commit 48b6ac0e97be72d6373151a830d8d90e7de52653
Date: Thu Jul 24 18:40:48 2014 -0400
Fixing Linux PyRosetta build
commit 6fe0ad033893b28fbbb69fed151ab90b944e2010
Merge: c9e965c 0c923ea
Date: Thu Jul 24 14:34:15 2014 -0700
resolving merge conflicts
commit 0c923ea1cdeb5042c3b56e8082a10ba0fa960601
Merge: 6287907 4e96b73
Date: Thu Jul 24 14:15:00 2014 -0700
Changing default values for -loops:outer_cycles to 5 and -loops:max_kic_perturber_samples to 2000
since our tests using the 45 loops benchmark set have shown considerable loop modeling performance
increases with these values.
These have already been the recommended values for next generation KIC, which is currently also
the recommended loop modeling protocol to use (I updated the documentation wiki for the loop
modeling app accordingly and will upload it once the server becomes accessible again).
Due to trajectory changes originating from changing the default values for those two
parameters, I expect the following list of integration tests to change:
rosetta_scripts_loops
antibody_H3
UBQ_E2_thioester_extra_bodies
kinematic_looprelax
KIC_refine
SnugDock
next_generation_KIC
AnchoredDesign
The following integration tests have already failed before and are not affected by this commit:
torsion_restricted_sampling
centroid_disulfide_scores
No other test changes expected.
commit 6287907c01d26b693fa6648c067e383f37fc4388
Merge: 5e65c27 3755921
Date: Thu Jul 24 12:44:36 2014 -0700
Changing default values for -loops:outer_cycles to 5 and -loops:max_kic_perturber_samples to 2000
since our tests using the 45 loops benchmark set have shown considerable loop modeling performance
increases with these values.
These have already been the recommended values for next generation KIC, which is currently also
the recommended loop modeling protocol to use (I updated the documentation wiki for the loop
modeling app accordingly and will upload it once the server becomes accessible again).
Due to trajectory changes originating from changing the default values for those two
parameters, I expect the following list of integration tests to change:
rosetta_scripts_loops
antibody_H3
UBQ_E2_thioester_extra_bodies
kinematic_looprelax
KIC_refine
SnugDock
next_generation_KIC
AnchoredDesign
The following integration tests have already failed before and are not affected by this commit:
torsion_restricted_sampling
centroid_disulfide_scores
No other test changes expected.
commit 4e96b73b98184aeac002e3d336e9e65d432f6b58
Date: Thu Jul 24 15:51:39 2014 -0400
delete_virtual_residues_after_FastRelax_='false' by
default in FastRelax constructor, since parse_my_tag in
rosetta_scripts alone may not be enough to specifically designate
default value for a user who uses command-line
commit 3755921d7c067211dea1ac2062ae9f8950b33178
Date: Thu Jul 24 15:29:37 2014 -0400
If a user wants, delete virtual residues after FastRelax for following rmsd calculation
commit d345e2f01af05861491dfc5d241d02ad2127796c
Date: Thu Jul 24 15:11:16 2014 -0400
Fixing some build errors on Windows platform
commit 0bb688136989855a60fe5fd5972668aa17ab2bfa
Date: Thu Jul 24 00:32:51 2014 -0400
Adjusting for dsbB
commit c5c1ce38ecc1fd58c9e2291027d9e85af08abd8e
Date: Wed Jul 23 23:38:55 2014 -0400
Updating basic version of membrane fastrelax protocol - possibly some bugs since global rmsd align = 0 in pymol
commit 4d64e5c85d5446a83cbe2dbaaa5049a45aa0f8d2
Date: Wed Jul 23 23:08:19 2014 -0400
Adding minimal refine membrane relax application - going to test it in a large scale setting
commit 5e65c277ebf73db5ba907f29981efe1ebc9b4c27
Date: Wed Jul 23 16:56:15 2014 -0700
Changing default values for -loops:outer_cycles to 5 and -loops:max_kic_perturber_samples to 2000
since our extensive tests using the 45 loops benchmark set have shown considerable performance
increases for all loop modeling protocols with these values.
These have already been the recommended values for next generation KIC.
Due to trajectory changes, I expect the following list of integration tests to change:
rosetta_scripts_loops
antibody_H3
UBQ_E2_thioester_extra_bodies
kinematic_looprelax
KIC_refine
SnugDock
next_generation_KIC
AnchoredDesign
The following integration tests have already failed before and are not affected by this commit:
torsion_restricted_sampling
centroid_disulfide_scores
commit 6fdbcd5e0599329c7643971c3be833fd480ac9d3
Merge: d6687d8 d153d53
Date: Wed Jul 23 16:40:58 2014 -0700
Revert LegacyKicSampler renaming.
The protocols::loop_modeling namespace uses the CamelCase convention for
class names. This commit reverts the change to LegacyKicSampler which
broke that convention.
commit d6687d8bf22ff41951f0832723cafec7fcc2090e
Date: Wed Jul 23 16:34:56 2014 -0700
Revert LegacyKicSampler renaming.
The protocols::loop_modeling namespace uses the CamelCase convention for
class names. This commit reverts a change to LegacyKicSampler which
broke that convention.
commit d153d53f002d54bea41c9f5f5c9c9cabe339e602
Date: Wed Jul 23 17:19:27 2014 -0400
this should fix broken mac.clang.build.debug
commit c9e965c12ef0833bdb339aa307671ca4005a5fb3
Date: Wed Jul 23 13:52:03 2014 -0700
changing name output of LegacyKIC_Sampler to fix Kale's unit tests
commit edf3490273e3c6680e53227e049a029dccc5fdf4
Date: Wed Jul 23 16:36:12 2014 -0400
fixed broken build
by
pose::PDBInfoCOP
->
pose::PDB_InfoCOP
commit 45ccfa53c97acf8edb0696b2bd413b3e1c8499a2
Date: Wed Jul 23 16:01:59 2014 -0400
[update of SandwichFeatures]
- newly introduced 4 more columns (like
num_PRO_in_starting_loop_and_1st_3rd_inter_sheet_loop) that seem to prevent aggregation
- technically finished all refactoring of SandwichFeatures for now
- should not change any integration tests other than (expected) features and features_database_schema (if any)
commit 09134edbb13e18ad0ddff7e70584e1cbdafc366b
Merge: 9a025a4 2aadce9
Date: Wed Jul 23 12:17:06 2014 -0700
Merge remote-tracking branch 'origin/master' into rpache/KIC_with_fragments
commit 2aadce9e227fee01785655d77ab0230be81cb5db
Merge: 12ffa68 b14c269
Date: Wed Jul 23 11:32:23 2014 -0700
Fixing initialization order in BackrubMover to get rid of warnings
commit b14c269e14eb80d23aac9086d492cbb33c882137
Date: Wed Jul 23 10:38:35 2014 -0700
Fixing initialization order in BackrubMover to get rid of warnings
commit 12ffa6860aa183c5274c3b2704573e700b9b02ea
Date: Wed Jul 23 12:32:40 2014 -0400
Revert "Debugged TaskOperationFeatures featurs reporter. The feature reporter"
Attempting to restore the build, step 2
This reverts commit afcf7f18ee5686f4ba3fb7b69c777b5382721495.
commit 3fc8dca3e5b5ac7ed22c2321f3ddbd82aebd4c07
Date: Wed Jul 23 12:28:23 2014 -0400
Revert "Revert "Fixed bug introduced by the "disable_design" xml option
of FastRelax where FastDesign stopped doing design by default. FastRelax
now has a class member variable that can be set by derived classes such
as FastDesign.""
attempting to restore build, step 1
This reverts commit 5cff772af35c0dff86b9841a7b60211269e2506a.
commit 3a81be627224f3e6d6f170865c1582cb248c3c97
Date: Wed Jul 23 11:46:05 2014 -0400
Pre-merge, current state of the branch. Not so worried if things break here
commit faa5fe4296d06821a6b9cb8a63bf11154e8022b9
Date: Wed Jul 23 11:36:55 2014 -0400
Updating doxygen in core/conformation/membrane objects
commit 5cff772af35c0dff86b9841a7b60211269e2506a
Date: Wed Jul 23 10:51:40 2014 -0400
Revert "Fixed bug introduced by the "disable_design" xml option of FastRelax where FastDesign stopped doing design by default. FastRelax now has a class member variable that can be set by derived classes such as FastDesign."
This reverts commit 4d84870a91b788f2ee30e0773a149bca7220ffc9.
commit 9a025a441ef9ab1ab831e7283d3dcaa4fc1f7a99
Merge: a0641b5 afcf7f1
Date: Tue Jul 22 20:15:22 2014 -0700
Merge remote-tracking branch 'origin/master' into rpache/KIC_with_fragments
Conflicts:
source/src/protocols.3.src.settings
source/src/protocols/comparative_modeling/LoopRelaxMover.cc
source/src/protocols/loop_modeling/samplers/LegacyKIC_Sampler.cc
commit a0641b5e25109fb7958838c87b970fef6c775bc4
Merge: 5dccbe3 840a017
Date: Tue Jul 22 19:27:33 2014 -0700
Merge branch 'rpache/KIC_with_fragments' of github.com:RosettaCommons/main into rpache/KIC_with_fragments
commit 5dccbe3148ccee1171f076cd304e42af76881555
Date: Tue Jul 22 19:17:33 2014 -0700
adding KIC_with_fragments integration test
commit 4689fac6ffa35e82902ce6208ca85390a8dbce26
Merge: e881ac0 86c3b46
Date: Tue Jul 22 22:14:51 2014 -0400
Merging in membrane relax code
commit e881ac04b0b5adea683d2b99a662a3f3a7643226
Date: Tue Jul 22 22:14:16 2014 -0400
Temporarily changing chain usage in pymol pyrosetta server - will be adding flags for this shortly
commit afcf7f18ee5686f4ba3fb7b69c777b5382721495
Date: Tue Jul 22 20:18:18 2014 -0400
Debugged TaskOperationFeatures featurs reporter. The feature reporter
reports the effects of individual task operations on every residue in a
pose. The effects of a feature reporter on a residue are whether the
residue becomes packable or designable due to the task operation.
The bug was that parse_my_tag had a subtly incorrect signature and the
the parse_my_tag of the FeaturesReporter base class was being called.
The new version of the feature reporter inherits from MetaWidget as a
method of inserting itself into the registrator/creator system rathter
than having an explicit regristrator and creator.
commit 4d84870a91b788f2ee30e0773a149bca7220ffc9
Date: Tue Jul 22 16:00:29 2014 -0700
Fixed bug introduced by the "disable_design" xml option of FastRelax where FastDesign stopped doing design by default. FastRelax now has a class member variable that can be set by derived classes such as FastDesign.
commit 8a5190e89f193e43f9deb2b762048edbc1fed0dc
Merge: 7c6cd5f 2976b84
Date: Tue Jul 22 15:47:15 2014 -0700
Update my hotfix branch to latest master
commit 2976b8424f5509240e2211398cd5f086b6f2c8fb
Merge: 732757f 6552098
Date: Tue Jul 22 14:48:45 2014 -0700
Added backrub rotation angle customization to BackrubMover
BackrubMover now has the following new data members:
bool custom_angle_ // true if backrub rotation angle is customizable
bool custom_angle() // gets custom_angle_
void set_custom_angle(bool) // sets custom_angle_
Real next_angle_ // the rotation angle for the next backrub move
Real next_angle() // gets the rotation angle for the next backrub move
set_next_angle(Real) // sets the rotation angle for the next backrub move
custom_angle_ is set to false by default to preserve normal backrub behavior
commit 732757f9040bf670df9c4a0fb902c1e98e72926e
Merge: 48471c6 0c317f5
Date: Tue Jul 22 14:42:15 2014 -0700
Added backrub rotation angle customization to BackrubMover
BackrubMover now has the following new data members:
bool custom_angle_ // true if backrub rotation angle is customizable
bool custom_angle() // gets custom_angle_
void set_custom_angle(bool) // sets custom_angle_
Real next_angle_ // the rotation angle for the next backrub move
Real next_angle() // gets the rotation angle for the next backrub move
set_next_angle(Real) // sets the rotation angle for the next backrub move
custom_angle_ is set to false by default to preserve normal backrub behavior
commit 65520983418baf54c31541a61837c364d777345f
Date: Tue Jul 22 17:31:04 2014 -0400
ResdidueProperties: improvements to auto-code-generation script
update_residue_properties.py now...
...only re-writes the files if changes have occured,
...ignores duplicated properties, and
...is more modular.
----------------------------------------
Unit test status: Not Run
Integration test status: Not Run
commit 14ffb5399279d3a03edd1c7f5ad82dd4fd2c24f5
Merge: 7b7ac14 e6ca4c6
Date: Tue Jul 22 17:28:08 2014 -0400
merging ResidueType branch into master
commit e6ca4c68842c95a2c9755811e8057150480c10a8
Date: Tue Jul 22 16:46:07 2014 -0400
ResiduePropeties: more modifications to update_residue_properties.py: files are only updated as needed
commit 7b7ac148574be48a5c2b1b890c87f5d5c1b15801
Date: Tue Jul 22 16:25:41 2014 -0400
PyRosetta. Updating dependency calculator.
commit 0c317f52c27df43ec043ab9177cbab8a1f9d9265
Date: Tue Jul 22 12:49:31 2014 -0700
Set backrub rotation angle customization to be false by default
Added custom_angle_(false) to BackrubMover constructor
commit 48471c6c57215d1db051de859fc2a2222f0479b2
Date: Tue Jul 22 14:30:58 2014 -0400
Fixing clang build
commit 766aa8b4fc6c5732e4683c0bdd27cee77d26d0a9
Date: Tue Jul 22 14:22:21 2014 -0400
Fixing PyRosetta build
commit 2b9f52401f3ba80166bdd3fd97b9e166d0d299dd
Date: Tue Jul 22 14:17:25 2014 -0400
ResidueProperties: improvements to auto-generation script to ignore duplicated entries
commit d3dc11011b3103f077fa427b0e0126684a632237
Date: Tue Jul 22 11:39:26 2014 -0500
Added case for D-proline in NtermTruncation patch
commit 2b97188dd4adf678e3a3423515c2f1afbe04b56c
Date: Tue Jul 22 12:23:09 2014 +0300
adding two integration tests for splice_in and splice_out for non-antibody cases
commit 485a6b17faf76632c9d5653a95f4fb4a785ac24b
Date: Tue Jul 22 12:21:37 2014 +0300
more bugfixes for non-antibody splices
commit abe01ab0175e6920b999c332a5b416195de69276
Date: Tue Jul 22 11:31:23 2014 +0300
fixing bugs in splice that prevented non-antibody proteins from working in splice out and in
commit 86c3b4658381441ddc3645ec14aabe36d39d4852
Date: Mon Jul 21 21:22:41 2014 -0400
Temporary updates to membrane_ddG application
commit 42980570f6e1af548b82e2bbb3f09112eac618e0
Date: Mon Jul 21 14:50:36 2014 -0700
Added backrub rotation angle customization to BackrubMover
BackrubMover now has the following new data members:
bool custom_angle_ // true if backrub rotation angle is customizable
bool custom_angle() // gets custom_angle_
void set_custom_angle(bool) // sets custom_angle_
Real next_angle_ // the rotation angle for the next backrub move
Real next_angle() // gets the rotation angle for the next backrub move
set_next_angle(Real) // sets the rotation angle for the next backrub move
commit 6404f96c20fe050ecb55693090c3fd11d7e8eb77
Merge: 6291b87 3490d15
Date: Mon Jul 21 17:01:27 2014 -0400
Reverting f8cb555; with Rhiju's commit just now, all unit tests should be restored
commit 6291b877d522527d2ee81b10945716da855313d2
Date: Mon Jul 21 17:01:27 2014 -0400
Reverting f8cb555 to fix all but one of the broken unit tests
commit 3490d1592278e7e1fdf3fc953b17e83081db5559
Date: Mon Jul 21 15:29:49 2014 -0400
removing newline from no_final_newline.txt in unit tests. Thanks Doug.
commit e5b7f939de21565c74bfbb09a8f05f4c3997d4fb
Merge: e3db1a8 91abef9
Date: Mon Jul 21 15:28:17 2014 -0400
restoring -Werror to unit test cmake build. Oops again, thanks Doug
commit e3db1a82282b1d0f8e5cc01eeafb511afb8a4196
Date: Mon Jul 21 15:25:51 2014 -0400
restoring -Werror to cmake build. Oops. Thanks, Doug.
commit 91abef97bcfa3749e3c181cf616d6b944ed43b57
Merge: b1fa4fe fc7eae4
Date: Mon Jul 21 15:19:06 2014 -0400
Fixing the unit test build following Rhiju's renaming; also fix Andrew Watkin's uninitialized variable warnings / errors.
commit b1fa4fe6eccfcae8e90a481ff51c93679807f469
Date: Mon Jul 21 15:19:06 2014 -0400
Fixing the unit test build following Rhiju's renaming
Also fixing up a handful of uninitialized variable warnings.
commit ff7ca63793acf041c449e95d4c155d757fbad777
Date: Mon Jul 21 15:11:41 2014 -0400
Updating membrane relax protocol - sending over to louis
commit fc7eae4a91aa8c85aa898cbc89e6e25a05668ab7
Date: Mon Jul 21 10:58:26 2014 -0700
Fixing a build error in PhenixInterface
commit 3a34bd9e3dc11e18525bb260a6b142e913aea8f2
Date: Mon Jul 21 09:48:13 2014 -0400
Updating relax executable for membranes
commit da759ea09dddfefacbf9deac1b2a381912e0135a
Date: Mon Jul 21 07:29:49 2014 -0400
Commenting the other mover out of the build settings again - going to start out with a plug in play - will just tweak movemap/min settings first then build up. Does not want to write cycles from scratch quite yet due to uncertainty here
commit 15b4898de299666468061854a67ebfb9d9cbfdda
Merge: 951edf4 2e01a30
Date: Mon Jul 21 12:47:08 2014 +0300
I hate git #n. Who knows why this file disappeared and reappeared. Anyway, bringing it back.
commit 951edf4503b48e723d09542f9be43692e3cf065c
Date: Mon Jul 21 12:42:14 2014 +0300
fixing poor behaviour in Splice when changing chain2
commit 3a0bd4353f6664bb39ae9760e7d5919c3eeec84a
Date: Mon Jul 21 00:21:09 2014 -0400
Adding relax mover to build settings
commit 26cd4f1243958d8fa7b2f12eb1319278878c3a8c
Date: Mon Jul 21 00:11:27 2014 -0400
Adding membrane fast relax movers down in protocols/membrane, should move later but will keep present for now as a framework app. Not part of the build yet
commit 0b3c7bb0c7295cda2b53b98135d6990a9046a71f
Date: Sun Jul 20 23:36:23 2014 -0400
Fixing signed vs. unsigned integer comparison issue introduced in membrane ddG mover - will hopefully resolve build issues
commit fd072cbcb43147b38b175f988dda95ffd6ef7e94
Date: Sun Jul 20 21:53:29 2014 -0400
Oops - thought I had resolved that merge conflict
commit 5935f7e6407e77521e4280744572129efe739160
Date: Sun Jul 20 21:51:47 2014 -0400
Oops - thought I had resolved that merge conflict
commit 264ee92a65e9ea2f003b8530005020a5d1c0bc2f
Date: Sun Jul 20 21:46:04 2014 -0400
Membrane Framework Updates: 7/20/14 (Part 2 :))
ddG/Design:
= Mutation Object: Store a position and residue to mutate to. Not so great - currently bypasses the resfile
reading interface, but makes it easy to do a ddG monomer style run where I can load in multiple mutationa
at once
= MembraneDDG Mover: Compute the ddG score given a pack radius and a Mutation (position, residue to mutate to).
Turns on the membrane framework, initializes the membrane position, computes native, repack & mutate and
then compute the ddG. This code is possibly some duplication from Liz Kellogg's ddG_monomer application, but
becasue that does not use the mover interface, nor is supported by JD2, it is much more difficult to plug
the membrane in using a generalizable/extensible approach.
= membrane_ddG: Application for running the membrane ddG mover (compute ddG with some refinement). Currently
includes methods for our 3 test cases - ompA, ompLA and brd7 - these will eventually be refactored out but
are present for convenience
PyMol Viewer:
= Bug fix: cast normal vector to a triple of floats (previously a triple of ints)
= Fixed cgo set transparency - setting an alpha value in the object will set transparency of only the planes
= Use triangle fan instead of triangle strip - cleaner rectangular planes
= Method present for drawing a normal cgo vector - still in progress, will need to parse additional info
SpanningTopology Object:
= Added additional comments, reformated, fixed potential bugs due to returning of raw objects
= Made documentation parseable by doxygen
Linux GCC Build:
= Removing unused variable warnings in spanfile_from_pdb
Sfxn Fingerprint Tests:
= These still may or may not run - I have no idea why...working on it?
Test Changes
= All unit tests should pass (unless there is dark magic on the test server)
= membrane_ddG integration test should change because it does something real now
commit 03eac2c6cdb3a8317f1e8877fb345b383933c085
Date: Sun Jul 20 21:25:19 2014 -0400
Adding some extra comments to pymol server, spanning topology
commit e348dd3af7928b94030017156cabd6ddcd60d77f
Merge: 51d0a0a 14873d0
Date: Sun Jul 20 21:15:19 2014 -0400
Removing another unused variable in the spanfile_from_pdb pilot app
commit 51d0a0a6287f4884223c651f4ab9a36c0e0c6654
Date: Sun Jul 20 20:52:21 2014 -0400
Membrane Framework Updates: 7/20/14
= Fixing broken unit test - SpanningTopology
= Integration test changes from the previous commit were expected and ok
= Fixing score function fingerprint tests to use spanfile flags
= Fixing integration tests to use updated spanfile flags
TODO:
Remove core/conformation/membrane/util.xx class. Methods should go in their
respective objects
commit e5db2eda710b1b89d0992cf3edcfa2acaf259432
Date: Sun Jul 20 20:39:23 2014 -0400
Fixing misplaced method in the library levels build
commit e5a9f8a12886f258644b3e37e0c61f7ad6b5653b
Date: Sun Jul 20 20:34:41 2014 -0400
Removing un-needed integration test due to recent code chanes ams smart ortho check xyz
commit e3a1ccdec3d384a16cace3609e4b8a5734a77636
Date: Sun Jul 20 20:16:49 2014 -0400
Updating spanning topology unit test - typo in input file
commit e030f4e4e14bbd10f14d8dd3f21a2ba77032cb41
Date: Sun Jul 20 18:34:40 2014 -0400
Fixing sfxn fingerprint tests to include the correct flags
commit 14873d08e673ac58a751083f1ecf78e238c84425
Date: Sun Jul 20 16:48:25 2014 -0400
Quick fixes to spanning topology test
commit e273586a858c50001a6dddcbef1324061f8a9323
Date: Sun Jul 20 15:31:50 2014 -0400
Doing a global find and replace for misnamed methods
commit 05ad0c0f313ffef26ed0a2a590854bf8c2a3414e
Date: Sun Jul 20 12:38:30 2014 -0400
Fixing formatting & doxygen and some potential bugs due to returning of raw objects in spanning topology objects. ALso renaming to convention
commit 68c448f407c891d7605befe3d1270f69af6d7bb7
Date: Sun Jul 20 11:43:44 2014 -0400
Adding quick fixes - will go back later for additions
commit 2e01a30044f104f836034d444df52c21f9351b07
Date: Sun Jul 20 11:30:01 2014 -0400
Somehow when I pulled master before pushing to sync changes, ResetBaselineMover.cc was changed and ResetBaselineMover.hh was not, leading to two inconsistent solutions to the unused parameter in its parse_my_tag function. Whoops!
commit 79d62c2fdf298cb2e923630521840c30d35bf400
Date: Sun Jul 20 10:25:25 2014 -0400
Added membrane ddG applicaiton
commit 6aba651d4d2305aa3974951b678c34191845a0f2
Date: Sun Jul 20 10:21:58 2014 -0400
Beautiful - fixing repack within radius
commit b56d0a7490da4f115885f18e4bf8b66543319adb
Merge: 5d1c093 f8cb555
Date: Sun Jul 20 04:08:38 2014 -0700
should restore unit test builds
commit 5d1c0939f3b87fe29f53cb6aedf4a8a7cf0dfe9e
Date: Sun Jul 20 04:08:01 2014 -0700
should restore unit test builds
commit 91e34844da16846d8a11101345a713718c33b060
Date: Sun Jul 20 00:32:51 2014 -0400
Fixed ddG code - will do upper and lower neighbors. Now just needs to put things together, clean up the interface, and we should be good on this front
commit e08ca8113264c5b8c2d5a3229732f02cd51ee93f
Date: Sun Jul 20 00:05:59 2014 -0400
Still fixing something wrong with this point graph code
commit f8cb555766f7fe10293fbdc4675434fe0574613c
Merge: 398d224 10307e7
Date: Sat Jul 19 23:57:16 2014 -0400
Support for homocysteine and D-homocysteine disulfides.
Earlier, I implemented params files for a disulfide bonded homocystine and D-homocystine, and I further made it so that Conformation could conceive of these residue connections. That didn't mean that they would be scored, though, or that a variety of protocols that might
have been primed to think of disulfides strictly in terms of SG atoms and comparisons to aa::cys and such were any more prepared.
Now they are: every protocol I could find that had a special disulfide behavior that was specifically about cysteine disulfides (and shouldn't be) no longer makes that assumption.
Now, some caveats. There still aren't centroid files for NCAAs, which include homocysteine and D-homocysteine. I didn't implement them. That said, whenever they're implemented, disulfides formed from them will work, so that's nice. Essentially, I didn't bend over backwards to implement new protocols or new functionality, but my aim was that--for protocols that ought to be agnostic to cysteine type but that for some reason were married to tepid ol' cysteine, now they aren't. Importantly, since there really isn't a wealth of e.g. D-homocy
stine disulfide structural data, it's not easy to empirically validate these structures, but we're expanding our capabilities.
commit 398d2248c4b240e1dd9f51b25613d48c1dd14f97
Merge: 2356438 e1a66da
Date: Sat Jul 19 23:47:40 2014 -0400
Support for homocysteine and D-homocysteine disulfides.
Earlier, I implemented params files for a disulfide bonded homocystine and D-homocystine, and I further made it so that Conformation could conceive of these residue connections. That didn't mean that they would be scored, though, or that a variety of protocols that might have been primed to think of disulfides strictly in terms of SG atoms and comparisons to aa::cys and such were any more prepared.
Now they are: every protocol I could find that had a special disulfide behavior that was specifically about cysteine disulfides (and shouldn't be) no longer makes that assumption.
Now, some caveats. There still aren't centroid files for NCAAs, which include homocysteine and D-homocysteine. I didn't implement them. That said, whenever they're implemented, disulfides formed from them will work, so that's nice. Essentially, I didn't bend over backwards to implement new protocols or new functionality, but my aim was that--for protocols that ought to be agnostic to cysteine type but that for some reason were married to tepid ol' cysteine, now they aren't. Importantly, since there really isn't a wealth of e.g. D-homocy
stine disulfide structural data, it's not easy to empirically validate this stuff. But doing something poorly (and only poorly because there's no metric for improvement) is better than being unable to do it at all!
commit e1c5888290a998534a4eee5fc7ba9070158871dd
Date: Sat Jul 19 23:30:50 2014 -0400
Adding code to ideally print the neighbors list - possibly inefficient
commit 10307e741f0c0e5fc28e78f22f8fee4b290e0f2d
Merge: 840ca41 dc4aae7
Date: Sat Jul 19 19:55:24 2014 -0700
Renaming/cleanup of variables to better match conventions. Mostly affects stepwise stuff, but I have always been annoyed PDBInfo -- acronyms should be separated by underscores -- so this is now PDB_Info. Merge of master and rhiju/swm_cleanup. Integration tests checked -- all changes cosmetic.
commit dc4aae71ad26a083e1bd756ccfc78726328bb782
Date: Sat Jul 19 19:02:45 2014 -0700
Update the RestrictToLoops task operations.
This commit adds a RestrictToLoops task operation, which is closely
related to the RestrictToLoopsAndNeighbors task operation. Support for
rosetta scripts was implemented for both task operations, although the
documentation has not been updated to reflect this.
Unit tests were added for RestrictToLoops. No integration test changes
expected.
commit bcf1c1f5b73a8d0c27ca9aad16498da756d00898
Date: Sat Jul 19 18:45:05 2014 -0700
Add a RestrictToLoops task operation.
RestrictToLoops is unit tested and compatible with rosetta scripts.
commit 840ca411abc9d5c66bd8aa87d61066ddb7515902
Merge: 68a25f6 909e3d4
Date: Sat Jul 19 14:24:29 2014 -0700
merge from rhiju/swm_cleanup
commit 909e3d457b7c58d4101d770c0541be75b858ebb5
Merge: b561b73 aa7b537
Date: Sat Jul 19 14:22:58 2014 -0700
fix conflicts in name PDBInfo --> PDB_Info with master.
commit 235643847de5f12305042dd5fb06988facf03831
Date: Sat Jul 19 15:50:46 2014 -0400
[update of SandwichFeatures]
- added 'min_dis_between_sheets_by_all_res' column to see a relationship
between 'min_dis_between_sheets_by_all_res' and 'holes' (surprisingly,
no relationship found)
- refactored SandwichFeatures much more by introducing WriteToDBFromSandwichFeatures.cc
- should not change any integration tests other than (expected) features and features_database_schema (if any)
commit 68a25f6cf54d946afe86786bdab4c81dd9cfd0a8
Date: Sat Jul 19 13:46:35 2014 -0500
Fix Segfault with RestrictToInterfaceVectorOperation and nonexistant chains.
If you passed a chain number or jump to
RestrictToInterfaceVectorOperation which didn't exist in the pose, your
run would segfault. Look for the error and utility exit appropriately.
Fixes bug 0000039
Meiler lab powercoding with Alyssa Lokits.
commit b561b73cf159ebc185a03d56be01b57c656e996d
Date: Sat Jul 19 11:39:43 2014 -0700
fix to SAMPLE_BOTH_SUGAR_AND_BASE setting -- look at sample_res before activating this sampling.
commit fca9ce0d3501b9865f8e0ced778fa345ce8cf1a8
Date: Sat Jul 19 11:19:31 2014 -0700
get rid of deprecated comment
commit 540cb597d06ffa63da457cc1e90061e4e4d6c863
Date: Sat Jul 19 11:19:04 2014 -0700
update Rosetta RNA colors to match EteRNA colors
commit aa7b53799ffbe6b4c475f1ae31a92740569585b4
Merge: 9c0da88 f176cf1
Date: Sat Jul 19 12:38:21 2014 -0500
Make usage of boost::uint64_t explicit
Certain compiler/platforms get confused about uint64_t - make it explicit
that Rosetta is using the boost version (as it's more portable).
This fixes bug 0000332
Meiler lab powercoding with Alyssa Lokits
commit e1a66da77989cb1e786157f4010421afad488dc4
Date: Sat Jul 19 13:15:41 2014 -0400
Finished generalizing protocols and one public app to accept the
possibility of d and homocysteine disulfides. Pushing to my branch to
run tests on a cluster.
commit 9c0da88971665bf2a21b8cab326a05d57c735729
Date: Sat Jul 19 12:19:46 2014 -0400
bug fix in cmake Python script
commit f176cf1bac80b219bea41cfa8139df2e40a32811
Date: Sat Jul 19 11:09:11 2014 -0500
Specify boost for unit64_t.
commit 930887b2d1fd031a053f62b272a7fd0205c48ad2
Date: Sat Jul 19 10:15:30 2014 -0400
Fixing neighbor graph code for ddG to not just get the upper neighbors...urgh so annoying
commit 9c7b3eb78cb16ef4d6042be6c8fd01fa0e8a04bb
Date: Sat Jul 19 09:57:01 2014 -0400
Implemented pg neighbor count - going to check in pymol before I implement the rest of it
commit f2edd736eb5383662af2bf4d474ab5b8d4887ea3
Merge: 2aaa554 2cc6158
Date: Sat Jul 19 00:07:51 2014 -0400
ResidueType: Residue properties are now stored in a separate class.
This push is first in a series of major refactorings of how proeprties for
ResidueTypes are handled in Rosetta. I will be discussing more about WHY and
what I did at the developer meeting, but the highlights are thus:
* Properties, such as POLAR, TERMINUS, LIPID, METALBINDING, etc., are no
longer stored in a vector of strings AND a series of is_foo_ bools in
ResidueType; instead, they are stored in a ResidueProperties class, to which
ResidueType has an OP.
* Within ResidueProperties, the properties are stored in a vector of bools
keyed by a ResidueProperty enum.
* enum values are auto-generated by a script, found in core/chemical/
residue_properties.
* The script auto-runs at compile (like update_options) and the generated
code files are not tracked by git. (I modified Scons, cmake, & xcode.)
* To add new properties, simply add a new line to the core/chemical/
residue_properties/general_properties.list file.
* Any property can be accessed by
ResidueType.properties().has_property( PROPERTY ).
* Wrappers still exist in Residue and ResidueType to access current properties
indirectly, (such as is_protein(),) but those could be deprecated if we
decide on that.
----------------------------------------
Unit test status: Pass
Integration test status: 2 changes
rings & carbohydrates: intentional output changes
commit 6b492ec5df079c991b9b401aebf7a32f0551f9c7
Date: Fri Jul 18 23:49:48 2014 -0400
Membrane ddG application compiles with design tasks
commit c227ac3d3fc26be019ee93929d4b9f3fd414489f
Date: Fri Jul 18 23:40:29 2014 -0400
Adding a missing #include for core chemical AA in membrane ddG app
commit de06b4b38121d5a68351c4c58fb5c780b2cc404e
Date: Fri Jul 18 23:37:24 2014 -0400
Adding bacteriorhodopsin mutation task to pilot app - shoud now have three methods for returning this information (though I would prefer some much better comments
commit e4f223d0641a3fee1b5821db00d60548bd6e0685
Date: Fri Jul 18 23:20:28 2014 -0400
Customizing my membrane ddG application to use specific mutations - these should NOT get committed to master...
commit e6d5e0b663678330bc1baa08f9b5997c666016a3
Date: Fri Jul 18 23:07:02 2014 -0400
Version of the ddG code using the mutation object inteface compiles
commit 4ef6f03de3ccb5373808bb8994a7630bc07c3de0
Date: Fri Jul 18 22:57:03 2014 -0400
Updating internal interface to use mutation objects that I can setup by task in my pilot app for rapid generation of the data plots
commit 090439fc7a36443778f5bd6c5e46696a82a07b5a
Date: Fri Jul 18 22:55:49 2014 -0400
Reworking the ddG code to take in a generic list of mutations - this will enable me to build a flexible pilot app for running mutation tasks
commit 560ae0bb55d1f82f91fd7f4ea2e7d98375c25395
Date: Fri Jul 18 22:36:06 2014 -0400
Adding mutations object to ddG code to improve generality
commit 840a017b3fe85594872846b111a1d345e054a1f9
Merge: b326bfa c6e4ce1
Date: Fri Jul 18 17:16:13 2014 -0700
Merge commit 'c5e4ce1e050ea86c2bce46609a409a9e2a7d1143' into rpache/KIC_with_fragments
commit 2aaa55467391abbec2b786108bad067f8e5aa5b5
Date: Fri Jul 18 19:41:19 2014 -0400
[update of SandwichFeatures]
- refactored SandwichFeatures by introducing CheckForSandwichFeatures.cc
- better comments
- should not change any integration tests other than (expected) features and features_database_schema (if any)
commit c6e4ce1e050ea86c2bce46609a409a9e2a7d1143
Date: Fri Jul 18 18:35:23 2014 -0500
Attempt to fix builds.
commit b326bfa4bfd36dbdce87261b60b16a27c930ea87
Date: Fri Jul 18 16:02:59 2014 -0700
Update LoopModeler unit tests.
commit 7158e664d27d7e2c9c7b48c3defabfc425fa3f93
Date: Fri Jul 18 17:51:12 2014 -0400
Adding mutation class to build settings
commit 92a5f5b59a95534df08717ee0925c74228b5d381
Date: Fri Jul 18 17:47:52 2014 -0400
Adding mutation class - udpating ddg mover to do repacking. Will add teh ability to do this repacking soon
commit 183cbe257fdde8e3d35ba44c89cc89f8f89b2c35
Merge: 58f672e 0f55db2
Date: Fri Jul 18 13:15:40 2014 -0700
Merge remote-tracking branch 'origin/master' into loops-xml
commit 58f672e04d67e6ce117ce65c02260d42a39d9fd3
Merge: 6c3f004 a65064f
Date: Fri Jul 18 13:15:13 2014 -0700
Merge remote-tracking branch 'origin/rpache/KIC_with_fragments' into loops-xml
Conflicts:
source/src/protocols/comparative_modeling/LoopRelaxMover.cc
source/src/protocols/kinematic_closure/ClosureProblem.cc
source/src/protocols/kinematic_closure/KicMover.cc
source/src/protocols/loop_modeling/LoopBuilder.cc
source/src/protocols/loop_modeling/LoopBuilder.hh
source/src/protocols/loop_modeling/refiners/LocalMinimizationRefiner.cc
source/src/protocols/loop_modeling/utilities/LoopMoverGroup.cc
source/src/protocols/loop_modeling/utilities/LoopMoverGroup.hh
source/src/protocols/loops/loop_closure/kinematic_closure/KinematicPerturber.cc
commit 0f55db26652041ab7665974f6dbb8180e0da2dd1
Date: Fri Jul 18 15:54:32 2014 -0400
Forgot the apps. Removing unused variable. Fixing build.
commit 0c7e91f2627c91691994dc4d5b9df5c8eb67aaf3
Date: Fri Jul 18 14:38:09 2014 -0400
Removing unused variable. Fixing the build.
commit 6c3f004d54dd892ddf551c56e2c479e921dee9ff
Merge: c16f650 81518f5
Date: Fri Jul 18 09:55:15 2014 -0700
Merge branch 'master' of github.com:RosettaCommons/main
commit c16f650b9abd56b44db3d6b651968d1a2d5c47de
Date: Fri Jul 18 09:49:37 2014 -0700
Add LoopModeler (with a RosettaScripts interface).
The LoopModeler class is meant to supersede the loopmodel application.
I had to transcribe the code that reattaches the sidechains between
centroid and fullatom mode into the new framework, so I can't be sure
that my code works until I benchmark it. The RosettaScripts interface
is largely in place, but there are still a few tweaks I need to make.
commit 190b726eee8b7440d24a2affafd3ef5b36c02e3d
Date: Fri Jul 18 18:38:56 2014 +0200
Updates for unit test compile.
commit 81518f5ea29aec0b3307b66ce0359b56d7d8462f
Date: Fri Jul 18 12:14:38 2014 -0400
[update of SandwichFeatures]
- refactored SandwichFeatures by introducing WriteToFileFromSandwichFeatures.cc
- streamlined all inclusions
- better comments
- should not change any integration tests other than (expected) features and features_database_schema (if any)
commit 842c6fcc22088fc7aee883e93c5fe5b78c780407
Date: Fri Jul 18 11:28:45 2014 -0400
Adding weights file for turning on pH mode with fullaton menv energy function
commit 2885fc4417ae8a5ac2678e660577a01c61ebe896
Date: Fri Jul 18 08:23:05 2014 -0700
trying to fix test server linux gcc build which seems to misread a weirdly indented line as having a "label".
commit f29b86aa07ac6bd3528fe84176e2f2734d70fc93
Date: Fri Jul 18 11:09:02 2014 -0400
Also adding some code for turning on ph variant types (protonated D and E) though not quite sure how to turn on the energy function to the pH I would need and see those changes. Flags for full repacking would also be nice
commit 15603b9b3be0813e9bcc33f04b35a7574e642e2b
Date: Fri Jul 18 11:04:37 2014 -0400
Going to try a full repack, also leaving the show method for quick assurance
commit 1f93a3f4582be0ee501167d5700dea4f68cb134e
Date: Fri Jul 18 09:49:18 2014 -0500
Update TorsionClaim::yield_elements for DOFelements' error messages.
commit 5ee687a28a9be8e3c36697a4183709f8de4f99a4
Date: Fri Jul 18 07:54:15 2014 -0400
Updating ddG code to be more general - will now print a parseable file for quick data io and also iterate through a list of designed positions
commit ebae420bcc5042e7fbf22d5268f946ec8c3c95c4
Date: Fri Jul 18 07:30:49 2014 -0400
Adjusting the ddG code to do per residue design as done in PyRosetta - much better scheme for this
commit d0473ab69b36cced7dd53977f0efc5a778b37a4c
Date: Fri Jul 18 06:57:28 2014 -0400
Switching some calls to pose into copy_pose so the ddG score output should now be nonzero
commit 8e9d68caefb45ec133487260c2c95994d080311e
Date: Fri Jul 18 06:56:04 2014 -0400
Yes - I think I finally got this code to do some design
'
commit d3727fee835ffc8ea5849e8b59e60b31fece9679
Date: Fri Jul 18 06:43:00 2014 -0400
Going to try this code using a modified resfile - this should let me see if I can do design and restrict repacking in essence by hand
commit 2cc61581f58087aa15c58a00d5dfe685f3af119b
Merge: 39fd755 c920e1e
Date: Fri Jul 18 00:19:32 2014 -0400
merging in last non-broken commit from master to ensure no one made changes to ResidueType that would conflict with mine
commit 39fd7556e412c01bb4a8923bc870995c7fa7dd46
Date: Fri Jul 18 00:13:36 2014 -0400
Residue Properties: one more sugar patch file fix
commit f3b7a1a62608ca9146264b3a6eab3de2157af8ab
Date: Thu Jul 17 20:45:15 2014 -0700
change in app name from swm to stepwise -- updating integration tests
commit ef173ca82b3edc900fa718c024216b5321bf1c0f
Date: Thu Jul 17 20:16:31 2014 -0700
reorganization of stepwise/ apps in directories to better reflect what is about to be deprecated. Renaming swm to stepwise to make it less cryptic, and to emphasize how it will displace the old swa_rna_main, swa_protein_main, swa_rna_util apps.
commit 3f0831663019ae47466c2a2732ae71055f84a27f
Merge: c0c364f 2b62338
Date: Thu Jul 17 20:09:56 2014 -0700
merge changes used for linux-compile.
commit c0c364f0017b54e9aeb8c2b67b4dbaa2d9ba14a2
Date: Thu Jul 17 20:09:06 2014 -0700
Updating the README in apps/. (Also, getting rid of some insane empty files that I must have checked in by accident; how embarrassing.)
commit eb8dbd56d98f1951c3d34cf80f31d78f7764451b
Date: Thu Jul 17 19:57:05 2014 -0700
fix to RDAT.cc to compile on linux!
commit 2b623382b2f86b8ba4671c6b007d977b2b7f7cbf
Merge: 0bbf0ba 020f84b
Date: Thu Jul 17 19:57:29 2014 -0700
merge from renaming updates on laptop.
commit 0bbf0ba154a15557fad63c2d38e00792e9980686
Date: Thu Jul 17 19:57:05 2014 -0700
fix to RDAT.cc to compile on linux!
commit 020f84b2e5ad0627cf406fbcb73512faab34d448
Date: Thu Jul 17 19:42:39 2014 -0700
fixing PDBInfo --> PDB_Info, PDBPoseMap --> PDB_PoseMap, as I think this is Rosetta convention (underscores separating acronyms, for readability)
commit c5da49c4cff279bd01b12aab4657d817418a61b2
Date: Thu Jul 17 22:28:53 2014 -0400
Adding additional updates to ddG membrane code
commit d3bb61af13abade4c6bfb4ab0e6f5490d403c6e7
Date: Thu Jul 17 18:42:54 2014 -0700
Another camelcase fixup, Kic --> KIC_. In stepwise rotamer sampling, disambiguating add_rotamer to add_external_loop_rotamer & add_internal_loop_rotamer.
commit 82e7ac659253924035693841a61a33cd01e845cb
Date: Thu Jul 17 18:18:35 2014 -0700
changing fang name Rotamer --> RotamerSampler to prevent confusion with all the other Rosetta rotamer classes.
commit 03c20f1d12257d48a5b5fd2bd8a7ab00785000dc
Merge: b562e7f df62b87
Date: Thu Jul 17 18:15:41 2014 -0700
Introduces RDAT file format for RNA chemical mapping into Rosetta as well as an app that should reach wide use, rna_predict_chemical_map. First connection of Rosetta 3D modeling to chemical mapping measurements that are widespread in RNA biochemistry, are exploding in throughput, and that are being put on a quantitative footing by our and other labs. This is a merge from rhiju/dms_score before closeout of that branch. No changes in integration tests except a couple that were failing already, and a couple that always seem to change on my mac (match_1n9l & flex_pep_dock).
commit 3688c18fcc4718ac22110ece4e527cbd883dbcfa
Date: Thu Jul 17 17:57:47 2014 -0700
changing fang name McComb --> MC_Comb, to match Rosetta camel-case conventions.
commit dd8652d2696d0fb29655e62651f3e6ce63d46364
Date: Thu Jul 17 20:03:20 2014 -0400
Properties System: fix #inclusions in other files
commit 4beca9d6b60414c750952fd784ca682a65c943e0
Date: Thu Jul 17 19:50:46 2014 -0400
Properties System: fix #inclusions in other files
commit 6039fcc4eea2f93ad46c556c49f41bb6f61a9ade
Date: Thu Jul 17 19:22:10 2014 -0400
Properties System: transferred over code to the source file to remove #inlcusion of ResidueProperties.hh
commit b562e7f0d0f277e6be6c04f8b037b3cd49b09c69
Date: Thu Jul 17 16:09:48 2014 -0700
getting rid of an uninitialized variable
commit 8367197ce0ad8eb36c37b85151e4ae5a29aec990
Date: Thu Jul 17 18:07:47 2014 -0400
Carbohydrates: quick-fixed sugars to work with new properties system
commit a0117d9c26197afea34254150492527a370fcb6d
Date: Thu Jul 17 17:47:33 2014 -0400
Properties System: properties list can now include comments
commit 64b2be62a1815b534d86da6d69c6d469781f4b95
Date: Thu Jul 17 15:30:34 2014 -0500
ChiralMover orients on backbone atoms when not enough sidechain atoms
3 atoms are necessary for orienting a residue by the side chain but ALA
for example does not have 3 side chain atoms so added functionality to
use backbone atoms when necessary
commit df62b8793b540f3f4bb2b64ebb35f3fc1eb36270
Date: Thu Jul 17 13:08:54 2014 -0700
rna_predict_chem_map now outputs mean DMS and std-dev of DMS, not maxL.
commit 79e3d5751d41190d77a8babea38c903ce4ac934a
Date: Thu Jul 17 15:43:00 2014 -0400
Properties System: added WATER
commit 26ae3cb347412e19d0da1227daf08222c2e8aaad
Date: Thu Jul 17 11:23:42 2014 -0700
creating app rna_predict_chem_map, which currently predicts full log-likelihood profiles for DMS reactivity given structure.
commit 9349137429d4394b2513d8ac28e42e9f54f5f486
Date: Thu Jul 17 13:22:35 2014 -0400
Support for D-homocysteine (NC F26) forming a disulfide. Went through
protocols and ensured generality to L and D homo and standard cysteine.
commit 12885b78ac2a25c5bd5bd2cae32954ad6a0b275d
Date: Thu Jul 17 12:19:05 2014 -0500
Add residue selector annotation queue behavior to CutBiasClaim.
commit 2d2db28bc117b4d57d0902d9bd1bd2d40b23a82c
Date: Thu Jul 17 10:48:47 2014 -0400
copy_data bug fixes
commit 2dffb695fad044653556cc72370aefb57c899b3a
Date: Thu Jul 17 10:36:03 2014 -0400
Trying to enable repack within radii for ddG plots
commit 6c6488ddad3a325fe8cf4e4671a436c7c994d3e9
Merge: c44e7d9 849e268
Date: Thu Jul 17 12:18:41 2014 +0200
Merging changes in my pilot app with the trunk
commit c44e7d9472ecef0c9485249109d7a068ba77c854
Date: Thu Jul 17 12:18:24 2014 +0200
my call_mover pilot app now reads temperature from cmdline
commit 912b2aef1a6c1606089d616b875dcf4f1268db29
Date: Wed Jul 16 21:53:29 2014 -0400
How the hell did that entire file get wiped?
commit e9882a882b8ff60c4cd6272a1171169fbc5f1383
Date: Wed Jul 16 21:32:20 2014 -0400
Properties System: fixed major deep copy and copy constructor errors
commit bb913219eef6f014d622766c0241f06bc8aba7be
Date: Wed Jul 16 20:50:00 2014 -0400
Properties System: pilot app for testing
commit d79fac6e1c3a508ba32da7fa88faf34921f51a36
Date: Wed Jul 16 19:37:47 2014 -0400
Properties System: improved ResidueType::show() to output VariantTypes as well
commit a9d689750b2bfe2c60d04f4162189258891e844e
Date: Wed Jul 16 19:36:08 2014 -0400
Properties System: modified xcode Python script to match Scons and cmake
commit bc4665ef621d5eda36f00853379eef529fda588a
Date: Wed Jul 16 18:08:04 2014 -0500
Update backbone oxygen placement when chiral switch of upper_terminus
ChiralMover will update phi and psi to be -1.0 * original phi/psi. For
upper_terminus residues, psi is not defined and defaults to 0.0. This
was producing weird placement of backbone oxygens. This commit updates
the chiral residue N-CA-C-O torsion with -1.0 * original torsion. Not
sure if necessary to fix hydrogens for lower terminus but probably
should.
commit 57c00d1cf158f09920aaba4659a056931c6f5c35
Date: Wed Jul 16 18:04:46 2014 -0400
updating pyrosetta server settings, running ddG app but the design will most likely chain
commit 7af8875f6a8fa89039c219dc7abe0826982ec52e
Date: Wed Jul 16 14:19:53 2014 -0700
adding functionalities to infer sequences and structures for each RDAT entry based on annotations like sequence:ACGGGG, mutation:A39U, or structure:(((...)))
commit 1d488da641aeff9452274cc43de151e3c9bf76b8
Date: Wed Jul 16 16:12:25 2014 -0500
Messing with RosettaScripts parse behaviors.
commit 0b2b4ab6cfdd47d1ce20f6f30a381ee0843dcb25
Date: Wed Jul 16 16:05:16 2014 -0500
Create a 'NO_POSITION' definition for code readability.
commit b29c50a6fa02ed0fbacddb32bed875fd8de50535
Date: Wed Jul 16 15:45:49 2014 -0500
Implement XYZClaim and VirtResClaim rosetta scripts parse methods.
commit 8481aef8b38e298228346bb0bcd411efae64370a
Date: Wed Jul 16 15:36:43 2014 -0400
updating mmebrane ddg app, and adding ddG mover to compile in the new branch
commit ede176eba38177096f9740693fa19035500b948d
Date: Wed Jul 16 15:26:49 2014 -0400
Adding some ddG mover code I wrote a wile ago into a newly merged branch
commit 2543c04cb52c6c22742f54eacd9dd67c193343b4
Date: Wed Jul 16 14:21:46 2014 -0500
Now EnvironmentJump::test_autocut_placment uses TestClaimingMover.
commit e2d95f9ce387b069b03cd8fd18bc0b1faa6a49d4
Date: Wed Jul 16 14:21:10 2014 -0500
Add Jump::operator== and Jump::operator!=.
commit c50a1651a6e6490f27946f184f2c9a4600c2edfd
Date: Wed Jul 16 21:26:15 2014 +0200
Updates for unit test compilation.
commit 0a5776fdb705d439d24b0dc01e7574671b87aa64
Merge: 18526c4 d5ecedd
Date: Wed Jul 16 14:37:31 2014 -0400
updates to MPframework
Span:
= added shift method
= added not_valid methods
SpanningTopology:
= added add_span method
= added reorder_spans method
= added write_spanfile method
= added nres_topo as check
AddMembraneMover:
= changed jump to MEM in apply function: setup_membrane
core/conformation/membrane/util:
= get name of spanfile(s) from options
= normalized length of normal vector to 15
MPDocking:
= fixed namespace errors
DockingProtocol:
= added comments and reorganized it for better readability
= added comments about lowres/highres logic which is counterintuitive
other
= added show method to xyzMatrix
commit 18526c4fa1acff45c9d6df8ee5590b02cefe3f0d
Date: Wed Jul 16 14:36:14 2014 -0400
fixed flags in integration tests, added function to util to normalize normal vector
commit fc62dc5bf89bfe67b2311e86d1c2209cfb478cc3
Date: Wed Jul 16 14:35:17 2014 -0400
fixed SpanningTopology unit test using try/catch block and exception in is_valid() function
commit 0c86d3ed68a515d8e100a3b6580b7ccdaa5dc77e
Date: Wed Jul 16 13:07:51 2014 -0500
Cleaning up EnvironmentJump to have a few more functions use Tester framework.
commit d93058c987a750438b1cec50698d061fb36c922d
Date: Wed Jul 16 12:49:01 2014 -0500
Swap out EnvironmentJump::test_jump_moves using Tester framework.
commit 47f5c802cba6138fc6d8f5839126e49f4e0a3448
Date: Wed Jul 16 20:07:00 2014 +0200
Fix compilation issues with ProtectedPose.
commit 38261e13772356e0750d94dfad4b942c0bcde25c
Date: Wed Jul 16 10:14:15 2014 -0700
creating check_rdat() function for online consistency checking of RDAT class. Putting in const qualifiers to some functions in RDAT.
commit ae342f88f711c82245b81a5ae4a36ac044149dd0
Date: Wed Jul 16 12:44:10 2014 -0400
Properties System: overloaded ++ operator for ResidueProperty
commit b274be169d50df9e916c44e6d1b7fe99ac81dcb6
Date: Wed Jul 16 12:04:51 2014 -0400
InitialMembranePositionMover: normalized length of normal to 15 for better visualization
commit 63bed954b177b2c362fdad73b7fc670747f52e1b
Date: Wed Jul 16 08:17:53 2014 -0700
moving RDAT and RNA_DataReader to a more appropriate place, core/io/rna
commit 3222fdcbeaf40140d122a3019fcbf7bc8fad4a3c
Date: Wed Jul 16 11:16:31 2014 -0400
Properties System: adding missing file to git
commit ca3a2c39b251d1f43913c8d933d58438bcdd502b
Date: Wed Jul 16 09:44:39 2014 -0500
Fix a namespace inclusion issue in EnvironmentJump.
commit 1c641022efb7ba5c06416bf349cd3ba2b1f0836b
Date: Wed Jul 16 09:41:41 2014 -0500
Add new JumpClaim rosetta-scripts parsing test to EnvironmentJump unit test.
commit bfd5cc5699dec5bb6169de9c675f9bd5131e991a
Date: Wed Jul 16 09:34:15 2014 -0500
Remove duplicate TestClaimingMover code from ProtectedConf unit test.
commit 94cef6211ad4a11747a68ebbee657f24d99dca5c
Date: Wed Jul 16 16:46:53 2014 +0200
Fix several compilation issues with beginning of switch to new testing mover.
commit d5ecedd7f4176d2558bf2b5caf6780a527c9a375
Date: Wed Jul 16 10:44:15 2014 -0400
Framework Update (7/16/14):
= Added MEMBRANE to list of properties recognized by residue type. Called by is_membrane()
= Added membrane property to MEM params files in centroid and fullatom residue typesets
= Fixes annoying MEM CA bug that was occuring when additional membrane residues were added for representing the membrane planes
commit c498b9880e36c201cf736150d394625924596eb9
Date: Wed Jul 16 10:42:00 2014 -0400
Fixed membrane CA Bug with residue type update
commit 9da7edff874c158665da40edcdb8b15423b74c80
Date: Wed Jul 16 10:26:31 2014 -0400
Adding a temporary residue type check in atom index
commit 2b7a89224937e38f9e8e2b86de0240e6cd5081a0
Date: Wed Jul 16 10:25:29 2014 -0400
Adding membrane property to both MEM params files as per new residue type updates
commit 4bd349632aa3226e1273da126da262e3682d0016
Date: Wed Jul 16 09:21:14 2014 -0500
Add TestClaimingMover objects to share across environment-related tests.
commit 1dfb68739482447f3b5a6aa68c44d6ae69311ec9
Date: Wed Jul 16 09:50:25 2014 -0400
Adding property 'membrane' to residue type
commit 849e26810f5ab4942f4f7e0cb6cd5896180a5ede
Date: Wed Jul 16 14:43:55 2014 +0300
fixing build
commit f1f0a7e68ae6959c23ca005460ab04798f68b9da
Date: Wed Jul 16 13:47:21 2014 +0300
adding mover ResetBaseelineMover to reset the baselines of Operator and CompoundFilter movers. See wiki for details
commit 2452077a632d246f94805b831bcc224cdc3b7490
Date: Tue Jul 15 21:46:05 2014 -0700
RDAT class can now read in RDAT files! And can use the RDAT file format for -data_file readin in SWM, FARFAR rna_denovo, and rna_score
commit 73d2586ed99600ee9f4baa0eb55dc955c69b460b
Date: Tue Jul 15 23:41:11 2014 -0400
bug fix
commit 1968a6225f9198f1e0d180174877432b1f0d8636
Date: Tue Jul 15 23:33:49 2014 -0400
Properties System: fixing unit tests to reflect name changes
commit 93abf4202f13179ccebf28dc9d94fa9d7c16bd80
Date: Tue Jul 15 23:17:17 2014 -0400
Properties System: undoing last commit; I forgot I had hyphens in the property names; I guess carbs will be broken for a bit
commit 7f7085e0c301dcf7306e16618870c620be598b37
Date: Tue Jul 15 23:14:02 2014 -0400
Properties System: copied all of the sugar properties over so that carbohydrate code will run, until I can refactor further
commit 1eeccc917ac4fadac68971a95900ba0c80bdac00
Date: Tue Jul 15 23:07:56 2014 -0400
Properties System: replaced countless calls to renamed VariantTypes and type set tags; Rosetta compiles
commit d34afd43736c2b14baa65a985af8844a2999c767
Date: Tue Jul 15 21:41:18 2014 -0500
Fix a bug where JumpClaim would always claim its init strength to be the same as its control strength. Similar bug in XYZClaim and TorsionClaim.
commit d777d2e2fd04bce34935964c0f764ee80840abea
Date: Tue Jul 15 22:19:12 2014 -0400
Properties System: implemented show() for ResidueProperties
commit a77501a00312437365c4be1f30074f226fa39d19
Date: Tue Jul 15 21:53:45 2014 -0400
Properties System: wrote Python script to automate enumeration generation
commit c920e1e152b6a7f5fd4adfe0513193aa979fd2d1
Date: Tue Jul 15 17:22:37 2014 -0400
Adding support for FA constraints in DockingProtocol.
The assemble_domains_jd2 test has a trajectory change due to constraints
not being enabled in docking without the cst_file flag set.
commit c9008438fcd7b63d6962589606c2e12089b2e0a0
Date: Tue Jul 15 16:19:16 2014 -0400
Adjusting spacing in DockingProtocol header, unfriending the << oerator, because no one needs friends. Moving the implementation of << to show, making sure show is virtual. Calling ConstraintSetMover::register_options(), looking for cst_fa_file when determining if constraints should be used.
commit d72d3109edc91cd45a1b7fc300fde011336b5f8c
Date: Tue Jul 15 16:15:53 2014 -0400
Adding a register_options() to ConstraintSetMover and adjusting some of the spacing.
commit 3356ff3d2f0cd52537c47dd33335a386e381146d
Date: Tue Jul 15 10:08:40 2014 -0400
Adding another note about what needs to be investigated.
commit 7314e0aea099e8ce5b0785436aaaf272be419a7e
Date: Tue Jul 15 09:31:01 2014 -0400
Adding a few notes to DockingProtocol to keep track of how to add FA only constraints
commit 926d57296f5148520072ce479b7a7b8e48f78cc0
Date: Tue Jul 15 17:48:43 2014 -0700
adding RDAT class for i/o of RNA chemical mapping data, and checked use in rna_features.
commit 0ed7668dd7182e649c7d24787928eb5d81717d41
Date: Tue Jul 15 17:48:08 2014 -0700
getting rid of debugging messages.
commit d1427c7f78f49666889fd5be92145958c44de91e
Date: Tue Jul 15 17:47:55 2014 -0700
adding useful error message if user tries to specify deprecated -out:file:silent_struct_type binary_rna.
commit 4bc42fe45b130cec7b376f888d4401827899b707
Date: Tue Jul 15 20:33:53 2014 -0400
Fixing linux gcc builds
commit 64e355acc03b937f45d5f44ba950708ea1222eb8
Merge: 77e82b9 c7499e1
Date: Tue Jul 15 18:55:57 2014 -0400
resolved merge conflicts
commit 60fb8643105bdee0d72b57d9d9c789309624f319
Date: Tue Jul 15 17:43:09 2014 -0500
Add annotation calls to EnvClaimBroker.
commit 282d368a0258bcc07da158d3a694ea47f6f6a56a
Date: Tue Jul 15 17:38:04 2014 -0500
Develop system in EnvClaim that allows RsidueSelectors to make annotations for JumpClaims for use in claiming.
commit 77e82b9b78fb9b27f0b628f3068915d63ae7cf19
Date: Tue Jul 15 17:45:32 2014 -0400
working on mpdocking and mpfolding pilot apps
commit 89d0ced35e9b404f6aae89f4159859ec0fd35f97
Date: Tue Jul 15 17:44:49 2014 -0400
moved spanfile_name into util = gets name from options
commit a6aa9d2d840b591c6c3bd71f0376ac0075b8171b
Date: Tue Jul 15 17:19:21 2014 -0400
Properties System: adding enum to string map;
changing names of VariantTypes and type sets to avoid naming conflicts;
fixing bugs introduced;
beginning automation process;
etc.
commit a2cad4f5044494231c6192d3a7ddac23bc61c9db
Date: Tue Jul 15 16:15:54 2014 -0500
Add more sophisticated duplicate-checking in SequenceAnnotation (now checks if members are the same before failing.
commit d73e1dcf07c78dd64fe89e002e1667e7a68ac385
Date: Tue Jul 15 14:26:07 2014 -0400
Maybe this will fix residue_types.txt
commit f5bf83eae6d60246ebde02f8a0f4efca6744255c
Date: Tue Jul 15 11:53:17 2014 -0400
Shoot, residue_types.txt got left out. No longer.
commit 583edd552b0bc7af9ef1456a1fc342c17c03856d
Merge: 60ca2b8 5ec9afd
Date: Tue Jul 15 11:47:34 2014 -0400
Homocysteine (NC C26) can now form disulfides.
Modification to Conformation and to disulfide scoring allows NC C26, homocysteine, to form a disulfide residue type (HCD, by analogy to CYD) and be scored as appropriate. (It retains the C26 rotamer library.) Integration test log file changes expected merely due to changes in Conformation log output
commit 5ec9afddea344415b7843c5fc8e3ef889fa5b5e1
Date: Tue Jul 15 11:46:10 2014 -0400
removing my modded residue_types.txt
commit 5ad85f74688895117fce85732cbe1d2eb7a3c28e
Date: Tue Jul 15 11:44:44 2014 -0400
Fixing up typos and unnecessary output log diffs
commit 98cd5cca6a09b8b78c373c000d5831cdc5a53a07
Date: Tue Jul 15 10:17:02 2014 -0400
Homocysteine (NC C26) can now form disulfides.
Modification to Conformation and to disulfide scoring allows NC C26,
homocysteine, to form a disulfide residue type (HCD, by analogy to CYD)
and be scored as appropriate. (It retains the C26 rotamer library.)
Integration test log file changes expected merely due to changes in
Conformation log output.
commit c7499e16b8d4cb316181e9f70c99993ef4061a54
Date: Tue Jul 15 07:53:35 2014 -0400
Membrane Framework Update: 7/15/14
Updates:
= Movers no longer depend on an anchored foldtree
= Default foldtree setup is a 'simple' foldtree
= Unit tests updated to reflect this behavior
Builds
= Fixed a bug in UniformPositionMover - should correct the linux gcc build
Unit Tests: All Membrane Framework Unit Tests Pass
= Span
= SpanningTopology
= MembranePositionRT
= MembraneInfo
= MembraneConformation
= AddMembraneMover
= InitialMembranePosition
Unit tests can be run using the script run_membrane_utests.py in the Rosetta/main/source directory
but should be stripped out prior to master merge
Integration Tests: Running
= load_mpframework
= membrane_ddG
= membrane_relax
Integration tests can be run using the script run_membrane_itests.py in the Rosetta/tests/integration
directory but should be stripped out prior to master merge.
commit 6fbffef93036a37b09c9f25b4490035d03121615
Date: Tue Jul 15 07:49:37 2014 -0400
Adding script for running membrane framework integration tests
commit b9f631b0f9ce348dd23e681306660661e6a1fbb4
Merge: 060e00c 2050f91
Date: Tue Jul 15 07:22:32 2014 -0400
Merging in removed fold tree dependencies and additional mover checks
commit 060e00c2ac8920c7c3ef6347c746c6bc769242b9
Date: Tue Jul 15 07:22:13 2014 -0400
Adding run membrane unit tests script to membrane source directory (should be removed prior to merging in master) - all membrane info unit tests pass (n=7)
commit c62764835fe45810a8d966b9cf315c824cae069d
Date: Tue Jul 15 07:17:07 2014 -0400
Fixing indentation and namespacing error in uniform position mover that broke the linux gcc build
commit 2050f9128a30cf7b39da6613b07bc98f00b7a101
Date: Tue Jul 15 07:14:11 2014 -0400
Fixing jump number (defaults) in MmebraneInfo unit test. All tests should pass
commit 9b1c31df4f606c1efba76cd951d5592cc2a2ad0b
Date: Tue Jul 15 07:11:00 2014 -0400
Updating membrane conformaiton unit test to use position equal within delta method for normal approximation due to coordinate coorect in initial stub. Unit test passes
commit c4c56e2ea6e6109b2207501c28d1f44266d7b769
Date: Tue Jul 15 06:46:04 2014 -0400
Updating default behavior to use a simple foldtree - add membrane mover unit test passes
commit 60ca2b8cabc42e3647da80314d6f026dd3c44ae8
Date: Tue Jul 15 13:44:01 2014 +0300
adding flag omega to MinMover that defaults to true. If set to false, don't minimize the omega bb torsion. No test changes expected (except log changes where RosettaScripts use MinMover).
commit 3456a0792743397cf1dbd319230160e3837518f1
Date: Mon Jul 14 23:04:19 2014 -0400
Adding unit tests without fold tree anchor"
commit c9cd4d9af3af68d54a857f9e8d8ded9067fa7299
Date: Mon Jul 14 22:40:12 2014 -0400
Fixing membrane rt and initial membrane position mover
commit ca04bd1a105d6f90e00d71d89b6ae0a4e41ba474
Date: Mon Jul 14 22:13:21 2014 -0400
Fixing the RT movers to be independent of the foldtree - skips some steps and uses a straight set with ortho check
commit c65d0936120002691de031840658c62c901edb4a
Date: Mon Jul 14 21:47:38 2014 -0400
Getting rid of old membrane position perturb and transform movers
commit a65064fa527a0e93e4ad772ec07bd8fb3f05e5ef
Merge: 03a6e96 c9199ff
Date: Mon Jul 14 18:31:56 2014 -0700
Merge branch 'rpache/KIC_with_fragments' of github.com:RosettaCommons/main into rpache/KIC_with_fragments
commit 03a6e969b426bfb000667e6aa091e8ef63086d1c
Date: Mon Jul 14 18:29:45 2014 -0700
changing LoopBuilder to respect the max_kic_build_attempts flag
commit 08b746014e06bd2273593eee39559bcece074719
Date: Mon Jul 14 18:28:38 2014 -0700
changing KICMover to respect the max_kic_perturber_samples flag
commit 26078dd43ff457bfe4fc15ba955d839a4208499d
Date: Mon Jul 14 20:15:34 2014 -0400
Forgot to git add the pilot app membrane sampling - should fix the builds
commit ed62478d4d936f3fc31f2dd25cc6d076519a5463
Date: Mon Jul 14 19:08:06 2014 -0400
Fixing membrane position RT - finally makes the correct determinstic rotation by changing the normal vector outside of the stub
commit b66d90422a816863e233de8a31c8bbd03ddf9629
Date: Mon Jul 14 19:05:24 2014 -0400
All tests pass computing the rotation outside of the code
commit 2590c849225089271aeedb047d38149e4d565104
Date: Mon Jul 14 18:51:19 2014 -0400
updating membrane position rt mover to make exact rotation/translation moves
commit c17523312904eb01b269a7c1c36f081a207c42e4
Date: Mon Jul 14 18:43:24 2014 -0400
Membrane Framework Update: 7/14/14
= Updating Conformation udpate_membrane_position method - will do a stub ortho check during folding to ensure the coordinate
frame was not invalidated
= Adds update_membrane_position method back, but relies on a relative coordinate frame (be careful)
commit 334427ffde295e0ac0d168e49796be367457fb02
Date: Mon Jul 14 18:37:22 2014 -0400
Updating initial membrane position mover to contain the correct expected values
commit 69d18bc5bc19c9b3e705510c103446590b3a0c5d
Date: Mon Jul 14 15:24:33 2014 -0700
adding -graft_backbone_only option to rna_graft
commit fc454f9402f9825995e9b1e9e5bb8fe25e0decf3
Date: Mon Jul 14 18:23:14 2014 -0400
Jeff's suggestion + my updates seme to work really well together - going to push this
commit b66058f500520454666a35d858495400a01a3ad4
Date: Mon Jul 14 18:18:03 2014 -0400
Orthogonal coordinate frame checking works - going to adjust this in initial membrane position mover
commit e741d61a769ecee5704651ce3a90b6569e72b661
Date: Mon Jul 14 18:01:51 2014 -0400
fwd.hh to .hh for now
commit 2b059a64624e34271ad6d9fc1705bfa8b69ca747
Date: Mon Jul 14 18:01:22 2014 -0400
fwd.hh to .hh for now
commit b2a072dcbe0ac8ae37fdded014736b6549307523
Date: Mon Jul 14 17:56:31 2014 -0400
Properties System: removed all the property booleans from ResidueType and changed all the accessors/mutators
commit bb198c355cb7d3529c595faa10a10a51e9b811da
Date: Mon Jul 14 17:49:50 2014 -0400
Adding a method to conformation that validates the membrane xyz coordinates as a valid orthogonal coordinate frame
commit 683b37d1dd3e8ca1c62c3009d90ef96020e01801
Date: Mon Jul 14 23:41:40 2014 +0200
Fix one bug in currently broken pyrosetta build.
commit 34f9eacb669719ae0d447833a84b49e7a90a378b
Date: Mon Jul 14 17:29:53 2014 -0400
Membrane Framework Updates: 7/13/14
Determinstic Moves for the Membrane Position
= Params File: I used the xyz->spherical methods to compute a desired default set of internal
coordinates to give the xyz coords we want. Now, when you load in a membrane params file by default,
the center is at (0, 0, 0), normal is at (0, 0, 1).
= Params File: Thickness is currently along the x axis - Unfortunately placing it along the z axis will
create an invalid stub. This coordinate is never used in simulations, only sometimes for visualization
so I am not so concerned for the moment - its not going to stop any science and we have some pretty good tools to visualize in the meantime before we can think about a different solution.
= UniformPositionMover - Lives in protocols/simple_moves and will make a deterministic rotation or
translation (separate movers). Unit test passes. Not specific to membranes - can be used n the general
case.
= MembranePositionRTMover - uses uniform position mover and will translate/rotate a membrane position
from an old to new membrane position. Has a passing unit test
= InitialMembranePositionMover - uses membrane position rt mover to move the membrane to a structure
based starting position. Has a passing unit test. Currently fails on one case due to a weird negative
zero thing I have been taking to Brian about - safe to use, but use with caution.
Test Changes:
= Should fix the unit test build, all unit tests associated with the framework should pass
= All membrane framework integration tests will most likely change becuase the default stub has changed.
commit 6fc3780392a56b77a2413c3de175af02b5f27eed
Merge: 29735da 39c3d7e
Date: Mon Jul 14 17:24:35 2014 -0400
Resolving merge conflicts between crumb and ninja mpframework_devel
commit 29735da715f49dc1b5e3374e7f18ddd69e392b05
Date: Mon Jul 14 17:02:53 2014 -0400
updating centroid residue typeset file
commit 77b3a24f3e400f80abf7809a42cad5a872205142
Date: Mon Jul 14 17:01:08 2014 -0400
Updating membrane params file which updates the default thickness setting to be 15A along the x axis
commit 559da5674790b5ca29b951b785c001ac91eff864
Merge: 9b917f0 37484ff
Date: Mon Jul 14 22:46:26 2014 +0200
Myriad bug fixes and API improvements for Environment system. New (and improved) unit tests, construction of general LoopCM for managing dof-greedy loop modeling code, FragmentsMovers are now created as a tag inside the Environment in RosettaScripts.
No (new) unit test breakages; no (new) integration test failures.
commit 37484ffb21ea94463f05afb7e97635f3798b91f5
Merge: 69bdc08 c10bb69
Date: Mon Jul 14 22:21:32 2014 +0200
Merge branch 'justinrporter/env_devel' into justinrporter/env_release
commit 9b917f07fcf5cb493d5ecbc98763e788f2332aa4
Date: Mon Jul 14 16:16:48 2014 -0400
Adding Talaris2014 weight set
Adding a weight set and a flag -talaris2014 that incorporates two small
changes to the score function:
All the terms are scaled upwards by 25% so that fa_atr has a weight of 1.0.
The hydrogen bond terms are scaled downwards by 20%, which benchmarking
revealed to improve decoy discrimination, sequence recovery, and rotamer recovery.
commit 4a6e0292a6a220af7c020b824ba231e9edcbafd2
Date: Mon Jul 14 16:01:44 2014 -0400
Properties System: adding bulk of source file
commit 56ea6af471d36e50a29087bb3945ac28fade8df9
Date: Mon Jul 14 12:40:01 2014 -0700
updating rna_data_reader object so that it does not require pose upon initialization -- that was confusing, and I figure I should fix it now while I am revisiting the code. now also handles conventional numbering mapping in a more transparent way ...
commit ebb2da9a4714210f2b12f7f572ac193010778319
Merge: 70823ff 69bdc08
Date: Mon Jul 14 15:24:49 2014 -0400
OK. I see what happened. I tried to reindent the MembranePotential.cc
file because it's all kinds of poorly indented, but in so doing,
I uncommented some code that doesn't work. I'm commenting out that code
again.
commit 70823ffbeabe60db7b06dc50e017012f97709548
Date: Mon Jul 14 15:24:49 2014 -0400
OK. I see what happened. I tried to reindent the MembranePotential.cc
file because it's all kinds of poorly indented, but in so doing,
I uncommented some code that doesn't work. I'm commenting out that code
again.
commit 1377cfe0437ea9bb359126a7ef5e7365086b1526
Date: Mon Jul 14 14:46:29 2014 -0400
Properties System: adding header file
commit c9199ffaec7f98b24668fd37df7158b75943c9ce
Date: Mon Jul 14 11:38:07 2014 -0700
Consolidate the MinimizationRefiner hierarchy.
commit ebd860fca0a086ea62b103b4ecad6d034b56ff3a
Date: Mon Jul 14 14:17:34 2014 -0400
Adding random membrane position mover
commit cffbf1fff559f48035d95bb492468d410ed75148
Date: Mon Jul 14 14:07:27 2014 -0400
Playing around with a bunch of things - fixing cross product in membrane position rt mover
commit 8e6b998633fc170c18a5392b48ed68fc82e92e38
Date: Mon Jul 14 13:13:00 2014 -0400
Properties System: adding fwd header
commit 44943ea96d211c9af475f886b799ee1fd71dde5b
Merge: c574375 63b3063
Date: Mon Jul 14 13:04:13 2014 -0400
merging in master
commit c10bb69b7e0e6b73aea5030d776cc77a3adf8906
Date: Mon Jul 14 11:41:53 2014 -0500
Move invalid-DOF_ID allowing to base torsion id validaiton method, ProtectedConformaiton::valid( TorsionID ).
commit f81bc2f78fca6d47a5bacc4cd4778d830ee8c92a
Date: Mon Jul 14 09:51:08 2014 -0500
Beautification of TorsionClaim.cc
commit 69bdc0880056bf292b2536e95c54d0fc5e9c936a
Date: Mon Jul 14 09:28:04 2014 -0700
Turned -Werror back on for CMake builds
For "build," I turned on all -Werror, instead
of just one type, so hopefully that works.
Also modified the Werror_check integration test to
check all CMakeLists files.
commit 63b3063809cf28d2d80fb1dfb8487a41d4d20af4
Date: Mon Jul 14 11:21:46 2014 -0400
Fixing the build error I just added.
commit 2a2076c3b0523078eef5e0239243395da8296fbf
Date: Mon Jul 14 16:58:53 2014 +0200
Fix a bug in one of the ClaimTests unit tests.
commit bce1c9be093418b2cd5a7421ca06af1062fd4f52
Merge: c88a1be e2d579e
Date: Mon Jul 14 10:43:57 2014 -0400
Aaaaaaaa - these unused-private-field warnings are awful! I've spent an hour and am only
half way through core. I can't get anything done here. I'm giving up.
commit c88a1be30616a4ac5abbe4837379b871b4330d84
Date: Mon Jul 14 10:43:57 2014 -0400
Aaaaaaaa - these unused-private-field warnings are awful! I've spent an hour and am only
half way through core. I can't get anything done here. I'm giving up.
commit 0fc63bab9b048b1681b20616a22fc33f037dd81f
Date: Mon Jul 14 10:43:46 2014 -0400
Adding coordinate correct method - trying this out after a discussion about the weird negative 0 occurences
commit c696bdb2f9e9336bdee1f4ee327bf6dbf3b84a76
Date: Sun Jul 13 23:21:07 2014 -0400
updating membrane params file in centroid residue typeset to take new params file updates"
commit 58102415b5ae6ab4f865c6da343bf8bb7c946aad
Date: Sun Jul 13 23:19:29 2014 -0400
Reverting back to use the anchored fold tree - this would take you some more time to debug
commit 5811784cd3a4f128c4a8b50dc2da71ec91fd7094
Date: Sun Jul 13 23:14:30 2014 -0400
Fixing membrane position rotation mover test to depend on a simple fold tree
commit 8681a45837a0cdc6494f0ce0766a11ae32d4bf0c
Date: Sun Jul 13 23:00:11 2014 -0400
Adding correct version of initial position RT mover - the only issue I have right now is with the negative almost 0 rotation. Will ask someone in the lab tomorrow
commit 2a1ae30c9854209bfbcc5e0b698997c551925518
Date: Sun Jul 13 22:44:44 2014 -0400
Fixing expected values to be correct in uniform position rotation mover
commit 40e02416d1cc2fcf0862bf7d44bafaffce2a0f83
Date: Sun Jul 13 22:39:44 2014 -0400
Fixing spacing in membrane position rt mover in this branch
commit 924f512b66b40caeefa0c0da4e7065b0f9f986fb
Date: Sun Jul 13 22:37:24 2014 -0400
Membrane position RT test updated and passes - yay :)
commit 5f65e8085f24f877db042709b4c4c4cbf97bc645
Date: Sun Jul 13 22:24:19 2014 -0400
Adding uniform posiiton mover test to settings
commit 4b0ad17a59e4b30a400ccb0a4a8338790ede1a9b
Date: Sun Jul 13 20:33:11 2014 -0400
Updating membrane params enum to respect the new structure of the params file
commit 87c3caf5ac2a33ceffa0243672425ac1966c03e6
Date: Sun Jul 13 20:17:12 2014 -0400
Updating membrane params file to load in the correct normal parameter by default
commit c92ccdfe5c8ea02bb69c9a20eba2ea5ac729a0fb
Date: Sun Jul 13 13:21:11 2014 -0500
Add ClaimTests unit test for making sure Claim constructures et al are working.
commit 501c6524274f6a6d43b7673763666dd6f664bd82
Date: Sun Jul 13 12:38:49 2014 -0500
Fix a bug in ProtectedConformation that caused invalid-dof set_torsion calls to fail as security exceptions rather than be ignored (the new behavior).
commit b8aeb178ac39c5011d578feb8b980a449d6fa195
Date: Sun Jul 13 11:04:53 2014 -0500
Remove unused ClaimStrength unit test.
commit 7127baf1a3113c731c01d67e453f10da769ea446
Date: Sun Jul 13 10:55:25 2014 -0500
Fix use of ang_delta in LoopCM::apply for pose sandboxing.
commit e2d579e79f69db2c45a3132f60870fc3d6066e83
Date: Sun Jul 13 10:14:04 2014 +0300
Adding debug flag to SeqprofConsensus to limit the amount of text output. No test changes expected
commit a924c6192e17c51dbb698802ea1d3aabd370d553
Date: Sun Jul 13 09:50:57 2014 +0300
Ramachandran2B Size->int conversion fix
commit 434e2a39041dfeef41e7902248d996f7e9e314f1
Date: Sat Jul 12 19:07:05 2014 -0700
fixing moveable_jump setting in minimizing for FARFAR/rna_denovo
commit 74b0af997ec7ceeb6b64cfa7dd5c1a0a587f384f
Date: Sat Jul 12 19:07:05 2014 -0700
fixing moveable_jump setting in minimizing for FARFAR/rna_denovo
commit 9f731aa3a7cd8f394870aead898c7b34151c393e
Date: Sat Jul 12 14:59:00 2014 -0400
Fixing signed/unsigned integer comparison (that I guess gcc doesn't catch?)
commit 39c3d7ebe8bef08cf6cc40a184d14467c3d6fb7f
Date: Sat Jul 12 13:59:47 2014 -0400
Framework Update: Fixing Linux gcc and unit tests builds. Also - the menv smooth integration test change was due to the fact that it had never been run before and is therefore a false negative
commit 0c64ed57ba7a1411980eb4f0eb26b7ba36df3666
Date: Sat Jul 12 12:56:24 2014 -0500
Add std::endl to output in ScriptCM.
commit bbbe3010f4153a3636f7f9ddc2437cf2b36cf829
Date: Sat Jul 12 12:54:33 2014 -0500
Remove auto-fail check for ProtectedConformation::contains_carbohydrate_residues.
commit 50984235523d2e91486ec429b1b8c9946c56a25b
Date: Sat Jul 12 12:37:43 2014 -0400
Commenting lips acc file io out of the unit test build as it is unused in the current iteration of the code
commit 266b68907e922bd8a0ed0851621dac527d35e65e
Date: Sat Jul 12 12:21:06 2014 -0400
Missed a spot in transform into membrane mover
commit d3cf812dc52bd1e0c8a0ef6db832e0bd87686f34
Date: Sat Jul 12 12:17:08 2014 -0400
Removing ambigious reference to Real in - conflict between platform, numeric and core in RT< perturb and transform movers
commit e63cdbfb90e3157968db72559f39cf35b94c8763
Date: Sat Jul 12 11:53:35 2014 -0400
Removing unused variable chain from the build
commit 6a47441d7d2be0e0256badc19a07e5507b54884b
Date: Fri Jul 11 21:41:59 2014 -0400
fixed bugs from merging, added tracers for debugging
commit a75dd2670a340c6ae379301eebbfa4b5b810f464
Date: Fri Jul 11 21:41:28 2014 -0400
added tracers to apply for debugging
commit 3812926b7bf4429fbd9fd107005bb1fa574736b0
Date: Fri Jul 11 21:39:58 2014 -0400
fixed bug in AddMembraneMover and changed jump to MEM to 1 in setup function
commit 2da0c4ac0ad9b8eee22772728ca2bfed785e7b5d
Date: Fri Jul 11 21:34:56 2014 -0400
added mpfolding app, still working on pilot apps mpdocking_setup and testing rotations
commit 3f6fd873d1b6c0607cbd3cec2d97f506ee487c12
Date: Fri Jul 11 21:32:44 2014 -0400
added show method to xyzMatrix
commit c7f5e0de21cfe9d2e849bd2b621e47fae81a896e
Merge: a4eff6e b67406b
Date: Fri Jul 11 17:38:49 2014 -0400
Reducing the memory use for Rama and Rama2B.
This commit brings in modifications to the Ramachandran and Ramachandran2B
classes to dramatically reduce the memory usage needed to perform the
sampling used by KIC and the next-generation KIC loop modeling protocols.
Previously, the Ramachandran table would look at all 36x36 phi/psi bins
and write down the phi and psi angles for each bin with a probability
above some very small threshold; then it created a very large table
with several thousand entries and write down the phi/psi values into
that table proportionately. I.e., if one phi/psi bin had 10% probability
then if there were 2500 entries in the table, that bin would have its
entries written down 250 times. Then, this table could be use to
proprotionately draw phi/psi values.
The new strategy is to compute the cumulative distribution function
for the phi and psi bins, to then draw a random number between 0 and 1,
and then to find the phi/psi bin where its CDF value is less than
the random number and the next phi/psi bin's CDF value is greater than
the random number. This strategy has remarkably little memory overhead;
just as much as is needed to store the probabilities in the first place.
This brings NGK's memory use down from 5GB+ (since the Rama2B's memory
footprint was 20x larger) to basically the same memory overhead as the
rest of Rosetta.
Thanks to Brian for discussions on how to implement this and to Amelie and
Roland for running the loop modeling benchmarks to make sure nothing worsened.
All unit tests pass. Integration tests using KIC and next-generation KIC
all change.
commit fe72bad03518e9d7857cec9cb80084725f927b2c
Date: Fri Jul 11 17:36:10 2014 -0700
a little code cleanup. fixing camel case of Base_pair to BasePair, etc.; moving these classes from core/scoring/rna to core/pose/rna.
commit 6c2b0e2abbc5a04e5e2a81cb7a4f964710a1c8f1
Date: Fri Jul 11 20:20:46 2014 -0400
initial work to make homocysteine disulfides work
commit f3f66e6a04843cfc0e4b818e8be2c912e4d24aca
Date: Fri Jul 11 19:02:01 2014 -0500
Fix forgotten tolerance check in LoopCM::apply's sandboxing of its internal mover's apply.
commit 8be20f8fd9ea32de191183e1148ad0d956a03268
Date: Fri Jul 11 19:00:27 2014 -0500
Change TorsionClaim's yielding to be a bit better encapsulated in functions.
commit ee01f0013de7ec9d782e755b048ca4b4a3e1a6c9
Date: Fri Jul 11 17:46:09 2014 -0500
Fix a bug in TorsionClaim where it would claim invalid dofs if a cutpoint is part of the region.
commit d628ad4378eaa3b88f8d03e35612db9d5899ec94
Date: Fri Jul 11 17:24:07 2014 -0500
Improve output, fix a bug where Broking was completely broken.
commit 5c87d68decdc4cb24b5c96dc3ea49ef5e7e962a7
Date: Fri Jul 11 16:46:07 2014 -0500
Added invalid dof error during broking, updated ScriptCM with better output and an add_claim method.
commit b67406b625bd0d2e55e4abb990eb6b4129f38115
Merge: ef8b9a8 29b8beb
Date: Fri Jul 11 17:38:49 2014 -0400
Reducing the memory use for Rama and Rama2B.
This commit brings in modifications to the Ramachandran and Ramachandran2B
classes to dramatically reduce the memory usage needed to perform the
sampling used by KIC and the next-generation KIC loop modeling protocols.
Previously, the Ramachandran table would look at all 36x36 phi/psi bins
and write down the phi and psi angles for each bin with a probability
above some very small threshold; then it created a very large table
with several thousand entries and write down the phi/psi values into
that table proportionately. I.e., if one phi/psi bin had 10% probability
then if there were 2500 entries in the table, that bin would have its
entries written down 250 times. Then, this table could be use to
proprotionately draw phi/psi values.
The new strategy is to compute the cumulative distribution function
for the phi and psi bins, to then draw a random number between 0 and 1,
and then to find the phi/psi bin where its CDF value is less than
the random number and the next phi/psi bin's CDF value is greater than
the random number. This strategy has remarkably little memory overhead;
just as much as is needed to store the probabilities in the first place.
This brings NGK's memory use down from 5GB+ (since the Rama2B's memory
footprint was 20x larger) to basically the same memory overhead as the
rest of Rosetta.
Thanks to Brian for discussions on how to implement this and to Amelie and
Roland for running the loop modeling benchmarks to make sure nothing worsened.
All unit tests pass. Integration tests using KIC and next-generation KIC
all change.
commit c5206808000427be14f76bb359ba1633d02bd44d
Merge: 6b6b964 8ff5894
Date: Fri Jul 11 23:12:47 2014 +0200
Merge branch 'justinrporter/env_devel' of github.com:RosettaCommons/main into justinrporter/env_devel
commit 8ff589451abdb2b6217d9a0f7cd1d06ea2f365fe
Date: Fri Jul 11 16:08:32 2014 -0500
Increase usefulness of claim strength conflict error output.
commit e9d074d19474c9c23a4aad400ff0f66fe4701d98
Date: Fri Jul 11 16:08:02 2014 -0500
Add output method for ClaimStrengths.
commit 3bff4b2556e878125da7ab86b423ac46b346ea91
Date: Fri Jul 11 16:06:54 2014 -0500
Fix a bug where XYZClaims were claiming all dofs.
commit a4eff6ed2ccbf3ea8a31c62761c89ef0979a43d9
Date: Thu Jul 10 22:04:24 2014 -0700
adding -unvirtualize_phosphate_res flag to rna_graft for silly cyclic-diAMP case.
commit 29b8bebab9e47521fbfe6532cc056b4bc18fff28
Date: Fri Jul 11 15:20:12 2014 -0400
Fixing the buried_unsat_kinemage integration test which has been failing.
Forgot to add find_buns.cc to my last commit.
commit d0dffb44cc5245282832ec651527e7b41dc127d3
Date: Fri Jul 11 15:14:34 2014 -0400
Fixing the buried_unsat_kinemage integration test which has been failing.
Also fixing an initialization-list order error in some of Jared's code and
getting rid of copoius quantities of trailing whitespace.
commit 6ccc8b0c1d77e2abab86dbce9233fc40f42d4b2c
Date: Fri Jul 11 14:53:59 2014 -0400
fix more constructor variable ordering
commit c1d0d174678973b906ba302380fdf2eb472a585e
Merge: b1d3e69 544fc3a
Date: Fri Jul 11 14:02:20 2014 -0400
fix copy constructor ordering to fix gcc build
commit 54ec0458e306b226d0e5bfb7be0682b6cd9e230e
Date: Fri Jul 11 12:16:38 2014 -0500
output beautification.
commit 544fc3aab754be9f44aa10e8a3ee33ee2f9ee458
Date: Fri Jul 11 13:11:51 2014 -0400
fix copy constructor to fix gcc build
commit 6b6b96475cabcbde89767ab797a2e76a651c61cd
Date: Fri Jul 11 19:07:35 2014 +0200
Fix unix compilation issues.
commit 0b1be2a2dea7fb658a8973138052b736fb98ee57
Date: Fri Jul 11 13:07:30 2014 -0400
fixed namespace errors in mpdocking, changed MEM in AddMembraneMover to jump to first residue, added comment to DockingProtocol about weird logic in running lowres/highres
commit 9cff141cf9b0ecd7ad43e4cff55cd898a0657969
Date: Fri Jul 11 12:07:11 2014 -0500
Add XYZClaim to EnvClaim factory, update EnvClaim factory to allow for existence checking. Both in service of allowing ScriptCM to instantiate client movers on the fly.
commit b1d3e6953f8eececc4c0c1a2fd54a659414cfb4b
Date: Fri Jul 11 12:23:37 2014 -0400
Updating regression tests comparison logic, increasing full-diff log size.
commit 1463d07d94b401fa16ae59dd563a8dee531d0236
Date: Fri Jul 11 10:10:07 2014 +0300
Fixing FilterScan's resfile control when using deltafilters
commit 5b734360e341fc196ad7f1a8399ab67ea51edd4e
Date: Thu Jul 10 22:04:24 2014 -0700
adding -unvirtualize_phosphate_res flag to rna_graft for silly cyclic-diAMP case.
commit 48263c46a21e10a85592f386411802589b22abf2
Date: Thu Jul 10 18:56:54 2014 -0500
Fix whitespace issues in SecondaryStructure and add a comment.
commit 9d9d0bc05e31f00d4e73d06900240315f4d4fd6d
Date: Thu Jul 10 18:56:37 2014 -0500
Change AbscriptMover from taking a std_frags option to having a Fragments subtag.
commit 4f7f9388e5ddec1260cce927863c672b699d0691
Date: Tue Jul 8 18:14:14 2014 -0500
Allow UniformRigidBodyMover to parse its own tag when embedded in an UniformRigidBodyCM and create a conditional check for unparsed values.
commit f89b15eeb3a8aa53253dfd0dba7bda6a95af2e83
Date: Tue Jul 8 11:17:04 2014 -0500
Get rid of chi setting from loop refiner.
commit c57cd30285133aef1525bdec9faa0d87e7ddd812
Date: Tue Jul 8 11:06:01 2014 -0500
Fix a bug where LoopCM was toleranceless of numerical differences.
commit aede3d4589a32fa506ef09494c1815ea7e73bbc3
Date: Tue Jul 8 11:05:43 2014 -0500
Fix a bug with collected claims output.
commit f3857ca28d31dda21319fc1cc5f2f2abd4411632
Date: Mon Jul 7 11:38:45 2014 -0500
Fix a bug in ProtectedConformation where differing dofs were not compared based on absolute value.
commit 41050b41024c003d582ad062aff8552a2ad94099
Date: Thu Jul 10 19:49:45 2014 -0400
fixed bug in SpanningTopology, spanfile_from_pdb only writes single spanfile if PDB contains single chain
commit 41758265c1b7fc99fc3dec9eb5641351831a1760
Date: Thu Jul 10 18:06:22 2014 -0400
fixed bugs, added comments
commit 671dc14c542f97c573a01c1fef13c5a23f52f7bc
Merge: 9a44b63 6e96245
Date: Thu Jul 10 17:42:46 2014 -0400
Add a set of simple_movers for grafting, make all and GraftMovers and utility movers available to RS
This commit adds a set of simple movers to protocols/grafting, which are basically wrappers to some grafting utility functions.
Combined with SavePoseMover and the main GraftMovers, both CCDEndsGraftMover and AnchoredGraftMover, one can create a grafting protocol within RS.
Adds unit tests for all the simple movers
No integration test changes expected.
Here is an example RS for grafting CDRS from one renumbered antibody into another:
commit 9a44b63e4ea663345251fb70f6f46b5491947351
Merge: 0b5140c 5a4bf0e
Date: Thu Jul 10 17:06:30 2014 -0400
Merge pull request #46 from RosettaCommons/momeara/HBond_xmax_params_bug_fix
Fix broken H-Bond polynomials in Talaris2013
commit 6e9624551cf867d282ecce896e8bb7f0c4f27928
Date: Thu Jul 10 16:48:15 2014 -0400
remove dump pdb statements
commit 2b64b7cfea1faa776451fba666b5f8d6c6b58b47
Date: Thu Jul 10 16:44:52 2014 -0400
fix copy constructor of graftmovers. all clear
commit 04008aac7dabc5f46b4adfd71020fbe481cad3c0
Merge: 8b84164 c281500
Date: Thu Jul 10 16:42:10 2014 -0400
merge /rfalford12/mpframework_devel into jkleman/refactor2, resolve conflicts
commit 8b84164b3adbc06361bdc0659e3b4b539dab3ad5
Date: Thu Jul 10 16:24:45 2014 -0400
fixed bug in SpanningTopology, changed EXCN to utility_exits, added mpframework_test pilot app for easy testing, still debugging mpdocking_setup
commit 0b5140cf34509b146b76a1d71c867c55d45aa232
Merge: 1a0a927 fcaae8c
Date: Thu Jul 10 22:47:09 2014 +0300
Merge remote branch 'origin/master'
commit 1a0a927070d3f69527230fe11b4661d4d9818af4
Date: Thu Jul 10 22:45:47 2014 +0300
FilterScan's baseline was very messy. Now baseline only works if using delta_filters. Now, for each position undergoing filtering, the position is relaxed twice (by invoking packing without design), and the reference pose is set to the pose after these two steps. Then, the pose is relaxed one more time (same way) and its DeltaFilter value is saved as the baseline. Now, each substitution is done against the reference pose (saved after two relaxation steps). Mutation to self shows values of 0 now.
commit fcaae8c0c2a82202ab3a3cc0eb3491257bdec002
Date: Thu Jul 10 12:05:35 2014 -0700
further fix of bug in jump sampling for RNA denovo. output of rna_denovo filters when they are note passed. Added -extra_minimize_chi_res option to allow flexibility of ligand in RNA puzzle.
commit 59f9a8206230724ade4015b551a6bdf1ed0791a2
Date: Thu Jul 10 12:05:35 2014 -0700
further fix of bug in jump sampling for RNA denovo. output of rna_denovo filters when they are note passed. Added -extra_minimize_chi_res option to allow flexibility of ligand in RNA puzzle.
commit c2815005aa95b840fa99f7179cd3a4dcb30bd334
Date: Thu Jul 10 14:37:17 2014 -0400
Membrane Framework Updates (7/9/14)
============================================================
Movers
= Deterministic/Uniform Rotation & Translation movers added to protocols/simple_moves
= Membrane Position Rotation/Translation movers for moving the membrane residue
= Randomized position movers based with deterministic movers
Membrane Position Coordinates
= Removal of #update_membrane_position() method in conformation and methods for setting xyz
= Added correction in membrane_normal() to always pull a unit vector derived from the coordinate
= Updated InitialPositionMover to use base rotation/translation mover described above
Default FoldTree Settings
= Added behavior for a non-default membrane fold tree anchored by an additional virtual residue. Can be turned on using the flag -membrane_new:anchored_foldtree
Energy Terms
= Updated #includes to remove incomplete conformation definition warnings
= Fixed global namespacing errors
Lipophilicity
= Updated LipidAccInfo object to remove setters, meet coding conventions, clean ups, etc
= Removal of LipsFileIO class - object initialized from file at construction
= Modified MembraneInfo to take a single lipophilicity file (no more 'by chain') as well as corresponding options and input streams
= Updated MPLipoEnergy to use the new object structure from MembraneInfo
Smoothed Energy Function
= Addition of MPEnvSmooth energy term (framework adapted)
= Addition of a new fingerprint test, menv_smooth_sfxn containing smoothed fullatom energy function weights set
Unit Testing:
Updated the unit tests to include the following:
= MembraneInfo
= AddMembraneMover
= MembraneConformation
= MembranePositionRT
In addition to pre-existing unit tests for the membrane code, which include MPDatabaseIO test and Julia's new unit tests for SpanningTopology and Span objects.
Expected Integration Test Changes
= All Framework integration tests will change due to io output errors. This will also diff against master merge which will also most likely produce a series of changes.
commit 0b92325d8426f07a367b280bf07a93c67dabb323
Date: Thu Jul 10 14:35:47 2014 -0400
Adding flag to turn anchored fold tree on/off and also fixing method that was deleted temporarily in conformation - those changes will come later
commit 3a708c33ddf23ab6d55882d5c54fb2bff910a608
Date: Thu Jul 10 11:18:30 2014 -0700
Added cmake Werror check to integration test
commit 6b1556ca17c0df19b43fb5ddf4c2bdd5593c529b
Date: Thu Jul 10 10:20:51 2014 -0700
fixing bug in rna_denovo where chain_connections jumps were not sampled if connected residues were in rigid segments. big problem in rnapuzzle12 modeling!
commit 5ceede69795c761f791a9b6a4d0d39be08574f74
Date: Thu Jul 10 10:20:51 2014 -0700
fixing bug in rna_denovo where chain_connections jumps were not sampled if connected residues were in rigid segments. big problem in rnapuzzle12 modeling!
commit 89295229bb75c443b97a0fe8fa6af406d3e01080
Date: Wed Jul 9 15:19:20 2014 -0400
Fixing a bug that can cause full atom only Docking to ignore constraints.
Two integration tests change as a result of caching the constraints to
the pose before converting it to the full atom representation. These
tests are:
1) docking_distance_constraints
2) docking_site_constraints
The scores and final coordinates of the decoys that are produced by
these tests remain unchanged.
I observed changes in two matcher tests that resulted from swapping HIS
with HIS_D. This is a weird things that seems to occur sporadically (at
least on my system), and it is unlikely that these tests will change on
the test server. I wonder if there is anything we can do about that
because it's not great to ignore changing integration tests.
Big thanks to BK for discovering and reporting this bug.
commit cf19fc6d23b5bfb7fe9bfbf2ff93c36f2ad2b26b
Merge: 6f362f9 1319064
Date: Thu Jul 10 11:30:05 2014 -0400
Resolving merge conflicts between mpframework devel and parallel devel branch
commit 131906496f1c4942bc2b290a869eac74ac12c0ac
Date: Thu Jul 10 10:33:34 2014 -0400
Membrane Framework Updates: Visualization in PyMol
====================================================
Added a feature to the PyMol mover/viewer for viewing the membrane planes as CGO planes derived
from information in the membrane framework.
= MembranePlanes Object - stores location of plane defining virtual residues
= ShowMembranePlanesMover - mover for adding plane defining residues to the pose
= AddMembraneMover will now automatically setup the pose for visualization in pymol if specified by the user upon initial add of the framework
= PyMolMover contains a send_membrane_planes which sends over location of plane defining residues & other framework information
= PyMolPyRosettaServer.py will parse a message containing plane residue locations, draw planes from these points and update in pymol during a PyMol viewer enabled simulation
Updated: 7/10/14
commit db014dca4f2bef349d26a5df10949cd959ab4a83
Date: Thu Jul 10 15:32:19 2014 +0300
Limited the number of allowed rotamers to pack in Splice in
commit c95e5fb5458865f8ebbb0028afb34b862aafc959
Merge: e34bfb2 fc50e38
Date: Thu Jul 10 13:00:57 2014 +0300
Merge branch 'master' of github.com:RosettaCommons/main
commit e34bfb252f341e3ac942c9ccd596764ba5582a7c
Merge: 0733163 68a6af8
Date: Wed Jul 9 19:22:53 2014 +0300
Added tarcer messages to Splice.cc
commit fc50e38880f011d480c6dd09c3db42751906ca0c
Merge: 0733163 68a6af8
Date: Wed Jul 9 22:16:37 2014 -0700
Created TrajectoryReportToDB to enable use of the features reporter system for trajectory output
TrajectoryReportToDB is a child Mover of ReportToDB, meaning most of its functionality
is the same as ReportToDB (e.g. any existing features reporter can be used with it).
The new behavior is that the class counts how many times each pose (identified by JD2 output tag)
has been "applied" in the features reporter system. A new table,
"trajectory_structures_steps", keeps track of which step iteration a particular struct_id
represents. Struct_ids can be grouped from the same output by using the existing tag field.
The mover has also a stride option to control how often features are reported.
The mover works in Rosetta Scripts, and could be particular useful as part of a parsed protocol
that is called multiple times, as in the generic monte carlo mover.
In the process of creating this class, I refactored some of the other database and features code,
but behavior should be unchanged.
I also removed SZ_MAX from core/types.hh, as it was causing an unused variable
warning/error on my system, preventing compilation.
This commit merges branch kylebarlow/general_dev into master
Expected test changes:
features: test now uses new reporter
features_database_schema: new mapping table
ligand_dock_script: numerical instability
commit fbdd192d32fa74da4349277add87c6a1f5fbcb80
Date: Wed Jul 9 22:54:55 2014 -0400
Updating documentation for the pymol viewer code"
commit de6e89d3d463499f5a0f81294235b0aa7481bac1
Date: Wed Jul 9 22:28:43 2014 -0400
added add_span, reorder_spans, and write_spanfile methods to SpanningTopology
commit cdd4c8201b630a4711c489928403273856961769
Date: Wed Jul 9 21:41:11 2014 -0400
added shift and not_valid methods to Span
commit 68a6af82564192a91e6c90f66bdbe03a27034a67
Merge: f0e6e78 0733163
Date: Wed Jul 9 18:33:02 2014 -0700
Merge remote-tracking branch 'origin/master' into kylebarlow/general_dev
commit f0e6e78d5a4de68f6dff592f6f8ab311cc6a08d0
Date: Wed Jul 9 18:28:41 2014 -0700
Added stride to TrajectoryReportToDB tag
To make sure that this tag is parsed correctly
commit 0bc24bdf69e53ebbdfad92766682e870e2a87e87
Date: Wed Jul 9 18:26:26 2014 -0700
Added unit test for TrajectoryReportToDB
Unit test checks if cycle counting works correctly
It isn't the best unit test because it also tests that ReportToDB is initialized correctly,
but this isn't the worst, as there are no unit tests for ReportToDB currently.
I had to add a new getter to be able to access cycle counts
commit 073316304ccec5ad9493d03d20e300577495606d
Date: Wed Jul 9 18:11:25 2014 -0700
decided to not have rna_chem_map_lores term on during fragment assembly by default, based on benchmark runs.
commit b453a7c5a5a3f968670111f3869ad513f32aa08c
Date: Wed Jul 9 18:11:25 2014 -0700
decided to not have rna_chem_map_lores term on during fragment assembly by default, based on benchmark runs.
commit 64d843e51c49d5479f1ae95f2ca648161c8f6381
Date: Wed Jul 9 21:06:48 2014 -0400
Removing extra tracer statements from pymol membranes code
commit 887364bad1312205d67808633dccf6c433cda1d0
Date: Wed Jul 9 21:05:34 2014 -0400
Working version of the pymol viewer for membranes - beautiful
commit 2925f4f0a4756c92b2d6f7314e6f589a627b8bbd
Date: Wed Jul 9 20:58:12 2014 -0400
forgot to add files
commit 13f57192195843fe9e8e8cf3e2d4592a490ea510
Date: Wed Jul 9 20:55:43 2014 -0400
Added mpdocking_setup pilot app, still working on it
added nres_topo as check in SpanningTopology
small renames and comments
commit 173d04863abe7e4d9c1982235ae15ea30dfac7e4
Date: Wed Jul 9 17:44:11 2014 -0700
Removed trailing whitespace
commit 18ecf601f36adc2c07b80e4d2f4735f901d7c938
Date: Wed Jul 9 17:42:58 2014 -0700
Fixed other unit tests that used now non-existent report_features call
They also use fake tags now
commit a544db3766c72cb2b6e08e9840981d8667d5be1d
Date: Wed Jul 9 20:34:36 2014 -0400
Has a full version of the pymol draw planes code - however pymol seems to freeze when it comes time to draw the cgo planes
commit 2643afbfa10a6ae9b5b246bf2de8f75d0386f5ac
Date: Wed Jul 9 17:28:10 2014 -0700
Modified FeaturesReporterTests unit test to not need report_features function that was removed.
Removed function didn't require an output tag and input tag to be passed in.
Now they are set to arbitrary values and passed in.
I ran the unit tests before this change (with the old function added back in) to make sure
it passed both before and after this change.
An added benefit is this unit test is no longer dependent on JD2 to run.
commit b67192eadd92ce2bfd181f0f436fc56be5e72a60
Date: Wed Jul 9 15:36:17 2014 -0700
Removed unused variables
commit 155c71c28ff7b86ef516717682969d2d1f39f229
Date: Wed Jul 9 15:10:11 2014 -0700
Removed SZ_MAX, as it was causing unused variable warning/errors
It was annoying me and wasn't used in very many places.
If you want it back you probably need to make it extern in types.hh
and then set it in a new types.cc file
commit d796d552a4d6abd4c77bf9437364bbe435a10f19
Date: Wed Jul 9 18:22:17 2014 -0400
Updating server script and pymol viewer test pilot app
commit 2c737403aa836b4cd2b311c29dcaa12b45848684
Date: Wed Jul 9 17:34:34 2014 -0400
Adding additional method to pose for grabbing total number of atoms up to a given residue
commit 61a500ae42ad96b966eeb2da2c347f7a8427a833
Merge: 795694b e1acea1
Date: Wed Jul 9 13:37:36 2014 -0700
Merge remote-tracking branch 'origin/master' into kylebarlow/general_dev
commit 87e36983fb1a178129ec00b8cda504fe22d0ed4f
Date: Wed Jul 9 15:37:03 2014 -0400
Enabling pymol mover on the C++ side to send message over to the Python side - no reciever implemented yet
commit 795694b8cbfd4760c23a2cec016b942a34238a21
Date: Wed Jul 9 12:32:20 2014 -0700
Added TrajectoryReportToDB to features integration test
commit a447146b60ba6dac4093fb21677ed5d4cc05a399
Date: Wed Jul 9 15:29:40 2014 -0400
updating message formatting sent over by pymol to make it more like a splittable string"
commit 835518bb689345892032d568dd188afd71df1604
Date: Wed Jul 9 15:24:31 2014 -0400
Fixing a bug in the view in pymol method that was allowing send plane info prior to initialization of plane points
commit 968a0254817f8c29e561e67be341115a979a7fa6
Date: Wed Jul 9 15:23:36 2014 -0400
I give up. something stupid is keeping this from working in RS
commit dca2b00b25fe567b560fe787b79b018e153e0eb3
Date: Wed Jul 9 14:53:30 2014 -0400
Adding milestone 1: show planes viewer will add the membrane points on command
commit d9ad13ca27b05e370a9c388bd4296dfbfe8aa7cf
Date: Wed Jul 9 14:35:01 2014 -0400
Updating show membrane planes mover to support new options and remove support for a user provided radius (rg more reliable/practical
commit 80fd2a12617c2186cd26e0822fc315d1d54463d1
Date: Wed Jul 9 14:29:44 2014 -0400
updating membrane planes to print the correct plane points, show membrane planes mover adds points to membrane info, adding options now
commit 08b09f412ec27550268f226efceef8470f0d637b
Date: Wed Jul 9 14:18:10 2014 -0400
Allowing show planes mover to directly add point info to membrane info object
commit 0a83bb4eccf8b26098d2552ccd4a9175ed33aa2e
Date: Wed Jul 9 14:16:41 2014 -0400
Adding pymol viewer testing pilot app
commit 8a7e5139018c8f591957def9471e4d5037400c26
Date: Wed Jul 9 14:16:23 2014 -0400
Adding view in pymol option and plane info to read into membrane info
commit b097728225776301a14d527bfc71c5bdb4c97fb3
Date: Wed Jul 9 14:03:53 2014 -0400
Adding updated version of show membrane planes viewer
commit e363f388a8b5e891eca4ec157c3202995f2f91af
Date: Wed Jul 9 13:46:04 2014 -0400
Adding membrane planes object to build settings
commit 37cd92f7b6ed682603c0821c56549ab4ce915fb4
Date: Wed Jul 9 13:44:59 2014 -0400
Adding membrane planes classes
commit e1acea1c459267ac071f978c234013fb3124ca18
Merge: 178f2b6 d1c09ae
Date: Wed Jul 9 19:22:53 2014 +0300
Added tarcer messages to Splice.cc
commit 9e78f9c887a6ed866d2ab2683368712e502da9e3
Date: Wed Jul 9 13:32:52 2014 -0400
pdbinfo fixes
commit d1c09aebaf1b5721a975f17753a477e8b835baf8
Date: Wed Jul 9 10:35:44 2014 -0500
Fix signed compare errors that were breaking the build.
commit c4b73ed51b3bf8ee7bb9a3ee87048862a6ae1e69
Date: Wed Jul 9 11:34:10 2014 -0400
deleted files of renamed energy terms
commit 4965e0fe3fae0b0b14188525e0ac2cb4008a2d64
Date: Wed Jul 9 11:30:26 2014 -0400
Undoing commit where I renamed the membrane energy terms
All energy terms should again start with MP, renaming them was a bad idea in the first place
commit 11ab10e947b1089d71e8ad4530cb8a1f0cb628c6
Date: Wed Jul 9 11:13:50 2014 -0400
added comments to docking protocol
commit 76d8d12d3bbd480fdeb43098a9f765f1f3d29c7b
Date: Wed Jul 9 09:09:06 2014 -0400
Fixing build errors from global namespacing and andrew's get_score_function rename. Merging remote master up to Rocco's recent commit into ninja local master and into current mpframework devel. 7/9/14
commit c959a80a7aa8e88431e34a29b9d4d631eeb74979
Date: Wed Jul 9 04:30:29 2014 -0400
commit 049b97d0f67f642648e2c41b420b16522298c6ab
Date: Wed Jul 9 04:26:35 2014 -0400
added bogus internal coords record to VRT1.params to keep residue_io.cc
-- wow that code is such a mess!
commit 773b482422eb8b1a399513c7e3c7386962c44a75
Date: Wed Jul 9 04:25:30 2014 -0400
commit abefbdbbed69970cd2889f420e2d74e3a586bc52
Date: Wed Jul 9 00:54:12 2014 -0400
bugfixes
commit 8297c165a18fb0bda8668fc28b991d81aad4a0a1
Date: Tue Jul 8 23:28:58 2014 -0400
Updating scoring manager due to merge conflict
commit dca27af24b52bd269e02b57b4d623080d30454d1
Merge: 2e3d5a4 05685c8
Date: Tue Jul 8 22:47:21 2014 -0400
Merging recent master up to Rocco's commit (7/8/12) into current mpframework devel
commit 05685c84f52abd1e7a9b90ab4f47971fc8bd50b6
Merge: 2884d93 15059e4
Date: Tue Jul 8 22:47:10 2014 -0400
Resolving merge conflicts in master
commit 6f362f98d73cadb7bf525c469af5423e97d8c8eb
Date: Tue Jul 8 22:41:29 2014 -0400
Quick changes in conf & rt mover
commit e602a7027ae2ad0cfde6969ec7cb0852d64c05d9
Date: Tue Jul 8 22:18:40 2014 -0400
make Grafting classes parse pdb_num/res_num at apply time instead of construction time. This allows better integration with the use of SavePoseMovers
commit a7a2b1f631148b7841e3048905c9809aa5ae3b9c
Date: Tue Jul 8 21:28:56 2014 -0400
work on RS interface
commit 53df8519dbc8cd35e1ef37e72254d9b909e4324a
Merge: 092f51f e9323c6
Date: Tue Jul 8 19:39:54 2014 -0500
Fix performance benchmark (ContextDependentGeometricSolEnergy)
ContextDependentGeometricSolEnergy was using the HBondSet but not generating
it. This results in issues when run in a Scorefunction with only those
energy terms and no HBonding terms. Add cautious generation of the HBondSet in
the setup function (along the lines of the HBond terms).
No test changes expected.
commit 092f51f8df158a909654e928761ba1a64a069cff
Date: Tue Jul 8 19:39:54 2014 -0500
Fix performance benchmark (ContextDependentGeometricSolEnergy)
ContextDependentGeometricSolEnergy was using the HBondSet but not generating
it. This results in issues when run in a Scorefunction with only those
energy terms and no HBonding terms. Add cautious generation of the HBondSet in
the setup function (along the lines of the HBond terms).
No test changes expected.
commit e9323c627d01e4c6e68384de3bb5e1c685ffe30f
Merge: b7f4cde 15059e4
Date: Tue Jul 8 15:41:49 2014 -0700
another merge from my branch rhiju/dms_score, which introduces rna_chem_map_lores score term. This allows chemical mapping data to guide fragment assembly, and is being tested in the RNA puzzles blind trials. Integration tests show changes in KIC_refine, SnugDock, antibody_H3, and a few other tests that look like floating point deviations. This has happened to me before when I update ScoreType.hh -- I will pay attention to whether there is an effect on the test server...
commit b7f4cdee1edf4066651605ad1b65fb5920973587
Merge: 390557f d994b32
Date: Tue Jul 8 15:41:10 2014 -0700
another merge from my branch rhiju/dms_score, which introduces rna_chem_map_lores score term. This allows chemical mapping data to guide fragment assembly, and is being tested in the RNA puzzles blind trials. Integration tests show changes in KIC_refine, SnugDock, antibody_H3, and a few other tests that look like floating point deviations. This has happened to me before when I update ScoreType.hh -- I will pay attention to whether there is an effect on the test server...
commit 732bf70d8bee72d2034e895c10e18f5e88500f7f
Date: Tue Jul 8 17:34:19 2014 -0400
updated mpdocking weights
commit 15059e4a16593b3d215136963702530c284d4270
Date: Tue Jul 8 15:44:02 2014 -0500
Fix uninitialized variable in DdgFilter
This was was giving us the intermitant DdgFilter unit test failures.
No other test changes expected.
commit d994b32f3634e8895d9b484a7cbe591c83506f07
Date: Tue Jul 8 13:40:58 2014 -0700
further updates to allow rna_chem_map_lores scoring to occur during FARFAR with minimal computational cost
commit 390557fd7fa1b318799939a992035c08972f9c28
Date: Tue Jul 8 16:39:01 2014 -0400
Renaming core::scoring::getScoreFunction to core::scoring::get_score_function
This function violates our naming conventions, so I'm fixing it along with
getScoreFunctionLegacy.
Also fixing a bug in core/membrane/io/SpanFileIO.cc which was producing
unit test failures.
commit 10f7b0da11420d9db37b93d9713d2660dce1c1e2
Merge: 3d98ce7 e064566
Date: Tue Jul 8 16:37:09 2014 -0400
Renaming getScoreFunction to get_score_function to match our coding conventions.
Also fixing a bug in core/membrane/io/SpanFileIO.cc which was producing
unit test failures.
commit 3d98ce796d5abd3173ed666af933cca82f1b172c
Date: Tue Jul 8 15:57:41 2014 -0400
Renaming core::scoring::getScoreFunction to core::scoring::get_score_function
This function violates our naming conventions, so I'm fixing it along with
getScoreFunctionLegacy.
commit e0645664c97ad5c3f160edbbe316305808e166e1
Date: Tue Jul 8 14:31:24 2014 -0500
Fix atom name bug in alternate ResidueType::add_atom()
This does not affect the standard add_atom() function, so no change
expected.
New unit test function added.
commit 7967d01180eac70fa8cff810e6f36c61dac552ce
Date: Tue Jul 8 15:16:37 2014 -0400
updating rt mover test - includes deterministic translation via stub but should set translaiton via jump instead
commit f178c073a08d8bc52bb49f3329b6068cf79160b6
Date: Tue Jul 8 12:11:10 2014 -0700
Changed trajectory struct_id->steps mapping table name
commit f7357f24fab0b4d1e975b5139efe2df26a3259e0
Date: Tue Jul 8 11:50:56 2014 -0700
adding DMS-scoring potential for RNA for low-resolution stage.
commit 41a687de75046773d8a9c247609c83601fb5953b
Merge: 614c36a f448e80
Date: Tue Jul 8 11:43:59 2014 -0700
Merge remote-tracking branch 'origin/master' into kylebarlow/general_dev
commit 3cf362593440298ecf93b12e6197aaa291f227aa
Date: Tue Jul 8 14:36:06 2014 -0400
This is a fake all pass for rt position mover - translations are still inconsistent and should be done in a more generalizable way
commit 633ebb7f4c69cf8f4f84d86e28e6d4eccd704614
Date: Tue Jul 8 14:31:11 2014 -0400
Going back to explicit translation, will need to fix this later on...
commit b7cd0556e87740dc686370f4b00f851613fd84db
Date: Tue Jul 8 14:01:56 2014 -0400
updating uniform rotation and translation in membrane position rt mover
commit f448e8063abb56619f53142587d98a7cd3e2902a
Merge: 5925a1c db69e0e
Date: Tue Jul 8 10:57:48 2014 -0700
Changed JD2 behavior to fail and exit when a bad RosettaScript is parsed and fixed 2 integration tests that were not running
The affected tests that were failing silently are:
write_mol_file and features
If you care about these tests, you might want to make sure they work properly now.
If multiple inputs were passed, the prior behavior was to iterate over
all of these inputs, even if a bad RosettaScript was used that wouldn't
work on any of them.
I added a new catch block in JD2 to specifically catch RosettaScripts
option exceptions (already existing) and reraise this exception, instead
of trying to continue as before.
The other problem that this fixes is if an integration test used a bad RosettaScript,
perhaps because the script's parse_my_tag function changed, this would only be picked
up by the initial test server run, and would fail silently after that. The
script parsing error wasn't picked up because JD2 exited with a "0" exit code.
This commit merges branch 'kylebarlow/bugs' into master
Expected test changes:
write_mol_file (wasn't running before, should at least run now)
features (wasn't running before, should at least run now)
commit db69e0e3e32d570885f1cb33750a2a36a1a0f3bd
Merge: 2268e8b 5925a1c
Date: Tue Jul 8 10:56:42 2014 -0700
Merge remote-tracking branch 'origin/master' into kylebarlow/bugs
commit 0c99c80a8300d76ffd6c81048146ee48d9fa7b9f
Date: Tue Jul 8 13:53:20 2014 -0400
Trying non absolute translation in membrane posiiton rt mover
commit 2268e8b2c0e485aabfb446337b045a37d6406f21
Date: Tue Jul 8 10:50:31 2014 -0700
Removed errant "2" that I added
I must have been emacsing it up
commit c1b7d4bd9e47ae71e063c1635af0222a6e7b0c40
Date: Tue Jul 8 13:48:51 2014 -0400
add KeepRegionMover to mover creators
commit 1e7047f8fc72f826474645a756b6ac72e2be8dc6
Date: Tue Jul 8 10:44:12 2014 -0700
Fixing broken integration test
commit b904a96d786a6c417897817855972e5158ef9b09
Date: Tue Jul 8 13:39:39 2014 -0400
Updating membrane position mover unit test so the mover generalizes to any given jump - unit test still passes
commit ac2d21d8ad0e2c89fcb99518f857af01c7be1ffe
Date: Tue Jul 8 13:34:39 2014 -0400
Adding rotation & translation tests - all tests pass
'
commit d334fa7fcf8214627cd300d825c576af2574e303
Date: Tue Jul 8 13:23:37 2014 -0400
renamed argvs in MembraneInfo
commit 831c3af038c1bcea47aa5a621cd66a240ab121c3
Date: Tue Jul 8 13:22:47 2014 -0400
Adding check rotation pilot app - directly applying delta rot seems to fix the problems I was having - will change the rotation code to this and use flexible jump.set"
commit 7498e0a50ed43e46cdbb7442e4d364bf3d9ff7be
Date: Tue Jul 8 09:56:53 2014 -0700
Changed type of exception thrown when checking features reporter dependencies
Cherry picked from 614c36ad9a117ff4abe4c9f5ad2de899addd7b69
commit 324a0c147f586808f597e3a1407d8740f6f4b1a8
Date: Tue Jul 8 09:44:41 2014 -0700
Removed trailing whitespace
Cherry picked from b306f0469560c229b3c9f3f348751ad29da9ec3f
commit 6391f267a94e6e03bcad311feabf6188b4a4fc25
Date: Tue Jul 8 09:43:27 2014 -0700
Changed JD2 to not continue after a RosettaScripts exception is caught when inputting a pose
Cherry picked from c68c202211f42a12740f16610476aebaefbe717a
commit 614c36ad9a117ff4abe4c9f5ad2de899addd7b69
Date: Tue Jul 8 09:56:53 2014 -0700
Changed type of exception thrown when checking features reporter dependencies
commit b306f0469560c229b3c9f3f348751ad29da9ec3f
Date: Tue Jul 8 09:44:41 2014 -0700
Removed trailing whitespace
commit c68c202211f42a12740f16610476aebaefbe717a
Date: Tue Jul 8 09:43:27 2014 -0700
Changed JD2 to not continue after a RosettaScripts exception is caught when inputting a pose
commit b1d96e9d39ab890db11ad03571a8ae2f6c9f7606
Date: Tue Jul 8 12:33:05 2014 -0400
Adding renamed file to test settings
commit caefcb75d05221e597e5e261d3f04aacffadc8e1
Date: Tue Jul 8 12:15:25 2014 -0400
Renamign membrane rt position mover test
commit 985626f87b443eba3645f92df48efdae5ae07184
Date: Tue Jul 8 12:13:59 2014 -0400
Bug fixes in add membrane mover unit test
commit 61578cf999eb1a91a6868c8023a9fa6e63088883
Date: Tue Jul 8 12:02:40 2014 -0400
added renamed MP energy files
commit 1c9bae259d67dd6e84f0331e3ba065c5b5646d2b
Date: Tue Jul 8 12:01:49 2014 -0400
renamed MP energy terms
commit 825df0e27fc293c35213466d182fe5fb5959e91a
Date: Tue Jul 8 12:01:19 2014 -0400
deleted mpdocking files
commit 6c0a0d7ce928500427befe442f173d6b9da36650
Date: Tue Jul 8 12:01:03 2014 -0400
Updating doxygen on top of membrane conformation unit test. Also renaming add membrane mover unit test
commit 6fe424afb7a73f0dbc9d378dc5336d866d95c2d6
Date: Tue Jul 8 11:57:24 2014 -0400
Removing old unit tests and accompanying unit test files
commit aa652b9eb12df66703d16725a4b04dca58e56709
Date: Tue Jul 8 11:50:26 2014 -0400
Adding modified spanfile for post membrane add test"
commit 5925a1c46e76c18c46e5935851e7404864311e56
Date: Tue Jul 8 11:42:44 2014 -0400
Cleaning up random *.orig files.
commit fa66188f9857fb0b77d7fa6759021cb9f91547b4
Date: Tue Jul 8 11:49:42 2014 -0400
Adding unit test for membrane conformation
commit 224e7bb76b44cb3f5f60d72f15bed39bb9849d8d
Date: Tue Jul 8 11:39:43 2014 -0400
Correcting spanning topology object for membrane residue counted in spanfile
commit d365be6bff735110351f78725de5bac8a2061d9a
Date: Tue Jul 8 11:34:24 2014 -0400
Fixing membrane info unit test - all tests pass
'
commit 3e3b4861254d197629e7f5b84d4f7df50d194fe8
Date: Tue Jul 8 11:30:49 2014 -0400
Fixing build for both membrane info and membrane conformation unit tests
commit a356dee071d6bc640374314e3ce0a19babbe1319
Date: Tue Jul 8 11:21:07 2014 -0400
Fixing global namespacing errors in Justin's unit tests that broke my build, adding back a new membrane info unit test
commit 72f3025da638a236dfd97e933e9db1270a952ad7
Date: Tue Jul 8 11:02:38 2014 -0400
Adding new membrane info unit test to work with the updated version of the framework
commit 8f56b197b6990827c4173ed4ce6b53f736932ff9
Date: Mon Jul 7 23:09:45 2014 -0700
Moved SandwichFeatures down list in integration test so test will run
commit 212b1388e3dfd714c157cf4b7a3d6c51b375b6ed
Date: Tue Jul 8 00:03:47 2014 -0400
compile
commit 59f76e5bb8f14a63e269d045caede434fa94053d
Date: Mon Jul 7 23:57:13 2014 -0400
make sure to detect disulfides while doing any pose editing operations
commit 0d79b44e06bb0614ff683b132578efdc774d76c4
Date: Mon Jul 7 23:50:47 2014 -0400
add keep region mover, use pdb_num res_num designation for RS
commit 72cbf13fbee2684d3626e1e254817ec4b681e9a2
Date: Mon Jul 7 18:43:45 2014 -0700
Removed extra single quotation marks now that insert_or_ignore handles these
commit c52bc121a45118834a003b8e24855aad19cd5d56
Date: Mon Jul 7 20:12:57 2014 -0400
Adding torsion param for CE1-CT2-NH1-CT2
I think I have added a torsion parameter for CE1-CT2-NH1-CT2 about a million times and committed it zero times. This ends today!
commit 69b9e0dc0c2e12977a7fb477796104fa79e6a398
Date: Mon Jul 7 16:32:26 2014 -0700
additional small fixes to get rna_chem_map scoring in FARFAR.
commit 0484d83ae69bc02083cf3596ac179049eff263b4
Date: Mon Jul 7 15:52:41 2014 -0700
small fixes to allow rna_chem_map scoring in FARFAR after minimizing.
commit 92aaad44be03db5f2b48644cef0d2741c81550cd
Merge: 34573a5 f6ab99a
Date: Mon Jul 7 15:52:23 2014 -0700
merge from master to rhiju/dms_score branch.
commit 39dd16e78329899b54bc34f601ffca6117950b88
Merge: 02f52b3 f6ab99a
Date: Mon Jul 7 15:18:11 2014 -0700
Merge remote-tracking branch 'origin/master' into kylebarlow/general_dev
commit 2e3d5a4538d3673bfda1dd331114483dad9f4d27
Merge: 0581be1 bfe5732
Date: Mon Jul 7 18:14:31 2014 -0400
merge devel into jkleman/refactor2; resolved conflicts, compiles
commit 02f52b342d6dfa1ff08316768ce1050116328d17
Date: Mon Jul 7 14:54:35 2014 -0700
Added stride option to RosettaScripts tag
commit f6ab99abe73b42f8dccaa593a4a8e5ff4bafb721
Merge: 1b0153f 825ac9d
Date: Mon Jul 7 14:49:33 2014 -0700
merge from master -- allows modeling of cyclic-diAMP in RNA puzzle 2 by FARFAR, using CHAIN_CONNECTION format that allows non-contiguous sets of residues to be input.
commit 1b0153f78a7068dfa1b95351f2744c5386410a10
Merge: b08b588 5408a59
Date: Mon Jul 7 14:48:46 2014 -0700
merge from master -- allows modeling of cyclic-diAMP in RNA puzzle 2 by FARFAR, using CHAIN_CONNECTION format that allows non-contiguous sets of residues to be input.
commit 0581be1f6c7cb6698407f9adc073271bd63c79e9
Date: Mon Jul 7 17:42:54 2014 -0400
fixed unit tests for SpanningTopology, tests for Span and SpanningTopology finally run correctly
commit d502cdae3a0d077123b5cd2c68017a1d65d1e2f5
Date: Mon Jul 7 17:42:22 2014 -0400
added unit test for Span
commit 34573a5f41c8caf1dede40daadc697e535ee1244
Date: Mon Jul 7 07:05:59 2014 -0700
Fixes (some of) rhiju's code that break rosetta's linux gcc build.
1. Place placeholders for your unused variables:
src/core/scoring/rna/data/RNA_ChemicalMappingEnergy.cc
2.(40) RNA_DataInfo::RNA_DataInfo( RNA_DataInfo const & src ) :
utility::pointer::ReferenceCount(src)
{
.
.
.
}
commit 178f2b686e87e4749454e56d999b2c9ae26344cb
Merge: 00451be 825ac9d
Date: Tue Jul 8 00:18:51 2014 +0300
Merge branch 'master' of github.com:RosettaCommons/main
commit 00451be53f905696cfd28ed2f917c3027ec4de94
Date: Tue Jul 8 00:18:33 2014 +0300
Chages to Splice.cc
commit 01a3e05ae00578db74c97b274b2433ad4689e53c
Date: Mon Jul 7 14:11:48 2014 -0700
Changed default batch names for TrajectoryReportToDB
This is to ensure that that batch name is different than regular ReportToDB,
so that if both fo these movers are used simultaneously, they will receive
separate batch IDs.
Cherry-picked from 79aee5e9015440b79bcac2c966f1a9ad990aaaf5
commit 8676a340bfcb0743abb01c858a96608a0ec3cc17
Date: Mon Jul 7 14:13:04 2014 -0700
Features reporters table is updated for each batch and refactoring
Since a TrajectoryReportToDB mover and a ReportToDB mover can both exist
for the same protocol ID, but with different batch IDs, and with different
associated features reporters, we need to update the features reporter table
for each new batch OR new protocol ID. Before, it was only updated for new
protocol IDs.
To accomplish this, I did a bit of code refactoring as well to use the
sql_utils insert_or_ignore function. I didn't test the postgres case;
apologies if it doesn't work.
Cherry-picked from 9496451872e79b3ad40dc4eb7f2d4aed725ceac7
commit 88de2ee82d955da4b5eaab1d8dddadb775b39d35
Date: Mon Jul 7 17:08:29 2014 -0400
add copy constructors and other needed mover functions to graft movers
commit 34f31c45b809cc3cf15c1eb8dc46d929869243e2
Date: Mon Jul 7 16:56:37 2014 -0400
Peptoid compatibility for matcher FoldTree
The FoldTree for the scaffold matcher routes through CB--which is an issue for peptoids. Detect if the residue is a peptoid, and if so route FoldTree through CA1.
commit 825ac9d35451c1ccd134bed95103e7e7f59aa5ce
Merge: b08b588 c3c020f
Date: Mon Jul 7 16:25:03 2014 -0400
parameterize strength of stub constraint for matcher
The scaffold_matcher app relies on backbone stub constraints. Previously, this was hard-coded to the relatively arbitrary value of 5.0. Now it's a command-line parameter (stub_constraint_strength).
commit c3c020f4f4e53eee7ff33e9490b0b4f5f022c425
Date: Mon Jul 7 16:17:08 2014 -0400
Scaffold matcher now has a variable force constant parameter that
modulates bb_stub_constraint strength
commit 5408a59c0019eccca8b9e3b9f1f83a331809d2aa
Date: Mon Jul 7 11:46:13 2014 -0700
updates to RNA_StructureParameters that allow CHAIN_CONNECTION definition across noncontiguous SET1 and SET2 residue sets. Get rid of a scary warning when testing alternative chain connections.
commit b08b588a9048f64af6ed81505299df75e7076541
Merge: 380277e 3e1549a
Date: Mon Jul 7 13:25:26 2014 -0400
Merge branch 'master' of github.com:RosettaCommons/main
add clang version to build system, uncomment line in buns
commit 380277e8634dfb7f40373f48003e96a9cb1b6047
Date: Mon Jul 7 13:25:08 2014 -0400
commit 3e1549ae19e767e910e6892d7bd0c7090217eb93
Merge: 4fb7783 0341dbf
Date: Mon Jul 7 09:44:36 2014 -0700
Merge branch 'master' to commit fixes to linux debug build
Fixes linux debug build
commit 4fb7783dfe315a527c4588e97912cc32d068c576
Date: Mon Jul 7 09:41:46 2014 -0700
Fixes linux debug build
Several changes that fixes compilation issues.
commit 1ddbbcd005071ccba8fb47932c2eb88305d707e8
Merge: 9f482ed 0341dbf
Date: Mon Jul 7 11:42:52 2014 -0400
merge master into branch
commit cfc5ed2d43459a349c8edf710fa7e2ecf64bc743
Date: Mon Jul 7 17:34:21 2014 +0200
Update ProtectedConformation unit test for compliation.
commit b46302a8249c6a162461f3401f8518495a9e4ab6
Date: Mon Jul 7 10:10:32 2014 -0500
Build fixes into ProtectedConformation unit test.
commit d47ab918ebfdfd8dd765e3560f385cf822529400
Date: Mon Jul 7 11:08:38 2014 -0400
Fixing grabbing normal parameter from coordinates - seems correct and consistent now which is awesome
commit b5b8e05f962729dbd76c1fbc3b255daa97437bfc
Date: Mon Jul 7 10:04:44 2014 -0500
Make replace_conformation exception-safe.
commit 10dfff2981df0c8f775231db529da9b7be789352
Date: Mon Jul 7 11:03:28 2014 -0400
Updating add membrane mover to always fill the membrane residue with default initial coordinates prior to placement (doesn't want to deal with relative stub craziness)
commit 36143425625c3657b32ba2ca67dc6e1330b6b7dc
Date: Mon Jul 7 10:53:55 2014 -0400
Fixing the pilot apps build due to global namespacing errors - commenting out Julias mpdocking app for now until she can fix her namespacing issues
commit 4691873f16fb66195ccb68d1061d903e8bb4e7fd
Date: Mon Jul 7 10:28:46 2014 -0400
Updating computing membrane center/normal from the global frame in Conformation
commit 0341dbf239582a343367d15d40594ad9b29342fc
Merge: aff759e d4e65ee
Date: Mon Jul 7 07:28:33 2014 -0700
updates to RNA_DataInfo fixes -- thanks to Daniel for prior fixes to build.
commit aff759e12637e504b71847c57b7ada5f3f49136f
Date: Mon Jul 7 07:27:44 2014 -0700
updates to RNA_DataInfo fixes -- thanks to Daniel for prior fixes to build.
commit d4e65eebc60296776135e2d18945b2071a2a4915
Merge: 6a8df61 5bec2bc
Date: Mon Jul 7 17:26:08 2014 +0300
Merge branch 'master' of github.com:RosettaCommons/main
commit 6a8df615894b682be1173440dae4b77816ad6752
Date: Mon Jul 7 17:24:51 2014 +0300
added some debugging tracers and got splice to respect task_operations...
commit acb35ac42fd46299eaa8e0cf0566bf88f01d5a9d
Date: Mon Jul 7 10:10:01 2014 -0400
Fixing more global namespacing errors caused by reducing namespace scope for lipid acc info data
commit 5bec2bce046be7b563e3436b8ccd5e6a0837f1ed
Date: Mon Jul 7 07:05:59 2014 -0700
Fixes (some of) rhiju's code that break rosetta's linux gcc build.
1. Place placeholders for your unused variables:
src/core/scoring/rna/data/RNA_ChemicalMappingEnergy.cc
2.(40) RNA_DataInfo::RNA_DataInfo( RNA_DataInfo const & src ) :
utility::pointer::ReferenceCount(src)
{
.
.
.
}
commit d1ba8f453f1b9bcdeba92261007431fd16c666f0
Date: Mon Jul 7 09:39:15 2014 -0400
Fixing a quick namespacing error enabled my my global namespacing mistake and fix in lips acc object down in core2
commit 88a7a1abc0962335af9d267d62482aa9bf5747d0
Date: Mon Jul 7 09:38:10 2014 -0400
Updating doxygen in lipid acc info objects
commit 6c8523567e04aba0ef5efd85820ec9081ef12168
Date: Mon Jul 7 09:28:54 2014 -0400
Updating mlipo energy to match new interface in membrane info
commit 16350ce4345f99124729257bbd3839779f772f40
Date: Mon Jul 7 09:25:47 2014 -0400
Updating defaults for membrane_new option to match input types
commit b0d4105f3f940bb28e17b44531077a76e1903656
Date: Mon Jul 7 08:06:22 2014 -0400
Removing currently unused score types breaking the pyrosetta build from score type and socre types manager
commit 996ae9d00cfbb4ba23128d76a66caf8ecb653247
Date: Mon Jul 7 08:03:12 2014 -0400
Fixing add membrane mover to use the correct option key
commit f249194c48a95325adea2bd1d491b6e61c9a6718
Date: Mon Jul 7 08:02:07 2014 -0400
Updating option keys - changing lipsfiles to lipsfile
commit f35900facd73131acba539bb5d0c8a08aaaa8160
Date: Mon Jul 7 07:59:06 2014 -0400
Adapting lips file object to only take one file - finished fixing this in add membrane mover
commit f81b37676110f770ae03be6ee6f490b16b30eb72
Date: Mon Jul 7 07:57:10 2014 -0400
Fixing spanfile loader and things that were mistakenly commented out of the build
commit 3d44aa75c768c89cd7ae70e698b0772e261d4981
Date: Mon Jul 7 07:55:20 2014 -0400
Removing spanfile and lipid file io classes disabling object mutability
commit 3ff6ad2e25cbf1382c0f232a911127aaf9f0e7a9
Date: Sun Jul 6 22:23:10 2014 -0700
One more file to FIx pyrosetta compilation
Missing def MACRO in CoordinateArray_RMSD_FlatLookup.hh
commit a97161b9f81e7c76a416c0e4112e9dcdc80f2408
Merge: c2eb67a 1725813
Date: Sun Jul 6 22:01:05 2014 -0700
Merge branch 'master' of github.com:RosettaCommons/main
Bugfixes to FragmentLookupFilter and QCP
that break pyrosetta compilation
commit c2eb67ab8b7b018df1a0aa6589fcd069c4ba2cb7
Date: Sun Jul 6 21:58:49 2014 -0700
Fixs bugs tha break pyrosetta compilation.
Fixes bugs in:
protocols/indexed_structure_store/filters/FragmentLookupFilter*
Pyrosetta compiles fine now.
commit 1725813a2ad0b1d88dee1dbe668ed451297e7a02
Merge: e719285 f5b118c
Date: Sun Jul 6 19:34:59 2014 -0700
Merge from rhiju/dms_score bracnh: includes new score term for RNA chemical mapping (for now, just dimethyl sulfate reactivities). In integration tests, cosmetic changes due to one additional residue type, and change in score type names (in jd2_database tests). I am also seeing changes to match_1n9l & cstfile_to_theozyme, which look like late floating point deviations on my Mac, but I will monitor output from test server.
commit e719285c05db2df83cfd62b4e393aaf153a7c263
Date: Sun Jul 6 19:30:41 2014 -0700
break degeneracy in data_file in ligand_motif_design test
commit 031aa0c50e9a358d16208c0c60f4c773196d64d3
Date: Sun Jul 6 21:50:22 2014 -0400
Updating lipid accessibility info object - now reads independently
commit 9295ea52c8f5cac44ed1ff26c01bb5c42d99bff0
Merge: fad71b1 5c78555
Date: Sun Jul 6 18:34:57 2014 -0700
trying to complete merge from rhiju/dms_score to master
commit 5c7855502c25900064a514c84d97a4729f3f2027
Merge: 07e3e99 43d96d0
Date: Sun Jul 6 18:33:46 2014 -0700
merge from master, including fix from linux compile.
commit fad71b18ff36ba481ac505ddcff9e3f9fed5a6f1
Merge: 751edf5 43d96d0
Date: Sun Jul 6 18:33:12 2014 -0700
merge from rhiju/dms_score, includes several fixes needed for RNA puzzles & DMS data scoring
commit 07e3e99ab1ef096fab29dcc9d00dca2c86d1b897
Date: Sun Jul 6 18:31:15 2014 -0700
bunch of fixes to dms_score branch caught in integration tests.
commit 98f48015530e0e4e74d63703871b1deb91e04d2a
Date: Sun Jul 6 19:22:24 2014 -0400
Updating conformation to take a single lips acc object instead of a list - no more by chain access
commit 40bfc6c68ebbaebf54f7e5727434ddbb353c10f4
Date: Sun Jul 6 19:19:37 2014 -0400
Updating membrane info to take a single lipophilicity data object
commit 0f905cbb720d0ee241d163984c6432e7cbeba4d8
Date: Sun Jul 6 19:08:06 2014 -0400
Adding new fingerprint test for fullatom high resolution energy function with smoothed env derivative
commit 47bc8a7d2d8e484de994c3e2d2ee0f09350413d6
Date: Sun Jul 6 19:07:14 2014 -0400
Adding new high resolution weights set including the smooth menv term now adapted for mpframework
commit 441d02fb093b92a73e5d88dfc09762f514a81f7e
Date: Sun Jul 6 19:05:05 2014 -0400
Unhacking conformation and removing debugging tracers from old and new menv smooth energies
commit 090503ce70d0346c8f8f208e509c7eda19b16f18
Date: Sun Jul 6 19:00:02 2014 -0400
Integration check for fullatom membrane environment smooth term complete :)
commit ce01c9fa011523705abd1a566e1e837325f2a43d
Date: Sun Jul 6 18:07:58 2014 -0400
Fixing database file path and starting tag in fa menv smooth energy
commit f5b118c1833faa9b1a0b939e35e802cda4a95a44
Merge: 6413716 751edf5
Date: Thu Jul 3 12:14:42 2014 -0700
Added an overloaded operator= in SymmetricConformation with an 'other' of type Conformation. This fixes a bug where copying a symmetric pose used Conformation's operator= instead of SymmetricConformation's, and failed to copy its symmetry type.
commit 6413716e09e68fbf21566d14e166ef9c48de736e
Merge: c50299c 7ffd960
Date: Thu Jul 3 12:14:42 2014 -0700
Added an overloaded operator= in SymmetricConformation with an 'other' of type Conformation. This fixes a bug where copying a symmetric pose used Conformation's operator= instead of SymmetricConformation's, and failed to copy its symmetry type.
commit eeef6f3c7babc1803f5d569ddc0d3a8eea436ca3
Date: Sun Jul 6 17:32:17 2014 -0400
updating fullaotm energy function app to score with menv smooth score types
commit 6ee72550733e93766259b4ca465f90a0b9ba0c54
Date: Sun Jul 6 17:22:21 2014 -0400
Updating layer bounds in fullatom membrane environment term smoothed and using the framework residue depth. Otherwise, making no other changes for now
commit 14509b7051525aed655de419b262e4e3d88f4ac0
Date: Sun Jul 6 17:03:16 2014 -0400
Adding membrane env smooth energy to build settings, note lipophilicity energy is there but untested for the time being
commit 27f66ea587991d893c5a6687d534a88aa7715bc8
Date: Sun Jul 6 17:02:06 2014 -0400
Hooking fullatom env smooth energy into sfxn framework - adding score type FaMPEnvSmooth energy to ScoreType and score type manager
commit 566d8ca5d849e875fdbbab7ed28a2dc71c8da7f0
Date: Sun Jul 6 15:57:10 2014 -0400
Replacing old depth incremented parameter with new z dependent parameter per-residue
commit 12cddaec57e8d5fad7557644c58044e1da8389cc
Date: Sun Jul 6 15:52:42 2014 -0400
Continued updates to fullatom smooth energy - has a derivative
commit 1872cf67b66e68dc95065943ac350d835f50c15e
Date: Sun Jul 6 15:46:34 2014 -0400
Starting to update implementation of smoothed environment energy. Also adding new scoretype FaMPEnvSmooth
commit b1b2094b02776d9428fcb2927e333fdb6a2b60da
Date: Sun Jul 6 15:34:29 2014 -0400
Adding header for menv smooth term
commit 11a556415ac77543c62168acddf118fa879ec03d
Date: Sun Jul 6 15:27:07 2014 -0400
Adding starting files for fullaotm membrane smoothed environment term - will be adapted for mpframework
commit 5aaf00e8ed1d4e787637c04dabc8dd5bbaa4f627
Date: Sun Jul 6 15:22:25 2014 -0400
Temporarily removing secstruc and spanning penalties that were never implemented to clean up the directory and cleaning up lipophilicity energy (still needs work to break back down to not per-chain
commit 43d96d0c2ddf11398b24cadaa56f22272294d3b3
Date: Sun Jul 6 12:01:35 2014 -0700
missing include needed for linux compile
commit 4bda854d9dda4ae47f3c74d2a7960721b3d0ab22
Date: Sun Jul 6 11:45:35 2014 -0700
setting up RNA chemical mapping score during actual SWM (well, calculating score after minimizing...)
commit 7eea4728a09095fbfc03277a7853e467431b116d
Date: Sun Jul 6 11:32:13 2014 -0500
Change the EnvClaim::str_type method to EnvClaim::type. Fix a bug causing duplicate addition of EnvClaims to the master list in EnvClaimBroker. Re-add the Comparator helper class in EnvClaimBroker to avoid an infinite loop in broking.
commit 273da4396062f29a3ba4b46b4f29ec28a2284dcb
Date: Sun Jul 6 10:41:24 2014 -0500
Bind owner information to elements inside a pair in EnvClaimBroker::collect_*
commit 9691e5564a3efc415672382152676e5766334ef7
Date: Sun Jul 6 08:25:22 2014 -0700
database updates needed for RNA scoring with DMS data
commit 751edf53bce90d75c5191878c06b45125a1e8ddf
Merge: 3e23253 4711d28
Date: Sun Jul 6 11:39:45 2014 +0300
Merge branch 'master' of github.com:RosettaCommons/main
commit 3e23253b4e27447229afcc55925e7ccf323a62ef
Date: Sun Jul 6 11:36:40 2014 +0300
Added keep_native tag to Seqprofconcensus task-operation which adds the pose native aa to allowed identities
commit fa49eea85281de46cd451669d1c1006671204119
Date: Sun Jul 6 01:20:56 2014 -0400
Removing cc include guards from membrane info
commit 4711d28aea259e94c51d8046080bb4efc6275479
Date: Sat Jul 5 20:57:24 2014 -0700
Adding exception handling to ParsedProtocol to address a segmentation fault bug triggered when a mover in the protocol throws an exception.
Cosmetic tracer output changes for clarity.
Unit Tests: All Pass
commit 36c822a347acd50295f3628df58f0b2d993adf7e
Date: Sat Jul 5 17:25:34 2014 -0700
Have MissingEnergy and SWM use the same core function to calculate missing.
commit 425debd242d7a814652d54a1f3f24d46c4f7928c
Date: Sat Jul 5 17:20:16 2014 -0700
default setting of sample_res & working_res, and also allowing command-line specification. When computing missing, only look over working_res. When computing DMS score, only look over working res. Some slight refactoring of rna_score and RNA_DataInfo so that it does not have to be read in over and over again in rna_score.
commit fac34efe2d474fde374ea0b35f3cf152cce5a5f1
Date: Sat Jul 5 15:54:52 2014 -0700
Fixed segfault caused by unitialized mover
commit 23b264e655cd6e93558339cf25b38374cc2ea6e3
Date: Sat Jul 5 16:24:27 2014 -0500
Fix bug where JumpClaims would always allow their VRTs to be created if nessecary.
commit 17a4847169dfc7c8fe09e5c99dd126f498cb1635
Date: Sat Jul 5 16:04:21 2014 -0500
Fix bug in dof creation in XYZClaim where it would not claim all DOFs.
commit 8d9fcfb17b0f9b2445e3d2c4ddafc1e8378555b0
Date: Sat Jul 5 16:04:00 2014 -0500
Fix bug in topo_driver ProtectedConformation practice unit test.
commit ee36c6bedcf015230df62dec8e4c722c0ea2b68e
Date: Sat Jul 5 16:02:23 2014 -0500
Add ProtectedConformation unit test for replace_residue (because the call is kind of complicated). More to follow.
commit 5880868930a8dabb63570411a79f7956375a498f
Merge: 13109a4 6c1c48a
Date: Fri Jul 4 23:37:18 2014 -0700
Pulled origin master into sripakpa/develop branch.
Pulled origin master into sripakpa/develop branch.
commit 13109a4ce73d0fdc7a67e52c1451f825e5d607b6
Date: Fri Jul 4 23:30:47 2014 -0700
Fixes to get RNA chemical shift scoring to work with new RNA atom names.
Fixes to get RNA chemical shift scoring to work with new RNA atom names.
commit 414e2458fefd49455bc8d55aaaaea268c5f59aa0
Date: Fri Jul 4 16:15:05 2014 -0700
minor code cleanup to RNA_DMS_Potential. Allow bulged (not yet instantiated) A to give back scores too.
commit 62782958c87d2a893d62c6c7089fd476fe1da3ec
Date: Fri Jul 4 16:03:54 2014 -0700
fixes to potentials, including indexing and -DMS_separate_features flag
commit d961bd08eb05463d2c2d460cfb72d28ad62022f6
Date: Fri Jul 4 16:56:27 2014 -0500
Begin developing ProtectedConformation unit test using Tester class.
commit 924dffb133b7bbf7370e1f242232f41b049026db
Date: Fri Jul 4 16:51:00 2014 -0500
Add null pointer check in EnvClaimBroker::collect_claims.
commit 4b241e14c5013b39ccb0a3b199bf52e2a582c037
Date: Fri Jul 4 16:50:00 2014 -0500
Remove direct sandboxing of ProtectedConformation::replace_residue (using atom pairs parameter) because it resulted in double-sandboxing.
commit fac519b96b1fb00d67b4627779bcb44421afb161
Date: Fri Jul 4 16:48:27 2014 -0500
Remove unsandboxed call to loop mover in LoopCM::apply.
commit 156a94364af037f0767881452ad46db7b16794a3
Date: Fri Jul 4 14:01:48 2014 -0700
chemical mapping potential -- can now do DMS scoring based on stats.
commit 37f29740922adfe2a70576a3ba5c7273696f1149
Date: Fri Jul 4 14:29:30 2014 -0500
Fix issues with boost::bind (by removing it) in ProtectedConformation::replace_residue. System works now.
commit aee7d5e5cb0dbab2fbddecc6f1dd0c403c6a258e
Date: Fri Jul 4 14:28:48 2014 -0500
Add set_owner method in EnvClaim.
commit 60039c62cf032b56eb93d1251663c87b1edb786d
Date: Fri Jul 4 14:27:07 2014 -0500
Update clarity of Environment exception system.
commit bfe5732116008effbe904f9cc184d56e0939f991
Date: Thu Jul 3 22:02:51 2014 -0400
Fixing linux gcc build
commit 103abcdad132ab351b3dfc184d37acab5dfd6021
Date: Thu Jul 3 18:49:51 2014 -0700
Added new TrajectoryReportToDB mover to utilize features reporter framework in a trajectory setting
Code compiles now but isn't tested yet
commit 76feacd451561c18caadb509402b54de11b19447
Date: Thu Jul 3 21:33:01 2014 -0400
Removing unused varaible from the debug build in MPCBeta energy - also looked into integration test changes from the previous commit. These should be due to the deprecation of the use incorrect derivative option in hbonds energy which is reflected in the analagous commit in master
commit 3ebb32087cab3b400e89a64cdfb3f431c4b807f6
Date: Thu Jul 3 15:54:16 2014 -0700
small fixes to get rna puzzle 12 jobs to run
commit 3acc540c8b09bd0a040306494b52de9f8ef4648c
Date: Thu Jul 3 15:22:46 2014 -0700
Refactored ReportToDB to always store job input/output tags
Member variables already existed for these tags, but were usually null strings,
unless set by an outside piece of code. Only one piece of code currently does this.
Tags will be set to the current JD2 tags unless a custom tag has been set (new
bools store whether or not this is true).
As ReportToDB always has these tags now, I removed superfluous code
in StructureFeatures to get tags from JD2.
commit c396a62a2598b7c6f1b1f473a99ccd9e45a46b67
Date: Thu Jul 3 18:03:49 2014 -0400
Updating rosetta scripts hooks in all protocols/membrane movers
commit feef80a7cf4e459816a577f8f5c19f0baff435b2
Date: Thu Jul 3 17:35:39 2014 -0400
Adding new movers to hook into rosetta scripts init files and will test build next
commit f4cc3cb68ec91f5db2a97ce7b698a343aa84b5aa
Date: Thu Jul 3 17:31:00 2014 -0400
Fixed parse my tag for rosetta scripts in visualize membrane mover - not doing in show planes mover quite yet
commit 568d3c8b912cf9aeb8f24dd74e0ff10c1ce3228e
Date: Thu Jul 3 17:28:27 2014 -0400
Implementing parse my tag in all protocols/membrane package movers
commit 0fe1b8e1e1a770ceba230d73fe922033b53ba75e
Date: Thu Jul 3 15:56:58 2014 -0500
Updates to replace_residue-related helper methods.
commit 554ed64a59203ec694dd0589f209684810aea21e
Date: Thu Jul 3 16:50:10 2014 -0400
Implemented parse my tag in membrane normal perturb movers
commit 34bbd48d62761139c6a4b39260c802a2a621f8c8
Date: Thu Jul 3 16:41:34 2014 -0400
Implementing full parse my tag method in add membrane mover
commit cd473899d42601f35e0b70736d3a5c0e31134d7a
Merge: f8a38da 3d56141
Date: Thu Jul 3 16:20:11 2014 -0400
Resolving merge conflicts - adding initial membrane orientation code, anchoring code, fold tre emodifications, multibody setup, etc into parallel devel
commit e2a0d7ba5406326ab719692e821714fd6cf3f419
Date: Thu Jul 3 15:11:12 2014 -0500
Override second replace_residue function in ProtectedConformation; create general sandboxing method for doing replace_residue.
commit 9f482edeef60ec075d7645c79668d2e2658fa7f9
Date: Thu Jul 3 15:55:42 2014 -0400
add creators for GraftMover classes
commit f8a38dae69ccc865e5d40e4f427bfafbfef3c9f6
Date: Thu Jul 3 15:37:41 2014 -0400
Removing use incorrect derivtive option - not sure why this skipped the merge. Mirrored from master branch
commit ac799d104fa30cc9c0157a1538f248ccc8933e53
Merge: 7577a37 2884d93
Date: Thu Jul 3 15:29:57 2014 -0400
Fixing rhiju's merge conflict of rna features and dna test pilot app
commit 657924002d7eea86bce1f20d74506f389340abed
Merge: 2ea9a6b c50299c
Date: Thu Jul 3 12:28:43 2014 -0700
Merge remote-tracking branch 'origin/master' into kylebarlow/general_dev
commit 2884d9310b9904d89c4ed606c0039210b6b6fabf
Merge: 6b41774 c50299c
Date: Thu Jul 3 15:27:49 2014 -0400
Merging ninja local with remote master branch:
= PyRosetta build is currently broken. Will not be due to membrane changes
commit 3d5614198e745682e3576d5ccd989ce756f30e00
Date: Thu Jul 3 15:19:00 2014 -0400
Quick compile fixes in membrane position perturb movers
commit 7ffd960df80b364932330de3ecd0f83975cc5e6e
Date: Thu Jul 3 12:14:42 2014 -0700
Added an overloaded operator= in SymmetricConformation with an 'other' of type Conformation. This fixes a bug where copying a symmetric pose used Conformation's operator= instead of SymmetricConformation's, and failed to copy its symmetry type.
commit 75db96a4be5f6d8855e9ac5fcc8024cda67cb37c
Date: Thu Jul 3 15:13:29 2014 -0400
Implementing the rest of position perturb movers - not tested yet, but going to put this on hold until I can get the pymol communications going for testing
commit c21fee82ef4f9442a06de0aeac19540e030bf1d5
Date: Thu Jul 3 14:59:38 2014 -0400
Applying center and normal perturb moves in position perturb mover - just needs to implement the rest of the apply methods
commit edb982d64c947539c1a86ac4ffa15fbbd67050bf
Date: Thu Jul 3 14:44:39 2014 -0400
Perturb movers compile without apply or parse my tag
commit 5da1a765726cbcfc3bf961062c082126f5aed03a
Date: Thu Jul 3 14:09:20 2014 -0400
All of the shell code for perturb movers should be present
commit 10d32a6800a7093df22ea5255d0c3b23f5830384
Merge: 603053c f1f7794
Date: Thu Jul 3 14:08:23 2014 -0400
Merge master into branch
commit ef550ba622da53d196696010bc187fedceec8474
Date: Thu Jul 3 14:02:27 2014 -0400
Implementing membrane center and normal perturbation mover shells - everything but the apply mehtods
commit fa64d7a86857a906fcab75acd44ba3657be44e3b
Date: Thu Jul 3 13:48:05 2014 -0400
Updating implementation of small gaussian perturbation movers for membrane position
commit a6f236b861c3c0b0c3bff7babffe8909a4d5a8a3
Date: Thu Jul 3 10:28:39 2014 -0700
adding RNA_DMS_Potential for scoring DMS. Code compiles but not tested yet.
commit 761476c5e579eeb60a52e197677e577abf1c28c2
Date: Thu Jul 3 11:44:57 2014 -0400
Finished implementing membrane normal perturb mover
commit 3bcbf84798a87162b3721777629855145b24a0ef
Date: Thu Jul 3 10:42:27 2014 -0500
Improve failed DoF access error message.
commit 283d30f901d6264bd6f967f2a5739313c082c550
Date: Thu Jul 3 11:41:13 2014 -0400
Implementing membrane center perturbation mover header
commit e971a6b6280d93d5fdcb24a8448f9039c0d45795
Date: Thu Jul 3 11:27:38 2014 -0400
Starting to implement the basic parts of membrane psoition perturb mover
commit 43b1f4acda7a8c72c4cda594b49f1ec40b52038b
Date: Thu Jul 3 10:13:48 2014 -0500
Fix a bug where loops built from selections were claiming cuts at the first or last residue.
commit c22a2523dce77cf2829b5918bd2a3df4073d8a3c
Date: Thu Jul 3 10:13:13 2014 -0500
Comment clarificatin.
commit 121036f1c60d562be3ad6a11a34d486814c5bb47
Date: Thu Jul 3 11:10:01 2014 -0400
And we are good - needs 2 separate movers for protein and membranes - one that will move to an exact position specified, and another that will move relative to an existing position. The absolute vs relative is important for preserving membrane coordinate frames
commit f7f3179ade768a55aa5740df2cff762a7772727c
Date: Thu Jul 3 10:55:07 2014 -0400
updating membrane position rotation translation mover to not normalize input at constructor (makes a mess) and needs to think about those input checks to prevent crazy things from happening. Also starting to implement backbone of the perturb mover
commit 4e3ae178f0659eb45ca85113bd704e7c77ef0e7b
Date: Thu Jul 3 10:45:00 2014 -0400
Adjusting membrane position rt mover for generality - can apply to other jumps besides the membrane jump, whose number should now be specified in the constructor
commit e84e2121547210872367d82c90c6c9d924897f7c
Date: Thu Jul 3 09:56:14 2014 -0400
Making a quick adjustment to membrane posiiton RT mover to show the move generalizes to moving both the protein and the membrane position"
commit b56818cc8663344625fad6698d5c594ba2293360
Date: Thu Jul 3 09:31:31 2014 -0400
Updating core.3.src.settings
commit 47ed87c07cec2781d2f62c5e8afea58e2f205d59
Date: Thu Jul 3 00:58:27 2014 -0400
Getting rid of an old method in core for depth no longer used - now lives in membrane info
commit 2995799f4718b5e3410a2acc0a32af293c3775d5
Date: Thu Jul 3 00:55:54 2014 -0400
No longer allowing explicit setting of xyz coordinates in the membrane virtual - moves are occuring reliably - use those instead. Also getting rid of the embedding_methods class not in use and used to rely on ability to set xyz
commit 8c4edaea9a950f7e17d39ebd9882bb0452fcd44c
Date: Thu Jul 3 00:49:01 2014 -0400
Deleting random files that were added once...
commit d4c48e9a546f87f1341b2363990235de88c1ae7e
Date: Thu Jul 3 00:44:37 2014 -0400
Transform into membrane mover - also behaves reasonably now. Will add an additional unit test for this later
commit 219a79f54346246e1da964c76d0edcf3ed6bdfac
Date: Thu Jul 3 00:12:35 2014 -0400
Updating transform into membrane mover
commit d675721d58d953d01bab4433cea7397bffebad09
Date: Thu Jul 3 00:07:17 2014 -0400
Membrane normal now derived from directionality of local coordinate frame
commit 9f98fa97b443a24dfe89cde8960ac4bb3fd93ac3
Date: Thu Jul 3 00:06:12 2014 -0400
updating membrane conformation to return a sin inverted normal vector from the local coordinate frame - this ensures correctness just in case of transformations
commit 9a6b9ba1cba9df0e13910337d78867c4993c77b3
Date: Wed Jul 2 23:49:03 2014 -0400
Just for the commit history, global frame rotations are randomnly in the visualize membrane application
commit e587121581f0b5bd1a66e4e88fe6c15fef7396fd
Date: Wed Jul 2 23:45:42 2014 -0400
Membrane position rotations working in the global coordinate frame - great ;)
commit 50bfea5a76876f2ad51e4a8861c28589702f08e1
Date: Wed Jul 2 22:18:06 2014 -0400
Getting rid of initial orient mover, too hacky and detemrinistic
commit 7f3c10192a3a8cd03240195eabbbd74fe6bef8ea
Date: Wed Jul 2 21:44:29 2014 -0400
Fixing initial orient mover starting coordinates for a, b, c from stub. Had a and b reversed by accident
commit caf28e211ee58e2278823e0a3408e2866f7fe160
Date: Wed Jul 2 21:39:59 2014 -0400
Adding a membrane initial orient mover - will ensure that the normal axis of the membrane planes is pointing upwards along the z direction, also making the remaining computations more predictable and numerically reliable. In the future, the params file should just be setup to create a good default membrane stub but I am currently uncertain of the steps to do this
commit e3c90338d1853de40e0256f27347fb7c896c1c05
Date: Wed Jul 2 20:50:28 2014 -0400
Updating membrane position and initial position mover to use the updated rotation move
commit 650a0e47a90215fa32a43b7035881ddfb4b86843
Date: Wed Jul 2 20:40:46 2014 -0400
Updating membrane position mover - should make the correct rotations now
commit 22c058e66b956395946b2df1db99747d3130c446
Date: Wed Jul 2 19:06:44 2014 -0400
Fixed rotations - working all good now :)"
commit 6cec188f3d165bd8a387ffe721a47e7df6d1a0ce
Date: Wed Jul 2 18:51:03 2014 -0400
Ok - just like we explicitly set the center, I am going to explicitly create and set a new stub with my desired normal. It doesn't look like rotation about some arbitrary axis is a good approach - it will not guarantee the deterministic result. This follows the idea of a uniform and guranteed way of working in absolute coordinates when things in Rosetta are mostly relative
commit e528875470e16e35c84e6e3fba02c1ea92112531
Date: Wed Jul 2 18:16:33 2014 -0400
Hacking stubs...one way to get the correct result but it still feels wrong...
commit 616300da71034ec97714aa9a1624e006d395a75f
Date: Wed Jul 2 17:49:27 2014 -0400
Fixing default membrane params to give the proper stub orientation from initial positioning
commit 61fd819bb433e8d81d8fa969b133ca2fe09f1817
Date: Wed Jul 2 17:23:03 2014 -0400
Working on initial stub orientation and deterministic move
commit 6678fc299dd1101deae4d68d7738bc327272b288
Date: Wed Jul 2 14:20:20 2014 -0400
Updating initial mover to make transformation instead of a position rt transform
commit 9440f92c9a3be82667caf6ebcbd5130780164d0b
Date: Wed Jul 2 13:34:07 2014 -0400
Membrane moves and protein transform moves are occuring consistently - will add initial orientation mover now
commit ca0ebbb3ea4fe15585b05128e0e054b8877fd22f
Date: Wed Jul 2 13:27:33 2014 -0400
Updating membrane position RT mover to set 2 as the default membrane jump. Also fixing check reasonable membrane fold tree method to check valid jump point but not the specific jump number. Scheme seems to work out pretty well
commit bc867666f1b8a37f58ba13ea0465d277328c5745
Date: Wed Jul 2 12:48:17 2014 -0400
Adding anchoring virtual residue to protein and changing the default membrane jump number to 2. This now also being explicitly set in the add membrane setup mover. Not going to track protein jumps - that is protocol specific
commit 15e42a8dae33c045ad81441ecdb8a08f483f7e19
Date: Wed Jul 2 11:33:45 2014 -0400
Adding code for rotating about the jump
commit f5d7f8b9f9dd58affc5413bc7e6ba224a34e79e8
Date: Wed Jul 2 10:53:19 2014 -0400
Lots of things to commit: Starting files for membrane orient perturb mover, work on the fold tree, some outlines for needed modifications to the pymol mover and add membrane mover modifications
commit a03a82f4d36cc9f132026d870ccde98fade47424
Date: Tue Jul 1 22:53:10 2014 -0500
Fix a bug where Claims did not have access to PDBInfo object during claiming.
commit 3cba4126d3c9656a68bce81c65afb7ed468f7920
Merge: 6b828d5 cf36209
Date: Tue Jul 1 21:38:39 2014 -0500
Merge mystery remote changes and LooCM mover registrator fixes.
commit 6b41774e3e321a4a15c1b8a08535a41b4bdf30ca
Merge: a9312e5 5ae4a79
Date: Tue Jul 1 22:38:23 2014 -0400
Merging in branch master from remote into ninja local
commit 6b828d5c9eee323c9dd545ffc40fdb96094945c6
Date: Tue Jul 1 21:35:32 2014 -0500
Fix Registrator bugs and bug relating to Loops creation from selector
commit e7b8398f2f0a6b4d04b2d011845ca2c26734cc41
Date: Tue Jul 1 20:29:18 2014 -0500
Add LoopCM to Mover registration system.
commit cf3620931c7d90defa54813d4991f6708ff3f2fb
Date: Tue Jul 1 20:29:18 2014 -0500
Add LoopCM to Mover registration system.
commit cab6dc6c3cccdcba85371952c673b3c6b55fc0b7
Date: Tue Jul 1 17:28:42 2014 -0700
refactoring RNA_Data stuff a little to allow read in of actual DMS values and scoring.
commit 7577a37dce0fa6a4aca95467569eb899a3da902e
Date: Tue Jul 1 18:17:27 2014 -0400
Fixing a bug in the linux.gcc.debug build - did not explicitly declare the namespace required for use of core types in MembranePositionRotation mover. This should fix it
commit 0ddd30c51ee465cf7bf56e3c8e965e1f1a5096f1
Date: Tue Jul 1 18:06:22 2014 -0400
Membrane Framework Updates:
= Membrane Position RT Movers - Apply explicit rotations & translations to the membrane residue
without modifying the fold tree. Rearranges the current fold tree - so there will be expected integration test changes for membrane_relax and load_mpframework (and anything else that prints the fold tree in it's show statement)
= Fixed unit test build
= Added MembranePosition rotation/translation mover unit test. Should be more rigorous in the future,
but the basic test is present
= Adding shadows of pymol mover code from a previous merge. This is not the most up to date version,
and will be merged in at a later date
commit fbd698e9ed8b7ab7d3b96d84ddc46160bfa21800
Date: Tue Jul 1 17:57:02 2014 -0400
updating membrane position movers to take a general membrane jump, no longer hard coded to position 1
commit e198d432d8956a42e77411e02fedc10569e5b0f8
Date: Tue Jul 1 17:51:14 2014 -0400
Rotation code and unit test behaving reasonably - merging basic code into devel next
commit 8df0cdd47d556136336c86dddbca49b53ff387ee
Date: Tue Jul 1 17:16:57 2014 -0400
Adding current version of the code
commit 3857fb1b2e51f1878fee831766ff6a45a84cb499
Merge: 96e9119 0aa4dfe
Date: Tue Jul 1 10:51:57 2014 -0700
quick merge from swm_general to dms_score branch.
commit 0aa4dfea662065327bf1826a3de02f5abfb36f77
Date: Tue Jul 1 10:51:41 2014 -0700
getting linux to compile with Vector, which has a name conflict with some system library.
commit 96e91196d648ca97d8fb3c4408c158e4d3159215
Date: Tue Jul 1 10:49:56 2014 -0700
fix to constraint setup in SWM when reference pose has crazy numbers.
commit 88b90c671b6b0b3a0e4b5de4d30cc6ca4589a5af
Date: Tue Jul 1 10:48:43 2014 -0700
getting rid of a compiler error due to wrong order of initialization of variables
commit ebce9c942cec7d3736ffcbe06e82797531f5a55d
Date: Tue Jul 1 10:48:13 2014 -0700
updates to get pseudomethyl energies for DMS/RNA modeling
commit 8c31e19b544cdc91aab9726a18809923f53c22c9
Merge: 77a2ea3 9c4f067
Date: Tue Jul 1 10:22:22 2014 -0700
merge from master.
commit 88df09526ac577b4d6b8daa02a0e27ed121cc77d
Date: Mon Jun 30 23:16:39 2014 -0400
Currently has reasonable rotation code - will document tomorrow
commit 310cb74b1ccbb89bfa645ac75275ede5e105226e
Date: Mon Jun 30 22:46:17 2014 -0400
Oh that's beautiful, finally doing rotations :D And I'm not kidding this time
commit 04f4c2b0bd0110e2e0b8de92b836699d54702c37
Date: Mon Jun 30 21:53:36 2014 -0400
Trying rotation with new representation of the normal from Justin's suggesiton about handling deterministic rotation moves
commit 8f798bd4761e9aea32f667621fec150b5c2d5f86
Merge: 80ef402 7f54625
Date: Mon Jun 30 17:37:07 2014 -0700
Merge branch 'rpache/KIC_with_fragments' of github.com:RosettaCommons/main into rpache/KIC_with_fragments
commit 80ef4024a5f5c85acc5474c419e37cbd655dc24e
Date: Mon Jun 30 17:35:33 2014 -0700
changing format to tabs instead of spaces
commit 85d45557e305f719696345a95efee4efc1409acf
Merge: 430fd49 481fb5a
Date: Mon Jun 30 18:50:20 2014 -0500
Merge justinrporter/env_claimscript in anticipation of removal of that branch.
commit 481fb5aa54687675230ec8be99b27f1bfb302d45
Date: Mon Jun 30 18:49:15 2014 -0500
Add LoopCM Client-based mover to make KIC and CDD perturb and refine movers claim.
commit 8511cb57c0b05a28f895dfc029333f20b79ff6c8
Date: Mon Jun 30 18:48:11 2014 -0500
Add selector based constructor for TorsionClaim.
:
commit 7bcca9a2fc6c6d3fcb559e58cb1db64766d2f1c8
Date: Mon Jun 30 16:18:04 2014 -0400
added SpanningTopology test, compiles, doesn't run; fixed bug in geometryUtil test
commit fed1249aed37ad894c4b276f5e21834435ca1f6f
Date: Mon Jun 30 14:29:17 2014 -0500
Add vector1< bool > initializer for IndependentLoopMover.
commit a5638d44173fce2551526a09b2ab92a44cf7db66
Merge: dac4b73 6505c5b
Date: Mon Jun 30 14:06:06 2014 -0400
Merging in membrane stub moves which should become useful in the show planes viewer
commit 6505c5b57e607f92ca1d01d5ea9303308ce2a602
Date: Mon Jun 30 14:04:58 2014 -0400
Still bugs in rotation...
commit baf3b213deb13f151e84dc549b7268ae2a28fed6
Date: Mon Jun 30 11:56:46 2014 -0400
Updating mover creator and forward headers to relfect the actual state of the mover
commit 261403fea5c5c075d95ea9b557f0a4a888e771cd
Date: Mon Jun 30 11:51:17 2014 -0400
Implementing translation and rotation move as separate rb moves that can be composed in a top level mover - the reason these need to be separate, is because one is acting upon the actual RT in the jump, whereas the other deals with the actual coordinate position in the stub. It fixes the non-coherence issue with center being a point and nomal being a direction. finally
commit 3a18942a849b0870be57eebe8c5f94765639b3c8
Date: Mon Jun 30 10:36:04 2014 -0500
Modify FragmentMover to implement MoveMapMover interface.
commit 54332a1c339750e28fe3ff75a7f4bc550ad03122
Date: Mon Jun 30 11:34:54 2014 -0400
Has the independent moves that work - will just compose into 2 separate moves and things should be good
commit 112ded1edb668fb957a1c29efeb54447b8a65af1
Date: Mon Jun 30 10:53:33 2014 -0400
Membrane rt still has bugs, taking code to merge into another branch
commit ef8b9a8c74113ab0b88ca03a9f1da900e58b9be2
Date: Mon Jun 30 10:40:21 2014 -0400
Removing an errant std::cout statement; this code looks like it's ready to me.
commit 9c8543c8f708f6ab52874a4bc070dcb53b899304
Date: Mon Jun 30 10:27:37 2014 -0400
Adding unit tests for the CDF code in Ramachandran2B
commit dbab01fe587376df44875039fc9c3bc055e97be3
Date: Mon Jun 30 10:08:01 2014 -0400
Unit test finally doing something reasonable - going to implement the rest
commit 635d59852dde641e70fd692d12b19a8c937c377b
Date: Mon Jun 30 10:03:25 2014 -0400
Implement corrected rotation & translation in membrane position rt mover
commit 5e0bcae795a71bd8b932d00c834448caef81a4fb
Date: Mon Jun 30 09:52:42 2014 -0400
Finally got translations working - code in the unit test and needs to be back generalized to the mover, but got something working ;)
commit 804486aeb1c0663d0f56147baedaec298e79bc23
Date: Sun Jun 29 22:57:47 2014 -0400
Same orientation problem in setting the jump - code looks more reasonable now though
commit 2aab4ea6a199e9a96ba1c5d53f54cc701d9a56d1
Date: Sun Jun 29 22:48:29 2014 -0400
Updating membrane position mover - rotation matrix is correct, but trying to set it in the stub is more complex
commit 99515cce3e6e98bb8d53e1393e647b8b1d518460
Date: Sun Jun 29 22:37:21 2014 -0400
Correcting rotation move, things should hopefully work now
commit e8a5b6b22e14b1d3e5eaf371efcea25531cebe04
Date: Sun Jun 29 22:18:55 2014 -0400
Right now, I am explicitly setting the rotation matrix equal to the stub matrix which is flat out wrong so the test will not pass. Getting there though
'
commit b99647e6a689b0536ff45fa97214f816354a8c41
Date: Sun Jun 29 22:11:04 2014 -0400
Consecutive translation test passes - still doesn't check for this strange is_stub edge case that seems to be often relevant for membranes. The thing, is that its not invalid for the normal to be along the same axis as the center, which can happen. Will look into it
commit 02bc0022d8793d5c2c8a4bdd03804ed57521683e
Date: Sun Jun 29 21:59:39 2014 -0400
Forgot to add spanfile to protocols test settings - recompiling and copying over to default bin now
commit fa82db66f054bd5d0e63327e81216ea098e702ab
Date: Sun Jun 29 21:54:50 2014 -0400
Membrane rotation/translation position unit test compiles with just consecutive translation test implemented
commit cb173b56002e3c551a324d5c0920eb3c682e2809
Date: Sun Jun 29 21:33:07 2014 -0400
Adding bacteriorhodopsin pdb and spanfile for membrane pos rt unit test
commit 9c0c406d9418d46bb98ba5085c82a1edd91fe862
Date: Sun Jun 29 21:27:35 2014 -0400
Starting to implement membrane position RT test
commit ce96da913d4475dc1fab57472ce15707f32b28fe
Date: Sun Jun 29 21:23:31 2014 -0400
Remedied current unit test situation - everything commented out except for unit tests I know will work
commit 0194b6f04e8e9cb39756261b97c23755b4b6f376
Date: Sun Jun 29 21:18:06 2014 -0400
Getting rid of check_trans pilot app - code now implemented in the mover
commit 7a7a5938651a71c5eaabeec5b00a2d2025482f03
Date: Sun Jun 29 21:16:15 2014 -0400
Adding uniform RT to membrane stub to its new home in the mover
commit e44c4f7e3454bdbd38c44b34dd38c58a2b4fde4a
Date: Sun Jun 29 21:11:04 2014 -0400
Check trans now contains code for valid Uniform RT of the membrane stub - also reads pretty logically which is pretty exicting
commit c0213115dd2c8b2682ffa544c1215a61177e7cb6
Date: Sun Jun 29 21:07:12 2014 -0400
Downstream and upstream positions were flipped - does the translations correctly :)
commit b0a36e768c27422abb444ced62378d97baea86dc
Date: Sun Jun 29 21:02:04 2014 -0400
Check trans code contains some probably more acurate code for moving the membrane stub...still not perfect though
commit 39146cc9253a4d9af2749cea8289870958452ad2
Date: Sun Jun 29 21:01:17 2014 -0400
Check trans code contains some probably more acurate code for moving the membrane stub...still not perfect though
commit d1b8e9b7899444aeda67e087c5ffd8c92a85585f
Date: Sun Jun 29 19:19:21 2014 -0400
Translations are occuring correctly - now to just figure out rotations
commit 8968b8a6c9ff65f20d7521e43f1075b12a71e6a0
Date: Sun Jun 29 16:00:52 2014 -0400
Fixed a lot of bugs related to making rotations/translations but its still not doing what I need...working on it
commit 354bd82af40f9992c55e0e053e6d32731f1d6246
Date: Sun Jun 29 15:36:44 2014 -0400
I have no idea what is going on...pymol shows that the translation/rotation are occuring appropriately but the output in my check trans begs to differ
commit 9a50ca1331480cf58e048f6a404debc6991f61f6
Date: Sun Jun 29 15:14:32 2014 -0400
Adding pilot app as a check for this
commit 7f9661ef984932f9c5e823d6b02f43f4a0a52522
Date: Sun Jun 29 15:14:10 2014 -0400
Committing current work trying to fix moveable membranes
commit 883b889195bf1265092e83bd2b5dcbca689e4e78
Date: Sun Jun 29 13:33:40 2014 -0400
Implementing uniform rotation/translation move from the membrane stub
commit b9648fbfc0f0a22e65e4bd02a0f1db3638c6aa6f
Date: Sun Jun 29 13:18:31 2014 -0400
Dropping the requirement for membrane residue to be the root of a reasonable membrane fold tree (much more generic) and making the check fold tree method take a const reference for correct pose binding
commit dac4b73c4f8241dcff164ee907d30375c2ee3c0e
Merge: 8e28e36 ea08a10
Date: Sat Jun 28 22:28:53 2014 -0400
Merging branch mpframework devel into pymol mover viewer branch
commit 895f05a8af0c7840a07c15154a1bbafccbbed946
Date: Sat Jun 28 22:26:13 2014 -0400
All of the code compiles...except the move ;)
commit ffb8aa5f93054be6e3f27370d2a1f10d98c2aa56
Date: Sat Jun 28 22:02:22 2014 -0400
Implemented everything in the membrane uniform rt mover except the apply - going to need to do this one interactively
commit baf2009fc5ab1b3a9e80e02dbc8141893854002d
Date: Sat Jun 28 21:56:05 2014 -0400
Implemented mover creator header and forward header - also working on cc file
commit fe34ba207e49c8b7de0d9dde01e9989fff685204
Date: Sat Jun 28 21:51:00 2014 -0400
Making a shell for the cc file for membrane position RT mover
commit ec56f4c7e187469c1432827fa523c2a7ebbd7995
Date: Sat Jun 28 21:37:08 2014 -0400
Membrane residue cannot be the root for the move to work - changing this temporarily in teh code
commit 7b824ff1de2c73a812270f50fc4c091ec35aca0b
Date: Sat Jun 28 21:31:52 2014 -0400
Implemented header file for membrane position mover
commit 76c0f1ce33ec4e9239e85bc02d59d50d9c0a28a3
Date: Sat Jun 28 21:20:09 2014 -0400
Starting to think about how this move will actually work...
commit 3132a360d8a6e72e07e903c493725f5c689b69e7
Date: Sat Jun 28 21:05:23 2014 -0400
Initial add of files for Membrane Position RT mover
commit ea08a10921c15608485d1f2f24ab8d3eb8ba2dd3
Date: Sat Jun 28 18:38:58 2014 -0400
Membrane Framework Updates:
- Added enum MembraneParams.hh for referencing atom indicies more cleanly in the membrane residue
- Added arguments in the membrane info constructor for specifying the membrane jump number. Also added these methods to the copy constructor of MembraneInfo
- Added a check_membrane_fold_tree method that users should run - this will let them know if their fold tree is reasonable for use with things like the atom tree minimizer.
- Fixing ~20 files broken by the spanning topology updates - most due to lack of #include membrane info and incomplete type definitions. Includes resource manager code, energy term #include declarations, etc.
- Formatting fixes in Embedding classes for coding conventions
commit 2a04d0531503164bd3b45900431afa4e1eb40a87
Date: Sat Jun 28 18:15:10 2014 -0400
Membrane Framework Updates:
- Added enum MembraneParams.hh for referencing atom indicies more cleanly in the membrane residue
- Added arguments in the membrane info constructor for specifying the membrane jump number. Also added these methods to the copy constructor of MembraneInfo
- Added a check_membrane_fold_tree method that users should run - this will let them know if their fold tree is reasonable for use with things like the atom tree minimizer.
- Fixing ~20 files broken by the spanning topology updates - most due to lack of #include membrane info and incomplete type definitions. Includes resource manager code, energy term #include declarations, etc.
- Formatting fixes in Embedding classes for coding conventions
commit a27bc70465980e884372d478a13c3aa5bb0e65f1
Date: Sat Jun 28 17:48:51 2014 -0400
Membrane Framework Updates:
- Added enum MembraneParams.hh for referencing atom indicies more cleanly in the membrane residue
- Added arguments in the membrane info constructor for specifying the membrane jump number. Also added these methods to the copy constructor of MembraneInfo
- Added a check_membrane_fold_tree method that users should run - this will let them know if their fold tree is reasonable for use with things like the atom tree minimizer.
- Fixing ~20 files broken by the spanning topology updates - most due to lack of #include membrane info and incomplete type definitions. Includes resource manager code, energy term #include declarations, etc.
- Formatting fixes in Embedding classes for coding conventions
commit 765af5251fc43898a200d82910211bfecf5b345e
Date: Sat Jun 28 17:40:46 2014 -0400
Fixing lots of bugs resulting from julia's spanning topology commit
commit 46cab0fe5772297ef901a5164b77f0c62206f604
Date: Sat Jun 28 16:41:08 2014 -0400
Debugging some additional namespace and scope errors introduced in conformation and embedding-methods (even though that class is going away in less than 5 seconds...
commit a92913b9a23c88fac6965b57712ee95707d5ea69
Date: Sat Jun 28 16:39:48 2014 -0400
Adding the membrane jump constructor to conformation
commit 3ec9b571779f0ccfd6024588b907a9cfd7dd9a5c
Date: Sat Jun 28 16:35:23 2014 -0400
Implemented check membrane fold tree method in membrane info to check for a reasonable membrane fold tree
commit 6093934d784fb579e4bdf3d9de5f8d67ae5a0276
Date: Sat Jun 28 16:32:08 2014 -0400
Adding default argument to membrane info - can specify the membrane jump number. will become useful when fold trees become more sophisticated. All code & copy constructors changed accordingly
commit b2b5cbe1ae62f9d9fe577876b4a1ea8d40be42f0
Date: Sat Jun 28 16:13:40 2014 -0400
Cleaning up conformation with a beautiful enum, never did i think enums could be so awesome
commit f770b34cc7171ee1785609ad8c0ce61402dcb3c6
Date: Sat Jun 28 16:10:08 2014 -0400
Updating conformation #includes - also removing hacky set thicnkess method
commit 8b8f50b7c6a49a644c19af810ef391ca4e0e6945
Date: Sat Jun 28 16:03:56 2014 -0400
Adding membrane params enum for better index refereincing in conformation.hh
commit 93c6a8a534aebc2fa47f321d650df37210e642f3
Merge: d528bec 506873b
Date: Sat Jun 28 15:38:57 2014 -0400
Merging in most recent version of mpframework devel into membrane code fixes branch - accepting Julia's params files changes for now but will not accpet in flex sampling branch
commit 506873bd12edc57838167492d96c3337a9adb633
Date: Sat Jun 28 15:23:35 2014 -0400
Framework Updates:
Adding Integration Tests for Membrane Framework Application Development (for Rebecca's apps):
- load_mpframework: Load and initialize a membrane protein using the framework with add membrane mover and initial membrane position mover.
- membrane_ddG: Run C++ adapted version of membrane mutate, relax and compute total score ddGs
- memrbane_relax2: New custom membrane protein structure refinement/relax protocol. Currently just minimizes
- translate_membrane: Membrane pose translation mover - used often in visualization
Updatng Objects:
- SpanningTopology: Fixed show method to override ReferenceCount#show( ostream ) and trace with output. Also added copy constructor and assignment operators and removed unnecessary cc guards
- Conformation: Added show_membrane() method - show method used temporarily for showing membrane output. Composes MembraneInfo
- MembraneInfo: Added membrane_info.show() method to show base information in the object.
commit 28627e0d3e93963d04eeab0e8165c850fe70a0c4
Date: Sat Jun 28 15:21:58 2014 -0400
Framework Updates:
Adding Integration Tests for Membrane Framework Application Development (for Rebecca's apps):
- load_mpframework: Load and initialize a membrane protein using the framework with add membrane mover and initial membrane position mover.
- membrane_ddG: Run C++ adapted version of membrane mutate, relax and compute total score ddGs
- memrbane_relax2: New custom membrane protein structure refinement/relax protocol. Currently just minimizes
- translate_membrane: Membrane pose translation mover - used often in visualization
Updatng Objects:
- SpanningTopology: Fixed show method to override ReferenceCount#show( ostream ) and trace with output. Also added copy constructor and assignment operators and removed unnecessary cc guards
- Conformation: Added show_membrane() method - show method used temporarily for showing membrane output. Composes MembraneInfo
- MembraneInfo: Added membrane_info.show() method to show base information in the object.
commit bf0716cab75601e34e1694294f756e0bd0b41bed
Date: Sat Jun 28 15:12:53 2014 -0400
Updating membrane ddG command file to locate teh right executable
commit 4df3b8bf3522f95c0863d4594729813718f3c655
Date: Sat Jun 28 15:12:24 2014 -0400
Adding membrane ddG integration test inputs
commit 2a37434c7136ffc7d700716f0a84432a5b11bff3
Date: Sat Jun 28 15:11:21 2014 -0400
Adding starter files for membrane ddG integration test
commit 78abe0f15b0fdadda3858f26099ebf4c288ce710
Date: Sat Jun 28 15:03:47 2014 -0400
Adding test starter files for membrane relax integraiton test - just doing integration min right now
commit 5ee0d57a84079f9de838a1ed81efed7e0611e427
Date: Sat Jun 28 15:02:33 2014 -0400
Updating membrane ddg, membrane relax and translate membrane pose integration tests. Relax should compile now and will try setting up the next 2 integration tests
commit 843246dfcd5a98e7583501cf41e9095de6b0a6e4
Date: Sat Jun 28 14:34:41 2014 -0400
Adding extra space to spanfile integration output
commit a5f9330f75227b59bd8990d9293948b9fc6f1535
Date: Sat Jun 28 14:32:04 2014 -0400
Updating command file for translate membrane integration test
commit 066a14917bf12cad9db0a97d92c4f91fefdd0667
Date: Sat Jun 28 12:58:53 2014 -0400
Updating translate membrane command file
commit cb31f93727d7f994591559b81ae054bdf539b33f
Date: Sat Jun 28 12:58:04 2014 -0400
Quick fix to load mpframework integration test - all tests pass
'
commit 2d2cb62e93d61dbc34a31eeceef888e004a091cd
Date: Sat Jun 28 12:53:57 2014 -0400
Adding integration tests as a temporary add - still needs to add the executables for these guys
commit c1a2ed118455cd9b57263df75366258a99cc6759
Date: Sat Jun 28 12:52:49 2014 -0400
Commenting out membrane ddg test for now
commit 6ef8d6693b22140f33e7b98845676f77362576c3
Date: Sat Jun 28 12:38:25 2014 -0400
Adding membrane ddG and translate membrane pose integration executables to build settings
commit d1e5b2fb3194b96d11e1a6b14232aea5b4cad919
Date: Sat Jun 28 12:36:13 2014 -0400
Adding translate membrane integration test
commit eed4911d3fd55b71b991e6e4b86275b0d74e0f71
Date: Sat Jun 28 12:35:31 2014 -0400
Adding translate membrane pose application to be used in integration test
commit 70f9ecb987ed2fba4b4931baf5239a44a535826b
Date: Sat Jun 28 12:26:41 2014 -0400
Adding starter shell for membrane ddG application
commit a7a79a67ae60bc916f5e485ec06d5c3f246b1b09
Date: Sat Jun 28 12:26:20 2014 -0400
updating load membrane pose application - hopefully can fix the bug I was seeing with implicit cout construction. Also updated the conformation show_membrane method signature to take this required reference
commit 36417af23350c8a226db3062707f32255c3922c0
Date: Sat Jun 28 12:10:13 2014 -0400
Bug fixes in load membrane pose pilot application
commit 36d74c408e5a8d60eb27bf196ad624f8dae06a30
Date: Sat Jun 28 11:57:26 2014 -0400
Now its added to build settings
commit ff1e943b73c48f35b8977fa98d52c68592355fbb
Date: Sat Jun 28 11:38:13 2014 -0400
Putting together a full show_membrane method in conformation to display the information in both membrane info and derived from coordinates. Might want to do this differently since it requires an unintuitive composition of methods
commit a4c4e6559db6ade13f8e869376c14cf32980c8a8
Date: Sat Jun 28 11:31:27 2014 -0400
Implementing overrided show method in membraneInfo
commit 05e98271e61f14fb0af999d6001b05077587dfd5
Date: Sat Jun 28 11:29:39 2014 -0400
Implementing required assignment operator and deep copy constructor methods required by Rosetta in SpanningTopology - will do a doxygen update later
commit 4b343e71fe8f095abc5935ffbb2c0be8435a81d3
Date: Sat Jun 28 11:24:17 2014 -0400
Starting to write show method in membrane info and membrane conformaiton (haven't decided how I'm doing this yet) and fixing spanning topology object to conform to coding conventions and override base reference count methods where required
commit 877d4129c7c3bdd88085978c163b2bd072bdc8af
Date: Sat Jun 28 11:13:41 2014 -0400
Adding integration test files for load mpframework integration test - incudes bacteriorhodopsin pdb (1C3W), spanfile, bare minimum flags file and command file loading the load_membrane_pose executable
commit 57b8418fc57d04fbc4edb55ad922b1147dd63761
Date: Sat Jun 28 10:58:41 2014 -0400
Ammending the commit message: Integration tests expected to change from the previous commit are UBQ_E2_thioester_two_ubiquitins
app_exception_handling
broker_membrane
buried_unsat_kinemage
membrane_relax,
These were broken in a previous version of the framework - the top 4 are currently broken in the pulled thread in master and membrane_relax is changed due to Rebecca's current development of the membrane relax applicaiton
commit 8e28e36456d812e43bc519a3608923425aa56186
Date: Sat Jun 28 01:49:47 2014 -0400
Adding a bookmark in the pymol mover for membranes
commit 26ba29767e1dc0c47794389aa9b0f805ce439d54
Date: Sat Jun 28 01:42:13 2014 -0400
Compiling version of show membrane planes mover - not yet tested, needs some work and checks. Might also need to make some changes to get this to work in the visualization pipeline. In genera, the mover computes 3 points for the upper and lower planes such that pymol can draw 2 triangular planes from these points. These points are special virtual residues - they are connected by jump to the central membrane point. This means that if in the pose's conformation the membrane moves, the planes should move according to the viewer as well. This might be unintuitive to frames at first - but will show how you can sample the membrane position around the pose
commit 1b18aae09382c31deb9230a21f5d0fea3a7baf19
Date: Sat Jun 28 00:20:10 2014 -0400
Added options reading in mover construction, also adding ShowMembranePlanesMover to build settings
commit 44ffb8f68c17cef40ee91f0624277c99fbfefc42
Date: Sat Jun 28 00:19:09 2014 -0400
Implementing options reading in show planes mover and adding new visualize option for plane radius
commit 1a1bb5e3b6437f8530e8d6ce71ad98c315f3a137
Date: Fri Jun 27 23:54:10 2014 -0400
Adding mover creator header for show membrane planes mover rosetta scripts hook
commit 3c24615bdd87ab44a569b5ca268a1a67f2d4f648
Date: Fri Jun 27 23:51:25 2014 -0400
Implementing most of the body of show membrane planes mover - making progress
commit 8144345b4a06a9494292f6ee20b388769393d406
Date: Fri Jun 27 23:08:23 2014 -0400
Adding header and forward header for show membrane planes mover
commit 61930f9be2651a11c67dade5217aa03154e7824a
Date: Fri Jun 27 23:05:52 2014 -0400
Initial add of mover files - adding show membrane planes mover which will add 6 points for an upper and lower triangular membrane plane
commit f50d75cfb648daa9f170de5f833f761845171c1b
Date: Fri Jun 27 22:58:53 2014 -0400
fixed bug in spanfile_from_pdb
commit 5b34dc2c64fbac1769c0f0a453a4fd6b4d4da5d2
Date: Fri Jun 27 22:10:46 2014 -0400
added SpanningTopology unit tests, needs to be tested
commit af9b740da9aaa55c74522fa4ab603dc06e3f4b0f
Date: Fri Jun 27 22:10:16 2014 -0400
moved pose_info function from pilot app to core/membrane/geometry/util
commit cf24e7e158e0ad93bc76c6d6c560efce386c2084
Date: Fri Jun 27 22:09:00 2014 -0400
SpanningTopology: took function out of constructors and made them private
commit 3a91f944e4f0a997832d87fbcac373eb13a18760
Date: Fri Jun 27 22:07:03 2014 -0400
added testfiles for unit test
commit da5ca0c50f3b6b5514415e310e11a2772212357b
Date: Fri Jun 27 19:04:29 2014 -0400
added spanfile_from_pdb pilot app, compiles, runs
commit 40b9c7c11dc8ee5be3c6c8785c15e3021759d362
Date: Fri Jun 27 19:03:26 2014 -0400
implemented show function for Span
commit 1cbc262dd9c615bbfb9ef375f3fbf8b8b6f66a8c
Date: Fri Jun 27 19:02:41 2014 -0400
fixed bug in Embedding
commit 2ea9a6bb4aaaf02c621f45d4610c7120199b7c22
Merge: 7404c21 fab252a
Date: Fri Jun 27 14:39:31 2014 -0700
Merge remote-tracking branch 'origin/master' into kylebarlow/general_dev
commit 7c6cd5ff8570f054dc6a67724b08de92deebc894
Date: Fri Jun 27 11:15:44 2014 -0700
Added an option to HSSTriplet filter which ignores the direction of the strands and helix (default false). If set, the helix-sheet angle is normalized to a value between -90 and 90. HSS Triplets that score 180 degrees without this flag set are parallel to the sheet but pointing the wrong N->C direction, creating confusion among users who don't expect the filter to fail in that case. If this flag is set, these parallel sheet-helix triplets will pass the filter.
commit 41fa52bdf0e5ff5c9885f9519a4a71d4d623df6f
Date: Fri Jun 27 14:42:48 2014 -0400
More progress with the Ramachandran potential
Fixing a bug in how entries in the CDF array are drawn if the CDF is
meant to hold the exclusive cumulative sum. I shoudn't pick the first
entry with a given value, but instead the last entry with a given value.
commit 9fa1256bd581e4ce0623e0d3ca429ee4f1fbdccc
Date: Fri Jun 27 13:09:06 2014 -0400
Progress in testing the Ramachandran potential
commit 0ba99f15f4e4dacc9d8bad096fe7b1d9e8f2d562
Date: Fri Jun 27 09:36:35 2014 -0400
Getting rid of a penalties class that should have not been present due to merging
commit d528becf0df786b559e4b7dca498fc2f97d82c8b
Date: Fri Jun 27 09:30:34 2014 -0400
Adding some quick notes into the params files and conformation
commit ff30a2c40909b87cc33c596cca8140ad0a51f3d8
Merge: 7ff2ab4 04ec940
Date: Thu Jun 26 18:34:59 2014 -0400
Merging mpframework_devel into here
commit 04ec940daa960e15d0d27695d2822274e93bab0a
Date: Thu Jun 26 18:33:46 2014 -0400
fixing library level build
commit 7ff2ab4b25075e3eaccf62553278767e7696ca9b
Date: Thu Jun 26 18:13:16 2014 -0400
mpdocking: changed back to dock_mcm_protocol
commit 603053ce6d0741070cd5ace1a6a0f1fbb6a03c09
Date: Thu Jun 26 17:32:30 2014 -0400
fix syntax
commit bc535ebbf30cfb65f27eec77d633cd8a801b4c2b
Date: Thu Jun 26 17:28:29 2014 -0400
add parse_my_tag to the main GraftMovers, add has_branch function to RS util, add function to load movemaps into the datamap, then call separately from the parse_movemap functions
commit 41c8b8368ab7c720f080d1a89c740a41db3992d2
Date: Thu Jun 26 17:25:45 2014 -0400
Adding a unit tests for the CDF in the Ramachandran class, and providing
read access to data of the Ramachandran class in order to make sure that
the CDF is being calculated correctly.
commit 44a69d861f4926e8b99e94f8c3bc5b06807ccd63
Date: Thu Jun 26 15:46:38 2014 -0400
binary search over the CDF now works
commit c3b0e1842a1048d6418cf1a1265de0449611890e
Merge: d96d03b a790a63
Date: Thu Jun 26 15:27:45 2014 -0400
Pulling from mpframework_devel
commit d96d03beb12d0e4df4ac88a79764a8c3e54bf4e4
Date: Thu Jun 26 15:25:22 2014 -0400
put scores for MC simulation into -mc:log_scores_in_MC flag; should reverse 83 integration test changes in commit 5d88106ee718c5b0; the 2 scoring changes in this commit are fine.
commit 885811348e0cfcd92474c1bf445952bd2ea3924e
Date: Thu Jun 26 15:02:40 2014 -0400
debugging
commit 39a24d8d8a3159d967a2085a9e864a485991101d
Date: Thu Jun 26 14:44:57 2014 -0400
added pilot app spanfile_from_pdb
commit 543ed882e887f106d3409d395e786c1428c4ebe4
Date: Thu Jun 26 11:57:10 2014 -0400
OK. The refactoring now compiles.
commit a790a63464897ebcacbdf9ccde383ccd6dd71151
Date: Thu Jun 26 11:02:19 2014 -0400
Adjusting spacing.
commit ab61ddee0a3648715fd27f1ee41012be21e7c98b
Date: Thu Jun 26 10:05:55 2014 -0400
Separating out the ppo_torsion_bin into its own files; adding more functions
for working with ppo_torsion_bins
commit 5f30fdb2d92e5d0cd4b161140ea6e07e32aa1005
Date: Thu Jun 26 09:42:50 2014 -0400
fixed bug to display thickness correctly, adjusted MEM and EMB params files for that
commit a11ace3d79ca3579f92d3ea015895fbea4635283
Date: Thu Jun 26 09:00:58 2014 -0400
progress in refactoring the remainder of the loops code that used strings
to describe the torsion bins -- replacing these strings with
utility::vector0< core::conformation::ppo_torsion_bin >
commit 17c4888bba07ba68a19c00899fadf4f978e3242e
Date: Thu Jun 26 01:14:48 2014 -0400
added mpdocking files
commit 3b8c58b8b0189c15d3fc7dad2c31cec869c16727
Date: Thu Jun 26 01:13:27 2014 -0400
added regular docking protocol to mpdocking
commit d3a76bbb51768fdf803caa96a0d0c22848db18df
Date: Wed Jun 25 23:33:56 2014 -0400
forgot to add wts files, adding them now
commit ee5e31dbd00e31038cd94736fdb03353d9c9299a
Date: Wed Jun 25 23:33:11 2014 -0400
setup docking weights for centroid and FA, just quick and dirty, needs to be benchmarked
commit 2a978ea0e6295c20470f0e223d3df143d654cefc
Date: Wed Jun 25 22:48:17 2014 -0400
MPdocking: took code out of protocol into pilot app for faster compiling
commit 5d88106ee718c5b0aab6e049fc65bcc84e8e71d3
Date: Wed Jun 25 22:10:01 2014 -0400
fixed thickness in params files, both for centroid and FA
commit 1327e95b394f6a315b25f672344bc3fa19755846
Date: Wed Jun 25 21:47:50 2014 -0400
Massive refactoring of the taboo perturbers eliminating just a ton of duplicated code.
commit 7c9d51ce1b5b67cf5fe9eadc66a6a837a403ec0b
Merge: 9266d88 2f42fb8
Date: Wed Jun 25 21:27:58 2014 -0400
Updated SpanningTopology
Also added MPDocking, runs, but needs fixing
commit 2f42fb8efe5fe01a4bd8cae04db4b238f386c908
Date: Wed Jun 25 21:05:27 2014 -0400
MPDocking runs, but needs fixes
commit edaf14a542322a3cd9e242b48ac00a124a182729
Date: Wed Jun 25 19:08:56 2014 -0400
compiled
commit b43b92b7421a57d2302cbcef5911c03bf54df5d3
Date: Wed Jun 25 15:00:35 2014 -0400
First stab refactor of the KinematicPerturber and the KinematicMover so that they
aren't using strings but are instead using arrays of core::conformation::ppo_torsion_bins
commit d3d3d8e7419f582db82fad040503b1e74126c234
Date: Wed Jun 25 10:34:06 2014 -0400
Now both Ramachandran and Ramachandran2B implement the low-memory, CDF-based
methods for drawing phi/psi bins randomly, biased by their probability.
I still need to remove the use of strings from the Taboo kinematic perturber. *sigh*
commit b0ec683df639ae016c703711d2507ee903b43c6b
Date: Tue Jun 24 21:16:10 2014 -0400
work on simple movers
commit 8445d389fe8b3b929634886b2a20ff80ca475542
Date: Tue Jun 24 17:17:47 2014 -0400
added Pymol observer to MPDocking
commit 6dca3f30df5739e132727f89dac963b50abf6a32
Date: Tue Jun 24 17:05:41 2014 -0400
added MPDocking protocol, compiles, not tested
commit 77a2ea36ed8b83a6fc717e38215dd3df512430fc
Date: Tue Jun 24 14:03:51 2014 -0700
updates to rna_features to capture DMS data.
commit a76ec18a0fd6221d7aa1406c55d6ce69a7e0bdec
Date: Tue Jun 24 15:43:31 2014 -0400
Progress in reimplementing the Rama2B table-shrinking code.
commit 01c97092352bb7408dc21056d55113d250aec5fe
Merge: 8047629 5a3bcf7
Date: Tue Jun 24 13:55:29 2014 -0400
fixed merge conflict
commit 5a4bf0e914a55fdd72a161cd9aaa36b5d1f78508
Date: Tue Jun 24 13:38:27 2014 -0400
Extrapoliate Ser/Thr HBond parameters to H2O HBond Parameters
Make HBonds involving water compatable with Talaris2013 by
extrapolating the parameters derived from Ser/Thr to HBonds involving
H2O.
Accept utracets to resolve change with HBondsTest:test_hbond_compute_energy2
Expected integration test differences relative to d45953f:
app_exception_handling
buried_unsat_kinemage
-> broken in trunk
dna_interface_design
geometric_solvation
ligand_dock_script
readin_dna_rna_protein
sdf_reader
swm_protein_move_inside_coiledcoil_by_bond
commit 91ee33139fd1ec24e4a2570fdbf0544bafe2c9a5
Date: Mon Jun 23 23:02:29 2014 -0400
change name of file
commit cbf7b870b7386d1ec246d45a7784e7c4df639b8b
Date: Mon Jun 23 18:11:35 2014 -0700
fixing swm to not pack terminal 5' phosphate at root residue. its because the phosphate holds the root atom, and its not easy to move the root atom elsewhere. eventually we'll fix this by including a virtual residue as another root, and have a jump into the RNA root residue.
commit a9312e5bb6189844a78aff8fc163a2fefd621fcf
Merge: b739ef4 d9f84f8
Date: Mon Jun 23 20:26:09 2014 -0400
Merging in master
commit 9266d88d6a2ad57aeb68c4d4991b2203671e134e
Date: Mon Jun 23 20:15:29 2014 -0400
Bug fix patched from membrane perturb and score branch for old update of embedding cordinates upon scoring. Taking this out - should fix crazy coordinate errors
commit 8047629d0d6da8bc42193b509402a617b39f74b6
Date: Mon Jun 23 19:33:58 2014 -0400
Added length check for spanfile
Compiles, took out SpanfileLoader stuff
needs to be updated so it takes cmd line input and not resource manager
commit 7f546254bec2d1d7f86d180cb697cecdc7439d1c
Merge: 8bae369 a776c06
Date: Mon Jun 23 16:20:58 2014 -0700
Merge branch 'rpache/KIC_with_fragments' of github.com:RosettaCommons/main into rpache/KIC_with_fragments
commit 8bae36914286fcef42f4c623c0bd477647a0551a
Date: Mon Jun 23 15:42:39 2014 -0700
Make it easier to use fragments for loop building.
commit 7e3c6137379ea7276a096447c9cd514f8ff411f0
Date: Mon Jun 23 16:45:47 2014 -0400
Fixed flags to match single spanfile
Compiles, fingerprint energies are the same except membrane center has moved
Old location is 0, 0, 0, new location is different
Thickness is still off (is on y-axis instead of z-axis)
commit aeb805e976c128ae002f5a4d9afca4c03d5354b6
Date: Mon Jun 23 16:27:15 2014 -0400
Shortened reading in of spanfiles in AddMembraneMover
In AddMembraneMover: replace all arrays of spanfiles with a single spanfile
commit 2e43b3c4dbf70b2cb597c500328c3d39a38af950
Date: Mon Jun 23 15:53:07 2014 -0400
removing chain dependence in SpanningTopology
doesn't compile yet. We need to propagates changes into AddMembraneMover
commit 236b68e32284cb3240aaa97903f5d20ba1f43d4f
Date: Mon Jun 23 13:12:07 2014 -0700
Make the minimizer settings easier to control.
Amelie pointed out that legacy KIC uses different minimizer settings in
centroid and fullatom mode. This commit adds code to copy that behavior
in refactored KIC.
commit 5a3bcf703efe97a120ea3b79b31dd4ccff65feeb
Date: Mon Jun 23 15:53:07 2014 -0400
removing chain dependence in SpanningTopology; doesn't compile; propagates changes into AddMembraneMover
commit f39d0cc5a897a1731089d0eba4310fa0da01477d
Date: Mon Jun 23 11:46:32 2014 -0400
resolve merge conflicts, run fingerprints
commit ce5b73c2ab370b4fd6ab0fca5b3a8591ca629e34
Merge: 8724870 3e52d93
Date: Mon Jun 23 11:04:12 2014 -0400
resolved merge conflicts
commit 87248709d2e4040ecba927d936bb2ffa175b3852
Merge: 54b4234 e435904
Date: Mon Jun 23 10:49:36 2014 -0400
resolve merge conflict
commit d45953f07f86e57c598d3bf7022cbb56143d3e79
Date: Sun Jun 22 23:39:47 2014 -0400
Fix broken H-Bond polynomials in Talaris2013
ISSUE
The AHdis polynomials for
Trp donor -> Gln/Asn acceptor
H20 donor -> protein backbone
H-bonds in the sp2_elec_params HBond parameter set (used by Talaris2013) were
not being evaluated because the xmax was set to -1234.
RESOLUTION
To resolve the issue, this commit
1) extends the hbpoly_ahdist_aASN_dTRP_9gt3_hesmooth_min1p6 up by 2% and sets the xmin/xmax appropriately
2) replaces the polynomial poly_AHdist_ah_dOH_1 (used by
hbdon_H2O,hbacc_PBA bonds) with
hbpoly_ahdist_aGLY_dSER_9gt3_hesmooth_min1p6 (used by
hbdon_HXL,hbacc_PBA bonds). This new polynomial is compatable with
Talaris2013 where the old one is not.
3) adds consistency checks to numeric::Polynomial_1D constructors
and error handling to HBondDatabase::initialize_HBPoly1D()
4) adds unit tests polynomial.cxxtest.hh testing the consistency check code
5) accepts all unit test utracers
RAMIFICATIONS
Hydrogen bonds between
Trp donor -> Gln/Asn acceptor
H2O donor -> protein backbone
have been completely ignored in Talaris2013(!). This commit allows
these interactions to be scored. Note, the HOH residue type is by
default not recognized, so HBonds involving water won't appear unless
you ask for them.
ANTICIPATED TEST FAILURES
No unit test failures
Note, the following utracers have changed/been updated:
Modified source/test/core/scoring/hbonds/hbond_compute_energy.u
Modified source/test/core/scoring/hbonds/read_polynomials_from_database.u
-> These are changes are clear
Modified source/test/protocols/docking/DockingProtocolFunctions.u
Modified source/test/core/pack/RotamerTrials.u
Modified source/test/core/pack/SymmetricRotamerTrials.u
-> These are presumably because new HBonds are being evaluated
Modified source/test/core/scoring/fa_atr.data
Modified source/test/core/scoring/fa_intra_atr.data
Modified source/test/core/scoring/fa_intra_rep.data
Modified source/test/core/scoring/fa_rep.data
Modified source/test/core/scoring/symmetry/fa_atr.data
Modified source/test/core/scoring/symmetry/fa_intra_atr.data
Modified source/test/core/scoring/symmetry/fa_intra_rep.data
Modified source/test/core/scoring/symmetry/fa_rep.data
-> These shouldn't have changed, but by inspection they look to be due to platform specific rounding
Integration test failures with
$ uname -a
Linux contador 3.2.0-60-generic #91-Ubuntu SMP Wed Feb 19 03:54:44 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
$ clang --version
Ubuntu clang version 3.0-6ubuntu3 (tags/RELEASE_30/final) (based on LLVM 3.0)
Target: x86_64-pc-linux-gnu
Thread model: posix
relative to revision 2a3c16b
/////////////////////////
app_exception_handling
buried_unsat_kinemage
-> broken in master
docking_ensemble
enzdes
geometric_solvation
hotspot_hashing
kinematic_looprelax
ligand_water_docking
mpi_multistate_design
mr_protocols
pocket_relax
readin_dna_rna_protein
swa_protein_prepack
swm_protein_move_inside_helix_by_bond
UBQ_E2_thioester_extra_bodies
-> After inspection, these all look like trajectory changes
NOTES
Thanks Phil Bradley for the bug report.
commit 68d4e2c54e132df8fbc427a8d3e8e8dde6a509ba
Date: Sun Jun 22 19:38:12 2014 -0700
Fix a closure bug in refactored KIC.
This commit fixes a bug in KIC that was causing chain breaks for
perturbers that set either omega or a bond angle for the first residue
in the loop. These dofs are basically ignored by KIC because they are
outside the pivots, but they were still being improperly applied to the
pose. This bug was only noticeable when the IdealizePerturber was being
used, because no other perturber set omegas or bond angles.
commit 3e52d93b3c5959efd23e421083d2c49c1d95a304
Date: Sat Jun 21 15:07:31 2014 -0400
Updating membrane framework - adding rosetta scripts hooks to all movers and updated documentation dox throughout. Vector parameters still not working in rscripts, but will ask for help
commit fff27760f272f348560fb6aa15f547ec48e59249
Date: Sat Jun 21 14:49:10 2014 -0400
Adding all 4 movers now hooked into Rosetta scripts
commit 191d19b523b51ac32cf12b2cae0f01c33720e4fa
Date: Sat Jun 21 14:39:25 2014 -0400
Adding rosetta scripts hooks to initial membrane position mover
commit 27a3cdd1e2154fd71319d4e9ad3f6ed9f5d286ae
Date: Sat Jun 21 14:35:27 2014 -0400
Adding rosetta scripts hooks in add emmbrane mover but no parse my tag yet because of vectors
commit 61cd28f1d1013d7bb0a24b56761a66b02904bfea
Date: Sat Jun 21 14:27:54 2014 -0400
Adding mover creator headers for add membrane mover and initial membrane mover position
commit 5dd800b8fd6af545c6aa5b385eab23ff197ba01f
Date: Sat Jun 21 13:48:47 2014 -0400
replacing calles to embeddingMover with calles to InitializeMembranePosotionmover
commit 5f16ce7e6de5bda55e13c6e1aebd68242ab13ed5
Date: Sat Jun 21 13:47:30 2014 -0400
Updating documentation in conformation and replacing calls to update_embedding with calls to update_membrane_position
commit 2b3ceab5f547af8c1762f3251c78841ccc35bd8a
Date: Sat Jun 21 13:19:20 2014 -0400
Updating doxygen in membrane info object and adding required assignemnt operator
commit 6f3416c842048d2ae0c6b439bce3e4f337c72563
Date: Sat Jun 21 12:57:32 2014 -0400
Renaming embedding mover to initial membrane position mover - will eventually take sequence and structure based but for now just structure - also adding docuemntation to this mover and updating it in the build settings. I have not yet fixed upstream changes - will fix when I compile apps
commit ade097ccf8ad5de888f323f0cf128e4d16d0d01a
Date: Sat Jun 21 12:36:53 2014 -0400
Updating doxygen tags in AddMembraneMover
commit 146372f64acbe1b583df9a1f89339a1dcb15823c
Date: Fri Jun 20 18:31:25 2014 -0400
Merging membrane translation rotation into uniform mem mover, membrane visualization mover, and applications for executing these operations plus their respective cmd line options into mpframework-devel
commit 9c9bbae9cf686308918fd4eaa390eb60185fbb38
Date: Fri Jun 20 17:28:48 2014 -0400
Beginning the refactoring to bring down the memory use for the Rama2B and
Rama sampling done by next-generation KIC.
commit 5f19fbd7c7a8dd49c6f94b407624b4d664936044
Merge: 2a3b3c5 ea19c10
Date: Fri Jun 20 16:59:34 2014 -0400
Merging in the gcc fix I made this morning on crumb into ninja's remote
commit 2a3b3c50c62764a6d3dc80aca7d11667c913205b
Merge: fc1b5b0 a11ade7
Date: Fri Jun 20 16:56:23 2014 -0400
Resolving merge conflicts in my pilot app build
commit a11ade77e70c5a62a8fe10024d9a8083028f5ffa
Date: Fri Jun 20 16:42:13 2014 -0400
Fixing crazy thickness problem
commit dc6dd1a24629564a31d2d63ae964e66766b580c2
Date: Fri Jun 20 16:32:17 2014 -0400
Working transform and visualize pipeline
commit 90b986120caa79ec2f7267bc3cd33338dc69a14b
Date: Fri Jun 20 15:29:23 2014 -0400
Fixing residue labeling order in membrane params file
commit b14b6602b93458d24860454e2e067774035b7f44
Date: Fri Jun 20 15:25:15 2014 -0400
Adding output tracers
commit 54b4234bf6ed0fac1450237a2265eb7255c3fc5e
Date: Fri Jun 20 15:16:14 2014 -0400
SpanningTopology: added spanning method
commit 31957a5f68f6d62d7bf52bd9a07a28c01168d542
Date: Fri Jun 20 14:44:40 2014 -0400
SpanningTopology correct
commit 6a5a9af3dbdb6932b8db246cbc5950f1f2601034
Date: Fri Jun 20 14:31:30 2014 -0400
Updating membrane thicnkess method in conformation to print the correct thicnkess and set correctly in the virtual residue
commit 7b257f498273cfa320b667828d56498a968e8127
Date: Fri Jun 20 14:30:32 2014 -0400
Updating membrane thicnkess method in conformation to print the correct thicnkess and set correctly in the virtual residue
commit 92594661baba74587b99577ca802df309c87e6bf
Date: Fri Jun 20 14:12:36 2014 -0400
Adding more documentation to transform into membrane mover
commit dcee8c467184ae953d4c353c5e234bc5746636ec
Date: Fri Jun 20 14:02:25 2014 -0400
Updating rosetta scripts and full hooks in transform into membrane mover - will hook into registrators later this afternoon
commit f60bd26506e216452db9ff72491c835e34cd3391
Date: Fri Jun 20 13:04:45 2014 -0400
Pulling direct rosetta scripts hooks out for now - will reimplement with the rest of the movers
commit 74de6a6242e04cf78939e0bcec87b3033f4cc3ac
Date: Fri Jun 20 12:32:50 2014 -0400
Implementing rosetta scripts and full mover requirements in transform into membrane and visualize membrane mover creators
commit 12e0399450683a29d32e29f5af181f86154bd40f
Date: Fri Jun 20 12:12:18 2014 -0400
Fixing quick rscripts plug in compiler error
commit f8c1cc92fb8bf6e005025841b63c18e8b6a82dfc
Date: Fri Jun 20 11:34:45 2014 -0400
implementing the remainder of rosetta scripts tags
commit ee0e0085abffe3878a4066afdcfd8cac0d340e9c
Date: Fri Jun 20 10:53:37 2014 -0400
Continuing to implement rosetta scripts hook for visualize membrane mover and adding 2 new command line options and an option group to the membrane new keys for visualize:spacing and visualize:width
commit bdbd9ca4fd042a51ce5fc59648b2c3e7b2a4c88c
Date: Fri Jun 20 10:43:41 2014 -0400
Implementing mover creator header for visualize membrane mover and fleshing out the rest of the required mvoer methods
commit 1ad8d710673aa9128803dadc5d70ee566fd665fe
Date: Fri Jun 20 10:06:40 2014 -0400
work on simple movers, add comments to AlignChainMover and AddJobMover
commit ea19c1065b1a85ee4349ddf87a97c7688b7ab4c7
Date: Fri Jun 20 09:25:57 2014 -0400
Fixing bug introduced in residue energies breakdown application for membrane proteins - this fix should fix the linux gcc compile
commit e4359041dc658f5da4a59ce84b7d23a7354b70e2
Date: Fri Jun 20 08:29:53 2014 -0400
Fixing initialization order in julia's refactoring branch
commit 3ea390b4d7a3296c357214057c1c2bd1e5ada75c
Date: Thu Jun 19 22:13:11 2014 -0400
Adding jd2 compatibility to visualize membrane app
commit 857378016c95096c4655e24a027f9078ba508a22
Date: Thu Jun 19 21:55:28 2014 -0400
Updating pilot apps settings - should work more reasonably now
commit 3f07fc30711795899fa1dd5c24755ead5b98ded2
Date: Thu Jun 19 21:48:33 2014 -0400
Updating translate view membrane application which should translate all structures into a uniform and display the membrane planes as virtual residues. Works with jd2 to take a list of PDB files
commit 869981a17876b8ee09f2c81e44bce2b18a45bc3e
Date: Thu Jun 19 21:41:03 2014 -0400
Adding top level membrane visualize executable to build settings
commit fc1b5b04721c6a3fb7a166e309f43263777471ec
Merge: 0e3e231 d9bfb8b0
Date: Thu Jun 19 21:14:07 2014 -0400
Merging gcc fixes with mpframework devel local on ninja
commit 0e3e231146a38f0b77d6629afa90e3ee15b7b3e0
Date: Thu Jun 19 21:12:34 2014 -0400
Updating scoretypes enum to corectly list cd2b types
commit a776c062cf73f4f2dff3605e88b997f988b0386a
Date: Thu Jun 19 16:49:12 2014 -0700
removing tracer debug output from ConstantLengthFragSet::overlapping_with_region function;
this eliminates the need to mute that tracer to avoid long runtimes due to writing to the terminal;
tracer output in the FragmentPerturber class has been adapted to also provide the frame length
commit 4908734b19214f40c6e0becd8e282cf04bc0e5b4
Date: Thu Jun 19 16:46:05 2014 -0700
fix to unit tests for hbond_type_manager.
commit 2605101766840f95a6b28ca78ead9d8468b66038
Date: Thu Jun 19 19:27:07 2014 -0400
Membrane residue energies app compiles
commit 43ebca3e2a6853fc3bf49bef106607dfef04f90d
Date: Thu Jun 19 19:10:33 2014 -0400
fingerprint ref folder correct now, still missing the corrected app that prints all the scores
commit 28ffa954e43dac4d469aa7c069795171b6d904f5
Date: Thu Jun 19 16:39:27 2014 -0400
fixed spacing
commit 6f426273cca9f0beb0284211c3f474c776f2268a
Date: Thu Jun 19 16:33:44 2014 -0400
Adding membrane per-residue and per-atom energies breakdown applicaiton - addapted to take add membrane mover on the pose
commit 61b2da19475c89605210865b01ebe2eea964e849
Date: Thu Jun 19 16:28:16 2014 -0400
Updating visualize membrane mover and pilot app for transforming a set of structures into a signle app using pdb lists in jd2
commit 34bda2a913fd3895d4b2f28e0e3e0d8b1354ca85
Date: Thu Jun 19 16:25:13 2014 -0400
fixed indentation in Span
commit ab636e1fb28731e39265f38cdc6d8e58980fe1a0
Date: Thu Jun 19 16:02:22 2014 -0400
fixed constructor in Span.cc
commit fc6e4ce1b1d323811b32c31934babf7180e4d02a
Date: Thu Jun 19 15:36:13 2014 -0400
adding pdb files to ref
commit 903f96b9c8d3229d191d3d540840ff787970ffa1
Date: Thu Jun 19 15:34:25 2014 -0400
comparing fingerprint tests, MPFAEnv changes, probably numerical precision errors
commit b31d51c2c2ef90e01587673f200e7fc25e5215c3
Date: Thu Jun 19 15:07:48 2014 -0400
Starting to work on a pilot app that will enable me to translate all structures into a single membrane and them move that membrane position
commit f9060bbf8a0d00594d64d31a52ac0295c1c018f9
Date: Thu Jun 19 15:07:05 2014 -0400
Applying center shift move in visualize membrane mover. Also commenting back in rotation of membrane residues move - after looking into this deeper I think what it is doing is correct, but will test a bit more
commit 48a79f664d4636e8f6b208519501b41a4f68e704
Date: Thu Jun 19 10:56:05 2014 -0400
Applying center shift move in visualize membrane mover. Also commenting back in rotation of membrane residues move - after looking into this deeper I think what it is doing is correct, but will test a bit more
commit b2469020b8472295e34110e99e9230100b19c92e
Date: Thu Jun 19 00:20:52 2014 -0400
Updating implementation of visualize membrane mover - still missing center shift and not rotating correctly
commit d9bfb8b0c0d87c75a5f9dc63339375199a5e22a9
Merge: 4e90b0c bd6c66f
Date: Wed Jun 18 22:59:38 2014 -0400
Merge branch 'master' into rfalford12/mpframework_devel
commit bd6c66f7e5e685e0c675290051bf8f69abbcf441
Merge: f2b2788 5b65c19
Date: Wed Jun 18 21:14:40 2014 -0400
Fixing master mege conflict - merging master branch into mpframework devel to ideally fix pyrosetta build
commit f2b27883443d510744b0090f6fc469ad74586341
Date: Wed Jun 18 21:08:20 2014 -0400
Updating overwritten change to some master merge conflict
commit 4e90b0c2ff4c36a40fa2b5b2abf30d5bec0dca88
Date: Wed Jun 18 21:05:09 2014 -0400
Adding sfxn fingerprint reference results - contains full list of residue-atom scores for 1bd, 2bd, and wsd energies - this includes the low resolution and high resolution energy functions
commit 90ec06be999f7f177172cc5cf1a99a3c8bc10db7
Date: Wed Jun 18 20:57:32 2014 -0400
Fixing initialization order build error in Span. - note, base class should always be initialized prior to the member data
commit 426d1a95b1d6d6a8c9cd58d18218c4592157de0b
Date: Wed Jun 18 19:06:55 2014 -0400
added gitignore back
commit e0a89b79eabcdb03318acb8bb4238bfdc74cb182
Date: Wed Jun 18 19:05:01 2014 -0400
fixed compiler errors, membrane fingerprints fail, but the tests are wrong
commit 126b62ba2ab763670e60033dab32eaf4a89ffd27
Date: Wed Jun 18 19:02:02 2014 -0400
Made a quick change, but rotation is still not working and shift not even present. Visaulize mover still needs some work
commit 2bb6b521b443b04d33da618077d6c9d841eac3a8
Date: Wed Jun 18 18:43:26 2014 -0400
Adding visualize membrane app, has a relatively working version but would like to capitalize on the jump I can use
commit 3e2514ba2a80e574211314f6bc4b06a6f6a9f635
Date: Wed Jun 18 18:42:57 2014 -0400
Quick fixes to transform into mem
commit 4f810f0d55a91f56de42499953bcd13881f41e81
Date: Wed Jun 18 18:07:53 2014 -0400
Implementing visualize membrane mover, hope it works
commit 952afc42300a754465ec5a892c9d6880787aec08
Date: Wed Jun 18 17:50:49 2014 -0400
Adding visualize membrane mover - at least the pieces for it. probably won't compile yet
commit b108d13e8b8dc4a8f267033cc1dc5c926aaf4ce2
Date: Wed Jun 18 17:50:02 2014 -0400
Quick updates to transform membrane mover
commit 2a7a61500869b0d29ead8f33721157c13a499e3d
Date: Wed Jun 18 16:28:35 2014 -0400
Updating transform mover to apply and set jump, was missing those lines in the previous commit. COmpiles
commit da639d3d2dc46681628100545bbe6d4b3d4366a5
Date: Wed Jun 18 16:23:15 2014 -0400
Implementing rotation move about normal
commit ad387b82117e2df49a6ade44277f4833ac4b640b
Date: Wed Jun 18 16:13:56 2014 -0400
Removing crazy debug trancers from trans memb app - I know my center shift is reasonable, correct not sure. I also know from my quick tracer test that conformation.update_embeddding, soon to be renamed, is also working reasonably
commit f4b922e11e4080cf7a2891c8c7a07c9efeeaf167
Date: Wed Jun 18 15:57:53 2014 -0400
Fixing typos in transform into membrane mover forward declaration, also declaring a tracer in the pilot app to check if the update embedding method is working
commit c2e4f01e8d034125f84593cb7b3839484e215d0a
Date: Wed Jun 18 15:51:57 2014 -0400
Implementing membrane transform mover pilot app
commit a5ff2446eb0aa3ea52336c6e2aff0dbe2ba6ba9a
Date: Wed Jun 18 15:45:32 2014 -0400
Adding transform into membrane pilot app
commit 87d07d71b77abda9280b20bc4a4759772719242a
Date: Wed Jun 18 15:45:15 2014 -0400
Fixing compiler errors in transform into membrane mover, added to build settings too in protocols.3 settings
commit 5b50902e286d694c56e5fe0f49269dd00fc787ed
Date: Wed Jun 18 15:30:43 2014 -0400
Implementing center translate move in transform into membrane mover
commit 2c8338e061034a896892c83cfac7154f3a1aeebd
Date: Wed Jun 18 14:27:15 2014 -0400
Fixing typo in the name of the transform into membrane mover
commit 31965ccf31d8ed78234b880ac66b618d964bf2b2
Date: Wed Jun 18 14:20:03 2014 -0400
Adding starting files for transform into membrane mover and implementing forward header and header file
commit 264f41577ae5c3fa8e04781c810d78cb5352e438
Date: Wed Jun 18 14:11:14 2014 -0400
Removing new results directory from sfxn fingerprint tests - only ref should be committed
commit e66eab8a91b291ff49d499008097a15b45c56ea3
Date: Wed Jun 18 13:33:16 2014 -0400
fixing build, removed ref for fingerprints, compiles
commit a497b9a22e340149126fa5c57dde7fc5c0e3eff4
Date: Tue Jun 17 17:13:14 2014 -0400
resolving conflicts, 2 remaining
commit 5c40e0a485e9e285b6d658cef483f7a09e3f4cf9
Date: Tue Jun 17 15:22:30 2014 -0400
added core/membrane/geometry/Embedding.*, doesn't compile, need to add EmbeddingConfig
commit f97769918c6e7f71c0e44f1152d963ae7067ffa3
Merge: ddefea1 28abab5
Date: Tue Jun 17 17:25:22 2014 -0400
resolving conflict in settings file
commit ddefea12c47fd47137cd9c7638e3c426577ea55e
Merge: 894225c 6d00d1d
Date: Tue Jun 17 17:22:36 2014 -0400
pulling from devel
commit 28abab5113bee4b214b8238bac9f29f295af352b
Date: Tue Jun 17 15:21:26 2014 -0400
added core/conformation/membrane/Span.*, compiles, fingerprint tests pass
commit b6c6a72125426e76f82df3970048eadf49c32f3b
Date: Tue Jun 17 14:21:12 2014 -0400
added new files to fingerprint tests
commit df900a33a33221fdd3449374b1f407affb4e6322
Date: Tue Jun 17 14:20:30 2014 -0400
fingerprint tests finally run
commit 6d00d1d63a631150ab4e08e254dd94f22b30260d
Date: Tue Jun 17 09:28:53 2014 -0400
Getting rid of non-relevant unit tests and fixing header only build
commit 796791a16cf4f24a7cf6df755ab30adc9d884be3
Date: Tue Jun 17 07:41:07 2014 -0400
Fixing gcc build
commit 40a6eb7978367b1183cb6e6937ab6601fe1379a4
Date: Mon Jun 16 23:14:51 2014 -0400
FINGERPRINT TESTS RUN :)
commit 6e8b58aca89de1e4ce8ed4ed92eaefd0d0d1aece
Date: Mon Jun 16 22:59:40 2014 -0400
Removing extra resource manager file support
commit 375962ee617cfdd63f9d50dcac93d76de4778cc8
Date: Mon Jun 16 22:57:44 2014 -0400
Still deleting old files
commit fce662961223db21c14720b63e7c41b3ac399393
Date: Mon Jun 16 22:56:04 2014 -0400
Getting rid of more old unused files
commit 343c3175f03aa5bfcff134cf3f62f56c03530e81
Date: Mon Jun 16 22:55:02 2014 -0400
Removing more old files
commit 5b575c4076a6201e03e8a68e344eede867238b77
Date: Mon Jun 16 22:54:42 2014 -0400
Removing old config code, will not be used
commit 9cf59d227e329072eba48f64bb8911513d0f9338
Date: Mon Jun 16 22:49:38 2014 -0400
Updating flags files in membrane cen and membrane fa sfxn to correct sfxn fingerprint tests
commit dc69ec5b8f495c99c3fd435fe6aa8cb772673446
Date: Mon Jun 16 21:26:40 2014 -0400
Updating local minimize app - will minimize after structure based embedding update
commit 99381b28053e0bb6c9c55e97515c57d12eef2819
Date: Mon Jun 16 19:12:34 2014 -0400
Updating local minimize pilot app, added to build settings and it compiles
commit 87574333ec091ca6cd23d5346c57c35934193d06
Date: Mon Jun 16 19:02:28 2014 -0400
Updating structure based embedding mover so it compiles and local minimize app
commit 7d159955cff9ed95f846c372536d665ede12a60b
Date: Mon Jun 16 18:35:46 2014 -0400
Updating embedding mover to make structure based computation
commit a2ef3141a59be07a5b80610c6e412b857f016ede
Date: Mon Jun 16 18:34:02 2014 -0400
Updating optimize membrane mover
commit 894225cdf361d35e59e033f11bfa385b4cff48af
Merge: 167e012 e3aa166
Date: Mon Jun 16 17:41:32 2014 -0400
pulled from mpframework_devel
commit 167e012d56a918799fe528b96dbe6e301b27a3e3
Date: Mon Jun 16 17:39:04 2014 -0400
added ref for fingerprint tests
commit 6e341f3ad3fb60d9af69528aa9c1680e5e8725ea
Date: Mon Jun 16 16:40:11 2014 -0400
Writing my own custom membrane optimization mover - uses slightly different approach and scoring from previous monte carlo. Because my mover is essentially inside out allowing me to do a true monte carlo search isntead of a score vs. score search. hopefully this can smooth out minimization
commit 169d009415443f5ab22ccbfc3bf046fa8e6c29ec
Date: Mon Jun 16 15:36:24 2014 -0400
Filling in optimize membrane mover - but ran into a scorefunction bug
commit c83f54ac212e9266f35604d55e1aa3b1a58f03f8
Date: Mon Jun 16 15:13:47 2014 -0400
local_minimize.cc: pilot app for minimization of membrane proteins with the new framework. checking out optimization of mp moves, etc
commit 62acc5be86e0c3e873b2197f882938358201f178
Date: Mon Jun 16 14:48:17 2014 -0400
Adding local minimize app - just getting started, it won't compile yet without the opt membrane mover I am currently working on
commit 92c12f0bacf18cf7801f8768d0be5f6d59b2cd0e
Date: Mon Jun 16 14:40:11 2014 -0400
Starting to implement optimize membrane mover helper methods, taking a short break to outline the local minimize app that is the goal of this entire refactor
commit a26dd4c822b70f7e48be860cb830d223bfff741d
Date: Mon Jun 16 14:26:11 2014 -0400
Starting to implement optimize membrane mover header - still figuring out what options should or shoould not be user controlled. Will set defaults and allow command line/rscripts access anyway
commit 941e9759135f289d5e1dd0afe97a4545ac365a3c
Date: Mon Jun 16 14:16:53 2014 -0400
Adding starting files for optimize membrane mover and implementing forward header - should take the place of the old monte carlo protocol
commit c472d832e122b40faef5edb907f90fc9b901706a
Date: Mon Jun 16 13:50:19 2014 -0400
Well that is weird - scores match when I recompile the executable with a change. Must have just needed a force recompile to link the libraries
commit 69fd0e46b24589fe89564d2a6fb02a4c0337adaf
Date: Mon Jun 16 12:27:07 2014 -0400
add creators for the movers, finish DeleteRegionMover
commit 419fa36f69843d7522a585392ef2dd6c98d92411
Date: Mon Jun 16 12:02:33 2014 -0400
Trying to debug the introduced discrepancy in the membrane fullatom env term. Added debugging tracers to both base classes
commit 4d73eccae199f245bc86124c189f22c4cd0ff2b9
Date: Mon Jun 16 10:48:25 2014 -0400
Ok, just kidding. something crazy is happening with the old term, possibly in applying penalties, but that isn't so much a concern here
commit 1739668f193fb91f0af284bd07692ec41c9492ee
Date: Mon Jun 16 09:52:08 2014 -0400
Adding back membrane and membrane_fa executables to test sfxn differences between new and old - fa mpenv and cen env terms are the only ones not working in the new refactored code and I'm not sure why
commit 3430fa3a79c3d6df46ba738e74a59a6665f7fdaa
Date: Sun Jun 15 22:47:47 2014 -0400
Removing debug tracers from add membrane mover - solvation term working fine, environment term needs work
commit 08bed203a2981fb375c5ed3b2226577537d2e423
Date: Sun Jun 15 22:21:28 2014 -0400
Removing extra debugging tracers
commit 486574abed882008893af0ddf389824d908b1f51
Date: Sun Jun 15 21:45:12 2014 -0400
Starting to update fingerprint apps based on the new refactor
commit f060e668f820bbae2d51474f67f1d1b06045c31f
Date: Sun Jun 15 17:09:41 2014 -0400
Adding membrane framework integration executable, integration test not yet setup and the unit tests are probably in mass disarray
commit 4ac4c37cb04f0ebee24bf5c91f07411decbb975f
Date: Sun Jun 15 17:08:39 2014 -0400
Add membrane mover works - and that is a beautiful thing
commit 7a9467db33c8a6f61eb9acf400d08e289bde241d
Date: Sun Jun 15 16:24:03 2014 -0400
Adding framework integration test app
commit 7b36243002737291f470b7b94c487c0b892bda36
Date: Sun Jun 15 12:22:44 2014 -0400
Updating mover registrator, creators and resource loader creators to not depend on the old cpm movers
commit b53ff5d7644c1005a492cf3e8889154890ab77ec
Date: Sun Jun 15 11:41:34 2014 -0400
AddMembraneMover compiles :)
commit cf26dd2031a198abcd6287c7ddb9edee8ca40047
Date: Sun Jun 15 11:35:28 2014 -0400
Initial bug fixes in AddMembraneMover - trying to get it to compile would be good
commit ebb0f7d217c0c9c6e15853e64860f3a97596bec9
Date: Sun Jun 15 01:06:28 2014 -0400
Tiny build error in the .hh is breaking compilation in the .cc. Will figure this out tomorrow
commit 1b8ce0352fa3d1ebd999c276b6896b49407febef
Date: Sun Jun 15 01:05:29 2014 -0400
Initial build fixes to AddMembranemover, and removing CreateMembranePoseMover dependencies from FastRelax
commit a9e0b6fedb49cc9fca9d687dc1219b2c5e1432d9
Date: Sun Jun 15 00:34:13 2014 -0400
Removing an old dependency on EmbedDefOptions, IO and fallback from a previous iteration of the membrane code. This code is kept in an old branch but no longer in main development
commit 81589a4b857ba7b60ce6ea1a477e3d31d1e63136
Date: Sun Jun 15 00:25:30 2014 -0400
Fixed embedding methods dependency on membrane info, now to conf pass through method
commit 6bd12e662edb1d1a3e71cb1efd124495feba319f
Date: Sun Jun 15 00:21:38 2014 -0400
Updating hbond energy correction with new changes
commit 729eff76eebbfc5950c87e04b905dabc6707b10b
Date: Sun Jun 15 00:18:37 2014 -0400
Introducing mutability of fa derivatives into fa solv and fa env energy methods - intendend use here is ok and overcomes coupling problem mentioned before
commit 22c8f2f815e7339cf2a68c47f8d8aaebc83fab0f
Date: Sun Jun 15 00:14:09 2014 -0400
Adding add membrane mover setup options to options_rosetta.py in membrane_new setup group
commit 6b3bbe88c0894a6a48a07ab6e6bce1e5d94ab518
Date: Sat Jun 14 23:36:59 2014 -0400
ARGH CONST CORRECTNESS
commit 16d1e5a52a5009c04bd7cce3bca835dc91cef065
Date: Sat Jun 14 22:28:32 2014 -0400
Killing the old membrane penalites class
commit c85179bb72d27718ef10848087672f3eb228bf87
Date: Sat Jun 14 22:24:21 2014 -0400
Low resolution energy terms compile, still waiting on fullatom
commit 31a02573995ceae399efd4e53c9ce781f13c5d31
Date: Sat Jun 14 22:14:56 2014 -0400
Fixing constness issue, trying to get energy terms to compile again and praying I haven't started any fires here
commit a92e0378902f82b66b3e4bdf5dd5fca062105914
Date: Sat Jun 14 21:55:50 2014 -0400
Woohoo - core.2 compiles with the changes
commit 22eda2fa0e9738792c78df586d5559eca9cf0a06
Date: Sat Jun 14 21:45:45 2014 -0400
Updating conformaiton object with quick fixes
commit 5fd26857bad0813f608229bf52a43bdea754f288
Date: Sat Jun 14 21:15:54 2014 -0400
Getting rid of the corresponding un-needed data members fa_proj_deriv and fa_proj_deriv_coord
commit c147962ed05c77fabb61e0f879a507355a99b4c7
Date: Sat Jun 14 21:14:22 2014 -0400
Removing un-needed computing of derivatives in fambsolv
commit d957ca6bce25d5c1e4b6ce971594fe955a0341c5
Date: Sat Jun 14 21:08:28 2014 -0400
Ok - all of the derivatives live in their respective energy methods now, but still need to clean up the solvation term
commit 4ec2ea45439732a34d19b0849875a3dff6d5c93f
Date: Sat Jun 14 20:59:16 2014 -0400
ok, i've decided to initialize this stuff twice - mostly because I think this is the best way to guarantee the pose derived data is correct. if I find another way, I can always change it
commit 92e1bba014fe05aa7b320c9abd7e4519b1beeb7a
Date: Sat Jun 14 20:02:10 2014 -0400
Just kidding - what a mess. scoring needs fa projection, derivatves need their derivatives, but all of this data is derived from one another. what happens first. crazy setup collision
commit c9ac90fedc45eff133e6f96677b5b9f87f166efc
Date: Sat Jun 14 19:58:09 2014 -0400
In theory, fampenv will now compute its own derivatives as it should have originally, but the game only ends when it compiles...
commit 739a49f753f0b26cdd6dfb20a16251d047d06d5d
Date: Sat Jun 14 19:41:00 2014 -0400
Moving dE/dz derivative pre calculations into their respective energy methods - even though it means the methods will be duplicated, the operations are not slow and it will be more clear to the user what the energy method and gradient method actually entails
commit 15373a42cb284840469add9bbd695682d6ad3c99
Date: Sat Jun 14 19:12:55 2014 -0400
More updates to membrane info, still trying to figure out what to do with the derivatives, introducing an old problem
commit 61b3fb0e56ff202b29ea94e5f82c6af5b2ac3eb7
Date: Sat Jun 14 16:31:30 2014 -0400
Removing references to un-needed methods I deleted - but now membrane info is unhappy becasue it has derivatives it cannot compute - might just be doing this on the fly outside? not sure yet
commit 3c4054121d300ada6118023a0851fa24700c96ed
Date: Sat Jun 14 16:28:22 2014 -0400
Implemented update embedidng method which talks directly to conformation's copy of residueOPs which are mutable if you are an insider
commit aeded9dc9a2f682e7d1a4f0ca560baade7b0a128
Date: Sat Jun 14 16:19:08 2014 -0400
Implementing residue and atom z position method relative to the membrane in Cofnormation - easist way to separate derived coordinate responsibilities - will need to do this similarly with the fullatom derivatives supplied
commit e132d8f0ad7e915d97a6355d1a2cfd86ba8586c3
Date: Sat Jun 14 16:11:29 2014 -0400
Updating methods in conformation to play nicely with membrane info and AddMembraneMover - includes atom z position, residue z position, overloaded setup_membrane methods to match membrane info constructors but respect method constness, and updated getters that will eventually but not yet pass through to pose
commit 46df5c468b491de3f6bf7756576b341d33718fc3
Date: Sat Jun 14 14:05:25 2014 -0400
Updating protocols.3.src.settings to get rid of other code and use only add membrane mover (and some other movers I will add a bit later
commit 5b53087593de154fd1bb4a62a208f5689edd572e
Date: Sat Jun 14 14:03:17 2014 -0400
Removing old crazy code for creating membrane proteins - starting fresh
commit 0a9db00d98615315b2fd86c4d935a4282142e2cb
Date: Sat Jun 14 14:00:54 2014 -0400
Getting rid of lots of old dead code - starting fresh, starting from scratch. This commit gets rid of core files not used any more - will be doing the same with protocols files soon
commit bdeff62d2ed77e4eddab11593774c14bc90ba7f9
Date: Sat Jun 14 13:55:01 2014 -0400
Killing old un-needed code, adding membrane mover creator for rosetta scripts compatibility but not yet implemented
commit 920f0346d805f5a3f58efbc85a07898942795c66
Date: Sat Jun 14 13:52:17 2014 -0400
Adding a simplified membrane info interface - will break everything under the sun
commit 696b405c78da84a2c50cd383208a68cdde343de2
Date: Sat Jun 14 13:46:50 2014 -0400
Updating author info in AddMembraneMover
commit 01414419a2d06fd791ca949156978aa42e265e39
Date: Sat Jun 14 13:23:01 2014 -0400
Starting to kill the old membrane info conf internal containment scheme - working on one that separates knowledge of coordinates from position
commit c1b07428a3541dc008d4818b111bdae3de0b1bde
Date: Sat Jun 14 13:05:06 2014 -0400
Alright - we have reasonable version of the cc and hh for add membrane mover as well as an expected API from conformation and membrane Info. going to set those up next
commit 2331f61f245d9c91c01b9155039a90ca5e17471b
Date: Sat Jun 14 12:53:02 2014 -0400
Implemented default, custom/pyrsetta and copy constructors in AddMembraneMover
commit e9f307a35bd5d93eb5450314751a290344f90d03
Date: Sat Jun 14 12:32:47 2014 -0400
Got all of the pseudocode there for membrane protein setup - killing it
commit dc373fb4fae01388d3661e3e3f719200e88624de
Date: Sat Jun 14 11:06:33 2014 -0400
More updates to add membrane mover
commit 57f97522ff82ace966fb0bdb42fdb78c5c73162c
Date: Fri Jun 13 22:08:58 2014 -0400
Starting to implement new AddMembraneMover - will need to also modify membrane info constructor, ensure PyRosetta and Rosetta Scripts friendliness
commit 9e0b24667feaa818b3abfc3b37b34f52ef23ec0b
Date: Fri Jun 13 21:49:46 2014 -0400
Adding code for a new lightweight membrane protein setup - minimal and only creates the objects we need while maintaining a good API
commit e3aa16647ddf00f103630313be5b7702b82af4b7
Date: Fri Jun 13 21:03:45 2014 -0400
Updating pilot apps
commit 0bb3138bd64c3f23bd2eeacdba5c814294f2a1d9
Merge: 8a4d4a4 b739ef4
Date: Fri Jun 13 18:03:41 2014 -0400
merging devel in local devel
commit 8a4d4a480ed517ae2c829dc25339e181bb1d5e24
Date: Fri Jun 13 18:02:12 2014 -0400
setup scorefxn fingerprint for MPs
commit e1064ebfc67dcaaf3af1f36b5837611e02eca1bd
Date: Fri Jun 13 16:46:07 2014 -0400
begin adding simple_movers to namespace for use in RS
commit b739ef41f73bff20a44db49cb19029360506823f
Date: Fri Jun 13 12:56:18 2014 -0400
updating sfxn fingerprint tests for membrane centroid and fullatom energy functions
commit 2e3ecdaa6954daeb95d82137af115480cd6bf6ce
Date: Fri Jun 13 11:35:24 2014 -0400
Adding membrane unit test fixes
commit 566f738c09886fc7132d1f133b2483bbdb102c3f
Merge: 1eedcea cc13434
Date: Fri Jun 13 09:48:32 2014 -0400
Merging remote master into ninja local master contianing mpframework devel branch
commit 1eedcea0140327b1001d8ba930d1c3e372df0223
Merge: a541608 d9a7f83
Date: Thu Jun 12 21:47:00 2014 -0400
continuing to merge remote master into ninja local master
commit a541608b7f583e2e33c1640092f1df8ea00b2345
Merge: e296f5f a118c71
Date: Thu Jun 12 08:37:32 2014 -0400
continuing to merge msater into this "pre-merged" branch while I wait for a broken pyrosetta build
commit e296f5fddf740b77dc9d4c0a17e9a8d68165a602
Date: Thu Jun 12 08:31:02 2014 -0400
Stripping out mp apps and scripts from master merge
commit 3d3d74d57e73131ee20d0ef35ad3a1a6ff8a0584
Merge: 8d5e88e b35da3d
Date: Wed Jun 11 21:36:24 2014 -0400
mergning in ninja naive docking application and membrane framework relax starting copy into mpframework devel
commit 8d5e88e35da7cdde33bdbe3e917eae1dabc37ba8
Merge: 6a00b07 f6d8ff4
Date: Wed Jun 11 21:35:39 2014 -0400
merging ninja mpframework devel with ninja master pulled on 6/11/14
commit f6d8ff43f424a08f33cb2aba1716460935abac48
Merge: 21e17b8 6115db3
Date: Wed Jun 11 21:34:56 2014 -0400
merging branch master on remote into ninja master 6/11/14
commit b35da3d1e4889928ae3d9e1f585fcf2cb2b3a7f0
Date: Wed Jun 11 21:24:16 2014 -0400
Compilation fixes to embedding methods
commit 34d6e032318ed06d6cee491b28f4de33fa71d325
Date: Wed Jun 11 21:00:31 2014 -0400
Bug fixes, should compile and do embedding update from structure. Downside is that scoring is still caling the shots, and should be done via lazy update from pose
commit de0eec40082b5d47b98d0aa11f177a980fadd090
Date: Wed Jun 11 20:46:31 2014 -0400
removing hacky embedding update methods - moving into a static methods class
commit 28c06d6bd87176a371fb5fd712d4daed8135d0b6
Date: Wed Jun 11 20:15:25 2014 -0400
Adding a reasonable version of relax, and starting files for separated embedding mehtods and new mover class
commit 1cf7a0e23d8d87459f37bda254eb2fd6627d1762
Date: Wed Jun 11 10:50:34 2014 -0400
Making some multithreading fixes without much luck
commit 1bc04b3504b2e106ee92ea2cc3c54b2defe56b1a
Date: Wed Jun 11 10:09:12 2014 -0400
Killing internal creation of a membrane pose in fast relax protocol - not the right way to go
commit 6eb14d55e07d91de20783a92039f6a9afb7a51b5
Date: Wed Jun 11 09:10:26 2014 -0400
Trying to get the framework relax version to run in parallel with jd2 - temporarily removing conformation warnings...wait not a good idea hold on
commit 1f9bf2e059d3d24c64429efd693f42fab595af3c
Merge: 99e6f89 9fa4440
Date: Tue Jun 10 10:21:06 2014 -0400
Merging in mprelax branch into mpdocking branch so I can get the mp solvation term fix
commit 9fa444010ca041061daf6515cbc81190cfdb0971
Date: Mon Jun 9 19:57:08 2014 -0400
Adding penalty terms to fullatom membrane weights
commit 0e9a6cc6d4cb9f758e6bd1c8093df44ba70a6ea1
Date: Mon Jun 9 18:22:11 2014 -0400
Updating fullatom energy terms to do a hacky structure-based embedding update for now - also added an update method in conformaiton becasue it seems like the OP in membrane info isn't really talking to conf very well
commit c4ff0304e6eb955c620477bb1940b062ec2c53c8
Date: Mon Jun 9 12:16:10 2014 -0400
Making temporary updates to membrane relax protocol - will make fixes later to the actual runtime events"
commit 99e6f89112cc21ada2eebefe155eec3957a99e24
Date: Sun Jun 8 12:20:04 2014 -0400
Adding a ridiculously naive version of a membrane protein-protein docking application
commit 6a00b07c11d04ad92c7d94b53add6da85f231c6a
Date: Sun Jun 8 10:42:56 2014 -0400
Adding warning boxes for deprecated old membrane scoring code
commit 859829d44047db089afcd9600cc691b69c61c652
Date: Sat Jun 7 18:31:20 2014 -0400
Adding dissulfide fix
commit 2b15e4c7a0cbae2c5fd71d3f132078a5494490ac
Date: Sat Jun 7 00:23:48 2014 -0400
Updating membrane fullatom weights file
commit 954149a2eabe36aec46dc184b1a3937578209b56
Date: Fri Jun 6 19:46:02 2014 -0400
Turning fullatom solvation energy back on for membranes - going to start debugging what's wrong
commit 53541aecd8ee0d69214c1f05f7259473256aaa93
Date: Fri Jun 6 16:29:43 2014 -0400
Membrane relax plus JD2 - up and running. Now to just make structures work
commit 88c2bf6dbef6de880ab05ba86dab220d8ae70518
Date: Fri Jun 6 09:12:27 2014 -0400
Bug fix for residue com method - used to be ambiguous when moved to protocols
commit d47ef09342df78e5863d6cfb150ba516f6bb0190
Merge: 004fc5d 21e17b8
Date: Fri Jun 6 07:58:25 2014 -0400
Merging master into mpframework devel in test branch
commit 21e17b840f5c97c6ac10ba50141a9d3874c1b642
Merge: 063af32 9d8fff5
Date: Fri Jun 6 07:56:35 2014 -0400
Merging remote master into ninja local master
commit 77bfd958d3bc466e12d95d06db52e202ece9efcc
Date: Thu Jun 5 22:47:10 2014 -0400
Updating membrane relax app with some quick debugging changes
commit f557261cfee4e8791f32652b4d7dcd69502ecc6b
Date: Thu Jun 5 18:05:40 2014 -0400
Starting to debug crazy twobody energy bug
commit 7ef0a1efa58d4c89d14eb3c40c33e1a3f695e349
Merge: b92b7b0 004fc5d
Date: Thu Jun 5 17:22:50 2014 -0400
Merging mpframework_devel updates into membrane relax branch
commit 004fc5df82f7020b05ba445758718043e02f4a2c
Date: Thu Jun 5 17:02:13 2014 -0400
Turning on hbond correction in fullatom scoring function fingerprint test
commit 0ed0183c1795910bffcaccab64ce78a6f506347a
Date: Thu Jun 5 16:02:41 2014 -0400
Adding sfxn fingerprint tests to use version mpscorefunction app extending from andrew's original score fprint app
commit be2b444ddb0d98f977238f5c94ad37c8b94eadce
Date: Thu Jun 5 16:00:48 2014 -0400
Adding membrane scorefunction fingerprint application
commit 15bad3057f57791b30d615a1830773eae97859b8
Date: Thu Jun 5 09:49:26 2014 -0400
Updating centroid membrane sfxn fingerprint test - now runs
commit bfab09df18cffb514b2d97790ffc74ffed81458d
Date: Thu Jun 5 09:25:22 2014 -0400
Updating fullatom weights and command file to correct sfxn fingerprint test
commit b84e247ca6e777e86448248d7ec31937c480eb38
Date: Thu Jun 5 09:05:19 2014 -0400
Adding readme in membrane directory
commit 5af6265389ac9a52c241a40fffb3427f27edf3e2
Date: Thu Jun 5 09:03:53 2014 -0400
Organizing pilot/ralford apps directory and commenting old apps from the build
commit b92b7b04278a23f86ccf987d8556b3bf2e65e992
Date: Thu Jun 5 08:51:13 2014 -0400
Adding membrane fullatom weights
commit 07a0d31e55bdafb15b84788f24cdbe8dc40d9596
Date: Thu Jun 5 08:48:55 2014 -0400
Updating membrane relax application - uses fullatom 2014 terms for membranes but crashes on number of 2 body energy types - most likely due to readable CA mismatch
commit db2e4863477d8664c5b90b3b59958e4c9609c58e
Date: Wed Jun 4 17:58:58 2014 -0700
changing max KIC perturber samples default value back to 2000
commit 815df0a1640cc5d9992ab49910c2709d5459e84f
Date: Wed Jun 4 16:22:30 2014 -0400
Turning off old membrane terms in relax and turning on new membrane framework compatible terms
commit cf56e909a079495baaf5cb8c5cc7719a73f4371c
Date: Wed Jun 4 12:53:28 2014 -0400
Updating membrane info, pilot apps and fast relax to include new membrane relax corrections
commit 8fb3caf284b4d596c2b6292f226acfaba88be5fd
Date: Tue Jun 3 12:11:24 2014 -0700
adding the standard Rama perturber before the given custom perturber
during initial loop build (in LoopBuilder class); this ensures that the
initial loop build is not biased towards the starting structure by
discarding all starting loop torsions and replacing them with random
values from Rama space; the given custom perturber can change those
torsions afterwards
commit 6faa1799d3244a759e7fd6c01ee13f758160e9cf
Date: Tue Jun 3 12:05:08 2014 -0700
restoring max KIC perturber samples to 2000
commit 6fbd6ecbc0ef4bfe5aa374655500f03a832df875
Date: Tue Jun 3 12:01:47 2014 -0700
checking if requested min_overlap is too large for the given region in ConstantLengthFragSet
commit 8021bfeeffcdfe826ffe0d000063f2b12cf16583
Date: Tue Jun 3 14:50:58 2014 -0400
Removing annoying time consuming tracer from membrane fa_embed code
commit a99752e3f0e0576813be39f177709a7bb6c66c6f
Date: Tue Jun 3 13:39:54 2014 -0400
Adding membrane relax executable to build settings
commit af29c4c4d3a190f6429dcbb2cbdaae48367934cf
Date: Tue Jun 3 13:36:41 2014 -0400
Adding membrane scorefunction corrections for relax protocol in new if option for protocol setup
commit 2a082927f8ec88a11cacd816ea4da81c4379ec4a
Date: Mon Jun 2 23:34:22 2014 -0400
Still needs to add the executable
commit b8102f868e5462c9002d0846b28f1a038c917596
Date: Mon Jun 2 23:34:03 2014 -0400
Adding starting files to membrane relax application
commit d2dd53e39bff1ea26cccd1ca49888ac5090f9b71
Date: Mon Jun 2 16:27:59 2014 -0400
Adding relax:membrane scorefunction modifications for mpframework relax mode
commit 063af324d3aa8d3eff6c0dd8f3b961841f6f4d7c
Merge: 0a5903b cc89ba4
Date: Fri May 30 10:09:11 2014 -0400
Merging branch remote master with lcoal ninja master
commit ff2106eb3416a24fcb6bcfbe8455164f43e2001b
Date: Wed May 28 10:45:31 2014 -0400
Updating most recent outline updates
commit d915166b205a4855fd8554badbd9cf7ff64cd4b0
Date: Tue May 27 10:44:35 2014 -0400
Adding additional outline for header in new mpf class design
commit 61a2a24939ef4a335dea1d46ebe47c020d350f1a
Date: Tue May 27 10:35:11 2014 -0400
Adding membrane protein creator class outline to top of cc file, probably needs a header outline as well
commit 3f521472aeb6bfbdef515de9c491e90c2d0f53a9
Date: Tue May 27 09:26:59 2014 -0400
Updating changes to membrane score function fingerprint tests
commit 7fa159618fe0a001ccf567a192666008cff58092
Date: Sat May 17 13:57:35 2014 -0400
Fixing order of arg initialization in membrane info - caused a bug in GCC
commit d9807dace4d3481625e33d960b58b117b7b8e22a
Date: Sat May 17 11:29:02 2014 -0400
Oops! Forgot to add spanfiles in sfxn fingerprint tests
'
'
commit c416d6c68d6166ff2d3883115758e5699f4d6682
Date: Sat May 17 11:15:32 2014 -0400
Removing +30 on layer bounds and method for computing z position
commit 745589ac7e4bee1f650ac66f80a7d06c251b8ab1
Date: Sat May 17 10:37:11 2014 -0400
Updating non +30 layer bounds in membrane environment term
commit b5e2e936adb4007f3d5fb24ce6a68ee93b8cb5f8
Merge: 7ed7873 4d1e665
Date: Fri May 16 22:49:25 2014 -0400
Merging branch mpframework_devel and new fullatom energy function with sfxn fingerprint tests
commit 4d1e665e1eb9e9dbbab03e3d9ebc0574cce38ee6
Date: Fri May 16 21:21:36 2014 -0400
Fixing command files for sfxn fingerprint tests
commit 656d209c9625929c241f5b09967f48dd6e5224dd
Date: Fri May 16 21:08:20 2014 -0400
Adding new centroid and fullatom membrane sfxn integration tests for new terms
commit 413ddeaaca3260ea5b63081f6773000d3543977d
Date: Fri May 16 21:07:43 2014 -0400
Removing old centroid integration test
commit ee2e702656fb57e9b9093afa8b9a6585def97104
Date: Fri May 16 20:24:35 2014 -0400
Fixing membrnae fullatom scoring terms - scoring terms pass integration tests
commit 0a5903b84f7fa5d063f0b5b61004e418ac835214
Merge: 9e8f7ff d26320a
Date: Thu May 15 20:53:59 2014 -0400
Merging local and ninja master
commit e5b630bc665613c2709b756e8c15c8014dd9e26c
Date: Thu May 15 20:46:46 2014 -0400
Adding bug fixes and updates to membrane info and fa mbenv energy
commit 7ed7873cf02506fb4aa377df365becb607482072
Merge: e3eb632 7f998ef
Date: Thu May 15 16:39:03 2014 -0400
resolve merge conflict
commit e3eb6326330a0150c7acc3cc7fe06e8c6c5194f0
Date: Thu May 15 16:25:57 2014 -0400
fix errors, compiles
commit c417e0cc62394793f8abcc28210743d0bda7612b
Merge: 7d0bc12 fa06be4
Date: Thu May 15 15:58:06 2014 -0400
merged mpframework_devel into here, resolved conflicts
commit 5d9e166bab7447f69f60fb35809af697390e4437
Date: Thu May 15 15:57:41 2014 -0400
updating membrane fa sfxn fingerprint executable and addint to pilot/membrane build settings
commit adb05cf613ca9e9a2f451856172b51c80176129e
Date: Thu May 15 15:50:20 2014 -0400
Adding fa mp env and fa mp solv energy method registrators to init.cc
commit 67e3a7d8563946684498a001edebeb12f2a11e14
Date: Thu May 15 15:47:56 2014 -0400
Bug fixes to compile FaMPEnvEnergy term
commit 7d0bc120af78c7262688eea0a6213ab2116f0204
Date: Thu May 15 15:39:38 2014 -0400
trying to fix the silent file stuff
commit eb10885862baeb19ca798215c1bd26b22caa8295
Date: Thu May 15 15:27:39 2014 -0400
Started a pilot app that will eventually execute the fa sfxn fingerprint tests
commit 4ab2fae433fe10c8dd2c16455396ad25e573f69d
Date: Thu May 15 15:27:05 2014 -0400
Adding fa accessors to membrane info and bug fixes to get compilation in FaMPSolvEnergy
commit 1fe4f7676f2457afe5bd038edeb3b342b70b9f74
Date: Thu May 15 13:57:22 2014 -0400
Fixing typos in hbond options class with new mphbond option
commit 41d225c97968e9132e13d551ec7b378ac2197240
Date: Thu May 15 13:55:28 2014 -0400
added comments
commit 114bbea640f29a481c3b63fa286fb8a23642ea8c
Date: Thu May 15 13:55:14 2014 -0400
Adding membrane framework supported hbond correction
commit 7880ed30cebcb2332f33a521fd9a5f2263b6260e
Date: Thu May 15 13:54:34 2014 -0400
Adding membrane framework supported hbond correction
commit f246478732919016db2fd129d1a2b5f837dc86ca
Date: Thu May 15 13:51:58 2014 -0400
removing methods I thought I needed but dont from hbonds.cc
commit a8d4e79f3d8d3d7fcc980d655b9669cc5ac3af47
Date: Thu May 15 13:51:41 2014 -0400
removing methods I thought I needed but dont from hbonds.cc
commit fa06be4cbfa25db9d287852ef5c780e5848731e0
Merge: ca5bfc8 c22033c
Date: Thu May 15 13:46:14 2014 -0400
pulling from remote
commit 057e7b20b2bc75636099489c3d17b5c68cbd253f
Date: Thu May 15 13:41:27 2014 -0400
Adding steepness getter to membrane info for use in hbonding code
commit e87400f3820c3cf5c8e178d1342d75cdf040f3ac
Date: Thu May 15 13:40:38 2014 -0400
Adding steepness getter to membrane info for use in hbonding code
commit ed99cd5eb4522a7ad6cd4cb3ebfbdf3a5cf480df
Date: Thu May 15 13:33:54 2014 -0400
Adding mphbond to hbond options object
commit 09e4aaba8283153f832804ba7f34bea84fc80012
Date: Thu May 15 13:25:01 2014 -0400
Adding membrane_new:scoring:hbond option for turning on framework supported hydrogen bodning correction in code
commit ca5bfc89c2554d8cdb648b3983fbb4165f77095a
Date: Thu May 15 13:13:07 2014 -0400
fixed documentation for input options
commit 7af79562fb280179eb2b4e2c0e070f04a15d5c9c
Date: Thu May 15 11:53:21 2014 -0400
Adding missing score types to ScoreType.hh files
commit 85ad9f7d356a8328a28b605b93c7df3d641755f8
Date: Thu May 15 10:45:22 2014 -0400
Initial big fixes to fix the build of FaMPSolv and FaMPEnv + score type fixes
commit f377c037cc91ce95417812362c53d429ebe4ab35
Date: Thu May 15 10:17:06 2014 -0400
Oops - made all of the membrane info methods private by accident
'
commit 80515b7c57a78389275eb2328b7093ac073c451e
Date: Thu May 15 10:14:35 2014 -0400
Finishing clean ups in membrane info class for new fullatom code
commit 350b262fcff2970c91f1bc087306478c129598bf
Date: Thu May 15 09:10:13 2014 -0400
Cleaned up and adapted membrane info object to do setup with fullatom information
commit 3d54737520366cb6c56625ed81d6ed79a83065a9
Date: Thu May 15 08:55:38 2014 -0400
Cleaning up the header for membrane info - should make it more comprehensible
commit 0cb5358aa1a59bd93a70cd80e7a6698c06288eb9
Date: Wed May 14 20:31:37 2014 -0400
Implementing env and solv energy creator methods
commit b1e5c41ebf5c7c9532aa193a03ecc0f4503aa878
Date: Wed May 14 20:12:36 2014 -0400
Implementing the rest of fullatom solvation energies
commit 18e24603bfcc3aea7c45e39857ea25c9cd2b238b
Date: Wed May 14 17:51:11 2014 -0400
Implementing more of the solvation energy term"
commit b0e51077e4669dfba8abcfa7a976ccd69dfe2d1c
Date: Wed May 14 17:11:29 2014 -0400
Starting to implement the solvation energy term
commit ce08454301fd397c756706ca39e04872f9db0fd7
Date: Wed May 14 15:50:28 2014 -0400
Implemented rough version of fullatom membrane environemnt energy
commit aed653521043a161a070f84b2f38dbb88d8439a1
Date: Wed May 14 15:34:15 2014 -0400
Moving stuff back into membrane info
commit 80e652a5871ebddf574f57e3d2bc10f1f096c2ba
Date: Wed May 14 13:20:52 2014 -0400
Adding fullatom score types to score type manager
commit fa00ed8d9897fa5c0a2d2b735de8092b5cbdd875
Date: Wed May 14 13:18:17 2014 -0400
Adding new utility class for fa calculations, starting to implement these in derivative setup in env term, also adapting membrnae info to hold this new data. Maybe I can make it so this is not typeset dependent whatsoever??
commit 7eaedd8b8cdc3cc9a310af394742f8717ef6425e
Date: Tue May 13 22:37:33 2014 -0400
Adding header, fwd header and starter cc code for new fa env and solv terms
commit ba7bac5e06d5cf68e3ea9b6b0e7a6e74e9c81049
Date: Tue May 13 22:14:11 2014 -0400
Implementing pieces of the fa env term
commit 9e1ad1c0e6d7848ae57d21e6a198d275d07c6538
Date: Tue May 13 22:03:12 2014 -0400
Adding templates for new fa solv and env energy terms which will be framework adapted
commit c22033c9492bfdb76b5703bab7c54113950fdb8c
Date: Tue May 13 19:04:02 2014 -0400
Quick bug fixes - membrane etable with new annotations compiles
commit adc9babea0f8c1569cce200f343a5eae41a00057
Date: Tue May 13 18:55:43 2014 -0400
Adding finished header to forward file and staging hh file for commit"
commit 4629ead2f04d91af93d405772b762cf1fc5410bc
Date: Tue May 13 18:54:42 2014 -0400
Adding more comments and updates to annotated sfxn
commit 09a9d1b3f9af39525e7496a6b7ff62dc0e0796c6
Date: Tue May 13 18:46:17 2014 -0400
Removing a ton more dead code in membrane etable
commit 9f0fa9ba66523eedf523bce7fd598ce0ca0c4c93
Date: Tue May 13 18:10:42 2014 -0400
Cleaning up membrane etable hh file, adding comments and formatting fixes. Also started updating base memb etable but then realized its no longer used
commit c5743752b26e21de3b52e657d2107d1631995492
Date: Tue May 13 17:57:18 2014 -0400
ResidueType: added VIRTUAL_RESIDUE property
commit 39de8304ddbfd37a16de088b8a8a45a10b506f7d
Merge: e2321a9 ce2af8c
Date: Tue May 13 17:33:39 2014 -0400
pull from remote
commit 5fa019ad69ccf44c7902738ce6e25580484a04a8
Date: Tue May 13 11:42:55 2014 -0400
Removing hundreds of lines of dead code in the membrane etable code
commit ce2af8c1a1931174f34fc6e56c76f2ee11f224e1
Date: Tue May 13 09:59:54 2014 -0400
I prematurely merged in msater into this branch. Wasn't ready, so I reset the branch to remote. It looks like everything is ok here - the branch builds. So I am goign to go ahead and push, but if we find issues we can always revert the work
commit ca52b2cd2fb3dbb30a392bf29bf9740173c7a4ed
Date: Tue May 13 09:57:28 2014 -0400
Fixing spacing in membrane data class so it reads much more nicely...
commit 0dc9e645a5c3ddc70a73426806491d8090aacdd1
Date: Mon May 5 13:51:37 2014 -0500
resolved merge conflicts in MEM and EMB params files
commit f59cd1a92b1385a0b50bf0b064b07cb1970ef04f
Merge: e3fa230 9e8f7ff
Date: Sat May 3 23:00:30 2014 -0400
Merging branch master 5/3/14 with mpframework devel into a merge testing branch. The only unresovled merge conflicts are in the membrane residue params files which needs to be corrected by julia
commit 9e8f7ffc4720825fedc7e138c48e4727a21d5eae
Merge: c968d61 fe5d0b7
Date: Sat May 3 22:55:33 2014 -0400
Merge of ninja local master with mpframework devel merge testing branch
commit e3fa23021a4211b3f19bf8e0b06e87c361e88c33
Merge: 4ff8b62 a67748c
Date: Sat May 3 21:53:07 2014 -0400
Merging of branch mpframework_devel and mpframework_sfxn
commit a67748c5cee9b511e11b394e464508afb848c6a2
Date: Sat May 3 21:49:13 2014 -0400
Fixing indentation issues that don't respect coding conventions
commit 9da7eebf4a6f3c773136a695feaf2579202b1f0e
Date: Sat May 3 21:44:03 2014 -0400
Removing old unit tests for membrane scoring - this functionality is covered more appropriately in an integration test
commit a4044f6a89cb3999f52812670bd0d50a90eeb988
Date: Sat May 3 19:45:21 2014 -0400
Adding passing membrane centroid scorefunciton integration test for new socres
commit 10101f3f4da99710a0703f00f5a2d6c51811b156
Date: Sat May 3 19:44:55 2014 -0400
updating membrane scorefunction app
commit 84dcecab54078220923ff7baeef80935711d5a0f
Date: Fri May 2 23:02:29 2014 -0400
Modifying resource definition file to take files from the current working directory
commit 30c7bcf90da20fedca9eea3544524b94a356586a
Date: Fri May 2 23:01:54 2014 -0400
Adding required input files for integration test
commit 785343f0fde130e27d884e7e9a1f6dc2c6cfb892
Date: Fri May 2 22:59:42 2014 -0400
Adding integration test dir for membrane sfxn
commit 7213ea392c19dfe29f72e030b67a3e50142599a9
Date: Fri May 2 22:59:24 2014 -0400
Adding integration test for membrane centroid score function
commit 120ffaed621477d564869ee1ec4d652d9962275a
Date: Wed Apr 30 13:39:37 2014 -0400
outlined test for pair term, still unsure about some issues though
commit 856e7e0ce5a9ca80b23430c728f0d036eb616148
Date: Wed Apr 30 13:32:40 2014 -0400
Updating Menv energy cases
commit 9fba307df9cbf72adc7d316fbbb1708992d75949
Date: Wed Apr 30 13:30:35 2014 -0400
Outlining tests in MPEnv energy unit test
commit 8a2ed5e5f10a1b8cfd5448c40ab3bf4fc9d9635e
Date: Wed Apr 30 13:21:04 2014 -0400
Updating MPEnvEnergy test and adding template for mp cbeta energy
commit 4fa1473b52910af48dbd763d54360416d9a092d3
Date: Wed Apr 30 10:56:38 2014 -0400
updating Menv energy unit test template
commit d2466784b73078e65b04f710cafdeeeb14ff5b48
Date: Wed Apr 30 08:24:36 2014 -0400
Adding some new files to test directory that got deleted earlier plus normal and x pos debugging tracers in membrane info
commit b14ec210a0ed6c05283cb87b28637ad3efe19a1e
Date: Tue Apr 29 22:55:34 2014 -0400
Still working on unit tests
commit 43a5b89f269309103ad3c9b59606500d442733e6
Date: Tue Apr 29 20:46:39 2014 -0400
Adding cytB test data and updating full menv energy unit test
commit d3022497efb9c448efe111be710124333300df94
Date: Tue Apr 29 20:08:42 2014 -0400
Adding structure of 1afo for scoring test data
commit 4fa31ae1735bb40ca4f28e0da68e5fa4c77f53e5
Date: Tue Apr 29 16:58:42 2014 -0400
Adding bug fixes in MP env energy
commit f17adf51b55a0c8ad36328d568baa81829d6ef66
Date: Tue Apr 29 16:54:53 2014 -0400
Fixing membrane info unit test with z position changes and updating mp environment energy unit test
commit 4ff8b624cd9ae6170461f62be3799ae25a7a04f7
Date: Tue Apr 29 13:51:29 2014 -0400
Fixing more merge conflicts and resolving reversed coding convention updates
commit 6aef0547579581fdaa53d8297153c019e58b2bd2
Date: Tue Apr 29 13:08:06 2014 -0400
Fixing spacing in core settings
commit a84066e54a96361d2af506bbc41909d00a61cc7a
Merge: 46305274 1e1999d
Date: Tue Apr 29 13:00:52 2014 -0400
Resolving merge conflicts in spanfile io and merging mpframework devel into julia's branch first
commit c968d614535389cddb723e9e071f9073eacf9705
Merge: 7b359f1 55e4f83
Date: Tue Apr 29 12:54:17 2014 -0400
updating ninja local master with remote master
commit 80ccad48733d1a43ef0b9c32450cfaa06b98d59c
Date: Tue Apr 29 12:53:23 2014 -0400
Working on local updates for unit tests
commit ba7f2ad279ace08331cfb8599f3a86e63a2d03f7
Date: Fri Apr 25 13:53:15 2014 -0400
Removing non helix penalty debugging tracers - this is a bogus term for now
commit 7798d888c781206040c2db2f6c6055741f99f7a7
Date: Fri Apr 25 12:58:55 2014 -0400
Fixing score type full names so they fit on the score file
commit c740335003e64e98389ac5b3c3d00e80d6079b4a
Date: Fri Apr 25 12:50:53 2014 -0400
Updating penalties to incldue corrections for virtual residues - all of the scors are correct except for non helix socres.
commit 38fc2850e54d9fccb87693febe75803c1cd6536c
Date: Fri Apr 25 09:13:49 2014 -0400
Adding new residue energies breakdown class from Rocco's pilot app so it can be used in Unit tests
commit f33b4122351b1c5b9e1ed03d677690e5c35aef32
Date: Fri Apr 25 08:25:13 2014 -0400
Remvoing the bug in mp cbeta energy and m pair energy - three working energy terms :D
commit 30a8b20aa3155402bac8aafacf9207e8ad65fd35
Date: Fri Apr 25 00:27:49 2014 -0400
Debugged issue in membrane cbeta term - removing debugging tracers
commit 85a60cb22610a0422829e222e8934f0292d1e46e
Date: Wed Apr 23 15:30:33 2014 -0700
fragment libraries are now passed to the FragmentPerturber as const reference
commit f90ce13b764237e64b618df84767249010ade7af
Date: Wed Apr 23 16:39:06 2014 -0400
Debugging of apps after merge
commit d20ca1b6758dd7938e3c4644397e5bbfcb59681d
Date: Wed Apr 23 14:59:26 2014 -0400
Reverting to old z_position containing membrane info files
commit c99213f3e32bc7b51e5d20ba5b8ef8677308e1eb
Date: Wed Apr 23 14:17:31 2014 -0400
Adding new app for analyzing new mp energy terms
commit 50b3e81e87f865975cbd17fc30c0506bba821910
Merge: 3097032 1e1999d
Date: Wed Apr 23 13:40:14 2014 -0400
Resolving merge conflicts from mpframework devel into mpframework scoring function
commit 30970328e2a493a6a93597484c14b70742fe918e
Date: Wed Apr 23 13:30:38 2014 -0400
Adding new weights files for new membrane scoring terms
commit 61444971e2834f11848125950a0a61365bf5664c
Date: Wed Apr 23 13:30:20 2014 -0400
Adding quick fix to non helix penalty
commit 536998ebe44f9b864fa883479ed66f25ed9ea8fb
Date: Tue Apr 22 14:11:20 2014 -0700
implementation of the FragmentPerturber class; this finally enables sampling using KIC with fragments
commit 1c022533998d7fd1d4bb5dac5d23724de635c4ce
Date: Tue Apr 22 14:07:50 2014 -0700
throwing a BadInput exception if KIC with fragments is enabled, but no fragment libraries are provided;
also fixes a bug where the refine stage would still use standard KIC even if KIC with fragments is set
commit 5fb929d2f111aceb1c922a8bf399a5c6b8a5f8df
Date: Tue Apr 22 16:37:41 2014 -0400
Pushing some debugging changes..haven't pushed in a while
commit c8de331b0b6be14424a58157cb3d50333927b8d2
Date: Sun Apr 20 22:55:02 2014 -0400
Fixing the scoring feature reporter so neighbor computation is more efficient and can actually finish on larger cases
commit cca14de1a1ef5cdd21fdb6e1b71f05449e1925e6
Date: Sat Apr 19 23:31:27 2014 -0400
Adding centroid membrane weights all weighted at 1.0 for generating of unit test reference scores
commit e13e26e06897899d7902fcafae5e7538a9305baa
Date: Fri Apr 18 11:35:50 2014 -0400
added file
commit 711960f9824ce7f5db8fd3f6b6341b762484a980
Date: Fri Apr 18 11:35:25 2014 -0400
change to mp_apps
commit fe71316a412273695a0284432ccab995b5032774
Merge: 191b217 3d1edb0
Date: Thu Apr 17 15:57:00 2014 -0400
merging crumb pyrosetta-friendly version with ninja local
commit 6b448e257801d9401feb9483bb0ae52791cb3982
Date: Wed Apr 16 17:05:16 2014 -0700
adding the function overlapping_with_region, which returns the number
and list of all fragment alignment frames that somehow overlap with the
given region (also allows those frames that start before the region and reach into it);
currently only implemented for ConstantLengthFragSet (the FragSet parent class
simply calls the region method by default)
commit 191b217d1bf8cadd5772b7e2f203a216041fb726
Date: Wed Apr 16 15:07:58 2014 -0400
Finished C++ version of scoring features reporter
commit 03adc6c9822ef0b9574050a27ee51ab4ed4c7fca
Date: Tue Apr 15 23:49:18 2014 -0400
Adding a features reporting app - shouldn't build because I amde some chnages after I first ran it. Work in progress
commit 521d913b7fbb79a427840754c8d241df089a2d3c
Date: Tue Apr 15 14:45:42 2014 -0700
including Frame.hh (instead of Frame.fwd.hh) in FrameList.hh to fix compilation;
this is needed due to FrameList inheriting from vector1
commit 606f429c9168df05d662d859e8d3f2da11278d53
Date: Tue Apr 15 13:35:54 2014 -0400
Ediding pilot apps settings for rosetta bin build
commit 3d1edb0bdbbb6bd05178f86e744957ef9c942e98
Date: Wed Apr 9 17:09:17 2014 -0400
Reversing bug fixes I made that were fixed for real in master
commit 76e1af72eed9c28b17a7d1bdc7fd80d4b7da43a0
Merge: 247619e 83f5c18
Date: Wed Apr 9 16:42:19 2014 -0400
Merge branch 'master' into rfalford12/mpframework_sfxn
commit 247619eb233e31285f7caccbb60fdb51e0544808
Merge: f95b08d ac9be95
Date: Wed Apr 9 16:03:53 2014 -0400
Merge of mpframework_sfxn branch with remote master
commit f95b08dce534b2989f6213d99caf3ae366e028e8
Date: Wed Apr 9 10:09:27 2014 -0400
Fixing case sensitive typos in mp score terms that broke the gcc build
commit 7160ba19db710933171ab0bb70f977e5cf241a29
Date: Wed Apr 9 09:58:09 2014 -0400
Renaming MPCbeta energy classes to have consistent file names - case typos broke build
commit bd538d85e5f78c2d78a9991d988757ef02fa8b32
Merge: c97a34d 836ac40
Date: Wed Apr 9 09:21:43 2014 -0400
Merge branch 'rfalford12/mpframework_sfxn' of github.com:RosettaCommons/main into rfalford12/mpframework_sfxn
commit 1e1999d37ec9bbd252929b5528887c9bdac84e01
Date: Tue Apr 8 10:56:29 2014 -0400
Fixed linking error for clang 5.1 unit tests
commit 756a6789e83ef93c0dd010bd90b2660b1cf622a6
Date: Tue Apr 8 10:34:34 2014 -0400
Editing resource loader creators such as to not include old code
commit 680daee49586793c6fa6bf0b2fe7a6bcbefa338b
Merge: d405b32 fe404b2
Date: Tue Apr 8 00:51:47 2014 -0400
Merging in coding conventions...agaIN
commit d405b324d035f57fb2b0ef285c10781f188b45b4
Date: Tue Apr 8 00:43:48 2014 -0400
Temp local changes
commit 714fd3e73bc8ad2177e412aa7aa5b0823b54ee09
Date: Tue Apr 8 00:04:14 2014 -0400
Making quick changes to tests - everything should compile
commit bd21b22f6a50762c0bd9daa7212e0293614877ba
Date: Mon Apr 7 23:23:06 2014 -0400
Merge of mpframework devel and coding convention updates
commit fe404b25645537b11a4637ed46a8c210b2f3ec5c
Date: Mon Apr 7 22:55:26 2014 -0400
Updating unit tests to sync with new coding convention changes
commit 8e5984b01803d0578cc889f475f371d712eaae29
Date: Mon Apr 7 22:31:54 2014 -0400
Some bug fixes to coding convention updates
commit 8a398b541c5d430fbe0c9a8befc0bcb602f9c552
Date: Mon Apr 7 22:14:38 2014 -0400
updating spanning topology for coding conventiosn
commit e34907616a6616c65c144729e36724fc0d52c22b
Date: Mon Apr 7 22:12:40 2014 -0400
Updating lipid acc info and membrane info for the coding conventions
commit b504457f2b7a9c17ef4a9de4cbb39492bf57535a
Date: Mon Apr 7 21:51:52 2014 -0400
More coding convention updates
commit 107693b7baa23faa0a6670a8db2a0fcc351f7da0
Date: Mon Apr 7 21:47:45 2014 -0400
Removing embed search params fallback confguration (old code) from file system
commit 1cfcf818ae4574ddf4f31c9750f8d19038388851
Date: Mon Apr 7 21:43:57 2014 -0400
Updating IO code to obey the coding conventions and getting rid of old resource manager code
commit d1964793c3548e95b91887028725c1c695d78cee
Date: Mon Apr 7 21:35:50 2014 -0400
More coding convention updates in membrane protein factory
commit 9e1164af1ed7bfd2f95f366ca5380b66985db21d
Date: Mon Apr 7 21:34:11 2014 -0400
Updating geometry util and membrane protein factory to accommodate coding conventions
commit 8b52a654be6810d525b83b218d7e3f5864f89ffe
Date: Mon Apr 7 19:01:21 2014 -0400
Quick coding convention updates in EmbeddingFactory - much of this code will get changed anyways
commit baf7cd231866df6fc41115541a788cc1c2fa91e7
Date: Mon Apr 7 18:59:39 2014 -0400
Getting rid of the random awkward header in MembraneProteinFactory
commit 20a7f9f02b3cb830deb315b2c570a8a97a70d30d
Date: Mon Apr 7 18:56:37 2014 -0400
Adding coding convention updates in core/membrane/geometry/MembraneResidueFactory
commit 8408e77d462eaeaa33947b16ad09941cfdad47f0
Date: Mon Apr 7 18:46:12 2014 -0400
Updating coding convention issues in geometry/util. in the framework code
commit 63f795d152275dc6bb2a14dc8c6c41cb34a5108e
Date: Mon Apr 7 11:49:32 2014 -0400
added pose.total_atoms, compiles, runs as expected
commit b8995c6df6d60f06dc9dde82740a4184b65fc3fa
Date: Sun Apr 6 14:38:00 2014 -0400
added files that I forgot to add in last commit
commit 8472b8d057ebd3559356e459c59cc0b8ec9a34d1
Date: Sun Apr 6 14:36:59 2014 -0400
added functionality in dump_pdb for writing out membrane, compiles, runs as expected
commit 8d902a1ccef5e710ac693e3508c7155f2655230b
Merge: e72d240 6be1270
Date: Sat Apr 5 01:30:56 2014 -0400
need input options in this branch
commit e72d2406a29d0bdde35b498989688cb4ad560114
Date: Sat Apr 5 01:30:48 2014 -0400
added file
commit 01d8a3778cf78e4f8c040d0b29bbe34ee5fc957a
Date: Sat Apr 5 01:30:18 2014 -0400
added function in file_data
commit 5506b3d0747b2e50f4f3d13c99d92ecd25d63d04
Date: Sat Apr 5 01:26:57 2014 -0400
Commenting out unfinished membrane app from the build
commit 6be1270a1dbce2d127b2c0f23b77e6446b406720
Date: Fri Apr 4 16:17:39 2014 -0400
updated position of MEM and EMB, compiles, runs correctly
commit e26fb5a131f4805424b1137eb9e64d004343522b
Date: Fri Apr 4 14:29:56 2014 -0400
fixed indents
commit b50539f8ab3c76db2cd972bbabd280be05b2818b
Date: Fri Apr 4 14:26:38 2014 -0400
Updating embedding MCM search
commit 836ac4042497a3eac638664955677cda58b0621f
Date: Fri Apr 4 01:31:04 2014 -0400
Added embedding mcm search and a couple of quick changes
commit ac62d454001f8ab6562bb6bf6a603cd0647d7463
Date: Fri Apr 4 01:17:40 2014 -0400
Initial add of developmental embedding mcm search method
commit f19e6e9cf57eaf187fb0693aca3bc33d673ddf9d
Date: Thu Apr 3 20:01:02 2014 -0700
fixing compilation of LoopRelaxMover
commit c97a34dc1791016c475bdaa02bcd1d4ecc086382
Date: Thu Apr 3 22:37:17 2014 -0400
Resolivng issue with some warnings turned errors
commit 266e2bdcc73a2933d5a0977a50478050d0baaa97
Date: Thu Apr 3 22:31:55 2014 -0400
Correcting typo created in a merge conflict resolution in MmebraneInfo
commit e82bf4129b02e4f2310a96af2f10c0e0d1a05db0
Merge: c94b8a0 8e63058
Date: Thu Apr 3 22:04:54 2014 -0400
Resolving merge conflicts between ninja master and crumb
commit ece27a314a01c4b132ecf33e88d2b08c20f01fbb
Date: Thu Apr 3 18:57:18 2014 -0700
adding FragmentPerturber class and registering it in protocols.3.src.settings; still requires implementation
commit 46b10661476e12e30a113295b615a1a134fb5d9d
Date: Thu Apr 3 18:44:24 2014 -0700
adapting the LoopRelaxMover to execute KIC with fragments when the
given flags are set (currently in debug mode for testing purposes)
commit 8e6305896977e966ebbd073b8d2aebd2afe2987e
Date: Thu Apr 3 18:56:35 2014 -0400
Membrane lips compiles
commit 618cb33dd41f61f4352292fd9320004c2d8d4409
Date: Thu Apr 3 18:45:00 2014 -0400
Adding residue zpos method in tm proj penalty
commit 46305274eb1daeeb61f25a1238071d1dd30966e5
Date: Thu Apr 3 18:29:07 2014 -0400
changed exceptions, moved MPfactory to protocols, updated mp_apps
commit 99a4c89717bc297a9bb514b2719ca4be2671095b
Date: Thu Apr 3 18:28:36 2014 -0400
Updating design of tm proj penalty to split up computation and checks
commit 5c44c52d936d7594aab4e38d4dbc5a6a49a21eee
Date: Thu Apr 3 15:56:05 2014 -0400
Just kidding on that last one - tm proj is a whole structure penalty - changed it by mistake
commit 8882d4683c014cf7614fb2ff448a517eff6015c6
Date: Thu Apr 3 15:55:06 2014 -0400
Fixing documentation issue from copying in mp nonhelix pen and working on implementing onebody interface in tm proj penalty
commit fbf7a534b6607261f3fccb871a753990dd803049
Date: Thu Apr 3 15:51:49 2014 -0400
Fixing indentation and documentation in MP tm proj penalty method
commit 9ad408ab0c395f9018f71f935b78123f52f02656
Date: Thu Apr 3 15:47:36 2014 -0400
Fixing compilation errors in mp non helix penalty
commit 568728c016b565cb72656fe0837a445a5a6a8864
Date: Thu Apr 3 15:29:47 2014 -0400
fixing bug
commit 51a29dca011b71cedced79439198d74e7f7b415c
Date: Thu Apr 3 15:15:06 2014 -0400
updating non helix penalty to separate evaluation from edge case handling - also cleaned up and made a one body energy
commit 7bee135bec5656ba02be4de457a8005aaf4b003e
Date: Thu Apr 3 15:05:46 2014 -0400
Also removing symmetry from NonHelix - will put it back, I promise :)
commit 6b1b12e85e1065ea67fe9ceacbced17dd6b3e806
Date: Thu Apr 3 15:04:04 2014 -0400
Temporarily removing symmetry from the energy terms as it simplifies use of the framework
commit c80b7164a84c361686dd0936e8cba928994a50c6
Date: Thu Apr 3 14:56:14 2014 -0400
Just made an awesome framework update - framework gets z_pos in one line of code vs 4 on the old frmwk
commit 4a2e67aa7e8a93841fb28cec8fede2f7dd78aae6
Date: Thu Apr 3 14:45:50 2014 -0400
Fixing indentation in MPNonHelix penalty
commit 868bd686d77570af0c01f5413b042b09ec1a7fdc
Date: Thu Apr 3 14:44:30 2014 -0400
Fixing compilation errors in the new MP termini penalty - everything in that class compiles
commit 4f0c5fca7d9b22aaa84e30a04d842031288adf49
Date: Thu Apr 3 14:39:08 2014 -0400
Reimplemented MPTermini penalty as a one body context dependent energy
commit 48998cf3444a476ee0809ef1bb2fb1c4cb4a9049
Date: Thu Apr 3 14:34:26 2014 -0400
moved MPfactory to protocols.a.4
commit 5b8bcdc7e51a830df37e32a335f6f0dfce3c1e8d
Date: Thu Apr 3 14:22:24 2014 -0400
Updating energy term documentation in MPPairEnergy
commit 393db99fa62e5137801d838f96db16909dc69fd4
Date: Thu Apr 3 14:16:24 2014 -0400
Updating energy term documentation in MPEnv energy
commit ab8205579f985491f7662ad51a6d24a1b5c55649
Date: Thu Apr 3 14:08:14 2014 -0400
Updating Energy term documentation in MPCbeta Energy
commit b4b0db11227c40af86a557849b3f2761677fc70b
Date: Thu Apr 3 02:38:52 2014 -0400
Adding notes for mp sec struc penalty
commit 1672f6a3e95dca645a030310a02ecf24377c0b57
Date: Thu Apr 3 02:03:17 2014 -0400
Starting to implement secstruc as a residue onebody penalty. Also adding new score types for secstruc and span to the enum
commit 959ce604c9fe0e6e0666053a9bffbce92bf89f1f
Date: Thu Apr 3 01:51:19 2014 -0400
Updating fwd header and creator header for secstruct penalty and adding header info in cc and hh
commit 445686325b5bc198f6966536b294e5e97324ca0c
Date: Thu Apr 3 01:13:31 2014 -0400
Renaming MP sec struct penalty from SS penalty
commit 931eaeea8a0276655c3a49623f7834f950dabe78
Date: Thu Apr 3 01:07:59 2014 -0400
Much more compiles - but still has a way to go
commit 50588fac39001897bd0f9519225100ae66e744a7
Date: Thu Apr 3 00:47:58 2014 -0400
Also finished resdesign of non helix and tm proj penalty
commit 946eefc43e60eab2785e7fc6513bd90a35722a62
Date: Thu Apr 3 00:32:59 2014 -0400
Depth be gone in core/conformation/membrnae
commit bd3fea4585ffa3b33ff791d2fdacd223bf2b9501
Date: Thu Apr 3 00:27:48 2014 -0400
Depth be gone from scoring :D
commit f96b3367adb78524daacaf02224e37028357a23e
Date: Thu Apr 3 00:22:02 2014 -0400
Renaming MPBasePotential => MembraneData in core/scoring/membrane
commit a3c403d9f31f4a17be9aca8e77e80d5ef91371b2
Date: Thu Apr 3 00:10:35 2014 -0400
Adding new method for temrini to header
commit d830f16bd3765375f17471ee472bb0b593211ac3
Date: Thu Apr 3 00:09:35 2014 -0400
Updating mplipo energy without spit and temrini penalty with redesign for funciton
commit 862581ad9c7dfa070758bc7dcc28c71e0e362323
Date: Wed Apr 2 22:36:17 2014 -0400
temp change
commit e2321a91e2b2b7ba58f3eab72b12f4bdca110e80
Merge: dfa28ff 3f24752
Date: Wed Apr 2 21:32:49 2014 -0400
getting mp scripts
commit 3f24752a34f7b002ec950819e4ce695566c8c2df
Date: Wed Apr 2 19:46:08 2014 -0400
Adding python equivalents for shared mp scripts
commit 8a630d48ba7d03ec3a87b3d896e0decda855e48b
Date: Wed Apr 2 19:43:04 2014 -0400
Adding shared scripts directory including coloring scripts, python scripts for computing topo, etc
commit 765a2b326e75bc1cbd65fcf5e748c1ec20d236e8
Merge: 049109d e8ddf4d
Date: Wed Apr 2 19:42:19 2014 -0400
merge of jkleman updates
commit 8d4b6cc8fa91ee3f973a4b1245820d2f8e659000
Date: Wed Apr 2 19:42:04 2014 -0400
QUick updates
commit df42d05a10327dd936ffa5632582439dfa35881b
Date: Wed Apr 2 15:58:23 2014 -0400
Implementing MPLipo energy creator and fwd header
commit 91bafac1e401fc9b60ae5e861ffae1415d31a142
Date: Wed Apr 2 15:42:24 2014 -0400
Started to fix termini penalty - and then I realized these should possibly be per residue - will stop for now and ask about it today
commit 12fc2c9e66a51131303e75f20e7ab97ecf03bec2
Date: Wed Apr 2 15:28:56 2014 -0400
Fixing indentation of classes in MPPair, MPCbeta, and MPEnv terms
commit adae9c50a9df42c18c5d8ffcffa48fa3c9691ce7
Date: Wed Apr 2 15:26:19 2014 -0400
Fixing indentation in mpair term
commit 8ed84ab28b17bf7d56bdb126880a76ca85e9e4c9
Date: Wed Apr 2 15:25:50 2014 -0400
Some additional clean ups to the mpair term
commit ed6989a0854c3d542327cb9ee02f6c1f44d03ab2
Date: Wed Apr 2 15:20:22 2014 -0400
updating pair term to split computation of score with rsd and pose inputs
commit e8fd9bc2babd7ae5c17956a62eb676feef6090d7
Date: Wed Apr 2 14:25:32 2014 -0400
Updating comput env score to work with function inputs
commit 69de7d0a6131e0dafaf2713d4d717a1a6537aeaa
Date: Wed Apr 2 13:57:52 2014 -0400
Compute mp cbeta score
commit 22be2aa1f9cae9065a6901aec7869ebd78026899
Date: Wed Apr 2 13:29:12 2014 -0400
Updating energy method MPCBetaEnergy - redesigned for testing - separated the actual computaiton of score from rosetta objects
commit e118a4f1df7aa0565eace3c123e53394b06bb38d
Date: Wed Apr 2 11:21:48 2014 -0400
Updating MPBasePotential to be called MembraneData - somewhat more appropriately named thanks brian
commit 76bb2e04bd7b0045d0324c7469cea573743b8558
Date: Tue Apr 1 23:32:55 2014 -0400
Reversing constness - turns out the log tables do need to somewhat change internally. Can either reformat this or change later
commit 1af58048e8ccfea875634e4eefb21dec5524d74b
Date: Tue Apr 1 23:23:08 2014 -0400
Hopefully updating const correctness in mp potential class
commit 2d79ff4dcdddf27f88f5359dd7543b82da71d7c7
Date: Tue Apr 1 23:21:51 2014 -0400
Updating indentation in MPBaePotential
commit 72e0844d855f846a90ffe8a2087940f90beef9cd
Date: Tue Apr 1 23:18:52 2014 -0400
changed pose_from_pdb to fxn in core3.io.pdb, compiles, runs
commit b37dae522d75cf0ad5b6f8f127381d06413bb937
Date: Tue Apr 1 22:23:07 2014 -0400
Quick notes in this app
commit e645fbf4b9836ebe6a28b62f5904eeedfc94a7ff
Date: Tue Apr 1 22:21:46 2014 -0400
Adding pilot apps for testing new membrane energy terms
commit ad4d9480428fb8d0ed3f864927146a209a2824c0
Date: Tue Apr 1 20:26:48 2014 -0400
debugged, doesn't compile
commit 7b359f191854de8e306a29507a29913f57dd69e1
Merge: f2557e3 3bdade7
Date: Tue Apr 1 17:40:30 2014 -0400
Resolving merge conflicts with membrane FA potential
commit 587028ad198510514c7bcc8e9abac0a52392e8f1
Date: Tue Apr 1 14:32:26 2014 -0700
refactoring LoopBuild main function to load fragment data whenever fragment files
are given on the command line; this implicitly enables fragment loading for KIC with fragments
commit 1ae1eba72a2d4d278cbf4599856c17258bfff8cf
Date: Tue Apr 1 01:54:46 2014 -0400
added files to mp_apps
commit 9dce53db4ef8d56de738ceef301fa28927de61de
Date: Tue Apr 1 01:49:22 2014 -0400
added functions for reading inputs, doesn't compile
commit 9369e1b020a3a8c1951a1a1cc694ff33cd0aaf18
Date: Mon Mar 31 23:18:28 2014 -0400
Restoring embedding factory to initial stage - wants to do this change in a separate branch
commit 18d0aba6ba13b8a463bba1616b4cb2137b18e1a2
Date: Mon Mar 31 23:10:51 2014 -0400
Updating the Embedding factory interface to work with some cleaner internal behaviors - this will temporarily break the build until I correct the implementations
commit 0451f4d76a5e6369d64f853b41d619537f5f0518
Date: Mon Mar 31 18:19:09 2014 -0700
fixing compilation of LoopBuilder with custom perturber constructor;
the given custom perturber can overwrite bond lengths, angles and
omega torsions after idealization if so desired
commit dfa28ff01f73fe22a6ee36053c0f6f25263d8d66
Merge: 5bdddd7 cce2f56
Date: Mon Mar 31 21:12:22 2014 -0400
Resolving merge conflicts in merge of jkleman branch recent updates
commit 5bdddd7d4df2639b255a64d785779fd4836caa1c
Date: Mon Mar 31 21:05:52 2014 -0400
Patching MPFramework Namespacing bug fixes into branch from mpframework_devel post 3/27
commit cce2f56071a2e08d84d6e06c56f3a6b9424fb094
Date: Mon Mar 31 19:58:25 2014 -0400
fixed namespacing in tests EmbedSearchParamsLoader and SpanFileIO
commit c94b8a0fb333afcbfbbac697bcae953f9e63f26e
Merge: 6637cce 4159d25
Date: Mon Mar 31 19:54:57 2014 -0400
Merge branch 'rfalford12/mpframework_sfxn' of github.com:RosettaCommons/main into rfalford12/mpframework_sfxn
commit 4159d2572b04156454eb77b0c9c4659e303c4f5c
Date: Mon Mar 31 19:10:55 2014 -0400
Adding stub code for lipo, sspred, and mp spanning penalty
commit 6637cceebe7fe447db9cdf84865b1ba7afb29397
Date: Mon Mar 31 18:24:41 2014 -0400
Removing unused variables in MembraneInfo
commit 4057f09b8c08d13d7169dec53d00d04961460eeb
Date: Mon Mar 31 16:55:33 2014 -0400
created pilot app to read spans from commandline and adjusting the MPfactory constructor, compiles
commit c96f9b986c5299cd2f63ac5a19ec76bc525f5258
Date: Mon Mar 31 16:47:18 2014 -0400
Adding MPPair unit test - only does one total energy check
commit f621b6044eb383c9bf3d61195ddd8b52e7c918e6
Date: Mon Mar 31 15:19:41 2014 -0400
More work on the unit testing template - still figuring this out
commit 384f86d85af42ad1f67af1a347191671d42b838a
Date: Mon Mar 31 15:05:28 2014 -0400
Adding membrane penalties to energy method registrators
commit 26db3f81acfca08f80e261aec26d3280f79ae5b8
Date: Mon Mar 31 15:01:09 2014 -0400
Adding mp scoring template unit test to build sttings
commit 9eb16edc7bbef94749f7953f5cfdb7d642a62d9f
Date: Mon Mar 31 14:53:18 2014 -0400
Added MP TM projection penalty to build settings
commit 12df3cd0d3ec3548965ebdce9ea4bbe3996bd1d0
Date: Mon Mar 31 14:48:45 2014 -0400
Implemented full MP tm proj penalty
commit 43af59bf7510c998ccf6b24bfe70cfeff97c155d
Date: Mon Mar 31 14:46:27 2014 -0400
Implemented tm proj forward and creator headers
commit 4c398d868ca991388c613830331eae84527bfcf3
Date: Mon Mar 31 14:42:12 2014 -0400
Quick documentation fix in MP non helix penalty creator header
commit 067db8cd90ab3d2d9c03c7330764e6566532877c
Date: Mon Mar 31 14:41:27 2014 -0400
Quick bug fixes - MPNonHelixPenalty compiles
commit 27dd9fe2ebec77a8549a0a6f212015c4d03d4ab0
Date: Mon Mar 31 14:39:29 2014 -0400
Implemented MP non helix penalty score tmer
commit 1d8baa62b5bc76d41358d865116dfe7268020433
Date: Mon Mar 31 14:34:19 2014 -0400
Added stub code for MP non helix penalty
commit f8e4cb8d31919511dfac508f92fc10da8a93cac7
Date: Mon Mar 31 14:30:06 2014 -0400
Quick fixes in MPTermini penalty - term compiles
commit b2d7a9acf5d099274a0a60436b6b865ed2179965
Date: Mon Mar 31 14:19:03 2014 -0400
Updating membrane penalties methods to include overhead methods for calls from energy terms
commit a33397c5d4fa2893f1e770a028db2d79120b2c38
Date: Mon Mar 31 14:12:39 2014 -0400
Adding overloaded methods to penalties for use with scoring methods
commit c20896fa3079ed0f10b6fb719f2b03c33636f842
Date: Mon Mar 31 00:53:40 2014 -0400
Started to implement termini penalty as a scoring method
commit 7d87abdabc42bc9078889dc06f65b746f5d5c0f3
Date: Mon Mar 31 00:23:56 2014 -0400
Initial add of penalties energy terms - framework supported
commit 3fd384427e6cc4c0b8e20217296b2e29a82c1ee3
Date: Sun Mar 30 21:21:22 2014 -0400
checking options done, compiles, runs as expected; only need to make sure that EMB and MEM do what they are supposed to
commit 72def467ff4449e87245efc210fdc34ebefe0c69
Date: Sun Mar 30 13:07:06 2014 -0400
Setting up unit test template for new mp energy terms to score with one term and test with it
commit 463c3f1f170ac001c572ee4e8cf56d57668bb2b3
Date: Sun Mar 30 12:45:28 2014 -0400
Adding shell code for mp energy term unit tests and fixing namespace icnludes in new energy method creators for mp terms
commit 3bdc46e36159d94195b776124293dc93dea5e2a5
Date: Sun Mar 30 12:21:27 2014 -0400
Registering new MP energy methods in init.cc - I think
commit 103e054267c228cd0659c5b7b9987f625bfcd550
Date: Sun Mar 30 12:15:11 2014 -0400
All three new mpframework energy terms compile - plugged into score tpes but not the methods yet
commit df27bf72fea04a4f62ae7b6095fba5bd90483daf
Date: Sun Mar 30 11:45:12 2014 -0400
MPEnv Energy method compiles
commit 3d6e8ffbc623c65e91bbe14a343c3ae529871b1a
Date: Sun Mar 30 11:31:16 2014 -0400
Quick fixes in MPCbeta energy so it compiles
commit 89a1ea0b151f33cc76813b0af0f4d418fd89b01e
Date: Sun Mar 30 11:21:36 2014 -0400
Adding new mpframework score types to ScoreType.cc and ScoreTypeManager.cc
commit ab79423cc03ce63e3cb2bb90fe4ef673c6445a51
Date: Sun Mar 30 11:12:25 2014 -0400
Debugging MPCbeta energy term and adding const member acces into MembraneINfo in Conformation
commit 373b8f4b0fa1093accf3a58dde1ac9d5181b1d5a
Date: Sun Mar 30 10:36:05 2014 -0400
commented out unwanted options
commit 7b6e1562ee7ee3492b4336fe5de5c7311fc21866
Date: Sun Mar 30 00:21:24 2014 -0400
Bug fixes in the scoring manager - should be all set
commit 6a3dd957370e743892f563919b53f7be06d65137
Date: Sun Mar 30 00:17:47 2014 -0400
Adding MPBase potential hooks into the scoring manager - pray it compiles and I didn't just kill all of rosetta
commit 1169455f017ba1a4e2ca951a03a14e22671e1b33
Date: Sun Mar 30 00:10:28 2014 -0400
Taking MP energies out of the build for now - needs to do a few other updates beforehand
commit 2ef47acd0f48c1167d0f34295df772158cf4ae30
Date: Sun Mar 30 00:08:32 2014 -0400
Const correct :) new MembraneInfo with improved interface compiles
commit de795111b519a5c5b0050c382b402bdddca01c28
Date: Sun Mar 30 00:05:12 2014 -0400
Correcting set xyz compiler error in membrane info
commit e0eda40c1a6109abec518d8bafb2d1dd882e56a9
Date: Sun Mar 30 00:04:09 2014 -0400
Correcting set xyz compiler error in membrane info
commit 5ecbdbb3302e089a79a8a84d9e17a493ad2f649f
Date: Sat Mar 29 23:29:03 2014 -0400
Updating membrane info with recent refactoring updates - will need to fix compiler errors in setting xyz info
commit eca2c87157ff66d4bd0476485edc0da6e7a62dc9
Date: Sat Mar 29 23:20:13 2014 -0400
Quick change in pair energy for now - also adding energy methods to build temporarily so they can be re-indexed by XCode
commit fd5277e8be003a84cbb6233a45f4657691586525
Date: Sat Mar 29 23:17:19 2014 -0400
Implemented MPPair energies - rough estimate. We now have all three terms roughly implemented though are not yet compiled. everything has creators but currently relies on some important dependencies
commit 3e527858d73766de5b8dd7a67d5a34640cf4ea56
Date: Sat Mar 29 22:41:36 2014 -0400
Adding MPEnv energy creator and MPenv energy methods
commit 54d2df5567ac93a4452a064ce1ce780b2a6c59d7
Date: Fri Mar 28 22:18:06 2014 -0400
Updating CBeta and MPair energies
commit 25689ffe1f64b0028775401db294c38a22f0a759
Date: Fri Mar 28 22:01:25 2014 -0400
Adding MPair energy creator header
commit 73857f768e39c5c03feb2ca69d984735d5efdff0
Date: Fri Mar 28 21:58:57 2014 -0400
Adjusting new cbeta method to use internal base potential
commit 0a7ffc131a0bb7d95790cea93aea4018894b2801
Date: Fri Mar 28 21:47:03 2014 -0400
Implemented MPCbeta energy method
commit eeabbaad6e6c09f139019b61fd9f8454854873a3
Date: Fri Mar 28 21:30:05 2014 -0400
Adding creator class header for mp cbeta energy
commit 46cbccf06d544683908e81a9dfe5afcc5fa476a0
Date: Fri Mar 28 18:51:07 2014 -0400
Implementing stub interface in MPCbeta method
commit 58d3451dea92998888a549e559a0ab95fe370f59
Date: Fri Mar 28 18:47:25 2014 -0400
Implemented MCbeta header
commit 86600ea342bbe85b169778629adccdaf6377f569
Date: Fri Mar 28 18:36:54 2014 -0400
Adding stub code in cc and hh files for MEnv term
commit 8344084fa1d8b324e8b2dbebef7998d985613758
Date: Fri Mar 28 18:34:55 2014 -0400
Adding stub code in cc and hh files for MCbeta term
commit 80105713c667df4b438d55d214850c3757cf4517
Date: Fri Mar 28 18:32:24 2014 -0400
Adding stub code in cc and hh files for MPair term
commit e070fa7226029fc214bb664a130362dcf626d604
Date: Fri Mar 28 18:30:32 2014 -0400
Initial add of mp energy term files for Menv, MCbeta, and Mpair and implemented forward headers
commit d9b9a69839323413326c9c9834af2ca90d07b783
Merge: 1dd9654 e8ddf4d
Date: Fri Mar 28 16:30:13 2014 -0400
need the binary apps for testing the corrected EMB & MEM residues
commit f175d778e007fa728362e50c827f63a6a31a0590
Date: Fri Mar 28 16:25:42 2014 -0400
Yay - MPBasePotential compiles
'
commit 6a1f54d20512b3ae911fd4f4b223442dcf1939e1
Date: Fri Mar 28 16:19:39 2014 -0400
Changing cenist private member naming to include the _ so compilation isn't ambiguous
commit 0bf344a81f585b8d333c70fe4ad3647eeccfda4c
Date: Fri Mar 28 16:10:58 2014 -0400
Updating core.3 settings to build the base potential - still has trouble with the referencing issues in io silent struct that are legacy on clang 5.1 Otherwise there shouldn't be issues with the penalties unit tests
commit 21f33db946a9b54d651f8e55f83e3f840c87689c
Date: Fri Mar 28 16:09:22 2014 -0400
MPBasePotential - Implemented database IO, initialization, and access methods, Should be good from here - will try to compile it
commit 1dd9654ea80dbaba31a6de502e95dcb742f8d4d4
Date: Fri Mar 28 16:05:01 2014 -0400
corrected EMB and MEM residue types for fa_standard and centroid
commit 68aebf05e853c31cceb42822fe2d9bfa9aaa5533
Date: Fri Mar 28 15:44:20 2014 -0400
MPBasePotential: Finished adding methods to the base class
commit 49703cb71f3f737e7c8156ee276e68b85f284d29
Date: Fri Mar 28 15:36:49 2014 -0400
MPBasePotential: Adding class definition for the header
commit 2e3ca126e818a1eece1df4402b14db9a968012dc
Date: Fri Mar 28 15:27:11 2014 -0400
Implemented forward header - easiest part :)
commit f4effec36e7bcd363b100d7da1eab97dc1eb7ea0
Date: Fri Mar 28 15:24:38 2014 -0400
Updating headers and include guards in mp base potential fwd.hh, hh. and cc
commit cb065957cf7bdc95c3f8bee1af27afc645f574e3
Date: Fri Mar 28 15:20:45 2014 -0400
Crazy syntax error in core.3 build file prevented penalties from compiling - fixing now
commit f666dec480c4d76e70d45cc41fbf5c3256e6459f
Date: Fri Mar 28 15:19:17 2014 -0400
Adding membrane penalites test to version control
commit d1442109c0a4bdb2f17028c6d06430c32939937c
Date: Fri Mar 28 15:18:59 2014 -0400
I have added and built the membrane penalties code and test - but there seems to be a linking error in the unit tests. Might try rebuilding the libraries first from scratch
commit de45af77d026e14af16c051d7444f3ed7e759c3e
Date: Fri Mar 28 15:06:50 2014 -0400
Initial add of MP base potential files - going to write stub code
commit a35b70c8008f4e360ddd14b71329494ba563bef9
Date: Fri Mar 28 11:24:32 2014 -0400
Adding membrane penalties to mp sfxn branch
commit 7a67caba2593256ebeb5c17751a254e57623691f
Date: Thu Mar 27 22:43:24 2014 -0400
split up read and check function, doesn't compile
commit 049109d21442b08b06a044690002862a3eed1655
Date: Thu Mar 27 21:37:26 2014 -0400
updating local changes quick
commit b378c781be4930eda8ec2df5dbcfbb94bb2e58a6
Date: Thu Mar 27 18:04:49 2014 -0400
checking parameters compiles and runs correctly
commit e8ddf4d219ba9b61fc30d424ce976d525ca4d3cf
Merge: 5586904 257f668
Date: Thu Mar 27 11:54:43 2014 -0400
Merge branch 'rfalford12/mpframework_devel' of github.com:RosettaCommons/main into rfalford12/mpframework_devel
commit 55869043c862253fe3fe2c16e5eb78ff61ebcf68
Date: Thu Mar 27 11:54:07 2014 -0400
Adding renamed command files for mp apps
commit 257f66880ae43e7a02b5d9f0f3d4f31c6db714a6
Merge: 2d62022 b58f599
Date: Thu Mar 27 10:04:35 2014 -0400
merge of local ninja mpframework devel with remote and crumb
commit 2d6202289784777d52f6e699d743748b12145b36
Date: Thu Mar 27 10:04:00 2014 -0400
Removing unnecessary methods from the embedding factory and also updating read pose from seuqnece app that I am working on
commit b58f5993fd946f619383227be7a744bd4ff0d659
Date: Thu Mar 27 09:19:39 2014 -0400
Adding mp apps inputs and outputs into Rosetta/main
commit ef97e8309d1f8bba998dbc78fc34085d2aecbcb2
Date: Thu Mar 27 09:18:02 2014 -0400
Updating quick big dominik introduced into sequence profile
commit 5466c05c0ab2920414260c9fb1f6fc9661fd9e9f
Date: Thu Mar 27 09:07:07 2014 -0400
added to_string function in xyzVector
commit d2d3a587beaf0417f79c5458698148d11fe6977e
Date: Wed Mar 26 23:19:15 2014 -0400
Fixing some invalid tracers in the embed from topo app - woudl need to give it a subset of the pose for this or traverse the full embedding. being used out of its original context
commit 03db5367e03ec5db2a76c0c7738888d7f3adf4e1
Date: Wed Mar 26 23:05:37 2014 -0400
Forgot to change private member to one used by the inputs - fixing now
commit c9e4b50ca1aa317e11d0bc10c98be090c98c64bd
Date: Wed Mar 26 22:52:16 2014 -0400
oops...forgot to init from cmd in cmp mover
commit 592717265446328bce7ebfe0ccca4e2bfa6a886a
Date: Wed Mar 26 21:51:55 2014 -0400
Updating bugs so the apps complie - pushing to louis
commit 519296b4d636b8705180e619aa14a5083907fe3d
Merge: d3a113c 5f747a3
Date: Wed Mar 26 18:41:39 2014 -0700
resolving conflict in options.settings when merging-in master (rev. 56584)
commit d3a113ce5af8057b633f56828a3d880584680787
Date: Wed Mar 26 18:31:44 2014 -0700
making perturb_kic_refactor and perturb_kic_with_fragments report when initial kinematic closure failed
commit f825821e85255ca7a441cb6f40aefa534db9e342
Date: Wed Mar 26 18:29:40 2014 -0700
added clang 5.1 to option settings
commit 21c2e42f63facfea324dba0a4b14f66e6a47a318
Date: Wed Mar 26 21:11:28 2014 -0400
Commenting in embed from topo pilot app
commit 2ebe91431af1e8fd7483782f4e89e71b1cbb6bdb
Date: Wed Mar 26 20:43:39 2014 -0400
Fixing new embedding method to not use private members - accident sorry
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commit 4147bd84d9be74c09fde51dc2f466da4a8eb5cef
Date: Wed Mar 26 20:30:55 2014 -0400
Forgot to add src apps pilot membrane to github
commit fe5a9a7b9dc75777988e8173e63453ae54205af5
Date: Wed Mar 26 20:30:34 2014 -0400
Adding non initialization based embedding from topology method to the embedding factory, also adding some tester apps to src/pilot/apps/membrane
commit 174b28a025de7702c46dcfe52da79290cd2a3b51
Date: Wed Mar 26 20:13:08 2014 -0400
added show() funtion to xyzVector. Doesn't compile.
commit dad1ac1491b24cf8de47c50a272d1c61421af881
Date: Wed Mar 26 12:30:42 2014 -0400
added functions, compiles and runs
commit 1918f45dc39bed2c86f9372dc3efae03738f91ab
Date: Wed Mar 26 10:53:58 2014 -0400
added function
commit 192abfdd214f02f7fde570a75a8809868daaaffb
Date: Wed Mar 26 00:34:33 2014 -0400
Moving metrics into a more extensible location for sampling
commit 304eceee4d01b196bc56e65659dc5e8e93865327
Date: Tue Mar 25 18:54:22 2014 -0700
adding custom-perturber constructor to LoopBuilder;
this allows to use a custom perturber for picking phi/psi torsions during the initial loop build;
bond lengths and angles, as well as omega torsions are still idealized
commit fbf745d4aa998034e85d936ac5c9153eac71d1f8
Date: Tue Mar 25 21:06:53 2014 -0400
read_membrane function in parameter checking. Doesn't compile
commit 171605e09b227c5cc0cb5ee25a6f1588bc0c244b
Date: Tue Mar 25 12:11:50 2014 -0400
comment out parameter checking to put that into a new branch
commit 010263bd09f8ece48f52cc14331ed918ef8d5a91
Date: Tue Mar 25 11:40:19 2014 -0400
working on checking parameters
commit f2557e370867546b495f29cb00ec04d6c8e008a6
Date: Mon Mar 24 13:54:22 2014 -0400
updating fa potential with consistent include guards
commit 52158add4a8aeff2fdda0503707d3bb06ce0adaa
Merge: 8d4ace3 d544ed2
Date: Mon Mar 24 13:48:55 2014 -0400
Merge of ninja master with local master
commit 8d4ace3d6d103219b513b1c8c3a4f4d3d342047a
Date: Mon Mar 24 13:48:50 2014 -0400
Updating include guards in membrane potential to hopefully fix the pyRosetta build
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commit c299b31ed530ad6bae76e73bdb4f8dae6c205af5
Date: Mon Mar 24 11:52:35 2014 -0400
added parameter files for MPframework to database: membrane/, scoring/weights/membrane_parameters.patch, scoring/weights/membrane_penalties.patch, pilot app jkleman/mp_parameters.cc for reading in
commit b64af7504900b62ccf15d961d59d066f8dd5bf80
Date: Sun Mar 23 02:05:37 2014 -0400
Updating mac clang build to pass
commit 90b207e4c175bc950baa88687517d3e5dfe6f3d8
Date: Sat Mar 22 23:14:48 2014 +0100
Applying fix to mac 5.1 clang build
commit 0a8dd8eeb1b1191acd4eeb62a860cc1231a577a1
Date: Fri Mar 21 17:04:44 2014 -0700
adding perturb_kic_with_fragments and refine_kic_with_fragments options
commit 34671a5cc851b32c0035e48a457446b7c31ef1f0
Date: Fri Mar 21 17:03:10 2014 -0700
adding user-specific xcode IDE files to .gitignore
commit 7404c21214cad4075813f45e1d456d08f0502aa1
Merge: cb7a0e4 adcacd3
Date: Wed Mar 5 12:09:14 2014 -0800
Merge remote-tracking branch 'origin/master' into kylebarlow/general_dev