The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP. More...

Namespaces
	abinitio

	analysis

	anchored_design

	antibody

	antibody2

	backrub

	boinc

	branch_angle

	canonical_sampling

	cartesian

	checkpoint

	cluster

	coarse_rna

	comparative_modeling

	constraints_additional

	contact_map

	ddg

	ddG

	design_opt

	dna

	docking

	domain_assembly

	electron_density

	elscripts

	enzdes

	evaluation

	features

	fibril

	filters

	fldsgn

	flexpack

	flexpep_docking

	floppy_tail

	flxbb

	forge

	frag_picker

	frags

	genetic_algorithm

	geometry

	grafting

	hotspot_hashing

	hybridization

	id

	idealize

	init

	inputter

	jd2

	jobdist

	jumping

	kinmatch

	ligand_docking

	loop_build

	loophash

	loops

	MakeRotLib

	match

	medal

	motifs

	moves

	mpi

	multistate_design

	noesy_assign

	nonlocal

	optimize_weights

	outputter

	pack_daemon

	pb_potential

	pmut_scan

	pockets

	protein_interface_design

	qsar

	rbsegment_relax

	relax

	rigid

	rna

	rosetta_scripts

	rotamer_recovery

	RotamerDump

	sasa_scores

	scoring

	seeded_abinitio

	sic_dock

	simple_filters

	simple_moves

	sparta

	star

	surface_docking

	swa

	symmetric_docking

	toolbox

	topology_broker

	ub_e2c

	unfolded_state_energy_calculator

	viewer

	vip

	wum

	wum2

Classes
class	LoopRebuild
	The loop-rebuild protocol. More...

class	LoopRefine
	class LoopRefine for fullatom loop refinement More...

class	RBSegmentRelaxImpl

Typedefs
typedef utility::pointer::owning_ptr < AntibodyModeler >	AntibodyModelerOP

typedef utility::pointer::owning_ptr < AntibodyModeler const >	AntibodyModelerCOP

typedef utility::pointer::owning_ptr < RBSegmentRelaxImpl >	RBSegmentRelaxImplOP

Functions
void	print_ddgs (std::string ddg_out, std::string label, ddgs delta_e_components, ddgs, double total_ddgs)

void	read_in_mutations (utility::vector1< mutations > &res_to_mut, std::string filename, pose::Pose &pose)

int	ddG_main ()

static basic::Tracer	TR ("protocols.looprelax_protocols")

static numeric::random::RandomGenerator	RG (431111)

void	Tokenize (const std::string &str, utility::vector1< std::string > &tokens, const std::string &delimiters=" ")
	Helper function tokenizes a str. More...

int	RBSegmentRelax_main ()

Detailed Description

The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.

FIX THIS.

Restrict design to residues matching user-specified SASA criteria in the monomeric, bound, or unbound state.

Compare the sequences between a native and designed protein.

How many salt bridge interactions are there?

Compare the rotamer recovery between a native protein and a list of other proteins.

How many pi-pi interactiosn are there? pi-stacking considered are T-stacking and offset.

This Calculator tries to solvate all polar groups by docking explicit TP5 water molecules, then counts unsatisfied hydrogen bonds using the same criteria in BuriedUnsatisfiedHydrogenBondCalculator.

How many cation-pi interactions are there?

unit headers

unit headeers

Set of functions from Sparta class that don't actually manipulate any state in the class and have thus been removed.

Problems found during porting:

initialization protocols for symmetrical docking

Inserts a Fragment into a Pose, similar to old Rosetta++ main_frag_trial algorithm.

set of fragments for a certain alignment frame

Hold chi- tensor information for the Pseudocontact Shift calculation.

MPI Headers.

STL Headers.

Boost headers.

Numeric headers.

general functions for generating typical kinds of Loops sets.

kinematic closure move

TODO make this a .fwd.

TODO .fwd fails (why?)

Project Headings.

C++ headers.

metric for Gunn moves

Cost computation for Gunn Moves.

Project headers.

Unit Headers.

Utility headers.

class to compute projection of a protein structure to principal component (PCA) eigenvectors ( as defined in file )

Replace pack_region_ala_pose_ with a PoseOP to remove this header.

stores movable_jumps info for replica docking

This class will create instances of Mover ConformerSwitchMover for the MoverFactory.

very simple–pulls apart non-DNA (i.e. protein and friends) from DNA to facilitate DNA binding score calculation

Where is the ddGMover.fwd.hh include?

Project Headers.

Unit headers.

simple mover for stealing side chains from one pose and sticking them on another pose.

simple mover that applies another Mover, and then recovers the input sidechains from the input Pose.

LoopRelaxThreadingMover.hh.

LoopRelaxMover.hh.

stupid test file for visual studio c++

The instance of CheckPointer contained by AbrelaxApplication should be replaced by a CheckPointerOP

Author: Oliver Lange; Oliver Lange Archive class to collect structures such that variances of scores can be computed to determine normalized weights; Oliver Lange (olang.nosp@m.e@u..nosp@m.washi.nosp@m.ngto.nosp@m.n.edu)

Date: Wed Oct 20 12:08:31 2007

Detailed:

Author: Mike Tyka; James Thompson

C++ headers Utility headers Project headers

Author: ashworth

sets an appropriate fold tree for a non-DNA/DNA interface (including multichain non-DNA and/or DNA) and then simply separates non-DNA chain(s) from the DNA chain(s) with a single translation. More basic than RigidBodyMover (which maybe needs a new base class?)

Author: ashworth; Andrew Leaver-Fay via code_writer.py (aleav.nosp@m.erfa.nosp@m.y@gma.nosp@m.il.c.nosp@m.om); Zhe Zhang; Tim Jacobs; Tim jacobs; Sarel Fleishman (sarel.nosp@m.f@uw.nosp@m..edu); Javier Castellanos ( javie.nosp@m.rcv@.nosp@m.uw.ed.nosp@m.u )

Package headers

Package headers Utility headers Numeric headers

Package headers Numeric headers

Package headers Project headers ObjexxFCL headers Utility headers Numeric headers C++ headers

Package headers Project headers

Package headers Project headers C++ headers

Package headers Project headers Utility headers C++ headers TEMP

C++ headers

Package headers CREATE THE .FWD.HH FILE Project headers ObjexxFCL headers

Unit headers

CREATE THE FORWARD DECLARATION FILE
#INCLUDE IT HERE

Package headers ObjexxFCL headers

Package headers Project headers Utility headers

Author: possu; Dominik Gront (dgron.nosp@m.t@ch.nosp@m.em.uw.nosp@m..edu.nosp@m..pl); Oliver Lange ( olang.nosp@m.e@u..nosp@m.washi.nosp@m.ngto.nosp@m.n.edu )

Date: Wed Aug 22 12:08:31 2007

Code duplication alert: TorsionFragment is going to be phased out Please avoid writing any new code using these classes: look in core/fragment/ instead look in /protocols/abinitio/FragmentMover for usage examples

#include <ObjexxFCL/format.hh> // apl needed? using namespace ObjexxFCL;

Project headers Utility headers C++ headers

Author: Oliver Lange

this class replaces the frag_close routines in jumping_pairings.cc the short loop is copied into a special purpose pose that just contains the loop-fragment with the hope that things are speeded up... which may or may not be true! only the linear chainbreak score is used.

Author: Daniel J. Mandell (dmand.nosp@m.ell@.nosp@m.itsa..nosp@m.ucsf.nosp@m..edu)

Date: Tues Jan 08 12:08:31 2008

Author: Amelie Stein (ameli.nosp@m.e.st.nosp@m.ein@u.nosp@m.csf..nosp@m.edu), Oct 2012 – next-generation KIC

ObjexxFCL headers

/protocols/match/downstream/SecMatchEvaluatorFactory.cc

Author: Kui Chan (kuich.nosp@m.an@u.nosp@m.w.edu), oct 09

This should probably be a pilot app, but the way Rosetta Scripts is set up, it can't be in the pilot apps

Utility headers C++ headers

Author: Sarel Fleishman

EVIL EVIL

Author: Rhiju Das

Where the # total is how many proteins compared. resi_idx = residue index nat_bb_bin = dssp naming for bb pct_bb = fraction matching backbone bins nat_rot1 = chi 1 pct_rot1 = fraction matching chi bins If 999 appears, that means that the amino acid does not have that chi angle

Detailed:

Parameters

@return

Remarks

References: JBNMR 2008 41:179-189 schmitz et all will explains the tensor convention used

Christophe Schmitz

Last Modified: June 2009

Author: Eva-Maria Strauch (evas0.nosp@m.1@u..nosp@m.washi.nosp@m.ngto.nosp@m.n.edu), March 2011; Eva-Maria Strauch (evas0.nosp@m.1@u..nosp@m.washi.nosp@m.ngto.nosp@m.n.edu); Eva-Maria Strauch (evas0.nosp@m.1@u..nosp@m.washi.nosp@m.ngto.nosp@m.n.edu), September 2011; Eva-Maria Strauch (evas0.nosp@m.1@u..nosp@m.washi.nosp@m.ngto.nosp@m.n.edu), May 2011

Core headers Numeric headers Utility headers C++ Headers

Author: Ingemar Andre; Oliver Lange (olang.nosp@m.e@u..nosp@m.washi.nosp@m.ngto.nosp@m.n.edu)

Date: Wed Oct 20 12:08:31 2007#include <protocols/abinitio/WobbleMover.fwd.hh>

modified for use inside CS-Rosetta by Oliver Lange

Author: Oliver Lange

modified for use inside CS-Rosetta by Oliver Lange

Author: Oliver Lange; James Thompson; Rhiju Das (rhiju.nosp@m.@sta.nosp@m.nford.nosp@m..edu, Parin Sripakdeevong (sripa.nosp@m.kap@.nosp@m.stanf.nosp@m.ord..nosp@m.edu)

project headers

package headers project headers

CatPiCalculator

Detailed:: Not much detailed here. Iterate through the carbons of aromatic rings and compare that to the distance of the polar hydrogens in basic residues...histidine not considered. Default distance is 3.2A. Wait, you want to know how to use this? Well, within your protocol, you need to do the following: First, create the calculator. To do this, see below: core::pose::metrics::PoseMetricCalculatorOP cat_pi_calculator = new protocols::toolbox::pose_metric_calculators::SaltBridgeCalculator(); Then you must register this so that the pose understands it. See below: core::pose::metrics::CalculatorFactory::Instance().register_calculator( "cat_pi_metric", cat_pi_calculator ); To actually get the metric, you have to print it. For example: core::pose::Pose pose; pose.print_metric("cat_pi_metric", "cat_pi") Where cat_pi_metric is the name that it is registered under and "cat_pi" is the key, seen below.

Author: Steven Combs

Last Modified: October 22 2010

ExplicitWaterUnsatisfiedPolarsCalculator

Author: Chris King - dr.ch.nosp@m.ris..nosp@m.king@.nosp@m.gmai.nosp@m.l.com

Last Modified: 4.8.2011

PiPiCalculator

Detailed:: Not much detailed here. Iterate through the carbons of aromatic rings and compare that to the distance of the aromatic hydrogens. Default distance is 3.2A. Wait, you want to know how to use this? Well, within your protocol, you need to do the following: First, create the calculator. To do this, see below: core::pose::metrics::PoseMetricCalculatorOP pi_pi_calculator = new protocols::toolbox::pose_metric_calculators::SaltBridgeCalculator(); Then you must register this so that the pose understands it. See below: core::pose::metrics::CalculatorFactory::Instance().register_calculator( "pi_pi_metric", pi_pi_calculator ); To actually get the metric, you have to print it. For example: core::pose::Pose pose; pose.print_metric("pi_pi_metric", "pi_pi") Where pi_pi_metric is the name that it is registered under and "pi_pi" is the key, seen below.

Author: Steven Combs

Last Modified: October 22 2010

RotamerRecovery

Detailed:: This is an implementation taken from James Thompson. I am not even sure he knows I stole it from him. The main function that is called is the get_rotamer_recovery() function. You can pass this function a native pdb and a list of altered pdbs, or just 1 native and 1 alterd pdb. The rotamer recovery will be output to the screen. Output looks like:
total = 1

resi_idx nat_bb_bin pct_bb nat_rot1 pct_rot1 nat_rot2 pct_rot2 nat_rot3 pct_rot3 nat_rot4 pct_rot4 1 E 1.0000 1 1.0000 2 1.0000 1 1.0000 999 0.0000 2 B 1.0000 2 1.0000 1 1.0000 999 0.0000 999 0.0000 Where the # total is how many proteins compared. resi_idx = residue index nat_bb_bin = dssp naming for bb pct_bb = how many match the bb bins? nat_rot1 = chi 1 pct_rot1 = how many are correct If 999 appears, that means that the amino acid does not have that chi angle

Authors

Author: James Thompson (original author); Steven Combs (moved it to protocols for general use)

Last Modified: October 20 2010

SaltBridgeCalculator

Detailed:: Not much detailed here. Iterate through the oxygens of acidic residues and compare that to the distance of the polar hydrogens in basic residues. Default distance is 3.2A. Wait, you want to know how to use this? Well, within your protocol, you need to do the following: First, create the calculator. To do this, see below: core::pose::metrics::PoseMetricCalculatorOP sb_calculator = new protocols::toolbox::pose_metric_calculators::SaltBridgeCalculator(); Then you must register this so that the pose understands it. See below: core::pose::metrics::CalculatorFactory::Instance().register_calculator( "sb_metric", sb_calculator ); To actually get the metric, you have to print it. For example: core::pose::Pose pose; pose.print_metric("sb_metric", "salt_bridge") Where sb_metric is the name that it is registered under and "salt_bridge" is the key, seen below.

Author: Steven Combs

Last Modified: October 22 2010

SequenceComparison

Detailed:: This is an implementation taken from Ron Jacak, Douglas Renfrew, Matt O Mera. The main function that is called is the get_sequence_recovery() function. You can pass this function a list of native pdbs and designed pdbs, or just 1 native and 1 designed pdb. The sequence recovery will be output in a file called sequencerecovery.txt along with a substitution matrix in a file called submatrix.txt

References:: "Native sequences are close to optimal" paper

Authors: Ron Jacak, Douglas Renfrew (renfr.nosp@m.ew@u.nosp@m.nc.ed.nosp@m.u) ( added rotamer recovery, cleanup ) Steven Combs (moved it into a general use class)