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Rosetta 3.5
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Rosetta 3.5
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Grafting class adapted from Steven Lewis' pose_into_pose algorithm. Basic, and quick, but with many options. More...
#include <AnchoredGraftMover.hh>
Public Member Functions | |
| AnchoredGraftMover (Size const start, Size const end) | |
| Start and end are the residue numbers you want your insert to go between. start->Insert<-end. More... | |
| virtual | ~AnchoredGraftMover () |
| void | set_defaults () |
| void | set_scaffold_flexibility (Size const Nter_scaffold_flexibility, Size const Cter_scaffold_flexibility) |
| Sets scaffold flexiblity on either end of scaffold. More... | |
| void | set_insert_flexibility (Size const Nter_insert_flexibility, Size const Cter_insert_flexibility) |
| Sets insert flexibility on either end of insert. More... | |
| void | set_movemaps (MoveMapOP const scaffold_mm, MoveMapOP const insert_mm) |
| Advanced way to set options. Use if you know what you are doing. More... | |
| void | set_use_default_movemap_from_flexibility (bool def) |
| Instructs the class to ignore any movemaps from set_movemaps. More... | |
| void | set_cycles (Size cycles) |
| void | set_default_cen_scorefunction () |
| override of base class More... | |
| void | set_cen_scorefunction (core::scoring::ScoreFunctionOP scorefxn_) |
| override of base class More... | |
| void | set_mintype (std::string mintype) |
| Sets the mintype for the MinMover. More... | |
| void | set_skip_sampling (bool skip_sampling) |
| Sets the mover to skip the small mover sampling step. More... | |
| void | set_use_smooth_centroid_settings (bool use_smooth) |
| sets up the smooth centroid scorefunction + any changes to VDW. if false, switches back to default scorefunction. More... | |
| void | set_use_single_loop_double_CCD_arms (bool single_loop_double_arm) |
| Uses a single loop, two arm loop closer. More... | |
| void | set_use_double_loop_double_CCD_arms (bool double_loop_double_arm) |
| Keeps the insert frozen in cartesian space. Sets the algorithm to use two loops on either side in order to close the graft. (Please superimpose piece onto scaffold first) More... | |
| void | set_use_double_loop_quad_CCD_arms (bool double_loop_quad_arm) |
| Keeps the insert frozen in cartesian space. Sets the algorithm to use two loops on either side in order to close the graft. (Please superimpose piece onto scaffold first) More... | |
| Size | get_Cter_loop_end () |
| void | set_test_control_mode (bool test_control_mode) |
| TESTING ONLY Sets the protocol to 'randomize' the flexible residues before trying to graft. This is used to test the protocol by grafting a piece of a protein back onto itself and looking at RMSD. More... | |
| virtual void | apply (Pose &pose) |
| Grafts the piece into the pose, uses CCD to close the connection. Insert does not change dihedral space, but DOES change cartesian space by default. Pose is returned without repacking any sidechains. Use repack_connection after apply method. Deletes overhang and region between start and end if residues are present. More... | |
| virtual void | repack_connection_and_residues_in_movemap (Pose &pose, core::scoring::ScoreFunctionOP fa_scorefxn) |
| convenience function for AFTER apply method. More... | |
| virtual void | repack_connection_and_residues_in_movemap_and_piece (Pose &pose, core::scoring::ScoreFunctionOP fa_scorefxn) |
| convenience function for AFTER apply method. More... | |
 Public Member Functions inherited from protocols::grafting::GraftMoverBase | |
| GraftMoverBase (Size const start, Size const end, std::string mover_name) | |
| Start and end are the residue numbers you want your insert to go between. start->Insert<-end. More... | |
| virtual | ~GraftMoverBase () |
| copy ctor More... | |
| virtual void | set_piece (Pose &piece, Size Nter_overhang, Size Cter_overhang) |
| Sets the piece that will be inserted, and any overhang residues. More... | |
| virtual void | set_insert_region (Size const start, Size const end) |
| Set the region if changed since construction. More... | |
| virtual void | set_fa_scorefunction (core::scoring::ScoreFunctionOP score) |
| virtual void | set_default_fa_scorefunction () |
| Grabs the scorefunction from command line options. More... | |
| void | superimpose_overhangs_heavy (Pose const &pose, bool ca_only, bool silence_rms) |
| uses rms_util to superimpose piece onto pose. Not run during apply for added control to user. More... | |
| virtual std::string | get_name () const |
| Return the name of the Mover. More... | |
| Public Member Functions inherited from protocols::moves::Mover | |
| Mover () | |
| virtual | ~Mover () |
| virtual MoverSP | create () |
| virtual void | apply (core::io::serialization::PipeMap &pmap) |
| virtual void | parse_state (SerializableState const &state) |
| virtual void | parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache) |
| virtual void | save_state (SerializableState &state) |
| Mover (std::string const &type_name) | |
| sets the type for a mover; name_ has been removed (2010/05/14) More... | |
| Mover (Mover const &other) | |
| Mover & | operator= (Mover const &other) |
| assignment operator More... | |
| virtual core::Real | last_proposal_density_ratio () |
| std::string const & | type () const |
| std::string | get_current_tag () const |
| A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More... | |
| void | set_current_tag (std::string const &new_tag) |
| virtual void | set_input_pose (PoseCOP pose) |
| setter for poses contained for rms More... | |
| virtual void | set_native_pose (PoseCOP pose) |
| setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More... | |
| PoseCOP | get_input_pose () const |
| PoseCOP | get_native_pose () const |
| virtual void | test_move (Pose &pose) |
| : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More... | |
| void | type (const std::string &type_in) |
| virtual MoverOP | clone () const |
| clone has to be overridden only if clone invocation is expected. More... | |
| virtual void | parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose) |
| Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
| std::string | get_type () const |
| MoverStatus | get_last_move_status () const |
| end parser interface, start Job Distributor interface///////////// More... | |
| void | reset_status () |
| resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More... | |
| virtual core::pose::PoseOP | get_additional_output () |
| Mechanism by which a mover may return multiple output poses from a single input pose. More... | |
| virtual void | clear_info () |
| Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More... | |
| virtual Strings & | info () |
| non-const accessor More... | |
| virtual Strings const & | info () const |
| const accessor More... | |
| virtual bool | reinitialize_for_each_job () const |
| this function informs the job distributor (august 08 vintage) whether this object needs to be freshly regenerated on each use. More... | |
| virtual bool | reinitialize_for_new_input () const |
| this function informs the job distributor (august 08 vintage) whether this object needs to be regenerated when the input pose is about to change (for example, if the mover has special code on the first apply() that is only valid for that one input pose). More... | |
| virtual MoverOP | fresh_instance () const |
| this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More... | |
| void | set_current_job (protocols::jobdist::BasicJobCOP job) |
| jobdist::BasicJobCOP | get_current_job () const |
Private Attributes | |
| Size | cycles_ |
| std::string | mintype_ |
| bool | skip_sampling_ |
| bool | single_loop_double_arm_ |
| bool | double_loop_double_arm_ |
| bool | double_loop_quad_arm_ |
| bool | test_control_mode_ |
Additional Inherited Members | |
| Public Types inherited from protocols::moves::Mover | |
| typedef utility::tag::TagPtr | TagPtr |
| typedef core::pose::Pose | Pose |
| typedef core::pose::PoseCOP | PoseCOP |
| typedef protocols::filters::Filters_map | Filters_map |
| typedef std::list< std::string > | Strings |
| Static Public Member Functions inherited from protocols::moves::Mover | |
| static std::string | name () |
| static void | register_options () |
| overload this static method if you access options within the mover. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. More... | |
| Protected Member Functions inherited from protocols::grafting::GraftMoverBase | |
| Pose | insert_piece (Pose const &pose) |
| Steven Lewis' insertion method from insert_pose_into_pose. Wrapper to his function, using variables defined in this baseclass. More... | |
| virtual core::Real | perturb_backbone_for_test (Pose &pose, MoveMapOP mm) |
| Uses a small mover at high KT to perturb residues in the movemap for testing. More... | |
| MoveMapOP | combine_movemaps (MoveMap const &scaffold_mm, MoveMap const &insert_mm) |
| combines the two main movemaps to use after the insertion. More... | |
| void | delete_overhang_residues () |
| deletes overhang residues of the pose piece set. Recommended use is within apply method More... | |
| void | set_overhang (Size Nter_overhang, Size Cter_overhang) |
| Set overhang residues. More... | |
| virtual void | setup_movemap_and_regions (Pose &pose) |
| sets up either the default movemap or a new combined movemap at apply time. Updates regions as needed. More... | |
| virtual void | set_default_movemap () |
| Sets up the default movemap. More... | |
| virtual void | set_regions_from_flexibility () |
| Sets up the regions at apply using insert variables and flexibility. More... | |
| virtual void | set_regions_from_movemap (Pose &pose) |
| Sets up region variables from the class movemap for the combined pose. More... | |
| virtual void | setup_single_loop_single_arm_remodeling_foldtree (Pose &pose, Size const Nter_loop_start, Size const Cter_loop_end, bool loop_modeling=false) |
| ****Nter_loop_start-—>Piece-—> | Cter_loop_end**** Insert will move in cartesian space lower_cutpoint for CCD and loops is Cter_loop_end-1 More... | |
| virtual void | setup_single_loop_double_arm_remodeling_foldtree (Pose &pose, Size const Nter_loop_start, Size const Cter_loop_end, bool loop_modeling=false) |
| ****Nter_loop_start-—>Piece | <-—Nter_loop_end**** Insert will move in cartesian space lower_cutpoint for CCD and loops is end_-1 More... | |
| Protected Attributes inherited from protocols::grafting::GraftMoverBase | |
| Pose | piece_ |
| Size | start_ |
| Residue insertion will start from. More... | |
| Size | end_ |
| Residue insertion will end before here. Updates after insertion. More... | |
| Size | original_end_ |
| some functions need to only work on the original numbers. (combine movemaps) More... | |
| Size | insertion_length_ |
| core::scoring::ScoreFunctionOP | cen_scorefxn_ |
| core::scoring::ScoreFunctionOP | fa_scorefxn_ |
| Size | Nter_overhang_ |
| Number of overhang residues on N terminus. Updates on delete_overhang_residues. More... | |
| Size | Cter_overhang_ |
| Number of overhang residues on C terminus. Updates on delete_overhang_residues. More... | |
| MoveMapOP | movemap_ |
| MoveMapOP | scaffold_movemap_ |
| MoveMapOP | insert_movemap_ |
| bool | use_default_movemap_ |
| Size | Nter_scaffold_flexibility_ |
| Size | Nter_insert_flexibility_ |
| Size | Nter_loop_start_ |
| Size | Nter_loop_end_ |
| Size | Cter_scaffold_flexibility_ |
| Size | Cter_insert_flexibility_ |
| Size | Cter_loop_start_ |
| Size | Cter_loop_end_ |
Grafting class adapted from Steven Lewis' pose_into_pose algorithm. Basic, and quick, but with many options.
example: mover = AnchoredGraftMover(start, end) mover.set_piece(piece, cter_overhang, nter_overhang) mover.apply(pose)
see also: grafting/util.hh.
Uses a single loop and a single arm to close the loop by default. ****Nter_loop_start-—>Piece-—> | Cter_loop_end**** Default movemap keeps insert Frozen in dihedral angle space, But think of the insert as part of a giant arm. Default flexibility on Nter and Cter is only two residues (–> part of diagram). Will delete any residues between start and end, and any overhang residues from the insert.
Algorithm originally from pose_into_pose: The insert will be left unchanged in internal-coordinate space except for the phi on the first residue, and the psi/omega on the last residue, and atoms whose bonding partners change as a result of the insertion. Internally, apply performs the insertion, idealizes the loop residues (omegas to 180, peptide bonds idealized) and the newly made polymer connections at the insert point, and then attempts to close the loop(s). It is intended, but not guaranteed, to produce a loop with good rama, omega, and chainbreak/peptide_bond scores. It does NOT attempt to give a loop with good sidechains (it does not repack at all) or worry overmuch about van der Waals
Definition at line 55 of file AnchoredGraftMover.hh.
Start and end are the residue numbers you want your insert to go between. start->Insert<-end.
Definition at line 68 of file AnchoredGraftMover.cc.
References set_defaults().
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Definition at line 76 of file AnchoredGraftMover.cc.
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Grafts the piece into the pose, uses CCD to close the connection. Insert does not change dihedral space, but DOES change cartesian space by default. Pose is returned without repacking any sidechains. Use repack_connection after apply method. Deletes overhang and region between start and end if residues are present.
Implements protocols::moves::Mover.
Definition at line 200 of file AnchoredGraftMover.cc.
References core::pose::add_variant_type_to_pose_residue(), protocols::simple_moves::BackboneMover::angle_max(), protocols::loops::FoldTreeFromLoops::apply(), protocols::simple_moves::SwitchResidueTypeSetMover::apply(), protocols::simple_moves::ReturnSidechainMover::apply(), protocols::simple_moves::BackboneMover::apply(), protocols::simple_moves::MinMover::apply(), core::id::BB, protocols::moves::MonteCarlo::boltzmann(), protocols::grafting::GraftMoverBase::cen_scorefxn_, core::chemical::CENTROID, core::pose::Pose::conformation(), protocols::grafting::GraftMoverBase::Cter_loop_end_, protocols::grafting::GraftMoverBase::Cter_loop_start_, protocols::loops::Loop::cut(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, cycles_, double_loop_double_arm_, double_loop_quad_arm_, protocols::grafting::GraftMoverBase::end_, core::pose::Pose::fold_tree(), core::conformation::Conformation::insert_ideal_geometry_at_polymer_bond(), protocols::grafting::GraftMoverBase::insert_piece(), protocols::grafting::GraftMoverBase::insertion_length_, protocols::loops::FoldTreeFromLoops::loops(), mintype_, protocols::grafting::GraftMoverBase::movemap_, protocols::grafting::GraftMoverBase::Nter_loop_end_, protocols::grafting::GraftMoverBase::Nter_loop_start_, protocols::grafting::GraftMoverBase::perturb_backbone_for_test(), core::id::phi_torsion(), core::id::psi_torsion(), protocols::moves::MonteCarlo::recover_low(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), protocols::grafting::GraftMoverBase::setup_movemap_and_regions(), protocols::grafting::GraftMoverBase::setup_single_loop_double_arm_remodeling_foldtree(), protocols::grafting::GraftMoverBase::setup_single_loop_single_arm_remodeling_foldtree(), single_loop_double_arm_, skip_sampling_, protocols::grafting::GraftMoverBase::start_, test_control_mode_, and protocols::TR().
| core::Size protocols::grafting::AnchoredGraftMover::get_Cter_loop_end | ( | ) |
Definition at line 176 of file AnchoredGraftMover.cc.
References protocols::grafting::GraftMoverBase::Cter_loop_end_.
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convenience function for AFTER apply method.
flexible Nter and Cter residues plus the first and last residue of the insert. If passing movemaps, will respect those movemaps.
Definition at line 420 of file AnchoredGraftMover.cc.
References core::pack::task::TaskFactory::create_packer_task(), protocols::grafting::GraftMoverBase::end_, protocols::grafting::GraftMoverBase::movemap_, protocols::grafting::GraftMoverBase::start_, and core::pose::Pose::total_residue().
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convenience function for AFTER apply method.
flexible Nter and Cter residues plus the entire insert. If passing movemaps, will respect those movemaps.
Definition at line 444 of file AnchoredGraftMover.cc.
References core::pack::task::TaskFactory::create_packer_task(), protocols::grafting::GraftMoverBase::end_, protocols::grafting::GraftMoverBase::movemap_, protocols::grafting::GraftMoverBase::start_, and core::pose::Pose::total_residue().
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override of base class
Reimplemented from protocols::grafting::GraftMoverBase.
Definition at line 132 of file AnchoredGraftMover.cc.
References protocols::grafting::GraftMoverBase::cen_scorefxn_, and core::scoring::chainbreak.
| void protocols::grafting::AnchoredGraftMover::set_cycles | ( | Size | cycles) |
Definition at line 113 of file AnchoredGraftMover.cc.
References cycles_.
Referenced by set_defaults().
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override of base class
Reimplemented from protocols::grafting::GraftMoverBase.
Definition at line 118 of file AnchoredGraftMover.cc.
References core::scoring::cbeta, protocols::grafting::GraftMoverBase::cen_scorefxn_, core::scoring::cenpack, core::scoring::chainbreak, core::scoring::hbond_lr_bb, core::scoring::hbond_sr_bb, core::scoring::omega, core::scoring::pair, core::scoring::rama, and core::scoring::vdw.
Referenced by set_use_smooth_centroid_settings().
| void protocols::grafting::AnchoredGraftMover::set_defaults | ( | ) |
Definition at line 79 of file AnchoredGraftMover.cc.
References set_cycles(), set_insert_flexibility(), set_mintype(), set_scaffold_flexibility(), set_skip_sampling(), set_test_control_mode(), set_use_default_movemap_from_flexibility(), set_use_double_loop_double_CCD_arms(), set_use_double_loop_quad_CCD_arms(), set_use_single_loop_double_CCD_arms(), and set_use_smooth_centroid_settings().
Referenced by AnchoredGraftMover().
| void protocols::grafting::AnchoredGraftMover::set_insert_flexibility | ( | Size const | Nter_insert_flexibility, |
| Size const | Cter_insert_flexibility | ||
| ) |
Sets insert flexibility on either end of insert.
Definition at line 106 of file AnchoredGraftMover.cc.
References protocols::grafting::GraftMoverBase::Cter_insert_flexibility_, and protocols::grafting::GraftMoverBase::Nter_insert_flexibility_.
Referenced by set_defaults().
| void protocols::grafting::AnchoredGraftMover::set_mintype | ( | std::string | mintype) |
Sets the mintype for the MinMover.
Definition at line 140 of file AnchoredGraftMover.cc.
References mintype_.
Referenced by set_defaults().
| void protocols::grafting::AnchoredGraftMover::set_movemaps | ( | MoveMapOP const | scaffold_mm, |
| MoveMapOP const | insert_mm | ||
| ) |
Advanced way to set options. Use if you know what you are doing.
Will combine the movemaps for apply, and renumber everything. Flexible residues in multiple chains not recommended. single_loop_single_arm (Default) From the first bb flexible residue to the last will act as one loop. This can be amazing as you can use loop regions in various parts of your protein to help the insertion. single_loop_double_arm: One arm will be from first flexible N terminal residue to end_; Second arm will be from there to last flexible residue double_loop_double_arm: One arm Will go from first flexible N terminal residue to after start_+any contiguous residues on in the movemap from there. Opposite for Cter side. double_loop_quad_arm: same as double, but cutpoints will be at each new peptide bond.
Note: Will disregard flexibility settings, as the movemaps will be used as primary way to define flexibility.
Definition at line 191 of file AnchoredGraftMover.cc.
References protocols::grafting::GraftMoverBase::insert_movemap_, protocols::grafting::GraftMoverBase::scaffold_movemap_, and protocols::grafting::GraftMoverBase::use_default_movemap_.
| void protocols::grafting::AnchoredGraftMover::set_scaffold_flexibility | ( | Size const | Nter_scaffold_flexibility, |
| Size const | Cter_scaffold_flexibility | ||
| ) |
Sets scaffold flexiblity on either end of scaffold.
Definition at line 99 of file AnchoredGraftMover.cc.
References protocols::grafting::GraftMoverBase::Cter_scaffold_flexibility_, and protocols::grafting::GraftMoverBase::Nter_scaffold_flexibility_.
Referenced by set_defaults().
| void protocols::grafting::AnchoredGraftMover::set_skip_sampling | ( | bool | skip_sampling) |
Sets the mover to skip the small mover sampling step.
Definition at line 145 of file AnchoredGraftMover.cc.
References skip_sampling_.
Referenced by set_defaults().
| void protocols::grafting::AnchoredGraftMover::set_test_control_mode | ( | bool | test_control_mode) |
TESTING ONLY Sets the protocol to 'randomize' the flexible residues before trying to graft. This is used to test the protocol by grafting a piece of a protein back onto itself and looking at RMSD.
Definition at line 181 of file AnchoredGraftMover.cc.
References test_control_mode_.
Referenced by set_defaults().
| void protocols::grafting::AnchoredGraftMover::set_use_default_movemap_from_flexibility | ( | bool | def) |
Instructs the class to ignore any movemaps from set_movemaps.
Definition at line 186 of file AnchoredGraftMover.cc.
References protocols::grafting::GraftMoverBase::use_default_movemap_.
Referenced by set_defaults().
| void protocols::grafting::AnchoredGraftMover::set_use_double_loop_double_CCD_arms | ( | bool | double_loop_double_arm) |
Keeps the insert frozen in cartesian space. Sets the algorithm to use two loops on either side in order to close the graft. (Please superimpose piece onto scaffold first)
****Nter_loop_start--—> | Piece | <-—Nter_loop_end****
Definition at line 166 of file AnchoredGraftMover.cc.
References double_loop_double_arm_.
Referenced by set_defaults().
| void protocols::grafting::AnchoredGraftMover::set_use_double_loop_quad_CCD_arms | ( | bool | double_loop_quad_arm) |
Keeps the insert frozen in cartesian space. Sets the algorithm to use two loops on either side in order to close the graft. (Please superimpose piece onto scaffold first)
****Nter_loop_start-—> | <-— Piece --—> | <---— Cter_loop_end**** Use only if you have continuous flexibility in your insert from start and or end.
Definition at line 171 of file AnchoredGraftMover.cc.
References double_loop_quad_arm_.
Referenced by set_defaults().
| void protocols::grafting::AnchoredGraftMover::set_use_single_loop_double_CCD_arms | ( | bool | single_loop_double_arm) |
Uses a single loop, two arm loop closer.
****Nter_loop_start-—>Piece | <-—Nter_loop_end****
Definition at line 161 of file AnchoredGraftMover.cc.
References single_loop_double_arm_.
Referenced by set_defaults().
| void protocols::grafting::AnchoredGraftMover::set_use_smooth_centroid_settings | ( | bool | use_smooth) |
sets up the smooth centroid scorefunction + any changes to VDW. if false, switches back to default scorefunction.
Definition at line 150 of file AnchoredGraftMover.cc.
References protocols::grafting::GraftMoverBase::cen_scorefxn_, core::scoring::chainbreak, core::scoring::ScoreFunctionFactory::create_score_function(), and set_default_cen_scorefunction().
Referenced by set_defaults().
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Definition at line 158 of file AnchoredGraftMover.hh.
Referenced by apply(), and set_cycles().
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Definition at line 163 of file AnchoredGraftMover.hh.
Referenced by apply(), and set_use_double_loop_double_CCD_arms().
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Definition at line 164 of file AnchoredGraftMover.hh.
Referenced by apply(), and set_use_double_loop_quad_CCD_arms().
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Definition at line 160 of file AnchoredGraftMover.hh.
Referenced by apply(), and set_mintype().
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Definition at line 162 of file AnchoredGraftMover.hh.
Referenced by apply(), and set_use_single_loop_double_CCD_arms().
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Definition at line 161 of file AnchoredGraftMover.hh.
Referenced by apply(), and set_skip_sampling().
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Definition at line 165 of file AnchoredGraftMover.hh.
Referenced by apply(), and set_test_control_mode().
1.8.4