A class specifying DOFs to be flexible or fixed. More...

#include <MoveMap.hh>

Inheritance diagram for core::kinematics::MoveMap:

Collaboration diagram for core::kinematics::MoveMap:

Public Types
typedef id::AtomID	AtomID

typedef id::AtomID_Mask	AtomID_Mask

typedef id::DOF_Type	DOF_Type

typedef id::DOF_ID	DOF_ID

typedef id::DOF_ID_Mask	DOF_ID_Mask

typedef id::TorsionType	TorsionType

typedef id::TorsionID	TorsionID

typedef std::pair< Size, TorsionType >	MoveMapTorsionID
	Our own specific torsion_id TorsionType can BB, CHI and JUMP. Thefore it doesnt distinguish torsion,eg phi/psi/omega in BB torsion. Useful when setting residue k backbone fixed. should probably make this a class/struct. More...

typedef std::map< TorsionType, bool >	TorsionTypeMap
	flexible or fixed for this TorsionType (BB, CHI, JUMP), for all residues More...

typedef std::map < MoveMapTorsionID, bool >	MoveMapTorsionID_Map
	flexible or fixed for this TorsionType (BB, CHI, JUMP), for one residue, eg no distinction betwen phi/psi/omega More...

typedef std::map< TorsionID, bool >	TorsionID_Map
	flexible or fixed for a single torsion, eg, psi (BB torsion 2) of residue 10 More...

typedef std::map< DOF_Type, bool >	DOF_TypeMap
	flexible or fixed for this DOF_Type (PHI, THETA, D, RB1-6), for all atoms More...

typedef std::map< DOF_ID, bool >	DOF_ID_Map
	flexible or fixed for a single DOF, eg, D of atom 5 in residue 10 More...

typedef std::map< id::JumpID, bool >	JumpID_Map
	flexible or fixed jumps (fold-tree independent definition via residue pairs ) More...

Public Member Functions
virtual	~MoveMap ()
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...

	MoveMap ()
	default constructor More...

MoveMapOP	clone () const

void	clear ()
	clear – sets all to FALSE More...

void	set_bb (bool const setting)
	Set whether or not BB TorsionType is moveable. More...

void	set_bb (Size const seqpos, bool const setting)
	Sets whether or not the BB torsions of residue <seqpos> are movable. More...

void	set_bb (utility::vector1< bool > allow_bb)
	Sets BB torsions movable based on input array. More...

void	set_bb_true_range (Size const begin, Size const end)
	Sets the BB torsions between residues <begin> and <end> as movable, all other residues are non-movable. More...

void	set_ranges_unmodifiable (const std::vector< std::pair< Size, Size > > &ranges)
	Prevents backbone torsion modifications to the intervals specified by <ranges>. Each element of the vector is a pair, which specifies the begin and end indices. Counting begins with 1. More...

void	set_chi (bool const setting)
	Sets whether of not CHI TorsionType is movable. More...

void	set_chi (Size const seqpos, bool const setting)
	Sets whether or not the CHI torsions of residue <seqpos> are movable. More...

void	set_chi (utility::vector1< bool > allow_chi)
	set CHI torsions movable based on input array More...

void	set_chi_true_range (Size const begin, Size const end)
	Sets the chi torsions between residues <begin> and <end> as movable and all other residues are non-movable. More...

void	set_jump (bool const setting)
	Sets whether or not JUMP TorsionType is moveable. More...

void	set_jump (int const jump_number, bool const setting)
	Sets the movability of JUMP <jump_number> to <setting> More...

void	set_jump (Size const pos1, Size const pos2, bool const setting)
	set JUMP moveable or not for one specific residue pair this mechanism does not mix with the "jump_nr" mechanism... i.e., if you set jump_nr 3 = movable —> movemap does not know that this refers to say residue 23-89 More...

void	set_jump (id::JumpID const &jump, bool const setting)
	set/get for JumpIDs — fold-tree independent definition of jumps More...

void	set (TorsionType const &t, bool const setting)
	set a specific TorsionType moveable; currently BB, CHI, or JUMP More...

void	set (MoveMapTorsionID const &id, bool const setting)
	set TorsionType flexible or fixed for one residue, eg BB torsions for residue 10 More...

void	set (TorsionID const &id, bool const setting)
	set an individual Torsion moveable or now, eg, "BB torsion 2 of residue 4" More...

void	set (DOF_Type const &t, bool const setting)
	set atom tree DOF, eg D, PHI, THETA More...

void	set (DOF_ID const &id, bool const setting)
	set for an individual dof, eg "PHI of Atom 3 in Residue 5" More...

bool	get_bb (Size const seqpos) const
	Returns if BB torsions are movable or not for residue <seqpos> More...

bool	get_chi (int const seqpos) const
	Returns if SC torsions are movable or not for residue <seqpos> More...

bool	get_jump (int const jump_number) const
	Returns if JUMP <jump_number> is movable or not. More...

bool	get_jump (Size const pos1, Size const pos2) const

bool	get_jump (id::JumpID const &jump) const

bool	get (TorsionType const &t) const
	get setting for a specific TorsionType, such as "BB" More...

bool	get (MoveMapTorsionID const &id) const
	get TorsionType flexible or fixed for one residue, eg BB torsions for residue 10 More...

bool	get (TorsionID const &id) const

bool	get (DOF_Type const &t) const
	get the default for this type of DOF, eg "PHI" More...

bool	get (DOF_ID const &id) const
	get the setting for an individual dof, eg, PHI of Atom 3 in Residue 5 More...

TorsionTypeMap::const_iterator	find (TorsionType const &t) const
	find the explicit setting for the given TorsionType More...

MoveMapTorsionID_Map::const_iterator	find (MoveMapTorsionID const &id) const
	find the explicit setting for the given MoveMapTorsionID More...

TorsionID_Map::const_iterator	find (TorsionID const &id) const
	find the explicit setting for the given TorsionID More...

JumpID_Map::const_iterator	find (id::JumpID const &jump) const
	find the explicit setting for the given JumpID More...

DOF_TypeMap::const_iterator	find (DOF_Type const &t) const
	find the explicit setting for the given DOF_Type More...

DOF_ID_Map::const_iterator	find (DOF_ID const &id) const
	find the explicit setting for the given DOF_ID More...

TorsionTypeMap::const_iterator	torsion_type_begin () const
	return an iterator pointing just past the last element of the TorsionTypeMap More...

TorsionTypeMap::const_iterator	torsion_type_end () const
	return an iterator pointing at the first element of the TorsionTypeMap More...

MoveMapTorsionID_Map::const_iterator	movemap_torsion_id_begin () const
	return an iterator pointing at the first element of the MoveMapTorsionID_Map More...

MoveMapTorsionID_Map::const_iterator	movemap_torsion_id_end () const
	return an iterator pointing just past the last element of the MoveMapTorsionID_Map More...

TorsionID_Map::const_iterator	torsion_id_begin () const
	return an iterator pointing at the first element of the TorsionID_Map More...

TorsionID_Map::const_iterator	torsion_id_end () const
	return an iterator pointing just past the last element of the TorsionID_Map More...

DOF_TypeMap::const_iterator	dof_type_begin () const
	return an iterator pointing just past the last element of the DOF_TypeMap More...

DOF_TypeMap::const_iterator	dof_type_end () const
	return an iterator pointing at the first element of the DOF_TypeMap More...

DOF_ID_Map::const_iterator	dof_id_begin () const
	return an iterator pointing at the first element of the DOF_ID_Map More...

DOF_ID_Map::const_iterator	dof_id_end () const
	return an iterator pointing just past the last element of the DOF_ID_Map More...

JumpID_Map::const_iterator	jump_id_begin () const
	return an iterator pointing at the first element of the JumpID_Map More...

JumpID_Map::const_iterator	jump_id_end () const
	return an iterator pointing just past the last element of the JumpID_Map More...

Size	import (MoveMap const &rval)
	import settings from another MoveMap More...

Size	import_false (MoveMap const &rval)
	import only False settings from another MoveMap More...

Size	import_true (MoveMap const &rval)
	import only True settings from another MoveMap More...

void	init_from_file (std::string const &filename)
	Read MoveMap from file. More...

void	show (std::ostream &out, Size i) const
	gives the BB and CHI bool values up to a given residue number More...

void	show (Size i) const
	gives the BB and CHI bool values up to a given residue number wrapper for PyRosetta More...

void	show (std::ostream &out) const

void	show () const

Private Member Functions
Size	import (MoveMap const &rval, bool const import_true_settings, bool const import_false_settings)
	import settings from another MoveMap More...

Private Attributes
TorsionTypeMap	torsion_type_map_
	flexible or fixed for this TorsionType (BB, CHI, JUMP), for all residues More...

MoveMapTorsionID_Map	move_map_torsion_id_map_
	flexible or fixed for this TorsionType (BB, CHI, JUMP), for one residue, eg no distinction betwen phi/psi/omega More...

TorsionID_Map	torsion_id_map_
	flexible or fixed for a single torsion, eg, psi (BB torsion 2) of residue 10 More...

DOF_TypeMap	dof_type_map_
	flexible or fixed for this DOF_Type (PHI, THETA, D, RB1-6), for all atoms More...

DOF_ID_Map	dof_id_map_
	flexible or fixed for a single DOF, eg, D of atom 5 in residue 10 More...

JumpID_Map	jump_id_map_

Detailed Description

A class specifying DOFs to be flexible or fixed.

currently there are two groups of data, one is residue-based Torsion definition, such as BB, CHI and JUMP; the other is atom-based DOF definition, such as bond length D, bond angle THETA and torsion angle PHI which are used in atom-tree. MoveMap does not automatically handle conversion from one group to the other, i.e., setting PHI false for DOF_type does not affect setting for BB and CHI torsion though they are PHIs in atom-tree.

within each group, there are multiple levels of control (from general/high to specific/lower):

Torsion-based: TorsionType(BB, CHI, JUMP) -> MoveMapTorsionID (BB, CHI of one residue) -> TorsionID ( BB torsion 2 or CHI torsion 3 of one residue)
DOF-base: DOF_type( D, THETA, PHI ) -> DOF_ID (D, THETA, PHI of one atom)

setting for each level are stored in a map structure and they are only added to the map when setting methods are invoked. As a result, MoveMap does not behave like a "Boolean vector" which always contains setting for each residue or atom in a conformation. Setting for a higher level will override setting for lower levels (remove it from map); Similarly, when querying a lower level finds no setting, it will check setting for its higher level. For example, setting TorisionType BB to be true will remove any data of BB setting for a residue or a specific BB torsion ( such as backbone psi ) in a residue. And querying setting for BB torsion 2 of residue 4 will first check if there is any specific setting, if not, check if there is a setting for all BB torsions for residue 4, if not again, use setting for BB torsions for all residues.

example: movemap = MoveMap() See also: Pose MinMover ShearMover SmallMover

Definition at line 81 of file MoveMap.hh.

Member Typedef Documentation

typedef id::AtomID core::kinematics::MoveMap::AtomID

Definition at line 86 of file MoveMap.hh.

typedef id::AtomID_Mask core::kinematics::MoveMap::AtomID_Mask

Definition at line 87 of file MoveMap.hh.

typedef id::DOF_ID core::kinematics::MoveMap::DOF_ID

Definition at line 89 of file MoveMap.hh.

typedef std::map< DOF_ID, bool > core::kinematics::MoveMap::DOF_ID_Map

flexible or fixed for a single DOF, eg, D of atom 5 in residue 10

Definition at line 113 of file MoveMap.hh.

typedef id::DOF_ID_Mask core::kinematics::MoveMap::DOF_ID_Mask

Definition at line 90 of file MoveMap.hh.

typedef id::DOF_Type core::kinematics::MoveMap::DOF_Type

Definition at line 88 of file MoveMap.hh.

typedef std::map< DOF_Type, bool > core::kinematics::MoveMap::DOF_TypeMap

flexible or fixed for this DOF_Type (PHI, THETA, D, RB1-6), for all atoms

Definition at line 110 of file MoveMap.hh.

typedef std::map< id::JumpID, bool > core::kinematics::MoveMap::JumpID_Map

flexible or fixed jumps (fold-tree independent definition via residue pairs )

Definition at line 116 of file MoveMap.hh.

typedef std::pair< Size, TorsionType > core::kinematics::MoveMap::MoveMapTorsionID

Our own specific torsion_id TorsionType can BB, CHI and JUMP. Thefore it doesnt distinguish torsion,eg phi/psi/omega in BB torsion. Useful when setting residue k backbone fixed. should probably make this a class/struct.

Definition at line 98 of file MoveMap.hh.

typedef std::map< MoveMapTorsionID, bool > core::kinematics::MoveMap::MoveMapTorsionID_Map

flexible or fixed for this TorsionType (BB, CHI, JUMP), for one residue, eg no distinction betwen phi/psi/omega

Definition at line 104 of file MoveMap.hh.

typedef id::TorsionID core::kinematics::MoveMap::TorsionID

Definition at line 92 of file MoveMap.hh.

typedef std::map< TorsionID, bool > core::kinematics::MoveMap::TorsionID_Map

flexible or fixed for a single torsion, eg, psi (BB torsion 2) of residue 10

Definition at line 107 of file MoveMap.hh.

typedef id::TorsionType core::kinematics::MoveMap::TorsionType

Definition at line 91 of file MoveMap.hh.

typedef std::map< TorsionType, bool > core::kinematics::MoveMap::TorsionTypeMap

flexible or fixed for this TorsionType (BB, CHI, JUMP), for all residues

Definition at line 101 of file MoveMap.hh.

Constructor & Destructor Documentation

core::kinematics::MoveMap::~MoveMap ( )

virtual

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

Definition at line 46 of file MoveMap.cc.

core::kinematics::MoveMap::MoveMap ( )

inline

default constructor

Definition at line 119 of file MoveMap.hh.

Referenced by clone().

Member Function Documentation

void core::kinematics::MoveMap::clear ( )

clear – sets all to FALSE

all internal map data are cleared.

Definition at line 69 of file MoveMap.cc.

Referenced by protocols::protein_interface_design::movers::PrepackMover::apply(), protocols::swa::protein::StepWiseProteinCCD_Closer::figure_out_loop(), and protocols::antibody2::AntibodyInfo::get_MoveMap_for_Loops().

MoveMapOP core::kinematics::MoveMap::clone ( ) const

inline

Definition at line 121 of file MoveMap.hh.

References MoveMap().

Referenced by protocols::forge::remodel::RemodelLoopMover::create_fragment_movers(), and protocols::rna::RNA_Minimizer::setup_movemap().

DOF_ID_Map::const_iterator core::kinematics::MoveMap::dof_id_begin ( ) const

inline

return an iterator pointing at the first element of the DOF_ID_Map

Definition at line 492 of file MoveMap.hh.

References dof_id_map_.

Referenced by import(), and core::pose::setup_dof_mask_from_move_map().

DOF_ID_Map::const_iterator core::kinematics::MoveMap::dof_id_end ( ) const

inline

return an iterator pointing just past the last element of the DOF_ID_Map

Definition at line 497 of file MoveMap.hh.

References dof_id_map_.

Referenced by import(), and core::pose::setup_dof_mask_from_move_map().

DOF_TypeMap::const_iterator core::kinematics::MoveMap::dof_type_begin ( ) const

inline

return an iterator pointing just past the last element of the DOF_TypeMap

Definition at line 482 of file MoveMap.hh.

References dof_type_map_.

Referenced by import().

DOF_TypeMap::const_iterator core::kinematics::MoveMap::dof_type_end ( ) const

inline

return an iterator pointing at the first element of the DOF_TypeMap

Definition at line 487 of file MoveMap.hh.

References dof_type_map_.

Referenced by import().

MoveMap::TorsionTypeMap::const_iterator core::kinematics::MoveMap::find ( TorsionType const & t) const

find the explicit setting for the given TorsionType

Returns: iterator pointing to the TorsionType-bool pair, otherwise torsion_type_end()

Warning: Do not use this for general lookup, as it does not take into account the stringency levels. Only use this when you need to check if a setting explicitly exists.

Definition at line 310 of file MoveMap.cc.

MoveMap::MoveMapTorsionID_Map::const_iterator core::kinematics::MoveMap::find ( MoveMapTorsionID const & id) const

find the explicit setting for the given MoveMapTorsionID

Returns: iterator pointing to the MoveMapTorsionID-bool pair, otherwise movemap_torsion_id_end()

Warning: Do not use this for general lookup, as it does not take into account the stringency levels. Only use this when you need to check if a setting explicitly exists.

Definition at line 321 of file MoveMap.cc.

MoveMap::TorsionID_Map::const_iterator core::kinematics::MoveMap::find ( TorsionID const & id) const

find the explicit setting for the given TorsionID

Returns: iterator pointing to the TorsionID-bool pair, otherwise torsion_id_end()

Warning: Do not use this for general lookup, as it does not take into account the stringency levels. Only use this when you need to check if a setting explicitly exists.

Definition at line 332 of file MoveMap.cc.

MoveMap::JumpID_Map::const_iterator core::kinematics::MoveMap::find ( id::JumpID const & jump) const

find the explicit setting for the given JumpID

Returns: iterator pointing to the JumpID-bool pair, otherwise jump_id_end()

Warning: Do not use this for general lookup, as it does not take into account the stringency levels. Only use this when you need to check if a setting explicitly exists.

Definition at line 342 of file MoveMap.cc.

MoveMap::DOF_TypeMap::const_iterator core::kinematics::MoveMap::find ( DOF_Type const & t) const

find the explicit setting for the given DOF_Type

Returns: iterator pointing to the DOF_Type-bool pair, otherwise dof_type_end()

Warning: Do not use this for general lookup, as it does not take into account the stringency levels. Only use this when you need to check if a setting explicitly exists.

Definition at line 352 of file MoveMap.cc.

MoveMap::DOF_ID_Map::const_iterator core::kinematics::MoveMap::find ( DOF_ID const & id) const

find the explicit setting for the given DOF_ID

Returns: iterator pointing to the DOF_ID-bool pair, otherwise dof_id_end()

Warning: Do not use this for general lookup, as it does not take into account the stringency levels. Only use this when you need to check if a setting explicitly exists.

Definition at line 362 of file MoveMap.cc.

bool core::kinematics::MoveMap::get ( TorsionType const & t) const

get setting for a specific TorsionType, such as "BB"

get setting for a specific TorsionType, such as "BB" return false if no setting has been set for this TorsionType.

Definition at line 231 of file MoveMap.cc.

Referenced by core::fragment::BBTorsionAndAnglesSRFD::apply(), core::fragment::IndependentBBTorsionSRFD::apply(), protocols::loops::loop_closure::ccd::ccd_moves(), protocols::loops::loop_closure::ccd::fast_ccd_loop_closure(), core::fragment::IndependentBBTorsionSRFD::is_applicable(), core::fragment::BBTorsionSRFD::is_applicable(), core::optimization::symmetry::SymAtomTreeMinimizer::make_assymetric_movemap(), core::optimization::symmetry::SymAtomTreeMinimizer::make_semisymmetric_movemap(), core::pose::symmetry::make_symmetric_movemap(), protocols::swa::Output_movemap(), protocols::swa::rna::Output_movemap(), and core::pose::setup_dof_mask_from_move_map().

bool core::kinematics::MoveMap::get ( MoveMapTorsionID const & id) const

get TorsionType flexible or fixed for one residue, eg BB torsions for residue 10

get TorsionType flexible or fixed for one residue, eg BB torsions for residue 10 if no setting for this MoveMapTorsionID, use the setting for the TorsionType to which this MoveMapTorsionID belongs to.

Definition at line 245 of file MoveMap.cc.

References core::scoring::hbonds::t().

bool core::kinematics::MoveMap::get ( TorsionID const & id) const

get an individual torsion movable or not, eg BB torsion 2 of residue 4 if no setting for this specific TorsionID, use setting for the MoveMapTorsionID. eg, no setting for BB torsion 2 of residue 4, check setting for BB torsions of residue 4; if still not set, use setting for BB torsion type.

Definition at line 261 of file MoveMap.cc.

bool core::kinematics::MoveMap::get ( DOF_Type const & type) const

get the default for this type of DOF, eg "PHI"

get setting for this type of DOF, eg "PHI" return false if no setting has been set to this DOF_type

Definition at line 276 of file MoveMap.cc.

bool core::kinematics::MoveMap::get ( DOF_ID const & id) const

get the setting for an individual dof, eg, PHI of Atom 3 in Residue 5

get the setting for an individual dof, eg, PHI of Atom 3 in Residue 5 if no setting for this specific DOF_ID, get setting for the DOF type to which this DOF_ID belongs to.

Definition at line 292 of file MoveMap.cc.

bool core::kinematics::MoveMap::get_bb ( Size const seqpos) const

inline

Returns if BB torsions are movable or not for residue <seqpos>

example: movemap.get_bb(49)

Definition at line 340 of file MoveMap.hh.

References core::id::BB.

Referenced by protocols::jumping::close_chainbreaks(), protocols::abinitio::AllResiduesChanged::compute_insert_pos(), protocols::forge::remodel::RemodelLoopMover::count_moveable_residues(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::determine_loop(), protocols::abinitio::dump_movemap(), protocols::forge::methods::fold_tree_from_pose(), core::fragment::FragSet::generate_insert_map(), protocols::jumping::DisulfPairingLibrary::generate_jump_frags(), protocols::jumping::JumpSample::generate_jump_frags(), protocols::jumping::PairingLibrary::generate_jump_frags(), protocols::jumping::JumpSample::generate_jump_frames(), core::optimization::symmetry::SymAtomTreeMinimizer::make_assymetric_movemap(), protocols::forge::methods::replace(), core::optimization::CartesianMinimizerMap::setup(), protocols::forge::methods::shift_jumps(), core::kinematics::simple_visualize_fold_tree_and_movemap(), and core::kinematics::simple_visualize_fold_tree_and_movemap_bb_chi().

bool core::kinematics::MoveMap::get_chi ( int const seqpos) const

inline

Returns if SC torsions are movable or not for residue <seqpos>

example: movemap.get_chi(49)

Definition at line 352 of file MoveMap.hh.

References core::id::CHI.

Referenced by protocols::relax::ClassicRelax::check_default_full_repacker(), protocols::relax::ClassicRelax::check_default_rottrial(), protocols::forge::remodel::RemodelMover::design_refine(), core::optimization::symmetry::SymAtomTreeMinimizer::make_assymetric_movemap(), core::optimization::CartesianMinimizerMap::setup(), and core::kinematics::simple_visualize_fold_tree_and_movemap_bb_chi().

bool core::kinematics::MoveMap::get_jump ( int const jump_number) const

inline

Returns if JUMP <jump_number> is movable or not.

example: movemap.get_jump(1)

Definition at line 363 of file MoveMap.hh.

References core::id::JUMP.

Referenced by core::fragment::DownJumpSRFD::apply(), protocols::rigid::gaussian_jump_move(), protocols::jumping::ResiduePairJumpSetup::generate_jump_frags(), get_jump(), core::fragment::DownJumpSRFD::is_applicable(), protocols::swa::rna::Output_movemap(), protocols::rigid::RigidBodyPerturbMover::RigidBodyPerturbMover(), protocols::rigid::RigidBodyPerturbNoCenterMover::RigidBodyPerturbNoCenterMover(), and core::pose::setup_dof_mask_from_move_map().

bool core::kinematics::MoveMap::get_jump	(	Size const	pos1,
		Size const	pos2
	)		const

inline

Definition at line 371 of file MoveMap.hh.

References get_jump().

bool core::kinematics::MoveMap::get_jump ( id::JumpID const & jump) const

Definition at line 218 of file MoveMap.cc.

References core::id::JUMP.

Size core::kinematics::MoveMap::import ( MoveMap const & rval)

inline

import settings from another MoveMap

Returns: The total number of settings imported.

Remarks: This function calls set() for each setting that exists in the 'rval' MoveMap in order from lowest to highest stringency.

Definition at line 516 of file MoveMap.hh.

Size core::kinematics::MoveMap::import	(	MoveMap const &	rval,
		bool const	import_true_settings,
		bool const	import_false_settings
	)

private

import settings from another MoveMap

Parameters

[in]	rval	The MoveMap to import settings from.
[in]	import_true_settings	Import True settings?
[in]	import_false_settings	Import False settings?

Returns: The total number of settings imported.

Remarks: This function calls set() for each setting that exists in the 'rval' MoveMap in order from lowest to highest stringency.

Definition at line 572 of file MoveMap.cc.

References dof_id_begin(), dof_id_end(), dof_type_begin(), dof_type_end(), jump_id_begin(), jump_id_end(), movemap_torsion_id_begin(), movemap_torsion_id_end(), torsion_id_begin(), torsion_id_end(), torsion_type_begin(), and torsion_type_end().

Size core::kinematics::MoveMap::import_false ( MoveMap const & rval)

inline

import only False settings from another MoveMap

Returns: The total number of settings imported.

Remarks: This function calls set() for each setting that is marked as False in the 'rval' MoveMap in order from lowest to highest stringency.

Definition at line 526 of file MoveMap.hh.

Referenced by protocols::forge::remodel::RemodelLoopMover::enforce_false_movemap().

Size core::kinematics::MoveMap::import_true ( MoveMap const & rval)

inline

import only True settings from another MoveMap

Returns: The total number of settings imported.

Remarks: This function calls set() for each setting that is marked as True in the 'rval' MoveMap in order from lowest to highest stringency.

Definition at line 536 of file MoveMap.hh.

void core::kinematics::MoveMap::init_from_file ( std::string const & filename)

Read MoveMap from file.

reads lines of format and set movemap RESIDUE * CHI # set all residues chi movable RESIDUE 36 48 BBCHI # set res 36-48 bb & chi movable RESIDUE 89 NO # set res 89 unmovable JUMP * NO # set all jumps unmovable JUMP 1 YES # set jump 1 movable If a residue/default is not specified, mm defaults to current value. If a value for a jum is not given (e.g. "JUMP 4\n"), it defaults to movable (YES) Setting 'CHI' implies BB not movable, thus don't do: RESIDUE * CHI RESIDUE * BB Instead: RESIDUE * BBCHI

Definition at line 381 of file MoveMap.cc.

References core::io::pdb::split().

Referenced by protocols::canonical_sampling::MetropolisHastingsMover::add_shear_mover(), protocols::canonical_sampling::MetropolisHastingsMover::add_small_mover(), and protocols::canonical_sampling::canonical_sampling_main().

JumpID_Map::const_iterator core::kinematics::MoveMap::jump_id_begin ( ) const

inline

return an iterator pointing at the first element of the JumpID_Map

Definition at line 502 of file MoveMap.hh.

References jump_id_map_.

Referenced by import(), and protocols::swa::rna::Output_movemap().

JumpID_Map::const_iterator core::kinematics::MoveMap::jump_id_end ( ) const

inline

return an iterator pointing just past the last element of the JumpID_Map

Definition at line 507 of file MoveMap.hh.

References jump_id_map_.

Referenced by import(), and protocols::swa::rna::Output_movemap().

MoveMapTorsionID_Map::const_iterator core::kinematics::MoveMap::movemap_torsion_id_begin ( ) const

inline

return an iterator pointing at the first element of the MoveMapTorsionID_Map

Definition at line 462 of file MoveMap.hh.

References move_map_torsion_id_map_.

Referenced by protocols::grafting::GraftMoverBase::combine_movemaps(), import(), and protocols::forge::build::SegmentInsert::insert_pose_torsion_override_movemap().

MoveMapTorsionID_Map::const_iterator core::kinematics::MoveMap::movemap_torsion_id_end ( ) const

inline

return an iterator pointing just past the last element of the MoveMapTorsionID_Map

Definition at line 467 of file MoveMap.hh.

References move_map_torsion_id_map_.

Referenced by protocols::grafting::GraftMoverBase::combine_movemaps(), import(), and protocols::forge::build::SegmentInsert::insert_pose_torsion_override_movemap().

void core::kinematics::MoveMap::set	(	TorsionType const &	t,
		bool const	setting
	)

set a specific TorsionType moveable; currently BB, CHI, or JUMP

set a specific TorsionType movable or not, eg "CHI" setting this TorsionType will clear data for individual MoveMapTorsionID and TorsionID with this TorsionType to keep these three maps in sync. Then query for a specific TorsionID or MoveMapTorsionID will turn to setting for TorsionType.

Definition at line 93 of file MoveMap.cc.

References core::id::JUMP, and core::scoring::hbonds::t().

Referenced by protocols::idealize::basic_idealize(), core::pack::rotamer_set::build_lib_dna_rotamers(), protocols::swa::protein::StepWiseProteinCCD_Closer::figure_out_loop(), protocols::swa::rna::StepWiseRNA_Minimizer::Figure_out_moving_residues(), protocols::swa::Figure_out_moving_residues(), protocols::relax::fix_worst_bad_ramas(), protocols::swa::rna::StepWiseRNA_Minimizer::Freeze_sugar_torsions(), protocols::swa::rna::Freeze_sugar_torsions(), protocols::relax::RelaxProtocolBase::initialize_movemap(), protocols::swa::protein::StepWiseProteinPoseMinimizer::let_neighboring_chis_minimize(), protocols::loops::loops_set_move_map(), core::optimization::symmetry::SymAtomTreeMinimizer::make_assymetric_movemap(), core::optimization::symmetry::SymAtomTreeMinimizer::make_semisymmetric_movemap(), core::pose::symmetry::make_symmetric_movemap(), protocols::forge::remodel::RemodelLoopMover::mark_loop_moveable(), protocols::forge::build::SegmentRebuild::movemap(), protocols::forge::build::SegmentInsert::movemap(), set_bb(), set_chi(), set_jump(), protocols::LoopRebuild::set_looprlx_allow_move_map(), protocols::loops::set_move_map_for_centroid_loop(), protocols::rna::RNA_Minimizer::setup_movemap(), and protocols::loops::Loop::switch_movemap().

void core::kinematics::MoveMap::set	(	MoveMapTorsionID const &	id,
		bool const	setting
	)

set TorsionType flexible or fixed for one residue, eg BB torsions for residue 10

set TorsionType flexible or fixed for one residue, eg BB torsions for residue 10 setting this MoveMapTorsionID will clear data for individual TorsionID for this residue with this TorsionType.

Definition at line 136 of file MoveMap.cc.

void core::kinematics::MoveMap::set	(	TorsionID const &	id,
		bool const	setting
	)

set an individual Torsion moveable or now, eg, "BB torsion 2 of residue 4"

set an individual Torsion movable or now, eg, "BB torsion 2 of residue 4"

Definition at line 159 of file MoveMap.cc.

void core::kinematics::MoveMap::set	(	DOF_Type const &	t,
		bool const	setting
	)

set atom tree DOF, eg D, PHI, THETA

brief set for this type of DOF, eg "PHI" setting this DOF type will also clear setting for individual DOF_ID of this type in order to keep these two maps in sync,(query DOF_ID setting will turn to DOF_type setting now)

Definition at line 179 of file MoveMap.cc.

References core::scoring::hbonds::t().

void core::kinematics::MoveMap::set	(	DOF_ID const &	id,
		bool const	setting
	)

set for an individual dof, eg "PHI of Atom 3 in Residue 5"

Definition at line 206 of file MoveMap.cc.

void core::kinematics::MoveMap::set_bb ( bool const setting)

inline

Set whether or not BB TorsionType is moveable.

example: movemap.set_bb(True) See also: MoveMap MoveMap.set_chi Pose MinMover ShearMover SmallMover

Definition at line 142 of file MoveMap.hh.

References core::id::BB, and set().

Referenced by protocols::loops::add_loop_flank_residues_bb_to_movemap(), protocols::simple_moves::ProlineFixMover::apply(), protocols::simple_filters::SAXSScoreFilter::apply(), protocols::abinitio::ResolutionSwitcher::apply(), protocols::hybridization::CartesianSampler::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::idealize::basic_idealize(), protocols::nonlocal::BiasedFragmentMover::BiasedFragmentMover(), protocols::loophash::LoopHashSampler::build_structures(), protocols::abinitio::TemplateJumpSetup::clean_jumps(), protocols::forge::remodel::RemodelMover::confirm_sequence(), protocols::forge::remodel::RemodelMover::design_refine(), protocols::swa::rna::StepWiseRNA_Minimizer::Figure_out_moving_residues(), protocols::swa::Figure_out_moving_residues(), protocols::relax::fix_worst_bad_ramas(), protocols::swa::rna::floating_base_chain_closure_post_process(), protocols::swa::rna::floating_base_chain_closure_setup(), protocols::topology_broker::JumpClaimer::generate_claims(), protocols::loophash::LoopHashLibrary::get_all(), protocols::antibody2::AntibodyInfo::get_MoveMap_for_Loops(), protocols::loophash::LoopHashLibrary::graft_loop(), protocols::topology_broker::JumpClaimer::init_jumps(), protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator::init_minmover(), protocols::topology_broker::FragmentClaimer::initialize_dofs(), protocols::rna::RNA_LoopCloser::local_minimize_at_chainbreaks(), protocols::loops::loops_set_move_map(), core::optimization::symmetry::SymAtomTreeMinimizer::make_assymetric_movemap(), protocols::relax::make_dna_rigid(), protocols::loophash::LocalInserter_SimpleMin::make_local_bb_change(), protocols::loophash::LocalInserter_SimpleMin::make_local_bb_change_close_gaps(), core::pose::symmetry::make_symmetric_movemap(), protocols::forge::remodel::RemodelLoopMover::mark_loop_moveable(), protocols::swa::rna::minimize_all_sampled_floating_bases(), protocols::rna::RNA_HelixAssembler::minimize_base_step(), protocols::simple_moves::ShakeStructureMover::minimize_with_constraints(), protocols::ddg::ddGMover::minimize_with_constraints(), MinimizeInterface(), protocols::cartesian::MolecularDynamics::MolecularDynamics(), protocols::forge::build::SegmentSwap::movemap(), protocols::forge::build::Bridge::movemap(), protocols::forge::build::GrowLeft::movemap(), protocols::forge::build::GrowRight::movemap(), protocols::forge::build::SegmentRebuild::movemap(), protocols::forge::build::ConnectRight::movemap(), protocols::forge::build::SegmentInsert::movemap(), core::fragment::FragSet::region_all(), protocols::loops::select_loop_frags(), set_bb_true_range(), protocols::LoopRebuild::set_looprlx_allow_move_map(), protocols::loops::set_move_map_for_centroid_loop(), core::optimization::CartesianMinimizerMap::setup(), protocols::abinitio::AbrelaxApplication::setup_fold(), protocols::rna::RNA_Minimizer::setup_movemap(), protocols::rbsegment_relax::setup_pose_from_rbsegs(), SymMinimizeInterface(), protocols::rna::RNA_LoopCloser::tight_minimize(), and protocols::topology_broker::BBClaim::toggle().

void core::kinematics::MoveMap::set_bb	(	Size const	seqpos,
		bool const	setting
	)

inline

Sets whether or not the BB torsions of residue <seqpos> are movable.

example: movemap.set_bb(49,True) See also: MoveMap MoveMap.set_chi Pose MinMover ShearMover SmallMover

Definition at line 160 of file MoveMap.hh.

References core::id::BB, and set().

void core::kinematics::MoveMap::set_bb ( utility::vector1< bool > allow_bb)

inline

Sets BB torsions movable based on input array.

Definition at line 169 of file MoveMap.hh.

References core::id::BB, and set().

void core::kinematics::MoveMap::set_bb_true_range	(	Size const	begin,
		Size const	end
	)

inline

Sets the BB torsions between residues <begin> and <end> as movable, all other residues are non-movable.

example: movemap.set_bb_true_range(40,60) See also: MoveMap MoveMap.set_bb MoveMap.set_chi Pose MinMover ShearMover SmallMover

Definition at line 190 of file MoveMap.hh.

References core::sequence::end, and set_bb().

Referenced by protocols::surface_docking::SurfaceDockingProtocol::abinitio().

void core::kinematics::MoveMap::set_chi ( bool const setting)

inline

Sets whether of not CHI TorsionType is movable.

example: movemap.set_chi(True) See also: MoveMap MoveMap.set_bb Pose MinMover ShearMover SmallMover

Definition at line 217 of file MoveMap.hh.

References core::id::CHI, and set().

Referenced by protocols::simple_moves::ProlineFixMover::apply(), protocols::simple_filters::SAXSScoreFilter::apply(), protocols::abinitio::ResolutionSwitcher::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::protein_interface_design::movers::Splice::apply(), protocols::idealize::basic_idealize(), protocols::forge::remodel::RemodelMover::confirm_sequence(), protocols::forge::remodel::RemodelMover::design_refine(), protocols::swa::rna::StepWiseRNA_Minimizer::Figure_out_moving_residues(), protocols::swa::Figure_out_moving_residues(), protocols::swa::rna::floating_base_chain_closure_setup(), protocols::antibody2::AntibodyInfo::get_MoveMap_for_Loops(), protocols::swa::protein::StepWiseProteinPoseMinimizer::let_neighboring_chis_minimize(), protocols::loops::loops_set_move_map(), core::optimization::symmetry::SymAtomTreeMinimizer::make_assymetric_movemap(), protocols::relax::make_dna_rigid(), core::pose::symmetry::make_symmetric_movemap(), protocols::forge::remodel::RemodelLoopMover::mark_loop_moveable(), protocols::simple_moves::ShakeStructureMover::minimize_with_constraints(), protocols::cartesian::MolecularDynamics::MolecularDynamics(), protocols::forge::build::Bridge::movemap(), protocols::forge::build::GrowRight::movemap(), protocols::forge::build::GrowLeft::movemap(), protocols::forge::build::SegmentRebuild::movemap(), protocols::relax::FastRelax::parse_my_tag(), core::fragment::FragSet::region_all(), set_chi_true_range(), protocols::LoopRebuild::set_looprlx_allow_move_map(), protocols::loops::set_move_map_for_centroid_loop(), core::optimization::CartesianMinimizerMap::setup(), and protocols::rna::RNA_Minimizer::setup_movemap().

void core::kinematics::MoveMap::set_chi	(	Size const	seqpos,
		bool const	setting
	)

inline

Sets whether or not the CHI torsions of residue <seqpos> are movable.

example: movemap.set_chi(49,True) See also: MoveMap MoveMap.set_bb Pose MinMover ShearMover SmallMover inline

Definition at line 234 of file MoveMap.hh.

References core::id::CHI, and set().

void core::kinematics::MoveMap::set_chi ( utility::vector1< bool > allow_chi)

inline

set CHI torsions movable based on input array

Definition at line 243 of file MoveMap.hh.

References core::id::CHI, and set().

void core::kinematics::MoveMap::set_chi_true_range	(	Size const	begin,
		Size const	end
	)

inline

Sets the chi torsions between residues <begin> and <end> as movable and all other residues are non-movable.

Example: movemap.set_chi_true_range(40, 60) See also: MoveMap MoveMap.set_bb MoveMap.set_bb_true_range MoveMap.set_chi Pose MinMover ShearMover SmallMover

Definition at line 265 of file MoveMap.hh.

References core::sequence::end, and set_chi().

void core::kinematics::MoveMap::set_jump ( bool const setting)

inline

Sets whether or not JUMP TorsionType is moveable.

example: movemap.set_jump(True)

Definition at line 282 of file MoveMap.hh.

References core::id::JUMP, and set().

Referenced by protocols::hybridization::HybridizeProtocol::apply(), protocols::idealize::basic_idealize(), protocols::abinitio::TemplateJumpSetup::clean_jumps(), protocols::swa::rna::StepWiseRNA_Minimizer::Figure_out_moving_residues(), protocols::swa::Figure_out_moving_residues(), protocols::swa::rna::floating_base_chain_closure_setup(), protocols::topology_broker::JumpClaimer::generate_claims(), protocols::antibody2::AntibodyInfo::get_MoveMap_for_Loops(), protocols::antibody2::AntibodyInfo::get_MoveMap_for_LoopsandDock(), protocols::topology_broker::JumpClaimer::init_jumps(), protocols::topology_broker::FragmentClaimer::initialize_dofs(), protocols::rna::let_rigid_body_jumps_move(), protocols::loops::loops_set_move_map(), core::pose::symmetry::make_symmetric_movemap(), protocols::vip::VIP_Mover::minimize_conformation(), protocols::abinitio::DoubleLayerKinematicAbinitio::new_kinematics(), protocols::abinitio::LoopJumpFoldCst::new_kinematics(), core::fragment::FragSet::region_all(), set_jump(), protocols::LoopRebuild::set_looprlx_allow_move_map(), protocols::loops::set_move_map_for_centroid_loop(), protocols::relax::RelaxProtocolBase::set_up_constraints(), protocols::rna::RNA_Minimizer::setup_movemap(), protocols::rbsegment_relax::setup_pose_from_rbsegs(), protocols::rna::RNA_DeNovoProtocol::setup_rigid_body_mover(), and protocols::topology_broker::JumpClaim::toggle().

void core::kinematics::MoveMap::set_jump	(	int const	jump_number,
		bool const	setting
	)

inline

Sets the movability of JUMP <jump_number> to <setting>

example: movemap.set_jump(1,True)

Definition at line 293 of file MoveMap.hh.

References core::id::JUMP, and set().

void core::kinematics::MoveMap::set_jump	(	Size const	pos1,
		Size const	pos2,
		bool const	setting
	)

inline

set JUMP moveable or not for one specific residue pair this mechanism does not mix with the "jump_nr" mechanism... i.e., if you set jump_nr 3 = movable —> movemap does not know that this refers to say residue 23-89

Definition at line 305 of file MoveMap.hh.

References set_jump().

void core::kinematics::MoveMap::set_jump	(	id::JumpID const &	jump,
		bool const	setting
	)

set/get for JumpIDs — fold-tree independent definition of jumps

Definition at line 83 of file MoveMap.cc.

void core::kinematics::MoveMap::set_ranges_unmodifiable ( const std::vector< std::pair< Size, Size > > & ranges)

Prevents backbone torsion modifications to the intervals specified by <ranges>. Each element of the vector is a pair, which specifies the begin and end indices. Counting begins with 1.

Definition at line 48 of file MoveMap.cc.

References core::sequence::end, and core::scoring::pair.