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

#include <MoveMap.hh>

Inheritance 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. More...

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

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

typedef std::map< TorsionID, bool >	TorsionID_Map
	flexible or fixed for a single torsion, e.g., 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
	~MoveMap () override
	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 (Size const seqpos, Size const torsion_id, bool const setting)
	Sets whether or not the BB torsion of residue <seqpos> and torsion <torsion_id> 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 or 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 (core::uint const begin, core::uint const end)
	Sets the chi torsions between residues <begin> and <end> as movable and all other residues are non-movable. More...

void	set_nu (bool const setting)
	Set whether or not NU TorsionTypes are movable. More...

void	set_nu (core::uint const seqpos, bool const setting)
	Set whether or not the NU torsions of residue <seqpos> are movable. More...

void	set_nus (utility::vector1< bool > const &settings)
	Set which NU torsions are movable based on input array. More...

void	set_nu_true_range (core::uint const begin, core::uint const end)
	Set the NU torsions between residues <begin> and <end> as movable and all other residues are non-movable. More...

void	set_branches (bool const setting)
	Set whether or not BRANCH TorsionTypes are movable. More...

void	set_branches (core::uint const seqpos, bool const setting)
	Set whether or not the BRANCH torsions of residue <seqpos> are movable. More...

void	set_branches (utility::vector1< bool > const &settings)
	Set which BRANCH torsions are movable based on input array. More...

void	set_branches_true_range (core::uint const begin, core::uint const end)
	Set the BRANCH 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_atom (id::AtomID const &atom, bool const setting)
	Set a specific AtomID movable. This is specifically for cartesian-space kinematics. More...

void	set (TorsionType const &t, bool const setting)
	set a specific TorsionType movable: currently BB, CHI, NU, BRANCH, or JUMP More...

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

void	set (TorsionID const &id, bool const setting)
	set an individual Torsion movable for now, e.g., "BB torsion 2 of residue 4" More...

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

void	set (DOF_ID const &id, bool const setting)
	set for an individual DoF, e.g., "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_bb (Size const seqpos, Size const torsion_id) const
	Returns if a specific BB torsion is 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_nu (core::uint const seqpos) const
	Return if NU torsions are movable or not for residue <seqpos>. More...

bool	get_branches (core::uint const seqpos) const
	Return if BRANCH 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

std::map< AtomID, bool > const &	get_atoms () const
	Get specific AtomID settings (used to set specific atoms in CartesianMin) More...

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
	Give the TorsionType bool values up to a given residue number. More...

void	show (Size i) const
	Give the TorsionType 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, NU, BRANCH, JUMP), for all residues More...

MoveMapTorsionID_Map	move_map_torsion_id_map_
	flexible or fixed for this TorsionType (BB, CHI, NU, BRANCH, JUMP), for one residue, e.g., no distinction between 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_

std::map< AtomID, bool >	atom_id_map_
	flexible or fixed for a single specific ATOM. Used for fine control of cartesian minimization/protocols More...

Detailed Description

A class specifying DOFs to be flexible or fixed.

Currently there are two groups of data, one is a residue-based Torsion definition, such as BB, CHI, NU, and JUMP; the other is an atom-based DOF definition, such as bond length D, bond angle THETA, and torsion angle PHI, which are used in the AtomTree. 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, NU, BRANCH, 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)

Settings 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 TorsionType 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 the setting for BB torsion 2 of residue 4 will first check if there is any specific setting, if not, it will check if there is a setting for all BB torsions for residue 4, if not again, it will use the setting for BB torsions for all residues.

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

Member Typedef Documentation

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

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

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

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

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

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

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

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

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

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

Our own specific torsion_id.

TorsionType can be BB, CHI, NU, or JUMP. Therefore, it doesn't distinguish specific torsions, e.g., phi/psi/omega in BB torsion. Useful when setting residue k backbone fixed.

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

flexible or fixed for this TorsionType (BB, CHI, NU, BRANCH, JUMP), for one residue, e.g., no distinction between phi/psi/omega

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

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

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

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

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

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

Constructor & Destructor Documentation

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

overridedefault

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

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

inline

default constructor

Member Function Documentation

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

clear – sets all to FALSE

all internal map data are cleared.

Referenced by protocols::antibody::AntibodyInfo::get_MoveMap_for_AllCDRsSideChains_and_H3backbone(), and protocols::antibody::AntibodyInfo::get_MoveMap_for_Loops().

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

inline

Referenced by protocols::md::CartesianMD::CartesianMD(), protocols::forge::remodel::RemodelLoopMover::create_fragment_movers(), protocols::forge::remodel::RemodelLoopMover::create_fragment_movers_limit_size(), and core::kinematics::deep_copy().

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

References dof_id_map_.

Referenced by core::optimization::AtomTreeMinimizer::check_setup(), import(), core::optimization::symmetry::SymAtomTreeMinimizer::make_asymmetric_movemap(), 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

References dof_id_map_.

Referenced by core::optimization::AtomTreeMinimizer::check_setup(), import(), core::optimization::symmetry::SymAtomTreeMinimizer::make_asymmetric_movemap(), 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

References dof_type_map_.

Referenced by import(), and core::optimization::symmetry::SymAtomTreeMinimizer::make_asymmetric_movemap().

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

inline

return an iterator pointing at the first element of the DOF_TypeMap

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.

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.

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.

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.

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.

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.

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.

Referenced by core::fragment::BBTorsionAndAnglesSRFD::apply(), core::fragment::IndependentBBTorsionSRFD::apply(), core::optimization::AtomTreeMinimizer::check_setup(), protocols::stepwise::modeler::figure_out_moving_chain_break_res(), core::fragment::IndependentBBTorsionSRFD::is_applicable(), core::fragment::BBTorsionSRFD::is_applicable(), core::optimization::symmetry::SymAtomTreeMinimizer::make_semisymmetric_movemap(), core::pose::symmetry::make_symmetric_movemap(), protocols::stepwise::modeler::output_movemap(), protocols::recces::scratch::ThermalSamplingMover::set_residue_sampling_from_pose_and_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.

References protocols::hybridization::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.

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

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.

std::map< core::id::AtomID, bool > const & core::kinematics::MoveMap::get_atoms ( ) const

Get specific AtomID settings (used to set specific atoms in CartesianMin)

Per-atom interface not available to discourage general use IE - In order to ask if an ATOM is movable with the rest of the MM settings (as the other get functions do) , one would require a pose.

Referenced by import(), core::pose::symmetry::make_symmetric_movemap(), and core::optimization::CartesianMinimizerMap::setup().

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)

References core::id::BB.

Referenced by protocols::frags::add_vall_cheating_fragments(), protocols::frags::add_vall_fragments(), protocols::jumping::close_chainbreaks(), protocols::rna::movers::com_of_true_residues(), 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::PairingLibrary::generate_jump_frags(), protocols::jumping::JumpSample::generate_jump_frags(), protocols::jumping::JumpSample::generate_jump_frames(), core::kinematics::get_residues_from_movemap_bb_any_torsion(), core::kinematics::get_residues_from_movemap_bb_or_chi(), protocols::normalmode::NormalModeRelaxMover::initialize_NM_for_movemap(), protocols::forge::methods::replace(), protocols::moves::PyMOLMover::send_movemap(), 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_bb	(	Size const	seqpos,
		Size const	torsion_id
	)		const

inline

Returns if a specific BB torsion is movable or not for residue <seqpos>

example: movemap.get_bb(49)

References core::id::BB.

bool core::kinematics::MoveMap::get_branches ( core::uint const seqpos ) const

inline

Return if BRANCH torsions are movable or not for residue <seqpos>.

: Example: movemap.get_branches(49)

References core::id::BRANCH.

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)

References core::id::CHI.

Referenced by protocols::relax::ClassicRelax::check_default_full_repacker(), protocols::relax::ClassicRelax::check_default_rottrial(), protocols::rna::movers::com_of_true_residues(), protocols::forge::remodel::RemodelMover::design_refine(), core::kinematics::get_residues_from_movemap_bb_or_chi(), protocols::stepwise::modeler::StepWiseMinimizer::move_side_chain(), protocols::moves::PyMOLMover::send_movemap(), core::optimization::CartesianMinimizerMap::setup(), protocols::mpi_refinement::setup_packer(), 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)

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::stepwise::modeler::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

References get_jump().

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

References core::id::JUMP.

bool core::kinematics::MoveMap::get_nu ( core::uint const seqpos ) const

inline

Return if NU torsions are movable or not for residue <seqpos>.

: Example: movemap.get_nu(49)

References core::id::NU.

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.

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.

References dof_id_begin(), dof_id_end(), dof_type_begin(), dof_type_end(), get_atoms(), 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.

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.

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

References protocols::sparta::split().

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

inline

return an iterator pointing at the first element of the JumpID_Map

References jump_id_map_.

Referenced by import(), core::optimization::symmetry::SymAtomTreeMinimizer::make_asymmetric_movemap(), and protocols::stepwise::modeler::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

References jump_id_map_.

Referenced by import(), core::optimization::symmetry::SymAtomTreeMinimizer::make_asymmetric_movemap(), and protocols::stepwise::modeler::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

References move_map_torsion_id_map_.

Referenced by protocols::denovo_design::movers::FastDesign::create_default_task_factory(), core::kinematics::get_residues_from_movemap_with_id(), import(), protocols::forge::build::SegmentInsert::insert_pose_torsion_override_movemap(), and core::optimization::symmetry::SymAtomTreeMinimizer::make_asymmetric_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

References move_map_torsion_id_map_.

Referenced by protocols::denovo_design::movers::FastDesign::create_default_task_factory(), core::kinematics::get_residues_from_movemap_with_id(), import(), protocols::forge::build::SegmentInsert::insert_pose_torsion_override_movemap(), and core::optimization::symmetry::SymAtomTreeMinimizer::make_asymmetric_movemap().

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

set a specific TorsionType movable: currently BB, CHI, NU, BRANCH, or JUMP

Set a specific TorsionType movable or not, e.g., "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.

References core::id::JUMP, and protocols::hybridization::t.

Referenced by protocols::mpi_refinement::add_movemap_from_loopres(), protocols::idealize::basic_idealize(), core::pack::rotamer_set::build_lib_dna_rotamers(), core::select::movemap::MoveMapFactory::edit_movemap_given_pose(), protocols::relax::fix_worst_bad_ramas(), protocols::stepwise::modeler::rna::freeze_sugar_torsions(), protocols::relax::RelaxProtocolBase::initialize_movemap(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::let_neighboring_chis_minimize(), protocols::loops::loops_set_move_map(), core::optimization::symmetry::SymAtomTreeMinimizer::make_asymmetric_movemap(), core::optimization::symmetry::SymAtomTreeMinimizer::make_semisymmetric_movemap(), core::pose::symmetry::make_symmetric_movemap(), protocols::forge::remodel::RemodelLoopMover::mark_loop_moveable(), protocols::stepwise::modeler::StepWiseMinimizer::move_side_chain(), protocols::forge::build::SegmentRebuild::movemap(), protocols::forge::build::SegmentInsert::movemap(), protocols::mpi_refinement::ramp_minpack_loop(), protocols::mpi_refinement::WorkUnit_Sampler::ramp_minpack_loop2(), protocols::loop_grower::LoopGrower::refine_cycle(), set_bb(), set_branches(), set_chi(), core::pose::carbohydrates::set_glycan_iupac_bb_torsions(), core::pose::carbohydrates::set_glycan_iupac_chi_torsions(), set_jump(), protocols::LoopRebuild::set_looprlx_allow_move_map(), protocols::loops::set_move_map_for_centroid_loop(), set_nu(), set_nus(), protocols::rna::denovo::movers::RNA_Minimizer::setup_movemap(), core::pose::toolbox::AtomLevelDomainMap::setup_movemap(), protocols::loops::Loop::switch_movemap(), protocols::rna::movers::ErraserMinimizerMover::turn_off_for_chunks(), protocols::simple_moves::ConstrainToIdealMover::vary_bond_geometry(), and protocols::rna::movers::ErraserMinimizerMover::vary_bond_geometry().

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

set TorsionType flexible or fixed for one residue, e.g., BB torsions for residue 10

Setting this MoveMapTorsionID will clear data for individual TorsionID for this residue with this TorsionType.

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

set an individual Torsion movable for now, e.g., "BB torsion 2 of residue 4"

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

set atom tree DOF, e.g., D, PHI, THETA

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)

References protocols::hybridization::t.

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

set for an individual DoF, e.g., "PHI of Atom 3 in Residue 5"

void core::kinematics::MoveMap::set_atom	(	id::AtomID const &	atom,
		bool const	setting
	)

Set a specific AtomID movable. This is specifically for cartesian-space kinematics.

Referenced by core::pose::symmetry::make_symmetric_movemap(), and core::pose::carbohydrates::set_glycan_iupac_bb_torsions().

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 MoveMap.set_nu MoveMap.set_branches Pose MinMover ShearMover SmallMover

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

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 MoveMap.set_nu MoveMap.set_branches Pose MinMover ShearMover SmallMover

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

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

inline

Sets whether or not the BB torsion of residue <seqpos> and torsion <torsion_id> are movable.

example: movemap.set_bb(49, 1, True) See also: MoveMap MoveMap.set_chi MoveMap.set_nu MoveMap.set_branches Pose MinMover ShearMover SmallMover

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.

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 MoveMap.set_nu MoveMap.set_branches Pose MinMover ShearMover SmallMover

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

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

inline

Set whether or not BRANCH TorsionTypes are movable.

Example: movemap.set_branches( True )
See also:
MoveMap
MoveMap.set_bb
MoveMap.set_chi
MoveMap.set_nu
Pose
MinMover
ShearMover
SmallMover

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

Referenced by core::select::movemap::MoveMapFactory::edit_movemap_given_pose(), core::pose::symmetry::make_symmetric_movemap(), set_branches_true_range(), core::pose::carbohydrates::set_glycan_iupac_bb_torsions(), and core::optimization::CartesianMinimizerMap::setup().

void core::kinematics::MoveMap::set_branches	(	core::uint const	seqpos,
		bool const	setting
	)

inline

Set whether or not the BRANCH torsions of residue <seqpos> are movable.

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

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

void core::kinematics::MoveMap::set_branches ( utility::vector1< bool > const & settings )

inline

Set which BRANCH torsions are movable based on input array.

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

void core::kinematics::MoveMap::set_branches_true_range	(	core::uint const	begin,
		core::uint const	end
	)

inline

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

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

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

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

inline

Sets whether or not CHI TorsionType is movable.

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

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

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 MoveMap.set_nu MoveMap.set_branches Pose MinMover ShearMover SmallMover inline

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

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

void core::kinematics::MoveMap::set_chi_true_range	(	core::uint const	begin,
		core::uint 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 MoveMap.set_nu MoveMap.set_nu_true_range MoveMap.set_branches MoveMap.set_branches_true_range Pose MinMover ShearMover SmallMover

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)

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

Referenced by protocols::simple_moves::CombinePoseMover::apply(), protocols::rbsegment_relax::IdealizeHelicesMover::apply(), protocols::hybridization::BackboneTorsionSampler::apply(), protocols::hybridization::FoldTreeHybridize::apply(), protocols::hybridization::CartesianSampler::apply_frame(), protocols::pose_creation::MakeJunctionsMover::assign_seq(), protocols::idealize::basic_idealize(), protocols::abinitio::TemplateJumpSetup::clean_jumps(), core::select::movemap::MoveMapFactory::edit_movemap_given_pose(), protocols::stepwise::modeler::freeze_waters(), protocols::topology_broker::FragmentJumpClaimer::generate_claims(), protocols::antibody::AntibodyInfo::get_MoveMap_for_AllCDRsSideChains_and_H3backbone(), protocols::antibody::AntibodyInfo::get_MoveMap_for_Loops(), protocols::antibody::AntibodyInfo::get_MoveMap_for_LoopsandDock(), core::util::getMLweight(), core::util::getMLweight_cart(), protocols::topology_broker::FragmentJumpClaimer::init_jumps(), protocols::rna::denovo::movers::RNP_HighResMover::initialize(), protocols::topology_broker::FragmentClaimer::initialize_dofs(), protocols::rna::denovo::let_rigid_body_jumps_move(), protocols::loops::loops_set_move_map(), core::optimization::symmetry::SymAtomTreeMinimizer::make_asymmetric_movemap(), core::pose::symmetry::make_symmetric_movemap(), protocols::pose_creation::MergePDBatOverlapMover::merge_junction_sequence(), core::import_pose::RNA_HelixAssembler::minimize_append_res(), protocols::pose_creation::MergePDBatOverlapMover::minimize_overlap(), core::import_pose::RNA_HelixAssembler::minimize_prepend_res(), protocols::rna::movers::ErraserMinimizerMover::movemap_setup(), protocols::pose_creation::MergePDBMover::pack_and_minimize(), protocols::kinematic_closure::perturbers::FragmentPerturber::perturb_subset(), protocols::mpi_refinement::ramp_minpack_loop(), protocols::mpi_refinement::WorkUnit_Sampler::ramp_minpack_loop2(), core::fragment::FragSet::region_all(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::search_rigid_body_orientation(), set_jump(), protocols::LoopRebuild::set_looprlx_allow_move_map(), protocols::loops::set_move_map_for_centroid_loop(), protocols::hydrate::set_task_and_movemap(), protocols::relax::RelaxProtocolBase::set_up_constraints(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::setup_dock_into_density_mover(), protocols::rna::denovo::movers::RNA_Minimizer::setup_movemap(), core::pose::toolbox::AtomLevelDomainMap::setup_movemap(), protocols::rbsegment_relax::setup_pose_from_rbsegs(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::setup_rigid_body_mover(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::setup_rna_protein_docking_mover(), and protocols::topology_broker::claims::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)

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

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

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

inline

Set whether or not NU TorsionTypes are movable.

Example: movemap.set_nu(True)
See also:
MoveMap
MoveMap.set_bb
MoveMap.set_chi
MoveMap.set_branches
Pose
MinMover
ShearMover
SmallMover

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

Referenced by core::select::movemap::MoveMapFactory::edit_movemap_given_pose(), set_nu_true_range(), and core::optimization::CartesianMinimizerMap::setup().

void core::kinematics::MoveMap::set_nu	(	core::uint const	seqpos,
		bool const	setting
	)

inline

Set whether or not the NU torsions of residue <seqpos> are movable.

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

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

void core::kinematics::MoveMap::set_nu_true_range	(	core::uint const	begin,
		core::uint const	end
	)

inline

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

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

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

void core::kinematics::MoveMap::set_nus ( utility::vector1< bool > const & settings )

inline

Set which NU torsions are movable based on input array.

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

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.

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