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core::kinematics::MoveMap Class Reference

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

#include <MoveMap.hh>

Inheritance diagram for core::kinematics::MoveMap:
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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, boolTorsionID_Map
 flexible or fixed for a single torsion, e.g., psi (BB torsion 2) of residue 10 More...
 
typedef std::map< DOF_Type, boolDOF_TypeMap
 flexible or fixed for this DOF_Type (PHI, THETA, D, RB1-6), for all atoms More...
 
typedef std::map< DOF_ID, boolDOF_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, boolatom_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):

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

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

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

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

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.

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

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

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

Referenced by clone().

Member Function Documentation

void core::kinematics::MoveMap::clear ( )
MoveMapOP core::kinematics::MoveMap::clone ( ) const
inline
DOF_ID_Map::const_iterator core::kinematics::MoveMap::dof_id_begin ( ) const
inline
DOF_ID_Map::const_iterator core::kinematics::MoveMap::dof_id_end ( ) const
inline
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
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
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
bool core::kinematics::MoveMap::get_jump ( int const  jump_number) const
inline
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]rvalThe MoveMap to import settings from.
[in]import_true_settingsImport True settings?
[in]import_false_settingsImport 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
MoveMapTorsionID_Map::const_iterator core::kinematics::MoveMap::movemap_torsion_id_end ( ) const
inline
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().

Referenced by protocols::loops::add_loop_flank_residues_bb_to_movemap(), protocols::mpi_refinement::add_movemap_from_loopres(), protocols::simple_moves::CombinePoseMover::apply(), protocols::simple_moves::ProlineFixMover::apply(), protocols::rbsegment_relax::IdealizeHelicesMover::apply(), protocols::simple_filters::SAXSScoreFilter::apply(), protocols::abinitio::ResolutionSwitcher::apply(), protocols::hybridization::CartesianSampler::apply(), protocols::ncbb::SecStructMinimizeMover::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::rna::movers::ErraserMinimizerMover::apply(), protocols::hybridization::BackboneTorsionSampler::apply(), protocols::hybridization::FoldTreeHybridize::apply(), protocols::forge::remodel::RemodelLoopMover::apply(), protocols::hybridization::CartesianSampler::apply_frame(), protocols::pose_creation::MakeJunctionsMover::assign_seq(), protocols::idealize::basic_idealize(), protocols::nonlocal::BiasedFragmentMover::BiasedFragmentMover(), protocols::loophash::LoopHashSampler::build_structures(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::bulge_chain_minimize_legacy(), protocols::abinitio::TemplateJumpSetup::clean_jumps(), protocols::cryst::ReportGradientsMover::compute(), protocols::forge::remodel::RemodelMover::confirm_sequence(), protocols::forge::remodel::RemodelMover::design_refine(), core::select::movemap::MoveMapFactory::edit_movemap_given_pose(), protocols::relax::fix_worst_bad_ramas(), protocols::topology_broker::FragmentJumpClaimer::generate_claims(), protocols::loophash::LoopHashLibrary::get_all(), protocols::magnesium::MgMinimizer::get_mg_hoh_minimize_move_map(), protocols::antibody::AntibodyInfo::get_MoveMap_for_AllCDRsSideChains_and_H3backbone(), protocols::antibody::AntibodyInfo::get_MoveMap_for_Loops(), core::util::getMLweight(), core::util::getMLweight_cart(), protocols::loophash::LoopHashLibrary::graft_loop(), protocols::topology_broker::FragmentJumpClaimer::init_jumps(), protocols::topology_broker::FragmentClaimer::initialize_dofs(), protocols::loops::loops_set_move_map(), 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::pose_creation::MergePDBatOverlapMover::merge_junction_sequence(), protocols::stepwise::modeler::rna::sugar::minimize_all_sampled_floating_bases(), core::import_pose::RNA_HelixAssembler::minimize_append_res(), core::import_pose::RNA_HelixAssembler::minimize_base_step(), protocols::pose_length_moves::PossibleLoop::minimize_loop(), core::import_pose::RNA_HelixAssembler::minimize_prepend_res(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::minimize_sugar(), protocols::simple_moves::ShakeStructureMover::minimize_with_constraints(), protocols::ddg::ddGMover::minimize_with_constraints(), protocols::protein_interface_design::MinimizeInterface(), protocols::cartesian::MolecularDynamics::MolecularDynamics(), protocols::forge::build::SegmentSwap::movemap(), protocols::forge::build::Bridge::movemap(), protocols::forge::build::GrowRight::movemap(), protocols::forge::build::GrowLeft::movemap(), protocols::forge::build::SegmentRebuild::movemap(), protocols::forge::build::ConnectRight::movemap(), protocols::forge::build::SegmentInsert::movemap(), protocols::rna::movers::ErraserMinimizerMover::movemap_setup(), protocols::pose_creation::MergePDBMover::pack_and_minimize(), protocols::hybridization::BackboneTorsionSampler::perturb(), protocols::kinematic_closure::perturbers::FragmentPerturber::perturb_subset(), protocols::mpi_refinement::ramp_minpack_loop(), protocols::mpi_refinement::WorkUnit_Sampler::ramp_minpack_loop2(), protocols::hydrate::read_body(), protocols::hydrate::read_header(), protocols::loop_grower::LoopGrower::refine_cycle(), core::fragment::FragSet::region_all(), protocols::loops::select_loop_frags(), set_bb_true_range(), core::pose::carbohydrates::set_glycan_iupac_bb_torsions(), protocols::LoopRebuild::set_looprlx_allow_move_map(), protocols::loops::set_move_map_for_centroid_loop(), protocols::hydrate::set_task_and_movemap(), core::optimization::CartesianMinimizerMap::setup(), protocols::rna::denovo::movers::RNA_Minimizer::setup_movemap(), core::pose::toolbox::AtomLevelDomainMap::setup_movemap(), protocols::rbsegment_relax::setup_pose_from_rbsegs(), protocols::protein_interface_design::SymMinimizeInterface(), protocols::topology_broker::claims::BBClaim::toggle(), and protocols::rna::movers::ErraserMinimizerMover::turn_off_for_chunks().

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
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().

Referenced by protocols::mpi_refinement::add_movemap_from_loopres(), protocols::simple_moves::CombinePoseMover::apply(), protocols::simple_moves::ProlineFixMover::apply(), protocols::simple_filters::SAXSScoreFilter::apply(), protocols::abinitio::ResolutionSwitcher::apply(), protocols::hybridization::CartesianSampler::apply(), protocols::rna::movers::ErraserMinimizerMover::apply(), protocols::hybridization::BackboneTorsionSampler::apply(), protocols::hybridization::FoldTreeHybridize::apply(), protocols::forge::remodel::RemodelLoopMover::apply(), protocols::hybridization::CartesianSampler::apply_frame(), protocols::pose_creation::MakeJunctionsMover::assign_seq(), protocols::idealize::basic_idealize(), protocols::forge::remodel::RemodelMover::confirm_sequence(), protocols::forge::remodel::RemodelMover::design_refine(), core::select::movemap::MoveMapFactory::edit_movemap_given_pose(), protocols::antibody::AntibodyInfo::get_MoveMap_for_AllCDRsSideChains_and_H3backbone(), protocols::antibody::AntibodyInfo::get_MoveMap_for_Loops(), core::util::getMLweight(), core::util::getMLweight_cart(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::let_neighboring_chis_minimize(), protocols::loops::loops_set_move_map(), protocols::relax::make_dna_rigid(), core::pose::symmetry::make_symmetric_movemap(), protocols::forge::remodel::RemodelLoopMover::mark_loop_moveable(), protocols::pose_creation::MergePDBatOverlapMover::merge_junction_sequence(), core::import_pose::RNA_HelixAssembler::minimize_append_res(), core::import_pose::RNA_HelixAssembler::minimize_prepend_res(), protocols::simple_moves::ShakeStructureMover::minimize_with_constraints(), protocols::cartesian::MolecularDynamics::MolecularDynamics(), protocols::stepwise::modeler::StepWiseMinimizer::move_side_chain(), protocols::forge::build::Bridge::movemap(), protocols::forge::build::GrowLeft::movemap(), protocols::forge::build::GrowRight::movemap(), protocols::forge::build::SegmentRebuild::movemap(), 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(), protocols::loop_grower::LoopGrower::refine_cycle(), core::fragment::FragSet::region_all(), set_chi_true_range(), core::pose::carbohydrates::set_glycan_iupac_bb_torsions(), core::pose::carbohydrates::set_glycan_iupac_chi_torsions(), protocols::LoopRebuild::set_looprlx_allow_move_map(), protocols::loops::set_move_map_for_centroid_loop(), protocols::hydrate::set_task_and_movemap(), core::optimization::CartesianMinimizerMap::setup(), protocols::rna::denovo::movers::RNA_Minimizer::setup_movemap(), core::pose::toolbox::AtomLevelDomainMap::setup_movemap(), and protocols::rna::movers::ErraserMinimizerMover::turn_off_for_chunks().

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.

void core::kinematics::MoveMap::show ( std::ostream &  out,
Size  i 
) const

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

References protocols::comparative_modeling::features::A, and core::chemical::element::I.

Referenced by core::kinematics::operator<<().

void core::kinematics::MoveMap::show ( Size  i) const
inline

Give the TorsionType bool values up to a given residue number. wrapper for PyRosetta.

References show().

Referenced by show().

void core::kinematics::MoveMap::show ( std::ostream &  out) const
void core::kinematics::MoveMap::show ( ) const
inline

References show().

Referenced by show().

TorsionID_Map::const_iterator core::kinematics::MoveMap::torsion_id_begin ( ) const
inline
TorsionID_Map::const_iterator core::kinematics::MoveMap::torsion_id_end ( ) const
inline
TorsionTypeMap::const_iterator core::kinematics::MoveMap::torsion_type_begin ( ) const
inline
TorsionTypeMap::const_iterator core::kinematics::MoveMap::torsion_type_end ( ) const
inline

Member Data Documentation

std::map< AtomID, bool > core::kinematics::MoveMap::atom_id_map_
private

flexible or fixed for a single specific ATOM. Used for fine control of cartesian minimization/protocols

DOF_ID_Map core::kinematics::MoveMap::dof_id_map_
private

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

Referenced by dof_id_begin(), and dof_id_end().

DOF_TypeMap core::kinematics::MoveMap::dof_type_map_
private

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

Referenced by dof_type_begin(), and dof_type_end().

JumpID_Map core::kinematics::MoveMap::jump_id_map_
private

Referenced by jump_id_begin(), and jump_id_end().

MoveMapTorsionID_Map core::kinematics::MoveMap::move_map_torsion_id_map_
private

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

Referenced by movemap_torsion_id_begin(), and movemap_torsion_id_end().

TorsionID_Map core::kinematics::MoveMap::torsion_id_map_
private

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

Referenced by torsion_id_begin(), and torsion_id_end().

TorsionTypeMap core::kinematics::MoveMap::torsion_type_map_
private

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

Referenced by torsion_type_begin(), and torsion_type_end().


The documentation for this class was generated from the following files: