Rosetta
Public Member Functions | Private Member Functions | Private Attributes | List of all members
core::pose::toolbox::AtomLevelDomainMap Class Reference

#include <AtomLevelDomainMap.hh>

Inheritance diagram for core::pose::toolbox::AtomLevelDomainMap:
Inheritance graph
[legend]

Public Member Functions

 AtomLevelDomainMap (core::pose::Pose const &pose, bool const map_to_vanilla_pose=false, utility::vector1< Size > const &allow_insert_res=utility::vector1< Size >())
 
virtual AtomLevelDomainMapOP clone () const
 
bool has_domain (core::id::AtomID const &atom_id) const
 
bool get (Size const &i) const
 
bool get (core::id::AtomID const &atom_id) const
 
bool get (core::id::TorsionID const &torsion_id, core::conformation::Conformation const &conformation) const
 
bool get_jump (Size const &jump_number, core::conformation::Conformation const &conformation) const
 
Size get_domain (Size const &i) const
 
Size get_domain (core::id::AtomID const &atom_id) const
 
Size get_domain (core::id::NamedAtomID const &named_atom_id, core::pose::Pose const &pose) const
 
void set_domain (Size const &i, Size const &setting)
 
void set_domain (core::id::AtomID const &atom_id, Size const &setting, bool ok_if_missing=false)
 
void set_domain (core::id::NamedAtomID const &atom_id, core::pose::Pose const &pose, Size const &setting)
 
void set_domain (Size const &setting)
 
void set_phosphate_domain (core::Size const &i, core::pose::Pose const &pose, Size const &setting)
 
void set_phosphate (core::Size const &i, core::pose::Pose const &pose, bool const &setting)
 
void set_sugar_domain (core::Size const &i, core::pose::Pose const &pose, Size const &setting)
 
void set_sugar (core::Size const &i, core::pose::Pose const &pose, bool const &setting)
 
void set (Size const &i, bool const &setting)
 
void set (core::id::NamedAtomID const &named_atom_id, core::pose::Pose const &pose, bool const &setting)
 
void set (core::id::AtomID const &atom_id, bool const &setting)
 
void set (bool const &setting)
 
void set_fixed_if_moving (Size const &i)
 
void set_fixed_if_moving (core::id::AtomID const &atom_id)
 
void show (std::ostream &out=std::cout) const
 
std::map< core::id::AtomID, Size > calculate_atom_id_domain_map (core::pose::Pose const &pose) const
 
void renumber_after_variant_changes (core::pose::Pose const &pose)
 
void setup_movemap (core::kinematics::MoveMap &mm, core::pose::Pose const &pose, bool const &check_for_vrt_phos=false)
 
AtomID_MapperCOP atom_id_mapper () const
 
void disallow_movement_of_input_res (core::pose::Pose const &pose)
 
void update_to_move_chunks_with_domain (Size const &domain)
 

Private Member Functions

void initialize (core::pose::Pose const &pose, bool const map_to_vanilla_pose, utility::vector1< Size > const &allow_insert_res)
 
void update_to_move_internal_phosphates (core::pose::Pose const &pose)
 
void update_to_not_move_virtual_phosphates (core::pose::Pose const &pose)
 
void update_to_not_move_virtual_o2prime (core::pose::Pose const &pose)
 
void update_to_not_move_last_virtual_residue (core::pose::Pose const &pose)
 
void apply_allow_insert_res (utility::vector1< Size > const &allow_insert_res)
 

Private Attributes

std::map< core::id::AtomID, Size > domain_map_
 
AtomID_MapperCOP atom_id_mapper_
 

Constructor & Destructor Documentation

◆ AtomLevelDomainMap()

core::pose::toolbox::AtomLevelDomainMap::AtomLevelDomainMap ( core::pose::Pose const &  pose,
bool const  map_to_vanilla_pose = false,
utility::vector1< Size > const &  allow_insert_res = utility::vector1< Size >() 
)

References initialize().

Referenced by clone().

Member Function Documentation

◆ apply_allow_insert_res()

void core::pose::toolbox::AtomLevelDomainMap::apply_allow_insert_res ( utility::vector1< Size > const &  allow_insert_res)
private

References set().

Referenced by initialize().

◆ atom_id_mapper()

AtomID_MapperCOP core::pose::toolbox::AtomLevelDomainMap::atom_id_mapper ( ) const
inline

References atom_id_mapper_.

◆ calculate_atom_id_domain_map()

std::map< AtomID, Size > core::pose::toolbox::AtomLevelDomainMap::calculate_atom_id_domain_map ( core::pose::Pose const &  pose) const

References get_domain(), core::pose::Pose::residue_type(), and core::pose::Pose::size().

◆ clone()

AtomLevelDomainMapOP core::pose::toolbox::AtomLevelDomainMap::clone ( ) const
virtual

References AtomLevelDomainMap().

◆ disallow_movement_of_input_res()

void core::pose::toolbox::AtomLevelDomainMap::disallow_movement_of_input_res ( core::pose::Pose const &  pose)

analogous to fixed_domain setting in initialize(), but this looks at input_domain – so, for example, makes sure no movement even in 'extra_minimize_res'.

References atom_id_mapper_, domain_map_, core::pose::full_model_info::full_model_info_defined(), core::pose::full_model_info::get_input_domain_from_full_model_info_const(), core::pose::Pose::residue_type(), and core::pose::Pose::size().

◆ get() [1/3]

bool core::pose::toolbox::AtomLevelDomainMap::get ( core::id::AtomID const &  atom_id) const

References get_domain().

◆ get() [2/3]

bool core::pose::toolbox::AtomLevelDomainMap::get ( core::id::TorsionID const &  torsion_id,
core::conformation::Conformation const &  conformation 
) const

References core::pose::copydofs::FIXED_DOMAIN, get(), get_domain(), and core::conformation::Conformation::get_torsion_angle_atom_ids().

◆ get() [3/3]

bool core::pose::toolbox::AtomLevelDomainMap::get ( Size const &  i) const

References get_domain().

Referenced by get(), get_jump(), core::pose::rna::moveable_jump(), set_fixed_if_moving(), setup_movemap(), and update_to_not_move_last_virtual_residue().

◆ get_domain() [1/3]

Size core::pose::toolbox::AtomLevelDomainMap::get_domain ( core::id::AtomID const &  atom_id) const

References atom_id_mapper_, domain_map_, and core::pose::copydofs::FIXED_DOMAIN.

◆ get_domain() [2/3]

Size core::pose::toolbox::AtomLevelDomainMap::get_domain ( core::id::NamedAtomID const &  named_atom_id,
core::pose::Pose const &  pose 
) const

References get_domain(), and core::pose::named_atom_id_to_atom_id().

◆ get_domain() [3/3]

Size core::pose::toolbox::AtomLevelDomainMap::get_domain ( Size const &  i) const

References atom_id_mapper_.

Referenced by calculate_atom_id_domain_map(), get(), core::import_pose::libraries::ChunkSet::get_atom_id_domain_map_for_rosetta_library_chunk(), get_domain(), get_jump(), core::pose::rna::moveable_jump(), show(), update_to_move_chunks_with_domain(), and update_to_move_internal_phosphates().

◆ get_jump()

bool core::pose::toolbox::AtomLevelDomainMap::get_jump ( Size const &  jump_number,
core::conformation::Conformation const &  conformation 
) const

References get(), get_domain(), and core::conformation::Conformation::get_jump_atom_ids().

Referenced by setup_movemap().

◆ has_domain()

bool core::pose::toolbox::AtomLevelDomainMap::has_domain ( core::id::AtomID const &  atom_id) const

References atom_id_mapper_.

◆ initialize()

void core::pose::toolbox::AtomLevelDomainMap::initialize ( core::pose::Pose const &  pose,
bool const  map_to_vanilla_pose,
utility::vector1< Size > const &  allow_insert_res 
)
private

References apply_allow_insert_res(), atom_id_mapper_, domain_map_, core::pose::full_model_info::full_model_info_defined(), core::pose::full_model_info::get_fixed_domain_from_full_model_info_const(), core::pose::Pose::residue_type(), core::pose::Pose::size(), update_to_move_internal_phosphates(), update_to_not_move_last_virtual_residue(), update_to_not_move_virtual_o2prime(), and update_to_not_move_virtual_phosphates().

Referenced by AtomLevelDomainMap().

◆ renumber_after_variant_changes()

void core::pose::toolbox::AtomLevelDomainMap::renumber_after_variant_changes ( core::pose::Pose const &  pose)

References atom_id_mapper_.

◆ set() [1/4]

void core::pose::toolbox::AtomLevelDomainMap::set ( bool const &  setting)

References core::pose::copydofs::FIXED_DOMAIN, and set_domain().

◆ set() [2/4]

void core::pose::toolbox::AtomLevelDomainMap::set ( core::id::AtomID const &  atom_id,
bool const &  setting 
)

References core::pose::copydofs::FIXED_DOMAIN, and set_domain().

◆ set() [3/4]

void core::pose::toolbox::AtomLevelDomainMap::set ( core::id::NamedAtomID const &  named_atom_id,
core::pose::Pose const &  pose,
bool const &  setting 
)

References core::pose::named_atom_id_to_atom_id(), set_domain(), and set_fixed_if_moving().

◆ set() [4/4]

void core::pose::toolbox::AtomLevelDomainMap::set ( Size const &  i,
bool const &  setting 
)

References core::pose::copydofs::FIXED_DOMAIN, and set_domain().

Referenced by apply_allow_insert_res(), and update_to_not_move_last_virtual_residue().

◆ set_domain() [1/4]

void core::pose::toolbox::AtomLevelDomainMap::set_domain ( core::id::AtomID const &  atom_id,
Size const &  setting,
bool  ok_if_missing = false 
)

References atom_id_mapper_, and domain_map_.

◆ set_domain() [2/4]

void core::pose::toolbox::AtomLevelDomainMap::set_domain ( core::id::NamedAtomID const &  atom_id,
core::pose::Pose const &  pose,
Size const &  setting 
)

References core::pose::named_atom_id_to_atom_id(), and set_domain().

◆ set_domain() [3/4]

void core::pose::toolbox::AtomLevelDomainMap::set_domain ( Size const &  i,
Size const &  setting 
)

References atom_id_mapper_.

Referenced by set(), set_domain(), set_fixed_if_moving(), set_phosphate_domain(), set_sugar_domain(), update_to_move_chunks_with_domain(), and update_to_not_move_virtual_o2prime().

◆ set_domain() [4/4]

void core::pose::toolbox::AtomLevelDomainMap::set_domain ( Size const &  setting)

References domain_map_.

◆ set_fixed_if_moving() [1/2]

void core::pose::toolbox::AtomLevelDomainMap::set_fixed_if_moving ( core::id::AtomID const &  atom_id)

References core::pose::copydofs::FIXED_DOMAIN, get(), and set_domain().

◆ set_fixed_if_moving() [2/2]

void core::pose::toolbox::AtomLevelDomainMap::set_fixed_if_moving ( Size const &  i)

References atom_id_mapper_.

Referenced by set().

◆ set_phosphate()

void core::pose::toolbox::AtomLevelDomainMap::set_phosphate ( core::Size const &  i,
core::pose::Pose const &  pose,
bool const &  setting 
)

References core::pose::copydofs::FIXED_DOMAIN, and set_phosphate_domain().

Referenced by update_to_move_internal_phosphates(), and update_to_not_move_virtual_phosphates().

◆ set_phosphate_domain()

void core::pose::toolbox::AtomLevelDomainMap::set_phosphate_domain ( core::Size const &  i,
core::pose::Pose const &  pose,
Size const &  setting 
)

References core::chemical::rna::atoms_involved_in_phosphate_torsion, core::conformation::Residue::is_coarse(), core::pose::named_atom_id_to_atom_id(), core::pose::Pose::residue(), and set_domain().

Referenced by set_phosphate().

◆ set_sugar()

void core::pose::toolbox::AtomLevelDomainMap::set_sugar ( core::Size const &  i,
core::pose::Pose const &  pose,
bool const &  setting 
)

References core::pose::copydofs::FIXED_DOMAIN, and set_sugar_domain().

◆ set_sugar_domain()

void core::pose::toolbox::AtomLevelDomainMap::set_sugar_domain ( core::Size const &  i,
core::pose::Pose const &  pose,
Size const &  setting 
)

References core::conformation::Residue::is_coarse(), core::pose::named_atom_id_to_atom_id(), core::pose::Pose::residue(), set_domain(), and core::chemical::rna::sugar_atoms.

Referenced by set_sugar().

◆ setup_movemap()

void core::pose::toolbox::AtomLevelDomainMap::setup_movemap ( core::kinematics::MoveMap &  mm,
core::pose::Pose const &  pose,
bool const &  check_for_vrt_phos = false 
)

References atom_id_mapper_, core::chemical::ResidueType::atom_index(), core::id::BB, core::kinematics::Edge::CHEMICAL, core::id::CHI, core::pose::Pose::conformation(), core::chemical::CUTPOINT_UPPER, core::id::D, core::chemical::FIVEPRIME_CAP, core::pose::Pose::fold_tree(), get(), get_jump(), core::kinematics::FoldTree::get_residue_edge(), core::conformation::Residue::has_variant_type(), core::chemical::ResidueTypeBase::has_variant_type(), core::chemical::rings::PHI, core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::kinematics::FoldTree::root(), core::kinematics::MoveMap::set(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_jump(), core::pose::Pose::size(), and core::chemical::VIRTUAL_PHOSPHATE.

◆ show()

void core::pose::toolbox::AtomLevelDomainMap::show ( std::ostream &  out = std::cout) const

References atom_id_mapper_, get_domain(), core::chemical::element::I, and core::conformation::membrane::out.

Referenced by core::import_pose::libraries::ChunkSet::get_atom_id_domain_map_for_rosetta_library_chunk().

◆ update_to_move_chunks_with_domain()

void core::pose::toolbox::AtomLevelDomainMap::update_to_move_chunks_with_domain ( Size const &  domain)

References atom_id_mapper_, get_domain(), and set_domain().

◆ update_to_move_internal_phosphates()

void core::pose::toolbox::AtomLevelDomainMap::update_to_move_internal_phosphates ( core::pose::Pose const &  pose)
private

References get_domain(), core::chemical::ResidueTypeBase::has_variant_type(), core::chemical::ResidueTypeBase::is_RNA(), core::pose::Pose::residue_type(), set_phosphate(), core::pose::Pose::size(), and core::chemical::VIRTUAL_PHOSPHATE.

Referenced by initialize().

◆ update_to_not_move_last_virtual_residue()

void core::pose::toolbox::AtomLevelDomainMap::update_to_not_move_last_virtual_residue ( core::pose::Pose const &  pose)
private

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_vrt, get(), core::pose::Pose::residue_type(), set(), and core::pose::Pose::size().

Referenced by initialize().

◆ update_to_not_move_virtual_o2prime()

void core::pose::toolbox::AtomLevelDomainMap::update_to_not_move_virtual_o2prime ( core::pose::Pose const &  pose)
private

References core::chemical::DEOXY_O2PRIME, core::pose::copydofs::FIXED_DOMAIN, core::chemical::ResidueTypeBase::has_variant_type(), core::pose::named_atom_id_to_atom_id(), core::pose::Pose::residue_type(), set_domain(), and core::pose::Pose::size().

Referenced by initialize().

◆ update_to_not_move_virtual_phosphates()

void core::pose::toolbox::AtomLevelDomainMap::update_to_not_move_virtual_phosphates ( core::pose::Pose const &  pose)
private

References core::chemical::ResidueTypeBase::has_variant_type(), core::pose::Pose::residue_type(), set_phosphate(), core::pose::Pose::size(), and core::chemical::VIRTUAL_PHOSPHATE.

Referenced by initialize().

Member Data Documentation

◆ atom_id_mapper_

AtomID_MapperCOP core::pose::toolbox::AtomLevelDomainMap::atom_id_mapper_
private

Referenced by atom_id_mapper(), disallow_movement_of_input_res(), get_domain(), has_domain(), initialize(), renumber_after_variant_changes(), set_domain(), set_fixed_if_moving(), setup_movemap(), show(), and update_to_move_chunks_with_domain().

◆ domain_map_

std::map< core::id::AtomID, Size > core::pose::toolbox::AtomLevelDomainMap::domain_map_
private

Referenced by disallow_movement_of_input_res(), get_domain(), initialize(), and set_domain().

The documentation for this class was generated from the following files:
Generated on Mon Sep 4 2023 05:13:09 for Rosetta by doxygen 1.9.1