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core::pose::toolbox::AtomLevelDomainMap Class Reference

#include <AtomLevelDomainMap.hh>

Inheritance diagram for core::pose::toolbox::AtomLevelDomainMap:
Inheritance graph
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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, Sizecalculate_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, Sizedomain_map_
 
AtomID_MapperCOP atom_id_mapper_
 

Constructor & Destructor Documentation

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

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

References set().

Referenced by initialize().

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

References atom_id_mapper_.

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

References AtomLevelDomainMap().

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::chemical::ResidueType::natoms(), core::pose::Pose::residue_type(), and core::pose::Pose::size().

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

References get_domain().

Referenced by core::pose::rna::moveable_jump().

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

References get_domain().

bool core::pose::toolbox::AtomLevelDomainMap::get ( core::id::TorsionID const &  torsion_id,
core::conformation::Conformation const &  conformation 
) const
Size core::pose::toolbox::AtomLevelDomainMap::get_domain ( Size const &  i) const
Size core::pose::toolbox::AtomLevelDomainMap::get_domain ( core::id::AtomID const &  atom_id) const
Size core::pose::toolbox::AtomLevelDomainMap::get_domain ( core::id::NamedAtomID const &  named_atom_id,
core::pose::Pose const &  pose 
) const
bool core::pose::toolbox::AtomLevelDomainMap::get_jump ( Size const &  jump_number,
core::conformation::Conformation const &  conformation 
) const
bool core::pose::toolbox::AtomLevelDomainMap::has_domain ( core::id::AtomID const &  atom_id) const

References atom_id_mapper_.

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

References atom_id_mapper_.

void core::pose::toolbox::AtomLevelDomainMap::set ( Size const &  i,
bool const &  setting 
)
void core::pose::toolbox::AtomLevelDomainMap::set ( core::id::NamedAtomID const &  named_atom_id,
core::pose::Pose const &  pose,
bool const &  setting 
)
void core::pose::toolbox::AtomLevelDomainMap::set ( core::id::AtomID const &  atom_id,
bool const &  setting 
)
void core::pose::toolbox::AtomLevelDomainMap::set ( bool const &  setting)
void core::pose::toolbox::AtomLevelDomainMap::set_domain ( Size const &  i,
Size const &  setting 
)
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_.

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

References domain_map_.

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

References atom_id_mapper_.

Referenced by set().

void core::pose::toolbox::AtomLevelDomainMap::set_fixed_if_moving ( core::id::AtomID const &  atom_id)
void core::pose::toolbox::AtomLevelDomainMap::set_phosphate ( core::Size const &  i,
core::pose::Pose const &  pose,
bool const &  setting 
)
void core::pose::toolbox::AtomLevelDomainMap::set_phosphate_domain ( core::Size const &  i,
core::pose::Pose const &  pose,
Size const &  setting 
)
void core::pose::toolbox::AtomLevelDomainMap::set_sugar ( core::Size const &  i,
core::pose::Pose const &  pose,
bool const &  setting 
)
void core::pose::toolbox::AtomLevelDomainMap::set_sugar_domain ( core::Size const &  i,
core::pose::Pose const &  pose,
Size const &  setting 
)
void core::pose::toolbox::AtomLevelDomainMap::setup_movemap ( core::kinematics::MoveMap mm,
core::pose::Pose const &  pose,
bool const &  check_for_vrt_phos = false 
)
void core::pose::toolbox::AtomLevelDomainMap::show ( std::ostream &  out = std::cout) const
void core::pose::toolbox::AtomLevelDomainMap::update_to_move_chunks_with_domain ( Size const &  domain)
void core::pose::toolbox::AtomLevelDomainMap::update_to_move_internal_phosphates ( core::pose::Pose const &  pose)
private
void core::pose::toolbox::AtomLevelDomainMap::update_to_not_move_last_virtual_residue ( core::pose::Pose const &  pose)
private
void core::pose::toolbox::AtomLevelDomainMap::update_to_not_move_virtual_o2prime ( core::pose::Pose const &  pose)
private
void core::pose::toolbox::AtomLevelDomainMap::update_to_not_move_virtual_phosphates ( core::pose::Pose const &  pose)
private

Member Data Documentation

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

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