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protocols::toolbox::AllowInsert Class Reference

#include <AllowInsert.hh>

Inheritance diagram for protocols::toolbox::AllowInsert:
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Collaboration diagram for protocols::toolbox::AllowInsert:
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Public Member Functions

 AllowInsert (core::pose::Pose const &pose)
 
virtual ~AllowInsert ()
 
AllowInsert & operator= (AllowInsert const &src)
 
 AllowInsert (AllowInsert const &src)
 
virtual AllowInsertOP clone () 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
 
Size get_domain (Size const &i) const
 
bool has_domain (core::id::AtomID const &atom_id) const
 
Size get_domain (core::id::AtomID const &atom_id) const
 
void set_domain (Size const &i, Size const &setting)
 
void set_domain (core::id::AtomID const &atom_id, Size const &setting)
 
void set_domain (Size const &setting)
 
void and_allow_insert (AllowInsertOP allow_insert_in)
 
core::Size nres ()
 
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 (Size const &i, bool const &setting)
 
void set (core::id::AtomID const &atom_id, bool const &setting)
 
void set (bool const &setting)
 
void show ()
 
std::map< core::id::AtomID,
Size > const & 		calculated_atom_id_domain_map ()
 
std::map< core::id::AtomID,
Size > const & 		calculate_atom_id_domain_map (core::pose::Pose const &pose)
 
void renumber_after_variant_changes (core::pose::Pose const &pose)
 
void calculate_atom_id_map (core::pose::Pose const &pose, std::map< core::Size, core::Size > const &res_map, core::kinematics::FoldTree const &scratch_fold_tree, std::map< core::id::AtomID, core::id::AtomID > &atom_id_map)
 
void set_force_ideal_chainbreak (bool const &setting)
 
void append_residue (core::pose::Pose const &pose, Size const &i, bool const &setting)
 

Private Member Functions

void initialize (core::pose::Pose const &pose)
 

Private Attributes

std::map< core::id::AtomID, Size > allow_insert_
 
std::map
< core::id::NamedAtomID,
core::id::AtomID > 		named_atom_id_map_
 
utility::vector1
< utility::vector1
< core::id::AtomID > > 		atom_ids_in_res_
 
std::map< core::id::AtomID, Size > calculated_atom_id_domain_map_
 
std::map< core::id::AtomID,
core::id::AtomID > 		map_to_original_
 
core::Size nres_
 
bool force_ideal_chainbreak_
 

Detailed Description

Definition at line 50 of file AllowInsert.hh.

Constructor & Destructor Documentation

protocols::toolbox::AllowInsert::AllowInsert ( core::pose::Pose const &  pose)

Definition at line 51 of file AllowInsert.cc.

References initialize().

Referenced by clone().

protocols::toolbox::AllowInsert::~AllowInsert ( )
virtual

Definition at line 59 of file AllowInsert.cc.

protocols::toolbox::AllowInsert::AllowInsert ( AllowInsert const &  src)

Definition at line 91 of file AllowInsert.cc.

Member Function Documentation

void protocols::toolbox::AllowInsert::and_allow_insert ( AllowInsertOP  allow_insert_in)

Definition at line 293 of file AllowInsert.cc.

References allow_insert_.

void protocols::toolbox::AllowInsert::append_residue ( core::pose::Pose const &  pose,
Size const &  i,
bool const &  setting 
)

Definition at line 497 of file AllowInsert.cc.

References allow_insert_, core::conformation::atom_id_to_named_atom_id(), atom_ids_in_res_, protocols::toolbox::FIXED_DOMAIN, map_to_original_, named_atom_id_map_, core::conformation::Residue::natoms(), nres_, and core::pose::Pose::residue().

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

Definition at line 475 of file AllowInsert.cc.

References calculated_atom_id_domain_map_, get_domain(), core::chemical::ResidueType::natoms(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

Referenced by initialize(), and renumber_after_variant_changes().

void protocols::toolbox::AllowInsert::calculate_atom_id_map ( core::pose::Pose const &  pose,
std::map< core::Size, core::Size > const &  res_map,
core::kinematics::FoldTree const &  scratch_fold_tree,
std::map< core::id::AtomID, core::id::AtomID > &  atom_id_map 
)

Definition at line 315 of file AllowInsert.cc.

References core::id::AtomID::atomno(), core::kinematics::FoldTree::is_cutpoint(), map_to_original_, core::chemical::ResidueType::natoms(), core::pose::Pose::residue_type(), and core::id::AtomID::rsd().

std::map< AtomID, Size > const & protocols::toolbox::AllowInsert::calculated_atom_id_domain_map ( )

Definition at line 309 of file AllowInsert.cc.

References calculated_atom_id_domain_map_.

AllowInsertOP protocols::toolbox::AllowInsert::clone ( ) const
virtual

Definition at line 63 of file AllowInsert.cc.

References AllowInsert().

bool protocols::toolbox::AllowInsert::get ( Size const &  i) const

Definition at line 134 of file AllowInsert.cc.

References get_domain().

bool protocols::toolbox::AllowInsert::get ( core::id::AtomID const &  atom_id) const

Definition at line 140 of file AllowInsert.cc.

References get_domain().

bool protocols::toolbox::AllowInsert::get ( core::id::TorsionID const &  torsion_id,
core::conformation::Conformation const &  conformation 
) const

Definition at line 146 of file AllowInsert.cc.

References get_domain(), and core::conformation::Conformation::get_torsion_angle_atom_ids().

Size protocols::toolbox::AllowInsert::get_domain ( Size const &  i) const

Definition at line 163 of file AllowInsert.cc.

References atom_ids_in_res_, and nres_.

Referenced by calculate_atom_id_domain_map(), and get().

Size protocols::toolbox::AllowInsert::get_domain ( core::id::AtomID const &  atom_id) const

Definition at line 184 of file AllowInsert.cc.

References allow_insert_, and map_to_original_.

bool protocols::toolbox::AllowInsert::has_domain ( core::id::AtomID const &  atom_id) const

Definition at line 177 of file AllowInsert.cc.

References map_to_original_.

void protocols::toolbox::AllowInsert::initialize ( core::pose::Pose const &  pose)
private

Definition at line 101 of file AllowInsert.cc.

References allow_insert_, atom_ids_in_res_, core::chemical::ResidueType::atom_name(), calculate_atom_id_domain_map(), map_to_original_, named_atom_id_map_, core::chemical::ResidueType::natoms(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

Referenced by AllowInsert().

core::Size protocols::toolbox::AllowInsert::nres ( )
inline

Definition at line 96 of file AllowInsert.hh.

References nres_.

AllowInsert & protocols::toolbox::AllowInsert::operator= ( AllowInsert const &  src)

Definition at line 71 of file AllowInsert.cc.

References allow_insert_, atom_ids_in_res_, calculated_atom_id_domain_map_, force_ideal_chainbreak_, map_to_original_, named_atom_id_map_, and nres_.

void protocols::toolbox::AllowInsert::renumber_after_variant_changes ( core::pose::Pose const &  pose)

Definition at line 384 of file AllowInsert.cc.

References core::chemical::ResidueType::atom_name(), calculate_atom_id_domain_map(), force_ideal_chainbreak_, core::chemical::ResidueType::is_coarse(), core::chemical::ResidueType::is_RNA(), map_to_original_, named_atom_id_map_, core::chemical::ResidueType::natoms(), nres_, core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

void protocols::toolbox::AllowInsert::set ( Size const &  i,
bool const &  setting 
)

Definition at line 259 of file AllowInsert.cc.

References set_domain().

void protocols::toolbox::AllowInsert::set ( core::id::AtomID const &  atom_id,
bool const &  setting 
)

Definition at line 265 of file AllowInsert.cc.

References set_domain().

void protocols::toolbox::AllowInsert::set ( bool const &  setting)

Definition at line 253 of file AllowInsert.cc.

References set_domain().

void protocols::toolbox::AllowInsert::set_domain ( Size const &  i,
Size const &  setting 
)

Definition at line 199 of file AllowInsert.cc.

References atom_ids_in_res_.

Referenced by set(), and set_phosphate_domain().

void protocols::toolbox::AllowInsert::set_domain ( core::id::AtomID const &  atom_id,
Size const &  setting 
)

Definition at line 207 of file AllowInsert.cc.

References allow_insert_, and map_to_original_.

void protocols::toolbox::AllowInsert::set_domain ( Size const &  setting)

Definition at line 225 of file AllowInsert.cc.

References allow_insert_.

void protocols::toolbox::AllowInsert::set_force_ideal_chainbreak ( bool const &  setting)
inline

Definition at line 136 of file AllowInsert.hh.

References force_ideal_chainbreak_.

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

Definition at line 272 of file AllowInsert.cc.

References set_phosphate_domain().

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

Definition at line 234 of file AllowInsert.cc.

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

Referenced by set_phosphate().

void protocols::toolbox::AllowInsert::show ( )

Definition at line 281 of file AllowInsert.cc.

References allow_insert_, atom_ids_in_res_, and nres_.

Member Data Documentation

std::map< core::id::AtomID, Size > protocols::toolbox::AllowInsert::allow_insert_
private

Definition at line 149 of file AllowInsert.hh.

Referenced by and_allow_insert(), append_residue(), get_domain(), initialize(), operator=(), set_domain(), and show().

utility::vector1< utility::vector1< core::id::AtomID > > protocols::toolbox::AllowInsert::atom_ids_in_res_
private

Definition at line 151 of file AllowInsert.hh.

Referenced by append_residue(), get_domain(), initialize(), operator=(), set_domain(), and show().

std::map< core::id::AtomID, Size > protocols::toolbox::AllowInsert::calculated_atom_id_domain_map_
private

Definition at line 153 of file AllowInsert.hh.

Referenced by calculate_atom_id_domain_map(), calculated_atom_id_domain_map(), and operator=().

bool protocols::toolbox::AllowInsert::force_ideal_chainbreak_
private

Definition at line 159 of file AllowInsert.hh.

Referenced by operator=(), renumber_after_variant_changes(), and set_force_ideal_chainbreak().

std::map< core::id::AtomID, core::id::AtomID > protocols::toolbox::AllowInsert::map_to_original_
private

Definition at line 155 of file AllowInsert.hh.

Referenced by append_residue(), calculate_atom_id_map(), get_domain(), has_domain(), initialize(), operator=(), renumber_after_variant_changes(), and set_domain().

std::map< core::id::NamedAtomID, core::id::AtomID > protocols::toolbox::AllowInsert::named_atom_id_map_
private

Definition at line 150 of file AllowInsert.hh.

Referenced by append_residue(), initialize(), operator=(), and renumber_after_variant_changes().

core::Size protocols::toolbox::AllowInsert::nres_
private

Definition at line 157 of file AllowInsert.hh.

Referenced by append_residue(), get_domain(), nres(), operator=(), renumber_after_variant_changes(), and show().

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