protocols::motifs::Motif Class Reference

#include <Motif.hh>

Inheritance diagram for protocols::motifs::Motif:

Collaboration diagram for protocols::motifs::Motif:

Public Member Functions
	Motif (std::string const resname1, std::string const res1_atom1, std::string const res1_atom2, std::string const res1_atom3, std::string const resname2, std::string const res2_atom1, std::string const res2_atom2, std::string const res2_atom3, core::kinematics::Jump const &orientation)
	Motif (core::pose::Pose const &pose, Size const pdb_residue_position_1, char const pdb_chain_id1, std::string const res1_atom1, std::string const res1_atom2, std::string const res1_atom3, Size const pdb_residue_position_2, char const pdb_chain_id2, std::string const res2_atom1, std::string const res2_atom2, std::string const res2_atom3)
	Motif (core::pose::Pose const &pose, Size const pdb_residue_position_1, std::string const res1_atom1, std::string const res1_atom2, std::string const res1_atom3, Size const pdb_residue_position_2, std::string const res2_atom1, std::string const res2_atom2, std::string const res2_atom3)
	Motif (core::conformation::Residue const &res1, core::conformation::Residue const &res2)
	Motif (core::conformation::Residue const &res1, core::conformation::Residue const &res2, utility::vector1< Size > const res2_atoms)
	Motif (std::string const resname1, std::string const res1_atom1, std::string const res1_atom2, std::string const res1_atom3, std::string const res2_atom1, std::string const res2_atom2, std::string const res2_atom3, core::kinematics::Jump const &orientation)
	Motif (Motif const &src)
MotifOP	clone () const
virtual	~Motif ()
virtual bool	forward_check (core::conformation::Residue const &check_res) const
virtual bool	backward_check (core::conformation::Residue const &check_res) const
virtual bool	apply_check (core::pose::Pose const &pose, Size const pos) const
virtual core::pack::rotamer_set::RotamerSetOP	build_rotamers (core::pose::Pose &pose, Size const rotamer_build_position, bool use_forward, Size const ex_, bool res2=false) const
virtual core::pack::rotamer_set::RotamerSetOP	build_inverted_rotamers (core::pose::Pose &pose, Size const motif_anchor_position, bool use_forward, Size rotamer_build_position=0) const
virtual void	place_residue (core::conformation::Residue const &fixed, core::conformation::Residue &mobile, bool one_three=true) const
virtual void	place_atoms (core::conformation::Residue const &fixed, core::conformation::Residue &mobile, utility::vector1< std::string > const &atoms, bool one_three=true) const
virtual void	place_atom (core::conformation::Residue const &fixed, core::conformation::Residue &mobile, core::conformation::Atom &atm, bool one_three=true, std::string const atomtype="C1*") const
virtual void	place_residue_ (core::conformation::Residue const &fixed, core::conformation::Residue &mobile, bool forward, bool one_three=true) const
virtual void	place_atom_ (core::conformation::Residue const &fixed, core::conformation::Residue &mobile, bool forward, core::conformation::Atom &atm, bool one_three=true, std::string const atomtype="C1*") const
virtual void	place_atoms_ (core::conformation::Residue const &fixed, core::conformation::Residue &mobile, bool forward, utility::vector1< std::string > const &atoms, bool one_three=true) const
virtual void	place_residue (core::conformation::Residue const &fixed, core::conformation::Residue &mobile, Size const &res2_atom1_index_in, Size const &res2_atom2_index_in, Size const &res2_atom3_index_in, bool one_three=true) const
virtual void	place_atoms (core::conformation::Residue const &fixed, core::conformation::Residue &mobile, utility::vector1< Size > const &atoms, Size const &res2_atom1_index_in, Size const &res2_atom2_index_in, Size const &res2_atom3_index_in, bool one_three=true) const
virtual void	place_atom (core::conformation::Residue const &fixed, core::conformation::Residue &mobile, core::conformation::Atom &atm, Size const &res2_atom1_index_in, Size const &res2_atom2_index_in, Size const &res2_atom3_index_in, Size const &atomtype, bool one_three=true) const
virtual void	place_residue_ (core::conformation::Residue const &fixed, core::conformation::Residue &mobile, bool forward, Size const &res2_atom1_index_in, Size const &res2_atom2_index_in, Size const &res2_atom3_index_in, bool one_three=true) const
virtual void	place_atom_ (core::conformation::Residue const &fixed, core::conformation::Residue &mobile, bool forward, core::conformation::Atom &atm, Size const &res2_atom1_index_in, Size const &res2_atom2_index_in, Size const &res2_atom3_index_in, Size const &atomtype, bool one_three=true) const
virtual void	place_atoms_ (core::conformation::Residue const &fixed, core::conformation::Residue &mobile, bool forward, utility::vector1< Size > const &atoms, Size const &res2_atom1_index_in, Size const &res2_atom2_index_in, Size const &res2_atom3_index_in, bool one_three=true) const
virtual void	print (std::ostream &os) const
virtual std::string	print () const
void	store_remark (std::string const &remark_in)
void	store_path (std::string const &path_in)
std::string const &	restype_name1 () const
std::string const &	res1_atom1_name () const
std::string const &	res1_atom2_name () const
std::string const &	res1_atom3_name () const
int const &	res1_atom1_int () const
int const &	res1_atom2_int () const
int const &	res1_atom3_int () const
Size const &	res1_atom1_index () const
Size const &	res1_atom2_index () const
Size const &	res1_atom3_index () const
std::string const &	restype_name2 () const
std::string const &	res2_atom1_name () const
std::string const &	res2_atom2_name () const
std::string const &	res2_atom3_name () const
int const &	res2_atom1_int () const
int const &	res2_atom2_int () const
int const &	res2_atom3_int () const
Size const &	res2_atom1_index () const
Size const &	res2_atom2_index () const
Size const &	res2_atom3_index () const
core::kinematics::Jump const &	forward_jump () const
core::kinematics::Jump const &	backward_jump () const
bool	has_remark () const
bool	has_path () const
std::string const &	remark () const
std::string const &	path () const

Private Attributes
std::string	restype_name1_
std::string	res1_atom1_name_
std::string	res1_atom2_name_
std::string	res1_atom3_name_
int	res1_atom1_int_
int	res1_atom2_int_
int	res1_atom3_int_
Size	res1_atom1_index_
Size	res1_atom2_index_
Size	res1_atom3_index_
std::string	restype_name2_
std::string	res2_atom1_name_
std::string	res2_atom2_name_
std::string	res2_atom3_name_
int	res2_atom1_int_
int	res2_atom2_int_
int	res2_atom3_int_
Size	res2_atom1_index_
Size	res2_atom2_index_
Size	res2_atom3_index_
core::kinematics::Jump	forward_jump_
core::kinematics::Jump	backward_jump_
std::string	remark_
std::string	path_
bool	has_remark_
bool	has_path_

Static Private Attributes
static std::map< std::string, utility::vector1< std::string > >	motifAtomIDs
static std::map< std::string, utility::vector1< std::string > >	basebaseAtomIDs

Friends
std::ostream &	operator<< (std::ostream &os, Motif const &mot)

Detailed Description

Definition at line 44 of file Motif.hh.

Constructor & Destructor Documentation

protocols::motifs::Motif::Motif	(	std::string const	resname1,
		std::string const	res1_atom1,
		std::string const	res1_atom2,
		std::string const	res1_atom3,
		std::string const	resname2,
		std::string const	res2_atom1,
		std::string const	res2_atom2,
		std::string const	res2_atom3,
		core::kinematics::Jump const &	orientation
	)

Definition at line 59 of file Motif.cc.

References core::chemical::FA_STANDARD, core::chemical::ChemicalManager::get_instance(), core::chemical::ResidueTypeSet::name_map(), res1_atom1_index_, res1_atom1_name_, res1_atom2_index_, res1_atom2_name_, res1_atom3_index_, res1_atom3_name_, res2_atom1_index_, res2_atom1_name_, res2_atom2_index_, res2_atom2_name_, res2_atom3_index_, res2_atom3_name_, restype_name1_, and restype_name2_.

Referenced by clone().

protocols::motifs::Motif::Motif	(	core::pose::Pose const &	pose,
		Size const	pdb_residue_position_1,
		char const	pdb_chain_id1,
		std::string const	res1_atom1,
		std::string const	res1_atom2,
		std::string const	res1_atom3,
		Size const	pdb_residue_position_2,
		char const	pdb_chain_id2,
		std::string const	res2_atom1,
		std::string const	res2_atom2,
		std::string const	res2_atom3
	)

Definition at line 93 of file Motif.cc.

References core::chemical::FA_STANDARD, core::chemical::ChemicalManager::get_instance(), core::chemical::ResidueTypeSet::name_map(), res1_atom1_index_, res1_atom1_name_, res1_atom2_index_, res1_atom2_name_, res1_atom3_index_, res1_atom3_name_, res2_atom1_index_, res2_atom1_name_, res2_atom2_index_, res2_atom2_name_, res2_atom3_index_, res2_atom3_name_, restype_name1_, and restype_name2_.

protocols::motifs::Motif::Motif	(	core::pose::Pose const &	pose,
		Size const	pdb_residue_position_1,
		std::string const	res1_atom1,
		std::string const	res1_atom2,
		std::string const	res1_atom3,
		Size const	pdb_residue_position_2,
		std::string const	res2_atom1,
		std::string const	res2_atom2,
		std::string const	res2_atom3
	)

Definition at line 135 of file Motif.cc.

References core::chemical::FA_STANDARD, core::chemical::ChemicalManager::get_instance(), core::chemical::ResidueTypeSet::name_map(), res1_atom1_index_, res1_atom1_name_, res1_atom2_index_, res1_atom2_name_, res1_atom3_index_, res1_atom3_name_, res2_atom1_index_, res2_atom1_name_, res2_atom2_index_, res2_atom2_name_, res2_atom3_index_, res2_atom3_name_, restype_name1_, and restype_name2_.

protocols::motifs::Motif::Motif	(	core::conformation::Residue const &	res1,
		core::conformation::Residue const &	res2
	)

Definition at line 267 of file Motif.cc.

References core::conformation::Residue::atom(), backward_jump_, basebaseAtomIDs, protocols::dna::dna_full_name3(), core::chemical::FA_STANDARD, forward_jump_, core::chemical::ChemicalManager::get_instance(), core::conformation::Residue::is_DNA(), core::conformation::Residue::is_protein(), motifAtomIDs, protocols::motifs::mt(), core::conformation::Residue::name3(), core::chemical::ResidueTypeSet::name_map(), res1_atom1_index_, res1_atom1_name_, res1_atom2_index_, res1_atom2_name_, res1_atom3_index_, res1_atom3_name_, res2_atom1_index_, res2_atom1_name_, res2_atom2_index_, res2_atom2_name_, res2_atom3_index_, res2_atom3_name_, restype_name1_, restype_name2_, core::kinematics::Jump::reversed(), and core::conformation::Atom::xyz().

protocols::motifs::Motif::Motif	(	core::conformation::Residue const &	res1,
		core::conformation::Residue const &	res2,
		utility::vector1< Size > const	res2_atoms
	)

Definition at line 177 of file Motif.cc.

References core::conformation::Residue::atom(), core::conformation::Residue::atom_type(), core::chemical::AtomType::atom_type_name(), backward_jump_, core::chemical::FA_STANDARD, forward_jump_, core::chemical::ChemicalManager::get_instance(), core::conformation::Residue::is_ligand(), core::conformation::Residue::is_protein(), motifAtomIDs, protocols::motifs::mt(), core::conformation::Residue::name3(), core::chemical::ResidueTypeSet::name_map(), res1_atom1_index_, res1_atom1_name_, res1_atom2_index_, res1_atom2_name_, res1_atom3_index_, res1_atom3_name_, res2_atom1_index_, res2_atom1_name_, res2_atom2_index_, res2_atom2_name_, res2_atom3_index_, res2_atom3_name_, restype_name1_, restype_name2_, core::kinematics::Jump::reversed(), and core::conformation::Atom::xyz().

protocols::motifs::Motif::Motif	(	std::string const	resname1,
		std::string const	res1_atom1,
		std::string const	res1_atom2,
		std::string const	res1_atom3,
		std::string const	res2_atom1,
		std::string const	res2_atom2,
		std::string const	res2_atom3,
		core::kinematics::Jump const &	orientation
	)

Definition at line 227 of file Motif.cc.

References core::chemical::ChemicalManager::atom_type_set(), backward_jump_, core::chemical::FA_STANDARD, forward_jump_, core::chemical::ChemicalManager::get_instance(), core::chemical::ResidueTypeSet::name_map(), res1_atom1_index_, res1_atom1_name_, res1_atom2_index_, res1_atom2_name_, res1_atom3_index_, res1_atom3_name_, res2_atom1_int_, res2_atom1_name_, res2_atom2_int_, res2_atom2_name_, res2_atom3_int_, res2_atom3_name_, restype_name1_, restype_name2_, and core::kinematics::Jump::reversed().

protocols::motifs::Motif::Motif

(

Motif const &

src)

Definition at line 324 of file Motif.cc.

protocols::motifs::Motif::~Motif ( )

virtual

Definition at line 361 of file Motif.cc.

Member Function Documentation

bool protocols::motifs::Motif::apply_check ( core::pose::Pose const &  pose, Size const  pos  ) const

virtual

Definition at line 381 of file Motif.cc.

References protocols::dna::dna_full_name3(), core::conformation::Residue::is_DNA(), core::conformation::Residue::name3(), core::pose::Pose::residue(), restype_name1_, and restype_name2_.

Referenced by build_inverted_rotamers().

bool protocols::motifs::Motif::backward_check ( core::conformation::Residue const &  check_res) const

virtual

Definition at line 373 of file Motif.cc.

References core::conformation::Residue::name3(), and restype_name2().

core::kinematics::Jump const& protocols::motifs::Motif::backward_jump ( ) const

inline

Definition at line 350 of file Motif.hh.

References backward_jump_.

core::pack::rotamer_set::RotamerSetOP protocols::motifs::Motif::build_inverted_rotamers ( core::pose::Pose &  pose, Size const  motif_anchor_position, bool  use_forward, Size  rotamer_build_position = 0  ) const

virtual

Definition at line 531 of file Motif.cc.

References apply_check(), build_rotamers(), forward_check(), protocols::motifs::mt(), place_residue(), and core::pose::Pose::residue().

core::pack::rotamer_set::RotamerSetOP protocols::motifs::Motif::build_rotamers ( core::pose::Pose &  pose, Size const  rotamer_build_position, bool  use_forward, Size const  ex_, bool  res2 = false  ) const

virtual

Definition at line 467 of file Motif.cc.

References core::chemical::aa_from_name(), core::pack::create_packer_graph(), core::pack::task::TaskFactory::create_packer_task(), core::pack::task::EX_FOUR_HALF_STEP_STDDEVS, core::scoring::fa_atr, core::scoring::fa_rep, core::chemical::num_canonical_aas, core::pose::Pose::residue(), restype_name1(), restype_name2(), and core::scoring::ScoreFunction::set_weight().

Referenced by build_inverted_rotamers().

MotifOP protocols::motifs::Motif::clone

(

)

const

Definition at line 356 of file Motif.cc.

References Motif().

Referenced by protocols::motifs::MotifLibrary::add_to_library(), and protocols::motifs::BuildPosition::keep_motif().

bool protocols::motifs::Motif::forward_check ( core::conformation::Residue const &  check_res) const

virtual

Definition at line 365 of file Motif.cc.

References core::conformation::Residue::name3(), and restype_name1().

Referenced by build_inverted_rotamers().

core::kinematics::Jump const& protocols::motifs::Motif::forward_jump ( ) const

inline

Definition at line 349 of file Motif.hh.

References forward_jump_.

Referenced by print().

bool protocols::motifs::Motif::has_path ( ) const

inline

Definition at line 352 of file Motif.hh.

References has_path_.

bool protocols::motifs::Motif::has_remark ( ) const

inline

Definition at line 351 of file Motif.hh.

References has_remark_.

Referenced by print().

std::string const& protocols::motifs::Motif::path ( ) const

inline

Definition at line 354 of file Motif.hh.

References path_.

void protocols::motifs::Motif::place_atom ( core::conformation::Residue const &  fixed, core::conformation::Residue &  mobile, core::conformation::Atom &  atm, bool  one_three = true, std::string const  atomtype = "C1*"  ) const

virtual

Definition at line 764 of file Motif.cc.

References place_atom_().

void protocols::motifs::Motif::place_atom ( core::conformation::Residue const &  fixed, core::conformation::Residue &  mobile, core::conformation::Atom &  atm, Size const &  res2_atom1_index_in, Size const &  res2_atom2_index_in, Size const &  res2_atom3_index_in, Size const &  atomtype, bool  one_three = true  ) const

virtual

Definition at line 608 of file Motif.cc.

References place_atom_().

void protocols::motifs::Motif::place_atom_ ( core::conformation::Residue const &  fixed, core::conformation::Residue &  mobile, bool  forward, core::conformation::Atom &  atm, bool  one_three = true, std::string const  atomtype = "C1*"  ) const

virtual

Definition at line 980 of file Motif.cc.

References core::conformation::Residue::atom(), backward_jump_, forward_jump_, core::kinematics::Stub::from_four_points(), core::kinematics::Stub::global2local(), core::kinematics::Stub::local2global(), core::kinematics::Jump::make_jump(), res1_atom1_index_, res1_atom2_index_, res1_atom3_index_, res2_atom1_index_, res2_atom2_index_, res2_atom3_index_, core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().

Referenced by place_atom().

void protocols::motifs::Motif::place_atom_ ( core::conformation::Residue const &  fixed, core::conformation::Residue &  mobile, bool  forward, core::conformation::Atom &  atm, Size const &  res2_atom1_index_in, Size const &  res2_atom2_index_in, Size const &  res2_atom3_index_in, Size const &  atomtype, bool  one_three = true  ) const

virtual

Definition at line 656 of file Motif.cc.

References core::conformation::Residue::atom(), backward_jump_, forward_jump_, core::kinematics::Stub::from_four_points(), core::kinematics::Stub::global2local(), core::kinematics::Stub::local2global(), core::kinematics::Jump::make_jump(), res1_atom1_index_, res1_atom2_index_, res1_atom3_index_, core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().

void protocols::motifs::Motif::place_atoms ( core::conformation::Residue const &  fixed, core::conformation::Residue &  mobile, utility::vector1< std::string > const &  atoms, bool  one_three = true  ) const

virtual

Definition at line 738 of file Motif.cc.

References protocols::dna::dna_full_name3(), protocols::motifs::mt(), core::conformation::Residue::name3(), place_atoms_(), restype_name1_, and restype_name2_.

void protocols::motifs::Motif::place_atoms ( core::conformation::Residue const &  fixed, core::conformation::Residue &  mobile, utility::vector1< Size > const &  atoms, Size const &  res2_atom1_index_in, Size const &  res2_atom2_index_in, Size const &  res2_atom3_index_in, bool  one_three = true  ) const

virtual

Definition at line 574 of file Motif.cc.

References protocols::dna::dna_full_name3(), protocols::motifs::mt(), core::conformation::Residue::name3(), place_atoms_(), restype_name1_, and restype_name2_.

void protocols::motifs::Motif::place_atoms_ ( core::conformation::Residue const &  fixed, core::conformation::Residue &  mobile, bool  forward, utility::vector1< std::string > const &  atoms, bool  one_three = true  ) const

virtual

Definition at line 1058 of file Motif.cc.

References core::conformation::Residue::atom(), backward_jump_, forward_jump_, core::kinematics::Stub::from_four_points(), core::kinematics::Stub::global2local(), core::kinematics::Stub::local2global(), core::kinematics::Jump::make_jump(), res1_atom1_name_, res1_atom2_name_, res1_atom3_name_, res2_atom1_name_, res2_atom2_name_, res2_atom3_name_, core::conformation::Residue::set_xyz(), core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().

Referenced by place_atoms().

void protocols::motifs::Motif::place_atoms_ ( core::conformation::Residue const &  fixed, core::conformation::Residue &  mobile, bool  forward, utility::vector1< Size > const &  atoms, Size const &  res2_atom1_index_in, Size const &  res2_atom2_index_in, Size const &  res2_atom3_index_in, bool  one_three = true  ) const

virtual

Definition at line 1139 of file Motif.cc.

References core::conformation::Residue::atom(), backward_jump_, forward_jump_, core::kinematics::Stub::from_four_points(), core::kinematics::Stub::global2local(), core::kinematics::Stub::local2global(), core::kinematics::Jump::make_jump(), res1_atom1_name_, res1_atom2_name_, res1_atom3_name_, core::conformation::Residue::set_xyz(), core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().

void protocols::motifs::Motif::place_residue ( core::conformation::Residue const &  fixed, core::conformation::Residue &  mobile, bool  one_three = true  ) const

virtual

Definition at line 794 of file Motif.cc.

References protocols::dna::dna_full_name3(), protocols::motifs::mt(), core::conformation::Residue::name3(), place_residue_(), restype_name1_, and restype_name2_.

Referenced by build_inverted_rotamers().

void protocols::motifs::Motif::place_residue ( core::conformation::Residue const &  fixed, core::conformation::Residue &  mobile, Size const &  res2_atom1_index_in, Size const &  res2_atom2_index_in, Size const &  res2_atom3_index_in, bool  one_three = true  ) const

virtual

Definition at line 625 of file Motif.cc.

References protocols::dna::dna_full_name3(), protocols::motifs::mt(), core::conformation::Residue::name3(), place_residue_(), restype_name1_, and restype_name2_.

void protocols::motifs::Motif::place_residue_ ( core::conformation::Residue const &  fixed, core::conformation::Residue &  mobile, bool  forward, bool  one_three = true  ) const

virtual

Definition at line 819 of file Motif.cc.

References core::conformation::Residue::atom(), backward_jump_, forward_jump_, core::kinematics::Stub::from_four_points(), core::kinematics::Stub::global2local(), core::kinematics::Stub::local2global(), core::kinematics::Jump::make_jump(), core::conformation::Residue::natoms(), res1_atom1_name_, res1_atom2_name_, res1_atom3_name_, res2_atom1_name_, res2_atom2_name_, res2_atom3_name_, core::conformation::Residue::set_xyz(), core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().

Referenced by place_residue().

void protocols::motifs::Motif::place_residue_ ( core::conformation::Residue const &  fixed, core::conformation::Residue &  mobile, bool  forward, Size const &  res2_atom1_index_in, Size const &  res2_atom2_index_in, Size const &  res2_atom3_index_in, bool  one_three = true  ) const

virtual

Definition at line 901 of file Motif.cc.

References core::conformation::Residue::atom(), backward_jump_, forward_jump_, core::kinematics::Stub::from_four_points(), core::kinematics::Stub::global2local(), core::kinematics::Stub::local2global(), core::kinematics::Jump::make_jump(), core::conformation::Residue::natoms(), res1_atom1_name_, res1_atom2_name_, res1_atom3_name_, core::conformation::Residue::set_xyz(), core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().

void protocols::motifs::Motif::print ( std::ostream &  os) const

virtual

Definition at line 1222 of file Motif.cc.

References forward_jump(), has_remark(), remark(), res1_atom1_name(), res1_atom2_name(), res1_atom3_name(), res2_atom1_name(), res2_atom2_name(), res2_atom3_name(), restype_name1(), and restype_name2().

Referenced by protocols::motifs::operator<<().

std::string protocols::motifs::Motif::print ( ) const

virtual

Definition at line 1242 of file Motif.cc.

std::string const& protocols::motifs::Motif::remark ( ) const

inline

Definition at line 353 of file Motif.hh.

References remark_.

Referenced by print().

Size const& protocols::motifs::Motif::res1_atom1_index ( ) const

inline

Definition at line 336 of file Motif.hh.

References res1_atom1_index_.

int const& protocols::motifs::Motif::res1_atom1_int ( ) const

inline

Definition at line 333 of file Motif.hh.

References res1_atom1_int_.

std::string const& protocols::motifs::Motif::res1_atom1_name ( ) const

inline

Definition at line 330 of file Motif.hh.

References res1_atom1_name_.

Referenced by print().

Size const& protocols::motifs::Motif::res1_atom2_index ( ) const

inline

Definition at line 337 of file Motif.hh.

References res1_atom2_index_.

int const& protocols::motifs::Motif::res1_atom2_int ( ) const

inline

Definition at line 334 of file Motif.hh.

References res1_atom2_int_.

std::string const& protocols::motifs::Motif::res1_atom2_name ( ) const

inline

Definition at line 331 of file Motif.hh.

References res1_atom2_name_.

Referenced by print().

Size const& protocols::motifs::Motif::res1_atom3_index ( ) const

inline

Definition at line 338 of file Motif.hh.

References res1_atom3_index_.

int const& protocols::motifs::Motif::res1_atom3_int ( ) const

inline

Definition at line 335 of file Motif.hh.

References res1_atom3_int_.

std::string const& protocols::motifs::Motif::res1_atom3_name ( ) const

inline

Definition at line 332 of file Motif.hh.

References res1_atom3_name_.

Referenced by print().

Size const& protocols::motifs::Motif::res2_atom1_index ( ) const

inline

Definition at line 346 of file Motif.hh.

References res2_atom1_index_.

int const& protocols::motifs::Motif::res2_atom1_int ( ) const

inline

Definition at line 343 of file Motif.hh.

References res2_atom1_int_.

std::string const& protocols::motifs::Motif::res2_atom1_name ( ) const

inline

Definition at line 340 of file Motif.hh.

References res2_atom1_name_.

Referenced by print().

Size const& protocols::motifs::Motif::res2_atom2_index ( ) const

inline

Definition at line 347 of file Motif.hh.

References res2_atom2_index_.

int const& protocols::motifs::Motif::res2_atom2_int ( ) const

inline

Definition at line 344 of file Motif.hh.

References res2_atom2_int_.

std::string const& protocols::motifs::Motif::res2_atom2_name ( ) const

inline

Definition at line 341 of file Motif.hh.

References res2_atom2_name_.

Referenced by print().

Size const& protocols::motifs::Motif::res2_atom3_index ( ) const

inline

Definition at line 348 of file Motif.hh.

References res2_atom3_index_.

int const& protocols::motifs::Motif::res2_atom3_int ( ) const

inline

Definition at line 345 of file Motif.hh.

References res2_atom3_int_.

std::string const& protocols::motifs::Motif::res2_atom3_name ( ) const

inline

Definition at line 342 of file Motif.hh.

References res2_atom3_name_.

Referenced by print().

std::string const& protocols::motifs::Motif::restype_name1 ( ) const

inline

Definition at line 329 of file Motif.hh.

References restype_name1_.

Referenced by build_rotamers(), forward_check(), and print().

std::string const& protocols::motifs::Motif::restype_name2 ( ) const

inline

Definition at line 339 of file Motif.hh.

References restype_name2_.

Referenced by backward_check(), build_rotamers(), and print().

void protocols::motifs::Motif::store_path

(

std::string const &

path_in)

Definition at line 457 of file Motif.cc.

References has_path_, and path_.

void protocols::motifs::Motif::store_remark

(

std::string const &

remark_in)

Definition at line 447 of file Motif.cc.

References has_remark_, and remark_.

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  os, Motif const &  mot  )

friend

Definition at line 1249 of file Motif.cc.

Member Data Documentation

core::kinematics::Jump protocols::motifs::Motif::backward_jump_

private

Definition at line 380 of file Motif.hh.

Referenced by backward_jump(), Motif(), place_atom_(), place_atoms_(), and place_residue_().

std::map< std::string, utility::vector1< std::string > > protocols::motifs::Motif::basebaseAtomIDs

staticprivate

Definition at line 48 of file Motif.hh.

Referenced by Motif().

core::kinematics::Jump protocols::motifs::Motif::forward_jump_

private

Definition at line 379 of file Motif.hh.

Referenced by forward_jump(), Motif(), place_atom_(), place_atoms_(), and place_residue_().

bool protocols::motifs::Motif::has_path_

private

Definition at line 385 of file Motif.hh.

Referenced by has_path(), and store_path().

bool protocols::motifs::Motif::has_remark_

private

Definition at line 384 of file Motif.hh.

Referenced by has_remark(), and store_remark().

std::map< std::string, utility::vector1< std::string > > protocols::motifs::Motif::motifAtomIDs

staticprivate

Definition at line 47 of file Motif.hh.

Referenced by Motif().

std::string protocols::motifs::Motif::path_

private

Definition at line 383 of file Motif.hh.

Referenced by path(), and store_path().

std::string protocols::motifs::Motif::remark_

private

Definition at line 382 of file Motif.hh.

Referenced by remark(), and store_remark().

Size protocols::motifs::Motif::res1_atom1_index_

private

Definition at line 365 of file Motif.hh.

Referenced by Motif(), place_atom_(), and res1_atom1_index().

int protocols::motifs::Motif::res1_atom1_int_

private

Definition at line 362 of file Motif.hh.

Referenced by res1_atom1_int().

std::string protocols::motifs::Motif::res1_atom1_name_

private

Definition at line 359 of file Motif.hh.

Referenced by Motif(), place_atoms_(), place_residue_(), and res1_atom1_name().

Size protocols::motifs::Motif::res1_atom2_index_

private

Definition at line 366 of file Motif.hh.

Referenced by Motif(), place_atom_(), and res1_atom2_index().

int protocols::motifs::Motif::res1_atom2_int_

private

Definition at line 363 of file Motif.hh.

Referenced by res1_atom2_int().

std::string protocols::motifs::Motif::res1_atom2_name_

private

Definition at line 360 of file Motif.hh.

Referenced by Motif(), place_atoms_(), place_residue_(), and res1_atom2_name().

Size protocols::motifs::Motif::res1_atom3_index_

private

Definition at line 367 of file Motif.hh.

Referenced by Motif(), place_atom_(), and res1_atom3_index().

int protocols::motifs::Motif::res1_atom3_int_

private

Definition at line 364 of file Motif.hh.

Referenced by res1_atom3_int().

std::string protocols::motifs::Motif::res1_atom3_name_

private

Definition at line 361 of file Motif.hh.

Referenced by Motif(), place_atoms_(), place_residue_(), and res1_atom3_name().

Size protocols::motifs::Motif::res2_atom1_index_

private

Definition at line 375 of file Motif.hh.

Referenced by Motif(), place_atom_(), and res2_atom1_index().

int protocols::motifs::Motif::res2_atom1_int_

private

Definition at line 372 of file Motif.hh.

Referenced by Motif(), and res2_atom1_int().

std::string protocols::motifs::Motif::res2_atom1_name_

private

Definition at line 369 of file Motif.hh.

Referenced by Motif(), place_atoms_(), place_residue_(), and res2_atom1_name().

Size protocols::motifs::Motif::res2_atom2_index_

private

Definition at line 376 of file Motif.hh.

Referenced by Motif(), place_atom_(), and res2_atom2_index().

int protocols::motifs::Motif::res2_atom2_int_

private

Definition at line 373 of file Motif.hh.

Referenced by Motif(), and res2_atom2_int().

std::string protocols::motifs::Motif::res2_atom2_name_

private

Definition at line 370 of file Motif.hh.

Referenced by Motif(), place_atoms_(), place_residue_(), and res2_atom2_name().

Size protocols::motifs::Motif::res2_atom3_index_

private

Definition at line 377 of file Motif.hh.

Referenced by Motif(), place_atom_(), and res2_atom3_index().

int protocols::motifs::Motif::res2_atom3_int_

private

Definition at line 374 of file Motif.hh.

Referenced by Motif(), and res2_atom3_int().

std::string protocols::motifs::Motif::res2_atom3_name_

private

Definition at line 371 of file Motif.hh.

Referenced by Motif(), place_atoms_(), place_residue_(), and res2_atom3_name().

std::string protocols::motifs::Motif::restype_name1_

private

Definition at line 358 of file Motif.hh.

Referenced by apply_check(), Motif(), place_atoms(), place_residue(), and restype_name1().

std::string protocols::motifs::Motif::restype_name2_

private

Definition at line 368 of file Motif.hh.

Referenced by apply_check(), Motif(), place_atoms(), place_residue(), and restype_name2().

---

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

• src/protocols/motifs/Motif.hh
• src/protocols/motifs/Motif.cc