#include <SingleMotif.hh>

Inheritance diagram for protocols::motifs::SingleMotif:

Public Member Functions
	SingleMotif (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)

	SingleMotif (core::pose::Pose const &pose, core::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, core::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)

	SingleMotif (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)

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

	SingleMotif (core::conformation::Residue const &res1, core::conformation::Residue const &res2)

	SingleMotif (SingleMotif const &src)

Public Member Functions inherited from 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)

	Motif (core::pose::Pose const &pose, core::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, core::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, core::Size const pdb_residue_position_1, std::string const &res1_atom1, std::string const &res1_atom2, std::string const &res1_atom3, core::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< core::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

	~Motif () override

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, core::Size const pos) const

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

virtual core::pack::rotamer_set::RotamerSetOP	build_inverted_rotamers (core::pose::Pose &pose, core::Size const motif_anchor_position, bool &use_forward, core::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, core::Size const &res2_atom1_index_in, core::Size const &res2_atom2_index_in, core::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< core::Size > const &atoms, core::Size const &res2_atom1_index_in, core::Size const &res2_atom2_index_in, core::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, core::Size const &res2_atom1_index_in, core::Size const &res2_atom2_index_in, core::Size const &res2_atom3_index_in, core::Size const &atomtype, bool one_three=true) const

virtual void	place_residue_ (core::conformation::Residue const &fixed, core::conformation::Residue &mobile, bool forward, core::Size const &res2_atom1_index_in, core::Size const &res2_atom2_index_in, core::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, core::Size const &res2_atom1_index_in, core::Size const &res2_atom2_index_in, core::Size const &res2_atom3_index_in, core::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< core::Size > const &atoms, core::Size const &res2_atom1_index_in, core::Size const &res2_atom2_index_in, core::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
	WARNING res_atom_int() values are not consistently initialized in constructors. More...

int const &	res1_atom2_int () const

int const &	res1_atom3_int () const

core::Size const &	res1_atom1_index () const

core::Size const &	res1_atom2_index () const

core::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
	WARNING res_atom_int() values are not consistently initialized in constructors. More...

int const &	res2_atom2_int () const

int const &	res2_atom3_int () const

core::Size const &	res2_atom1_index () const

core::Size const &	res2_atom2_index () const

core::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

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

Constructor & Destructor Documentation

protocols::motifs::SingleMotif::SingleMotif	(	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
	)

protocols::motifs::SingleMotif::SingleMotif	(	core::pose::Pose const &	pose,
		core::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,
		core::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
	)

protocols::motifs::SingleMotif::SingleMotif	(	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
	)

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

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

protocols::motifs::SingleMotif::SingleMotif ( SingleMotif const & src )

default

Friends And Related Function Documentation

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

friend

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

src/protocols/motifs/SingleMotif.hh
src/protocols/motifs/SingleMotif.cc

Public Member Functions

Friends

Constructor & Destructor Documentation

Friends And Related Function Documentation