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protocols::motifs::Motif Class Reference

#include <Motif.hh>

Inheritance diagram for protocols::motifs::Motif:
Inheritance graph
[legend]

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, 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
 

Private Member Functions

void place_residue_helper (core::kinematics::Stub &end_stub, core::kinematics::Stub &mobile_stub, 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) const
 
void place_residue_helper (core::kinematics::Stub &end_stub, core::kinematics::Stub &mobile_stub, core::conformation::Residue const &fixed, core::conformation::Residue &mobile, bool forward, bool one_three) 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_
 
core::Size res1_atom1_index_
 
core::Size res1_atom2_index_
 
core::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_
 
core::Size res2_atom1_index_
 
core::Size res2_atom2_index_
 
core::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)
 

Constructor & Destructor Documentation

◆ Motif() [1/7]

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() [2/7]

protocols::motifs::Motif::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() [3/7]

protocols::motifs::Motif::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() [4/7]

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

◆ Motif() [5/7]

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

◆ Motif() [6/7]

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 
)

◆ Motif() [7/7]

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

◆ ~Motif()

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

Member Function Documentation

◆ apply_check()

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

◆ backward_check()

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

◆ backward_jump()

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

References backward_jump_.

◆ build_inverted_rotamers()

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

◆ build_rotamers()

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

◆ clone()

MotifOP protocols::motifs::Motif::clone ( ) const

◆ forward_check()

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

◆ forward_jump()

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

References forward_jump_.

Referenced by print().

◆ has_path()

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

References has_path_.

◆ has_remark()

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

References has_remark_.

Referenced by print().

◆ path()

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

References path_.

◆ place_atom() [1/2]

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

References place_atom_().

◆ place_atom() [2/2]

void protocols::motifs::Motif::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

References place_atom_().

◆ place_atom_() [1/2]

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

◆ place_atom_() [2/2]

void protocols::motifs::Motif::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

◆ place_atoms() [1/2]

void protocols::motifs::Motif::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

◆ place_atoms() [2/2]

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

◆ place_atoms_() [1/2]

void protocols::motifs::Motif::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

◆ place_atoms_() [2/2]

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

◆ place_residue() [1/2]

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

◆ place_residue() [2/2]

void protocols::motifs::Motif::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

◆ place_residue_() [1/2]

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

◆ place_residue_() [2/2]

void protocols::motifs::Motif::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

◆ place_residue_helper() [1/2]

void protocols::motifs::Motif::place_residue_helper ( core::kinematics::Stub end_stub,
core::kinematics::Stub mobile_stub,
core::conformation::Residue const &  fixed,
core::conformation::Residue mobile,
bool  forward,
bool  one_three 
) const
private

◆ place_residue_helper() [2/2]

void protocols::motifs::Motif::place_residue_helper ( core::kinematics::Stub end_stub,
core::kinematics::Stub mobile_stub,
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 
) const
private

◆ print() [1/2]

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

◆ print() [2/2]

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

◆ remark()

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

References remark_.

Referenced by print().

◆ res1_atom1_index()

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

References res1_atom1_index_.

◆ res1_atom1_int()

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

WARNING res*_atom*_int() values are not consistently initialized in constructors.

References res1_atom1_int_.

◆ res1_atom1_name()

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

References res1_atom1_name_.

Referenced by print().

◆ res1_atom2_index()

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

References res1_atom2_index_.

◆ res1_atom2_int()

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

References res1_atom2_int_.

◆ res1_atom2_name()

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

References res1_atom2_name_.

Referenced by print().

◆ res1_atom3_index()

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

References res1_atom3_index_.

◆ res1_atom3_int()

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

References res1_atom3_int_.

◆ res1_atom3_name()

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

References res1_atom3_name_.

Referenced by print().

◆ res2_atom1_index()

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

References res2_atom1_index_.

◆ res2_atom1_int()

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

WARNING res*_atom*_int() values are not consistently initialized in constructors.

References res2_atom1_int_.

◆ res2_atom1_name()

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

References res2_atom1_name_.

Referenced by print().

◆ res2_atom2_index()

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

References res2_atom2_index_.

◆ res2_atom2_int()

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

References res2_atom2_int_.

◆ res2_atom2_name()

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

References res2_atom2_name_.

Referenced by print().

◆ res2_atom3_index()

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

References res2_atom3_index_.

◆ res2_atom3_int()

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

References res2_atom3_int_.

◆ res2_atom3_name()

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

References res2_atom3_name_.

Referenced by print().

◆ restype_name1()

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

References restype_name1_.

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

◆ restype_name2()

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

References restype_name2_.

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

◆ store_path()

void protocols::motifs::Motif::store_path ( std::string const &  path_in)

References has_path_, and path_.

◆ store_remark()

void protocols::motifs::Motif::store_remark ( std::string const &  remark_in)

Friends And Related Function Documentation

◆ operator<<

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

Member Data Documentation

◆ backward_jump_

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

◆ basebaseAtomIDs

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

Referenced by Motif().

◆ forward_jump_

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

◆ has_path_

bool protocols::motifs::Motif::has_path_
private

Referenced by has_path(), and store_path().

◆ has_remark_

bool protocols::motifs::Motif::has_remark_
private

Referenced by has_remark(), and store_remark().

◆ motifAtomIDs

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

Referenced by Motif().

◆ path_

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

Referenced by path(), and store_path().

◆ remark_

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

Referenced by remark(), and store_remark().

◆ res1_atom1_index_

core::Size protocols::motifs::Motif::res1_atom1_index_
private

◆ res1_atom1_int_

int protocols::motifs::Motif::res1_atom1_int_
private

Referenced by res1_atom1_int().

◆ res1_atom1_name_

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

◆ res1_atom2_index_

core::Size protocols::motifs::Motif::res1_atom2_index_
private

◆ res1_atom2_int_

int protocols::motifs::Motif::res1_atom2_int_
private

Referenced by res1_atom2_int().

◆ res1_atom2_name_

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

◆ res1_atom3_index_

core::Size protocols::motifs::Motif::res1_atom3_index_
private

◆ res1_atom3_int_

int protocols::motifs::Motif::res1_atom3_int_
private

Referenced by res1_atom3_int().

◆ res1_atom3_name_

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

◆ res2_atom1_index_

core::Size protocols::motifs::Motif::res2_atom1_index_
private

◆ res2_atom1_int_

int protocols::motifs::Motif::res2_atom1_int_
private

Referenced by Motif(), and res2_atom1_int().

◆ res2_atom1_name_

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

◆ res2_atom2_index_

core::Size protocols::motifs::Motif::res2_atom2_index_
private

◆ res2_atom2_int_

int protocols::motifs::Motif::res2_atom2_int_
private

Referenced by Motif(), and res2_atom2_int().

◆ res2_atom2_name_

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

◆ res2_atom3_index_

core::Size protocols::motifs::Motif::res2_atom3_index_
private

◆ res2_atom3_int_

int protocols::motifs::Motif::res2_atom3_int_
private

Referenced by Motif(), and res2_atom3_int().

◆ res2_atom3_name_

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

◆ restype_name1_

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

◆ restype_name2_

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

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