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protocols::motifs::SingleMotif Class Reference

#include <SingleMotif.hh>

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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, 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)
 
 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, 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)
 
 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, 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
 

Friends

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

Detailed Description

Definition at line 35 of file SingleMotif.hh.

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 
)

Definition at line 50 of file SingleMotif.cc.

protocols::motifs::SingleMotif::SingleMotif ( 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 73 of file SingleMotif.cc.

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 
)

Definition at line 140 of file SingleMotif.cc.

protocols::motifs::SingleMotif::SingleMotif ( 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 100 of file SingleMotif.cc.

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

Definition at line 123 of file SingleMotif.cc.

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

Definition at line 132 of file SingleMotif.cc.

Friends And Related Function Documentation

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

Definition at line 161 of file SingleMotif.cc.

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