Rosetta 3.4
Public Member Functions | Friends
protocols::motifs::Motif Class Reference

#include <Motif.hh>

Inheritance diagram for protocols::motifs::Motif:
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Collaboration diagram for protocols::motifs::Motif:
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List of all members.

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 void generate_atom_ints ()
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, Motif const &mot)

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

Member Function Documentation

bool protocols::motifs::Motif::apply_check ( core::pose::Pose const &  pose,
Size const  pos 
) const [virtual]
bool protocols::motifs::Motif::backward_check ( core::conformation::Residue const &  check_res) const [virtual]
core::kinematics::Jump const& protocols::motifs::Motif::backward_jump ( ) const [inline]
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]
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]
MotifOP protocols::motifs::Motif::clone ( ) const
bool protocols::motifs::Motif::forward_check ( core::conformation::Residue const &  check_res) const [virtual]
core::kinematics::Jump const& protocols::motifs::Motif::forward_jump ( ) const [inline]

Referenced by print().

void protocols::motifs::Motif::generate_atom_ints ( ) [virtual]
bool protocols::motifs::Motif::has_path ( ) const [inline]
bool protocols::motifs::Motif::has_remark ( ) const [inline]

Referenced by print().

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

References place_atom_().

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_().

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]
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]
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]
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]
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]
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]
void protocols::motifs::Motif::place_residue ( core::conformation::Residue const &  fixed,
core::conformation::Residue mobile,
bool  one_three = true 
) const [virtual]
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]
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]
void protocols::motifs::Motif::place_residue_ ( core::conformation::Residue const &  fixed,
core::conformation::Residue mobile,
bool  forward,
bool  one_three = true 
) const [virtual]
void protocols::motifs::Motif::print ( std::ostream &  os) const [virtual]
std::string protocols::motifs::Motif::print ( ) const [virtual]
std::string const& protocols::motifs::Motif::remark ( ) const [inline]

Referenced by print().

Size const& protocols::motifs::Motif::res1_atom1_index ( ) const [inline]

Referenced by generate_atom_ints().

int const& protocols::motifs::Motif::res1_atom1_int ( ) const [inline]
std::string const& protocols::motifs::Motif::res1_atom1_name ( ) const [inline]

Referenced by print().

Size const& protocols::motifs::Motif::res1_atom2_index ( ) const [inline]

Referenced by generate_atom_ints().

int const& protocols::motifs::Motif::res1_atom2_int ( ) const [inline]
std::string const& protocols::motifs::Motif::res1_atom2_name ( ) const [inline]

Referenced by print().

Size const& protocols::motifs::Motif::res1_atom3_index ( ) const [inline]

Referenced by generate_atom_ints().

int const& protocols::motifs::Motif::res1_atom3_int ( ) const [inline]
std::string const& protocols::motifs::Motif::res1_atom3_name ( ) const [inline]

Referenced by print().

Size const& protocols::motifs::Motif::res2_atom1_index ( ) const [inline]
int const& protocols::motifs::Motif::res2_atom1_int ( ) const [inline]
std::string const& protocols::motifs::Motif::res2_atom1_name ( ) const [inline]

Referenced by print().

Size const& protocols::motifs::Motif::res2_atom2_index ( ) const [inline]
int const& protocols::motifs::Motif::res2_atom2_int ( ) const [inline]
std::string const& protocols::motifs::Motif::res2_atom2_name ( ) const [inline]

Referenced by print().

Size const& protocols::motifs::Motif::res2_atom3_index ( ) const [inline]
int const& protocols::motifs::Motif::res2_atom3_int ( ) const [inline]
std::string const& protocols::motifs::Motif::res2_atom3_name ( ) const [inline]

Referenced by print().

std::string const& protocols::motifs::Motif::restype_name1 ( ) const [inline]
std::string const& protocols::motifs::Motif::restype_name2 ( ) const [inline]
void protocols::motifs::Motif::store_path ( std::string const &  path_in)
void protocols::motifs::Motif::store_remark ( std::string const &  remark_in)

Friends And Related Function Documentation

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

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