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core::scoring::constraints::ConstraintIO Class Reference

#include <ConstraintIO.hh>

Inheritance diagram for core::scoring::constraints::ConstraintIO:
Inheritance graph
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Static Public Member Functions

static ConstraintSetOP read_constraints (std::string const &filename, ConstraintSetOP cst_set, pose::Pose const &pose, bool const force_pdb_info_mapping=false)
 
static ConstraintSetOP read_constraints (std::istream &data, ConstraintSetOP cst_set, pose::Pose const &pose, bool const force_pdb_info_mapping=false)
 
static void write_constraints (std::ostream &, ConstraintSet const &cst_set, core::pose::Pose const &)
 
static void write_constraints (std::string const &filename, ConstraintSet const &cst_set, core::pose::Pose const &)
 
static func::FuncFactoryget_func_factory ()
 
static ConstraintFactoryget_cst_factory ()
 
static ConstraintOP parse_atom_pair_constraint (std::istream &data, core::pose::Pose pose, bool const force_pdb_info_mapping=false)
 
static ConstraintSetOP read_constraints_new (std::string const &fname, ConstraintSetOP cset, pose::Pose const &pose, bool const force_pdb_info_mapping=false)
 
static ConstraintSetOP read_constraints_new (std::istream &data, ConstraintSetOP cset, pose::Pose const &pose, bool const force_pdb_info_mapping=false)
 
static ConstraintOP read_individual_constraint_new (std::istream &data, core::pose::Pose const &pose, func::FuncFactory const &func_factory, bool const force_pdb_info_mapping=false)
 read one individual constraint defined. More...
 
static ConstraintOP read_individual_constraint_new (std::istream &data, core::pose::Pose const &pose, func::FuncFactory const &func_factory, std::string type, bool const force_pdb_info_mapping=false)
 read one individual constraint defined. More...
 
static ConstraintOP parse_coordinate_constraint (std::istream &data, core::pose::Pose pose, bool const force_pdb_info_mapping=false)
 
static void parse_residue (pose::Pose const &pose, std::string const &residue_string, Size &residue_num, bool const force_pdb_info_mapping=false)
 
static Size parse_residue (pose::Pose const &pose, int const resnum, char const chain=0, bool const force_pdb_info_numbering=false)
 

Static Protected Member Functions

static void read_cst_bindingsites (std::istream &data, std::string &next_section, ConstraintSet &, pose::Pose const &, bool const force_pdb_info_mapping=false)
 
static void read_cst_atom_pairs (std::istream &data, std::string &next_section, ConstraintSet &, pose::Pose const &, bool const force_pdb_info_mapping=false)
 
static void read_cst_coordinates (std::istream &data, std::string &next_section, ConstraintSet &, pose::Pose const &, bool const force_pdb_info_mapping=false)
 
static void read_cst_angles (std::istream &data, std::string &next_section, ConstraintSet &, pose::Pose const &, bool const force_pdb_info_mapping=false)
 

Private Member Functions

 ConstraintIO ()
 

Private Attributes

func::FuncFactory func_factory_
 

Friends

class utility::SingletonBase< ConstraintIO >
 

Constructor & Destructor Documentation

core::scoring::constraints::ConstraintIO::ConstraintIO ( )
inlineprivate

Member Function Documentation

ConstraintFactory & core::scoring::constraints::ConstraintIO::get_cst_factory ( )
static
func::FuncFactory & core::scoring::constraints::ConstraintIO::get_func_factory ( )
static
ConstraintOP core::scoring::constraints::ConstraintIO::parse_atom_pair_constraint ( std::istream &  data,
core::pose::Pose  pose,
bool const  force_pdb_info_mapping = false 
)
static
ConstraintOP core::scoring::constraints::ConstraintIO::parse_coordinate_constraint ( std::istream &  data,
core::pose::Pose  pose,
bool const  force_pdb_info_mapping = false 
)
static
void core::scoring::constraints::ConstraintIO::parse_residue ( pose::Pose const &  pose,
std::string const &  residue_string,
Size residue_num,
bool const  force_pdb_info_mapping = false 
)
static
Size core::scoring::constraints::ConstraintIO::parse_residue ( pose::Pose const &  pose,
int const  resnum,
char const  chain = 0,
bool const  force_pdb_info_numbering = false 
)
static
ConstraintSetOP core::scoring::constraints::ConstraintIO::read_constraints ( std::string const &  fname,
ConstraintSetOP  cset,
pose::Pose const &  pose,
bool const  force_pdb_info_mapping = false 
)
static

All the heavy lifting is done by read_constraints( istream &, ConstraintSetOP, Pose const & ), or by read_constraints_new( istream &, ConstraintSetOP, Pose const & ), but the logic for deciding which of two execution paths to follow that lives inside read_constraints( isteam &, ... ) will not work if given an izstream constructed from a zipped file. SO instead, we check the file format of the input constraint file here and then rewind to the beginning of the file using the izstream seek_beg() function.

References core::scoring::constraints::get_section_name(), read_constraints_new(), protocols::sparta::section(), and core::scoring::constraints::tr().

Referenced by protocols::ddg::ddGMover::setup_constraints().

ConstraintSetOP core::scoring::constraints::ConstraintIO::read_constraints ( std::istream &  data,
ConstraintSetOP  cst_set,
pose::Pose const &  pose,
bool const  force_pdb_info_mapping = false 
)
static
ConstraintSetOP core::scoring::constraints::ConstraintIO::read_constraints_new ( std::string const &  fname,
ConstraintSetOP  cset,
pose::Pose const &  pose,
bool const  force_pdb_info_mapping = false 
)
static

read in constraints with new format from a file

References core::scoring::constraints::tr().

Referenced by read_constraints().

ConstraintSetOP core::scoring::constraints::ConstraintIO::read_constraints_new ( std::istream &  data,
ConstraintSetOP  cset,
pose::Pose const &  pose,
bool const  force_pdb_info_mapping = false 
)
static
void core::scoring::constraints::ConstraintIO::read_cst_angles ( std::istream &  data,
std::string &  next_section,
ConstraintSet cst_set,
pose::Pose const &  pose,
bool const  force_pdb_info_mapping = false 
)
staticprotected
void core::scoring::constraints::ConstraintIO::read_cst_atom_pairs ( std::istream &  data,
std::string &  next_section,
ConstraintSet cst_set,
pose::Pose const &  pose,
bool const  force_pdb_info_mapping = false 
)
staticprotected
void core::scoring::constraints::ConstraintIO::read_cst_bindingsites ( std::istream &  data,
std::string &  next_section,
ConstraintSet cst_set,
pose::Pose const &  pose,
bool const  force_pdb_info_mapping = false 
)
staticprotected
void core::scoring::constraints::ConstraintIO::read_cst_coordinates ( std::istream &  data,
std::string &  next_section,
ConstraintSet cst_set,
pose::Pose const &  pose,
bool const  force_pdb_info_mapping = false 
)
staticprotected
ConstraintOP core::scoring::constraints::ConstraintIO::read_individual_constraint_new ( std::istream &  data,
core::pose::Pose const &  pose,
func::FuncFactory const &  func_factory,
bool const  force_pdb_info_mapping = false 
)
static

read one individual constraint defined.

read in each individual constraint. The constraints could be single-line ones such as AtomPair, Angle and Diehedral, or multi-line ones such as Multiconstraint and Ambiguous. Return owing pointer of the constraint if read in successfully, otherwise return NULL. Identify the type of constraint and call each constraint's read_def function to finish reading. Skip lines beginning with '#' or '
' May be called recursively in the case of Multiconstraint and AmbiguousConstraint.

Note
the istream data should point to the beginning of a line when this function is called.

References core::pack::dunbrack::c, and core::scoring::constraints::tr().

Referenced by protocols::constraint_movers::CstInfoMover::get_constraints_from_file(), read_constraints_new(), core::scoring::constraints::AmbiguousConstraint::read_def(), and core::scoring::constraints::KofNConstraint::read_def().

ConstraintOP core::scoring::constraints::ConstraintIO::read_individual_constraint_new ( std::istream &  data,
core::pose::Pose const &  pose,
func::FuncFactory const &  func_factory,
std::string  type,
bool const  force_pdb_info_mapping = false 
)
static
void core::scoring::constraints::ConstraintIO::write_constraints ( std::ostream &  out,
ConstraintSet const &  cst_set,
core::pose::Pose const &  pose 
)
static
void core::scoring::constraints::ConstraintIO::write_constraints ( std::string const &  filename,
ConstraintSet const &  cst_set,
core::pose::Pose const &  pose 
)
static

References write_constraints().

Friends And Related Function Documentation

friend class utility::SingletonBase< ConstraintIO >
friend

Member Data Documentation

func::FuncFactory core::scoring::constraints::ConstraintIO::func_factory_
private

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