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

#include <ConstraintIO.hh>

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Static Public Member Functions

static ConstraintIO * get_instance ()
 
static ConstraintSetOP read_constraints (std::string const &filename, ConstraintSetOP cst_set, pose::Pose const &pose)
 
static ConstraintSetOP read_constraints (std::istream &data, ConstraintSetOP cst_set, pose::Pose const &pose)
 
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 FuncFactory & get_func_factory (void)
 
static ConstraintFactory & get_cst_factory (void)
 
static ConstraintOP parse_atom_pair_constraint (std::istream &data, core::pose::Pose pose)
 
static ConstraintSetOP read_constraints_new (std::string const &fname, ConstraintSetOP cset, pose::Pose const &pose)
 
static ConstraintSetOP read_constraints_new (std::istream &data, ConstraintSetOP cset, pose::Pose const &pose)
 
static ConstraintOP read_individual_constraint_new (std::istream &data, core::pose::Pose const &pose, FuncFactory const &func_factory)
 read one individual constraint defined. More...
 
static ConstraintOP read_individual_constraint_new (std::istream &data, core::pose::Pose const &pose, FuncFactory const &func_factory, std::string type)
 read one individual constraint defined. More...
 
static ConstraintOP parse_coordinate_constraint (std::istream &data, core::pose::Pose pose)
 
static void parse_residue (pose::Pose const &pose, std::string const residue_string, Size &residue_num)
 

Static Protected Member Functions

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

Private Member Functions

 ConstraintIO ()
 

Static Private Attributes

static ConstraintIO * instance_ = 0
 
static FuncFactory func_factory_
 

Detailed Description

Definition at line 42 of file ConstraintIO.hh.

Constructor & Destructor Documentation

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

Definition at line 114 of file ConstraintIO.hh.

Referenced by get_instance().

Member Function Documentation

ConstraintFactory & core::scoring::constraints::ConstraintIO::get_cst_factory ( void  )
static

Definition at line 71 of file ConstraintIO.cc.

References core::scoring::constraints::ConstraintFactory::get_instance().

Referenced by read_individual_constraint_new().

FuncFactory & core::scoring::constraints::ConstraintIO::get_func_factory ( void  )
static

Definition at line 67 of file ConstraintIO.cc.

References func_factory_.

Referenced by protocols::abinitio::common_setup(), read_constraints_new(), read_cst_bindingsites(), protocols::topology_broker::CoordConstraintClaimer::read_tag(), and protocols::abinitio::AbrelaxApplication::setup().

ConstraintIO * core::scoring::constraints::ConstraintIO::get_instance ( )
static

Definition at line 60 of file ConstraintIO.cc.

References ConstraintIO(), and instance_.

Referenced by protocols::abinitio::Template::_read_constraints(), protocols::topology_broker::ConstraintClaimer::add_constraints(), protocols::abinitio::AbrelaxApplication::add_constraints(), core::scoring::constraints::add_constraints_from_cmdline_to_pose(), protocols::dna::add_constraints_from_file(), core::scoring::constraints::add_fa_constraints_from_cmdline_to_pose(), protocols::simple_moves::ConstraintSetMover::apply(), protocols::abinitio::AbrelaxApplication::fold(), protocols::forge::constraints::ConstraintFileRCG::generate_remodel_constraints(), protocols::loophash::MPI_LoopHashRefine::load_structures_from_cmdline_into_library(), protocols::constraints_additional::ConstraintEvaluator::prepare_pose(), protocols::topology_broker::CoordConstraintClaimer::read_constraints_from_file(), core::scoring::constraints::MultiConstraint::read_def(), protocols::relax::WorkUnit_BatchRelax::run(), protocols::medal::setup_atom_pair_constraints(), protocols::hybridization::setup_centroid_constraints(), protocols::swa::StepWisePoseSetup::setup_constraints(), and protocols::hybridization::setup_fullatom_constraints().

ConstraintOP core::scoring::constraints::ConstraintIO::parse_atom_pair_constraint ( std::istream &  data,
core::pose::Pose  pose 
)
static

Definition at line 140 of file ConstraintIO.cc.

References core::chemical::ResidueType::atom_index(), func_factory_, core::scoring::constraints::FuncFactory::func_types_, parse_residue(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), and core::scoring::constraints::tr().

ConstraintOP core::scoring::constraints::ConstraintIO::parse_coordinate_constraint ( std::istream &  data,
core::pose::Pose  pose 
)
static

Definition at line 247 of file ConstraintIO.cc.

References core::chemical::ResidueType::atom_index(), func_factory_, core::scoring::constraints::FuncFactory::func_types_, parse_residue(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), and core::scoring::constraints::tr().

void core::scoring::constraints::ConstraintIO::parse_residue ( pose::Pose const &  pose,
std::string const  residue_string,
Size &  residue_num 
)
static

Definition at line 676 of file ConstraintIO.cc.

References core::pose::Pose::pdb_info().

Referenced by parse_atom_pair_constraint(), parse_coordinate_constraint(), read_cst_angles(), read_cst_atom_pairs(), core::scoring::constraints::AngleConstraint::read_def(), core::scoring::constraints::DistancePairConstraint::read_def(), core::scoring::constraints::DihedralPairConstraint::read_def(), core::scoring::constraints::DihedralConstraint::read_def(), core::scoring::constraints::SiteConstraint::read_def(), core::scoring::constraints::CoordinateConstraint::read_def(), core::scoring::constraints::NamedAtomPairConstraint::read_def(), core::scoring::constraints::LocalCoordinateConstraint::read_def(), core::scoring::constraints::AtomPairConstraint::read_def(), and core::scoring::constraints::AmbiguousNMRDistanceConstraint::read_def().

ConstraintSetOP core::scoring::constraints::ConstraintIO::read_constraints ( std::string const &  fname,
ConstraintSetOP  cset,
pose::Pose const &  pose 
)
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.

Definition at line 510 of file ConstraintIO.cc.

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

Referenced by protocols::abinitio::Template::_read_constraints(), protocols::topology_broker::ConstraintClaimer::add_constraints(), protocols::abinitio::AbrelaxApplication::add_constraints(), core::scoring::constraints::add_constraints_from_cmdline_to_pose(), core::scoring::constraints::add_fa_constraints_from_cmdline_to_pose(), protocols::simple_moves::ConstraintSetMover::apply(), protocols::abinitio::AbrelaxApplication::fold(), protocols::forge::constraints::ConstraintFileRCG::generate_remodel_constraints(), protocols::loophash::MPI_LoopHashRefine::load_structures_from_cmdline_into_library(), protocols::constraints_additional::ConstraintEvaluator::prepare_pose(), protocols::topology_broker::CoordConstraintClaimer::read_constraints_from_file(), protocols::relax::WorkUnit_BatchRelax::run(), protocols::medal::setup_atom_pair_constraints(), protocols::swa::StepWisePoseSetup::setup_constraints(), and protocols::ddg::ddGMover::setup_constraints().

ConstraintSetOP core::scoring::constraints::ConstraintIO::read_constraints ( std::istream &  data,
ConstraintSetOP  cst_set,
pose::Pose const &  pose 
)
static

Definition at line 461 of file ConstraintIO.cc.

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

ConstraintSetOP core::scoring::constraints::ConstraintIO::read_constraints_new ( std::string const &  fname,
ConstraintSetOP  cset,
pose::Pose const &  pose 
)
static

read in constraints with new format from a file

Definition at line 537 of file ConstraintIO.cc.

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

Referenced by protocols::dna::add_constraints_from_file(), read_constraints(), protocols::hybridization::setup_centroid_constraints(), and protocols::hybridization::setup_fullatom_constraints().

ConstraintSetOP core::scoring::constraints::ConstraintIO::read_constraints_new ( std::istream &  data,
ConstraintSetOP  cset,
pose::Pose const &  pose 
)
static

Definition at line 550 of file ConstraintIO.cc.

References get_func_factory(), read_individual_constraint_new(), and core::scoring::constraints::tr().

void core::scoring::constraints::ConstraintIO::read_cst_angles ( std::istream &  data,
std::string &  next_section,
ConstraintSet &  cst_set,
pose::Pose const &  pose 
)
staticprotected

Definition at line 293 of file ConstraintIO.cc.

References core::scoring::constraints::ConstraintSet::add_constraint(), core::chemical::ResidueType::atom_index(), func_factory_, core::scoring::constraints::FuncFactory::func_types_, parse_residue(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), and core::scoring::constraints::tr().

Referenced by read_constraints().

void core::scoring::constraints::ConstraintIO::read_cst_atom_pairs ( std::istream &  data,
std::string &  next_section,
ConstraintSet &  cst_set,
pose::Pose const &  pose 
)
staticprotected

Definition at line 81 of file ConstraintIO.cc.

References core::scoring::constraints::ConstraintSet::add_constraint(), core::chemical::ResidueType::atom_index(), func_factory_, core::scoring::constraints::FuncFactory::func_types_, core::chemical::ResidueType::has_atom_name(), parse_residue(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), and core::scoring::constraints::tr().

Referenced by read_constraints().

void core::scoring::constraints::ConstraintIO::read_cst_bindingsites ( std::istream &  data,
std::string &  next_section,
ConstraintSet &  cst_set,
pose::Pose const &  pose 
)
staticprotected

Definition at line 420 of file ConstraintIO.cc.

References core::scoring::constraints::ConstraintSet::add_constraint(), get_func_factory(), core::scoring::constraints::ConstraintFactory::get_instance(), core::scoring::constraints::ConstraintFactory::newConstraint(), and core::scoring::constraints::tr().

Referenced by read_constraints().

void core::scoring::constraints::ConstraintIO::read_cst_coordinates ( std::istream &  data,
std::string &  next_section,
ConstraintSet &  cst_set,
pose::Pose const &  pose 
)
staticprotected

Definition at line 182 of file ConstraintIO.cc.

References core::scoring::constraints::ConstraintSet::add_constraint(), core::chemical::ResidueType::atom_index(), func_factory_, core::scoring::constraints::FuncFactory::func_types_, core::chemical::ResidueType::has_atom_name(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), and core::scoring::constraints::tr().

Referenced by read_constraints().

ConstraintOP core::scoring::constraints::ConstraintIO::read_individual_constraint_new ( std::istream &  data,
core::pose::Pose const &  pose,
FuncFactory const &  func_factory 
)
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.

Definition at line 623 of file ConstraintIO.cc.

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

Referenced by read_constraints_new(), core::scoring::constraints::AmbiguousConstraint::read_def(), core::scoring::constraints::KofNConstraint::read_def(), and core::scoring::constraints::MultiConstraint::read_def().

ConstraintOP core::scoring::constraints::ConstraintIO::read_individual_constraint_new ( std::istream &  data,
core::pose::Pose const &  pose,
FuncFactory const &  func_factory,
std::string  type 
)
static

read one individual constraint defined.

Definition at line 573 of file ConstraintIO.cc.

References get_cst_factory(), core::scoring::constraints::ConstraintFactory::newConstraint(), and core::scoring::constraints::tr().

void core::scoring::constraints::ConstraintIO::write_constraints ( std::ostream &  out,
ConstraintSet const &  cst_set,
core::pose::Pose const &  pose 
)
static

Definition at line 650 of file ConstraintIO.cc.

References core::scoring::constraints::ConstraintSet::show_definition().

Referenced by protocols::noesy_assign::NoesyModule::generate_constraint_files(), and write_constraints().

void core::scoring::constraints::ConstraintIO::write_constraints ( std::string const &  filename,
ConstraintSet const &  cst_set,
core::pose::Pose const &  pose 
)
static

Definition at line 655 of file ConstraintIO.cc.

References write_constraints().

Member Data Documentation

FuncFactory core::scoring::constraints::ConstraintIO::func_factory_
staticprivate

Definition at line 116 of file ConstraintIO.hh.

Referenced by get_func_factory(), parse_atom_pair_constraint(), parse_coordinate_constraint(), read_cst_angles(), read_cst_atom_pairs(), and read_cst_coordinates().

ConstraintIO * core::scoring::constraints::ConstraintIO::instance_ = 0
staticprivate

Definition at line 114 of file ConstraintIO.hh.

Referenced by get_instance().

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