#include <ConstraintIO.hh>

Inheritance diagram for core::scoring::constraints::ConstraintIO:

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::FuncFactory &	get_func_factory ()

static ConstraintFactory &	get_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

Referenced by read_individual_constraint_new().

func::FuncFactory & core::scoring::constraints::ConstraintIO::get_func_factory ( )

static

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

ConstraintOP core::scoring::constraints::ConstraintIO::parse_atom_pair_constraint	(	std::istream &	data,
		core::pose::Pose	pose,
		bool const	force_pdb_info_mapping = `false`
	)

static

References core::chemical::ResidueType::atom_index(), parse_residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), and core::scoring::constraints::tr().

ConstraintOP core::scoring::constraints::ConstraintIO::parse_coordinate_constraint	(	std::istream &	data,
		core::pose::Pose	pose,
		bool const	force_pdb_info_mapping = `false`
	)

static

References core::chemical::ResidueType::atom_index(), parse_residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), and core::scoring::constraints::tr().

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

a value of 0 for the chain means to ignore PDBInfo settings, and treat the resnum as Rosetta/Pose numbering.

References core::pose::full_model_info::const_full_model_info(), core::pose::full_model_info::full_model_info_defined(), core::pose::full_model_info::FullModelInfo::full_to_sub(), core::pose::Pose::pdb_info(), core::pose::Pose::size(), core::id::to_string(), and core::scoring::constraints::tr().

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

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,
		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

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,
		bool const	force_pdb_info_mapping = `false`
	)

staticprotected

References core::scoring::constraints::ConstraintSet::add_constraint(), core::chemical::ResidueType::atom_index(), parse_residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), 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,
		bool const	force_pdb_info_mapping = `false`
	)

staticprotected

References core::scoring::constraints::ConstraintSet::add_constraint(), core::chemical::ResidueType::atom_index(), core::chemical::ResidueType::has(), parse_residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), 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,
		bool const	force_pdb_info_mapping = `false`
	)

staticprotected

References core::scoring::constraints::ConstraintSet::add_constraint(), get_func_factory(), 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,
		bool const	force_pdb_info_mapping = `false`
	)

staticprotected

References core::scoring::constraints::ConstraintSet::add_constraint(), core::chemical::ResidueType::atom_index(), core::chemical::ResidueType::has(), parse_residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), 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,
		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

read one individual constraint defined.

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

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

Referenced by write_constraints().

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:

src/core/scoring/constraints/ConstraintIO.hh
src/core/scoring/constraints/ConstraintIO.cc

Static Public Member Functions

Static Protected Member Functions

Private Member Functions

Private Attributes

Friends

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation