#include <ConstraintIO.hh>

Static Public Member Functions
static ConstraintIO *	get_instance ()
	static function to get the instance of ( pointer to) this singleton class More...

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 func::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, func::FuncFactory const &func_factory)
	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)
	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 Member Functions
static ConstraintIO *	create_singleton_instance ()
	private singleton creation function to be used with utility::thread::threadsafe_singleton More...

Static Private Attributes
static ConstraintIO *	instance_ = 0

static func::FuncFactory	func_factory_

Constructor & Destructor Documentation

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

inlineprivate

Referenced by create_singleton_instance().

Member Function Documentation

ConstraintIO * core::scoring::constraints::ConstraintIO::create_singleton_instance ( )

staticprivate

private singleton creation function to be used with utility::thread::threadsafe_singleton

References ConstraintIO().

Referenced by get_instance().

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

static

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

Referenced by read_individual_constraint_new().

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

static

References func_factory_.

Referenced by read_constraints_new(), and read_cst_bindingsites().

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

static

static function to get the instance of ( pointer to) this singleton class

References create_singleton_instance(), instance_, and utility::thread::safely_create_singleton().

Referenced by core::scoring::constraints::add_constraints_from_cmdline_to_pose(), core::scoring::constraints::add_fa_constraints_from_cmdline_to_pose(), core::scoring::constraints::merge_constraints_from_cmdline_to_pose(), core::scoring::constraints::merge_fa_constraints_from_cmdline_to_pose(), and core::scoring::constraints::MultiConstraint::read_def().

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

static

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

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

static

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

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

static

References chain, and core::pose::Pose::pdb_info().

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.

References core::scoring::constraints::get_section_name(), getline(), read_constraints_new(), core::scoring::constraints::tr, and utility_exit_with_message.

Referenced by core::scoring::constraints::add_constraints_from_cmdline_to_pose(), core::scoring::constraints::add_fa_constraints_from_cmdline_to_pose(), core::scoring::constraints::merge_constraints_from_cmdline_to_pose(), and core::scoring::constraints::merge_fa_constraints_from_cmdline_to_pose().

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

static

References core::scoring::constraints::get_section_name(), getline(), read_constraints_new(), read_cst_angles(), read_cst_atom_pairs(), read_cst_bindingsites(), read_cst_coordinates(), core::scoring::constraints::tr, and utility_exit_with_message.

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

References core::scoring::constraints::tr, and utility_exit_with_message.

Referenced by read_constraints().

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

static

References core::scoring::constraints::ConstraintSet::add_constraint(), 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

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

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

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

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

References core::scoring::constraints::ConstraintSet::add_constraint(), get_func_factory(), core::scoring::constraints::ConstraintFactory::get_instance(), getline(), 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

References core::scoring::constraints::ConstraintSet::add_constraint(), core::chemical::ResidueType::atom_index(), func_factory_, core::scoring::func::FuncFactory::func_types_, getline(), core::chemical::ResidueType::has(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), core::scoring::constraints::tr, type, and utility_exit_with_message.

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
	)

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, tag, 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,
		func::FuncFactory const &	func_factory,
		std::string	type
	)

static

read one individual constraint defined.

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

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
	)