#include <EnzConstraintIO.hh>

Public Member Functions
	EnzConstraintIO (core::chemical::ResidueTypeSetCAP src_restype_set)
	@ brief constructor for EnzConstraintIO class, builds up function types More...

virtual	~EnzConstraintIO ()

void	read_enzyme_cstfile (std::string fname)
	reads the enzyme cstfile and for each block of residue residue constraints, creates a new More...

toolbox::match_enzdes_util::MatchConstraintFileInfoListCOP	mcfi_list (core::Size block) const

core::Size	num_mcfi_lists () const

void	add_constraints_to_pose (core::pose::Pose &pose, core::scoring::ScoreFunctionCOP scofx, bool accept_blocks_missing_header)

void	add_constraints_to_pose_for_block_without_clearing_and_header_processing (core::pose::Pose &pose, core::scoring::ScoreFunctionCOP scofx, core::Size cst_block) const
	BE CAREFUL when using this function, it generates constraints. More...

void	add_pregenerated_constraints_to_pose (core::pose::Pose &pose, core::scoring::ScoreFunctionCOP scofx) const
	convenience function that will add constraints to the pose if they have More...

void	remove_constraints_from_pose (core::pose::Pose &pose, bool const keep_covalent, bool const fail_on_constraints_missing) const

void	remove_constraints_from_pose_for_block (core::pose::Pose &pose, core::Size cst_block, bool const fail_on_constraints_missing) const

void	remove_position_from_template_res_for_block (core::pose::Pose &pose, core::Size pos, core::Size cst_block) const

void	remove_position_from_template_res (core::pose::Pose &pose, core::Size pos) const

void	process_pdb_header (core::pose::Pose &pose, bool accept_missing_blocks)
	reads the residue numbers that the constraints will be applied to. More...

bool	contains_position (core::pose::Pose const &pose, core::Size const seqpos) const
	are constraints specified for this position? More...

bool	is_backbone_only_cst (core::pose::Pose const &pose, core::Size const seqpos) const
	are the constraints specified at this position mediated through backbone interactions only? More...

void	update_pdb_remarks_for_backbone_params (core::pose::Pose &pose) const

utility::vector1< std::string >	allowed_res_name3_at_position (core::pose::Pose const &pose, core::Size const seqpos) const

void	show_cst_definitions () const

void	remap_resid (core::id::SequenceMapping const &smap)
	changing the constrained residues if the sequence length changes More...

void	set_position_for_missing_res_in_parameter_block (core::pose::Pose &pose, core::Size cst_block, core::Size respos) const

void	clear_active_pose_constraints_for_block (core::pose::Pose &pose, core::Size cst_block) const

void	set_external_position_for_resA_in_parameter_block (core::Size cst_block, core::Size respos)

void	set_external_position_for_resB_in_parameter_block (core::Size cst_block, core::Size respos)

EnzConstraintParametersCOP	enz_cst_params (core::Size block) const

utility::vector1 < EnzConstraintParametersCOP >	enz_cst_params_missing_in_pose (core::pose::Pose const &pose) const

utility::vector1< core::Size >	ordered_constrained_positions (core::pose::Pose const &pose) const

core::Size	mcfi_lists_size () const

core::Size	enz_cst_params_size ()

utility::vector1< std::pair < core::Size, core::Size > > const &	target_downstream_res () const

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

Protected Attributes
utility::vector1 < EnzConstraintParametersOP >	cst_pairs_

Private Member Functions
void	generate_pose_specific_data (core::pose::Pose &pose, core::scoring::ScoreFunctionCOP scofx) const
	prepares the class for reading in data from a pose/pdb More...

void	generate_pose_specific_data_for_block (core::pose::Pose &pose, core::scoring::ScoreFunctionCOP scofx, core::Size cst_block) const

void	determine_target_downstream_res ()

Static Private Member Functions
static EnzConstraintIO *	create_singleton_instance ()
	private singleton creation function to be used with utility::thread::threadsafe_singleton More...

Private Attributes
utility::vector1 < toolbox::match_enzdes_util::MatchConstraintFileInfoListOP >	mcfi_lists_

utility::vector1< std::pair < core::Size, core::Size > >	target_downstream_res_

core::chemical::ResidueTypeSetCAP	restype_set_

Static Private Attributes
static EnzConstraintIO *	generic_instance_

Constructor & Destructor Documentation

protocols::toolbox::match_enzdes_util::EnzConstraintIO::EnzConstraintIO ( core::chemical::ResidueTypeSetCAP src_restype_set )

@ brief constructor for EnzConstraintIO class, builds up function types

References cst_pairs_, mcfi_lists_, and restype_set_.

Referenced by create_singleton_instance().

protocols::toolbox::match_enzdes_util::EnzConstraintIO::~EnzConstraintIO ( )

virtual

Member Function Documentation

void protocols::toolbox::match_enzdes_util::EnzConstraintIO::add_constraints_to_pose	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunctionCOP	scofx,
		bool	accept_blocks_missing_header
	)

References add_constraints_to_pose_for_block_without_clearing_and_header_processing(), cst_pairs_, basic::options::OptionKeys::enzdes::enz_debug, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), basic::options::option, process_pdb_header(), remove_constraints_from_pose(), show_cst_definitions(), and protocols::toolbox::match_enzdes_util::tr.

void protocols::toolbox::match_enzdes_util::EnzConstraintIO::add_constraints_to_pose_for_block_without_clearing_and_header_processing	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunctionCOP	scofx,
		core::Size	cst_block
	)		const

BE CAREFUL when using this function, it generates constraints.

without clearing the internal data structures and reading in the information in the pdb REMARKs if you're unsure use the above one

References core::pose::Pose::add_constraints(), generate_pose_specific_data_for_block(), and protocols::toolbox::match_enzdes_util::get_enzdes_observer().

Referenced by add_constraints_to_pose(), add_pregenerated_constraints_to_pose(), and protocols::forge::remodel::RemodelEnzdesCstModule::apply().

void protocols::toolbox::match_enzdes_util::EnzConstraintIO::add_pregenerated_constraints_to_pose	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunctionCOP	scofx
	)		const

convenience function that will add constraints to the pose if they have

been previously generated. BE CAREFUL when using this function, it relies on the pose having the same residue types at the same constrained positions as in the pose that was originally used to generate the constraints. If in doubt, it's safer to regenerate the constraints before adding (i.e. use the above add_constraints_to_pose function.)

References core::pose::Pose::add_constraint(), add_constraints_to_pose_for_block_without_clearing_and_header_processing(), core::pose::Pose::constraint_set(), cst_pairs_, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), protocols::toolbox::match_enzdes_util::tr, and utility_exit_with_message.

utility::vector1< std::string > protocols::toolbox::match_enzdes_util::EnzConstraintIO::allowed_res_name3_at_position	(	core::pose::Pose const &	pose,
		core::Size const	seqpos
	)		const

References cst_pairs_, and protocols::toolbox::match_enzdes_util::get_enzdes_observer().

void protocols::toolbox::match_enzdes_util::EnzConstraintIO::clear_active_pose_constraints_for_block	(	core::pose::Pose &	pose,
		core::Size	cst_block
	)		const

References cst_pairs_, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), and runtime_assert.

bool protocols::toolbox::match_enzdes_util::EnzConstraintIO::contains_position	(	core::pose::Pose const &	pose,
		core::Size const	seqpos
	)		const

are constraints specified for this position?

References protocols::toolbox::match_enzdes_util::get_enzdes_observer().

EnzConstraintIO * protocols::toolbox::match_enzdes_util::EnzConstraintIO::create_singleton_instance ( )

staticprivate

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

References basic::options::OptionKeys::enzdes::cstfile, EnzConstraintIO(), FA_STANDARD, basic::options::option, and residue_type_set.

Referenced by get_instance().

void protocols::toolbox::match_enzdes_util::EnzConstraintIO::determine_target_downstream_res ( )

private

References mcfi_lists_, and target_downstream_res_.

Referenced by read_enzyme_cstfile().

EnzConstraintParametersCOP protocols::toolbox::match_enzdes_util::EnzConstraintIO::enz_cst_params ( core::Size block ) const

References cst_pairs_.

utility::vector1< EnzConstraintParametersCOP > protocols::toolbox::match_enzdes_util::EnzConstraintIO::enz_cst_params_missing_in_pose ( core::pose::Pose const & pose ) const

References cst_pairs_.

core::Size protocols::toolbox::match_enzdes_util::EnzConstraintIO::enz_cst_params_size ( )

inline

References cst_pairs_.

void protocols::toolbox::match_enzdes_util::EnzConstraintIO::generate_pose_specific_data	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunctionCOP	scofx
	)		const

private

prepares the class for reading in data from a pose/pdb

References cst_pairs_, and generate_pose_specific_data_for_block().

void protocols::toolbox::match_enzdes_util::EnzConstraintIO::generate_pose_specific_data_for_block	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunctionCOP	scofx,
		core::Size	cst_block
	)		const

private

References cst_pairs_, and protocols::toolbox::match_enzdes_util::tr.

Referenced by add_constraints_to_pose_for_block_without_clearing_and_header_processing(), and generate_pose_specific_data().

EnzConstraintIO * protocols::toolbox::match_enzdes_util::EnzConstraintIO::get_instance ( )

static

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

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

bool protocols::toolbox::match_enzdes_util::EnzConstraintIO::is_backbone_only_cst	(	core::pose::Pose const &	pose,
		core::Size const	seqpos
	)		const

are the constraints specified at this position mediated through backbone interactions only?

References cst_pairs_, and protocols::toolbox::match_enzdes_util::get_enzdes_observer().

toolbox::match_enzdes_util::MatchConstraintFileInfoListCOP protocols::toolbox::match_enzdes_util::EnzConstraintIO::mcfi_list ( core::Size block ) const

References mcfi_lists_, and runtime_assert.

Referenced by protocols::forge::remodel::RemodelEnzdesCstModule::apply(), and protocols::match::Matcher::initialize_from_file().

core::Size protocols::toolbox::match_enzdes_util::EnzConstraintIO::mcfi_lists_size ( ) const

References mcfi_lists_.

Referenced by protocols::match::Matcher::initialize_from_file().

core::Size protocols::toolbox::match_enzdes_util::EnzConstraintIO::num_mcfi_lists ( ) const

inline

References mcfi_lists_.

utility::vector1< core::Size > protocols::toolbox::match_enzdes_util::EnzConstraintIO::ordered_constrained_positions ( core::pose::Pose const & pose ) const

References protocols::toolbox::match_enzdes_util::get_enzdes_observer().

void protocols::toolbox::match_enzdes_util::EnzConstraintIO::process_pdb_header	(	core::pose::Pose &	pose,
		bool	accept_missing_blocks
	)

reads the residue numbers that the constraints will be applied to.

References cst_pairs_, utility::exit(), protocols::toolbox::match_enzdes_util::get_enzdes_observer(), mcfi_lists_, core::conformation::Residue::name3(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), protocols::toolbox::match_enzdes_util::split_up_remark_line(), tag, utility::to_string(), core::pose::Pose::total_residue(), and utility_exit_with_message.

Referenced by add_constraints_to_pose().

void protocols::toolbox::match_enzdes_util::EnzConstraintIO::read_enzyme_cstfile ( std::string fname )

reads the enzyme cstfile and for each block of residue residue constraints, creates a new

instance of EnzConstraintParameters

References cst_pairs_, determine_target_downstream_res(), getline(), key, mcfi_lists_, parameters, restype_set_, protocols::toolbox::match_enzdes_util::tr, and utility_exit_with_message.

Referenced by protocols::forge::remodel::RemodelEnzdesCstModule::RemodelEnzdesCstModule().

void protocols::toolbox::match_enzdes_util::EnzConstraintIO::remap_resid ( core::id::SequenceMapping const & smap )

changing the constrained residues if the sequence length changes

References cst_pairs_.

void protocols::toolbox::match_enzdes_util::EnzConstraintIO::remove_constraints_from_pose	(	core::pose::Pose &	pose,
		bool const	keep_covalent,
		bool const	fail_on_constraints_missing
	)		const

References cst_pairs_, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), and remove_constraints_from_pose_for_block().

Referenced by add_constraints_to_pose().

void protocols::toolbox::match_enzdes_util::EnzConstraintIO::remove_constraints_from_pose_for_block	(	core::pose::Pose &	pose,
		core::Size	cst_block,
		bool const	fail_on_constraints_missing
	)		const

References cst_pairs_, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), core::pose::Pose::remove_constraints(), and utility_exit_with_message.

Referenced by remove_constraints_from_pose().

void protocols::toolbox::match_enzdes_util::EnzConstraintIO::remove_position_from_template_res	(	core::pose::Pose &	pose,
		core::Size	pos
	)		const

References cst_pairs_, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), and remove_position_from_template_res_for_block().

void protocols::toolbox::match_enzdes_util::EnzConstraintIO::remove_position_from_template_res_for_block	(	core::pose::Pose &	pose,
		core::Size	pos,
		core::Size	cst_block
	)		const

References protocols::toolbox::match_enzdes_util::get_enzdes_observer().

Referenced by remove_position_from_template_res().

void protocols::toolbox::match_enzdes_util::EnzConstraintIO::set_external_position_for_resA_in_parameter_block	(	core::Size	cst_block,
		core::Size	respos
	)

References cst_pairs_, and runtime_assert.

void protocols::toolbox::match_enzdes_util::EnzConstraintIO::set_external_position_for_resB_in_parameter_block	(	core::Size	cst_block,
		core::Size	respos
	)

References cst_pairs_, and runtime_assert.

void protocols::toolbox::match_enzdes_util::EnzConstraintIO::set_position_for_missing_res_in_parameter_block	(	core::pose::Pose &	pose,
		core::Size	cst_block,
		core::Size	respos
	)		const

References cst_pairs_, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), and runtime_assert.

void protocols::toolbox::match_enzdes_util::EnzConstraintIO::show_cst_definitions ( ) const

References cst_pairs_, and protocols::toolbox::match_enzdes_util::tr.

Referenced by add_constraints_to_pose().

utility::vector1< std::pair< core::Size, core::Size> > const& protocols::toolbox::match_enzdes_util::EnzConstraintIO::target_downstream_res ( ) const

inline

References target_downstream_res_.

void protocols::toolbox::match_enzdes_util::EnzConstraintIO::update_pdb_remarks_for_backbone_params ( core::pose::Pose & pose ) const

References cst_pairs_, and utility_exit_with_message.

Member Data Documentation

utility::vector1< EnzConstraintParametersOP > protocols::toolbox::match_enzdes_util::EnzConstraintIO::cst_pairs_

protected

Referenced by add_constraints_to_pose(), add_pregenerated_constraints_to_pose(), allowed_res_name3_at_position(), protocols::forge::remodel::RemodelEnzdesCstModule::apply(), protocols::forge::remodel::RemodelEnzdesCstModule::blueprint_cst_definition(), clear_active_pose_constraints_for_block(), enz_cst_params(), enz_cst_params_missing_in_pose(), enz_cst_params_size(), EnzConstraintIO(), generate_pose_specific_data(), generate_pose_specific_data_for_block(), is_backbone_only_cst(), process_pdb_header(), read_enzyme_cstfile(), remap_resid(), remove_constraints_from_pose(), remove_constraints_from_pose_for_block(), remove_position_from_template_res(), set_external_position_for_resA_in_parameter_block(), set_external_position_for_resB_in_parameter_block(), set_position_for_missing_res_in_parameter_block(), show_cst_definitions(), and update_pdb_remarks_for_backbone_params().

EnzConstraintIO * protocols::toolbox::match_enzdes_util::EnzConstraintIO::generic_instance_

staticprivate

Referenced by get_instance().

utility::vector1< toolbox::match_enzdes_util::MatchConstraintFileInfoListOP > protocols::toolbox::match_enzdes_util::EnzConstraintIO::mcfi_lists_

private

Referenced by determine_target_downstream_res(), EnzConstraintIO(), mcfi_list(), mcfi_lists_size(), num_mcfi_lists(), process_pdb_header(), and read_enzyme_cstfile().

core::chemical::ResidueTypeSetCAP protocols::toolbox::match_enzdes_util::EnzConstraintIO::restype_set_

private

Referenced by EnzConstraintIO(), and read_enzyme_cstfile().

utility::vector1< std::pair< core::Size, core::Size> > protocols::toolbox::match_enzdes_util::EnzConstraintIO::target_downstream_res_

private

Referenced by determine_target_downstream_res(), and target_downstream_res().

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

src/protocols/toolbox/match_enzdes_util/EnzConstraintIO.hh
src/protocols/toolbox/match_enzdes_util/EnzConstraintIO.cc

Public Member Functions

Static Public Member Functions

Protected Attributes

Private Member Functions

Static Private Member Functions

Private Attributes

Static Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation