Functions
static thread_local basic::Tracer	tr ("protocols.enzdes.enzdes_util")

bool	is_catalytic_seqpos (core::pose::Pose const &pose, core::Size const seqpos)
	queries whether a certain position is considered catalytic, i.e. if the residue is constrained according to the enzdes constraint file More...

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

core::Real	sum_constraint_scoreterms (core::pose::Pose const &pose, int which_res)
	sums up coordinate, atom_pair, angle, and dihedral constraint scores for the residue in question. in case which_res is -1, the scores for the whole pose will be taken More...

void	read_pose_from_pdb (core::pose::Pose &pose, std::string const &filename)
	convenience function to read in a pose for enzdes this function basically just calls pose_from_pdb, but it will create an enzdes cacheable observer in the pose, also, 1, if a multimodel pdb is requested, if there are different ligand positions, these will be saved in the enzdes cacheable observer and 2, if option additional_packing_ligand_rb_confs is active, random ligand rigid body confs will be generated and added to the cacheable observer More...

void	make_continuous_true_regions_in_bool_vector (utility::vector1< bool > &the_vector, core::Size const min_number_continuous_trues)

core::pack::task::PackerTaskOP	recreate_task (core::pose::Pose const &pose, core::pack::task::PackerTask const &orig_task)

toolbox::match_enzdes_util::EnzConstraintIOCOP	get_enzcst_io (core::pose::Pose const &pose)
	convenience function to get enzdes cst io out of cst cache. note: may return empty pointer in case cst cache wasn't set yet More...

void	remove_remark_header_for_geomcst (core::pose::Pose &pose, core::Size geomcst)

void	create_remark_headers_from_cstcache (core::pose::Pose &pose)
	function to write proper remark headers from whatever is found in the pose cstcache More...

std::string	get_pdb_code_from_pose_tag (core::pose::Pose const &pose)

bool	is_digit (char *cha)
	delete and use cctype functions More...

bool	is_uppercase_letter (char *cha)
	delete and use cctype functions More...

bool	is_lowercase_letter (char *cha)
	delete and use cctype functions More...

void	disable_constraint_scoreterms (core::scoring::ScoreFunctionOP scorefxn)

void	enable_constraint_scoreterms (core::scoring::ScoreFunctionOP scorefxn)

bool	is_scofx_cstfied (core::scoring::ScoreFunctionCOP scorefxn)

void	scorefxn_update_from_options (core::scoring::ScoreFunctionOP scorefxn)

void	remove_all_enzdes_constraints (core::pose::Pose &pose)

void	get_resnum_from_cstid_list (std::string const &cstidlist, core::pose::Pose const &pose, utility::vector1< core::Size > &resnums)

core::Size	get_resnum_from_cstid (std::string const &cstid, core::pose::Pose const &pose)
	Extracts residue number from cstid string. More...

Function Documentation

utility::vector1< core::Size > protocols::enzdes::enzutil::catalytic_res ( core::pose::Pose const & pose )

References protocols::toolbox::match_enzdes_util::get_enzdes_observer(), core::chemical::ResidueType::is_ligand(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

Referenced by protocols::enzdes::EnzdesScorefileFilter::examine_pose(), and protocols::enzdes::EnzdesScorefileFilter::setup_pose_metric_calculators().

void protocols::enzdes::enzutil::create_remark_headers_from_cstcache ( core::pose::Pose & pose )

function to write proper remark headers from whatever is found in the pose cstcache

References protocols::toolbox::match_enzdes_util::assemble_remark_line(), protocols::toolbox::match_enzdes_util::get_enzdes_observer(), protocols::toolbox::match_enzdes_util::EnzdesCstParamCache::missing_in_pose(), core::conformation::Residue::name3(), core::pose::RemarkInfo::num, core::pose::Pose::pdb_info(), core::pose::Pose::residue(), protocols::toolbox::match_enzdes_util::split_up_remark_line(), protocols::toolbox::match_enzdes_util::EnzdesCstParamCache::template_res_cache(), protocols::toolbox::match_enzdes_util::EnzdesCstParamCache::template_res_cache_size(), utility_exit_with_message, and core::pose::RemarkInfo::value.

Referenced by protocols::enzdes::UpdateEnzdesHeaderMover::apply().

void protocols::enzdes::enzutil::disable_constraint_scoreterms ( core::scoring::ScoreFunctionOP scorefxn )

References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, core::scoring::coordinate_constraint, core::scoring::dihedral_constraint, and core::scoring::res_type_constraint.

Referenced by protocols::enzdes::RepackWithoutLigandFilter::compute().

void protocols::enzdes::enzutil::enable_constraint_scoreterms ( core::scoring::ScoreFunctionOP scorefxn )

References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, core::scoring::coordinate_constraint, core::scoring::dihedral_constraint, basic::options::option, core::scoring::res_type_constraint, and user.

Referenced by protocols::enzdes::LigInterfaceEnergyFilter::compute(), protocols::enzdes::EnzScoreFilter::compute(), protocols::enzdes::EnzRepackMinimize::ensure_scofx_cstfication(), and protocols::enzdes::LigInterfaceEnergyFilter::LigInterfaceEnergyFilter().

toolbox::match_enzdes_util::EnzConstraintIOCOP protocols::enzdes::enzutil::get_enzcst_io ( core::pose::Pose const & pose )

convenience function to get enzdes cst io out of cst cache. note: may return empty pointer in case cst cache wasn't set yet

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

Referenced by protocols::enzdes::SecondaryMatchProtocol::do_matching(), and protocols::enzdes::EnzdesBaseProtocol::enzdes_pack().

std::string protocols::enzdes::enzutil::get_pdb_code_from_pose_tag ( core::pose::Pose const & pose )

function not implemented very slick at the moment, need to find way to compile boost regex library :((

to extract the pdb code from the pose tag without a regular expression module, some explicit functions

have been written below

References core::pose::Pose::data(), basic::datacache::BasicDataCache::get_const_ptr(), is_digit(), is_lowercase_letter(), is_uppercase_letter(), protocols::kinmatch::str(), and utility::string_split().

Referenced by protocols::enzdes::DesignVsNativeComparison::compare_to_native().

core::Size protocols::enzdes::enzutil::get_resnum_from_cstid	(	std::string const &	cstid,
		core::pose::Pose const &	pose
	)

Extracts residue number from cstid string.

Expects cstid string to be of format [0-9]+[A-Z], where the number is constraint number and trailing letter is temlplate id i.e. either A or B

see enzdes style REMARKs format used to specify match type constraint between two residues (template A and template B)

References protocols::toolbox::match_enzdes_util::get_enzdes_observer(), runtime_assert, core::pose::Pose::total_residue(), and utility_exit_with_message.

Referenced by protocols::enzdes::EnzScoreFilter::compute(), and get_resnum_from_cstid_list().

void protocols::enzdes::enzutil::get_resnum_from_cstid_list	(	std::string const &	cstidlist,
		core::pose::Pose const &	pose,
		utility::vector1< core::Size > &	resnums
	)

References get_resnum_from_cstid(), runtime_assert, utility::string_split(), and core::pose::Pose::total_residue().

Referenced by protocols::enzdes::PackRotamersMoverPartGreedy::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), and protocols::enzdes::RepackWithoutLigandFilter::compute().

bool protocols::enzdes::enzutil::is_catalytic_seqpos	(	core::pose::Pose const &	pose,
		core::Size const	seqpos
	)

queries whether a certain position is considered catalytic, i.e. if the residue is constrained according to the enzdes constraint file

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

Referenced by protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::enzdes::ProteinLigandInterfaceUpweighter::apply(), protocols::enzdes::EnzdesBaseProtocol::design_targets(), and protocols::enzdes::EnzdesBaseProtocol::is_catalytic_position().

bool protocols::enzdes::enzutil::is_digit ( char * cha )

delete and use cctype functions

Referenced by get_pdb_code_from_pose_tag().

bool protocols::enzdes::enzutil::is_lowercase_letter ( char * cha )

delete and use cctype functions

Referenced by get_pdb_code_from_pose_tag().

bool protocols::enzdes::enzutil::is_scofx_cstfied ( core::scoring::ScoreFunctionCOP scorefxn )

References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, core::scoring::coordinate_constraint, and core::scoring::dihedral_constraint.

Referenced by protocols::enzdes::EnzRepackMinimize::ensure_scofx_cstfication().

bool protocols::enzdes::enzutil::is_uppercase_letter ( char * cha )

delete and use cctype functions

Referenced by get_pdb_code_from_pose_tag().

void protocols::enzdes::enzutil::make_continuous_true_regions_in_bool_vector	(	utility::vector1< bool > &	the_vector,
		core::Size const	min_number_continuous_trues
	)

References utility_exit_with_message.

Referenced by protocols::enzdes::EnzdesBaseProtocol::create_enzdes_movemap(), and protocols::enzdes::EnzdesFlexBBProtocol::determine_flexible_regions().

void protocols::enzdes::enzutil::read_pose_from_pdb	(	core::pose::Pose &	pose,
		std::string const &	filename
	)

convenience function to read in a pose for enzdes this function basically just calls pose_from_pdb, but it will create an enzdes cacheable observer in the pose, also, 1, if a multimodel pdb is requested, if there are different ligand positions, these will be saved in the enzdes cacheable observer and 2, if option additional_packing_ligand_rb_confs is active, random ligand rigid body confs will be generated and added to the cacheable observer

References protocols::enzdes::GenerateStoredRBConfs::apply(), clone(), protocols::toolbox::match_enzdes_util::get_enzdes_observer(), basic::options::option, core::import_pose::pose_from_pdb(), runtime_assert, and size().

Referenced by protocols::enzdes::EnzdesJobInputter::pose_from_job().

core::pack::task::PackerTaskOP protocols::enzdes::enzutil::recreate_task	(	core::pose::Pose const &	pose,
		core::pack::task::PackerTask const &	orig_task
	)

Referenced by protocols::enzdes::EnzdesFlexBBProtocol::apply(), protocols::enzdes::EnzdesBaseProtocol::enzdes_pack(), and protocols::enzdes::EnzdesFlexibleRegion::sort_ensemble_by_designability().

void protocols::enzdes::enzutil::remove_all_enzdes_constraints ( core::pose::Pose & pose )

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

Referenced by protocols::enzdes::RepackWithoutLigandFilter::compute().

void protocols::enzdes::enzutil::remove_remark_header_for_geomcst	(	core::pose::Pose &	pose,
		core::Size	geomcst
	)

References core::pose::Pose::pdb_info(), and protocols::toolbox::match_enzdes_util::split_up_remark_line().

void protocols::enzdes::enzutil::scorefxn_update_from_options ( core::scoring::ScoreFunctionOP scorefxn )

References core::scoring::methods::EnergyMethodOptions::exclude_protein_protein_fa_elec(), basic::options::option, and user.

Referenced by protocols::enzdes::EnzRepackMinimize::ensure_scofx_cstfication().

core::Real protocols::enzdes::enzutil::sum_constraint_scoreterms	(	core::pose::Pose const &	pose,
		int	which_res
	)

sums up coordinate, atom_pair, angle, and dihedral constraint scores for the residue in question. in case which_res is -1, the scores for the whole pose will be taken

References angle_constraint, atom_pair_constraint, coordinate_constraint, dihedral_constraint, core::pose::Pose::energies(), core::scoring::Energies::residue_total_energies(), core::scoring::Energies::total_energies(), and core::scoring::Energies::weights().

Referenced by protocols::enzdes::SecondaryMatchProtocol::add_enz_cst_interaction_to_pose(), protocols::enzdes::EnzdesScorefileFilter::compute_metrics_for_residue_subset(), and protocols::enzdes::EnzdesScorefileFilter::examine_pose().

static thread_local basic::Tracer protocols::enzdes::enzutil::tr ( "protocols.enzdes.enzdes_util" )

static

Functions

Function Documentation