core::util Namespace Reference

Classes
class	ChainbreakUtil

Functions
static basic::Tracer	TS ("core.scoring.cryst.util")
core::Real	getMLweight (core::scoring::ScoreFunction &scorefxn, core::pose::Pose &)
	get the optimal weight on the xtal ML energy More...
core::Real	getMLweight (core::scoring::ScoreFunction &scorefxn, core::pose::Pose &, core::kinematics::MoveMap &)
	get the optimal weight on the xtal ML energy considering only movable DOFs More...
core::Real	getMLweight_cart (core::scoring::ScoreFunction &scorefxn, core::pose::Pose &)
	get the optimal weight on the xtal ML energy More...
core::Real	getMLweight_cart (core::scoring::ScoreFunction &scorefxn, core::pose::Pose &, core::kinematics::MoveMap &)
	get the optimal weight on the xtal ML energy considering only movable DOFs More...
static basic::Tracer	TR ("protocols.toolbox.disulfide_util")
void	rebuild_disulfide (Pose &pose, Size lower_res, Size upper_res, core::Size const threads_to_request, PackerTaskOP packer_task, ScoreFunctionOP packer_score, MoveMapOP mm, ScoreFunctionOP minimizer_score)
void	rebuild_disulfide (core::pose::Pose &pose, utility::vector1< std::pair< core::Size, core::Size > > disulfides, core::Size const threads_to_request, core::pack::task::PackerTaskOP packer_task=nullptr, core::scoring::ScoreFunctionOP packer_score=nullptr, core::kinematics::MoveMapOP mm=nullptr, core::scoring::ScoreFunctionOP minimizer_score=nullptr)
	Rebuild a number of pairs of cysteines (and possibly surrounding residues) so that they form near-ideal disulfide bonds. More...
void	rebuild_disulfide (core::pose::Pose &pose, core::Size lower_res, core::Size upper_res, core::Size const threads_to_request, core::pack::task::PackerTaskOP packer_task=nullptr, core::scoring::ScoreFunctionOP packer_score=nullptr, core::kinematics::MoveMapOP mm=nullptr, core::scoring::ScoreFunctionOP minimizer_score=nullptr)
	Rebuild a pair of cysteines (and possibly surrounding residues) so that they form a near-ideal disulfide bond. Supports symmetric poses. More...
void	remove_cutpoint_variants (core::pose::Pose &pose)
	Removes cutpoint variants from pose by scanning the fold tree. More...
static basic::Tracer	TR ("core.util.metalloproteins_util")
void	add_covalent_linkage_helper (core::pose::Pose &pose, core::Size const res_pos, core::Size const Atpos, numeric::xyzVector< core::Real > const &, bool const remove_hydrogens)
	: This is a helper function for the add_covalent_linkage function. More...
void	add_covalent_linkage (core::pose::Pose &pose, Size const resA_pos, Size const resB_pos, Size const resA_At, Size const resB_At, bool const remove_hydrogens)
	: Adds an arbitrary covalent linkage between two atoms (resA_At and resB_At) in two residues (at positions resA_pos and resB_pos). More...
std::map< core::Size, utility::vector1< core::id::AtomID > >	find_metalbinding_atoms_for_complex (core::pose::Pose const &pose, core::Size const metal_position, core::Real const dist_cutoff_multiplier)
	Function that can find contacts to metal ions that are part of a larger complex. More...
utility::vector1< core::id::AtomID >	find_metalbinding_atoms_helper (core::pose::Pose const &pose, core::id::AtomID const &metal_atom, core::Real const dist_cutoff_multiplier)
	Helper function that finds contacts for metal atoms specified by AtomID. More...
utility::vector1< core::id::AtomID >	find_metalbinding_atoms (core::pose::Pose const &pose, core::Size const metal_position, core::Real const dist_cutoff_multiplier)
	Function that generates a list of metal-binding atoms that coordinate a metal in a protein. More...
void	add_covalent_linkages_to_metal (core::pose::Pose &pose, core::Size const metal_position, utility::vector1< core::id::AtomID > &liganding_atomids, bool const remove_hydrogens)
	Function to add covalent linkages between a metal atom and all the liganding atoms provided in a vector of AtomIDs. More...
void	auto_setup_all_metal_bonds (core::pose::Pose &pose, core::Real const dist_cutoff_multiplier, bool const remove_hydrogens)
	Function to auto-detect and add covalent connections to ALL metal ions in a pose. More...
void	add_constraints_to_metal (core::pose::Pose &pose, core::Size const metal_position, core::Real const distance_constraint_multiplier, core::Real const angle_constraint_multiplier, utility::vector1< core::id::AtomID > const &binders)
	Function to set up distance and angle constraints for a specified metal ion. More...
void	auto_setup_all_metal_constraints (core::pose::Pose &pose, core::Real const distance_constraint_multiplier, core::Real const angle_constraint_multiplier)
	Function to set up distance and angle constraints between metals and the residues that bind them. More...
void	auto_setup_all_metal_constraints (core::pose::Pose &pose, core::scoring::ScoreFunctionOP sfxn, core::Real const distance_constraint_multiplier, core::Real const angle_constraint_multiplier)
	Function to set up distance and angle constraints between metals and the residues that bind them. More...
static basic::Tracer	TR ("core.util.switchresiduetypeset")
void	switch_to_residue_type_set (core::pose::Pose &pose, core::chemical::ResidueTypeSet const &type_set, core::Size const threads_to_request, bool allow_sloppy_match, bool switch_protein_res_only, bool keep_energies)
void	switch_to_residue_type_set (core::pose::Pose &pose, core::chemical::TypeSetMode type_set_mode, core::Size const threads_to_request, bool allow_sloppy_match, bool switch_protein_res_only, bool keep_energies)
void	switch_to_residue_type_set (core::pose::Pose &pose, std::string const &type_set_name, core::Size const threads_to_request, bool allow_sloppy_match, bool switch_protein_res_only, bool keep_energies)
void	switch_to_centroid_rot_set (core::pose::Pose &pose, core::conformation::symmetry::SymmetryInfoCOP symm_info, core::chemical::ResidueTypeSet const &rsd_set, bool)
core::chemical::MutableResidueTypeOP	generate_replacement_restype (core::chemical::ResidueType const &restype, core::chemical::TypeSetMode mode)
	Attempt to generate a new residue type of the appropriate mode. If not possible, return a nullptr. More...
void	rebuild_fa_disulfides (core::pose::Pose &pose, core::Size const threads_to_request=0)
	Rebuild disulfides after a transition to a full atom ResidueTypeSet. More...

Variables
std::set< std::string > const	METALS = { "NA", "K", "MG", "LI", "CA", "CU", "CO", "NI", "FE", "ZN", "CR", "MN", "MO", "PD", "PT", "AG", "HG", "LA", "FE2"}
	: Set of element strings used to identify metal ions. More...

Function Documentation

add_constraints_to_metal()

void core::util::add_constraints_to_metal	(	core::pose::Pose &	pose,
		core::Size const	metal_position,
		core::Real const	distance_constraint_multiplier,
		core::Real const	angle_constraint_multiplier,
		utility::vector1< core::id::AtomID > const &	binders
	)

Function to set up distance and angle constraints for a specified metal ion.

Modified/taken from auto_setup_all_metal_constraints to allow constraint setup for only specified metal residues. Does not modify score function weights. Inputs: pose (The pose that we'll operate on, changed by operation) metal_position (The residue number of the metal to be constrained) distance_constraint_multiplier (A float for the strength of the metal - binding atom distance constraint. A value of 2.0 doubles it, for example.) angle_constraint_multiplier (A float for the strength of the metal - binding atom - binding atom parent angle constraint.)

Author

Sharon Guffy (guffy.nosp@m.@ema.nosp@m.il.un.nosp@m.c.ed.nosp@m.u); originally written by Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@uw.e.nosp@m.du) as part of auto_setup_all_metal_constraints

References core::pose::Pose::add_constraint(), core::chemical::ResidueType::atom_base(), core::conformation::Residue::atom_name(), core::chemical::ResidueConnection::atomno(), core::conformation::Residue::connect_map(), core::chemical::ResConnID::connid(), core::conformation::Residue::is_metal(), core::conformation::Residue::is_virtual(), core::scoring::metalbinding_constraint, core::conformation::Residue::n_possible_residue_connections(), core::conformation::Residue::name(), core::conformation::Residue::natoms(), core::chemical::ResConnID::resid(), core::pose::Pose::residue(), core::conformation::Residue::residue_connection(), core::pose::Pose::set_xyz(), core::conformation::Residue::type(), core::pose::Pose::xyz(), and core::conformation::Residue::xyz().

Referenced by protocols::simple_moves::SetupMetalsMover::apply(), and auto_setup_all_metal_constraints().

add_covalent_linkage()

void core::util::add_covalent_linkage	(	core::pose::Pose &	pose,
		Size const	resA_pos,
		Size const	resB_pos,
		Size const	resA_At,
		Size const	resB_At,
		bool const	remove_hydrogens
	)

: Adds an arbitrary covalent linkage between two atoms (resA_At and resB_At) in two residues (at positions resA_pos and resB_pos).

: This is useful for adding covalent linkages between metal-binding side-chains and metal atoms. This code was shamelessly stolen from Florian's EnzConstraintParameters.cc in protocols/toolbox/match_enzdes_utils, and was modified to permit deletion of unnecessary protons.

Author

: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu), Florian Richter (floso.nosp@m.pher.nosp@m.@gmai.nosp@m.l.co.nosp@m.m)

: This is useful for adding covalent linkages between metal-binding side-chains and metal atoms. This code was shamelessly stolen from Florian's EnzConstraintParameters.cc in protocols/toolbox/match_enzdes_utils, and was modified to permit deletion of unnecessary protons. NOTE: THIS CODE MODIFIES THE RESIDUE TYPE LIST, AND IS CURRENTLY NOT THREADSAFE.

Author

: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu), Florian Richter (floso.nosp@m.pher.nosp@m.@gmai.nosp@m.l.co.nosp@m.m)

References add_covalent_linkage_helper(), core::conformation::Residue::atom_name(), core::pose::Pose::conformation(), core::conformation::Conformation::declare_chemical_bond(), core::pose::Pose::residue(), TR(), and core::conformation::Residue::xyz().

Referenced by add_covalent_linkages_to_metal().

add_covalent_linkage_helper()

void core::util::add_covalent_linkage_helper	(	core::pose::Pose &	pose,
		core::Size const	res_pos,
		core::Size const	Atpos,
		numeric::xyzVector< core::Real > const &	,
		bool const	remove_hydrogens
	)

: This is a helper function for the add_covalent_linkage function.

: This is useful for adding covalent linkages between metal-binding side-chains and metal atoms. This code was shamelessly stolen from Florian's EnzConstraintParameters.cc but now does not modify the RTS and would be threadsafe.

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Florian Richter (floso.nosp@m.pher.nosp@m.@gmai.nosp@m.l.co.nosp@m.m)

Andy Watkins (andy..nosp@m.watk.nosp@m.ins2@.nosp@m.gmai.nosp@m.l.com)

References core::conformation::Residue::atom_index(), core::conformation::Residue::atom_name(), core::conformation::Residue::clone(), core::pose::get_restype_for_pose(), core::conformation::Residue::has(), core::chemical::ResidueType::is_metal(), core::conformation::Residue::is_metal(), core::chemical::ResidueTypeBase::mode(), core::conformation::Residue::natoms(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::chemical::residue_type_all_patches_name(), core::chemical::residue_type_base_name(), core::pose::Pose::set_xyz(), core::chemical::orbitals::strip_whitespace(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by add_covalent_linkage().

add_covalent_linkages_to_metal()

void core::util::add_covalent_linkages_to_metal	(	core::pose::Pose &	pose,
		core::Size const	metal_position,
		utility::vector1< core::id::AtomID > &	liganding_atomids,
		bool const	remove_hydrogens
	)

Function to add covalent linkages between a metal atom and all the liganding atoms provided in a vector of AtomIDs.

The inputs are: pose (The pose to be modified) metal_position (The residue number of the metal in the pose) liganding_atomids (A list of AtomIDs on other residues that will be covalently linked to the metal) remove_hydrogens (Should hydrogens on the liganding atoms be removed automatically? Default true.) This function uses core::pose::add_covalent_linkage, which can strip off extraneous hydrogens.

References add_covalent_linkage(), core::conformation::Residue::is_metal(), and core::pose::Pose::residue().

Referenced by protocols::simple_moves::SetupMetalsMover::apply(), and auto_setup_all_metal_bonds().

auto_setup_all_metal_bonds()

void core::util::auto_setup_all_metal_bonds	(	core::pose::Pose &	pose,
		core::Real const	dist_cutoff_multiplier,
		bool const	remove_hydrogens
	)

Function to auto-detect and add covalent connections to ALL metal ions in a pose.

Function to auto-detect and add covalent connections to all metal ions in a pose.

This function iteratively calls auto_setup_metal_bonds. Inputs: pose (The pose that we'll operate on, unchanged by operation) dist_cutoff_multiplier (A float for the distance cutoff multiplier; the cutoff is the sum of the Lennard-Jones radii times the multiplier) remove_hydrogesn (Should hydrogens on the liganding atoms be auto-removed? Default true.)

Author

Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@uw.e.nosp@m.du)

This function iteratively calls auto_setup_metal_bonds. Inputs: pose (The pose that we'll operate on, changed by operation) dist_cutoff_multiplier (A float for the distance cutoff multiplier; the cutoff is the sum of the Lennard-Jones radii times the multiplier) remove_hydrogesn (Should hydrogens on the liganding atoms be auto-removed? Default true.)

Author

Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@uw.e.nosp@m.du)

References add_covalent_linkages_to_metal(), find_metalbinding_atoms(), core::conformation::Residue::is_metal(), core::pose::Pose::residue(), core::pose::Pose::size(), and TR().

Referenced by protocols::simple_moves::SetupMetalsMover::apply(), and core::import_pose::build_pose_as_is2().

auto_setup_all_metal_constraints() [1/2]

void core::util::auto_setup_all_metal_constraints	(	core::pose::Pose &	pose,
		core::Real const	distance_constraint_multiplier,
		core::Real const	angle_constraint_multiplier
	)

Function to set up distance and angle constraints between metals and the residues that bind them.

This function constrains the distances to be whatever they are in the input pose. This version does not set the weights for the constraints terms in the scorefunction. Inputs: pose (The pose that we'll operate on, changed by operation) distance_constraint_multiplier (A float for the strength of the metal - binding atom distance constraint. A value of 2.0 doubles it, for example.) angle_constraint_multiplier (A float for the strength of the metal - binding atom - binding atom parent angle constraint.)

Author

Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@uw.e.nosp@m.du)

References add_constraints_to_metal(), core::conformation::Residue::is_metal(), core::pose::Pose::residue(), core::pose::Pose::size(), and TR().

Referenced by protocols::simple_moves::SetupMetalsMover::apply(), auto_setup_all_metal_constraints(), core::import_pose::build_pose_as_is2(), and protocols::jd2::PDBJobInputter::pose_from_job().

auto_setup_all_metal_constraints() [2/2]

void core::util::auto_setup_all_metal_constraints	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunctionOP	sfxn,
		core::Real const	distance_constraint_multiplier,
		core::Real const	angle_constraint_multiplier
	)

Function to set up distance and angle constraints between metals and the residues that bind them.

This function constrains the distances to be whatever they are in the input pose. This version sets the weights for the constraints terms in the scorefunction to 1.0 if they're off, or scales the constraints themselves appropriately if they're already on. Inputs: pose (The pose that we'll operate on, changed by operation) sfxn (An owning pointer to the scorefunction, changed by operation) distance_constraint_multiplier (A float for the strength of the metal - binding atom distance constraint. A value of 2.0 doubles it, for example.) angle_constraint_multiplier (A float for the strength of the metal - binding atom - binding atom parent angle constraint.)

Author

Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@uw.e.nosp@m.du)

References auto_setup_all_metal_constraints(), and core::scoring::metalbinding_constraint.

find_metalbinding_atoms()

utility::vector1< core::id::AtomID > core::util::find_metalbinding_atoms	(	core::pose::Pose const &	pose,
		core::Size const	metal_position,
		core::Real const	dist_cutoff_multiplier
	)

Function that generates a list of metal-binding atoms that coordinate a metal in a protein.

This function generates the list by looping through all residues and checking all metal-binding atoms of all metal-binding residues, so it's not super speedy. Inputs: pose (The pose that we'll operate on, unchanged by operation) metal_postion (The residue number of the metal) dist_cutoff_multiplier (A float for the distance cutoff multiplier; the cutoff is the sum of the Lennard-Jones radii times the multiplier)

Author

Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@uw.e.nosp@m.du)

References find_metalbinding_atoms_helper(), core::conformation::Residue::is_metal(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by protocols::simple_moves::SetupMetalsMover::apply(), and auto_setup_all_metal_bonds().

find_metalbinding_atoms_for_complex()

std::map< core::Size, utility::vector1< core::id::AtomID > > core::util::find_metalbinding_atoms_for_complex	(	core::pose::Pose const &	pose,
		core::Size const	metal_position,
		core::Real const	dist_cutoff_multiplier
	)

Function that can find contacts to metal ions that are part of a larger complex.

Identifies metal ions based on the METALS set defined in this file and passes those atoms to find_metalbinding_atoms_helper.

Author

Sharon Guffy (guffy.nosp@m.@ema.nosp@m.il.un.nosp@m.c.ed.nosp@m.u )

References core::conformation::Residue::atom_type(), core::chemical::AtomType::element(), find_metalbinding_atoms_helper(), METALS, and core::pose::Pose::residue().

Referenced by protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector(), and protocols::residue_selectors::LigandMetalContactSelector::apply().

find_metalbinding_atoms_helper()

utility::vector1< core::id::AtomID > core::util::find_metalbinding_atoms_helper	(	core::pose::Pose const &	pose,
		core::id::AtomID const &	metal_atom,
		core::Real const	dist_cutoff_multiplier
	)

Helper function that finds contacts for metal atoms specified by AtomID.

Code modified from Vikram's code originally in find_metalbinding_atoms

Author

Sharon Guffy (guffy.nosp@m.@ema.nosp@m.il.un.nosp@m.c.ed.nosp@m.u )

References core::conformation::Residue::atom_is_backbone(), core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type(), core::id::AtomID::atomno(), core::conformation::Residue::get_metal_binding_atoms(), core::conformation::Residue::is_metalbinding(), core::chemical::AtomType::lj_radius(), core::pose::Pose::residue(), core::id::AtomID::rsd(), core::pose::Pose::total_residue(), TR(), and core::conformation::Residue::xyz().

Referenced by protocols::constraint_generator::MetalContactsConstraintGenerator::apply(), find_metalbinding_atoms(), and find_metalbinding_atoms_for_complex().

generate_replacement_restype()

core::chemical::MutableResidueTypeOP core::util::generate_replacement_restype	(	core::chemical::ResidueType const &	restype,
		core::chemical::TypeSetMode	mode
	)

Attempt to generate a new residue type of the appropriate mode. If not possible, return a nullptr.

References core::chemical::CENTROID_t, core::chemical::FULL_ATOM_t, core::chemical::make_centroid(), and core::chemical::ResidueTypeBase::mode().

Referenced by switch_to_residue_type_set().

getMLweight() [1/2]

core::Real core::util::getMLweight	(	core::scoring::ScoreFunction &	scorefxn,
		core::pose::Pose &	pose
	)

get the optimal weight on the xtal ML energy

References core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), and core::kinematics::MoveMap::set_jump().

Referenced by protocols::cryst::SetCrystWeightMover::apply().

getMLweight() [2/2]

core::Real core::util::getMLweight	(	core::scoring::ScoreFunction &	scorefxn,
		core::pose::Pose &	pose_orig,
		core::kinematics::MoveMap &	move_map
	)

get the optimal weight on the xtal ML energy considering only movable DOFs

References core::scoring::ScoreFunction::clone(), core::pose::Pose::conformation(), core::optimization::MinimizerMap::copy_dofs_from_pose(), core::optimization::AtomTreeMultifunc::dfunc(), core::optimization::symmetry::SymAtomTreeMultifunc::dfunc(), core::pose::symmetry::is_symmetric(), core::optimization::symmetry::SymAtomTreeMinimizer::make_asymmetric_movemap(), core::optimization::symmetry::SymAtomTreeMinimizer::make_semisymmetric_movemap(), core::pose::symmetry::make_symmetric_movemap(), core::optimization::MinimizerMap::nangles(), core::optimization::MinimizerMap::setup(), TS(), and core::scoring::xtal_ml.

getMLweight_cart() [1/2]

core::Real core::util::getMLweight_cart	(	core::scoring::ScoreFunction &	scorefxn,
		core::pose::Pose &	pose
	)

get the optimal weight on the xtal ML energy

References core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), and core::kinematics::MoveMap::set_jump().

Referenced by protocols::cryst::SetCrystWeightMover::apply().

getMLweight_cart() [2/2]

core::Real core::util::getMLweight_cart	(	core::scoring::ScoreFunction &	scorefxn,
		core::pose::Pose &	pose,
		core::kinematics::MoveMap &	move_map
	)

get the optimal weight on the xtal ML energy considering only movable DOFs

References core::scoring::ScoreFunction::clone(), core::pose::Pose::conformation(), core::optimization::CartesianMinimizerMap::copy_dofs_from_pose(), core::optimization::CartesianMultifunc::dfunc(), core::pose::symmetry::is_symmetric(), core::pose::symmetry::make_symmetric_movemap(), core::optimization::CartesianMinimizerMap::ndofs(), core::optimization::CartesianMinimizerMap::setup(), and core::scoring::xtal_ml.

rebuild_disulfide() [1/3]

void core::util::rebuild_disulfide	(	core::pose::Pose &	pose,
		core::Size	lower_res,
		core::Size	upper_res,
		core::Size const	threads_to_request,
		core::pack::task::PackerTaskOP	packer_task = nullptr,
		core::scoring::ScoreFunctionOP	packer_score = nullptr,
		core::kinematics::MoveMapOP	mm = nullptr,
		core::scoring::ScoreFunctionOP	minimizer_score = nullptr
	)

Rebuild a pair of cysteines (and possibly surrounding residues) so that they form a near-ideal disulfide bond. Supports symmetric poses.

rebuild_disulfide() [2/3]

void core::util::rebuild_disulfide	(	core::pose::Pose &	pose,
		utility::vector1< std::pair< core::Size, core::Size > >	disulfides,
		core::Size const	threads_to_request,
		core::pack::task::PackerTaskOP	packer_task,
		core::scoring::ScoreFunctionOP	packer_score,
		core::kinematics::MoveMapOP	mm,
		core::scoring::ScoreFunctionOP	minimizer_score
	)

Rebuild a number of pairs of cysteines (and possibly surrounding residues) so that they form near-ideal disulfide bonds.

Precondition

The two residues specified should already be disulfide-forming types with a bond defined between the sulphur atoms. This can be accomplished by first calling protocols::toolbox::form_disulfide().

To provide the most flexibility, this function does not restrict the degrees of freedom in the repacking and minimization steps. This is needed in some cases where the backbone position is not optimal for making a disulfide bond. However, if this function needs to be reasonably fast you should prevent repacking on all residues except the two targets.

Parameters

pose[in,out]	The pose to modify with a disulfides
disulfides[in]	A list of pairs of residue indices indicating pairs of disulfide- bonded residues.
threads_to_request	In the multi-threaded build only, this extra parameter allows more than one thread to be requested for packer setup.
packer_task[in]	A task to control repacking. Defaults to repacking lower_res & upper_res if ommitted or NULL.
packer_score[in]	A scoring function to use while repacking. Use default score function if ommitted or NULL.
mm[in]	A MoveMap to control minimization. Defaults to full degrees of freedom if ommitted or NULL.
minimizer_score[in]	The score to use for minimization. Defaults to packer_score if ommitted or NULL.

References core::pose::Pose::conformation(), core::pack::task::TaskFactory::create_packer_task(), core::pack::task::EX_SIX_QUARTER_STEP_STDDEVS, core::scoring::get_score_function(), core::conformation::is_disulfide_bond(), core::pose::symmetry::is_symmetric(), core::pose::symmetry::make_symmetric_movemap(), core::pack::pack_rotamers(), core::optimization::AtomTreeMinimizer::run(), core::optimization::symmetry::SymAtomTreeMinimizer::run(), core::pose::Pose::size(), TR(), and core::pose::Pose::update_residue_neighbors().

rebuild_disulfide() [3/3]

void core::util::rebuild_disulfide	(	Pose &	pose,
		Size	lower_res,
		Size	upper_res,
		core::Size const	threads_to_request,
		PackerTaskOP	packer_task,
		ScoreFunctionOP	packer_score,
		MoveMapOP	mm,
		ScoreFunctionOP	minimizer_score
	)

A convenience function for calling core::util:: rebuild_disulfide() with only a single disulfide bond. Supports symmetric poses.

Note

In multi-threaded builds, this function takes an extra parameter for the number of threads to request, for parallel interaction graph precomputation.

References protocols::comparative_modeling::features::A, core::chemical::element::B, core::pose::Pose::conformation_ptr(), core::pose::symmetry::is_symmetric(), and TR().

Referenced by protocols::protein_interface_design::movers::DisulfideMover::apply(), protocols::simple_moves::DisulfideInsertionMover::apply(), protocols::forge::remodel::build_and_score_disulfide(), protocols::denovo_design::DisulfidizeMover::make_disulfide(), protocols::forge::remodel::RemodelDesignMover::make_disulfide(), rebuild_fa_disulfides(), and protocols::fold_from_loops::NubInitioMover::repack_minimize_disulfides().

rebuild_fa_disulfides()

void core::util::rebuild_fa_disulfides	(	core::pose::Pose &	pose,
		core::Size const	threads_to_request
	)

Rebuild disulfides after a transition to a full atom ResidueTypeSet.

Note

In multi-threaded builds, this function takes an extra parameter for the number of threads to request, for parallel interaction graph precomputation.

References core::pose::Pose::conformation(), core::pack::task::TaskFactory::create_packer_task(), core::conformation::disulfide_bonds(), core::pose::Pose::is_fullatom(), core::conformation::Residue::is_protein(), rebuild_disulfide(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by switch_to_residue_type_set().

remove_cutpoint_variants()

void core::util::remove_cutpoint_variants

(

core::pose::Pose &

pose

)

Removes cutpoint variants from pose by scanning the fold tree.

References core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), core::pose::remove_variant_type_from_pose_residue(), and core::pose::Pose::size().

Referenced by protocols::medal::MedalMover::apply(), protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::rbsegment_relax::ConfChangeMover::apply(), protocols::loop_modeling::LoopMover::apply(), protocols::forge::remodel::RemodelLoopMover::boost_closure_stage(), protocols::LoopRebuild::build_random_loops(), protocols::forge::components::BDR::design_refine(), protocols::seeded_abinitio::CloseFold::fast_loopclose(), protocols::forge::remodel::RemodelLoopMover::independent_stage(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), protocols::forge::build::Bridge::modify_impl(), protocols::kinematic_closure::ClosureProblem::mutate_residues(), protocols::seeded_abinitio::CloseFold::quick_closure(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::forge::remodel::RemodelLoopMover::simultaneous_stage(), and protocols::star::StarAbinitio::tear_down_kinematics().

switch_to_centroid_rot_set()

void core::util::switch_to_centroid_rot_set	(	core::pose::Pose &	pose,
		core::conformation::symmetry::SymmetryInfoCOP	symm_info,
		core::chemical::ResidueTypeSet const &	rsd_set,
		bool
	)

References core::conformation::Residue::aa(), core::chemical::aa_unk, core::chemical::aa_vrt, core::conformation::Residue::atom(), core::conformation::Residue::atom_index(), core::conformation::Residue::atom_name(), core::conformation::Residue::atoms(), core::chemical::element::B, core::chemical::CENTROID_ROT_t, core::chemical::CENTROID_t, core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), core::chemical::ResidueType::first_sidechain_atom(), core::conformation::Residue::first_sidechain_atom(), core::chemical::FULL_ATOM_t, core::chemical::ResidueTypeSet::get_representative_type_name3(), core::conformation::Residue::is_terminus(), core::conformation::Residue::is_virtual(), core::pose::mass(), protocols::mean_field::max(), core::chemical::ResidueTypeBase::mode(), core::chemical::ResidueTypeSet::mode(), core::chemical::ResidueTypeBase::name(), core::conformation::Residue::name(), core::conformation::Residue::name3(), core::chemical::ResidueTypeSet::name_map(), core::conformation::Residue::nbr_atom(), core::conformation::Residue::nheavyatoms(), core::chemical::ResidueType::nheavyatoms(), core::pose::Pose::pdb_info(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::sequence(), core::pose::Pose::set_xyz(), core::chemical::string_from_type_set_mode(), core::pose::Pose::total_residue(), TR(), core::conformation::Residue::type(), and core::conformation::Atom::xyz().

Referenced by switch_to_residue_type_set().

switch_to_residue_type_set() [1/3]

void core::util::switch_to_residue_type_set	(	core::pose::Pose &	pose,
		core::chemical::ResidueTypeSet const &	type_set,
		core::Size const	threads_to_request,
		bool	allow_sloppy_match,
		bool	switch_protein_res_only,
		bool	keep_energies
	)

the function allows a pose to use a different residue_type_set to represent all its residues, such as from fullatom residues to centroid residues, or vice versa. During the switch, corresponding atoms will be copied. Redundant atoms will be removed (in case from fullatom to centroid) and missing atoms will be built by ideal geometry (in the case from centroid to fullatom).

References core::conformation::Residue::aa(), core::chemical::ResidueTypeFinder::aa(), core::chemical::aa_vrt, core::chemical::CENTROID_ROT_t, core::scoring::Energies::clear(), core::pose::Pose::conformation(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), core::conformation::ResidueFactory::create_residue(), core::pose::Pose::energies(), core::chemical::FULL_ATOM_t, generate_replacement_restype(), core::chemical::ResidueTypeFinder::get_representative_type(), core::chemical::ResidueTypeSet::get_representative_type_name3(), core::chemical::ResidueTypeSet::has_name(), core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), core::chemical::ResidueTypeBase::mode(), core::chemical::ResidueTypeSet::mode(), core::conformation::Conformation::modifiable_residue_type_set_for_conf(), core::chemical::ResidueTypeBase::name(), core::conformation::Residue::name(), core::chemical::ResidueTypeBase::name3(), core::conformation::Residue::name3(), core::chemical::ResidueTypeSet::name_mapOP(), rebuild_fa_disulfides(), core::pose::Pose::replace_residue(), core::conformation::Conformation::reset_residue_type_set_for_conf(), core::pose::Pose::residue(), core::conformation::Residue::seqpos(), core::pose::Pose::sequence(), core::chemical::ResidueType::show(), core::pose::Pose::size(), switch_to_centroid_rot_set(), TR(), core::conformation::Residue::type(), and core::chemical::ResidueTypeBase::variant_types().

Referenced by protocols::abinitio::StructureStore::add(), protocols::denovo_design::components::SheetDB::add_sheet(), protocols::abinitio::ResolutionSwitcher::apply(), protocols::domain_assembly::AssembleLinkerMover::apply(), protocols::ligand_docking::LigandDockProtocol::apply(), protocols::loophash::LoopHashDiversifier::apply(), protocols::loophash::LoopHashLibrary::apply(), protocols::loophash::LoopHashMoverWrapper::apply(), protocols::loophash::Mover_LoopHashRefine::apply(), protocols::medal::MedalMover::apply(), protocols::protein_interface_design::movers::DockWithHotspotMover::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::relax::FastRelax::apply(), protocols::relax::LocalRelax::apply(), protocols::relax::loop::LoopRelaxMover::apply(), protocols::relax::MiniRelax::apply(), protocols::rna::denovo::RNA_FragmentMonteCarlo::apply(), protocols::seeded_abinitio::GrowPeptides::apply(), protocols::simple_moves::SwitchResidueTypeSetMover::apply(), protocols::simple_filters::JScoreEvaluator::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::simple_filters::SAXSScoreFilter::apply(), protocols::flxbb::FlxbbDesign::apply(), protocols::forge::components::VarLengthBuild::apply(), protocols::forge::remodel::RemodelLoopMover::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::loophash::FastGapMover::apply(), protocols::relax::FastRelax::batch_apply(), protocols::simple_moves::StructProfileMover::calc_cenlist(), protocols::analysis::InterfaceAnalyzerMover::calc_centroid_dG(), protocols::fldsgn::BluePrintBDR::centroid_build(), protocols::forge::components::BDR::centroid_build(), protocols::forge::remodel::RemodelMover::centroid_build(), protocols::score_filters::ScoreTypeFilter::compute(), protocols::simple_filters::ResidueSetChainEnergyFilter::compute(), protocols::simple_filters::EnergyPerResidueFilter::compute(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::convert_to_centroid(), protocols::metal_interface::ZincHeterodimerMover::copy_to_centroid(), protocols::loophash::MPI_LoopHashRefine_Master::create_loophash_WUs(), protocols::pose_length_moves::NearNativeLoopCloser::create_potential_loops(), protocols::loop_modeling::utilities::PrepareForCentroid::do_apply(), protocols::loop_modeling::utilities::PrepareForFullatom::do_apply(), protocols::abinitio::AbrelaxApplication::do_distributed_rerun(), protocols::forge::remodel::RemodelLoopMover::fa_relax_stage(), protocols::noesy_assign::NoesyModule::generate_constraint_files(), protocols::seeded_abinitio::GrowPeptides::grow_from_vertices(), protocols::constraints_additional::BindingSiteConstraint::init(), protocols::topology_broker::RigidChunkClaimer::init_after_reading(), protocols::helical_bundle_predict::HelicalBundlePredictApplication::make_pose_from_sequence_file_contents(), protocols::loophash::LoopHashRelaxProtocol::manual_call(), protocols::topology_broker::RigidChunkClaimer::new_decoy(), protocols::frag_picker::FragmentCandidate::output_silent(), protocols::rna::denovo::RNA_DeNovoProtocol::output_to_silent_file(), protocols::scoring::methods::saxs::PDDFEnergy::PDDFEnergy(), protocols::RBSegmentRelaxImpl::RBSegmentRelaxImpl(), protocols::comparative_modeling::rebuild_loops_until_closed(), protocols::pose_metric_calculators::FragQualCalculator::recompute(), protocols::tcr::remodel_tcr_cdr_loops(), protocols::relax::WorkUnit_BatchRelax_and_PostRescore::rescore_all_decoys(), protocols::topology_broker::RigidChunkClaimer::RigidChunkClaimer(), protocols::helical_bundle_predict::HelicalBundlePredictApplication::run(), protocols::loophash::WorkUnit_LoopHash::run(), protocols::mpi_refinement::WorkUnit_LoopHash::run(), protocols::relax::WorkUnit_BatchRelax_and_PostRescore::set_defaults(), protocols::abinitio::AbrelaxApplication::setup(), protocols::pose_length_moves::PossibleLoop::setup_finalPose_copy_rotamers(), protocols::abinitio::ResolutionSwitcher::start_pose(), protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::switch_residue_type_set(), protocols::topology_broker::TopologyBroker::switch_to_fullatom(), switch_to_residue_type_set(), protocols::star::to_centroid(), protocols::medal::to_centroid(), protocols::nonlocal::SingleFragmentMover::to_centroid(), protocols::legacy_sewing::Assembly::to_pose(), protocols::sewing::data_storage::SmartAssembly::to_pose(), and protocols::jobdist::universal_main().

switch_to_residue_type_set() [2/3]

void core::util::switch_to_residue_type_set	(	core::pose::Pose &	pose,
		core::chemical::TypeSetMode	type_set_mode,
		core::Size const	threads_to_request = 0,
		bool	allow_sloppy_match = false,
		bool	switch_protein_res_only = false,
		bool	keep_energies = false
	)

the function allows a pose to use a different residue_type_set to represent all its residues, such as from fullatom residues to centroid residues, or vice versa. During the switch, corresponding atoms will be copied. Redundant atoms will be removed (in case from fullatom to centroid) and missing atoms will be built by ideal geometry (in the case from centroid to fullatom).

References core::pose::Pose::residue_type_set_for_pose(), and switch_to_residue_type_set().

switch_to_residue_type_set() [3/3]

void core::util::switch_to_residue_type_set	(	core::pose::Pose &	pose,
		std::string const &	type_set_name,
		core::Size const	threads_to_request = 0,
		bool	allow_sloppy_match = false,
		bool	switch_protein_res_only = false,
		bool	keep_energies = false
	)

the function allows a pose to use a different residue_type_set to represent all its residues, such as from fullatom residues to centroid residues, or vice versa. During the switch, corresponding atoms will be copied. Redundant atoms will be removed (in case from fullatom to centroid) and missing atoms will be built by ideal geometry (in the case from centroid to fullatom).

References switch_to_residue_type_set().

TR() [1/3]

static basic::Tracer core::util::TR ( "core.util.metalloproteins_util"  )

static

TR() [2/3]

static basic::Tracer core::util::TR ( "core.util.switchresiduetypeset"  )

static

TR() [3/3]

static basic::Tracer core::util::TR ( "protocols.toolbox.disulfide_util"  )

static

Referenced by add_covalent_linkage(), auto_setup_all_metal_bonds(), auto_setup_all_metal_constraints(), find_metalbinding_atoms_helper(), rebuild_disulfide(), switch_to_centroid_rot_set(), and switch_to_residue_type_set().

TS()

static basic::Tracer core::util::TS ( "core.scoring.cryst.util"  )

static

Referenced by getMLweight().

Variable Documentation

METALS

std::set< std::string > const core::util::METALS = { "NA", "K", "MG", "LI", "CA", "CU", "CO", "NI", "FE", "ZN", "CR", "MN", "MO", "PD", "PT", "AG", "HG", "LA", "FE2"}

: Set of element strings used to identify metal ions.

Referenced by find_metalbinding_atoms_for_complex().