Classes
class	ABEGO
	abego elments More...

class	ABEGOManager
	manager for abego More...

class	ChainbreakUtil

struct	Line
	struct More...

Typedefs
typedef utility::pointer::owning_ptr < ABEGOManager >	ABEGOManagerOP

typedef utility::pointer::owning_ptr < ABEGOManager const >	ABEGOManagerCOP

Functions
utility::vector1< std::string >	get_abego (core::pose::Pose const &pose, core::Size const level)
	utility for getting abego More...

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...

void	rebuild_disulfide (Pose &pose, Size lower_res, Size upper_res, 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::pack::task::PackerTaskOP packer_task=0, core::scoring::ScoreFunctionOP packer_score=0, core::kinematics::MoveMapOP mm=0, core::scoring::ScoreFunctionOP minimizer_score=0)
	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::pack::task::PackerTaskOP packer_task=0, core::scoring::ScoreFunctionOP packer_score=0, core::kinematics::MoveMapOP mm=0, core::scoring::ScoreFunctionOP minimizer_score=0)
	Rebuild a pair of cysteines (and possibly surrounding residues) so that they form a near-ideal disulfide bond. More...

void	remove_cutpoint_variants (core::pose::Pose &pose)
	Removes cutpoint variants from `pose` by scanning the fold tree. 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...

void	add_covalent_linkage_helper (core::pose::Pose &pose, core::Size const res_pos, core::Size const Atpos, numeric::xyzVector< core::Real > const partner_xyz, std::string &res_varname, bool const remove_hydrogens)
	: This is a helper function for the add_covalent_linkage function. You probably don't want to call it directly, unless you really know what you're doing. 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_metal_bonds (core::pose::Pose &pose, core::Size const metal_position, core::Real const dist_cutoff_multiplier, bool const remove_hydrogens)
	Function to auto-detect and add covalent connections to metal ions. 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	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...

void	switch_to_residue_type_set (core::pose::Pose &pose, std::string const &type_set_name, bool allow_sloppy_match)

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

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

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

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

Typedef Documentation

typedef utility::pointer::owning_ptr<ABEGOManager const> core::util::ABEGOManagerCOP

typedef utility::pointer::owning_ptr<ABEGOManager> core::util::ABEGOManagerOP

Function Documentation

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. 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(), core::pose::Pose::residue_type(), core::chemical::residue_type_base_name(), and core::conformation::Residue::xyz().

Referenced by add_covalent_linkages_to_metal().

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	partner_xyz,
		std::string &	res_varname,
		bool const	remove_hydrogens
	)

: This is a helper function for the add_covalent_linkage function. You probably don't want to call it directly, unless you really know what you're doing.

: 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 (colourful comments and all) in protocols/toolbox/match_enzdes_utils, and was modified to permit deletion of unnecessary protons and to remove EnzDes-specific stuff. 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)

Referenced by add_covalent_linkage().

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(), core::pose::Pose::residue(), and utility_exit_with_message.

Referenced by auto_setup_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 auto_setup_metal_bonds(), core::conformation::Residue::is_metal(), core::pose::Pose::n_residue(), nres, and core::pose::Pose::residue().

Referenced by core::import_pose::build_pose_as_is2().

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)

Referenced by auto_setup_all_metal_constraints(), and core::import_pose::build_pose_as_is2().

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 core::scoring::angle_constraint, core::scoring::atom_pair_constraint, auto_setup_all_metal_constraints(), core::scoring::ScoreFunction::get_weight(), and core::scoring::ScoreFunction::set_weight().

void core::util::auto_setup_metal_bonds	(	core::pose::Pose &	pose,
		core::Size const	metal_position,
		core::Real const	dist_cutoff_multiplier,
		bool const	remove_hydrogens
	)

Function to auto-detect and add covalent connections to metal ions.

Function to auto-detect and add covalent connections to a particular metal ion.

This function calls find_metalbinding_atoms and then passes the list of metal binding atoms to add_covalent_linkages_to_metal. 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) 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 calls find_metalbinding_atoms and then passes the list of metal binding atoms to add_covalent_linkages_to_metal. Inputs: pose (The pose that we'll operate on, changed 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) 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(), and find_metalbinding_atoms().

Referenced by auto_setup_all_metal_bonds().

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 core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type(), numeric::xyzVector< class >::distance_squared(), core::conformation::Residue::get_metal_binding_atoms(), core::conformation::Residue::is_metal(), core::conformation::Residue::is_metalbinding(), core::chemical::AtomType::lj_radius(), core::pose::Pose::n_residue(), nres, core::pose::Pose::residue(), utility_exit_with_message, and core::conformation::Residue::xyz().

Referenced by auto_setup_metal_bonds().

utility::vector1< std::string > core::util::get_abego	(	core::pose::Pose const &	pose,
		core::Size const	level
	)

utility for getting abego

References core::util::ABEGOManager::get_symbols().

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().

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::optimization::symmetry::SymMinimizerMap::copy_dofs_from_pose(), core::optimization::MinimizerMap::copy_dofs_from_pose(), core::optimization::AtomTreeMultifunc::dfunc(), core::optimization::symmetry::SymAtomTreeMultifunc::dfunc(), core::pose::symmetry::is_symmetric(), core::pose::symmetry::make_symmetric_movemap(), core::optimization::symmetry::SymMinimizerMap::nangles(), core::optimization::MinimizerMap::nangles(), core::optimization::MinimizerMap::setup(), core::scoring::symmetry::symmetrize_scorefunction(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), TS, vars, and core::scoring::xtal_ml.

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().

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::CartesianMultifunc::dfunc(), core::pose::symmetry::is_symmetric(), core::pose::symmetry::make_symmetric_movemap(), core::optimization::CartesianMinimizerMap::setup(), core::scoring::symmetry::symmetrize_scorefunction(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), vars, and core::scoring::xtal_ml.

void core::util::rebuild_disulfide	(	core::pose::Pose &	pose,
		core::Size	lower_res,
		core::Size	upper_res,
		core::pack::task::PackerTaskOP	packer_task = `0`,
		core::scoring::ScoreFunctionOP	packer_score = `0`,
		core::kinematics::MoveMapOP	mm = `0`,
		core::scoring::ScoreFunctionOP	minimizer_score = `0`
	)

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

void core::util::rebuild_disulfide	(	Pose &	pose,
		Size	lower_res,
		Size	upper_res,
		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

Referenced by switch_to_residue_type_set().

void core::util::rebuild_disulfide	(	core::pose::Pose &	pose,
		utility::vector1< std::pair< core::Size, core::Size > >	disulfides,
		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 cysteines with a bond defined between the SG 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
lower_res[in]	The first residue of the disulfide
upper_res[in]	The second residue of the disulfide
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::pack::pack_rotamers(), core::optimization::AtomTreeMinimizer::run(), core::pose::Pose::total_residue(), TR, core::pose::Pose::update_residue_neighbors(), and utility_exit.

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::pose::remove_variant_type_from_pose_residue(), and core::pose::Pose::total_residue().

void core::util::switch_to_residue_type_set	(	core::pose::Pose &	pose,
		std::string const &	type_set_name,
		bool	allow_sloppy_match
	)

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).

Variable Documentation

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

static

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

static

Referenced by core::util::ABEGOManager::index2symbol(), rebuild_disulfide(), switch_to_residue_type_set(), core::util::ABEGOManager::symbol2index(), and core::util::ABEGOManager::torsion2index().

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

static

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

static

Referenced by getMLweight().

Classes

Typedefs

Functions

Variables

Typedef Documentation

Function Documentation

Variable Documentation