metalloproteins_util.cc File Reference

#include <core/util/metalloproteins_util.hh>
#include <core/pose/copydofs/CopyDofs.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ResidueTypeSetCache.hh>
#include <core/chemical/Patch.hh>
#include <core/chemical/PatchOperation.hh>
#include <core/conformation/Conformation.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/AtomType.hh>
#include <core/chemical/ResidueConnection.hh>
#include <core/id/AtomID.hh>
#include <core/scoring/ScoreType.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/func/CircularHarmonicFunc.hh>
#include <core/scoring/func/ScalarWeightedFunc.hh>
#include <core/scoring/constraints/NamedAtomPairConstraint.hh>
#include <core/scoring/constraints/NamedAngleConstraint.hh>
#include <basic/Tracer.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <numeric/xyzVector.hh>
#include <numeric/xyz.functions.hh>
#include <utility/exit.hh>
#include <utility/string_util.hh>
#include <utility/vector1.hh>
#include <cmath>
#include <iostream>
#include <ObjexxFCL/string.functions.hh>

Namespaces
	core
	A class for reading in the atom type properties.
	core::util

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