metalloproteins_util.hh File Reference

Utilities for working with metalloproteins. More...

#include <map>
#include <set>
#include <numeric/xyzVector.hh>
#include <utility/vector1.fwd.hh>
#include <core/types.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/ResidueType.fwd.hh>
#include <core/chemical/VariantType.fwd.hh>
#include <core/id/AtomID.fwd.hh>
#include <core/id/AtomID_Map.fwd.hh>
#include <core/id/DOF_ID_Mask.fwd.hh>
#include <core/id/NamedAtomID.fwd.hh>
#include <core/id/NamedStubID.fwd.hh>
#include <core/id/TorsionID.fwd.hh>
#include <core/kinematics/FoldTree.fwd.hh>
#include <core/kinematics/Jump.fwd.hh>
#include <core/kinematics/MoveMap.fwd.hh>
#include <core/kinematics/RT.fwd.hh>
#include <core/kinematics/tree/Atom.fwd.hh>
#include <core/scoring/ScoreType.hh>
#include <core/id/SequenceMapping.fwd.hh>
#include <core/pose/util.tmpl.hh>
#include <core/pose/MiniPose.fwd.hh>
#include <utility/vector1.hh>
#include <core/kinematics/Jump.hh>
#include <core/pose/Pose.fwd.hh>

Namespaces
	core
	A class for defining atom parameters, known as atom_types.
	core::util

Macros
#define	DEFAULT_DIST_CUTOFF_MULTIPLIER   1.05

Functions
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...
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. 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_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	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::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...

Detailed Description

Utilities for working with metalloproteins.

Author

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

Macro Definition Documentation

#define DEFAULT_DIST_CUTOFF_MULTIPLIER   1.05