metalloproteins_util.hh File Reference

Utilities for working with metalloproteins. More...

#include <core/types.hh>
#include <core/id/AtomID.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <utility/vector1.hh>
#include <core/pose/Pose.fwd.hh>
#include <map>
#include <set>

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

Variables
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. More...

Detailed Description

Utilities for working with metalloproteins.

Author

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

Macro Definition Documentation

DEFAULT_DIST_CUTOFF_MULTIPLIER

#define DEFAULT_DIST_CUTOFF_MULTIPLIER   1.05