ligand_functions.cc File Reference

#include <protocols/ligand_docking/ligand_functions.hh>
#include <core/conformation/Residue.hh>
#include <core/id/AtomID.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <core/scoring/constraints/AmbiguousConstraint.hh>
#include <core/scoring/constraints/Constraint.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/DihedralConstraint.hh>
#include <core/scoring/func/CircularHarmonicFunc.hh>
#include <basic/Tracer.hh>
#include <protocols/ligand_docking/grid_functions.hh>
#include <numeric/angle.functions.hh>
#include <numeric/conversions.hh>
#include <core/pose/Pose.hh>
#include <utility/vector1.hh>

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::ligand_docking

Functions
static thread_local basic::Tracer	protocols::ligand_docking::TR ("protocols.ligand_docking.ligand_functions")
core::scoring::constraints::ConstraintOP	protocols::ligand_docking::torsion_constraints_from_mean_sd (core::Size rsd_no, core::Size chino, core::chemical::ResidueType const &rsd_type, utility::vector1< std::pair< core::Real, core::Real > > const &mean_sd_degrees)
	Helper function. More...
core::scoring::constraints::ConstraintOP	protocols::ligand_docking::torsion_constraints_from_rotamers (core::Size rsd_no, core::Size chino, utility::vector1< core::conformation::ResidueCOP > const &rsds, core::Real stddev_degrees)
	Produce an ambiguous dihedral restraint for the specified chi angle, assuming that the provided conformations represent (all) energetic minima. More...
core::scoring::constraints::ConstraintOP	protocols::ligand_docking::torsion_constraints_from_chi_rotamers (core::Size rsd_no, core::Size chino, core::chemical::ResidueType const &rsdtype)
	Produce an ambiguous dihedral restraint for the specified chi angle, assuming that ResidueType.chi_rotamers() lists (all) energetic minima. More...
void	protocols::ligand_docking::get_ligand_torsion_constraints (core::pose::Pose &pose, core::Size rsd_no, core::Real stddev_degrees, utility::vector1< core::scoring::constraints::ConstraintOP > &csts_out, bool const constrain_all_torsions_equally)
	Produce dihedral restraints for all chi angles in the specified residue, from chi_rotamers() if available, and from the rotamer library otherwise. More...
void	protocols::ligand_docking::constrain_ligand_torsions (core::pose::Pose &pose, core::Real stddev_degrees, bool constrain_all_torsions_equally=true)
	Call get_ligand_torsion_constraints() for all non-polymer residues and add the resulting constraints to the Pose. More...
utility::vector1< core::Size >	protocols::ligand_docking::get_ligand_seqpos (core::pose::Pose const &pose)
	simple function to scan the pose for all ligand residues More...

Detailed Description

Author

Ian W. Davis