util.cc File Reference

#include <protocols/ligand_docking/GALigandDock/util.hh>
#include <protocols/ligand_docking/GALigandDock/GridScorer.hh>
#include <core/chemical/AA.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/extra_pose_info_util.hh>
#include <core/pose/subpose_manipulation_util.hh>
#include <core/conformation/Residue.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/TwelveANeighborGraph.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreType.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/scoring/constraints/Constraint.fwd.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/hbonds/HBondSet.hh>
#include <core/scoring/hbonds/HBondDatabase.hh>
#include <core/scoring/hbonds/constants.hh>
#include <core/scoring/hbonds/HBondOptions.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/optimization/CartesianMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <numeric/random/random.functions.hh>
#include <numeric/random/random.hh>
#include <numeric/random/random_xyz.hh>
#include <numeric/conversions.hh>
#include <core/types.hh>
#include <basic/Tracer.hh>
#include <utility/vector1.hh>

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

Functions
static basic::Tracer	protocols::ligand_docking::ga_ligand_dock::TR ("protocols.ligand_docking.GALigandDock.util")
core::Size	protocols::ligand_docking::ga_ligand_dock::count_neighbors_on_coord (core::pose::Pose const &pose, core::Vector const &xyz1, std::string const atomname, core::Real const dcut)
utility::vector1< core::Size >	protocols::ligand_docking::ga_ligand_dock::count_neighbors (core::pose::Pose const &pose, std::string const atomname, core::Real const dcut)
utility::vector1< core::Size >	protocols::ligand_docking::ga_ligand_dock::get_atomic_contacting_sidechains (core::pose::Pose const &pose, utility::vector1< core::Size > const &ligids, core::Real const atomic_distance_cut)
void	protocols::ligand_docking::ga_ligand_dock::constraint_relax (core::pose::Pose &pose, utility::vector1< core::Size > const &ligids, utility::vector1< core::Size > const &movable_scs, core::Real maxiter)
void	protocols::ligand_docking::ga_ligand_dock::make_ligand_only_pose (core::pose::PoseOP pose_new, core::pose::PoseCOP pose, utility::vector1< core::Size > const &lig_resnos)
void	protocols::ligand_docking::ga_ligand_dock::perturb_ligand_rb (core::pose::Pose &pose, utility::vector1< core::Size > const &ligids, core::Real trans_step, core::Real rot_step)
void	protocols::ligand_docking::ga_ligand_dock::perturb_ligand_torsions (core::pose::Pose &pose, utility::vector1< core::Size > const &ligids, utility::vector1< core::Size > const &freeze_chi, core::Real chi_step)
core::Size	protocols::ligand_docking::ga_ligand_dock::get_ligand_jumpid (core::pose::Pose const &pose, utility::vector1< core::Size > const &ligids)
void	protocols::ligand_docking::ga_ligand_dock::get_ligand_resids (core::pose::Pose const &pose, utility::vector1< core::Size > &lig_resids)
bool	protocols::ligand_docking::ga_ligand_dock::is_hb_satisfied (core::scoring::ScoreFunctionOP sf, core::scoring::hbonds::HBondDatabaseCOP hb_database, core::scoring::hbonds::HBondOptions const &hbopt, hbAcc const &acc, hbDon const &don, core::Real const &maxHbdis2, core::Real const &hb_energy_cutoff, std::string const &metric)
void	protocols::ligand_docking::ga_ligand_dock::compute_nhbonds (core::pose::Pose const &pose, utility::vector1< core::Size > const &ligids, utility::vector1< core::Size > const &resids, core::Size &nhbonds_total, core::Size &nhbonds_max1, bool const &include_bb, std::string const &hb_metric)