util.cc File Reference

#include <protocols/antibody/constraints/util.hh>
#include <core/conformation/Residue.hh>
#include <core/id/AtomID.hh>
#include <core/scoring/constraints/Constraint.hh>
#include <core/scoring/constraints/ConstraintIO.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/DihedralConstraint.hh>
#include <core/scoring/func/CircularHarmonicFunc.hh>
#include <core/scoring/constraints/util.hh>
#include <protocols/antibody/AntibodyInfo.hh>
#include <iostream>
#include <fstream>
#include <basic/Tracer.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <numeric/conversions.hh>
#include <utility/file/FileName.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/excn/Exceptions.hh>

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

Functions
bool	protocols::antibody::constraints::cdr_has_res_constraints (AntibodyInfoCOP ab_info, core::pose::Pose &pose, CDRNameEnum const cdr, std::string const constraint_type)
	Check if all residues already have a specific constraint type. Useful for coordinate and dihedral constraints. More...
void	protocols::antibody::constraints::add_harmonic_cluster_cst_or_coordinate_cst (AntibodyInfoOP ab_info, core::pose::Pose &pose, CDRNameEnum const cdr, core::Real coord_cst_sd=.75)
	Adds harmonic cluster constraint or coordinate cst if the cluster does not have constraints associated with it. Requires AHO numbering. More...
void	protocols::antibody::constraints::add_harmonic_cluster_cst_or_coordinate_cst (AntibodyInfoOP ab_info, core::pose::Pose &pose, CDRNameEnum const cdr, clusters::CDRClusterEnum const cluster, core::Real coord_cst_sd=.75)
	Adds harmonic cluster constraint or coordinate cst if the cluster does not have constraints associated with it. Requires AHO numbering. More...
void	protocols::antibody::constraints::add_harmonic_cluster_cst_or_dihedral_cst (AntibodyInfoOP ab_info, core::pose::Pose &pose, CDRNameEnum const cdr, core::Real phi_sd_deg=20.0, core::Real psi_sd_deg=30.0)
	Add dihedral constraints to CDR with mean being the current phi/psi if no cluster constraints. More...
void	protocols::antibody::constraints::add_harmonic_cluster_cst_or_dihedral_cst (AntibodyInfoOP ab_info, core::pose::Pose &pose, CDRNameEnum const cdr, clusters::CDRClusterEnum const cluster, core::Real phi_sd_deg=20.0, core::Real psi_sd_deg=30.0)
	Add dihedral constraints to CDR with mean being the current phi/psi if no cluster constraints. More...
void	protocols::antibody::constraints::add_harmonic_dihedral_cst_general (AntibodyInfoOP ab_info, core::pose::Pose &pose, CDRNameEnum const cdr, core::Real phi_sd_deg=20.0, core::Real psi_sd_deg=30.0)
	Add dihedral constraints to CDR with mean being the current phi/psi. More...
std::map< CDRNameEnum, bool >	protocols::antibody::constraints::add_harmonic_cluster_constraints (AntibodyInfoOP ab_info, core::pose::Pose &pose)
	Adds dihedral harmonic constraints to Pose CDRs using cluster info in AntibodyInfo. More...
std::map< CDRNameEnum, bool >	protocols::antibody::constraints::add_harmonic_cluster_constraints (AntibodyInfoOP ab_info, core::pose::Pose &pose, utility::vector1< core::scoring::constraints::ConstraintCOP > constraints)
	Same as above, but adds constraints to the vector so they can be identified and removed from the pose if needed. More...
bool	protocols::antibody::constraints::add_harmonic_cluster_constraint (AntibodyInfoCOP ab_info, core::pose::Pose &pose, clusters::CDRClusterEnum const cluster)
	Adds a harmonic constraint to a Pose CDR based on cluster type. More...
bool	protocols::antibody::constraints::add_harmonic_cluster_constraint (AntibodyInfoCOP ab_info, core::pose::Pose &pose, clusters::CDRClusterEnum const cluster, utility::vector1< core::scoring::constraints::ConstraintCOP > constraints)
	Same as above, but adds constraints to the vector so they can be identified and removed from the pose if needed. More...
std::string	protocols::antibody::constraints::get_harmonic_cluster_constraint_filename (AntibodyInfoCOP ab_info, clusters::CDRClusterEnum const cluster)
	Gets the cluster constraint name. Returns NA if not found. More...

Variables
static basic::Tracer	TR ("antibody.constraints.util")

Detailed Description

Author

Jared Adolf-Bryfogle (jadol.nosp@m.fbr@.nosp@m.gmail.nosp@m..com)

Variable Documentation

basic::Tracer TR("antibody.constraints.util")

static