protocols::antibody::constraints Namespace Reference

Classes
class	CDRDihedralConstraintMover
	Add Cluster or General Dihedral CircularHarmonic constraints to a CDR. Cluster constraints currently only work for AHO renumbered CDRs. (This will be rafactored to create constraints on-the-fly from cluster Mean/SD instead of from cst files.) More...
class	CDRDihedralConstraintMoverCreator
class	ParatopeEpitopeSiteConstraintMover
	Add SiteConstraints from the Epitope to the Paratope and from the Paratope to the Epitope. Will only add the constraint if not already present. More...
class	ParatopeEpitopeSiteConstraintMoverCreator
class	ParatopeSiteConstraintMover
	Adds and removes ambiguous site constraints for the Antibody Paratope to antigen, defined for simplicity as the CDRs, however a set of paratope residues can be given to the class to use instead. More...
class	ParatopeSiteConstraintMoverCreator

Typedefs
typedef utility::pointer::shared_ptr< CDRDihedralConstraintMover >	CDRDihedralConstraintMoverOP
typedef utility::pointer::shared_ptr< CDRDihedralConstraintMover const >	CDRDihedralConstraintMoverCOP
typedef utility::pointer::shared_ptr< ParatopeEpitopeSiteConstraintMover >	ParatopeEpitopeSiteConstraintMoverOP
typedef utility::pointer::shared_ptr< ParatopeEpitopeSiteConstraintMover const >	ParatopeEpitopeSiteConstraintMoverCOP
typedef utility::pointer::shared_ptr< ParatopeSiteConstraintMover >	ParatopeSiteConstraintMoverOP
typedef utility::pointer::shared_ptr< ParatopeSiteConstraintMover const >	ParatopeSiteConstraintMoverCOP

Functions
bool	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	add_harmonic_dihedral_cst_general (AntibodyInfoCOP ab_info, core::pose::Pose &pose, CDRNameEnum const cdr, core::Real phi_sd_deg=16.0, core::Real psi_sd_deg=16.0)
	Add dihedral constraints to CDR with mean being the current phi/psi. More...

Typedef Documentation

CDRDihedralConstraintMoverCOP

typedef utility::pointer::shared_ptr< CDRDihedralConstraintMover const > protocols::antibody::constraints::CDRDihedralConstraintMoverCOP

CDRDihedralConstraintMoverOP

typedef utility::pointer::shared_ptr< CDRDihedralConstraintMover > protocols::antibody::constraints::CDRDihedralConstraintMoverOP

ParatopeEpitopeSiteConstraintMoverCOP

typedef utility::pointer::shared_ptr< ParatopeEpitopeSiteConstraintMover const > protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMoverCOP

ParatopeEpitopeSiteConstraintMoverOP

typedef utility::pointer::shared_ptr< ParatopeEpitopeSiteConstraintMover > protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMoverOP

ParatopeSiteConstraintMoverCOP

typedef utility::pointer::shared_ptr< ParatopeSiteConstraintMover const > protocols::antibody::constraints::ParatopeSiteConstraintMoverCOP

ParatopeSiteConstraintMoverOP

typedef utility::pointer::shared_ptr< ParatopeSiteConstraintMover > protocols::antibody::constraints::ParatopeSiteConstraintMoverOP

Function Documentation

add_harmonic_dihedral_cst_general()

void protocols::antibody::constraints::add_harmonic_dihedral_cst_general	(	AntibodyInfoCOP	ab_info,
		core::pose::Pose &	pose,
		CDRNameEnum const	cdr,
		core::Real	phi_sd_deg = 16.0,
		core::Real	psi_sd_deg = 16.0
	)

Add dihedral constraints to CDR with mean being the current phi/psi.

Values for avg SD for each cluster not including H3 were 16 and 16 degrees respectively. Using cluster outliers, values were at 21 and 23 degrees respectively. Mean SD for both dihedrals was 16 and 22 for without/with outliers. Use this especially if doing cartesian-space minimization

References core::pose::Pose::add_constraint(), core::conformation::Residue::atom_index(), core::pose::Pose::phi(), core::pose::Pose::psi(), and core::pose::Pose::residue().

Referenced by protocols::antibody::constraints::CDRDihedralConstraintMover::apply().

cdr_has_res_constraints()

bool protocols::antibody::constraints::cdr_has_res_constraints	(	AntibodyInfoCOP	ab_info,
		core::pose::Pose &	pose,
		CDRNameEnum	cdr,
		std::string const &	constraint_type
	)

Check if all residues already have a specific constraint type. Useful for coordinate and dihedral constraints.

References core::pose::Pose::constraint_set().