protocols::antibody::constraints Namespace Reference

Classes
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	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...

Typedefs
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_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	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	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	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	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 >	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 >	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	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	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	get_harmonic_cluster_constraint_filename (AntibodyInfoCOP ab_info, clusters::CDRClusterEnum const cluster)
	Gets the cluster constraint name. Returns NA if not found. More...

Typedef Documentation

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

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

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

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

Function Documentation

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.

Currently requires North_AHO numbering.

References core::pose::Pose::add_constraints(), get_harmonic_cluster_constraint_filename(), and protocols::antibody::TR().

Referenced by add_harmonic_cluster_constraints(), add_harmonic_cluster_cst_or_coordinate_cst(), and add_harmonic_cluster_cst_or_dihedral_cst().

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.

Returns true or false depending on success

References core::pose::Pose::add_constraints(), get_harmonic_cluster_constraint_filename(), protocols::antibody::clusters::NA, and protocols::antibody::TR().

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.

Currently requires North_AHO numbering. Returns map of success/failure

References add_harmonic_cluster_constraint().

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.

Returns map of success/failure

References add_harmonic_cluster_constraint().

void protocols::antibody::constraints::add_harmonic_cluster_cst_or_coordinate_cst	(	AntibodyInfoOP	ab_info,
		core::pose::Pose &	pose,
		CDRNameEnum const	cdr,
		core::Real	coordinate_cst_sd
	)

Adds harmonic cluster constraint or coordinate cst if the cluster does not have constraints associated with it. Requires AHO numbering.

References core::scoring::constraints::add_coordinate_constraints(), add_harmonic_cluster_constraint(), and protocols::antibody::TR().

void protocols::antibody::constraints::add_harmonic_cluster_cst_or_coordinate_cst	(	AntibodyInfoOP	ab_info,
		core::pose::Pose &	pose,
		CDRNameEnum const	cdr,
		CDRClusterEnum const	cluster,
		core::Real	coordinate_cst_sd
	)

Adds harmonic cluster constraint or coordinate cst if the cluster does not have constraints associated with it. Requires AHO numbering.

References core::scoring::constraints::add_coordinate_constraints(), add_harmonic_cluster_constraint(), and protocols::antibody::TR().

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.

Values for avg SD for each cluster not including H3 were 23 and 42 degrees respectively. Values chosen here are conservative. Mean SD for both dihedrals was 32.66 degrees Use this especially if doing cartesian-space minimization

References add_harmonic_cluster_constraint(), and add_harmonic_dihedral_cst_general().

Referenced by protocols::antibody::design::AntibodyGraftDesignMover::run_graft(), protocols::antibody::design::AntibodySeqDesignMover::setup_cdr_constraints(), and protocols::antibody::design::AntibodyDesignMover::setup_constraints().

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.

Values for avg SD for each cluster not including H3 were 23 and 42 degrees respectively. Values chosen here are conservative. Mean SD for both dihedrals was 32.66 degrees Use this especially if doing cartesian-space minimization

References add_harmonic_cluster_constraint(), add_harmonic_dihedral_cst_general(), and protocols::antibody::TR().

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.

Values for avg SD for each cluster not including H3 were 23 and 42 degrees respectively. Values chosen here are conservative. Mean SD for both dihedrals was 32.66 degrees 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(), numeric::conversions::radians(), and core::pose::Pose::residue().

Referenced by add_harmonic_cluster_cst_or_dihedral_cst().

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(), and x().

Referenced by protocols::antibody::design::AntibodySeqDesignMover::setup_cdr_constraints(), and protocols::antibody::design::AntibodyDesignMover::setup_constraints().

std::string protocols::antibody::constraints::get_harmonic_cluster_constraint_filename	(	AntibodyInfoCOP	ab_info,
		CDRClusterEnum const	cluster
	)

Gets the cluster constraint name. Returns NA if not found.

References utility::file::file_exists(), option, and protocols::antibody::TR().

Referenced by add_harmonic_cluster_constraint().