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Classes | Typedefs | Functions
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

Function Documentation

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().

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().