metrics.cc File Reference

Routines to measure antibodies. More...

#include <protocols/antibody/util.hh>
#include <protocols/antibody/metrics.hh>
#include <protocols/antibody/AntibodyInfo.hh>
#include <protocols/antibody/AntibodyEnum.hh>
#include <basic/Tracer.hh>
#include <core/id/SequenceMapping.hh>
#include <core/conformation/Residue.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/init_id_map.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/util.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/scoring/hbonds/HBondOptions.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/sasa/SasaCalc.hh>
#include <core/scoring/rms_util.hh>
#include <numeric/PCA.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/xyzVector.io.hh>
#include <utility/vector1.hh>

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

Functions
static basic::Tracer	TR ("antibody.metrics")
vector1< Real >	protocols::antibody::vl_vh_orientation_coords (const core::pose::Pose &pose_in, const AntibodyInfo &ab_info)
	calculate the VH_VL packing angle from 2 sheet definitions on each antibody chain More...
std::pair< core::Real, core::Real >	protocols::antibody::kink_dihedral (const core::pose::Pose &pose, const protocols::antibody::AntibodyInfo &ab_info, bool debug)
core::Real	protocols::antibody::kink_bb_Hbond (const core::pose::Pose &pose, const protocols::antibody::AntibodyInfo &ab_info)
core::Real	protocols::antibody::kink_RD_Hbond (const core::pose::Pose &pose, const protocols::antibody::AntibodyInfo &ab_info)
core::Real	protocols::antibody::kink_Trp_Hbond (const core::pose::Pose &pose, const protocols::antibody::AntibodyInfo &ab_info)
std::pair< ParatopeMetric< core::Real >, ParatopeMetric< core::Real > >	protocols::antibody::paratope_sasa (const core::pose::Pose &pose, const AntibodyInfo &ab_info, bool include_de_loop=false)
	calculate the SASA of the antibody paratope. Returns all and hydrophobic components. More...
core::SSize	protocols::antibody::pose_charge (core::pose::Pose const &pose)
	calculate the net charge of the antibody More...
ParatopeMetric< core::SSize >	protocols::antibody::paratope_charge (core::pose::Pose const &pose, const protocols::antibody::AntibodyInfo &abinfo, bool include_de_loop=false)
	calculate the net charge of the paratope More...
core::Real	protocols::antibody::cdr_energy (core::pose::Pose const &pose, AntibodyInfoCOP ab_info, core::scoring::ScoreFunctionCOP scorefxn, CDRNameEnum const &cdr)
	calculate dSASA of the paratope and antigen using result of InterfaceAnalyzerMover More...
core::Real	protocols::antibody::cdr_CN_anchor_distance (core::pose::Pose const &pose, AntibodyInfoCOP ab_info, CDRNameEnum const &cdr)
	Calculate the distance between the carbon and nitrogen of each residue before and after the CDR respectively. More...
vector1< Real >	protocols::antibody::cdr_backbone_rmsds (core::pose::Pose &p1, core::pose::Pose const &p2, AntibodyInfoOP const a1, AntibodyInfoOP const a2, core::Size aln_thresh=10)
	Align two sequence matching antibodies and calculate CDR rmsds (add OCD), then store in scores. More...

Detailed Description

Routines to measure antibodies.

Author

Jeffrey J. Gray

Oana Lungu

Nick Marze

Jared Adolf-Bryfogle

Jeffrey J. Gray, Jared Adolf-Bryfogle

Function Documentation

TR()

static basic::Tracer TR ( "antibody.metrics"  )

static

Referenced by protocols::antibody::cdr_backbone_rmsds(), protocols::antibody::kink_bb_Hbond(), protocols::antibody::kink_dihedral(), protocols::antibody::kink_Trp_Hbond(), protocols::antibody::paratope_charge(), protocols::antibody::paratope_sasa(), and protocols::antibody::vl_vh_orientation_coords().