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protocols::antibody::clusters::CDRClusterMatcher Class Reference

Simple class for identifying CDR clusters of an antibody or protein structure. More...

#include <CDRClusterMatcher.hh>

Inheritance diagram for protocols::antibody::clusters::CDRClusterMatcher:
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Public Member Functions

 CDRClusterMatcher ()
 
 ~CDRClusterMatcher () override
 
CDRClusterOP get_cdr_cluster (core::pose::Pose const &pose, CDRNameEnum const cdr, core::Size start, const core::Size end) const
 Get the cluster of an antibody CDR region, defined between start and end of the pose. Should it give out an OP or not? It's a small class... I don't have any idea... More...
 
CDRClusterOP get_closest_cluster (core::pose::Pose const &pose, core::Size const start, core::Size const end) const
 Get the closest cluster of a region. Used to detect CDR-like regions in normal proteins. More...
 
bool allow_rama_mismatches () const
 skip first grouping Cis and Trans for clusters in which a Cis/Trans designation currently does not exist. Default False More...
 
void allow_rama_mismatches (bool const allow)
 Set to skip first grouping Cis and Trans for clusters in which a Cis/Trans designation currently does not exist. Default False. More...
 

Private Member Functions

void load_center_data ()
 
std::map< std::string,
utility::vector1< core::Real > > 
get_pose_angles (core::pose::Pose const &pose, core::Size const start, core::Size const end) const
 

Private Attributes

std::string center_cluster_db_path_
 
utility::vector1< ClusterDatacluster_data_
 
bool allow_rama_mismatches_
 skip first grouping Cis and Trans for clusters in which a Cis/Trans designation currently does not exist. More...
 

Detailed Description

Simple class for identifying CDR clusters of an antibody or protein structure.

Main interface is through CDRClusterSet/AntibodyInfo. That is where AntibodyNumbering can be used to access specific CDRs and numbering scheme transformations.

Constructor & Destructor Documentation

protocols::antibody::clusters::CDRClusterMatcher::CDRClusterMatcher ( )
protocols::antibody::clusters::CDRClusterMatcher::~CDRClusterMatcher ( )
overridedefault

Member Function Documentation

bool protocols::antibody::clusters::CDRClusterMatcher::allow_rama_mismatches ( ) const
inline

skip first grouping Cis and Trans for clusters in which a Cis/Trans designation currently does not exist. Default False

References allow_rama_mismatches_.

void protocols::antibody::clusters::CDRClusterMatcher::allow_rama_mismatches ( bool const  allow)
inline

Set to skip first grouping Cis and Trans for clusters in which a Cis/Trans designation currently does not exist. Default False.

References allow_rama_mismatches_.

CDRClusterOP protocols::antibody::clusters::CDRClusterMatcher::get_cdr_cluster ( core::pose::Pose const &  pose,
CDRNameEnum const  cdr,
core::Size  start,
const core::Size  end 
) const
CDRClusterOP protocols::antibody::clusters::CDRClusterMatcher::get_closest_cluster ( core::pose::Pose const &  pose,
core::Size const  start,
core::Size const  end 
) const
std::map< std::string, vector1< core::Real > > protocols::antibody::clusters::CDRClusterMatcher::get_pose_angles ( core::pose::Pose const &  pose,
core::Size const  start,
core::Size const  end 
) const
private
void protocols::antibody::clusters::CDRClusterMatcher::load_center_data ( )
private

Member Data Documentation

bool protocols::antibody::clusters::CDRClusterMatcher::allow_rama_mismatches_
private

skip first grouping Cis and Trans for clusters in which a Cis/Trans designation currently does not exist.

Referenced by allow_rama_mismatches(), CDRClusterMatcher(), get_cdr_cluster(), and get_closest_cluster().

std::string protocols::antibody::clusters::CDRClusterMatcher::center_cluster_db_path_
private
utility::vector1< ClusterData > protocols::antibody::clusters::CDRClusterMatcher::cluster_data_
private

The documentation for this class was generated from the following files: