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:

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< ClusterData >	cluster_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

(

)

References allow_rama_mismatches_, center_cluster_db_path_, and load_center_data().

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

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...

References allow_rama_mismatches_, protocols::antibody::clusters::calculate_dihedral_distance(), protocols::antibody::clusters::ClusterData::cdr, protocols::antibody::clusters::ClusterData::cis_trans_conf, cluster_data_, core::kinematics::distance(), get_pose_angles(), protocols::antibody::clusters::get_pose_cis_trans_conformation(), protocols::antibody::clusters::ClusterData::length, protocols::mean_field::min(), protocols::antibody::clusters::NA, protocols::antibody::clusters::ClusterData::phis, protocols::antibody::clusters::ClusterData::psis, and protocols::antibody::clusters::TR().

CDRClusterOP protocols::antibody::clusters::CDRClusterMatcher::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.

References allow_rama_mismatches_, protocols::antibody::clusters::calculate_dihedral_distance(), protocols::antibody::clusters::ClusterData::cis_trans_conf, cluster_data_, core::kinematics::distance(), get_pose_angles(), protocols::antibody::clusters::get_pose_cis_trans_conformation(), protocols::antibody::l1, protocols::antibody::clusters::ClusterData::length, protocols::mean_field::min(), protocols::antibody::clusters::NA, protocols::antibody::clusters::ClusterData::phis, protocols::antibody::clusters::ClusterData::psis, and protocols::antibody::clusters::TR().

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

References core::sequence::end, core::pose::Pose::phi(), and core::pose::Pose::psi().

Referenced by get_cdr_cluster(), and get_closest_cluster().

void protocols::antibody::clusters::CDRClusterMatcher::load_center_data ( )

private

References protocols::antibody::clusters::ClusterData::cdr, center_cluster_db_path_, protocols::antibody::clusters::ClusterData::cis_trans_conf, protocols::antibody::clusters::ClusterData::cluster, cluster_data_, protocols::antibody::clusters::ClusterData::length, protocols::antibody::clusters::ClusterData::phis, protocols::antibody::clusters::ClusterData::psis, and protocols::sparta::split().

Referenced by CDRClusterMatcher().

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

Referenced by CDRClusterMatcher(), and load_center_data().

utility::vector1< ClusterData > protocols::antibody::clusters::CDRClusterMatcher::cluster_data_

private

Referenced by get_cdr_cluster(), get_closest_cluster(), and load_center_data().

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

• src/protocols/antibody/clusters/CDRClusterMatcher.hh
• src/protocols/antibody/clusters/CDRClusterMatcher.cc