protocols::antibody::clusters::CDRCluster Class Reference

Simple class to hold and access CDRCluster info for a region of the pose. More...

#include <CDRCluster.hh>

Inheritance diagram for protocols::antibody::clusters::CDRCluster:

Public Member Functions
	CDRCluster (core::pose::Pose const &pose, CDRNameEnum const cdr, core::Size const cdr_length, CDRClusterEnum const cluster, core::Size const start, core::Real const distance, bool cis_trans_match=true)
	CDRCluster (CDRCluster const &src)
CDRClusterOP	clone () const
	~CDRCluster () override
CDRNameEnum	cdr () const
CDRClusterEnum	cluster () const
core::Size	start () const
	return Rosetta start that was used for construction More...
core::Size	end () const
	return Rosetta end that was used for construction More...
core::Size	pdb_start () const
	return PDB start. Useful for CDR length changes in other parts of the antibody when combined with numbering scheme ala AbInfo More...
core::Size	pdb_end () const
	return PDB end. Useful for CDR length changes in other parts of the antibody when combined with numbering scheme ala AbInfo More...
char	chain () const
	return PDB chain More...
core::Real	distance () const
core::Real	length_normalized_distance () const
core::Real	normalized_distance_in_degrees () const
bool	cis_trans_match () const
	Does the closest cluster match at cis_trans positions? Currently, this should always be True. More...

Private Member Functions
void	set_pdb_numbering (core::pose::Pose const &pose, core::Size start, core::Size end)

Private Attributes
CDRNameEnum	cdr_
CDRClusterEnum	cluster_
core::Real	distance_
core::Real	normalized_distance_
core::Size	pdb_start_
core::Size	pdb_end_
char	pdb_start_insertion_code_
char	pdb_end_insertion_code_
core::Size	start_
core::Size	end_
char	chain_
bool	cis_trans_match_

Detailed Description

Simple class to hold and access CDRCluster info for a region of the pose.

Constructor & Destructor Documentation

protocols::antibody::clusters::CDRCluster::CDRCluster	(	core::pose::Pose const &	pose,
		CDRNameEnum const	cdr,
		core::Size const	cdr_length,
		CDRClusterEnum const	cluster,
		core::Size const	start,
		core::Real const	distance,
		bool	cis_trans_match = true
	)

References end_, normalized_distance_, and set_pdb_numbering().

protocols::antibody::clusters::CDRCluster::CDRCluster ( CDRCluster const &  src )

default

protocols::antibody::clusters::CDRCluster::~CDRCluster ( )

overridedefault

Member Function Documentation

CDRNameEnum protocols::antibody::clusters::CDRCluster::cdr ( ) const

inline

References cdr_.

char protocols::antibody::clusters::CDRCluster::chain ( ) const

inline

return PDB chain

References chain_.

bool protocols::antibody::clusters::CDRCluster::cis_trans_match ( ) const

inline

Does the closest cluster match at cis_trans positions? Currently, this should always be True.

References cis_trans_match_.

CDRClusterOP protocols::antibody::clusters::CDRCluster::clone

(

)

const

CDRClusterEnum protocols::antibody::clusters::CDRCluster::cluster ( ) const

inline

References cluster_.

core::Real protocols::antibody::clusters::CDRCluster::distance ( ) const

inline

References distance_.

core::Size protocols::antibody::clusters::CDRCluster::end ( ) const

inline

return Rosetta end that was used for construction

References end_.

core::Real protocols::antibody::clusters::CDRCluster::length_normalized_distance ( ) const

inline

References normalized_distance_.

core::Real protocols::antibody::clusters::CDRCluster::normalized_distance_in_degrees

(

)

const

References normalized_distance_.

core::Size protocols::antibody::clusters::CDRCluster::pdb_end ( ) const

inline

return PDB end. Useful for CDR length changes in other parts of the antibody when combined with numbering scheme ala AbInfo

References pdb_end_.

core::Size protocols::antibody::clusters::CDRCluster::pdb_start ( ) const

inline

return PDB start. Useful for CDR length changes in other parts of the antibody when combined with numbering scheme ala AbInfo

References pdb_start_.

void protocols::antibody::clusters::CDRCluster::set_pdb_numbering ( core::pose::Pose const &  pose, core::Size  start, core::Size  end  )

private

References chain_, pdb_end_, pdb_end_insertion_code_, core::pose::Pose::pdb_info(), pdb_start_, and pdb_start_insertion_code_.

Referenced by CDRCluster().

core::Size protocols::antibody::clusters::CDRCluster::start ( ) const

inline

return Rosetta start that was used for construction

References start_.

Member Data Documentation

CDRNameEnum protocols::antibody::clusters::CDRCluster::cdr_

private

Referenced by cdr().

char protocols::antibody::clusters::CDRCluster::chain_

private

Referenced by chain(), and set_pdb_numbering().

bool protocols::antibody::clusters::CDRCluster::cis_trans_match_

private

Referenced by cis_trans_match().

CDRClusterEnum protocols::antibody::clusters::CDRCluster::cluster_

private

Referenced by cluster().

core::Real protocols::antibody::clusters::CDRCluster::distance_

private

Referenced by distance().

core::Size protocols::antibody::clusters::CDRCluster::end_

private

Referenced by CDRCluster(), and end().

core::Real protocols::antibody::clusters::CDRCluster::normalized_distance_

private

Referenced by CDRCluster(), length_normalized_distance(), and normalized_distance_in_degrees().

core::Size protocols::antibody::clusters::CDRCluster::pdb_end_

private

Referenced by pdb_end(), and set_pdb_numbering().

char protocols::antibody::clusters::CDRCluster::pdb_end_insertion_code_

private

Referenced by set_pdb_numbering().

core::Size protocols::antibody::clusters::CDRCluster::pdb_start_

private

Referenced by pdb_start(), and set_pdb_numbering().

char protocols::antibody::clusters::CDRCluster::pdb_start_insertion_code_

private

Referenced by set_pdb_numbering().

core::Size protocols::antibody::clusters::CDRCluster::start_

private

Referenced by start().

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

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