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protocols::antibody::CDRSetOptions Class Reference

Class that holds instructions for a single CDR for loading from the antibody database. Default is instructions to load all CDRs from the database. More...

#include <CDRSetOptions.hh>

Inheritance diagram for protocols::antibody::CDRSetOptions:
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Public Member Functions

 CDRSetOptions (bool load=true)
 
 CDRSetOptions (CDRNameEnum cdr, bool load=true)
 
 CDRSetOptions (CDRSetOptions const &src)
 
 ~CDRSetOptions () override
 
void set_cdr (CDRNameEnum cdr)
 
CDRNameEnum cdr () const
 
void load (bool load)
 
bool load () const
 
void length_type (core::Size const type, bool const setting)
 Set to only sample with clusters of the given type for this CDR. More...
 
utility::vector1< boollength_type () const
 
void min_length (core::Size length)
 set the minimum cdr length to sample. Nothing shorter then this will be used during graft. More...
 
core::Size min_length () const
 
void max_length (core::Size length)
 set the maximum cdr length to sample. Nothing longer then this will be used. Useful for H3. More...
 
core::Size max_length () const
 
void exclude_pdbs (utility::vector1< std::string > exclude_pdbids)
 
void exclude_pdbs_add (std::string pdbid)
 
void exclude_pdbs_clear ()
 
utility::vector1< std::string > exclude_pdbs () const
 
void include_only_pdbs (utility::vector1< std::string > include_pdbids)
 
void include_only_pdbs_add (std::string pdbid)
 
void include_only_pdbs_clear ()
 
utility::vector1< std::string > include_only_pdbs () const
 
void exclude_clusters (utility::vector1< clusters::CDRClusterEnum > exclude)
 
void exclude_clusters_add (clusters::CDRClusterEnum exclude)
 
void exclude_clusters_clear ()
 
utility::vector1
< clusters::CDRClusterEnum
exclude_clusters () const
 
void include_only_clusters (utility::vector1< clusters::CDRClusterEnum > include_only)
 
void include_only_clusters_add (clusters::CDRClusterEnum include_only)
 
void include_only_clusters_clear ()
 
utility::vector1
< clusters::CDRClusterEnum
include_only_clusters () const
 
void exclude_species (utility::vector1< std::string > exclude)
 
void exclude_species_add (std::string exclude)
 
void exclude_species_clear ()
 
utility::vector1< std::string > exclude_species () const
 
void include_only_species (utility::vector1< std::string > include_only)
 
void include_only_species_add (std::string include_only)
 
void include_only_species_clear ()
 
utility::vector1< std::string > include_only_species () const
 
void exclude_germlines (utility::vector1< std::string > exclude)
 
void exclude_germlines_add (std::string exclude)
 
void exclude_germlines_clear ()
 
utility::vector1< std::string > exclude_germlines () const
 
void include_only_germlines (utility::vector1< std::string > include_only)
 
void include_only_germlines_add (std::string include_only)
 
void include_only_germlines_clear ()
 
utility::vector1< std::string > include_only_germlines () const
 
void include_only_current_cluster (bool only_current_cluster)
 If antibody CDRs are loaded in relation to the current PDB in whatever algorithm or app is using this, Should we only pull clusters of the same type as this PDB? More...
 
bool include_only_current_cluster () const
 
void include_only_center_clusters (bool centers_only)
 Do we only include the center members of the clusters in the CDRSet? More...
 
bool include_only_center_clusters () const
 
void cluster_sampling_cutoff (core::Size cutoff)
 Set a sampling cutoff. Use zero for no cutoff as default. More...
 
core::Size cluster_sampling_cutoff () const
 
CDRSetOptionsOP clone () const
 
void set_defaults ()
 

Private Attributes

CDRNameEnum cdr_
 
bool load_
 
bool only_current_cluster_
 
bool only_center_clusters_
 
utility::vector1< boollength_types_
 
utility::vector1< std::string > exclude_pdb_ids_
 
utility::vector1< std::string > include_only_pdb_ids_
 
utility::vector1
< clusters::CDRClusterEnum
exclude_clusters_
 
utility::vector1
< clusters::CDRClusterEnum
include_only_clusters_
 
core::Size min_length_
 
core::Size max_length_
 
utility::vector1< std::string > exclude_species_
 
utility::vector1< std::string > include_only_species_
 
utility::vector1< std::string > exclude_germlines_
 
utility::vector1< std::string > include_only_germlines_
 
core::Size sampling_cutoff_
 

Detailed Description

Class that holds instructions for a single CDR for loading from the antibody database. Default is instructions to load all CDRs from the database.

Constructor & Destructor Documentation

protocols::antibody::CDRSetOptions::CDRSetOptions ( bool  load = true)

References set_defaults().

protocols::antibody::CDRSetOptions::CDRSetOptions ( CDRNameEnum  cdr,
bool  load = true 
)

References set_defaults().

protocols::antibody::CDRSetOptions::CDRSetOptions ( CDRSetOptions const &  src)
protocols::antibody::CDRSetOptions::~CDRSetOptions ( )
overridedefault

Member Function Documentation

CDRNameEnum protocols::antibody::CDRSetOptions::cdr ( ) const
inline

References cdr_.

Referenced by set_cdr().

CDRSetOptionsOP protocols::antibody::CDRSetOptions::clone ( ) const
void protocols::antibody::CDRSetOptions::cluster_sampling_cutoff ( core::Size  cutoff)

Set a sampling cutoff. Use zero for no cutoff as default.

References sampling_cutoff_.

core::Size protocols::antibody::CDRSetOptions::cluster_sampling_cutoff ( ) const

References sampling_cutoff_.

void protocols::antibody::CDRSetOptions::exclude_clusters ( utility::vector1< clusters::CDRClusterEnum exclude)

References exclude_clusters_.

utility::vector1< CDRClusterEnum > protocols::antibody::CDRSetOptions::exclude_clusters ( ) const

References exclude_clusters_.

void protocols::antibody::CDRSetOptions::exclude_clusters_add ( clusters::CDRClusterEnum  exclude)

References exclude_clusters_.

void protocols::antibody::CDRSetOptions::exclude_clusters_clear ( )

References exclude_clusters_.

void protocols::antibody::CDRSetOptions::exclude_germlines ( utility::vector1< std::string >  exclude)

References exclude_germlines_.

utility::vector1< std::string > protocols::antibody::CDRSetOptions::exclude_germlines ( ) const

References exclude_germlines_.

void protocols::antibody::CDRSetOptions::exclude_germlines_add ( std::string  exclude)

References exclude_germlines_.

void protocols::antibody::CDRSetOptions::exclude_germlines_clear ( )

References exclude_germlines_.

void protocols::antibody::CDRSetOptions::exclude_pdbs ( utility::vector1< std::string >  exclude_pdbids)

References exclude_pdb_ids_.

utility::vector1< std::string > protocols::antibody::CDRSetOptions::exclude_pdbs ( ) const

References exclude_pdb_ids_.

void protocols::antibody::CDRSetOptions::exclude_pdbs_add ( std::string  pdbid)

References exclude_pdb_ids_.

void protocols::antibody::CDRSetOptions::exclude_pdbs_clear ( )

References exclude_pdb_ids_.

void protocols::antibody::CDRSetOptions::exclude_species ( utility::vector1< std::string >  exclude)

References exclude_species_.

utility::vector1< std::string > protocols::antibody::CDRSetOptions::exclude_species ( ) const

References exclude_species_.

void protocols::antibody::CDRSetOptions::exclude_species_add ( std::string  exclude)

References exclude_species_.

void protocols::antibody::CDRSetOptions::exclude_species_clear ( )

References exclude_species_.

void protocols::antibody::CDRSetOptions::include_only_center_clusters ( bool  centers_only)

Do we only include the center members of the clusters in the CDRSet?

References only_center_clusters_.

bool protocols::antibody::CDRSetOptions::include_only_center_clusters ( ) const

References only_center_clusters_.

void protocols::antibody::CDRSetOptions::include_only_clusters ( utility::vector1< clusters::CDRClusterEnum include_only)
utility::vector1< CDRClusterEnum > protocols::antibody::CDRSetOptions::include_only_clusters ( ) const
void protocols::antibody::CDRSetOptions::include_only_clusters_add ( clusters::CDRClusterEnum  include_only)
void protocols::antibody::CDRSetOptions::include_only_clusters_clear ( )
void protocols::antibody::CDRSetOptions::include_only_current_cluster ( bool  only_current_cluster)

If antibody CDRs are loaded in relation to the current PDB in whatever algorithm or app is using this, Should we only pull clusters of the same type as this PDB?

May or may not be used. In AntibodyGraftDesign, this is used.

References only_current_cluster_.

bool protocols::antibody::CDRSetOptions::include_only_current_cluster ( ) const

References only_current_cluster_.

void protocols::antibody::CDRSetOptions::include_only_germlines ( utility::vector1< std::string >  include_only)
utility::vector1< std::string > protocols::antibody::CDRSetOptions::include_only_germlines ( ) const
void protocols::antibody::CDRSetOptions::include_only_germlines_add ( std::string  include_only)
void protocols::antibody::CDRSetOptions::include_only_germlines_clear ( )
void protocols::antibody::CDRSetOptions::include_only_pdbs ( utility::vector1< std::string >  include_pdbids)

References include_only_pdb_ids_.

utility::vector1< std::string > protocols::antibody::CDRSetOptions::include_only_pdbs ( ) const

References include_only_pdb_ids_.

void protocols::antibody::CDRSetOptions::include_only_pdbs_add ( std::string  pdbid)

References include_only_pdb_ids_.

void protocols::antibody::CDRSetOptions::include_only_pdbs_clear ( )

References include_only_pdb_ids_.

void protocols::antibody::CDRSetOptions::include_only_species ( utility::vector1< std::string >  include_only)

References include_only_species_.

utility::vector1< std::string > protocols::antibody::CDRSetOptions::include_only_species ( ) const

References include_only_species_.

void protocols::antibody::CDRSetOptions::include_only_species_add ( std::string  include_only)

References include_only_species_.

void protocols::antibody::CDRSetOptions::include_only_species_clear ( )

References include_only_species_.

void protocols::antibody::CDRSetOptions::length_type ( core::Size const  type,
bool const  setting 
)

Set to only sample with clusters of the given type for this CDR.

References length_types_.

utility::vector1<bool> protocols::antibody::CDRSetOptions::length_type ( ) const
inline

References length_types_.

void protocols::antibody::CDRSetOptions::load ( bool  load)

References load(), and load_.

bool protocols::antibody::CDRSetOptions::load ( ) const
inline

References load_.

Referenced by load().

void protocols::antibody::CDRSetOptions::max_length ( core::Size  length)

set the maximum cdr length to sample. Nothing longer then this will be used. Useful for H3.

References max_length_.

core::Size protocols::antibody::CDRSetOptions::max_length ( ) const
inline

References max_length_.

void protocols::antibody::CDRSetOptions::min_length ( core::Size  length)

set the minimum cdr length to sample. Nothing shorter then this will be used during graft.

References min_length_.

core::Size protocols::antibody::CDRSetOptions::min_length ( ) const
inline

References min_length_.

void protocols::antibody::CDRSetOptions::set_cdr ( CDRNameEnum  cdr)

References cdr(), and cdr_.

void protocols::antibody::CDRSetOptions::set_defaults ( )

Member Data Documentation

CDRNameEnum protocols::antibody::CDRSetOptions::cdr_
private

Referenced by cdr(), and set_cdr().

utility::vector1< clusters::CDRClusterEnum > protocols::antibody::CDRSetOptions::exclude_clusters_
private
utility::vector1< std::string > protocols::antibody::CDRSetOptions::exclude_germlines_
private
utility::vector1< std::string > protocols::antibody::CDRSetOptions::exclude_pdb_ids_
private
utility::vector1< std::string > protocols::antibody::CDRSetOptions::exclude_species_
private
utility::vector1< clusters::CDRClusterEnum > protocols::antibody::CDRSetOptions::include_only_clusters_
private
utility::vector1< std::string > protocols::antibody::CDRSetOptions::include_only_germlines_
private
utility::vector1< std::string > protocols::antibody::CDRSetOptions::include_only_pdb_ids_
private
utility::vector1< std::string > protocols::antibody::CDRSetOptions::include_only_species_
private
utility::vector1< bool> protocols::antibody::CDRSetOptions::length_types_
private

Referenced by length_type(), and set_defaults().

bool protocols::antibody::CDRSetOptions::load_
private

Referenced by load().

core::Size protocols::antibody::CDRSetOptions::max_length_
private

Referenced by max_length(), and set_defaults().

core::Size protocols::antibody::CDRSetOptions::min_length_
private

Referenced by min_length(), and set_defaults().

bool protocols::antibody::CDRSetOptions::only_center_clusters_
private
bool protocols::antibody::CDRSetOptions::only_current_cluster_
private
core::Size protocols::antibody::CDRSetOptions::sampling_cutoff_
private

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