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:

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< bool >	length_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< bool >	length_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

)

References include_only_clusters_.

utility::vector1< CDRClusterEnum > protocols::antibody::CDRSetOptions::include_only_clusters

(

)

const

References include_only_clusters_.

void protocols::antibody::CDRSetOptions::include_only_clusters_add

(

clusters::CDRClusterEnum

include_only

)

References include_only_clusters_.

void protocols::antibody::CDRSetOptions::include_only_clusters_clear

(

)

References include_only_clusters_.

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

)

References include_only_germlines_.

utility::vector1< std::string > protocols::antibody::CDRSetOptions::include_only_germlines

(

)

const

References include_only_germlines_.

void protocols::antibody::CDRSetOptions::include_only_germlines_add

(

std::string

include_only

)

References include_only_germlines_.

void protocols::antibody::CDRSetOptions::include_only_germlines_clear

(

)

References include_only_germlines_.

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

(

)

References exclude_clusters_, exclude_germlines_, exclude_pdb_ids_, exclude_species_, include_only_clusters_, include_only_germlines_, include_only_pdb_ids_, include_only_species_, length_types_, max_length_, min_length_, only_center_clusters_, only_current_cluster_, and sampling_cutoff_.

Referenced by CDRSetOptions().

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

Referenced by exclude_clusters(), exclude_clusters_add(), exclude_clusters_clear(), and set_defaults().

utility::vector1< std::string > protocols::antibody::CDRSetOptions::exclude_germlines_

private

Referenced by exclude_germlines(), exclude_germlines_add(), exclude_germlines_clear(), and set_defaults().

utility::vector1< std::string > protocols::antibody::CDRSetOptions::exclude_pdb_ids_

private

Referenced by exclude_pdbs(), exclude_pdbs_add(), exclude_pdbs_clear(), and set_defaults().

utility::vector1< std::string > protocols::antibody::CDRSetOptions::exclude_species_

private

Referenced by exclude_species(), exclude_species_add(), exclude_species_clear(), and set_defaults().

utility::vector1< clusters::CDRClusterEnum > protocols::antibody::CDRSetOptions::include_only_clusters_

private

Referenced by include_only_clusters(), include_only_clusters_add(), include_only_clusters_clear(), and set_defaults().

utility::vector1< std::string > protocols::antibody::CDRSetOptions::include_only_germlines_

private

Referenced by include_only_germlines(), include_only_germlines_add(), include_only_germlines_clear(), and set_defaults().

utility::vector1< std::string > protocols::antibody::CDRSetOptions::include_only_pdb_ids_

private

Referenced by include_only_pdbs(), include_only_pdbs_add(), include_only_pdbs_clear(), and set_defaults().

utility::vector1< std::string > protocols::antibody::CDRSetOptions::include_only_species_

private

Referenced by include_only_species(), include_only_species_add(), include_only_species_clear(), and set_defaults().

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

Referenced by include_only_center_clusters(), and set_defaults().

bool protocols::antibody::CDRSetOptions::only_current_cluster_

private

Referenced by include_only_current_cluster(), and set_defaults().

core::Size protocols::antibody::CDRSetOptions::sampling_cutoff_

private

Referenced by cluster_sampling_cutoff(), and set_defaults().

---

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

• src/protocols/antibody/database/CDRSetOptions.hh
• src/protocols/antibody/database/CDRSetOptions.cc