Rosetta
Public Member Functions | Private Attributes | List of all members
core::chemical::bcl::BCLFragmentHandler Class Reference

#include <BCLFragmentHandler.hh>

Inheritance diagram for core::chemical::bcl::BCLFragmentHandler:
Inheritance graph
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Public Member Functions

 BCLFragmentHandler ()
 default constructor More...
 
MutableResidueTypeCOP get_rosetta_restype () const
 construct with BCL fragment More...
 
IndexVDMapping const & get_index_to_vd () const
 Get how the most recently created ResidueType corresponds to the underlying fragment. More...
 
VDIndexMapping const & get_vd_to_index () const
 Get mapping of restype vertex descriptors to indices of the bcl fragments. More...
 
core::Size get_nbr () const
 Get the atom used as the neighbor atom when restype is generated. More...
 
void set_rosetta_restype (MutableResidueTypeCOP restype)
 Set the BCL molecule. More...
 
void set_nbr (core::Size nbr)
 Which atom in the fragment to use as the neighbor atom when the a restype is generated. More...
 

Private Attributes

MutableResidueTypeCOP rosetta_restype_
 molecule in Rosetta format More...
 
IndexVDMapping index_to_vd_
 How the fragment indices map to the most recently created ResidueType. More...
 
VDIndexMapping vd_to_index_
 Mapping of restype vertex descriptors to indices of the bcl fragments Uses utility::get_undefined_size() for non-represented BCL indices. More...
 
core::Size nbr_
 Which index in the fragment is used for the neighbor atom. utility::get_undefined_size() means autodetermine. More...
 

Constructor & Destructor Documentation

◆ BCLFragmentHandler()

core::chemical::bcl::BCLFragmentHandler::BCLFragmentHandler ( )

default constructor

Member Function Documentation

◆ get_index_to_vd()

IndexVDMapping const & core::chemical::bcl::BCLFragmentHandler::get_index_to_vd ( ) const

Get how the most recently created ResidueType corresponds to the underlying fragment.

References index_to_vd_.

◆ get_nbr()

core::Size core::chemical::bcl::BCLFragmentHandler::get_nbr ( ) const

Get the atom used as the neighbor atom when restype is generated.

References nbr_.

◆ get_rosetta_restype()

MutableResidueTypeCOP core::chemical::bcl::BCLFragmentHandler::get_rosetta_restype ( ) const

construct with BCL fragment

Return a Rosetta molecule as a MutableResidueType.

construct with Rosetta residue

Return the BCL molecule as a standard FragmentComplete

Return a Rosetta molecule as a MutableResidueType

References rosetta_restype_.

◆ get_vd_to_index()

VDIndexMapping const & core::chemical::bcl::BCLFragmentHandler::get_vd_to_index ( ) const

Get mapping of restype vertex descriptors to indices of the bcl fragments.

References vd_to_index_.

◆ set_nbr()

void core::chemical::bcl::BCLFragmentHandler::set_nbr ( core::Size  nbr)

Which atom in the fragment to use as the neighbor atom when the a restype is generated.

References protocols::sic_dock::scores::nbr, and nbr_.

◆ set_rosetta_restype()

void core::chemical::bcl::BCLFragmentHandler::set_rosetta_restype ( MutableResidueTypeCOP  restype)

Set the BCL molecule.

Set the Rosetta molecule.

Set the Rosetta molecule

References rosetta_restype_.

Member Data Documentation

◆ index_to_vd_

IndexVDMapping core::chemical::bcl::BCLFragmentHandler::index_to_vd_
private

How the fragment indices map to the most recently created ResidueType.

Referenced by get_index_to_vd().

◆ nbr_

core::Size core::chemical::bcl::BCLFragmentHandler::nbr_
private

Which index in the fragment is used for the neighbor atom. utility::get_undefined_size() means autodetermine.

Referenced by get_nbr(), and set_nbr().

◆ rosetta_restype_

MutableResidueTypeCOP core::chemical::bcl::BCLFragmentHandler::rosetta_restype_
private

molecule in Rosetta format

Referenced by get_rosetta_restype(), and set_rosetta_restype().

◆ vd_to_index_

VDIndexMapping core::chemical::bcl::BCLFragmentHandler::vd_to_index_
private

Mapping of restype vertex descriptors to indices of the bcl fragments Uses utility::get_undefined_size() for non-represented BCL indices.

Referenced by get_vd_to_index().


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