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Public Member Functions | Private Member Functions | Private Attributes | List of all members
core::chemical::rdkit::RDMolToRestype Class Reference

#include <RDMolToRestype.hh>

Public Member Functions

 RDMolToRestype (::RDKit::ROMol const &rdmol)
 
MutableResidueTypeOP generate_restype (VDIndexMapping const &mapping={})
 Convert the stored molecule into a ResidueType. More...
 
MutableResidueTypeOP generate_restype (MutableResidueType const &orig_restype, VDIndexMapping const &mapping)
 Convert the stored molecule into a ResidueType, extracting additional information from the provided restype mapping is a mapping of the residue type atoms onto the rdmol atoms. More...
 
MutableResidueTypeOP generate_restype (IndexNameMapping const &mapping)
 
MutableResidueTypeOP generate_restype (MutableResidueType const &orig_restype, IndexNameMapping const &mapping)
 
IndexVDMapping const & index_to_vd () const
 Get how the most recently created ResidueType corresponds to the underlying fragment. 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 Member Functions

 RDMolToRestype ()
 

Private Attributes

core::Size nbr_
 Which index in the fragment is used for the neighbor atom. utility::get_undefined_size() means autodetermine. More...
 
IndexVDMapping index_to_vd_
 How the fragments indicies map to the most recently created ResidueType. More...
 
::RDKit::ROMol rdmol_
 

Constructor & Destructor Documentation

core::chemical::rdkit::RDMolToRestype::RDMolToRestype ( ::RDKit::ROMol const &  rdmol)
core::chemical::rdkit::RDMolToRestype::RDMolToRestype ( )
private

Member Function Documentation

MutableResidueTypeOP core::chemical::rdkit::RDMolToRestype::generate_restype ( VDIndexMapping const &  mapping = {})
MutableResidueTypeOP core::chemical::rdkit::RDMolToRestype::generate_restype ( MutableResidueType const &  orig_restype,
VDIndexMapping const &  mapping 
)

Convert the stored molecule into a ResidueType, extracting additional information from the provided restype mapping is a mapping of the residue type atoms onto the rdmol atoms.

Currently, it just pulls the following:

  • The type sets
  • name/name1/name3 and related
  • atom name information for atoms with valid mappings.

References core::chemical::MutableResidueType::all_atoms(), core::chemical::MutableResidueType::atom_name(), and generate_restype().

MutableResidueTypeOP core::chemical::rdkit::RDMolToRestype::generate_restype ( IndexNameMapping const &  mapping)
MutableResidueTypeOP core::chemical::rdkit::RDMolToRestype::generate_restype ( MutableResidueType const &  orig_restype,
IndexNameMapping const &  mapping 
)
IndexVDMapping const& core::chemical::rdkit::RDMolToRestype::index_to_vd ( ) const
inline

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

References index_to_vd_.

void core::chemical::rdkit::RDMolToRestype::set_nbr ( core::Size  nbr)
inline

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_.

Member Data Documentation

IndexVDMapping core::chemical::rdkit::RDMolToRestype::index_to_vd_
private

How the fragments indicies map to the most recently created ResidueType.

Referenced by generate_restype(), and index_to_vd().

core::Size core::chemical::rdkit::RDMolToRestype::nbr_
private

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

Referenced by generate_restype(), and set_nbr().

::RDKit::ROMol core::chemical::rdkit::RDMolToRestype::rdmol_
private

Referenced by generate_restype().


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