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 = {}

)

Convert the stored molecule into a ResidueType.

References core::chemical::ChemicalManager::atom_type_set(), core::chemical::ChemicalManager::element_set(), core::chemical::ResidueTypeBase::interchangeability_group(), core::chemical::ChemicalManager::mm_atom_type_set(), core::chemical::ResidueTypeBase::name(), core::chemical::ResidueTypeBase::name1(), core::chemical::ResidueTypeBase::name3(), and core::chemical::ChemicalManager::orbital_type_set().

Referenced by generate_restype().

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

)

References core::chemical::ChemicalManager::atom_type_set(), core::chemical::ChemicalManager::element_set(), generate_restype(), core::chemical::ResidueTypeBase::interchangeability_group(), core::chemical::ChemicalManager::mm_atom_type_set(), core::chemical::ResidueTypeBase::name(), core::chemical::ResidueTypeBase::name1(), core::chemical::ResidueTypeBase::name3(), and core::chemical::ChemicalManager::orbital_type_set().

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

References core::chemical::ResidueTypeBase::atom_type_set_ptr(), core::chemical::AtomRefMapping< FromRef, ToRef >::clear(), core::chemical::rdkit::convert_from_rdkit_bondtype(), core::chemical::AtomRefMapping< FromRef, ToRef >::count(), core::chemical::ResidueTypeBase::element_set_ptr(), core::chemical::AtomRefMapping< FromRef, ToRef >::erase(), core::chemical::find_bonds_in_rings(), core::chemical::find_nbr_dist(), core::chemical::ResidueTypeBase::gasteiger_atom_typeset(), index_to_vd_, core::chemical::ResidueTypeBase::interchangeability_group(), core::chemical::ResidueTypeBase::mm_atom_types_ptr(), core::chemical::ResidueTypeBase::name(), core::chemical::ResidueTypeBase::name1(), core::chemical::ResidueTypeBase::name3(), nbr_, core::chemical::MutableResidueType::null_vertex, core::chemical::ResidueTypeBase::orbital_types_ptr(), rdmol_, core::chemical::rename_atoms(), core::chemical::rosetta_recharge_fullatom(), and core::chemical::rosetta_retype_fullatom().

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().

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

• src/core/chemical/rdkit/RDMolToRestype.hh
• src/core/chemical/rdkit/RDMolToRestype.cc