Rosetta: core::chemical::rdkit::RestypeToRDMol Class Reference

Rosetta

#include <RestypeToRDMol.hh>

Public Member Functions
	RestypeToRDMol (MutableResidueType const &res, bool neutralize=true, bool keep_hydro=false, bool sanitize=true, bool noImplicitHs=false, bool skipHs=false)
	Convert ResidueType to an RDKit RWMol object. More...

	RestypeToRDMol (MutableResidueType const &res, RestypeToRDMolOptions const &options)

VDIndexMapping const &	vd_to_index () const
	Return the corespondance from the input ResidueType VD to the RDKit atom index. More...

IndexVDMapping const &	index_to_vd () const

std::map< core::Size, core::Size > const &	get_atomIndexMap_Rd2Res () const

::RDKit::RWMOL_SPTR	Mol ()
	Return an RDKit RWMol object which represents the residue type. More...

Private Member Functions
	RestypeToRDMol ()

Private Attributes
MutableResidueType const &	res_

RestypeToRDMolOptions	options_

bool	neutralize_

bool	keep_hydro_

bool	sanitize_

bool	noImplicitHs_

bool	skipHs_

bool	aro2double_ = false

VDIndexMapping	vd_to_index_
	Mapping of restype vertex descriptors to indices of the rdkit object. More...

IndexVDMapping	index_to_vd_

std::map< core::Size, core::Size >	atomIndexMap_Rd2Res_

Constructor & Destructor Documentation

◆ RestypeToRDMol() [1/3]

core::chemical::rdkit::RestypeToRDMol::RestypeToRDMol	(	MutableResidueType const &	res,
		bool	neutralize = `true`,
		bool	keep_hydro = `false`,
		bool	sanitize = `true`,
		bool	noImplicitHs = `false`,
		bool	skipHs = `false`
	)

Convert ResidueType to an RDKit RWMol object.

If neutralize is true, attempt to reprotonate into a neutral (non-formally charged) molecule. (Charges due to heavy atoms, like quaternary amines, will still be present.)

If keep_hydro is true, represent hydrogens as physical atoms, rather than "explicit" annotations (see below).

Note that due to implementation details, "neutralize = true" will not play well with "keep_hydro = true".

RDKit is "aware" of three types of hydrogens.

1) Physical hydrogens: actual atoms in the atom graph and can have coordinates. 2) "Explicit" hydrogens: don't have existence in the atom graph or coordinates, but are instead represented by a field on the heavy atom ("This atom has 3 hydrogens attached to it") 3) "Implicit" hydrogens: aren't annotated anywhere, but instead are implied by the difference in the expected valence of the heavy atom and the number of valences which are currently occupied by bonds and/or "explicit" hydrogens.

Most of RDKit is written around the assumption of non-physical hydrogens, the exception being things like energy minimization which needs coordinates. On the other hand, "implicit" hydrogens cause issues in certain cases with kekulization. Because of this, the default conversion here is to remove the physical hydrogens, and replace them with "explicit" hydrogen annotations.

Much of RDKit (especially the metric calculations) assumes neutral protonation. (e.g. what you'd see in an aprotic organic solvent), which is why we neutralize the residues by default.

References keep_hydro_, neutralize_, sanitize_, and core::chemical::rdkit::TR().

◆ RestypeToRDMol() [2/3]

core::chemical::rdkit::RestypeToRDMol::RestypeToRDMol	(	MutableResidueType const &	res,
		RestypeToRDMolOptions const &	options
	)

References core::chemical::rdkit::RestypeToRDMolOptions::aro2double, aro2double_, core::chemical::rdkit::RestypeToRDMolOptions::keep_hydro, keep_hydro_, core::chemical::rdkit::RestypeToRDMolOptions::neutralize, neutralize_, core::chemical::rdkit::RestypeToRDMolOptions::noImplicitHs, noImplicitHs_, options_, core::chemical::rdkit::RestypeToRDMolOptions::sanitize, sanitize_, core::chemical::rdkit::RestypeToRDMolOptions::skipHs, and skipHs_.

◆ RestypeToRDMol() [3/3]

core::chemical::rdkit::RestypeToRDMol::RestypeToRDMol ( )

private

Member Function Documentation

◆ get_atomIndexMap_Rd2Res()

std::map<core::Size, core::Size> const& core::chemical::rdkit::RestypeToRDMol::get_atomIndexMap_Rd2Res ( ) const

inline

References atomIndexMap_Rd2Res_.

◆ index_to_vd()

IndexVDMapping const& core::chemical::rdkit::RestypeToRDMol::index_to_vd ( ) const

inline

References index_to_vd_.

Referenced by protocols::ligand_docking::ga_ligand_dock::MCSAligner::apply().

◆ Mol()

RDKit::RWMOL_SPTR core::chemical::rdkit::RestypeToRDMol::Mol ( )

Return an RDKit RWMol object which represents the residue type.

References core::chemical::MutableResidueType::all_atoms(), aro2double_, core::chemical::AROMATIC, core::chemical::MutableResidueType::atom(), core::chemical::MutableResidueType::atom_index(), atomIndexMap_Rd2Res_, core::chemical::MutableResidueType::bond(), core::chemical::Bond::bond_name(), core::chemical::AtomRefMapping< FromRef, ToRef >::clear(), core::chemical::rdkit::convert_to_rdkit_bondtype(), protocols::simple_filters::coords(), core::chemical::Atom::element_type(), core::chemical::rdkit::final_neutralize(), core::chemical::Atom::formal_charge(), core::chemical::MutableResidueType::graph(), core::chemical::Atom::ideal_xyz(), index_to_vd_, core::chemical::AtomRefMapping< FromRef, ToRef >::invalid_entry(), core::chemical::Atom::is_virtual(), keep_hydro_, core::chemical::Atom::name(), core::chemical::ResidueTypeBase::name(), neutralize_, core::chemical::rdkit::neutralize_rdmol(), noImplicitHs_, core::chemical::Bond::order(), core::chemical::PseudoBondOrder, res_, sanitize_, skipHs_, core::chemical::rdkit::TR(), and vd_to_index_.

Referenced by protocols::drug_design::RDKitMetricsMover::add_scores_for_residue(), protocols::drug_design::ReactionBasedAnalogSampler::apply(), protocols::drug_design::ReactionFragment::apply(), protocols::drug_design::ReactionGrow::apply(), protocols::drug_design::ReactionMultiTransform::apply(), protocols::drug_design::SubstituentReplace::apply(), protocols::drug_design::SubstructureReplace::apply(), protocols::ligand_docking::ga_ligand_dock::MCSAligner::apply(), protocols::drug_design::RDKitMetric::calculate(), protocols::drug_design::RDKitMetricFilter::compute(), protocols::drug_design::SAScoreFilter::compute(), protocols::rotamer_gen::RDKitRotamers::generate_conformers(), and protocols::ligand_evolution::FragmentLibrary::generate_rotamers().

◆ vd_to_index()

VDIndexMapping const& core::chemical::rdkit::RestypeToRDMol::vd_to_index ( ) const

inline

Return the corespondance from the input ResidueType VD to the RDKit atom index.

References vd_to_index_.

Referenced by protocols::drug_design::ReactionBasedAnalogSampler::apply(), protocols::drug_design::ReactionFragment::apply(), protocols::drug_design::ReactionGrow::apply(), protocols::drug_design::ReactionMultiTransform::apply(), protocols::drug_design::SubstituentReplace::apply(), protocols::drug_design::SubstructureReplace::apply(), protocols::rotamer_gen::RDKitRotamers::generate_conformers(), and protocols::ligand_evolution::FragmentLibrary::generate_rotamers().

Member Data Documentation

◆ aro2double_

bool core::chemical::rdkit::RestypeToRDMol::aro2double_ = false

private

Referenced by Mol(), and RestypeToRDMol().

◆ atomIndexMap_Rd2Res_

std::map<core::Size, core::Size> core::chemical::rdkit::RestypeToRDMol::atomIndexMap_Rd2Res_

private

Referenced by get_atomIndexMap_Rd2Res(), and Mol().

◆ index_to_vd_

IndexVDMapping core::chemical::rdkit::RestypeToRDMol::index_to_vd_

private

Referenced by index_to_vd(), and Mol().

◆ keep_hydro_

bool core::chemical::rdkit::RestypeToRDMol::keep_hydro_

private

Referenced by Mol(), and RestypeToRDMol().

◆ neutralize_

bool core::chemical::rdkit::RestypeToRDMol::neutralize_

private

Referenced by Mol(), and RestypeToRDMol().

◆ noImplicitHs_

bool core::chemical::rdkit::RestypeToRDMol::noImplicitHs_

private

Referenced by Mol(), and RestypeToRDMol().

◆ options_

RestypeToRDMolOptions core::chemical::rdkit::RestypeToRDMol::options_

private

Referenced by RestypeToRDMol().

◆ res_

MutableResidueType const& core::chemical::rdkit::RestypeToRDMol::res_

private

Referenced by Mol().

◆ sanitize_

bool core::chemical::rdkit::RestypeToRDMol::sanitize_

private

Referenced by Mol(), and RestypeToRDMol().

◆ skipHs_

bool core::chemical::rdkit::RestypeToRDMol::skipHs_

private

Referenced by Mol(), and RestypeToRDMol().

◆ vd_to_index_

VDIndexMapping core::chemical::rdkit::RestypeToRDMol::vd_to_index_

private

Mapping of restype vertex descriptors to indices of the rdkit object.

Referenced by Mol(), and vd_to_index().

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

src/core/chemical/rdkit/RestypeToRDMol.hh
src/core/chemical/rdkit/RestypeToRDMol.cc