protocols::drug_design::ConformationSelectionToRDMol Class Reference

#include <ConformationSelectionToRDMol.hh>

Public Member Functions
	ConformationSelectionToRDMol (core::conformation::Conformation const &conf, utility::vector1< core::Size > const &res, bool neutralize=true, bool keep_hydro=false)
	Convert ResidueType to an RDKit RWMol object. More...
::RDKit::RWMOL_SPTR	Mol ()
	Return an RDKit RWMol object which represents the residue type. More...

Private Member Functions
	ConformationSelectionToRDMol ()

Private Attributes
core::conformation::Conformation const &	conf_
utility::vector1< core::Size >	res_
bool	neutralize_
bool	keep_hydro_

Constructor & Destructor Documentation

ConformationSelectionToRDMol() [1/2]

protocols::drug_design::ConformationSelectionToRDMol::ConformationSelectionToRDMol	(	core::conformation::Conformation const &	conf,
		utility::vector1< core::Size > const &	res,
		bool	neutralize = true,
		bool	keep_hydro = 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_, and neutralize_.

ConformationSelectionToRDMol() [2/2]

protocols::drug_design::ConformationSelectionToRDMol::ConformationSelectionToRDMol ( )

private

Member Function Documentation

Mol()

RDKit::RWMOL_SPTR protocols::drug_design::ConformationSelectionToRDMol::Mol

(

)

Return an RDKit RWMol object which represents the residue type.

References core::chemical::AROMATIC, core::chemical::ResidueType::atom_name(), core::chemical::ResidueConnection::atomno(), core::chemical::ResidueType::bonded_neighbor(), core::chemical::ResidueType::bonded_neighbor_ringnesses(), core::chemical::ResidueType::bonded_neighbor_types(), core::chemical::BondInRing, conf_, core::chemical::rdkit::convert_to_rdkit_bondtype(), protocols::simple_filters::coords(), core::chemical::ResidueType::element_type(), core::chemical::rdkit::final_neutralize(), core::chemical::ResidueType::first_sidechain_atom(), core::chemical::ResidueType::formal_charge(), core::chemical::ResidueTypeBase::has_property(), core::chemical::ResidueType::is_virtual(), keep_hydro_, core::chemical::ResidueType::n_possible_residue_connections(), protocols::sic_dock::scores::nbr, neutralize_, core::chemical::rdkit::neutralize_rdmol(), res_, core::conformation::Conformation::residue(), core::conformation::Residue::residue_connection(), core::conformation::Residue::residue_connection_conn_id(), core::conformation::Residue::residue_connection_partner(), core::conformation::Conformation::residue_type(), core::chemical::SingleBond, protocols::drug_design::TR(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by protocols::drug_design::RDKitMetric::calculate().

Member Data Documentation

conf_

core::conformation::Conformation const& protocols::drug_design::ConformationSelectionToRDMol::conf_

private

Referenced by Mol().

keep_hydro_

bool protocols::drug_design::ConformationSelectionToRDMol::keep_hydro_

private

Referenced by ConformationSelectionToRDMol(), and Mol().

neutralize_

bool protocols::drug_design::ConformationSelectionToRDMol::neutralize_

private

Referenced by ConformationSelectionToRDMol(), and Mol().

res_

utility::vector1< core::Size > protocols::drug_design::ConformationSelectionToRDMol::res_

private

Referenced by Mol().

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

• src/protocols/drug_design/ConformationSelectionToRDMol.hh
• src/protocols/drug_design/ConformationSelectionToRDMol.cc