Classes
class	RDMolToRestype

class	RestypeToRDMol

Typedefs
typedef std::vector< std::pair < ::RDKit::RWMolOP, int > >	ChargeTransformList

Functions
static basic::Tracer	TR ("core.chemical.rdkit.RDMolToRestype")

static basic::Tracer	TR ("core.chemical.rdkit.RestypeToRDMol")

static basic::Tracer	TR ("core.chemical.rdkit.util")

static basic::Tracer	TR_RDKit ("RDKit")

void	initialize_rdkit_random (int seed)
	Initialize the RDKit random number generator. More...

void	initialize_rdkit_tracers ()
	Initialize the RDKit output levels with the Rosetta commandline settings. More...

::RDKit::Bond::BondType	convert_to_rdkit_bondtype (core::chemical::BondName bondtype)
	Convert a Rosetta BondName enum to an RDKit BondType value. More...

core::chemical::BondName	convert_from_rdkit_bondtype (::RDKit::Bond::BondType bondtype)
	Convert an RDKit BondType value to a Rosetta BondName enum. More...

std::string	get_name (::RDKit::ROMol const &mol)
	Get the name of the RDMol. More...

bool	has_physical_Hs (::RDKit::ROMol const &mol)
	Does the molecule have physical hydrogens? More...

bool	has_explicit_Hs (::RDKit::ROMol const &mol)
	Does the molecule have "explicit" (but not physical) hydrogens? More...

bool	has_implicit_Hs (::RDKit::ROMol const &mol)
	Does the molecule have implicit hydrogens? More...

::RDKit::ForceFieldOP	get_forcefield (::RDKit::ROMol &mol, int conf_num=-1)
	Load an RDKit forcefield. Will prefer MMFF, but will fall back to UFF. More...

void	softSanitize (::RDKit::RWMol &mol)
	Non strict sanitization, useful if working with molecules which aren't 100% acceptable by RDKit (e.g. protonation/kekulization issues) More...

void	remove_excess_protons (::RDKit::RWMol &rdmol)
	Remove any excess hydrogens, where "excess" is defined as any which contribute to a positive formal charge (Assumes a graph-hydrogen removed form.) More...

void	remove_most_charges (::RDKit::RWMol &rdmol)

void	apply_charge_transforms (::RDKit::RWMol &rdmol, ChargeTransformList const &transforms)
	Reset the charges on particular groups (Assumes a graph-hydrogen removed form.) More...

void	reprotonate_rdmol (::RDKit::RWMol &rdmol)
	Change the protonation state on an rdmol to match physiological pH. Will reset the molecule to an graph-explicit hydrogen form. More...

void	neutralize_rdmol (::RDKit::RWMol &rdmol, bool addHs=true)
	Remove any pH-dependent charges on the molecule If addHs is true, then the resultant molecule with have hydrogens added. If addHs is false, then the resultant molecule will be without hydrogens. More...

void	label_with_index (::RDKit::ROMol &rdmol, std::string const &index_prop)
	Label a molecule with it's index values (for find_mapping, later) More...

core::chemical::IndexIndexMapping	convert_match_vect_to_index_index_map (::RDKit::MatchVectType const &match_vect)
	Convert the MatchVectType to an IndexIndex map, going query->molecule Use -1 as the invalid value, as zero is a valid one. More...

core::chemical::IndexIndexMapping	find_mapping (::RDKit::ROMOL_SPTR from,::RDKit::ROMOL_SPTR to, std::string const &index_prop)
	Find a mapping from one RDMol to another. More...

void	load_sdf (std::string const &filename, utility::vector1< ::RDKit::ROMolOP > &mol_vector, bool removeHs)
	Load molecules from file and append them to mol_vector. More...

std::map< std::string, std::string >	get_metric_names ()
	Return a set containing all the valid names for the rdkit_metric() function mapped to short descriptions. More...

core::Real	rdkit_metric (::RDKit::ROMol const &mol, std::string const &metric)
	Return the value of a given RDKit metric for the given mol. More...

Typedef Documentation

typedef std::vector< std::pair< ::RDKit::RWMolOP, int > > core::chemical::rdkit::ChargeTransformList

Function Documentation

void core::chemical::rdkit::apply_charge_transforms	(	::RDKit::RWMol &	rdmol,
		ChargeTransformList const &	transforms
	)

Reset the charges on particular groups (Assumes a graph-hydrogen removed form.)

Referenced by neutralize_rdmol(), and reprotonate_rdmol().

core::chemical::BondName core::chemical::rdkit::convert_from_rdkit_bondtype ( ::RDKit::Bond::BondType bondtype )

Convert an RDKit BondType value to a Rosetta BondName enum.

References core::chemical::AROMATIC, core::chemical::AromaticBond, core::chemical::DoubleBond, core::chemical::SingleBond, TR(), core::chemical::TripleBond, and core::chemical::UnknownBond.

Referenced by core::chemical::rdkit::RDMolToRestype::generate_restype().

core::chemical::IndexIndexMapping core::chemical::rdkit::convert_match_vect_to_index_index_map ( ::RDKit::MatchVectType const & match_vect )

Convert the MatchVectType to an IndexIndex map, going query->molecule Use -1 as the invalid value, as zero is a valid one.

Referenced by find_mapping().

RDKit::Bond::BondType core::chemical::rdkit::convert_to_rdkit_bondtype ( core::chemical::BondName bondtype )

Convert a Rosetta BondName enum to an RDKit BondType value.

References core::chemical::AROMATIC, core::chemical::AromaticBond, core::chemical::DoubleBond, core::chemical::SingleBond, TR(), and core::chemical::TripleBond.

Referenced by core::chemical::rdkit::RestypeToRDMol::Mol().

core::chemical::IndexIndexMapping core::chemical::rdkit::find_mapping	(	::RDKit::ROMOL_SPTR	from,
		::RDKit::ROMOL_SPTR	to,
		std::string const &	index_prop
	)

Find a mapping from one RDMol to another.

Find a mapping from one RDMol to another If index_prop is found, it will be used (if present) as the starting index.

References core::chemical::combine(), convert_match_vect_to_index_index_map(), core::chemical::AtomRefMapping< FromRef, ToRef >::empty(), core::chemical::AtomRefMapping< FromRef, ToRef >::reverse(), and TR().

RDKit::ForceFieldOP core::chemical::rdkit::get_forcefield	(	::RDKit::ROMol &	mol,
		int	conf_num
	)

Load an RDKit forcefield. Will prefer MMFF, but will fall back to UFF.

References TR().

std::map< std::string, std::string > core::chemical::rdkit::get_metric_names ( )

Return a set containing all the valid names for the rdkit_metric() function mapped to short descriptions.

Referenced by protocols::drug_design::RDKitMetricsMover::add_scores_for_residue(), and protocols::drug_design::RDKitMetric::rdkit_metric().

std::string core::chemical::rdkit::get_name ( ::RDKit::ROMol const & mol )

Get the name of the RDMol.

Referenced by protocols::kinematic_closure::KicMover::get_children_names(), protocols::abinitio::abscript::FragmentCM::passport_updated(), protocols::kinematic_closure::perturbers::Perturber::perturb_subset_with_balance(), protocols::loop_grower::LoopGrower::provide_citation_info(), core::chemical::ResidueType::show(), protocols::abinitio::abscript::FragmentCM::yield_claims(), and protocols::environment::CoMTrackerCM::yield_claims().

bool core::chemical::rdkit::has_explicit_Hs ( ::RDKit::ROMol const & mol )

Does the molecule have "explicit" (but not physical) hydrogens?

bool core::chemical::rdkit::has_implicit_Hs ( ::RDKit::ROMol const & mol )

Does the molecule have implicit hydrogens?

bool core::chemical::rdkit::has_physical_Hs ( ::RDKit::ROMol const & mol )

Does the molecule have physical hydrogens?

void core::chemical::rdkit::initialize_rdkit_random ( int seed )

Initialize the RDKit random number generator.

Note that seed is an int to match the seed generated in core/init.cc

References TR().

Referenced by core::init::init().

void core::chemical::rdkit::initialize_rdkit_tracers ( )

Initialize the RDKit output levels with the Rosetta commandline settings.

You can set the global RDKit output by controlling the "RDKit" tracer.

References TR_RDKit().

Referenced by core::init::init_tracers().

void core::chemical::rdkit::label_with_index	(	::RDKit::ROMol &	rdmol,
		std::string const &	index_prop
	)

Label a molecule with it's index values (for find_mapping, later)

void core::chemical::rdkit::load_sdf	(	std::string const &	filename,
		utility::vector1< ::RDKit::ROMolOP > &	mol_vector,
		bool	removeHs
	)

Load molecules from file and append them to mol_vector.

Load the structures from the given file into the provided vector Structures will be appended to the ones already in the vector.

References TR().

void core::chemical::rdkit::neutralize_rdmol	(	::RDKit::RWMol &	rdmol,
		bool	addHs
	)

Remove any pH-dependent charges on the molecule If addHs is true, then the resultant molecule with have hydrogens added. If addHs is false, then the resultant molecule will be without hydrogens.

References apply_charge_transforms(), remove_excess_protons(), remove_most_charges(), and softSanitize().

Referenced by core::chemical::rdkit::RestypeToRDMol::Mol().

core::Real core::chemical::rdkit::rdkit_metric	(	::RDKit::ROMol const &	mol,
		std::string const &	metric
	)

Return the value of a given RDKit metric for the given mol.

Referenced by protocols::drug_design::RDKitMetricsMover::add_scores_for_residue(), and protocols::drug_design::RDKitMetric::calculate().

void core::chemical::rdkit::remove_excess_protons ( ::RDKit::RWMol & rdmol )

Remove any excess hydrogens, where "excess" is defined as any which contribute to a positive formal charge (Assumes a graph-hydrogen removed form.)

References protocols::mean_field::min().

Referenced by neutralize_rdmol(), and reprotonate_rdmol().

void core::chemical::rdkit::remove_most_charges ( ::RDKit::RWMol & rdmol )

Referenced by neutralize_rdmol().

void core::chemical::rdkit::reprotonate_rdmol ( ::RDKit::RWMol & rdmol )

Change the protonation state on an rdmol to match physiological pH. Will reset the molecule to an graph-explicit hydrogen form.

References apply_charge_transforms(), remove_excess_protons(), and softSanitize().

void core::chemical::rdkit::softSanitize ( ::RDKit::RWMol & mol )

Non strict sanitization, useful if working with molecules which aren't 100% acceptable by RDKit (e.g. protonation/kekulization issues)

Referenced by neutralize_rdmol(), and reprotonate_rdmol().

static basic::Tracer core::chemical::rdkit::TR ( "core.chemical.rdkit.util" )

static

static basic::Tracer core::chemical::rdkit::TR ( "core.chemical.rdkit.RestypeToRDMol" )

static

static basic::Tracer core::chemical::rdkit::TR ( "core.chemical.rdkit.RDMolToRestype" )

static

Referenced by convert_from_rdkit_bondtype(), convert_to_rdkit_bondtype(), find_mapping(), get_forcefield(), initialize_rdkit_random(), load_sdf(), and core::chemical::rdkit::RestypeToRDMol::Mol().

static basic::Tracer core::chemical::rdkit::TR_RDKit ( "RDKit" )

static

Referenced by initialize_rdkit_tracers().

Classes

Typedefs

Functions

Typedef Documentation

Function Documentation