rdkit¶

Bindings for core::chemical::rdkit namespace

class pyrosetta.rosetta.core.chemical.rdkit.RDMolToRestype¶

Bases: pybind11_object

generate_restype(*args, **kwargs)¶

Overloaded function.

generate_restype(self: pyrosetta.rosetta.core.chemical.rdkit.RDMolToRestype) -> pyrosetta.rosetta.core.chemical.MutableResidueType
generate_restype(self: pyrosetta.rosetta.core.chemical.rdkit.RDMolToRestype, mapping: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t) -> pyrosetta.rosetta.core.chemical.MutableResidueType

Convert the stored molecule into a ResidueType.

C++: core::chemical::rdkit::RDMolToRestype::generate_restype(const class core::chemical::AtomRefMapping<void *, unsigned long> &) –> class std::shared_ptr<class core::chemical::MutableResidueType>

generate_restype(self: pyrosetta.rosetta.core.chemical.rdkit.RDMolToRestype, orig_restype: pyrosetta.rosetta.core.chemical.MutableResidueType, mapping: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t) -> pyrosetta.rosetta.core.chemical.MutableResidueType

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.

C++: core::chemical::rdkit::RDMolToRestype::generate_restype(const class core::chemical::MutableResidueType &, const class core::chemical::AtomRefMapping<void *, unsigned long> &) –> class std::shared_ptr<class core::chemical::MutableResidueType>

index_to_vd(self: pyrosetta.rosetta.core.chemical.rdkit.RDMolToRestype) → pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t¶

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

C++: core::chemical::rdkit::RDMolToRestype::index_to_vd() const –> const class core::chemical::AtomRefMapping<unsigned long, void *> &

set_nbr(self: pyrosetta.rosetta.core.chemical.rdkit.RDMolToRestype, nbr: int) → None¶

Which atom in the fragment to use as the neighbor atom when the a restype is generated.

C++: core::chemical::rdkit::RDMolToRestype::set_nbr(unsigned long) –> void

class pyrosetta.rosetta.core.chemical.rdkit.RestypeToRDMol¶

Bases: pybind11_object

get_atomIndexMap_Rd2Res(self: pyrosetta.rosetta.core.chemical.rdkit.RestypeToRDMol) → pyrosetta.rosetta.std.map_unsigned_long_unsigned_long¶: C++: core::chemical::rdkit::RestypeToRDMol::get_atomIndexMap_Rd2Res() const –> const class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > > &

index_to_vd(self: pyrosetta.rosetta.core.chemical.rdkit.RestypeToRDMol) → pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t¶: C++: core::chemical::rdkit::RestypeToRDMol::index_to_vd() const –> const class core::chemical::AtomRefMapping<unsigned long, void *> &

vd_to_index(self: pyrosetta.rosetta.core.chemical.rdkit.RestypeToRDMol) → pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t¶

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

C++: core::chemical::rdkit::RestypeToRDMol::vd_to_index() const –> const class core::chemical::AtomRefMapping<void *, unsigned long> &

class pyrosetta.rosetta.core.chemical.rdkit.RestypeToRDMolOptions¶

Bases: pybind11_object

property aro2double¶

assign(self: pyrosetta.rosetta.core.chemical.rdkit.RestypeToRDMolOptions, : pyrosetta.rosetta.core.chemical.rdkit.RestypeToRDMolOptions) → pyrosetta.rosetta.core.chemical.rdkit.RestypeToRDMolOptions¶: C++: core::chemical::rdkit::RestypeToRDMolOptions::operator=(const struct core::chemical::rdkit::RestypeToRDMolOptions &) –> struct core::chemical::rdkit::RestypeToRDMolOptions &

property keep_hydro¶

property neutralize¶

property noImplicitHs¶

property sanitize¶

property skipHs¶

pyrosetta.rosetta.core.chemical.rdkit.convert_from_rdkit_bondtype(bondtype: RDKit::Bond::BondType) → pyrosetta.rosetta.core.chemical.BondName¶

Convert an RDKit BondType value to a Rosetta BondName enum

C++: core::chemical::rdkit::convert_from_rdkit_bondtype(RDKit::Bond::BondType) –> enum core::chemical::BondName

pyrosetta.rosetta.core.chemical.rdkit.convert_to_rdkit_bondtype(*args, **kwargs)¶

Overloaded function.

convert_to_rdkit_bondtype(bondtype: pyrosetta.rosetta.core.chemical.BondName) -> RDKit::Bond::BondType
convert_to_rdkit_bondtype(bondtype: pyrosetta.rosetta.core.chemical.BondName, aro2double: bool) -> RDKit::Bond::BondType

Convert a Rosetta BondName enum to an RDKit BondType value

C++: core::chemical::rdkit::convert_to_rdkit_bondtype(enum core::chemical::BondName, bool) –> RDKit::Bond::BondType

pyrosetta.rosetta.core.chemical.rdkit.get_forcefield(*args, **kwargs)¶

Overloaded function.

get_forcefield(mol: pyrosetta.rosetta.RDKit.ROMol) -> ForceFields::ForceField
get_forcefield(mol: pyrosetta.rosetta.RDKit.ROMol, conf_num: int) -> ForceFields::ForceField

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

C++: core::chemical::rdkit::get_forcefield(class RDKit::ROMol &, int) –> class std::shared_ptr<class ForceFields::ForceField>

pyrosetta.rosetta.core.chemical.rdkit.get_metric_names() → pyrosetta.rosetta.std.map_std_string_std_string¶

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

C++: core::chemical::rdkit::get_metric_names() –> class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > >

pyrosetta.rosetta.core.chemical.rdkit.get_name(mol: pyrosetta.rosetta.RDKit.ROMol) → str¶

Get the name of the RDMol

C++: core::chemical::rdkit::get_name(const class RDKit::ROMol &) –> std::string

pyrosetta.rosetta.core.chemical.rdkit.has_explicit_Hs(mol: pyrosetta.rosetta.RDKit.ROMol) → bool¶

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

C++: core::chemical::rdkit::has_explicit_Hs(const class RDKit::ROMol &) –> bool

pyrosetta.rosetta.core.chemical.rdkit.has_implicit_Hs(mol: pyrosetta.rosetta.RDKit.ROMol) → bool¶

Does the molecule have implicit hydrogens?

C++: core::chemical::rdkit::has_implicit_Hs(const class RDKit::ROMol &) –> bool

pyrosetta.rosetta.core.chemical.rdkit.has_physical_Hs(mol: pyrosetta.rosetta.RDKit.ROMol) → bool¶

Does the molecule have physical hydrogens?

C++: core::chemical::rdkit::has_physical_Hs(const class RDKit::ROMol &) –> bool

pyrosetta.rosetta.core.chemical.rdkit.initialize_rdkit_random(seed: int) → None¶

Initialize the RDKit random number generator.

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

C++: core::chemical::rdkit::initialize_rdkit_random(int) –> void

pyrosetta.rosetta.core.chemical.rdkit.initialize_rdkit_tracers() → None¶

Initialize the RDKit output levels with the Rosetta commandline settings

You can set the global RDKit output by controlling the “RDKit” tracer.

C++: core::chemical::rdkit::initialize_rdkit_tracers() –> void

pyrosetta.rosetta.core.chemical.rdkit.label_with_index(*args, **kwargs)¶

Overloaded function.

label_with_index(rdmol: pyrosetta.rosetta.RDKit.ROMol) -> None
label_with_index(rdmol: pyrosetta.rosetta.RDKit.ROMol, index_prop: str) -> None

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

C++: core::chemical::rdkit::label_with_index(class RDKit::ROMol &, const std::string &) –> void

pyrosetta.rosetta.core.chemical.rdkit.neutralize_rdmol(*args, **kwargs)¶

Overloaded function.

neutralize_rdmol(rdmol: pyrosetta.rosetta.RDKit.RWMol) -> None
neutralize_rdmol(rdmol: pyrosetta.rosetta.RDKit.RWMol, addHs: bool) -> None

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.

C++: core::chemical::rdkit::neutralize_rdmol(class RDKit::RWMol &, bool) –> void

pyrosetta.rosetta.core.chemical.rdkit.rdkit_metric(mol: pyrosetta.rosetta.RDKit.ROMol, metric: str) → float¶

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

C++: core::chemical::rdkit::rdkit_metric(const class RDKit::ROMol &, const std::string &) –> double

pyrosetta.rosetta.core.chemical.rdkit.remove_excess_protons(rdmol: pyrosetta.rosetta.RDKit.RWMol) → None¶

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

C++: core::chemical::rdkit::remove_excess_protons(class RDKit::RWMol &) –> void

pyrosetta.rosetta.core.chemical.rdkit.reprotonate_rdmol(rdmol: pyrosetta.rosetta.RDKit.RWMol) → None¶

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

C++: core::chemical::rdkit::reprotonate_rdmol(class RDKit::RWMol &) –> void

pyrosetta.rosetta.core.chemical.rdkit.softSanitize(mol: pyrosetta.rosetta.RDKit.RWMol) → None¶

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

C++: core::chemical::rdkit::softSanitize(class RDKit::RWMol &) –> void