schrodinger.livedesign.registration module¶

Control the registration of entities in LiveDesign.

class schrodinger.livedesign.registration.RegistrationData(serialized_rdmol: str, entity_class: str, deduplication_hash: str, display_string: str, input_string: ~typing.Optional[str] = None, input_property_data: dict = <factory>, computed_data: dict = <factory>, child_data: dict = <factory>, to_deprecate_sdf: ~typing.Optional[str] = None, to_deprecate_no_stereo_hash: ~typing.Optional[str] = None)¶

Bases: object

Registration data for a single entity.

Parameters:

serialized_rdmol – base64 encoded binary string of the rdkit mol
entity_class – input-specified or auto-detected classification
deduplication_hash – hash used to collapse virtuals
display_string – string used to represent the entity in the first column in the LD UI
input_string – original input string used to create the entity, required to map back to input
input_property_data – column data present on input
computed_data – column data computed from the mol
child_data – relational data for derived children
to_deprecate_sdf – SDF representation of the mol
to_deprecate_no_stereo_hash – deduplication hash ignoring stereochemistry

serialized_rdmol: str¶

entity_class: str¶

deduplication_hash: str¶

display_string: str¶

input_string: Optional[str] = None¶

input_property_data: dict¶

computed_data: dict¶

child_data: dict¶

to_deprecate_sdf: Optional[str] = None¶

to_deprecate_no_stereo_hash: Optional[str] = None¶

__init__(serialized_rdmol: str, entity_class: str, deduplication_hash: str, display_string: str, input_string: ~typing.Optional[str] = None, input_property_data: dict = <factory>, computed_data: dict = <factory>, child_data: dict = <factory>, to_deprecate_sdf: ~typing.Optional[str] = None, to_deprecate_no_stereo_hash: ~typing.Optional[str] = None) → None¶

class schrodinger.livedesign.registration.RegistrationOptions(preprocessor_options: ~schrodinger.livedesign.preprocessor.PreprocessorOptions = PreprocessorOptions(MAX_NUM_ATOMS=None, STRICT=True, KEEP_ONLY_LARGEST_STRUCTURE=True, STRIP_SALTS=None, NEUTRALIZE=True, TRANSFORMATIONS=('[#7+0;v5:1]=[#8+0:2]>>[#7+:1]-[#8-:2]', '[#6:3][P+:1]([#6:4])([#6:5])[#6-:2]>>[#6:3][P-0:1]([#6:4])([#6:5])=[#6+0:2]', '[#6:3][P-:1]([#6:4])([#6:5])[#6+:2]>>[#6:3][P-0:1]([#6:4])([#6:5])=[#6+0:2]', '[#6:3][S+:1]([#6:4])-[#8-:2]>>[#6:3][S;X3+0:1]([#6:4])=[#8-0:2]', '[#6:3][P+:1]([#8;X2:4])([#8;X2:5])[#8-:2]>>[#6:3][P+0:1]([#8:4])([#8:5])=[#8-0:2]', '[#6:3][S+:1]([#6:4])([#8-:2])=[O:5]>>[#6:3][S+0:1]([#6:4])(=[#8-0:2])=[O:5]', '[#7;A;X2-:1][N;X2+:2]#[N;X1:3]>>[#7-0:1]=[N+:2]=[#7-:3]', '[#6;X3-:1][N;X2+:2]#[N;X1:3]>>[#6-0;A:1]=[N+:2]=[#7-:3]'), CHOOSE_CANONICAL_TAUTOMER=False, RESOLVE_AMBIGUOUS_TAUTOMERS=False, CHIRAL_FLAG_0_MEANING=<ChiralFlag0Meaning.UNGROUPED_ARE_ABSOLUTE: 1>, STRIP_AND_GROUPS_ON_SINGLE_ATOM=False, PRESERVE_ENHANCED_STEREO_GROUP_IDS=False, REMOVE_PROPERTIES=False, GENERATE_COORDINATES=<GenerateCoordinates.FULL_ALIGNED: 3>, EXPLICIT_HYDROGENS=<ExplicitHydrogens.REMOVE_ALL: 1>, CLEAR_INVALID_WEDGE_BONDS=True, WEDGE_TWO_BONDS_AROUND_CHIRAL_ATOMS=False), hash_scheme: ~rdkit.Chem.RegistrationHash.HashScheme = HashScheme.ALL_LAYERS, data_field_names: ~typing.Optional[~typing.Iterable[str]] = None, fasta_single_entity_mapping: ~typing.Optional[~typing.Dict] = None, rdmol_based_hashing: bool = 0, set_input_string: bool = True)¶

Bases: NamedTuple

Options controlling Registration in LiveDesign.

Deduplication is a combination of “preprocessing” and “hashing”

preprocessor_options: PreprocessorOptions¶: Alias for field number 0

hash_scheme: HashScheme¶: Alias for field number 1

data_field_names: Optional[Iterable[str]]¶: Alias for field number 2

fasta_single_entity_mapping: Optional[Dict]¶: Alias for field number 3

rdmol_based_hashing: bool¶: Alias for field number 4

set_input_string: bool¶: Alias for field number 5

schrodinger.livedesign.registration.get_registration_data(input_data: str, input_format: Format, options: RegistrationOptions) → Iterator[RegistrationData]¶

Runs through the registration pipeline for the compound provided in the input data, which includes the preprocessor and canonicalization.

Parameters:

data – input text string to be deserialized into RDKit mols
options – registration options

schrodinger.livedesign.registration.to_binary(mol: Mol) → str¶

Parameters:: mol – rdkit mol
Returns:: base64 encoded binary string of the mol