schrodinger.livedesign.bbchem_endpoints module

Collection of functions intended as bbchem web endpoints.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.livedesign.bbchem_endpoints.RegistrationDescriptors(average_molecular_weight, exact_molecular_weight, total_charge, molecular_formula)

Bases: tuple

average_molecular_weight: float

Alias for field number 0

exact_molecular_weight: float

Alias for field number 1

total_charge: int

Alias for field number 2

molecular_formula: str

Alias for field number 3

__contains__(key, /)

Return key in self.

__len__()

Return len(self).

count(value, /)

Return number of occurrences of value.

index(value, start=0, stop=9223372036854775807, /)

Return first index of value.

Raises ValueError if the value is not present.

class schrodinger.livedesign.bbchem_endpoints.RegistrationData(sdf, requested_hash, no_stereo_hash, display_smiles, descriptors, has_attachment_point)

Bases: tuple

sdf: Union[str, bytes]

Alias for field number 0

requested_hash: str

Alias for field number 1

no_stereo_hash: str

Alias for field number 2

display_smiles: str

Alias for field number 3

descriptors: schrodinger.livedesign.bbchem_endpoints.RegistrationDescriptors

Alias for field number 4

has_attachment_point: bool

Alias for field number 5

__contains__(key, /)

Return key in self.

__len__()

Return len(self).

count(value, /)

Return number of occurrences of value.

index(value, start=0, stop=9223372036854775807, /)

Return first index of value.

Raises ValueError if the value is not present.

schrodinger.livedesign.bbchem_endpoints.registration_process(data: Union[str, bytes], options: Optional[schrodinger.livedesign.preprocessor.PreprocessorOptions] = None, hash_scheme: schrodinger.livedesign.molhash.HashScheme = HashScheme.ALL_LAYERS, data_field_names: Optional[Iterable] = None, escape: Optional[str] = None) → Iterator[schrodinger.livedesign.bbchem_endpoints.RegistrationData]

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

Parameters

• data – input text string to be deserialized into RDKit mols

• options – preprocessor options

class schrodinger.livedesign.bbchem_endpoints.FingerprintUse(value)

Bases: enum.Enum

An enumeration.

SUBSTRUCTURE_SEARCH = 1

SIMILARITY_SCORE = 2

schrodinger.livedesign.bbchem_endpoints.generate_fingerprint(mol: rdkit.Chem.rdchem.Mol, use: schrodinger.livedesign.bbchem_endpoints.FingerprintUse, substructure_options: Optional[schrodinger.livedesign.substructure.QueryOptions] = None) → rdkit.DataStructs.cDataStructs.ExplicitBitVect

Generates a substructure or similarity fingerprint for a given mol.

Parameters

• mol – RDKit mol to generate fingerprint of

• fingerprint_type – type of fingerprint to generate

• substructure_options – substructure matching options

schrodinger.livedesign.bbchem_endpoints.generate_image(mol: rdkit.Chem.rdchem.Mol, alignment_mol: Optional[rdkit.Chem.rdchem.Mol] = None, substructure_options: Optional[schrodinger.livedesign.substructure.QueryOptions] = None, highlight_mol: Optional[rdkit.Chem.rdchem.Mol] = None, draw_options: Optional[schrodinger.livedesign.draw.ImageGenOptions] = None) → Union[str, bytes]

Generates an image used in LiveDesign which may have a request for compound alignment, or substructure highlighting, or both.

Parameters

• mol – compound to generate an image of

• alignment_mol – molecule to align to prior to image generation

• substructure_options – substructure matching options

• highlight_mol – core to highlight in generated image

• draw_options – image generation options

Returns

generated image as a string

schrodinger.livedesign.bbchem_endpoints.generate_reaction_image(rxn: rdkit.Chem.rdChemReactions.ChemicalReaction, draw_options: Optional[schrodinger.livedesign.draw.ImageGenOptions] = None) → Union[str, bytes]

Generates an image of a reaction used in LiveDesign

Parameters

• rxn – reaction to generate an image of

• draw_options – image generation options

Returns

generated image as a string

schrodinger.livedesign.bbchem_endpoints.generate_sar_analysis_image(match_mol: rdkit.Chem.rdchem.Mol, scaffold_mol: rdkit.Chem.rdchem.Mol, substructure_options: Optional[schrodinger.livedesign.substructure.QueryOptions] = None, draw_options: Optional[schrodinger.livedesign.draw.ImageGenOptions] = None) → Union[str, bytes]

Generates an image used in LiveDesign that is specifically from SAR analysis output, highlighting the core and all r-groups from the decomposition.

Parameters

• match_mol – source molecule for R-group decomposition to highlight and generate image of

• scaffold_mol – scaffold molecule on which to find R-groups

• substructure_options – substructure matching options

• draw_options – image generation options

Returns

generated image as a string

schrodinger.livedesign.bbchem_endpoints.pop_properties(mol: rdkit.Chem.rdchem.Mol) → dict

Parameters

mol – molecule to extract, then clear all properties from

Returns

map of all removed properties as strings

schrodinger.livedesign.bbchem_endpoints.set_properties(mol: rdkit.Chem.rdchem.Mol, new_props: dict)

Parameters

• mol – molecule to clear, then set given properties on

• new_props – map of properties to add onto the molecule

schrodinger.livedesign.bbchem_endpoints.split_fragments(mol: rdkit.Chem.rdchem.Mol)

Param

input molecule

Returns

iterable containing each fragment mol

schrodinger.livedesign.bbchem_endpoints.num_substructure_matches(match_mol: rdkit.Chem.rdchem.Mol, query_mol: rdkit.Chem.rdchem.Mol, options: Optional[schrodinger.livedesign.substructure.QueryOptions] = None) → int

Returns the number of substructure matches between two molecules.

Parameters

• match_mol – molecule to find substructure matches in

• query_mol – substructure molecule on which to find matches

• options – substructure query options

Returns

number of substructure matches found

schrodinger.livedesign.bbchem_endpoints.has_substructure_match(match_mol: rdkit.Chem.rdchem.Mol, query_mol: rdkit.Chem.rdchem.Mol, options: Optional[schrodinger.livedesign.substructure.QueryOptions] = None) → bool

Parameters

• match_mol – molecule to find substructure matches in

• query_mol – substructure molecule on which to find matches

• options – substructure query options

Returns

whether a substructure match was found

schrodinger.livedesign.bbchem_endpoints.enumerate_stereoisomers(mol: rdkit.Chem.rdchem.Mol, max_stereoisomers: int = 512) → Iterator[rdkit.Chem.rdchem.Mol]

Generates stereoisomers from a specified SDF structure string.

Parameters

• structure – structure from which to generate stereoisomers

• max_stereoisomers – maximum number of stereoisomers to generate

Returns

generated stereoisomers

schrodinger.livedesign.bbchem_endpoints.rgroup_decompose(scaffold_mol: rdkit.Chem.rdchem.Mol, match_mol: rdkit.Chem.rdchem.Mol, options: Optional[schrodinger.livedesign.substructure.QueryOptions] = None) → List[dict]

Decomposes a molecule into its core and R-groups given a scaffold

Parameters

• scaffold_mol – scaffold molecule on which to find R-groups

• match_mol – source molecule for R-group decomposition

• stereospecific – whether to consider bond stereochemistry and atom chirality of scaffold

Returns

list of dicts of R-group matches

schrodinger.livedesign.bbchem_endpoints.get_rgroup_labels(scaffold_mol: rdkit.Chem.rdchem.Mol) → List[str]

Parameters

scaffold_mol – scaffold molecule

Returns

R-group labels present on the scaffold

schrodinger.livedesign.bbchem_endpoints.setup_reaction(rxn_input: str) → str

Tidy up and convert user sketched reactions into a format that can be used for reaction enumeration.

Parameters

rxn_input – a SMARTS string describing the user’s reaction.

Returns

a SMARTS string describing the cleaned up reaction