schrodinger.livedesign.bbchem_endpoints module

Collection of functions intended as bbchem web endpoints.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.livedesign.bbchem_endpoints.RegistrationData(sdf, hash_layers, molecular_weight, molecular_formula, has_attachment_point)[source]

Bases: tuple

sdf: Union[str, bytes]

Alias for field number 0

hash_layers: schrodinger.livedesign.molhash.Layers

Alias for field number 1

molecular_weight: float

Alias for field number 2

molecular_formula: str

Alias for field number 3

has_attachment_point: bool

Alias for field number 4

__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) → Iterator[schrodinger.livedesign.bbchem_endpoints.RegistrationData][source]

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

schrodinger.livedesign.bbchem_endpoints.pop_properties(mol: rdkit.Chem.rdchem.Mol) → dict[source]
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)[source]
Parameters
  • mol – molecule to clear, then set given properties on

  • new_props – map of properties to add onto the molecule

schrodinger.livedesign.bbchem_endpoints.num_substructure_matches(match_mol: rdkit.Chem.rdchem.Mol, query_mol: rdkit.Chem.rdchem.Mol) → int[source]

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

Returns

number of substructure matches found

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

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_mols: List[rdkit.Chem.rdchem.Mol], stereospecific: bool = True) → List[dict][source]

Returns R-groups of a scaffold given a list of match cores.

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

  • match_mol – source molecules for R-group decomposition

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

Returns

list of dicts of R-group matches