schrodinger.livedesign.bbchem_endpoints module¶
Collection of functions intended as bbchem web endpoints.
Copyright Schrodinger, LLC. All rights reserved.
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class
schrodinger.livedesign.bbchem_endpoints.
RegistrationData
(sdf, hash_layers, molecular_weight, molecular_formula, has_attachment_point)[source]¶ Bases:
tuple
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sdf
: Union[str, bytes]¶ Alias for field number 0
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hash_layers
: schrodinger.livedesign.molhash.Layers¶ Alias for field number 1
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molecular_weight
: float¶ Alias for field number 2
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molecular_formula
: str¶ Alias for field number 3
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has_attachment_point
: bool¶ Alias for field number 4
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__contains__
(key, /)¶ Return key in self.
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__len__
()¶ Return len(self).
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count
(value, /)¶ Return number of occurrences of value.
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index
(value, start=0, stop=9223372036854775807, /)¶ Return first index of value.
Raises ValueError if the value is not present.
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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
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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
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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
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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
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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
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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