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Refactor inorganics filter #13

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merged 2 commits into from
May 17, 2024
Merged

Refactor inorganics filter #13

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685ff76
remove print statement
c-w-feldmann May 17, 2024
57b1eed
only check small molecules to improve performance
c-w-feldmann May 17, 2024
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11 changes: 7 additions & 4 deletions molpipeline/mol2mol/filter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -221,6 +221,7 @@ class InorganicsFilter(_MolToMolPipelineElement):
"""Filters Molecules which do not contain any organic (i.e. Carbon) atoms."""

CARBON_INORGANICS = ["O=C=O", "[C-]#[O+]"] # CO2 and CO are not organic
CARBON_INORGANICS_MAX_ATOMS = 3

def __init__(
self,
Expand Down Expand Up @@ -258,8 +259,10 @@ def pretransform_single(self, value: RDKitMol) -> OptionalMol:
return InvalidInstance(
self.uuid, "Molecule contains no organic atoms.", self.name
)
smiles = Chem.MolToSmiles(value)
print(smiles)
if smiles in self.CARBON_INORGANICS:
return InvalidInstance(self.uuid, "Molecule is not organic.", self.name)

# Only check for inorganic molecules if the molecule is small enough
if value.GetNumAtoms() <= self.CARBON_INORGANICS_MAX_ATOMS:
smiles = Chem.MolToSmiles(value)
if smiles in self.CARBON_INORGANICS:
return InvalidInstance(self.uuid, "Molecule is not organic.", self.name)
return value
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