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Upgrade Morgan Fingerprint Generation to Use Modern RDKit API #323

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Merged
merged 1 commit into from
Oct 3, 2024
Merged

Upgrade Morgan Fingerprint Generation to Use Modern RDKit API #323

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5 changes: 4 additions & 1 deletion bot_services/discord/principal_component_analysis.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@

from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import rdFingerprintGenerator
from rdkit.Chem.Draw import rdDepictor
from rdkit.Chem.Draw import rdMolDraw2D
from rdkit.Chem import DataStructs
Expand Down Expand Up @@ -133,7 +134,9 @@ def mol2fparr(self, mol):
'''

arr = np.zeros((0,))
fp = AllChem.GetMorganFingerprintAsBitVect(mol, self.morgan_radius, nBits=self.bit_representation)
# fp = AllChem.GetMorganFingerprintAsBitVect(mol, self.morgan_radius, nBits=self.bit_representation)
morgan_gen = rdFingerprintGenerator.GetMorganGenerator(radius=self.morgan_radius, fpSize=self.bit_representation)
fp = morgan_gen.GetFingerprint(mol)
DataStructs.ConvertToNumpyArray(fp, arr)
return arr

Expand Down
14 changes: 9 additions & 5 deletions global_chem_extensions/global_chem_extensions/cheminformatics/applications/decoder_engine.py
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Expand Up @@ -14,6 +14,7 @@
from rdkit.Chem import AllChem
from rdkit.Chem import DataStructs
from rdkit.Chem import BRICS
from rdkit.Chem import rdFingerprintGenerator

from global_chem import GlobalChem

Expand All @@ -40,11 +41,14 @@ def generate_morgan_fingerprint(smiles):

molecule = Chem.MolFromSmiles(smiles)

bit_string = AllChem.GetMorganFingerprintAsBitVect(
molecule,
2,
nBits=512
).ToBitString()
# bit_string = AllChem.GetMorganFingerprintAsBitVect(
# molecule,
# 2,
# nBits=512
# ).ToBitString()
morgan_gen = rdFingerprintGenerator.GetMorganGenerator(radius=2, fpSize=512)
bit_string = morgan_gen.GetFingerprint(molecule).ToBitString()


return bit_string

Expand Down
5 changes: 4 additions & 1 deletion ..._chem_extensions/global_chem_extensions/cheminformatics/applications/node_pca_analysis.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,7 @@
from rdkit.Chem.Draw import rdMolDraw2D
from rdkit.Chem import DataStructs
rdDepictor.SetPreferCoordGen(True)
from rdkit.Chem import rdFingerprintGenerator


# Graphing Imports
Expand Down Expand Up @@ -139,7 +140,9 @@ def mol2fparr(self, mol):
'''

arr = np.zeros((0,))
fp = AllChem.GetMorganFingerprintAsBitVect(mol, self.morgan_radius, nBits=self.bit_representation)
# fp = AllChem.GetMorganFingerprintAsBitVect(mol, self.morgan_radius, nBits=self.bit_representation)
morgan_gen = rdFingerprintGenerator.GetMorganGenerator(radius=self.morgan_radius, fpSize=self.bit_representation)
fp = morgan_gen.GetFingerprint(mol)
DataStructs.ConvertToNumpyArray(fp, arr)
return arr

Expand Down
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