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45 tests use old fingerprint method (part 2) #53

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merged 3 commits into from
Jul 17, 2024
Merged

45 tests use old fingerprint method (part 2) #53

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186a666
use GetMorganGenerator
c-w-feldmann Jul 5, 2024
6a7335e
update tests to new fp
c-w-feldmann Jul 12, 2024
a3afdc2
Merge branch 'main' into 45-tests-use-old-fingerprint-method
c-w-feldmann Jul 12, 2024
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5 changes: 3 additions & 2 deletions tests/utils/fingerprints.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
from rdkit import Chem

# pylint: disable=no-name-in-module
from rdkit.Chem.AllChem import GetMorganFingerprintAsBitVect
from rdkit.Chem import rdFingerprintGenerator as rdkit_fp
from rdkit.DataStructs import ExplicitBitVect
from scipy import sparse

Expand All @@ -34,9 +34,10 @@ def make_sparse_fp(
Feature matrix.
"""
vector_list = []
morgan_fp = rdkit_fp.GetMorganGenerator(radius=radius, fpSize=n_bits)
for smiles in smiles_list:
mol = Chem.MolFromSmiles(smiles) # pylint: disable=no-member
vector = GetMorganFingerprintAsBitVect(mol, radius=radius, nBits=n_bits)
vector = morgan_fp.GetFingerprintAsNumPy(mol)
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vector_list.append(sparse.csr_matrix(vector))
return sparse.vstack(vector_list)

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