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Update SA score to use FingerprintGenerators (#7795)

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* modernize Contrib/SA_Score/sascorer.py

this is impacted by some new deprecation warning:
we need to use rdFingerprintGenerator

* we need to use the "legacy" Morgan fingerprint length
to keep the obtained scores invariant

* Update Contrib/SA_Score/sascorer.py

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* Update Contrib/SA_Score/sascorer.py

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

---------

Co-authored-by: Francois Berenger <ligand@free.fr>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
This commit is contained in:
François Bérenger
2024-09-17 19:19:23 +09:00
committed by GitHub
parent aeb70c4dfc
commit 75771be090
1 changed files with 3 additions and 3 deletions
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6
Contrib/SA_Score/sascorer.py
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@@ -22,7 +22,7 @@ import pickle
from collections import defaultdict
from rdkit import Chem
from rdkit.Chem import rdMolDescriptors
from rdkit.Chem import rdMolDescriptors, rdFingerprintGenerator
_fscores = None
@@ -46,14 +46,14 @@ def numBridgeheadsAndSpiro(mol, ri=None):
nBridgehead = rdMolDescriptors.CalcNumBridgeheadAtoms(mol)
return nBridgehead, nSpiro
mfpgen = rdFingerprintGenerator.GetMorganGenerator(radius=2)
def calculateScore(m):
if _fscores is None:
readFragmentScores()
# fragment score
fp = rdMolDescriptors.GetMorganFingerprint(m,
2) # <- 2 is the *radius* of the circular fingerprint
fp = mfpgen.GetSparseCountFingerprint(m)
fps = fp.GetNonzeroElements()
score1 = 0.
nf = 0