add a script for benchmarking fingerprint screenout and substructure performance (#2523)

* add fingerprint_screenout script to benchmarking suite * cleanup * simplification
2026-06-03 21:44:30 +08:00 · 2019-07-03 04:54:10 +02:00
parent 76ed536c87
commit 36599e9ac3
1 changed files with 110 additions and 0 deletions
--- a/Regress/Scripts/fingerprint_screenout.py
+++ b/Regress/Scripts/fingerprint_screenout.py
@@ -0,0 +1,110 @@
+#
+#  Copyright (C) 2019 Greg Landrum
+#
+#   @@ All Rights Reserved @@
+#  This file is part of the RDKit.
+#  The contents are covered by the terms of the BSD license
+#  which is included in the file license.txt, found at the root
+#  of the RDKit source tree.
+#
+import time
+import gzip
+import rdkit
+from rdkit import Chem
+from rdkit import DataStructs
+from rdkit.Chem import AllChem
+from rdkit.RDLogger import logger
+import argparse
+
+logger = logger()
+
+parser = argparse.ArgumentParser(
+    description="benchmark and test fingerprint screenout and substructure searching")
+parser.add_argument("--validate", dest='validateResults', default=False, action='store_true',
+                    help="validate that the screenout isn't missing anything")
+parser.add_argument("--short", dest='doShort', default=False, action='store_true',
+                    help="run a small subset of the molecules")
+args = parser.parse_args()
+
+ts = []
+
+logger.info('mols from smiles')
+mols = []
+t1 = time.time()
+# find this file here: https://raw.githubusercontent.com/greglandrum/rdkit_blog/master/data/chembl21_25K.pairs.txt.gz
+with gzip.open('../Data/chembl21_25K.pairs.txt.gz', 'rb') as inf:
+    for line in inf:
+        line = line.decode().strip().split()
+        smi1 = line[1]
+        smi2 = line[3]
+        mols.append(Chem.MolFromSmiles(smi1))
+        mols.append(Chem.MolFromSmiles(smi2))
+        if args.doShort and len(mols) >= 1000:
+            break
+t2 = time.time()
+ts.append(t2 - t1)
+logger.info(f'Results{len(ts)}: {t2-t1 : .2f} seconds, {len(mols)} mols')
+
+
+logger.info('queries from smiles')
+t1 = time.time()
+# find this file here: https://raw.githubusercontent.com/greglandrum/rdkit_blog/master/data/zinc.frags.500.q.smi
+frags = [Chem.MolFromSmiles(x.split()[0]) for x in open('../Data/zinc.frags.500.q.smi', 'r')]
+# find this file here: https://raw.githubusercontent.com/greglandrum/rdkit_blog/master/data/zinc.leads.500.q.smi
+leads = [Chem.MolFromSmiles(x.split()[0]) for x in open('../Data/zinc.leads.500.q.smi', 'r')]
+# find this file here: https://raw.githubusercontent.com/greglandrum/rdkit_blog/master/data/fragqueries.q.txt
+pieces = [Chem.MolFromSmiles(x) for x in open('../Data/fragqueries.q.txt', 'r')]
+t2 = time.time()
+ts.append(t2 - t1)
+logger.info(f'Results{len(ts)}: {t2-t1 : .2f} seconds')
+
+
+logger.info('generating pattern fingerprints for mols')
+t1 = time.time()
+mfps = [Chem.PatternFingerprint(m) for m in mols]
+t2 = time.time()
+ts.append(t2 - t1)
+logger.info(f'Results{len(ts)}: {t2-t1 : .2f} seconds')
+
+
+logger.info('generating pattern fingerprints for queries')
+t1 = time.time()
+fragsfps = [Chem.PatternFingerprint(m, 2048) for m in frags]
+leadsfps = [Chem.PatternFingerprint(m, 2048) for m in leads]
+piecesfps = [Chem.PatternFingerprint(m, 2048) for m in pieces]
+t2 = time.time()
+ts.append(t2 - t1)
+logger.info(f'Results{len(ts)}: {t2-t1 : .2f} seconds')
+
+for nm, qs, qfps in [('frags', frags, fragsfps), ('leads', leads, leadsfps), ('pieces', pieces, piecesfps)]:
+    logger.info(f'testing {nm} queries')
+    t1 = time.time()
+    nPossible = 0
+    nTested = 0
+    nFound = 0
+    nErrors = 0
+    for i, fragfp in enumerate(qfps):
+        for j, mfp in enumerate(mfps):
+            nPossible += 1
+            if args.validateResults:
+                matched = mols[j].HasSubstructMatch(qs[i])
+                fpMatch = DataStructs.AllProbeBitsMatch(fragfp, mfp)
+                if fpMatch:
+                    nTested += 1
+                if matched:
+                    nFound += 1
+                    if not fpMatch:
+                        nErrors += 1
+                        logger.error(f"ERROR: mol {j} query {i}")
+            else:
+                if DataStructs.AllProbeBitsMatch(fragfp, mfp):
+                    nTested += 1
+                    if mols[j].HasSubstructMatch(qs[i]):
+                        nFound += 1
+    t2 = time.time()
+    ts.append(t2 - t1)
+    logger.info(
+        f'Results{len(ts)}: {t2-t1 : .2f} seconds. {nTested} tested ({nTested/nPossible :.4f} of total), {nFound} found, {nFound/nTested : .2f} accuracy. {nErrors} errors.')
+
+
+print(f"| {rdkit.__version__} | {' | '.join(['%.1f' % x for x in ts])} |")