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import time
import gzip
import random
import os
import sys
import rdkit
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.RDLogger import logger
dname = os.path.dirname(__file__)
def data(fname):
return os.path.join(dname, '..', 'Data', fname)
logger = logger()
tests = [1] * 1001
if len(sys.argv) > 1:
tests = [0] * 1001
for x in sys.argv[1:]:
x = int(x)
tests[x] = 1
ts = []
mols = []
if tests[0]:
lines = gzip.open(data('znp.50k.smi.gz'), 'rt').readlines()
logger.info('mols from smiles')
nMols = 0
nBad = 0
t1 = time.time()
for line in lines:
line = line.strip().split(' ')
m = Chem.MolFromSmiles(line[0])
if m:
nMols += 1
mols.append(m)
else:
nBad += 1
t2 = time.time()
logger.info('Results1: %.2f seconds, %d passed, %d failed' % (t2 - t1, nMols, nBad))
ts.append(t2 - t1)
if tests[1]:
logger.info('Writing: Canonical SMILES')
t1 = time.time()
for mol in mols:
smi = Chem.MolToSmiles(mol, True)
t2 = time.time()
logger.info('Results2: %.2f seconds' % (t2 - t1))
ts.append(t2 - t1)
if tests[2]:
sdData = gzip.open(data('mols.1000.sdf.gz'), 'rb').read()
logger.info('mols from sdf')
suppl = Chem.SDMolSupplier()
suppl.SetData(sdData)
nMols = 0
nBad = 0
t1 = time.time()
for i in range(10):
for m in suppl:
if m:
nMols += 1
# mols.append(m)
else:
nBad += 1
t2 = time.time()
logger.info('Results1: %.2f seconds, %d passed, %d failed' % (t2 - t1, nMols, nBad))
ts.append(t2 - t1)
if tests[3] or tests[4] or tests[5]:
pattData = gzip.open(data('queries.txt.gz'), 'rt').readlines()
pattData = [x.strip().replace('[H]', '').replace('()', '') for x in pattData]
logger.info('patterns from smiles')
patts = []
nMols = 0
t1 = time.time()
for line in pattData:
m = Chem.MolFromSmarts(line)
if m:
nMols += 1
patts.append(m)
else:
nBad += 1
t2 = time.time()
logger.info('Results3: %.2f seconds, %d passed, %d failed' % (t2 - t1, nMols, nBad))
ts.append(t2 - t1)
random.seed(23)
random.shuffle(patts)
patts = patts[:100]
if tests[4]:
logger.info('Matching1: HasSubstructMatch')
t1 = time.time()
for mol in mols:
for patt in patts:
mol.HasSubstructMatch(patt)
t2 = time.time()
logger.info('Results4: %.2f seconds' % (t2 - t1))
ts.append(t2 - t1)
if tests[5]:
logger.info('Matching2: GetSubstructMatches')
t1 = time.time()
for mol in mols:
for patt in patts:
mol.GetSubstructMatches(patt)
t2 = time.time()
logger.info('Results5: %.2f seconds' % (t2 - t1))
ts.append(t2 - t1)
if tests[6] or tests[7] or tests[8]:
logger.info('reading SMARTS')
patts = []
t1 = time.time()
for line in open(data('RLewis_smarts.txt')):
line = line.strip()
if line == '' or line[0] == '#':
continue
splitL = line.split(' ')
sma = splitL[0]
m = Chem.MolFromSmarts(sma)
if m:
patts.append(m)
t2 = time.time()
logger.info('Results6: %.2f seconds for %d patterns' % (t2 - t1, len(patts)))
ts.append(t2 - t1)
if tests[7]:
logger.info('Matching3: HasSubstructMatch')
t1 = time.time()
for mol in mols:
for patt in patts:
mol.HasSubstructMatch(patt)
t2 = time.time()
logger.info('Results7: %.2f seconds' % (t2 - t1))
ts.append(t2 - t1)
if tests[8]:
logger.info('Matching4: GetSubstructMatches')
t1 = time.time()
for mol in mols:
for patt in patts:
mol.GetSubstructMatches(patt)
t2 = time.time()
logger.info('Results8: %.2f seconds' % (t2 - t1))
ts.append(t2 - t1)
if tests[9]:
logger.info('Writing: Mol blocks')
t1 = time.time()
for mol in mols:
mb = Chem.MolToMolBlock(mol)
t2 = time.time()
logger.info('Results10: %.2f seconds' % (t2 - t1))
ts.append(t2 - t1)
if tests[10]:
from rdkit.Chem import BRICS
logger.info('BRICS decomposition')
t1 = time.time()
for mol in mols:
d = BRICS.BreakBRICSBonds(mol)
t2 = time.time()
logger.info('Results11: %.2f seconds' % (t2 - t1))
ts.append(t2 - t1)
if tests[11]:
logger.info('Generate 2D coords')
t1 = time.time()
for mol in mols:
AllChem.Compute2DCoords(mol)
t2 = time.time()
logger.info('Results12: %.2f seconds' % (t2 - t1))
ts.append(t2 - t1)
if tests[12]:
logger.info('Generate topological fingerprints')
t1 = time.time()
for mol in mols:
Chem.RDKFingerprint(mol)
t2 = time.time()
logger.info('Results16: %.2f seconds' % (t2 - t1))
ts.append(t2 - t1)
if tests[13]:
logger.info('Generate morgan fingerprints')
t1 = time.time()
for mol in mols:
AllChem.GetMorganFingerprint(mol, radius=2)
t2 = time.time()
logger.info('Results16: %.2f seconds' % (t2 - t1))
ts.append(t2 - t1)
print(f"| {rdkit.__version__} | {' | '.join(['%.1f' % x for x in ts])} |")
|
