rdkit/Regress/Scripts/timings.py

import gzip
import os
import random
import sys
import time

import rdkit
from rdkit import Chem
from rdkit.Chem import AllChem, Recap
from rdkit.RDLogger import logger

logger = logger()

tests = [1] * 1001
if len(sys.argv) > 1:
  tests = [0] * 1001
  tests[1] = 1
  for x in sys.argv[1:]:
    x = int(x)
    tests[x] = 1
ts = []

sdData = gzip.open('../Data/mols.1000.sdf.gz').read()
logger.info('mols from sdf')
suppl = Chem.SDMolSupplier()
suppl.SetData(sdData)
mols = []
nMols = 0
nBad = 0
t1 = time.time()
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[2]:
  lines = gzip.open('../Data/mols.1000.txt.gz').readlines()
  logger.info('mols from smiles')
  nMols = 0
  nBad = 0
  t1 = time.time()
  for line in lines:
    line = line.decode().strip().split(' ')
    m = Chem.MolFromSmiles(line[1])
    if m:
      nMols += 1
    else:
      nBad += 1
  t2 = time.time()
  logger.info('Results2: %.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').readlines()
  pattData = [x.decode().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: Canonical SMILES')
  t1 = time.time()
  for mol in mols:
    smi = Chem.MolToSmiles(mol)
  t2 = time.time()
  logger.info('Results9: %.2f seconds' % (t2 - t1))
  ts.append(t2 - t1)

if tests[10]:
  logger.info('Generate 2D coords')
  t1 = time.time()
  for mol in mols:
    AllChem.Compute2DCoords(mol)
  t2 = time.time()
  logger.info('Results10: %.2f seconds' % (t2 - t1))
  ts.append(t2 - t1)

if tests[11]:
  logger.info('Writing: Mol blocks')
  t1 = time.time()
  for mol in mols:
    mb = Chem.MolToMolBlock(mol)
  t2 = time.time()
  logger.info('Results11: %.2f seconds' % (t2 - t1))
  ts.append(t2 - t1)

if tests[12]:
  logger.info('RECAP decomposition')
  t1 = time.time()
  for mol in mols:
    d = Recap.RecapDecompose(mol)
  t2 = time.time()
  logger.info('Results12: %.2f seconds' % (t2 - t1))
  ts.append(t2 - t1)

if tests[13]:
  logger.info('Generate 3D coords for 50 molecules with ETKDG')
  mols3d = mols[200:250]
  t1 = time.time()
  nBad = 0
  for mol in mols3d:
    cid = AllChem.EmbedMolecule(mol, randomSeed=0xF00D, useExpTorsionAnglePrefs=True,
                                useBasicKnowledge=True)
    if cid < 0:
      nBad += 1
  t2 = time.time()
  logger.info('Results13: %.2f seconds %d failures' % (t2 - t1, nBad))
  ts.append(t2 - t1)

if tests[14]:
  logger.info('UFF optimizing those:')
  t1 = time.time()
  for mol in mols3d:
    if not mol.GetNumConformers():
      continue
    mol = Chem.Mol(mol)
    needMore = 1
    while needMore:
      needMore = AllChem.UFFOptimizeMolecule(mol, maxIters=200)
  t2 = time.time()
  logger.info('Results14: %.2f seconds' % (t2 - t1))
  ts.append(t2 - t1)

if tests[15]:
  logger.info('MMFF optimizing the molecules:')
  t1 = time.time()
  for i, mol in enumerate(mols3d):
    mol = Chem.Mol(mol)
    if not mol.GetNumConformers():
      continue
    if not AllChem.MMFFHasAllMoleculeParams(mol):
      continue
    needMore = 1
    while needMore:
      try:
        needMore = AllChem.MMFFOptimizeMolecule(mol, maxIters=200)
      except ValueError:
        logger.warning('Problems with MMFF and mol %d' % i)
        break
  t2 = time.time()
  logger.info('Results15: %.2f seconds' % (t2 - t1))
  ts.append(t2 - t1)

if tests[16]:
  logger.info('Find unique subgraphs')
  t1 = time.time()
  for mol in mols:
    Chem.FindUniqueSubgraphsOfLengthN(mol, 6)
  t2 = time.time()
  logger.info('Results16: %.2f seconds' % (t2 - t1))
  ts.append(t2 - t1)

if tests[17]:
  logger.info('Generate topological fingerprints')
  t1 = time.time()
  for mol in mols:
    Chem.RDKFingerprint(mol)
  t2 = time.time()
  logger.info('Results17: %.2f seconds' % (t2 - t1))
  ts.append(t2 - t1)

if tests[18]:
  logger.info('Generate morgan fingerprints')
  t1 = time.time()
  for mol in mols:
    AllChem.GetMorganFingerprint(mol, radius=2)
  t2 = time.time()
  logger.info('Results18: %.2f seconds' % (t2 - t1))
  ts.append(t2 - t1)

print(f"| {rdkit.__version__} | {' | '.join(['%.1f' % x for x in ts])} |")