rdkit/Projects/DbCLI/SearchDb.py

# $Id$
#
#  Copyright (c) 2007-2013, Novartis Institutes for BioMedical Research Inc.
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# modification, are permitted provided that the following conditions are
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#     * Redistributions of source code must retain the above copyright
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#       disclaimer in the documentation and/or other materials provided
#       with the distribution.
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# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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#  Created by Greg Landrum, July 2007
#

_version = "0.14.0"
_description = """
     The sd filename argument can be either an SD file or an MDL mol 
     file.
     

  NOTES:

    - The property names may have been altered on loading the
      database.  Any non-alphanumeric character in a property name
      will be replaced with '_'. e.g."Gold.Goldscore.Constraint.Score" becomes
      "Gold_Goldscore_Constraint_Score".

    - Property names are not case sensitive in the database.

 """
import argparse
import os
import sys
import time

from rdkit import RDConfig
from rdkit.Dbase.DbConnection import DbConnect
from rdkit.RDLogger import logger

logger = logger()
import zlib

from rdkit import Chem, DataStructs
from rdkit.Chem.MolDb import FingerprintUtils
from rdkit.Chem.MolDb.FingerprintUtils import (BuildSigFactory, DepickleFP,
                                               LayeredOptions,
                                               supportedSimilarityMethods)


def _molFromPkl(pkl):
  if isinstance(pkl, (bytes, str)):
    mol = Chem.Mol(pkl)
  else:
    mol = Chem.Mol(str(pkl))
  return mol


def GetNeighborLists(probes, topN, pool, simMetric=DataStructs.DiceSimilarity, simThresh=-1.,
                     silent=False, **kwargs):
  probeFps = [x[1] for x in probes]
  validProbes = [x for x in range(len(probeFps)) if probeFps[x] is not None]
  validFps = [probeFps[x] for x in validProbes]
  from rdkit.DataStructs.TopNContainer import TopNContainer
  if simThresh <= 0:
    nbrLists = [TopNContainer(topN) for x in range(len(probeFps))]
  else:
    nbrLists = [TopNContainer(-1) for x in range(len(probeFps))]

  nDone = 0
  for nm, fp in pool:
    nDone += 1
    if not silent and not nDone % 1000:
      logger.info('  searched %d rows' % nDone)
    if (simMetric == DataStructs.DiceSimilarity):
      scores = DataStructs.BulkDiceSimilarity(fp, validFps)
      for i, score in enumerate(scores):
        if score > simThresh:
          nbrLists[validProbes[i]].Insert(score, nm)
    elif (simMetric == DataStructs.TanimotoSimilarity):
      scores = DataStructs.BulkTanimotoSimilarity(fp, validFps)
      for i, score in enumerate(scores):
        if score > simThresh:
          nbrLists[validProbes[i]].Insert(score, nm)
    elif (simMetric == DataStructs.TverskySimilarity):
      av = float(kwargs.get('tverskyA', 0.5))
      bv = float(kwargs.get('tverskyB', 0.5))
      scores = DataStructs.BulkTverskySimilarity(fp, validFps, av, bv)
      for i, score in enumerate(scores):
        if score > simThresh:
          nbrLists[validProbes[i]].Insert(score, nm)
    else:
      for i in range(len(probeFps)):
        pfp = probeFps[i]
        if pfp is not None:
          score = simMetric(probeFps[i], fp)
          if score > simThresh:
            nbrLists[validProbes[i]].Insert(score, nm)
  return nbrLists


def GetMolsFromSmilesFile(dataFilename, errFile, nameProp):
  dataFile = open(dataFilename, 'r')
  for idx, line in enumerate(dataFile):
    try:
      smi, nm = line.strip().split(' ')
    except ValueError:
      continue
    m = Chem.MolFromSmiles(smi)
    if not m:
      if errFile:
        print(idx, nm, smi, file=errFile)
      continue
    yield (nm, smi, m)


def GetMolsFromSDFile(dataFilename, errFile, nameProp):
  suppl = Chem.SDMolSupplier(dataFilename)

  for idx, m in enumerate(suppl):
    if not m:
      if errFile:
        if hasattr(suppl, 'GetItemText'):
          d = suppl.GetItemText(idx)
          errFile.write(d)
        else:
          logger.warning('full error file support not complete')
      continue
    smi = Chem.MolToSmiles(m, True)
    if m.HasProp(nameProp):
      nm = m.GetProp(nameProp)
      if not nm:
        logger.warning('molecule found with empty name property')
    else:
      nm = 'Mol_%d' % (idx + 1)
    yield nm, smi, m


def RunSearch(options, queryFilename):
  global sigFactory
  if options.similarityType == 'AtomPairs':
    fpBuilder = FingerprintUtils.BuildAtomPairFP
    simMetric = DataStructs.DiceSimilarity
    dbName = os.path.join(options.dbDir, options.pairDbName)
    fpTableName = options.pairTableName
    fpColName = options.pairColName
  elif options.similarityType == 'TopologicalTorsions':
    fpBuilder = FingerprintUtils.BuildTorsionsFP
    simMetric = DataStructs.DiceSimilarity
    dbName = os.path.join(options.dbDir, options.torsionsDbName)
    fpTableName = options.torsionsTableName
    fpColName = options.torsionsColName
  elif options.similarityType == 'RDK':
    fpBuilder = FingerprintUtils.BuildRDKitFP
    simMetric = DataStructs.FingerprintSimilarity
    dbName = os.path.join(options.dbDir, options.fpDbName)
    fpTableName = options.fpTableName
    if not options.fpColName:
      options.fpColName = 'rdkfp'
    fpColName = options.fpColName
  elif options.similarityType == 'Pharm2D':
    fpBuilder = FingerprintUtils.BuildPharm2DFP
    simMetric = DataStructs.DiceSimilarity
    dbName = os.path.join(options.dbDir, options.fpDbName)
    fpTableName = options.pharm2DTableName
    if not options.fpColName:
      options.fpColName = 'pharm2dfp'
    fpColName = options.fpColName
    FingerprintUtils.sigFactory = BuildSigFactory(options)
  elif options.similarityType == 'Gobbi2D':
    from rdkit.Chem.Pharm2D import Gobbi_Pharm2D
    fpBuilder = FingerprintUtils.BuildPharm2DFP
    simMetric = DataStructs.TanimotoSimilarity
    dbName = os.path.join(options.dbDir, options.fpDbName)
    fpTableName = options.gobbi2DTableName
    if not options.fpColName:
      options.fpColName = 'gobbi2dfp'
    fpColName = options.fpColName
    FingerprintUtils.sigFactory = Gobbi_Pharm2D.factory
  elif options.similarityType == 'Morgan':
    fpBuilder = FingerprintUtils.BuildMorganFP
    simMetric = DataStructs.DiceSimilarity
    dbName = os.path.join(options.dbDir, options.morganFpDbName)
    fpTableName = options.morganFpTableName
    fpColName = options.morganFpColName

  extraArgs = {}
  if options.similarityMetric == 'tanimoto':
    simMetric = DataStructs.TanimotoSimilarity
  elif options.similarityMetric == 'dice':
    simMetric = DataStructs.DiceSimilarity
  elif options.similarityMetric == 'tversky':
    simMetric = DataStructs.TverskySimilarity
    extraArgs['tverskyA'] = options.tverskyA
    extraArgs['tverskyB'] = options.tverskyB

  if options.smilesQuery:
    mol = Chem.MolFromSmiles(options.smilesQuery)
    if not mol:
      logger.error('could not build query molecule from smiles "%s"' % options.smilesQuery)
      sys.exit(-1)
    options.queryMol = mol
  elif options.smartsQuery:
    mol = Chem.MolFromSmarts(options.smartsQuery)
    if not mol:
      logger.error('could not build query molecule from smarts "%s"' % options.smartsQuery)
      sys.exit(-1)
    options.queryMol = mol

  if options.outF == '-':
    outF = sys.stdout
  elif options.outF == '':
    outF = None
  else:
    outF = open(options.outF, 'w+')

  molsOut = False
  if options.sdfOut:
    molsOut = True
    if options.sdfOut == '-':
      sdfOut = sys.stdout
    else:
      sdfOut = open(options.sdfOut, 'w+')
  else:
    sdfOut = None
  if options.smilesOut:
    molsOut = True
    if options.smilesOut == '-':
      smilesOut = sys.stdout
    else:
      smilesOut = open(options.smilesOut, 'w+')
  else:
    smilesOut = None

  if queryFilename:
    try:
      tmpF = open(queryFilename, 'r')
    except IOError:
      logger.error('could not open query file %s' % queryFilename)
      sys.exit(1)

    if options.molFormat == 'smiles':
      func = GetMolsFromSmilesFile
    elif options.molFormat == 'sdf':
      func = GetMolsFromSDFile

    if not options.silent:
      msg = 'Reading query molecules'
      if fpBuilder:
        msg += ' and generating fingerprints'
      logger.info(msg)
    probes = []
    i = 0
    nms = []
    for nm, smi, mol in func(queryFilename, None, options.nameProp):
      i += 1
      nms.append(nm)
      if not mol:
        logger.error('query molecule %d could not be built' % (i))
        probes.append((None, None))
        continue
      if fpBuilder:
        probes.append((mol, fpBuilder(mol)))
      else:
        probes.append((mol, None))
      if not options.silent and not i % 1000:
        logger.info("  done %d" % i)
  else:
    probes = None

  conn = None
  idName = options.molIdName
  ids = None
  names = None
  molDbName = os.path.join(options.dbDir, options.molDbName)
  molIdName = options.molIdName
  mConn = DbConnect(molDbName)
  cns = [(x.lower(), y) for x, y in mConn.GetColumnNamesAndTypes('molecules')]
  idCol, idTyp = cns[0]
  if options.propQuery or options.queryMol:
    conn = DbConnect(molDbName)
    curs = conn.GetCursor()
    if options.queryMol:
      if not options.silent:
        logger.info('Doing substructure query')
      if options.propQuery:
        where = 'where %s' % options.propQuery
      else:
        where = ''
      if not options.silent:
        curs.execute('select count(*) from molecules %(where)s' % locals())
        nToDo = curs.fetchone()[0]

      join = ''
      doSubstructFPs = False
      fpDbName = os.path.join(options.dbDir, options.fpDbName)
      if os.path.exists(fpDbName) and not options.negateQuery:
        curs.execute("attach database '%s' as fpdb" % (fpDbName))
        try:
          curs.execute('select * from fpdb.%s limit 1' % options.layeredTableName)
        except Exception:
          pass
        else:
          doSubstructFPs = True
          join = 'join fpdb.%s using (%s)' % (options.layeredTableName, idCol)
          query = LayeredOptions.GetQueryText(options.queryMol)
          if query:
            if not where:
              where = 'where'
            else:
              where += ' and'
            where += ' ' + query

      cmd = 'select %(idCol)s,molpkl from molecules %(join)s %(where)s' % locals()
      curs.execute(cmd)
      row = curs.fetchone()
      nDone = 0
      ids = []
      while row:
        id, molpkl = row
        if not options.zipMols:
          m = _molFromPkl(molpkl)
        else:
          m = Chem.Mol(zlib.decompress(molpkl))
        matched = m.HasSubstructMatch(options.queryMol)
        if options.negateQuery:
          matched = not matched
        if matched:
          ids.append(id)
        nDone += 1
        if not options.silent and not nDone % 500:
          if not doSubstructFPs:
            logger.info('  searched %d (of %d) molecules; %d hits so far' %
                        (nDone, nToDo, len(ids)))
          else:
            logger.info('  searched through %d molecules; %d hits so far' % (nDone, len(ids)))
        row = curs.fetchone()
      if not options.silent and doSubstructFPs and nToDo:
        nFiltered = nToDo - nDone
        logger.info('   Fingerprint screenout rate: %d of %d (%%%.2f)' %
                    (nFiltered, nToDo, 100. * nFiltered / nToDo))

    elif options.propQuery:
      if not options.silent:
        logger.info('Doing property query')
      propQuery = options.propQuery.split(';')[0]
      curs.execute('select %(idCol)s from molecules where %(propQuery)s' % locals())
      ids = [x[0] for x in curs.fetchall()]
    if not options.silent:
      logger.info('Found %d molecules matching the query' % (len(ids)))

  t1 = time.time()
  if probes:
    if not options.silent:
      logger.info('Finding Neighbors')
    conn = DbConnect(dbName)
    cns = conn.GetColumnNames(fpTableName)
    curs = conn.GetCursor()

    if ids:
      ids = [(x, ) for x in ids]
      curs.execute('create temporary table _tmpTbl (%(idCol)s %(idTyp)s)' % locals())
      curs.executemany('insert into _tmpTbl values (?)', ids)
      join = 'join  _tmpTbl using (%(idCol)s)' % locals()
    else:
      join = ''

    if cns[0].lower() != idCol.lower():
      # backwards compatibility to the days when mol tables had a guid and
      # the fps tables did not:
      curs.execute("attach database '%(molDbName)s' as mols" % locals())
      curs.execute("""
  select %(idCol)s,%(fpColName)s from %(fpTableName)s join
      (select %(idCol)s,%(molIdName)s from mols.molecules %(join)s)
    using (%(molIdName)s)
""" % (locals()))
    else:
      curs.execute('select %(idCol)s,%(fpColName)s from %(fpTableName)s %(join)s' % locals())

    def poolFromCurs(curs, similarityMethod):
      row = curs.fetchone()
      while row:
        id, pkl = row
        fp = DepickleFP(pkl, similarityMethod)
        yield (id, fp)
        row = curs.fetchone()

    topNLists = GetNeighborLists(probes, options.topN, poolFromCurs(curs, options.similarityType),
                                 simMetric=simMetric, simThresh=options.simThresh, **extraArgs)
    uniqIds = set()
    nbrLists = {}
    for i, nm in enumerate(nms):
      topNLists[i].reverse()
      scores = topNLists[i].GetPts()
      nbrNames = topNLists[i].GetExtras()
      nbrs = []
      for j, nbrGuid in enumerate(nbrNames):
        if nbrGuid is None:
          break
        else:
          uniqIds.add(nbrGuid)
          nbrs.append((nbrGuid, scores[j]))
      nbrLists[(i, nm)] = nbrs
    t2 = time.time()
    if not options.silent:
      logger.info('The search took %.1f seconds' % (t2 - t1))

    if not options.silent:
      logger.info('Creating output')

    curs = mConn.GetCursor()
    ids = list(uniqIds)

    ids = [(x, ) for x in ids]
    curs.execute('create temporary table _tmpTbl (%(idCol)s %(idTyp)s)' % locals())
    curs.executemany('insert into _tmpTbl values (?)', ids)
    curs.execute('select %(idCol)s,%(molIdName)s from molecules join _tmpTbl using (%(idCol)s)' %
                 locals())
    nmDict = {}
    for guid, id in curs.fetchall():
      nmDict[guid] = str(id)

    ks = list(nbrLists.keys())
    ks.sort()
    if not options.transpose:
      for i, nm in ks:
        nbrs = nbrLists[(i, nm)]
        nbrTxt = options.outputDelim.join(
          [nm] + ['%s%s%.3f' % (nmDict[id], options.outputDelim, score) for id, score in nbrs])
        if outF:
          print(nbrTxt, file=outF)
    else:
      labels = ['%s%sSimilarity' % (x[1], options.outputDelim) for x in ks]
      if outF:
        print(options.outputDelim.join(labels), file=outF)
      for i in range(options.topN):
        outL = []
        for idx, nm in ks:
          nbr = nbrLists[(idx, nm)][i]
          outL.append(nmDict[nbr[0]])
          outL.append('%.3f' % nbr[1])
        if outF:
          print(options.outputDelim.join(outL), file=outF)
  else:
    if not options.silent:
      logger.info('Creating output')
    curs = mConn.GetCursor()
    ids = [(x, ) for x in set(ids)]
    curs.execute('create temporary table _tmpTbl (%(idCol)s %(idTyp)s)' % locals())
    curs.executemany('insert into _tmpTbl values (?)', ids)
    molIdName = options.molIdName
    curs.execute('select %(idCol)s,%(molIdName)s from molecules join _tmpTbl using (%(idCol)s)' %
                 locals())
    nmDict = {}
    for guid, id in curs.fetchall():
      nmDict[guid] = str(id)
    if outF:
      print('\n'.join(nmDict.values()), file=outF)
  if molsOut and ids:
    molDbName = os.path.join(options.dbDir, options.molDbName)
    cns = [x.lower() for x in mConn.GetColumnNames('molecules')]
    if cns[-1] != 'molpkl':
      cns.remove('molpkl')
      cns.append('molpkl')

    curs = mConn.GetCursor()
    #curs.execute('create temporary table _tmpTbl (guid integer)'%locals())
    #curs.executemany('insert into _tmpTbl values (?)',ids)
    cnText = ','.join(cns)
    curs.execute('select %(cnText)s from molecules join _tmpTbl using (%(idCol)s)' % locals())

    row = curs.fetchone()
    molD = {}
    while row:
      row = list(row)
      m = _molFromPkl(row[-1])
      guid = row[0]
      nm = nmDict[guid]
      if sdfOut:
        m.SetProp('_Name', nm)
        print(Chem.MolToMolBlock(m), file=sdfOut)
        for i in range(1, len(cns) - 1):
          pn = cns[i]
          pv = str(row[i])
          print >> sdfOut, '> <%s>\n%s\n' % (pn, pv)
        print('$$$$', file=sdfOut)
      if smilesOut:
        smi = Chem.MolToSmiles(m, options.chiralSmiles)
      if smilesOut:
        print('%s %s' % (smi, str(row[1])), file=smilesOut)
      row = curs.fetchone()
  if not options.silent:
    logger.info('Done!')


# ---- ---- ---- ----  ---- ---- ---- ----  ---- ---- ---- ----  ---- ---- ---- ----


def initParser():
  """ Initialize the command line parser """
  parser = argparse.ArgumentParser(usage='SearchDB [optional arguments] <sdffilename>',
                                   description=_description,
                                   formatter_class=argparse.RawDescriptionHelpFormatter)

  parser.add_argument('filename', nargs='?', help='File containg molecules for searching')
  parser.add_argument('--version', action='version', version='%(prog)s ' + _version)

  parser.add_argument(
    '--dbDir', default='', help=
    'name of the directory containing the database information. The default is the current directory'
  )
  parser.add_argument('--molDbName', default='Compounds.sqlt', help='name of the molecule database')
  parser.add_argument('--molIdName', default='compound_id', help='name of the database key column')
  parser.add_argument('--regName', default='molecules', help='name of the molecular registry table')
  parser.add_argument('--pairDbName', default='AtomPairs.sqlt',
                      help='name of the atom pairs database')
  parser.add_argument('--pairTableName', default='atompairs', help='name of the atom pairs table')
  parser.add_argument('--pairColName', default='atompairfp', help='name of the atom pair column')
  parser.add_argument(
    '--torsionsDbName', default='AtomPairs.sqlt',
    help='name of the topological torsions database (usually the same as the atom pairs database)')
  parser.add_argument(
    '--torsionsTableName', default='atompairs',
    help='name of the topological torsions table (usually the same as the atom pairs table)')
  parser.add_argument('--torsionsColName', default='torsionfp', help='name of the atom pair column')
  parser.add_argument('--fpDbName', default='Fingerprints.sqlt',
                      help='name of the 2D fingerprints database')
  parser.add_argument('--fpTableName', default='rdkitfps', help='name of the 2D fingerprints table')
  parser.add_argument('--layeredTableName', default='layeredfps',
                      help='name of the layered fingerprints table')
  parser.add_argument('--fpColName', default='',
                      help='name of the 2D fingerprint column, a sensible default is used')
  parser.add_argument('--descrDbName', default='Descriptors.sqlt',
                      help='name of the descriptor database')
  parser.add_argument('--descrTableName', default='descriptors_v1',
                      help='name of the descriptor table')
  parser.add_argument('--descriptorCalcFilename',
                      default=os.path.join(RDConfig.RDBaseDir, 'Projects', 'DbCLI', 'moe_like.dsc'),
                      help='name of the file containing the descriptor calculator')
  parser.add_argument('--outputDelim', default=',',
                      help='the delimiter for the output file. The default is %(default)s')
  parser.add_argument(
    '--topN', default=20, type=int,
    help='the number of neighbors to keep for each query compound. The default is %(default)s')

  parser.add_argument('--outF', '--outFile', default='-',
                      help='The name of the output file. The default is the console (stdout).')

  parser.add_argument(
    '--transpose', default=False, action="store_true", help=
    'print the results out in a transposed form: e.g. neighbors in rows and probe compounds in columns'
  )

  parser.add_argument('--molFormat', default='sdf', choices=('smiles', 'sdf'),
                      help='specify the format of the input file')
  parser.add_argument(
    '--nameProp', default='_Name', help=
    'specify the SD property to be used for the molecule names. Default is to use the mol block name'
  )

  parser.add_argument('--smartsQuery', '--smarts', '--sma', default='',
                      help='provide a SMARTS to be used as a substructure query')
  parser.add_argument('--smilesQuery', '--smiles', '--smi', default='',
                      help='provide a SMILES to be used as a substructure query')
  parser.add_argument('--negateQuery', '--negate', default=False, action='store_true',
                      help='negate the results of the smarts query.')
  parser.add_argument('--propQuery', '--query', '-q', default='',
                      help='provide a property query (see the NOTE about property names)')

  parser.add_argument('--sdfOut', '--sdOut', default='',
                      help='export an SD file with the matching molecules')
  parser.add_argument('--smilesOut', '--smiOut', default='',
                      help='export a smiles file with the matching molecules')
  parser.add_argument('--nonchiralSmiles', dest='chiralSmiles', default=True, action='store_false',
                      help='do not use chiral SMILES in the output')
  parser.add_argument('--silent', default=False, action='store_true',
                      help='Do not generate status messages.')

  parser.add_argument('--zipMols', '--zip', default=False, action='store_true',
                      help='read compressed mols from the database')

  parser.add_argument('--pharm2DTableName', default='pharm2dfps',
                      help='name of the Pharm2D fingerprints table')
  parser.add_argument('--fdefFile', '--fdef', default=os.path.join(RDConfig.RDDataDir,
                                                                   'Novartis1.fdef'),
                      help='provide the name of the fdef file to use for 2d pharmacophores')
  parser.add_argument('--gobbi2DTableName', default='gobbi2dfps',
                      help='name of the Gobbi2D fingerprints table')

  parser.add_argument(
    '--similarityType', '--simType', '--sim', default='RDK', choices=supportedSimilarityMethods,
    help=
    'Choose the type of similarity to use, possible values: RDK, AtomPairs, TopologicalTorsions, Pharm2D, Gobbi2D, Avalon, Morgan. The default is %(default)s'
  )
  parser.add_argument('--morganFpDbName', default='Fingerprints.sqlt',
                      help='name of the morgan fingerprints database')
  parser.add_argument('--morganFpTableName', default='morganfps',
                      help='name of the morgan fingerprints table')
  parser.add_argument('--morganFpColName', default='morganfp',
                      help='name of the morgan fingerprint column')

  parser.add_argument(
    '--similarityMetric', '--simMetric', '--metric', default='',
    choices=('tanimoto', 'dice', 'tversky', ''), help=
    'Choose the type of similarity to use, possible values: tanimoto, dice, tversky. The default is determined by the fingerprint type'
  )
  parser.add_argument('--tverskyA', default=0.5, type=float, help='Tversky A value')
  parser.add_argument('--tverskyB', default=0.5, type=float, help='Tversky B value')
  parser.add_argument(
    '--simThresh', default=-1, type=float,
    help='threshold to use for similarity searching. If provided, this supersedes the topN argument'
  )
  return parser


if __name__ == '__main__':

  parser = initParser()
  options = parser.parse_args()

  if options.filename is None and not (options.smilesQuery or options.smartsQuery
                                       or options.propQuery):
    parser.error('please either provide a query filename argument or do a data or smarts query')

  queryFilename = options.filename
  options.queryMol = None
  RunSearch(options, queryFilename)