Source Code for Module rdkit.Chem.MolDb.Loader

  1  # $Id: Loader.py 997 2009-02-25 06:12:43Z glandrum $ 
  2  # 
  3  #  Copyright (C) 2007-2008 Greg Landrum 
  4  #   @@ All Rights Reserved @@ 
  5  # 
  6  from rdkit import Chem 
  7  from rdkit.Chem import AllChem 
  8  from rdkit.Chem import Lipinski,Descriptors,Crippen 
  9  from rdkit.Dbase.DbConnection import DbConnect 
 10  from rdkit.Dbase import DbModule 
 11  import re 
 12   
 13  #set up the logger: 
 14  import rdkit.RDLogger as logging 
 15  logger = logging.logger() 
 16  logger.setLevel(logging.INFO) 
 17   
 18 -def ProcessMol(mol,typeConversions,globalProps,nDone,nameProp='_Name',nameCol='compound_id', 
 19                 redraw=False,keepHs=False, 
 20                 skipProps=False,addComputedProps=False, 
 21                 skipSmiles=False, 
 22                 uniqNames=None,namesSeen=None): 
 23    if not mol: 
 24      raise ValueError,'no molecule' 
 25    if keepHs: 
 26      Chem.SanitizeMol(mol) 
 27    try: 
 28      nm = mol.GetProp(nameProp) 
 29    except KeyError: 
 30      nm = None 
 31    if not nm: 
 32      nm = 'Mol_%d'%nDone 
 33    if uniqNames and nm in namesSeen: 
 34      logger.error('duplicate compound id (%s) encountered. second instance skipped.'%nm) 
 35      return None 
 36    namesSeen.add(nm) 
 37    row = [nm] 
 38    if not skipProps: 
 39      if addComputedProps: 
 40        nHD=Lipinski.NumHDonors(mol) 
 41        mol.SetProp('DonorCount',str(nHD)) 
 42        nHA=Lipinski.NumHAcceptors(mol) 
 43        mol.SetProp('AcceptorCount',str(nHA)) 
 44        nRot=Lipinski.NumRotatableBonds(mol) 
 45        mol.SetProp('RotatableBondCount',str(nRot)) 
 46        MW=Descriptors.MolWt(mol) 
 47        mol.SetProp('AMW',str(MW)) 
 48        logp=Crippen.MolLogP(mol) 
 49        mol.SetProp('MolLogP',str(logp)) 
 50   
 51      pns = list(mol.GetPropNames()) 
 52      pD={} 
 53      for pi,pn in enumerate(pns): 
 54        if pn.lower()==nameCol.lower(): continue 
 55        pv = mol.GetProp(pn).strip() 
 56        if pv.find('>')<0 and pv.find('<')<0: 
 57          colTyp = globalProps.get(pn,2) 
 58          while colTyp>0: 
 59            try: 
 60              tpi = typeConversions[colTyp][1](pv) 
 61            except: 
 62              colTyp-=1 
 63            else: 
 64              break 
 65          globalProps[pn]=colTyp 
 66          pD[pn]=typeConversions[colTyp][1](pv) 
 67        else: 
 68          pD[pn]=pv 
 69    else: 
 70      pD={} 
 71    if redraw: 
 72      AllChem.Compute2DCoords(m) 
 73    if not skipSmiles: 
 74      row.append(Chem.MolToSmiles(mol,True)) 
 75    row.append(DbModule.binaryHolder(mol.ToBinary())) 
 76    row.append(pD) 
 77    return row 
 78   
 79 -def ConvertRows(rows,globalProps,defaultVal,skipSmiles): 
 80    for i,row in enumerate(rows): 
 81      newRow = [] 
 82      newRow.append(row[0]) 
 83      pD=row[-1] 
 84      for pn in globalProps: 
 85        pv = pD.get(pn,defaultVal) 
 86        newRow.append(pv) 
 87      newRow.append(row[1]) 
 88      if not skipSmiles: 
 89        newRow.append(row[2]) 
 90      rows[i] = newRow 
 91   
 92 -def LoadDb(suppl,dbName,nameProp='_Name',nameCol='compound_id',silent=False, 
 93             redraw=False,errorsTo=None,keepHs=False,defaultVal='N/A',skipProps=False, 
 94             regName='molecules',skipSmiles=False,maxRowsCached=-1, 
 95             uniqNames=False,addComputedProps=False,lazySupplier=False): 
 96    if not lazySupplier: 
 97      nMols = len(suppl) 
 98    else: 
 99      nMols=-1 
100    if not silent: 
101      logger.info("Generating molecular database in file %s"%dbName) 
102      if not lazySupplier: 
103        logger.info("  Processing %d molecules"%nMols) 
104    rows = [] 
105    globalProps = {} 
106    namesSeen = set() 
107    nDone = 0 
108    typeConversions={0:('varchar',str),1:('float',float),2:('int',int)} 
109    for m in suppl: 
110      nDone +=1 
111      if not m: 
112        if errorsTo: 
113          if hasattr(suppl,'GetItemText'): 
114            d = suppl.GetItemText(nDone-1) 
115            errorsTo.write(d) 
116          else: 
117            logger.warning('full error file support not complete') 
118        continue 
119   
120      row=ProcessMol(m,typeConversions,globalProps,nDone,nameProp=nameProp, 
121                     nameCol=nameCol,redraw=redraw, 
122                     keepHs=keepHs,skipProps=skipProps, 
123                     addComputedProps=addComputedProps,skipSmiles=skipSmiles, 
124                     uniqNames=uniqNames,namesSeen=namesSeen) 
125      if row is None: continue 
126      rows.append(row) 
127      if not silent and not nDone%100: 
128        logger.info('  done %d'%nDone) 
129      if len(rows)==maxRowsCached: 
130        break 
131   
132    nameDef='%s varchar not null'%nameCol 
133    if uniqNames: 
134      nameDef += ' unique' 
135    typs = [nameDef] 
136    pns = [] 
137    for pn,v in globalProps.iteritems(): 
138      addNm = re.sub(r'[\W]','_',pn) 
139      typs.append('%s %s'%(addNm,typeConversions[v][0])) 
140      pns.append(pn.lower()) 
141   
142    if not skipSmiles: 
143      if 'smiles' not in pns: 
144        typs.append('smiles varchar') 
145      else: 
146        typs.append('cansmiles varchar') 
147    typs.append('molpkl %s'%(DbModule.binaryTypeName)) 
148    conn = DbConnect(dbName) 
149    curs = conn.GetCursor() 
150    try: 
151      curs.execute('drop table %s'%regName) 
152    except: 
153      pass 
154    curs.execute('create table %s (%s)'%(regName,','.join(typs))) 
155    qs = ','.join([DbModule.placeHolder for x in typs]) 
156   
157   
158    ConvertRows(rows,globalProps,defaultVal,skipSmiles) 
159    curs.executemany('insert into %s values (%s)'%(regName,qs),rows) 
160    conn.Commit() 
161   
162    rows = [] 
163    while 1: 
164      nDone +=1 
165      try: 
166        m = suppl.next() 
167      except StopIteration: 
168        break 
169      if not m: 
170        if errorsTo: 
171          if hasattr(suppl,'GetItemText'): 
172            d = suppl.GetItemText(nDone-1) 
173            errorsTo.write(d) 
174          else: 
175            logger.warning('full error file support not complete') 
176        continue 
177      tmpProps={} 
178      row=ProcessMol(m,typeConversions,globalProps,nDone,nameProp=nameProp, 
179                     nameCol=nameCol,redraw=redraw, 
180                     keepHs=keepHs,skipProps=skipProps, 
181                     addComputedProps=addComputedProps,skipSmiles=skipSmiles, 
182                     uniqNames=uniqNames,namesSeen=namesSeen) 
183      if not row: continue 
184      rows.append(row) 
185      if not silent and not nDone%100: 
186        logger.info('  done %d'%nDone) 
187      if len(rows)==maxRowsCached: 
188        ConvertRows(rows,globalProps,defaultVal,skipSmiles) 
189        curs.executemany('insert into %s values (%s)'%(regName,qs),rows) 
190        conn.Commit() 
191        rows = [] 
192    if len(rows): 
193      ConvertRows(rows,globalProps,defaultVal,skipSmiles) 
194      curs.executemany('insert into %s values (%s)'%(regName,qs),rows) 
195      conn.Commit() 
196