Source Code for Module rdkit.Chem.MolDb.Loader_orig

  1  # $Id: Loader_orig.py 1528 2010-09-26 17:04:37Z glandrum $ 
  2  # 
  3  #  Copyright (C) 2007-2008 Greg Landrum 
  4  #   @@ All Rights Reserved @@ 
  5  #  This file is part of the RDKit. 
  6  #  The contents are covered by the terms of the BSD license 
  7  #  which is included in the file license.txt, found at the root 
  8  #  of the RDKit source tree. 
  9  # 
 10  from rdkit import Chem 
 11  from rdkit.Chem import AllChem 
 12  from rdkit.Chem import Lipinski,Descriptors,Crippen 
 13  from rdkit.Dbase.DbConnection import DbConnect 
 14  from rdkit.Dbase import DbModule 
 15  import re 
 16   
 17  #set up the logger: 
 18  import rdkit.RDLogger as logging 
 19  logger = logging.logger() 
 20  logger.setLevel(logging.INFO) 
 21   
 22 -def ProcessMol(mol,typeConversions,globalProps,nDone,nameProp='_Name',nameCol='compound_id', 
 23                 redraw=False,keepHs=False, 
 24                 skipProps=False,addComputedProps=False, 
 25                 skipSmiles=False, 
 26                 uniqNames=None,namesSeen=None): 
 27    if not mol: 
 28      raise ValueError,'no molecule' 
 29    if keepHs: 
 30      Chem.SanitizeMol(mol) 
 31    try: 
 32      nm = mol.GetProp(nameProp) 
 33    except KeyError: 
 34      nm = None 
 35    if not nm: 
 36      nm = 'Mol_%d'%nDone 
 37    if uniqNames and nm in namesSeen: 
 38      logger.error('duplicate compound id (%s) encountered. second instance skipped.'%nm) 
 39      return None 
 40    namesSeen.add(nm) 
 41    row = [nm] 
 42    if not skipProps: 
 43      if addComputedProps: 
 44        nHD=Lipinski.NumHDonors(mol) 
 45        mol.SetProp('DonorCount',str(nHD)) 
 46        nHA=Lipinski.NumHAcceptors(mol) 
 47        mol.SetProp('AcceptorCount',str(nHA)) 
 48        nRot=Lipinski.NumRotatableBonds(mol) 
 49        mol.SetProp('RotatableBondCount',str(nRot)) 
 50        MW=Descriptors.MolWt(mol) 
 51        mol.SetProp('AMW',str(MW)) 
 52        logp=Crippen.MolLogP(mol) 
 53        mol.SetProp('MolLogP',str(logp)) 
 54   
 55      pns = list(mol.GetPropNames()) 
 56      pD={} 
 57      for pi,pn in enumerate(pns): 
 58        if pn.lower()==nameCol.lower(): continue 
 59        pv = mol.GetProp(pn).strip() 
 60        if pv.find('>')<0 and pv.find('<')<0: 
 61          colTyp = globalProps.get(pn,2) 
 62          while colTyp>0: 
 63            try: 
 64              tpi = typeConversions[colTyp][1](pv) 
 65            except: 
 66              colTyp-=1 
 67            else: 
 68              break 
 69          globalProps[pn]=colTyp 
 70          pD[pn]=typeConversions[colTyp][1](pv) 
 71        else: 
 72          pD[pn]=pv 
 73    else: 
 74      pD={} 
 75    if redraw: 
 76      AllChem.Compute2DCoords(m) 
 77    if not skipSmiles: 
 78      row.append(Chem.MolToSmiles(mol,True)) 
 79    row.append(DbModule.binaryHolder(mol.ToBinary())) 
 80    row.append(pD) 
 81    return row 
 82   
 83 -def ConvertRows(rows,globalProps,defaultVal,skipSmiles): 
 84    for i,row in enumerate(rows): 
 85      newRow = [row[0],row[1]] 
 86      pD=row[-1] 
 87      for pn in globalProps: 
 88        pv = pD.get(pn,defaultVal) 
 89        newRow.append(pv) 
 90      newRow.append(row[2]) 
 91      if not skipSmiles: 
 92        newRow.append(row[3]) 
 93      rows[i] = newRow 
 94   
 95 -def LoadDb(suppl,dbName,nameProp='_Name',nameCol='compound_id',silent=False, 
 96             redraw=False,errorsTo=None,keepHs=False,defaultVal='N/A',skipProps=False, 
 97             regName='molecules',skipSmiles=False,maxRowsCached=-1, 
 98             uniqNames=False,addComputedProps=False,lazySupplier=False): 
 99    if not lazySupplier: 
100      nMols = len(suppl) 
101    else: 
102      nMols=-1 
103    if not silent: 
104      logger.info("Generating molecular database in file %s"%dbName) 
105      if not lazySupplier: 
106        logger.info("  Processing %d molecules"%nMols) 
107    rows = [] 
108    globalProps = {} 
109    namesSeen = set() 
110    nDone = 0 
111    typeConversions={0:('varchar',str),1:('float',float),2:('int',int)} 
112    for m in suppl: 
113      nDone +=1 
114      if not m: 
115        if errorsTo: 
116          if hasattr(suppl,'GetItemText'): 
117            d = suppl.GetItemText(nDone-1) 
118            errorsTo.write(d) 
119          else: 
120            logger.warning('full error file support not complete') 
121        continue 
122   
123      row=ProcessMol(m,typeConversions,globalProps,nDone,nameProp=nameProp, 
124                     nameCol=nameCol,redraw=redraw, 
125                     keepHs=keepHs,skipProps=skipProps, 
126                     addComputedProps=addComputedProps,skipSmiles=skipSmiles, 
127                     uniqNames=uniqNames,namesSeen=namesSeen) 
128      if row is None: continue 
129      rows.append([nDone]+row) 
130      if not silent and not nDone%100: 
131        logger.info('  done %d'%nDone) 
132      if len(rows)==maxRowsCached: 
133        break 
134   
135    nameDef='%s varchar not null'%nameCol 
136    if uniqNames: 
137      nameDef += ' unique' 
138    typs = ['guid integer not null primary key',nameDef] 
139    pns = [] 
140    for pn,v in globalProps.iteritems(): 
141      addNm = re.sub(r'[\W]','_',pn) 
142      typs.append('%s %s'%(addNm,typeConversions[v][0])) 
143      pns.append(pn.lower()) 
144   
145    if not skipSmiles: 
146      if 'smiles' not in pns: 
147        typs.append('smiles varchar') 
148      else: 
149        typs.append('cansmiles varchar') 
150    typs.append('molpkl %s'%(DbModule.binaryTypeName)) 
151    conn = DbConnect(dbName) 
152    curs = conn.GetCursor() 
153    try: 
154      curs.execute('drop table %s'%regName) 
155    except: 
156      pass 
157    curs.execute('create table %s (%s)'%(regName,','.join(typs))) 
158    qs = ','.join([DbModule.placeHolder for x in typs]) 
159   
160   
161    ConvertRows(rows,globalProps,defaultVal,skipSmiles) 
162    curs.executemany('insert into %s values (%s)'%(regName,qs),rows) 
163    conn.Commit() 
164   
165    rows = [] 
166    while 1: 
167      nDone +=1 
168      try: 
169        m = suppl.next() 
170      except StopIteration: 
171        break 
172      if not m: 
173        if errorsTo: 
174          if hasattr(suppl,'GetItemText'): 
175            d = suppl.GetItemText(nDone-1) 
176            errorsTo.write(d) 
177          else: 
178            logger.warning('full error file support not complete') 
179        continue 
180      tmpProps={} 
181      row=ProcessMol(m,typeConversions,globalProps,nDone,nameProp=nameProp, 
182                     nameCol=nameCol,redraw=redraw, 
183                     keepHs=keepHs,skipProps=skipProps, 
184                     addComputedProps=addComputedProps,skipSmiles=skipSmiles, 
185                     uniqNames=uniqNames,namesSeen=namesSeen) 
186      if not row: continue 
187      rows.append([nDone]+row) 
188      if not silent and not nDone%100: 
189        logger.info('  done %d'%nDone) 
190      if len(rows)==maxRowsCached: 
191        ConvertRows(rows,globalProps,defaultVal,skipSmiles) 
192        curs.executemany('insert into %s values (%s)'%(regName,qs),rows) 
193        conn.Commit() 
194        rows = [] 
195    if len(rows): 
196      ConvertRows(rows,globalProps,defaultVal,skipSmiles) 
197      curs.executemany('insert into %s values (%s)'%(regName,qs),rows) 
198      conn.Commit() 
199