Source Code for Module rdkit.Dbase.DbReport

  1  # $Id: DbReport.py 997 2009-02-25 06:12:43Z glandrum $ 
  2  # 
  3  #  Copyright (C) 2003-2006  Rational Discovery LLC 
  4  # 
  5  #   @@ All Rights Reserved  @@ 
  6  # 
  7  try: 
  8    from reportlab import platypus 
  9  except ImportError: 
 10    import sys 
 11    sys.stderr.write('ReportLab module could not be imported.  Db->PDF functionality not available') 
 12    GetReportlabTable = None 
 13    QuickReport = None 
 14  else: 
 15    from rdkit import Chem 
 16    try: 
 17      from pyRDkit.utils import chemdraw 
 18    except ImportError: 
 19      hasCDX=0 
 20    else: 
 21      hasCDX=1 
 22    from rdkit.utils import cactvs   
 23    from rdkit.Chem import rdDepictor 
 24    from rdkit.Chem.Draw import DrawUtils 
 25    from rdkit.Dbase.DbConnection import DbConnect 
 26    from rdkit.Dbase import DbInfo 
 27    from rdkit.Reports.PDFReport import PDFReport,ReportUtils 
 28    import os,tempfile,sys 
 29     
 30 -  def GetReportlabTable(self,*args,**kwargs): 
 31      """ this becomes a method of DbConnect  """ 
 32      dbRes = self.GetData(*args,**kwargs) 
 33      rawD = [dbRes.GetColumnNames()] 
 34      colTypes = dbRes.GetColumnTypes() 
 35      binCols = [] 
 36      for i in range(len(colTypes)): 
 37        if colTypes[i] in DbInfo.sqlBinTypes or colTypes[i]=='binary': 
 38          binCols.append(i) 
 39      nRows = 0 
 40      for entry in dbRes: 
 41        nRows += 1 
 42        for col in binCols: 
 43          entry = list(entry) 
 44          entry[col] = 'N/A' 
 45        rawD.append(entry) 
 46        #if nRows >10: break 
 47      
 48      res = platypus.Table(rawD) 
 49      return res 
 50   
 51    from reportlab.lib.units import inch 
 52 -  class CDXImageTransformer(object): 
 53 -    def __init__(self,smiCol,width=1,verbose=1,tempHandler=None): 
 54        self.smiCol = smiCol 
 55        if tempHandler is None: 
 56          tempHandler = ReportUtils.TempFileHandler() 
 57        self.tempHandler = tempHandler 
 58        self.width = width*inch 
 59        self.verbose=verbose 
 60 -    def __call__(self,arg): 
 61        res = list(arg) 
 62        if self.verbose: 
 63          print 'Render:',res[0] 
 64        if hasCDX: 
 65          smi = res[self.smiCol] 
 66          tmpName = self.tempHandler.get('.jpg') 
 67          try: 
 68            img = chemdraw.SmilesToPilImage(smi) 
 69            w,h = img.size 
 70            aspect = float(h)/w 
 71            img.save(tmpName) 
 72            img = platypus.Image(tmpName) 
 73            img.drawWidth = self.width 
 74            img.drawHeight = aspect*self.width 
 75            res[self.smiCol] = img 
 76          except: 
 77            import traceback 
 78            traceback.print_exc() 
 79            res[self.smiCol] = 'Failed' 
 80        return res 
 81   
 82 -  class CactvsImageTransformer(object): 
 83 -    def __init__(self,smiCol,width=1.,verbose=1,tempHandler=None): 
 84        self.smiCol = smiCol 
 85        if tempHandler is None: 
 86          tempHandler = ReportUtils.TempFileHandler() 
 87        self.tempHandler = tempHandler 
 88        self.width = width*inch 
 89        self.verbose=verbose 
 90 -    def __call__(self,arg): 
 91        res = list(arg) 
 92        if self.verbose: 
 93          sys.stderr.write('Render(%d): %s\n'%(self.smiCol,str(res[0]))) 
 94        smi = res[self.smiCol] 
 95        tmpName = self.tempHandler.get('.gif') 
 96        aspect = 1 
 97        width = 300 
 98        height = aspect*width 
 99        ok = cactvs.SmilesToGif(smi,tmpName,(width,height)) 
100        if ok: 
101          try: 
102            img = platypus.Image(tmpName) 
103            img.drawWidth = self.width 
104            img.drawHeight = aspect*self.width 
105          except: 
106            ok = 0 
107        if ok: 
108          res[self.smiCol] = img 
109        else: 
110          # FIX: maybe include smiles here in a Paragraph? 
111          res[self.smiCol] = 'Failed' 
112        return res 
113           
114   
115    from rdkit.sping.ReportLab.pidReportLab import RLCanvas as Canvas 
116    from rdkit.Chem.Draw.MolDrawing import MolDrawing 
117 -  class ReportLabImageTransformer(object): 
118 -    def __init__(self,smiCol,width=1.,verbose=1,tempHandler=None): 
119        self.smiCol = smiCol 
120        self.width = width*inch 
121        self.verbose=verbose 
122 -    def __call__(self,arg): 
123        res = list(arg) 
124        if self.verbose: 
125          sys.stderr.write('Render(%d): %s\n'%(self.smiCol,str(res[0]))) 
126        smi = res[self.smiCol] 
127        aspect = 1 
128        width = self.width 
129        height = aspect*width 
130        try: 
131          mol = Chem.MolFromSmiles(smi) 
132          Chem.Kekulize(mol) 
133          canv = Canvas((width,height)) 
134          drawing = MolDrawing() 
135          drawing.atomLabelMinFontSize=3 
136          drawing.minLabelPadding=(.5,.5) 
137          drawing.bondLineWidth=0.5 
138          if not mol.GetNumConformers(): 
139            rdDepictor.Compute2DCoords(mol) 
140          drawing.AddMol(mol,canvas=canv) 
141          ok = True 
142        except: 
143          if self.verbose: 
144            import traceback 
145            traceback.print_exc() 
146          ok = False 
147   
148        if ok: 
149          res[self.smiCol] = canv.drawing 
150        else: 
151          # FIX: maybe include smiles here in a Paragraph? 
152          res[self.smiCol] = 'Failed' 
153        return res 
154           
155   
156 -  class RDImageTransformer(object): 
157 -    def __init__(self,smiCol,width=1.,verbose=1,tempHandler=None): 
158        self.smiCol = smiCol 
159        if tempHandler is None: 
160          tempHandler = ReportUtils.TempFileHandler() 
161        self.tempHandler = tempHandler 
162        self.width = width*inch 
163        self.verbose=verbose 
164 -    def __call__(self,arg): 
165        res = list(arg) 
166        if self.verbose: 
167          sys.stderr.write('Render(%d): %s\n'%(self.smiCol,str(res[0]))) 
168        smi = res[self.smiCol] 
169        tmpName = self.tempHandler.get('.jpg') 
170        aspect = 1 
171        width = 300 
172        height = aspect*width 
173        ok = DrawUtils.SmilesToJpeg(smi,tmpName,size=(width,height)) 
174        if ok: 
175          try: 
176            img = platypus.Image(tmpName) 
177            img.drawWidth = self.width 
178            img.drawHeight = aspect*self.width 
179          except: 
180            ok = 0 
181        if ok: 
182          res[self.smiCol] = img 
183        else: 
184          # FIX: maybe include smiles here in a Paragraph? 
185          res[self.smiCol] = 'Failed' 
186        return res 
187           
188 -  def QuickReport(conn,fileName,*args,**kwargs): 
189      from reportlab.lib import colors 
190      from reportlab.lib.styles import getSampleStyleSheet 
191      from reportlab.lib.units import inch 
192   
193      styles = getSampleStyleSheet() 
194      title = 'Db Report' 
195      if kwargs.has_key('title'): 
196        title = kwargs['title'] 
197        del kwargs['title'] 
198   
199      names = [x.upper() for x in conn.GetColumnNames()] 
200      try: 
201        smiCol = names.index('SMILES') 
202      except ValueError: 
203        try: 
204          smiCol = names.index('SMI') 
205        except ValueError: 
206          smiCol = -1 
207      if smiCol >-1: 
208        if hasCDX: 
209          tform = CDXImageTransformer(smiCol) 
210        elif 1: 
211          tform = ReportLabImageTransformer(smiCol) 
212        else: 
213          tform = CactvsImageTransformer(smiCol) 
214   
215      else: 
216        tform = None 
217      kwargs['transform'] = tform 
218      tbl = conn.GetReportlabTable(*args,**kwargs) 
219      tbl.setStyle(platypus.TableStyle([('GRID',(0,0),(-1,-1),1,colors.black), 
220                                        ('FONT',(0,0),(-1,-1),'Times-Roman',8), 
221                                        ])) 
222   
223       
224      if smiCol >-1 and tform: 
225        tbl._argW[smiCol] = tform.width*1.2 
226      elements = [tbl] 
227      reportTemplate = PDFReport() 
228      reportTemplate.pageHeader = title 
229   
230      doc = platypus.SimpleDocTemplate(fileName) 
231      doc.build(elements,onFirstPage=reportTemplate.onPage, 
232                onLaterPages=reportTemplate.onPage) 
233       
234    DbConnect.GetReportlabTable = GetReportlabTable 
235   
236  if __name__=='__main__': 
237    import sys 
238    dbName = sys.argv[1] 
239    tblName = sys.argv[2] 
240    fName = 'report.pdf' 
241    conn = DbConnect(dbName,tblName) 
242    QuickReport(conn,fName,where="where mol_id in ('1','100','104','107')") 
243