Source Code for Module rdkit.Dbase.DbReport

  1  # $Id$ 
  2  # 
  3  #  Copyright (C) 2003-2006  Rational Discovery LLC 
  4  # 
  5  #   @@ All Rights Reserved @@ 
  6  #  This file is part of the RDKit. 
  7  #  The contents are covered by the terms of the BSD license 
  8  #  which is included in the file license.txt, found at the root 
  9  #  of the RDKit source tree. 
 10  # 
 11  from __future__ import print_function 
 12  try: 
 13    from reportlab import platypus 
 14  except ImportError: 
 15    import sys 
 16    sys.stderr.write('ReportLab module could not be imported.  Db->PDF functionality not available') 
 17    GetReportlabTable = None 
 18    QuickReport = None 
 19  else: 
 20    from rdkit import Chem 
 21    try: 
 22      from pyRDkit.utils import chemdraw 
 23    except ImportError: 
 24      hasCDX=0 
 25    else: 
 26      hasCDX=1 
 27    from rdkit.utils import cactvs   
 28    from rdkit.Chem import rdDepictor 
 29    from rdkit.Chem.Draw import DrawUtils 
 30    from rdkit.Dbase.DbConnection import DbConnect 
 31    from rdkit.Dbase import DbInfo 
 32    from rdkit.Reports.PDFReport import PDFReport,ReportUtils 
 33    import os,tempfile,sys 
 34     
 35 -  def GetReportlabTable(self,*args,**kwargs): 
 36      """ this becomes a method of DbConnect  """ 
 37      dbRes = self.GetData(*args,**kwargs) 
 38      rawD = [dbRes.GetColumnNames()] 
 39      colTypes = dbRes.GetColumnTypes() 
 40      binCols = [] 
 41      for i in range(len(colTypes)): 
 42        if colTypes[i] in DbInfo.sqlBinTypes or colTypes[i]=='binary': 
 43          binCols.append(i) 
 44      nRows = 0 
 45      for entry in dbRes: 
 46        nRows += 1 
 47        for col in binCols: 
 48          entry = list(entry) 
 49          entry[col] = 'N/A' 
 50        rawD.append(entry) 
 51        #if nRows >10: break 
 52      
 53      res = platypus.Table(rawD) 
 54      return res 
 55   
 56    from reportlab.lib.units import inch 
 57 -  class CDXImageTransformer(object): 
 58 -    def __init__(self,smiCol,width=1,verbose=1,tempHandler=None): 
 59        self.smiCol = smiCol 
 60        if tempHandler is None: 
 61          tempHandler = ReportUtils.TempFileHandler() 
 62        self.tempHandler = tempHandler 
 63        self.width = width*inch 
 64        self.verbose=verbose 
 65 -    def __call__(self,arg): 
 66        res = list(arg) 
 67        if self.verbose: 
 68          print('Render:',res[0]) 
 69        if hasCDX: 
 70          smi = res[self.smiCol] 
 71          tmpName = self.tempHandler.get('.jpg') 
 72          try: 
 73            img = chemdraw.SmilesToPilImage(smi) 
 74            w,h = img.size 
 75            aspect = float(h)/w 
 76            img.save(tmpName) 
 77            img = platypus.Image(tmpName) 
 78            img.drawWidth = self.width 
 79            img.drawHeight = aspect*self.width 
 80            res[self.smiCol] = img 
 81          except Exception: 
 82            import traceback 
 83            traceback.print_exc() 
 84            res[self.smiCol] = 'Failed' 
 85        return res 
 86   
 87 -  class CactvsImageTransformer(object): 
 88 -    def __init__(self,smiCol,width=1.,verbose=1,tempHandler=None): 
 89        self.smiCol = smiCol 
 90        if tempHandler is None: 
 91          tempHandler = ReportUtils.TempFileHandler() 
 92        self.tempHandler = tempHandler 
 93        self.width = width*inch 
 94        self.verbose=verbose 
 95 -    def __call__(self,arg): 
 96        res = list(arg) 
 97        if self.verbose: 
 98          sys.stderr.write('Render(%d): %s\n'%(self.smiCol,str(res[0]))) 
 99        smi = res[self.smiCol] 
100        tmpName = self.tempHandler.get('.gif') 
101        aspect = 1 
102        width = 300 
103        height = aspect*width 
104        ok = cactvs.SmilesToGif(smi,tmpName,(width,height)) 
105        if ok: 
106          try: 
107            img = platypus.Image(tmpName) 
108            img.drawWidth = self.width 
109            img.drawHeight = aspect*self.width 
110          except Exception: 
111            ok = 0 
112        if ok: 
113          res[self.smiCol] = img 
114        else: 
115          # FIX: maybe include smiles here in a Paragraph? 
116          res[self.smiCol] = 'Failed' 
117        return res 
118           
119   
120    from rdkit.sping.ReportLab.pidReportLab import RLCanvas as Canvas 
121    from rdkit.Chem.Draw.MolDrawing import MolDrawing,DrawingOptions 
122 -  class ReportLabImageTransformer(object): 
123 -    def __init__(self,smiCol,width=1.,verbose=1,tempHandler=None): 
124        self.smiCol = smiCol 
125        self.width = width*inch 
126        self.verbose=verbose 
127 -    def __call__(self,arg): 
128        res = list(arg) 
129        if self.verbose: 
130          sys.stderr.write('Render(%d): %s\n'%(self.smiCol,str(res[0]))) 
131        smi = res[self.smiCol] 
132        aspect = 1 
133        width = self.width 
134        height = aspect*width 
135        try: 
136          mol = Chem.MolFromSmiles(smi) 
137          Chem.Kekulize(mol) 
138          canv = Canvas((width,height)) 
139          options = DrawingOptions() 
140          options.atomLabelMinFontSize=3 
141          options.bondLineWidth=0.5 
142          drawing = MolDrawing(options=options) 
143          if not mol.GetNumConformers(): 
144            rdDepictor.Compute2DCoords(mol) 
145          drawing.AddMol(mol,canvas=canv) 
146          ok = True 
147        except Exception: 
148          if self.verbose: 
149            import traceback 
150            traceback.print_exc() 
151          ok = False 
152   
153        if ok: 
154          res[self.smiCol] = canv.drawing 
155        else: 
156          # FIX: maybe include smiles here in a Paragraph? 
157          res[self.smiCol] = 'Failed' 
158        return res 
159           
160   
161 -  class RDImageTransformer(object): 
162 -    def __init__(self,smiCol,width=1.,verbose=1,tempHandler=None): 
163        self.smiCol = smiCol 
164        if tempHandler is None: 
165          tempHandler = ReportUtils.TempFileHandler() 
166        self.tempHandler = tempHandler 
167        self.width = width*inch 
168        self.verbose=verbose 
169 -    def __call__(self,arg): 
170        res = list(arg) 
171        if self.verbose: 
172          sys.stderr.write('Render(%d): %s\n'%(self.smiCol,str(res[0]))) 
173        smi = res[self.smiCol] 
174        tmpName = self.tempHandler.get('.jpg') 
175        aspect = 1 
176        width = 300 
177        height = aspect*width 
178        ok = DrawUtils.SmilesToJpeg(smi,tmpName,size=(width,height)) 
179        if ok: 
180          try: 
181            img = platypus.Image(tmpName) 
182            img.drawWidth = self.width 
183            img.drawHeight = aspect*self.width 
184          except Exception: 
185            ok = 0 
186        if ok: 
187          res[self.smiCol] = img 
188        else: 
189          # FIX: maybe include smiles here in a Paragraph? 
190          res[self.smiCol] = 'Failed' 
191        return res 
192           
193 -  def QuickReport(conn,fileName,*args,**kwargs): 
194      from reportlab.lib import colors 
195      from reportlab.lib.styles import getSampleStyleSheet 
196      from reportlab.lib.units import inch 
197   
198      styles = getSampleStyleSheet() 
199      title = 'Db Report' 
200      if kwargs.has_key('title'): 
201        title = kwargs['title'] 
202        del kwargs['title'] 
203   
204      names = [x.upper() for x in conn.GetColumnNames()] 
205      try: 
206        smiCol = names.index('SMILES') 
207      except ValueError: 
208        try: 
209          smiCol = names.index('SMI') 
210        except ValueError: 
211          smiCol = -1 
212      if smiCol >-1: 
213        if hasCDX: 
214          tform = CDXImageTransformer(smiCol) 
215        elif 1: 
216          tform = ReportLabImageTransformer(smiCol) 
217        else: 
218          tform = CactvsImageTransformer(smiCol) 
219   
220      else: 
221        tform = None 
222      kwargs['transform'] = tform 
223      tbl = conn.GetReportlabTable(*args,**kwargs) 
224      tbl.setStyle(platypus.TableStyle([('GRID',(0,0),(-1,-1),1,colors.black), 
225                                        ('FONT',(0,0),(-1,-1),'Times-Roman',8), 
226                                        ])) 
227   
228       
229      if smiCol >-1 and tform: 
230        tbl._argW[smiCol] = tform.width*1.2 
231      elements = [tbl] 
232      reportTemplate = PDFReport() 
233      reportTemplate.pageHeader = title 
234   
235      doc = platypus.SimpleDocTemplate(fileName) 
236      doc.build(elements,onFirstPage=reportTemplate.onPage, 
237                onLaterPages=reportTemplate.onPage) 
238       
239    DbConnect.GetReportlabTable = GetReportlabTable 
240   
241  if __name__=='__main__': 
242    import sys 
243    dbName = sys.argv[1] 
244    tblName = sys.argv[2] 
245    fName = 'report.pdf' 
246    conn = DbConnect(dbName,tblName) 
247    QuickReport(conn,fName,where="where mol_id in ('1','100','104','107')") 
248