# $Id$ # # Copyright (C) 2003-2006 Rational Discovery LLC # # @@ All Rights Reserved @@ # This file is part of the RDKit. # The contents are covered by the terms of the BSD license # which is included in the file license.txt, found at the root # of the RDKit source tree. # try: from reportlab import platypus except ImportError: import sys sys.stderr.write('ReportLab module could not be imported. Db->PDF functionality not available') GetReportlabTable = None QuickReport = None else: from rdkit import Chem try: from pyRDkit.utils import chemdraw except ImportError: hasCDX=0 else: hasCDX=1 from rdkit.utils import cactvs from rdkit.Chem import rdDepictor from rdkit.Chem.Draw import DrawUtils from rdkit.Dbase.DbConnection import DbConnect from rdkit.Dbase import DbInfo from rdkit.Reports.PDFReport import PDFReport,ReportUtils import os,tempfile,sys def GetReportlabTable(self,*args,**kwargs): """ this becomes a method of DbConnect """ dbRes = self.GetData(*args,**kwargs) rawD = [dbRes.GetColumnNames()] colTypes = dbRes.GetColumnTypes() binCols = [] for i in range(len(colTypes)): if colTypes[i] in DbInfo.sqlBinTypes or colTypes[i]=='binary': binCols.append(i) nRows = 0 for entry in dbRes: nRows += 1 for col in binCols: entry = list(entry) entry[col] = 'N/A' rawD.append(entry) #if nRows >10: break res = platypus.Table(rawD) return res from reportlab.lib.units import inch class CDXImageTransformer(object): def __init__(self,smiCol,width=1,verbose=1,tempHandler=None): self.smiCol = smiCol if tempHandler is None: tempHandler = ReportUtils.TempFileHandler() self.tempHandler = tempHandler self.width = width*inch self.verbose=verbose def __call__(self,arg): res = list(arg) if self.verbose: print 'Render:',res[0] if hasCDX: smi = res[self.smiCol] tmpName = self.tempHandler.get('.jpg') try: img = chemdraw.SmilesToPilImage(smi) w,h = img.size aspect = float(h)/w img.save(tmpName) img = platypus.Image(tmpName) img.drawWidth = self.width img.drawHeight = aspect*self.width res[self.smiCol] = img except: import traceback traceback.print_exc() res[self.smiCol] = 'Failed' return res class CactvsImageTransformer(object): def __init__(self,smiCol,width=1.,verbose=1,tempHandler=None): self.smiCol = smiCol if tempHandler is None: tempHandler = ReportUtils.TempFileHandler() self.tempHandler = tempHandler self.width = width*inch self.verbose=verbose def __call__(self,arg): res = list(arg) if self.verbose: sys.stderr.write('Render(%d): %s\n'%(self.smiCol,str(res[0]))) smi = res[self.smiCol] tmpName = self.tempHandler.get('.gif') aspect = 1 width = 300 height = aspect*width ok = cactvs.SmilesToGif(smi,tmpName,(width,height)) if ok: try: img = platypus.Image(tmpName) img.drawWidth = self.width img.drawHeight = aspect*self.width except: ok = 0 if ok: res[self.smiCol] = img else: # FIX: maybe include smiles here in a Paragraph? res[self.smiCol] = 'Failed' return res from rdkit.sping.ReportLab.pidReportLab import RLCanvas as Canvas from rdkit.Chem.Draw.MolDrawing import MolDrawing,DrawingOptions class ReportLabImageTransformer(object): def __init__(self,smiCol,width=1.,verbose=1,tempHandler=None): self.smiCol = smiCol self.width = width*inch self.verbose=verbose def __call__(self,arg): res = list(arg) if self.verbose: sys.stderr.write('Render(%d): %s\n'%(self.smiCol,str(res[0]))) smi = res[self.smiCol] aspect = 1 width = self.width height = aspect*width try: mol = Chem.MolFromSmiles(smi) Chem.Kekulize(mol) canv = Canvas((width,height)) options = DrawingOptions() options.atomLabelMinFontSize=3 options.bondLineWidth=0.5 drawing = MolDrawing(options=options) if not mol.GetNumConformers(): rdDepictor.Compute2DCoords(mol) drawing.AddMol(mol,canvas=canv) ok = True except: if self.verbose: import traceback traceback.print_exc() ok = False if ok: res[self.smiCol] = canv.drawing else: # FIX: maybe include smiles here in a Paragraph? res[self.smiCol] = 'Failed' return res class RDImageTransformer(object): def __init__(self,smiCol,width=1.,verbose=1,tempHandler=None): self.smiCol = smiCol if tempHandler is None: tempHandler = ReportUtils.TempFileHandler() self.tempHandler = tempHandler self.width = width*inch self.verbose=verbose def __call__(self,arg): res = list(arg) if self.verbose: sys.stderr.write('Render(%d): %s\n'%(self.smiCol,str(res[0]))) smi = res[self.smiCol] tmpName = self.tempHandler.get('.jpg') aspect = 1 width = 300 height = aspect*width ok = DrawUtils.SmilesToJpeg(smi,tmpName,size=(width,height)) if ok: try: img = platypus.Image(tmpName) img.drawWidth = self.width img.drawHeight = aspect*self.width except: ok = 0 if ok: res[self.smiCol] = img else: # FIX: maybe include smiles here in a Paragraph? res[self.smiCol] = 'Failed' return res def QuickReport(conn,fileName,*args,**kwargs): from reportlab.lib import colors from reportlab.lib.styles import getSampleStyleSheet from reportlab.lib.units import inch styles = getSampleStyleSheet() title = 'Db Report' if kwargs.has_key('title'): title = kwargs['title'] del kwargs['title'] names = [x.upper() for x in conn.GetColumnNames()] try: smiCol = names.index('SMILES') except ValueError: try: smiCol = names.index('SMI') except ValueError: smiCol = -1 if smiCol >-1: if hasCDX: tform = CDXImageTransformer(smiCol) elif 1: tform = ReportLabImageTransformer(smiCol) else: tform = CactvsImageTransformer(smiCol) else: tform = None kwargs['transform'] = tform tbl = conn.GetReportlabTable(*args,**kwargs) tbl.setStyle(platypus.TableStyle([('GRID',(0,0),(-1,-1),1,colors.black), ('FONT',(0,0),(-1,-1),'Times-Roman',8), ])) if smiCol >-1 and tform: tbl._argW[smiCol] = tform.width*1.2 elements = [tbl] reportTemplate = PDFReport() reportTemplate.pageHeader = title doc = platypus.SimpleDocTemplate(fileName) doc.build(elements,onFirstPage=reportTemplate.onPage, onLaterPages=reportTemplate.onPage) DbConnect.GetReportlabTable = GetReportlabTable if __name__=='__main__': import sys dbName = sys.argv[1] tblName = sys.argv[2] fName = 'report.pdf' conn = DbConnect(dbName,tblName) QuickReport(conn,fName,where="where mol_id in ('1','100','104','107')")