# $Id$ # # 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 from rdkit.sping.ReportLab.pidReportLab import RLCanvas as Canvas from rdkit.Chem.Draw.MolDrawing import MolDrawing, DrawingOptions from reportlab.lib import colors from reportlab.lib.units import inch import 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) res = platypus.Table(rawD) return res 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 Exception: 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 Exception: ok = 0 if ok: res[self.smiCol] = img else: # FIX: maybe include smiles here in a Paragraph? res[self.smiCol] = 'Failed' return res 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 Exception: 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 Exception: 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): title = 'Db Report' if 'title' in kwargs: 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__': 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')")