# $Id$ # # Copyright (C) 2002-2006 Greg Landrum and 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. # """ tools for interacting with chemdraw """ import string,tempfile,os,time try: import pythoncom from win32com.client import gencache,Dispatch,constants import win32com.client.gencache cdxModule = win32com.client.gencache.EnsureModule("{5F646AAB-3B56-48D2-904C-A68D7989C251}", 0, 7, 0) except: cdxModule = None _cdxVersion=0 raise ImportError,"ChemDraw version (at least version 7) not found." else: _cdxVersion=7 if cdxModule: from win32com.client import Dispatch import win32gui import re cdApp = None theDoc = None theObjs = None selectItem = None cleanItem = None centerItem = None def StartChemDraw(visible=True,openDoc=False,showDoc=False): """ launches chemdraw """ global cdApp,theDoc,theObjs,selectItem,cleanItem,centerItem if cdApp is not None: # if called more than once, do a restart holder = None selectItem = None cleanItem = None centerItem = None theObjs = None theDoc = None cdApp = None cdApp = Dispatch('ChemDraw.Application') if openDoc: theDoc = cdApp.Documents.Add() theObjs = theDoc.Objects else: theDoc = None selectItem = cdApp.MenuBars(1).Menus(2).MenuItems(8) cleanItem = cdApp.MenuBars(1).Menus(5).MenuItems(6) if _cdxVersion == 6: centerItem = cdApp.MenuBars(1).Menus(4).MenuItems(1) else: centerItem = cdApp.MenuBars(1).Menus(4).MenuItems(7) if visible: cdApp.Visible=1 if theDoc and showDoc: theDoc.Activate() def ReactivateChemDraw(openDoc=True,showDoc=True): global cdApp,theDoc,theObjs cdApp.Visible=1 if openDoc: theDoc = cdApp.Documents.Add() if theDoc and showDoc: theDoc.Activate() theObjs = theDoc.Objects # ------------------------------------------------------------------ # interactions with Chemdraw # ------------------------------------------------------------------ def CDXConvert(inData,inFormat,outFormat): """converts the data passed in from one format to another inFormat should be one of the following: chemical/x-cdx chemical/cdx chemical/x-daylight-smiles chemical/daylight-smiles chemical/x-mdl-isis chemical/mdl-isis chemical/x-mdl-molfile chemical/mdl-molfile chemical/x-mdl-rxn chemical/mdl-rxn chemical/x-mdl-tgf chemical/mdl-tgf chemical/x-questel-F1 chemical/x-questel-F1-query outFormat should be one of the preceding or: image/x-png image/png image/x-wmf image/wmf image/tiff application/postscript image/gif """ global theObjs,theDoc if cdApp is None: StartChemDraw() if theObjs is None: if theDoc is None: theDoc = cdApp.Documents.Add() theObjs = theDoc.Objects theObjs.SetData(inFormat,inData,pythoncom.Missing) outD = theObjs.GetData(outFormat) theObjs.Clear() return outD def CDXClean(inData,inFormat,outFormat): """calls the CDXLib Clean function on the data passed in. CDXLib_Clean attempts to clean (prettify) the data before doing an output conversion. It can be thought of as CDXConvert++. CDXClean supports the same input and output specifiers as CDXConvert (see above) """ global cdApp,theDoc,theObjs,selectItem,cleanItem if cdApp is None: StartChemDraw() if theObjs is None: if theDoc is None: theDoc = cdApp.Documents.Add() theObjs = theDoc.Objects theObjs.SetData(inFormat,inData,pythoncom.Missing) theObjs.Select() cleanItem.Execute() outD = theObjs.GetData(outFormat) theObjs.Clear() return outD def CDXDisplay(inData,inFormat='chemical/cdx',clear=1): """ displays the data in Chemdraw """ global cdApp,theDoc,theObjs,selectItem,cleanItem,centerItem if cdApp is None: StartChemDraw() try: theDoc.Activate() except: ReactivateChemDraw() theObjs = theDoc.Objects if clear: theObjs.Clear() theObjs.SetData(inFormat,inData,pythoncom.Missing) return def CDXGrab(outFormat='chemical/x-mdl-molfile'): """ returns the contents of the active chemdraw document """ global cdApp,theDoc if cdApp is None: res = "" else: cdApp.Visible=1 if not cdApp.ActiveDocument: ReactivateChemDraw() try: res = cdApp.ActiveDocument.Objects.GetData(outFormat) except: res = "" return res def CloseChemdraw(): """ shuts down chemdraw """ global cdApp try: cdApp.Quit() except: pass Exit() def Exit(): """ destroys our link to Chemdraw """ global cdApp cdApp = None def SaveChemDrawDoc(fileName='save.cdx'): """force chemdraw to save the active document NOTE: the extension of the filename will determine the format used to save the file. """ d = cdApp.ActiveDocument d.SaveAs(fileName) def CloseChemDrawDoc(): """force chemdraw to save the active document NOTE: the extension of the filename will determine the format used to save the file. """ d = cdApp.ActiveDocument d.Close() def RaiseWindowNamed(nameRe): # start by getting a list of all the windows: cb = lambda x,y: y.append(x) wins = [] win32gui.EnumWindows(cb,wins) # now check to see if any match our regexp: tgtWin = -1 for win in wins: txt = win32gui.GetWindowText(win) if nameRe.match(txt): tgtWin=win break if tgtWin>=0: win32gui.ShowWindow(tgtWin,1) win32gui.BringWindowToTop(tgtWin) def RaiseChemDraw(): e = re.compile('^ChemDraw') RaiseWindowNamed(e) try: from PIL import Image import cStringIO def SmilesToPilImage(smilesStr): """takes a SMILES string and returns a PIL image using chemdraw """ return MolToPilImage(smilesStr,inFormat='chemical/daylight-smiles',outFormat='image/gif') def MolToPilImage(dataStr,inFormat='chemical/daylight-smiles',outFormat='image/gif'): """takes a molecule string and returns a PIL image using chemdraw """ # do the conversion... res = CDXConvert(dataStr,inFormat,outFormat) dataFile = cStringIO.StringIO(str(res)) img = Image.open(dataFile).convert('RGB') return img except ImportError: def SmilesToPilImage(smilesStr): print 'You need to have PIL installed to use this functionality' return None def MolToPilImage(dataStr,inFormat='chemical/daylight-smiles',outFormat='image/gif'): print 'You need to have PIL installed to use this functionality' return None # ------------------------------------------------------------------ # interactions with Chem3D # ------------------------------------------------------------------ c3dApp = None def StartChem3D(visible=0): """ launches Chem3D """ global c3dApp c3dApp = Dispatch('Chem3D.Application') if not c3dApp.Visible: c3dApp.Visible = visible def CloseChem3D(): """ shuts down Chem3D """ global c3dApp c3dApp.Quit() c3dApp = None availChem3DProps = ('DipoleMoment','BendEnergy','Non14VDWEnergy','StericEnergy', 'StretchBendEnergy','StretchEnergy','TorsionEnergy','VDW14Energy') def Add3DCoordsToMol(data,format,props={}): """ adds 3D coordinates to the data passed in using Chem3D **Arguments** - data: the molecular data - format: the format of _data_. Should be something accepted by _CDXConvert_ - props: (optional) a dictionary used to return calculated properties """ global c3dApp if c3dApp is None: StartChem3D() if format != 'chemical/mdl-molfile': molData = CDXClean(data,format,'chemical/mdl-molfile') else: molData = data molFName = tempfile.mktemp('.mol') open(molFName,'wb+').write(molData) doc = c3dApp.Documents.Open(molFName) if not doc: print 'cannot open molecule' raise ValueError,'No Molecule' # set up the MM2 job job = Dispatch('Chem3D.MM2Job') job.Type=1 job.DisplayEveryIteration=0 job.RecordEveryIteration=0 # start the calculation... doc.MM2Compute(job) # and wait for it to finish while doc.ComputeStatus in [0x434f4d50,0x50454e44]: pass #outFName = tempfile.mktemp('.mol') # this is horrible, but apparently Chem3D gets pissy with tempfiles: outFName = os.getcwd()+'/to3d.mol' doc.SaveAs(outFName) # generate the properties for prop in availChem3DProps: props[prop] = eval('doc.%s'%prop) doc.Close(0) os.unlink(molFName) c3dData = open(outFName,'r').read() gone = 0 while not gone: try: os.unlink(outFName) except: time.sleep(.5) else: gone = 1 return c3dData def OptimizeSDFile(inFileName,outFileName,problemFileName='problems.sdf', restartEvery=20): """ optimizes the structure of every molecule in the input SD file **Arguments** - inFileName: name of the input SD file - outFileName: name of the output SD file - problemFileName: (optional) name of the SD file used to store molecules which fail during the optimization process - restartEvery: (optional) Chem3D will be shut down and restarted every _restartEvery_ molecules to try and keep core leaks under control """ inFile = open(inFileName,'r') outFile = open(outFileName,'w+') problemFile = None props = {} lines = [] nextLine = inFile.readline() skip = 0 nDone = 0 t1 = time.time() while nextLine != '': if nextLine.find('M END') != -1: lines.append(nextLine) molBlock = string.join(lines,'') try: newMolBlock = Add3DCoordsToMol(molBlock,'chemical/mdl-molfile',props=props) except: badBlock = molBlock skip = 1 lines = [] else: skip = 0 lines = [newMolBlock] elif nextLine.find('$$$$') != -1: t2 = time.time() nDone += 1 print 'finished molecule %d in %f seconds'%(nDone,time.time()-t1) t1 = time.time() if nDone%restartEvery == 0: CloseChem3D() StartChem3D() outFile.close() outFile = open(outFileName,'a') if not skip: for prop in props.keys(): lines.append('> <%s>\n%f\n\n'%(prop,props[prop])) lines.append(nextLine) outFile.write(string.join(lines,'')) lines = [] else: skip = 0 lines.append(nextLine) if problemFile is None: problemFile = open(problemFileName,'w+') problemFile.write(badBlock) problemFile.write(string.join(lines,'')) lines = [] else: lines.append(nextLine) nextLine = inFile.readline() outFile.close() if problemFile is not None: problemFile.close() if __name__=='__main__': inStr = 'CCC(C=O)CCC' img = SmilesToPilImage(inStr) img.save('foo.jpg') convStr = CDXClean(inStr,'chemical/x-daylight-smiles','chemical/x-daylight-smiles') print 'in:',inStr print 'out:',convStr convStr = CDXConvert(inStr,'chemical/x-daylight-smiles','chemical/x-mdl-molfile') print 'in:',inStr print 'out:',convStr convStr2 = CDXClean(convStr,'chemical/x-mdl-molfile','chemical/x-mdl-molfile') print 'out2:',convStr2 inStr = 'COc1ccc(c2onc(c2C(=O)NCCc3ccc(F)cc3)c4ccc(F)cc4)c(OC)c1' convStr = CDXConvert(inStr,'chemical/x-daylight-smiles','chemical/x-mdl-molfile') out = open('test.mol','w+') out.write(convStr) out.close()