Hello, First I want to apologize if this is a trivial question or the wrong place to ask.
I'm maintain a Database for GC-MS spectra. Recently I updated the web frontend to display the chemical structures using the ChemDoodle Web Components (http://web.chemdoodle.com/) plugin. However, I notice that some structure are displayed correct (i.g. see here: http://gmd.mpimp-golm.mpg.de/Metabolites/f4f207ff-8ff8-4789-99a1-147ae0a36673.aspx) whereas others are displayed incorrect (http://gmd.mpimp-golm.mpg.de/Metabolites/0c450b43-c901-4435-9e74-051222d815ea.aspx). I mean they get displayed, but not very nice. I think that ChemDoodle is not the problem that the chemical structure can't be recognized from the displayed picture. The scaling of the picture (or of the mol-Files) seems somehow odd. And, other chemical software solutions seem to handle this to a better degree. >From my understanding (being not a chemist) I suspect, that I have some >problems in the mol-Files. The coordinates between correct and incorrect >mol-Files seem to differ by an order of magnitude. My question is now, How can I use OpenBabel to re-render (repaint, re-layout) an "incorrect" mol-File into a "standard compliant" mol-File? mol.Center() did not the trick. Here is my C# code OBConversion obconv = new OBConversion(); OBMol mol = new OBMol(); obconv.SetInFormat("mol"); obconv.SetOutFormat("mol"); obconv.ReadString(mol, source); mol.Center(); obconv.WriteFile(mol, dest); Thank you very much for any help. Jan ------------------------------------------------------------------------------ Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d _______________________________________________ OpenBabel-scripting mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
