On 10/06/2011 19:59, aun syed wrote: > Hi, > > i am trying to explore the features of OpenBabel, i have a PDF structure of a > natural drug..I am trying to convert it into SDF format, but still i did not > get. I just uses the raw text sheet as input that carries the information > regarding name, chemical formula, total number of atoms, chemical weight..but > output file is not giving the appropriate results..Kindly fix this problem, > how can i convert these information into relevant format...is there any video > demo of openBabel available, in this way i can sort out the actual > procedure...
OpenBabel normally expects its input to be in a well-defined data structure of some sort - it does not do "data-mining", that is collecting data from un-formatted text. In your text data sheet look to see if there is any mention of SMILES or InChI. If not, I doubt you have sufficient chemical structural information to make an SDF file. If there is, you can cut an paste information to the OpenBabel GUI. Click the box on the left labelled "Input below(ignore input file)". The box will go yellow. Set the Output Format to sdf and choose the name of the output file. If there is InChI, set the Input Format to inchi and paste the text data into the yellow box. The InChI text will probably be found ok, but if it doesn't work, copy just the text starting "InChi=" to the end of the line. Click the box in the middle "Generate 2D coordinates" (or alternatively you may want 3D coordinates). Click Convert. If there is SMILES, set the input format appropriately and copy the SMILES string (which will look something like c1cc(ccc1C(=O)O)O ). It is necessary to be more precise with SMILES input, for instance no leading spaces. Hope this helps. Chris > > thanks for help > > Aun > Bioinformatics > IUPUI, Indianapolis, Indiana > ------------------------------------------------------------------------------ EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-dev2dev _______________________________________________ OpenBabel-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
