On 12/21/10 1:55 PM, erapp wrote: > All, > > I have a question about using OpenBabel to fragment a molecule. Is there > any way to fragment a given molecule such that detailed information is > provided about the given fragment (i.e. all bonds for each atom in addition > to the other atoms in the fragment and associated bonds). I need to be able > to find all unique fragments for a molecule of a given length (i.e. number > of atoms in fragment) and provide information about what makes it unique. I > tried mna but that doesn't seem to provide the detailed information I need > (or not in the GUI.....or I don't have the options set correctly). This is an uncomputable problem. It can be done for very small molecules, but when you have more than a few dozen atoms, the number of fragments explodes. And it really gets bad in a hurry for a molecule with complex rings, which can have a virtually uncountable number of ways you can "fragment" it.
If you limit your "bond breaking" in some ways, say only break non-ring bonds, or some other algorithm that produces "reasonable" fragments, then the problem might be solvable. If you do find an algorithm that produces a reasonable number of fragments, the canonical SMILES generator might be useful. It has the ability to generate fragment SMILES. You can specify a list of atoms to include in the SMILES and it will generate a canonical SMILES for just those atoms, but using the electronic configuration for the whole molecule. For example, in "Cc1ccccc1C", you can generate a canonical SMILES for "CccC". This would probably be a good way for you to record all of the fragments that you generate. To use it, you don't actually have to break the bonds of the molecule. Just specify the atoms that you want as part of the fragment and then generate the canonical SMILES. Craig ------------------------------------------------------------------------------ Forrester recently released a report on the Return on Investment (ROI) of Google Apps. They found a 300% ROI, 38%-56% cost savings, and break-even within 7 months. Over 3 million businesses have gone Google with Google Apps: an online email calendar, and document program that's accessible from your browser. Read the Forrester report: http://p.sf.net/sfu/googleapps-sfnew _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
