I am working with several ligands from a database stored in a SMILES format. I am using the SMILES string to get three dimensional coordinates (pdb format file) using a third-party program called libcheck.
For some of these molecules the SMILES string sterochemistry in the database is entered in incorrectly such that the SMILES input to libcheck returns a mangled coordinate file with rings clashing with each other . Inputting SMILES string without the stereochemistry makes libcheck behave correctly. Is there a way to use rdkit to cleanup the stereochemistry in the SMILES string. Thanks for your help in advance Hari ------------------------------------------------------------------------------ Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
