Hi everyone. Just a quick question. Basically I'm at the final part of my research and I don't really know what to do in terms of procedure.
Background: I have SDF file with the 3d coordinates of every molecule of interest. My ultimate goal is to take molecule A, align it to molecule B and then "delete" all atoms from molecule B and molecule A which are not present in each other. These aligned atoms of molecule B, will then be compared with the atoms from Molecule A and their differences in electronegativity will be calculated for the Molecules. I have tried doing an MCS alignment but it can be 'broken easily' For example: Molecule A : CCCCSCCO Molecule B: CCCCNCCO MCS : CCCC Ideal alignment: CCCC_CCO Problem: The CCO atoms are present in both but this method tends to 'lose' information. I have tried obfit: command: obfit SMART PATTERN MoleculeA.sdf MoleculeB.sdf > aligned.sdf The input Smart Pattern is the MCS generated but the aligned.sdf contains the same atoms as Molecule B (atoms which aren't in common aren't removed). What methods can I use which may assist with what I want/ What am i missing? Thank you!
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