Dear Prof. Hutchison,
Yes, thats what I want to do.
I followed your suggestions, at least as far as I understood it.
1. I built a new side chain w/ 3D coordinates from OBBuilder (stored as OBMol
newSideChain)
2. Deleted the required sidechain atoms from the origMol.
3. Added all the atoms of newSideChain to origMol. (using AddAtom)
I am not sure how to put the connections in place.
Thanks for any suggestions,
Prashanth
On Dec 28, 2011, at 2:24 PM, Prashanth Athri wrote:
> I was wondering if there is an 'optimal' path to do the following using OB
> C++ library:
> 1. Read protein (PDB -- well formatted)
> 2. Mutate one residue with another at specific points (say I have a vector of
> OBMol's with all amino acids to do the replacement)
If I follow your question, you're saying that you want to change the residue
information, say from TRP to ARG, and substitute/place atoms from another
source.
You'd want to change the OBResidue object associated with the mutation point,
delete any atoms from the first side chain, and then build out the new one. The
last part is easily done from the OBBuilder class.
If you want more concrete code, let us know, preferably on the openbabel-devel
list and I'll think about it more carefully.
Hope that helps,
-Geoff
--
Prashanth Athri
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