Dear All,
Enthused by all the great talks at the UGM, for the last couple of days I have
been getting more hands-on with RDKit than I have in quite a while!
I was keen to work with some peptides/proteins in 3D, but am having some
problems when adding hydrogens...
I have uploaded a GIST to demonstrate the issue (apologies - the py3Dmol js
doesn't render in the nbviewer, but this doesn't affect understanding):
https://gist.github.com/jepdavidson/f5220187c18be0fc9e119f9da2e7d955
The main problem is that added hydrogens don't automatically get assigned
monomer info from the monomer they are being added to, but there are other
issues as well (the hydrogens are marked 'HETATM', the occupancy for the ATOM
blocks are set to "-nan", and the CONECT block doesn't list the added Hs).
Propagating the monomer info from the amino acids to the added Hs isn't too
difficult (can call atom.GetNeighbors() and take the info from the neighbouring
atom) - but there are also some preferred (or required?) naming and numbering
conventions to adhere to ("H" for the backbone NH, "HA" for the hydrogen on the
alpha carbon, etc).
Perhaps I am missing something here (a secret 'flavour' option? :)) - but if
not, it would be interesting to hear what behaviour others would expect when
adding explicit hydrogens (I think the same issues will relate to any sequence
where monomer information is present).
Kind regards
James
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