James,
On Thu, Oct 24, 2013 at 7:27 PM, James Davidson <j.david...@vernalis.com>wrote:
> Hi Greg (et al.),****
>
> ** **
>
> Thanks for the beta! I have been going through some of the recently-added
> functionality, and had a couple of questions regarding the PDB reading /
> writing.
>
Thanks for the bug reports!
> **
>
> **1. **Do I remember correctly that there was a proposal (from
> Roger) to add some auto bond-type perception to the PDB parser for ligands
> (or is that just wishful thinking!)?
>
Roger will have to confirm this, but I believe he said something along the
lines of "that way lies madness".
> 2. **If not, I notice that there is an
> AssignBondOrdersFromTemplate() method – but the example in the doc-string
> only shows (I think) the case where the input PDB is just a single small
> molecule – so the matching is pretty easy! I think a more real-World case
> is when one wants to set the bond orders for multiple ligands (HETATM
> residues) based on substructure matches – which will then return an atom
> index selection that can be used as a start point. Is there any way to
> have the AssignBondOrdersFromTemplate() convenience function optionally
> accept a list of atom indexes to specify a substructure?
>
Sereina? Is that doable?
> ****
>
> **3. **Is there some explanation for what the ‘flavor’ option does
> for reading/writing PDB?
>
I'm not sure about the reader. Roger, can you answer that?
This is what's in the C++ for the PDBWriter:
// PDBWriter support multiple "flavors" of PDB output
// flavor & 1 : Write MODEL/ENDMDL lines around each record
// flavor & 2 : Don't write any CONECT records
// flavor & 4 : Write CONECT records in both directions
// flavor & 8 : Don't use multiple CONECTs to encode bond order
// flavor & 16 : Write MASTER record
// flavor & 32 : Write TER record
This is now in the docs for both the Python and C++ code.
> ****
>
> **4. **Having read in a PDB file I see the correct atoms flagged as
> HETATM (from GetIsHeteroAtom()). But when call Chem.MolToPDBBlock() these
> atoms get written as ATOM records… Also, a Chem.MolToPDBFile() method
> would be nice for completeness / symmetry : )
>
The HETATM thing was the result of a dumb copy and paste error from me.
It's fixed.
Re: Chem.MolToPDBFile()
that's missing because there's no corresponding Chem.MolToMolFile()
This is an odd oversight, which I've now fixed.
> ****
>
> **5. **It seems to me that GetResidueNumber() and GetSerialNumber()
> may have got mixed-up at some point(?). At least, when I call
> GetSerialNumber() I see what appears to be the residue number; and when I
> call GetResidueNumber() I get “0”!
>
This was another dumb bug from me. It's fixed.
> ****
>
> **6. **I also seem to be seeing all of the bonds (for all residues)
> being written out in CONECT records – such that they all appear as single
> bonds in eg PyMOL – is this expected behaviour at the moment?
>
Another one for Roger.
-greg
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