Thanks Greg! Much appreciated.
-
Jean-Paul Ebejer
Early Stage Researcher
On 15 January 2014 08:38, Greg Landrum <greg.land...@gmail.com> wrote:
>
> On Tue, Jan 14, 2014 at 11:48 AM, Greg Landrum <greg.land...@gmail.com>wrote:
>
>> ok, it looks like something bad happened[1] when the PDB branch was
>> merged into trunk before the last release. Here's an example that worked
>> properly at the time of the UGM:
>>
>> In [5]: m =Chem.MolFromPDBFile('data/2FVD.pdb')
>> In [6]: Chem.MolToSmiles(m,canonical=False)
>> Out[6]: 'NC(C(O)NC(C .... '
>>
>> Here's the notebook showing what's supposed to happen:
>>
>> http://nbviewer.ipython.org/github/rdkit/UGM_2013/blob/master/Notebooks/Whats_new.ipynb
>>
>> I'll look into this as soon as I can and get it fixed.
>>
>
> I just tracked this down and fixed it. The changes are checked into
> github. Details about what happened are below.
>
> Here's my example from above now:
>
> In [3]: m = Chem.MolFromPDBFile('./2FVD.pdb')
> In [4]: Chem.MolToSmiles(m,canonical=False)
> Out[4]: 'NC(C(=O)NC(C(=O)NC(C(=O....'
>
>
> This is, IMO, a major enough problem that it's worth doing a patch release
> to address it. Over the next few days, I will put together a list of fixes
> (not new features) that should be in the 2013_09_2 release and adjust the
> milestones for those issues. Please feel free to suggest additions. The
> list (currently empty) can be found here:
> https://github.com/rdkit/rdkit/issues?milestone=6
>
> For those who care, here's how the bug came about.
> The bond-type assignment code for standard PDB residues tests bonded atoms
> to make sure they are in the same residue. This code compares the two
> atoms' AtomPDBResidueInfo structures. Shortly before the 2013_09_1 release,
> I added an explicit residueNumber property to the AtomPDBResidueInfo class
> and switched the serialNumber property (previously used to store the
> residueNumber) to capture the actual serial number of the atom. I forgot to
> update the residue comparison code to reflect this change, so
> the SamePDBResidue() function was returning false unless the two atoms were
> the same. silly mistake.
>
> Best,
> -greg
>
>
>
>
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