Re: [Rdkit-discuss] Yet another PropertyMol Question

[Greg L. <gre...@gm...>]

Hi Markus,

On Fri, Oct 16, 2009 at 2:40 PM, markus kossner <m.k...@tu...> wrote:
> Hi there,
> I recently noticed some unexpected behavior of the PropertyMol.
> Note that I have installed the Q1_2009 installation currently.
> Look at that:
>>>> from rdkit import Chem
>>>> mol=Chem.MolFromSmiles('c1ccccc1')
>>>> mol.SetProp('_Name','benzene')
>>>> w=Chem.SDWriter('test.sdf')
>>>> w.write(mol)
>>>> from Chem.PropertyMol import *
>>>> pm=PropertyMol(mol)
>>>> w.write(pm)
>>>> exit()
>
> Everything works fine, but when I look at the produced sd file,
> only the first of the two entries has the string 'benzene' in the header
> line.

Nice catch. The problem is fixed in subversion (and in the release,
which I be completed this weekend). Here's an explanation of the
problem, if you are interested: PropertyMol is a python object and the
extra functionality I added to capture properties such that they could
be pickled was only updating the python object. So when you called a
C++ function (SDWriter.write), it wasn't getting the new properties. I
modified the PropertyMol object so that it places the properties in
the C++ object as well.

A shortcoming to the current fix is that if you pickle a PropertyMol
and *then* write it into an SD file, the properties don't go into the
file. Since the PropertyMol is a bit of a hack, there are going to be
a lot of these edge cases. I'll enter a bug against this one and fix
it sometime in the near future, but it won't be in this release.


> !-!-!-!-!-!-!-!-!-!-!
>        Script: test_list.py.  Failed 1 (of 15) tests in 27.15 seconds
>                (GraphMol): python test_list.py

If you want some more detail about what failed, switch to the
Code/GraphMol directory and run python test_list.py in there. Then
you'll see the failing tests.

> And b.t.w. why does my RDKit work fairly well despite the failed
> GraphMol things? :-)

you aren't using the broken bits. ;-)

-greg