One minor refinement to Christos' answer. If you create an SDWriter and do
not call SetProps(), it *should* write all non-computed properties each
molecule has. This should work from both Python and Java
Here's a very simple example of that from Python, the Java should behave
the same way:
In [1]: from rdkit import Chem
In [2]: import StringIO
In [3]: sio = StringIO.StringIO()
In [4]: m = Chem.MolFromSmiles('C')
In [5]: m.SetProp('p1','1')
In [7]: m2 = Chem.MolFromSmiles('C')
In [8]: m2.SetProp('p2','2')
In [9]: m2.SetProp('p3','1')
In [10]: w = Chem.SDWriter(sio)
In [12]: w.write(m)
In [13]: w.write(m2)
In [14]: w.flush()
In [15]: w=None
In [16]: print sio.getvalue()
RDKit
1 0 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
M END
> <p1> (1)
1
$$$$
RDKit
1 0 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
M END
> <p2> (2)
2
> <p3> (2)
1
$$$$
The property values getting lost while pickling molecules is a known
shortcoming of the RDKit that is probably fixable in a future version
(there are a few other good reasons to make the changes required for that).
Best,
-greg
On Thu, Mar 12, 2015 at 4:46 PM, Christos Kannas <[email protected]>
wrote:
> Hi Mathew,
>
> In order to store the tags and the data associated with them prior to
> writing the molecule to SDF/SMILES file you have to use SetProps(props)
> e.g. outfile.SetProps(props), where props is a list of the tags names your
> molecules have.
>
> In regards to when you pickle molecules you loose that extra
> information,you can convert your molecules to PropertyMol, e.g. from
> rdkit.Chem.PropertyMol import PropertyMol pmol = PropertyMol(mol)
>
> Hope the information above helps a bit.
>
> Regards,
>
> Christos
>
> Christos Kannas
>
> Researcher
> Ph.D Student
>
> [image: View Christos Kannas's profile on LinkedIn]
> <http://cy.linkedin.com/in/christoskannas>
>
> On 12 March 2015 at 15:33, Matthew Lardy <[email protected]> wrote:
>
>> Hi,
>>
>> I've noticed some strangeness between the Java and Python wrappers that I
>> have spent some time battling. If I load a SD file, via the SDMolSupplier
>> and then write out the file with SDWriter I lose all of the tags for the
>> molecules. Also if I pickle an SD file, reload it and then iterate over it
>> the tags are missing again. Is this the expected behaviour, or I am doing
>> something wrong?
>>
>> Thanks in advance!
>> Matthew
>>
>>
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