Hi Christos,
Thanks, presently I iterate over all of the tags and copy them over.
That's really ugly and is identical to your suggestion. I was hopeful that
there was a more elegant way of doing things but I guess not. The pickling
thing really caught me by surprise. I can't tell you how many hours I
burned until I realized that was the problem.
Thanks for the quick response!
Matthew
On Thu, Mar 12, 2015 at 8:46 AM, Christos Kannas <chriskan...@gmail.com>
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 <mla...@gmail.com> 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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