I could only imagine the errors when using threading/multiprocessing +
reusing SDMolSupplier object... So if I understand correctly the official
line of RDKit is: "a multimol file => supplier => file(-like) objects".
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
[email protected]
2016-10-03 14:53 GMT+02:00 Brian Kelley <[email protected]>:
> I'll admit that using StringIO here feels more pythonic, although SetData
> can be reused without a reconstructing the class.
>
> I suppose I would prefer having something like
>
> MolToSDDataBlock
>
> Which can be used in conjunction with MolToMolBlock. I have often found
> that many times data changes without molecule change so perhaps both could
> be useful.
>
> ----
> Brian Kelley
>
> > On Oct 3, 2016, at 7:08 AM, Andrew Dalke <[email protected]>
> wrote:
> >
> >> On Oct 2, 2016, at 10:48 PM, Maciek Wójcikowski wrote:
> >> Yes I get it, but obviously there is no MolFromSDBlock, so one would
> suspect MolFromMolBlock to support both formats. As I understand correctly
> the only way of reading SD from variable is as presented in my example? Or
> is there some marvelous undocumented API? ;)
> >
> > Six years ago, Greg Landrum at http://www.mail-archive.com/
> [email protected]/msg01436.html suggested:
> >
> > nsuppl = Chem.SDMolSupplier()
> > nsuppl.SetData(mb)
> > mol = nsuppl.next()
> >
> > This is simpler than passing in a StringIO().
> >
> > I knew about this posting because my own code has MolFromSDBlock()
> wrapper layer, and a comment pointing to that URL as explanation.
> >
> >
> >> On Oct 2, 2016, at 11:06 PM, Brian Kelley wrote:
> >> The general idea, I believe, is that if the format can result in
> multiple molecules a supplier should be used.
> >
> > I wrote the function to make it easier to deal with web service input or
> database records where the text contains one and only one record in SD
> format. This is a proper subset of the SD format, which contains 0 or more
> records.
> >
> > If there are no records then my function returns a None, so I don't need
> to deal with a StopIteration. I don't care if there is more than one
> record, so I ignore anything past the first record.
> >
> > The use case occurs pretty frequently in my work, so I figured a
> MolFromSDBlock() for my own use was worthwhile.
> >
> > Cheers,
> >
> > Andrew
> > [email protected]
> >
> >
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