On 15 March 2011 15:36, Egon Willighagen <egon.willigha...@gmail.com> wrote:
> On Mon, Mar 14, 2011 at 2:55 PM, Vincent Le Guilloux
> <vincent.le-guill...@univ-orleans.fr> wrote:
> > Fair enough :) I think it's not so much unusual: when it's time to test
> your
> > new outstanding chemoinformatics library, you often want to use some
> > molecules you already known as basic test cases, and the simplest and
> > cleanest way is to store them in dedicated files (IMHO).
>
> You can still do that with the IteratingMDLReader...
>
>
Being aware it might be controversial and / or time consuming redesign,
can't help to throw this idea in:
1) Having iterating readers as the basis of all full-file readers, with
basic functionality just splitting the file into records and providing text
buffers for each record iteratively.
2) Simple "one-record" readers for actually parsing the one-record content
into a chemical object in memory
Thus, iterative readers could be the default, and other readers, loading all
the file in memory, are built on top of them, and used only when really
necessary.
Regards,
Nina
> > Of course one may use hardcoded SMILES as alternatives, but I found that
> > using SDF is less prone to reading / parsing errors...
>
> Very true!
>
> >> That's what we have this mailing list for (and the book).
> >>
> >> Anyway, I will file bug/feature reports for:
> >>
> >> 1. split SDFReader from MDLV2000Reader (if not in master already; need
> >> to check that)
>
>
> https://sourceforge.net/tracker/?func=detail&aid=3213262&group_id=20024&atid=370024
>
> >> 2. have IChemObjectReader.read() throw an EOF exception when called a
> >> second time
>
>
> https://sourceforge.net/tracker/?func=detail&aid=3213264&group_id=20024&atid=120024
>
> >> 3. clearer JavaDoc, as outlined above
>
>
> https://sourceforge.net/tracker/?func=detail&aid=3213267&group_id=20024&atid=120024
>
> Thanx guys!
>
> Egon
>
> --
> Dr E.L. Willighagen
> Postdoctoral Researcher
> Institutet för miljömedicin
> Karolinska Institutet
> Homepage: http://egonw.github.com/
> LinkedIn: http://se.linkedin.com/in/egonw
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: http://www.citeulike.org/user/egonw/tag/papers
>
>
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