[Owl-devel] Null Pointer Exception in readCrystalData

[Jose M. Duarte]

Ok answering to my self. I can see what's the problem now with that cif
file... the crystal parameter fields are optional, NMR entries won't have
them (2l02 is NMR). Will see if I can fix that.

Jose


On 1 September 2010 14:33, Jose M. Duarte <jose.m.duarte at gmail.com> wrote:

> Hi Henning
>
> (posting to owl-devel directly)
>
> Thanks for that, I didn't even know this was happening. Just checked with
> 2l02 and indeed I can reproduce the problem, I think there might be
> something strange in that entry, the parsing tests do pass (which means that
> the tests are not good enough!). Have you seen the problem with other cif
> files too?
>
> Re the casp file problems, do you have an example of one of those casp
> files? I think both problems should be easily solvable without having to go
> for optional parsing. If you can send me one example I'll look into it.
>
> Cheers
>
> Jose
>
>
>
> On 09/01/2010 12:37 PM, Henning Stehr wrote:
>
> Continuing with the next problem right away...
>
> I'm getting such errors when loading cif files (e.g. 2l02):
>
> Exception in thread "main" java.lang.NullPointerException
>         at owl.core.structure.CiffilePdb.readCrystalData(CiffilePdb.java:374)
>
>         at owl.core.structure.CiffilePdb.parseCifFile(CiffilePdb.java:296)
>         at owl.core.structure.CiffilePdb.load(CiffilePdb.java:173)
>         at owl.core.structure.Pdb.load(Pdb.java:259)
>         at owl.casp.tools.MapStru2Seq.main(MapStru2Seq.java:69)
>
> I had similar problems earlier with the new b-factor parsing and when
> I checked I found that Casp models often break the correct format for
> b-factors (which we had previously ignored). As a workaround I fixed
>
> the format in the files but I probably can't do that for cyrstal data.
> Can we somehow make parsing all these things optional? I'm not sure
> how to best implement this, but mabe some kind of legacy or lenient
>
> parse mode?
>
> Thanks,
> Henning
>
>
>
>
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