[Owl-devel] Null Pointer Exception in readCrystalData

[Jose M. Duarte]

I commited a fix for the CIF parsing problem. Let me know if something
doesn't work.

Jose


On 1 September 2010 14:39, Jose M. Duarte <jose.m.duarte at gmail.com> wrote:

> 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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