Daniel,
On Sun, Nov 3, 2013 at 1:45 PM, Daniel Moser <
[email protected]> wrote:
>
>
> Okay.. I started this mail some time ago. In the meantime things have
> changed a little. I was curious if the problems could be related to
> unittest so I commented all tests except test84PDBBasics out. Now the test
> succeeds.
>
> So I started to successively enable the other tests. What I finally found
> was that if any of the following tests is run before test84PDBBasics,
> test84PDBBasics fails:
>
> test23MolFileParsing
>
> test25SDMolSupplier
>
> test29SDWriterLoop
>
> test39Issue273
>
> test41SetStreamIndices
>
> test48Issue1928819
>
> test56LazySDMolSupplier
>
> test58Issue2983794
>
> test63Issue3313539
>
> test65StreamSupplier
>
> test66StreamSupplierIter
>
> test67StreamSupplierStringIO
>
> test68ForwardSupplierUsingFilename
>
> test69StreamSupplierStreambuf
>
> test70StreamSDWriter
>
> test71StreamSmilesWriter
>
> test72StreamTDTWriter
>
> test74Issue3510149
>
>
>
> In fact, the following little script already fails (i.e. m is None) when
> the for-loop is present. Only creating the supplier is no problem.
>
> from rdkit import RDConfig, rdBase
>
> import os
>
> from rdkit import Chem
>
>
>
> fileN = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','FileParsers',
> 'test_data','NCI_aids_few.sdf')
>
> sdSup = Chem.SDMolSupplier(fileN)
>
> for mol in sdSup :
>
> print mol.GetProp("_Name")
>
> sdSup.reset()
>
>
>
> fileN =
> os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','FileParsers','test_data','1CRN.pdb')
>
> m = Chem.MolFromPDBFile(fileN)
>
> print m is not None # prints False
>
>
>
Well, that at least is a nice small test case. I tried this on my CentOS
6.4 VM (still using the system Python and boost installations) and,
unfortunately, I cannot reproduce the problem.
-greg
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