Dear Greg,
thanks a lot for your help!
Cheers,
Paul
>
> The solution from the mailing list
>
http://www.mail-archive.com/[email protected]/msg02127.html^
> "
> file_name = sys.argv[1]+".onlylargestfrag.sdf.gz"
> test_output = gzip.open(file_name,'w+')
> test_cpd_out = Chem.SDWriter(test_output)
> # [...] inside a loop..
> test_cpd_out.write(largest_frag)
> # outside the loop
> test_cpd_out.flush()
> test_output.flush()
> test_cpd_out=None
> test_output=None
> "
>
> gives a sdf.gz, but it seems to be corrupted when trying to gunzip
> on the command line:
> "gzip: f.sdf.gz.onlylargestfrag.sdf.gz: unexpected end of file"
>
>
> When unzipping the file via "gunzip < a.sdf.gz > blubb.sdf"
> =>
> Here comes the very last part of this file:
> "
> $$$$
> CHEMBL70380
> RDKit 3D
>
> 30 33 0 0 0 0 0 0 0 0999 V2000
> -0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1.2320 0.8556 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
> 2.5379 0.1177 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 2.4393 -1.3791 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> 3.9294 0.6779 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 5.0376 -0.3330 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
> 6.4672 0.1213 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 6.7885 1.5865 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> 7.575
> "
>
>
> Apparently, the flush didn't do a good job, since the outputted file
> is not complete.
> When moving the flush part into the loop (in which I loop over the
> compounds_to_be_outputted) does not work as well.
>
>
> Does anyone have a suggestion?
>
> It seems like you have to call the .close() method, not flush().
> Here's an example.
>
> This is the equivalent of what you are doing:
>
> In [36]: gz = gzip.open('out.sdf.gz','w+')
>
> In [37]: w = Chem.SDWriter(gz)
>
> In [38]: for m in ms: w.write(m)
>
> In [39]: w.flush()
>
> In [40]: gz.flush()
>
> and it produces an error:
>
> In [41]: !gzcat out.sdf.gz | tail
>
> gzip: out.sdf.gz: unexpected end of file
> > <NUM_ROTATABLEBONDS> (200)
> 2
>
> > <P1> (200)
> 2.17
>
> > <SMILES> (200)
> CC(=O)Nc1cc(C)cc(C)c1
>
> $$$$
>
> But if I use close() it seems to work:
>
> In [30]: gz = gzip.open('out.sdf.gz','w+')
>
> In [31]: w = Chem.SDWriter(gz)
>
> In [32]: for m in ms: w.write(m)
>
> In [33]: w.close()
>
> In [34]: gz.close()
>
> In [35]: !gzcat out.sdf.gz | tail
> > <NUM_ROTATABLEBONDS> (200)
> 2
>
> > <P1> (200)
> 2.17
>
> > <SMILES> (200)
> CC(=O)Nc1cc(C)cc(C)c1
>
> $$$$
>
> I will take a look at the underlying C++ code and see if I can
> figure out some way to make at least some of that unnecessary.
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