Dear RDKitters,
I would like to write out sdf.gz files.
When looking into the manual:
http://www.rdkit.org/docs/api/rdkit.Chem.rdmolfiles.SDWriter-class.html
"
file_name = sys.argv[1]+".onlylargestfrag.sdf.gz"
test_output = gzip.open(file_name,'w+')
test_cpd_out = Chem.ForwardSDMolSupplier(test_output)
"
this does not work =>
"
AttributeError: 'ForwardSDMolSupplier' object has no attribute 'write'
"
I guess that the documentation is not correct in this respect.
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?
Cheers,
Paul
This message and any attachment are confidential and may be privileged or
otherwise protected from disclosure. If you are not the intended recipient, you
must not copy this message or attachment or disclose the contents to any other
person. If you have received this transmission in error, please notify the
sender immediately and delete the message and any attachment from your system.
Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not accept
liability for any omissions or errors in this message which may arise as a
result of E-Mail-transmission or for damages resulting from any unauthorized
changes of the content of this message and any attachment thereto. Merck KGaA,
Darmstadt, Germany and any of its subsidiaries do not guarantee that this
message is free of viruses and does not accept liability for any damages caused
by any virus transmitted therewith.
Click http://www.merckgroup.com/disclaimer to access the German, French,
Spanish and Portuguese versions of this disclaimer.------------------------------------------------------------------------------
Master HTML5, CSS3, ASP.NET, MVC, AJAX, Knockout.js, Web API and
much more. Get web development skills now with LearnDevNow -
350+ hours of step-by-step video tutorials by Microsoft MVPs and experts.
SALE $99.99 this month only -- learn more at:
http://p.sf.net/sfu/learnmore_122812
_______________________________________________
Rdkit-discuss mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
