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Messages - Bernhard10

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Bug reports / JSON output should escape backslashes
« on: November 29, 2018, 04:39:59 am »
When I give DSSR a filename which contains a backslash (e.g. as a path seperator on Windows), this backslash gets included in the created JSON in the fields "command", "input_file" and possibly "str_id".
This makes the JSON invalid and impossible to parse, because backslashes are escape characters in JSON and have to be escaped as "\\" to produce valid JSON.

rename 1rnk.pdb into '1rnk\something.pdb'
./x3dna-dssr -i='1rnk\something.pdb' --json

Gives a JSON including
{"command":"x3dna-dssr -i=1rnk\something.pdb --json","input_file":"1rnk\something.pdb","str_id":"1rnk\something"

instead of
{"command":"x3dna-dssr -i=1rnk\\something.pdb --json","input_file":"1rnk\\something.pdb","str_id":"1rnk\\something"

It seems that 'O5'' is actually correct.

The error was caused by using a non-integer model number.

Thanks for the help.

It seems there is a bug in biopython. I have submitted a bugreport and I'm testing the fix:


I noticed that the cif files created with biopython are not supported by DSSR.
Biopython `Bio.PDB.MMCIFIO' writes rather minimal cif files which ONLY contain the following loop:

ATOM   1   O  'O5'' . C   A ? 1 ? 23.308 21.309 18.480 1.0 17.2  1  A ' '

When I analyze these biopython-generated cif files with DSSR, I get the following error: "no nucleotides found."

Could you tell me which dictionary keys of the cif format are essential for DSSR, so I can decide if I can extend biopython's cif writer to make it compatible with dssr.

(Attached is an example file. This is 333D.cif read with biopython and written to a new file. Tested with cif version v1.7.1-2017nov01)

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.