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Messages - Bernhard10

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1
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.

Example:
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"

2
It seems that 'O5'' is actually correct.

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

3
Thanks for the help.

It seems there is a bug in biopython. I have submitted a bugreport and I'm testing the fix: https://github.com/biopython/biopython/issues/1784

4
Hallo,

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:

Quote
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.pdbx_PDB_ins_code
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.auth_seq_id
_atom_site.auth_asym_id
_atom_site.pdbx_PDB_model_num
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.