ViewDockX: Mol2 reader makes duplicate bonds

[i.ihnatenko@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.17763
ChimeraX Version: 0.9 (2019-05-21)
Description
Opening a mol2-file generated by GOLD which has two or multiple molecules / conformations of a molecule causes this issue. The file cannot be opened. 
The problem does not occur in the earlier viersion UCSF ChimeraX version 0.9 (2019-03-18).

Log:
UCSF ChimeraX version: 0.9 (2019-05-21)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Users/Irina/PowerFolders/Arbeit/Grundlegende pdb-files/Andere ,
Debugs/deux résultats.mol2"

Summary of feedback from opening
C:/Users/Irina/PowerFolders/Arbeit/Grundlegende pdb-files/Andere , Debugs/deux
résultats.mol2  
---  
warnings | line 120: ignoring section 'SET'  
line 242: ignoring section 'SET'  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 141, in <lambda>  
lambda e, what=what, self=self: self.handle_scheme(what),  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 96, in handle_scheme  
run(self.session, f'{value}')  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2632, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 69, in open  
_handle_unexpected_keyword_error(e)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 64, in open  
path_models = session.models.open(paths, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 602, in open  
session, filenames, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 477, in open_multiple_data  
models, status = open_data(session, fspec, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 433, in open_data  
models, status = open_func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\viewdockx\\__init__.py", line 43, in open_file  
return open_mol2(session, path, file_name, auto_style, atomic)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\viewdockx\io.py", line 5, in open_mol2  
p = Mol2Parser(session, stream, file_name, auto_style, atomic)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\viewdockx\io.py", line 81, in __init__  
self._make_structure()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\viewdockx\io.py", line 201, in _make_structure  
s.new_bond(origin, target)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1494, in new_bond  
return f(self._c_pointer, atom1._c_pointer, atom2._c_pointer)  
TypeError: Bond already exists between these atoms  
  
TypeError: Bond already exists between these atoms  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1494, in new_bond  
return f(self._c_pointer, atom1._c_pointer, atom2._c_pointer)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 23.20.16.4973
OpenGL renderer: Intel(R) HD Graphics 510
OpenGL vendor: Intel

[Eric Pettersen]

Reported by Irina Ihnatenko

[Conrad Huang]

Hi, Irina.

Can you please send me the mol2 file that generated this error? Thanks.

Conrad

[i.ihnatenko@…]

Hi Conrad,

please find attached one of the files which causes the problem.

Kind regards,

Irina

Am 23.05.2019 um 21:05 schrieb ChimeraX:

deux résultats.mol2​

[i.ihnatenko@…]

Added by email2trac

[Conrad Huang]

Hi, Irina.

There was a problem with parsing mol2 files that did not have comment lines that start with '#'. The bug should be fixed in tomorrow's daily build (dated May 30 or later). Can you please give it a try and let me know if it's working? Thanks.

Conrad

[i.ihnatenko@…]

Hi Conrad,

the files can now be opened correctly, thank you very much for fixing 
the bug! You can find the log below.

Kind regards,

Irina

[Conrad Huang]

Fix worked!