Parsing complaint about Ligand Expo cif files

[Tristan Croll]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1127.13.1.el7.x86_64-x86_64-with-centos-7.8.2003-Core
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
The attached .cif file is the concatenation of a set of templates pulled from ligand-expo (corresponding to the set of residues currently covered by ISOLDE's "core" forcefield). If I open it with:

{{{
from chimerax.atomic import mmcif
mmcif.load_mmCIF_templates('core_components.cif')
}}}

... then I get the following message printed to the log:

Loading template file failed: left square bracket is illegal outside of quotes in CIF 1.1 near line 419

(and many more of them if I load the files individually). The templates themselves still appear to be loaded, so the message is a little misleading. Anyway, the four lines starting from line 419 look like the following:

{{{
TRP_LSN3 SMILES_CANONICAL CACTVS               3.341 [NH3+][C@@H](Cc1c[nH]c2ccccc12)[C-]=O                                                          
TRP_LSN3 SMILES           CACTVS               3.341 [NH3+][CH](Cc1c[nH]c2ccccc12)[C-]=O                                                            
TRP_LSN3 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1ccc2c(c1)c(c[nH]2)C[C@@H]([C-]=O)[NH3+]                                                      
TRP_LSN3 SMILES           "OpenEye OEToolkits" 1.5.0 c1ccc2c(c1)c(c[nH]2)CC([C-]=O)[NH3+]                                                           
}}}

A case of the wwPDB breaking their own rules?

Log:
UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show Shell

/opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
UserWarning: IPython History requires SQLite, your history will not be saved  
warn("IPython History requires SQLite, your history will not be saved")  




OpenGL version: 3.3.0 NVIDIA 450.51.05
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            62G        6.4G         46G        210M        9.5G         55G
	Swap:          4.9G          0B        4.9G

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:11df]	
	Kernel driver in use: nvidia
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8
File attachment: core_components.cif

core_components.cif​

[Tristan Croll]

Added by email2trac

[Greg Couch]

Yes, that is illegal according to the CIF standard, ​https://www.iucr.org/resources/cif/spec/version1.1/cifsyntax, paragraph 19:

Matching square bracket characters, [ and ], are reserved for possible future introduction as delimiters of multi-line data values. At this revision of the CIF specification a data value may not begin with an unquoted left square bracket character '['.