findclash gives traceback unless "test self" specified

[Elaine Meng]

Re the closed ticket #502:

Don’t know how much of a fix this is, since using the command gives a traceback now. The “test other” option is the default, but it gives the traceback. Thus one has to explicitly use a different “test” value. Unfortunately usage also shows “test atomspec” and “test model” but they are not implemented either and give a similar traceback. The only allowed value is “test self” … so including the lack of hbond correction and the misleading usage info, it isn’t particularly usable. I haven’t documented it.

I would guess (I may be wrong) that the simplest fix would be to implement the other "test" options. I understand everybody's too busy, just making a ticket so it doesn't fall into a black hole forever. May need to be reassigned.

Example:
open 1zik
findclash protein
Traceback (most recent call last):
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/cmd_line/tool.py", line 158, in execute
cmd.run(cmd_text)
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/cli.py", line 2255, in run
result = ci.function(session, kw_args)
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/exp_cmd/findclash.py", line 29, in findclash
raise LimitationError("findclash test \"%s\" not implemented" % test)
chimerax.core.errors.LimitationError: findclash test "other" not implemented

[Conrad Huang]

"findclash" was implemented to demo RINalyzer using only distance criteria and was not intended as a "real" command. When the hydrogen bond finder is available, we can revisit.

[Eric Pettersen]

Since this demo version of findclash has been withdrawn, this bug report is now moot. The "real" findclash will be ported at some point.