Changes between Version 120 and Version 121 of Needed Command Functionality

Timestamp:

Nov 6, 2015, 12:57:57 PM (10 years ago)

Author:

Elaine Meng

Comment:

--

Needed Command Functionality

@@ -6 +6 @@
 - [http://www.cgl.ucsf.edu/home/meng/chi2/frameatom_spec2.html atomspec]
 - [http://www.cgl.ucsf.edu/home/meng/chi2/surface.html surface]
-- [http://www.cgl.ucsf.edu/home/meng/chi2/color.html color] (omnibus, including color-by-value; currently I favor this over separate color-by-value [http://www.cgl.ucsf.edu/home/meng/chi2/vcolor.html vcolor])
+- [http://www.cgl.ucsf.edu/home/meng/chi2/color.html color]
 - [http://www.cgl.ucsf.edu/home/meng/chi2/transparency.html transparency]
 - [http://www.cgl.ucsf.edu/home/meng/chi2/alias.html alias] (we decided to make this '''namespec''')
 - [http://www.cgl.ucsf.edu/home/meng/chi2/macro.html macro] (we decided to leave this as '''alias''')
 Potential renaming of Chimera1 commands (up for discussion):
-- ~~Chimera1 '''freeze''' → Chimera2 '''stop'''~~ (done) (the latter no longer used for exiting the program; if no ongoing motion '''stop''' should remind user of this!)
--  '''~select/select''' (whole-model activation/deactivation function) → '''freeze/~freeze'''
+- ~~Chimera1 '''freeze''' → Chimera2 '''stop'''~~ (done)
+ - Nov 5 2015 Greg will add Log message to remind users of '''stop''' function if no ongoing motion
+-  ~~'''~select/select''' (model activation/deactivation) → '''freeze/~freeze'''~~
+ - Nov 5 2015 decided activation concept not needed in Chimear2
 - ~~'''window, focus''' → '''view ''spec'' '''~~ (done)
-- '''windowsize''' → '''window'''
+- ~~'''windowsize''' → '''window'''~~
+ - Nov 5 2015 deemed unnecessary now that it can be truncated (since the '''window''' command is not present)
 - ~~'''scale''' → '''zoom'''~~ (done)
 - '''display/modeldisplay''' → '''show/hide'''
-- '''alias''' (target-defining function) → '''namespec'''
+ - Nov 2 2015 agreed to proceed with this, with '''~show''' as an undocumented alias to '''hide'''
+- '''alias''' (target-defining function) → '''namespec''' (previously agreed upon)
+ - Nov 5 2015 for the other (command-defining) function of '''alias''', agreed to change syntax for listing and deleting aliases, and to use analogous approach for other commands that also allow the user to assign names to definitions ('''namespec''', '''colordef''', ''etc.''...'''view''' is already that way)
+    - '''alias''' → '''alias list'''
+    - '''~alias ''name''''' → '''alias delete (''name''|all)'''
 - ~~'''2dlabels''' → '''title'''~~ (done)
 - ~~'''ribbon''' → '''cartoon'''~~ (done but we still have '''ribbon''' as a synonym)
@@ -23 +30 @@
 == Late summer release ==
 
-Initial versions (not necessarily full implementations, could be partial) of:
+Initial versions (not necessarily full implementations) of:
 * '''open''' (suggest same general syntax as Chimera1, possibly adjusting prefixes; covers both local files and web-fetch)
   - for this release: PDB, PDB/mmCIF, density maps, sessions
   - as of Nov 2 2015 done for the above except sessions
   - prefixes (''e.g.'' '''pdb:''' should allow opening file with non-standard suffix as that format; currently only treats the string as an ID code)
-* ~~'''close'''~~ (done for models; might want to add session option later)
+  - Nov 5 2015 intend to add keywords '''from''' to specify database for web fetch and '''format''' which could useful for both fetch and local files, and possibly other keywords; retain colon syntax as alternative
+* ~~'''close'''~~ (done for models; might want to add '''session''' and/or '''all''' keywords later)
 * ~~'''exit, quit''' or equivalent~~ (done)
-  - maybe '''stop''' should instead work like Chimera1 '''freeze''' (stop motion), and '''freeze''' could be repurposed for deactivation (the older function of Chimera1 '''~select''')
-* ~~something like Chimera1 '''focus''' and/or '''window''' (although I might rename as '''view''')~~ (done)
-  - '''window''' may be better for windowsize specification
-* '''display''', '''modeldisplay''' (maybe replace with '''show/hide''')
-  - this could control pseudobonds indirectly if they are hidden automatically when endpoint atoms are hidden, but we may want to make it act on them directly, or else '''setattr''' (see below) might be the only way
-  - as of Nov 2 2015 implemented as '''display''' and its options (EM: seems good to me)
+* ~~something like Chimera1 '''focus''' and/or '''window''' (rename as '''view''')~~ (done)
+* '''display''', '''modeldisplay''' (plan to replace with '''show/hide''')
+  - as of Nov 2 2015 implemented as '''display''' and its options 
 * '''cartoon''' including spline, path-smoothing, and any other whole-chain parameters as options
   - see [http://www.cgl.ucsf.edu/home/meng/chi2/ribbons.html ribbons writeup]