Changes between Version 58 and Version 59 of Needed Command Functionality

Timestamp:

May 14, 2015, 4:14:21 PM (10 years ago)

Author:

Elaine Meng

Comment:

--

Needed Command Functionality

@@ -17 +17 @@
   - see [[SurfaceCategories]] discussion of categories and command design
   - see [http://www.cgl.ucsf.edu/home/meng/chi2/surface.html surface manpage mockup] based on subsequent discussion
-* '''repr''', '''ribrepr''', '''ribscale''', '''surfrepr''' (maybe consolidate into a new '''style''' command, generalizing ribbon to cartoon as per [http://www.cgl.ucsf.edu/home/meng/chi2/ribbons.html ribbons writeup], and including pseudobonds; I'm not sure consolidation is better, however, since consolidation makes longer commands, and for such frequently used functionality we need easy-to-type commands)
-  - styles for this release include atom/bond '''stick, bs, sphere'''; surface (volume and molecular) '''solid, mesh'''; and at least a default style or a few possibilities for ribbons/cartoons (I suggest at least '''smooth''' and '''edged''' with default scaling; '''tube''' should actually be easier although not listed until the '''Would be nice''' section)
+* '''repr''', '''ribrepr''', '''ribscale''', '''surfrepr''' (maybe consolidate into a new '''style''' command, generalizing ribbon to cartoon as per [http://www.cgl.ucsf.edu/home/meng/chi2/ribbons.html ribbons writeup], and including pseudobonds; I'm not sure consolidation is better, however, since consolidation makes longer commands, and these will be used frequently); styles for this release:
+  - atom/bond '''stick, bs, sphere'''
+  - pseudobond '''dashedStick''' (since TomG already added it), maybe '''solidStick''' and/or '''solidLine''' (if easy or already present)
+  - surface (volume and molecular) '''solid, mesh'''
+  - a default style or a few possibilities for ribbons/cartoons (say '''smooth''' and '''edged''' with default scaling; '''tube''' should be easier even though it's down in the '''Would be nice''' section)
+  - each style could have sub-options (''e.g.'' stick radius), or if it's too complicated to include them in the '''style''' command, they could be adjusted with '''setattr'''
 * '''color''' (leaving color-by-attr as in '''rangecolor''', color-by-scalar-field as in '''scolor''', and '''rainbow''' for later and separate from '''color''')
 * '''volume''' control over isosurface display (redundancy with show/hide/color etc. OK with me, but should review structure and keywords ''vs.'' the negotiable [http://www.cgl.ucsf.edu/home/meng/chi2/command-structure.html command guidelines])
@@ -44 +48 @@
 The following functionality is listed for the December release, but not necessarily as commands:
 * '''transparency''' (similar to '''color'''; takes care of individual settings, whereas '''set''' or another command would be used for related global parameters)
-* pseudobonds that could be intermodel (implying need for '''distance''' and maybe '''hbond, findclash''' functionality)
+* pseudobonds that could be intermodel (implying need for '''distance''')
 * '''clip''', '''section''', '''thickness''' (suggest combining into single command to control global clipping, say '''clip''' or '''gclip''')
 * '''mclip''' per-model clipping, plane or slab
-* capping of all solid objects ('''set''' if global, '''setattr''' if per-object; could also be options in '''clip''' and/or '''mclip''')
+* capping of all solid objects ('''set''' if global, '''setattr''' if per-object; could also be an option in '''clip''' and/or '''mclip''')
 * single-layer transparency ('''set''' or other command control)
-* '''freeze''' or something like that to control model activation for motion (in Chimera1, '''freeze''' is something different)
+* '''freeze''' or some other command to control model activation for motion (in Chimera1, '''freeze''' is something different)
+* '''help''' to bring up command documentation
 
 Expanded functionality of existing commands:
@@ -58 +63 @@
 * more built-in specs like '''protein, nucleic acid''',''etc.''
 * full atomspecs (see [http://www.cgl.ucsf.edu/home/meng/chi2/frameatom_spec2.html Chimera2 atomspec writeup])
+* translation of menu actions into commands (if needed for full logging... maybe it's not?)
 
 == Highly desirable ==
 
 Again listed but not necessarily as commands:
+* smart molecule display (does that imply '''preset''' functionality?)
 * '''findhbond'''
 * '''rangecolor''' or equivalent for color-by-attribute
@@ -83 +90 @@
 
 Expanded functionality of existing commands:
-* '''style''' options for pseudobonds '''dashed, dotted, dotdash''', with 3D versions preferred over lines
+* '''style''' options for pseudobonds '''solidStick, dottedStick, dotdashStick, solidLine, dottedLine, dashedLine, dotdashLine'''
 
 Command accoutrements: