Bob, Thanks for the replies.
> Note -- this is all 10.x > > Dave, > > [EMAIL PROTECTED] wrote: > > >Bob, > > > >Here is my suggested list of desirable functionality. > >I think all these are fairly minor changes, or in some cases > >no change at all. > >Let me what you think. > > > >1. Measurement table should display all measurements in current > >measurement list. > >By measurement list I mean the data accessed by the viewer api > >getMeasurementCount() and getMeasurementCountPlusIndices() > > > > > > > If this is not current operation, it's a bug. Let me know. > The measurement table does not update when a measurement is deleted in the viewer and the measurement then becomes un-selectable in the table. > >2. 'measure ON/OFF' should control *display* of current measurement > >list, > >not delete anything. If this breaks backward-compatibility, you could > >have > >new keywords 'measure DISPLAYON/DISPLAYOFF' > > > > > > > yes, we'll need those keywords. Very good idea. Very simple, too, > because with the visibility business I have set up, it's trivial to add > an additional flag that adds this level of detail. > good! > >3. 'measure DELETEALL' deletes all measurements from measurement list > > > > > this is just > > measures off > OK, maybe no need for 'measure DELETEALL'. IMHO the measure ON/OFF syntax is confusing -- if measure OFF deletes all measurements, measure ON cannot restore them, so what does measure ON do exactly? But if it's documented, maybe no need to change it. > >'measure x y' creates new measurement > > > > > where x and y can be either two atom numbers (running sequentially > through ALL models; 1-based) or two atom expressions. In the case of > atom expressions, unless the ALL keyword is used, the FIRST atom in any > given atom expression is used. > yep. I meant x and y to be atom expressions. > >'measure DELETE x y' deletes this measurement > > > > > > > I've implemented this specifically for atom expressions. If you think > it's important to do so with raw atom numbers, let me know. > > No, atom expressions fine for me. > >4. On measurement table: > >'Delete All' button is equivalent to 'measure DELETEALL' > > > > > currently DeleteAll > > >'Delete' button equivalent to 'measure DELETE x y', where x y is > >selected > >measurement. > > > > > current action > currently there is no 'measure DELETE' option. 'measure x y' on an already existing measurement deletes that measurement. This is fine, I was just suggesting a more intuitive syntax for writing scripts. BUT, as noted above, deleting measurements doesn't update the measurement table. Maybe this is just a case of calling updateTables() or something, haven't looked. > >5. In viewer: > >selecting a measurement with clicking is equivalent to > >'measure x y' > > > > > current action > yes. > >selecting an already selected measurement with clicking > >is equivalent to 'measure DELETE x y' > > > > > > > current action > yes, need to update measurement table as above. > >6. The above commands apply to the current frame only, > >unless 'set measureAllModels ON' is set, in which case they apply > >to the same measurement in all frames. > > > > > > > current action > Need to include deletion of measurements in this -- it is not carried across all models, as per my original request. > >7. The 'measure ALL x y' syntax in 10.x should be restricted to > >the current frame, only extended if 'set measureAllModels ON' > >is set, as with all other 'measure' commands. > > > > > ah, THAT's a good idea! Excellent! > > >8. It should be possible to create measurements between atoms in > >different > >frames (using e.g. measure 1/1 1/2) If 'set measureAllModels ON' is set, > >this measurement should > >be created between the first selected atom in the current frame, and the > >other > >atoms in all frames (e.g. you could track the distance moved by one atom > >over an MD trajectory). > > > > > > > current action -- no special keywords required. Because we are being so > specific, the code recognizes the intent. > > > >9. The 'set measurement' commands should remain as present. > > > > > > > ok > > >10. The atom boxes in the measurement table should label both the atom > >number and the frame number, e.g. 23/1 H. > > > > > > > done (yesterday) > > >11. The menu and popup Measurement tick boxes should be equivalent > >to 'measure ON/OFF' > > > > > > > Let's think more about what the menu options should be and where they > should be. Here you mean DISPLAYON/DISPLAYOFF, I think. > Agreed. > OK, so that's not so bad. I see two modifications to make: > > a) displayon/displayoff > b) "ALL" with current model only > > That sound right? > Yes, that would be great, plus keeping the measurement table up to date on deletion, doing deletion across models when 'set measureAllModels ON' is set, and fixing the menu tick boxes to use displayon/displayoff properly. > You might want to look into using the JmolViewer interface function: > > abstract public Object getProperty(String returnType, String infoType, > String paramInfo); > > specifically > > getProperty(null,"measurementInfo") > This sound great. I have been using getProperty(null,"atomInfo") and getProperty(null,"bondInfo"), and converting to a CDK object, so I can run then same classes from the command line as from Jmol, also because I need all the connection info to do J-coupling calculations. -- Dave Evans [EMAIL PROTECTED] http://www.davidaevans.org _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
