Simple programming features in ChimeraX command language?
Hi, Is there any possibility of adding simple scripting features to the ChimeraX command syntax in the future? Obviously more complex things will be done in a python script, but if/then/for/while statements would be very handy to add to the power of one liners and aliases on the command line - e.g. for each chain in molecule1, if chain is protein, fit to map, things like that? Cheers Oli
Hi Oli, First off, thanks for all the suggestions and feedback — we love it. Keep it coming (this applies to everyone!). The sticking point of course is though ChimeraX does a lot of things that Chimera doesn’t, the converse is also true: Chimera does a lot of things that ChimeraX doesn’t, and we are working hard to close that gap. So working on suggestions from you and others has to be prioritized and slotted into that process. So some suggestions may get incorporated quickly while others “wait their turn” — it doesn’t mean we’ve forgotten them. As for this specific suggestion for simple programming-like language features, it could be the hardest one for us to do. It really it something much easier to integrate if it is part of your original design rather than a later addition. The command line parsing is already quite complex to allow non-core bundles to add commands and to add keywords to the open and save commands. There was no provision for multi-line command constructs. Though I could be overlooking some means of implementing this without a major overhaul of the command parsing — I am not the true expert on the parser (that would be Greg Couch). I guess it might be possible to implement some kind of preprocessor that looks at the original input with it’s simple logic constructs, and executes it and generates a series of one-line commands that would be executed by the “real” command processor. Would it be a problem if these constructs were only available if you had opened a script file, rather than directly typing them? —Eric Eric Pettersen UCSF Computer Graphics Lab
On May 7, 2017, at 12:46 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi,
Is there any possibility of adding simple scripting features to the ChimeraX command syntax in the future? Obviously more complex things will be done in a python script, but if/then/for/while statements would be very handy to add to the power of one liners and aliases on the command line - e.g. for each chain in molecule1, if chain is protein, fit to map, things like that?
Cheers Oli _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Eric, Absolutely understand re priorities and feasibility etc - I’ll keep sending feedback/wish-list stuff as it comes to mind, and you guys can decide if/when it should be implemented :-) Totally get that altering the underlying syntax is hard - if it is feasible, I think it would expand the capabilities of what one could do ‘on-the-fly’ quite substantially, but I understand that it may not be worth the effort. I guess what’s in my head is the flexibility that one gets from using if/for/while etc constructs in bash one-liners, without having to resort to writing a script per se. By the way, I just found the option to use the right mouse button to adjust the density level - that it a fantastic feature, improves usability massively! Cheers Oli
On May 8, 2017, at 7:10 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Oli, First off, thanks for all the suggestions and feedback — we love it. Keep it coming (this applies to everyone!). The sticking point of course is though ChimeraX does a lot of things that Chimera doesn’t, the converse is also true: Chimera does a lot of things that ChimeraX doesn’t, and we are working hard to close that gap. So working on suggestions from you and others has to be prioritized and slotted into that process. So some suggestions may get incorporated quickly while others “wait their turn” — it doesn’t mean we’ve forgotten them. As for this specific suggestion for simple programming-like language features, it could be the hardest one for us to do. It really it something much easier to integrate if it is part of your original design rather than a later addition. The command line parsing is already quite complex to allow non-core bundles to add commands and to add keywords to the open and save commands. There was no provision for multi-line command constructs. Though I could be overlooking some means of implementing this without a major overhaul of the command parsing — I am not the true expert on the parser (that would be Greg Couch). I guess it might be possible to implement some kind of preprocessor that looks at the original input with it’s simple logic constructs, and executes it and generates a series of one-line commands that would be executed by the “real” command processor. Would it be a problem if these constructs were only available if you had opened a script file, rather than directly typing them?
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On May 7, 2017, at 12:46 PM, Oliver Clarke <olibclarke@gmail.com <mailto:olibclarke@gmail.com>> wrote:
Hi,
Is there any possibility of adding simple scripting features to the ChimeraX command syntax in the future? Obviously more complex things will be done in a python script, but if/then/for/while statements would be very handy to add to the power of one liners and aliases on the command line - e.g. for each chain in molecule1, if chain is protein, fit to map, things like that?
Cheers Oli _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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Eric Pettersen -
Oliver Clarke