Re: [Jmol-users] Compare SMILES Question
Yes, I think that is appropriate.
$ print "C1=CC=CC=C1".find("smiles", "c1c1")
6
$ print "C1=CC=CC=C1".find("smiles", "/aromaticdefined/c1c1")
0
The first allows for different types of aromatic descriptions to be
matched; the second does not.
These "directives" are described in Table 8 of
https://jcheminf.springeropen.com/articles/10.1186/s13321-016-0160-4
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[Jmol-users] Compare SMILES Question
Bob, I'm writing this question because I discovered that something is working that I thought should not work. With Jmol compare SMILES (key studentAnswer), I'm getting a match with the following: C1=CC=CC=C1 (JME) c1c1 (Jmol) C1=CC=CC=C1 is the Key c1c1 is the student answer This is matching. Is that correct? Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Java support in browsers
I don't have any *insider* information of any kind, but their "About" page seems pretty clear that they're in favor of allowing users to use Java and any other plugins if they wish. Also revealing is this page from their blog: https://www.waterfoxproject.org/blog/waterfox-52.0-release-download which indicates that the project may soon fork and only get security updates from now on (because of a major structural change that Firefox is introducing). Anyways, on that page they also list NPAPI support as part of the feature-set of Waterfox, so hopefully that doesn't change any time soon. It doesn't need to last forever, at some stage the performance differences between jsmol and jmol will be negligible for all but the largest structures on modern computers. On Wed, Mar 29, 2017 at 3:59 PM, Angel Herráez wrote: > (I'm following another thread started by David Hibbitts but this is a > different > topic, so I changed the subject) > > David, > May I ask what is the information you have regarding future support of Java > by Waterfox? > > > On 29 Mar 2017 at 15:14, David Hibbitts wrote: > > It's hard to know how much any of us should invest in these > java-specific issues given the aggressive nature of browsers toward > javascript -- > > but my website really serves my research group, not the general public, > and there I can certainly get the users to install Waterfox+JAVA. > > > --- > El software de antivirus Avast ha analizado este correo electrónico en > busca de virus. > https://www.avast.com/antivirus > > -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] R: Java support in browsers
I wonder if it is the time to let Java go since every browser has issues with Java. A big problem for sure for Jsmol too? Pino Messaggio originale Da: angel.herr...@uah.es Data: 29-mar-2017 21.59 A: Ogg: [Jmol-users] Java support in browsers (I'm following another thread started by David Hibbitts but this is a different topic, so I changed the subject) David, May I ask what is the information you have regarding future support of Java by Waterfox? On 29 Mar 2017 at 15:14, David Hibbitts wrote: > It's hard to know how much any of us should invest in these java-specific > issues given the aggressive nature of browsers toward javascript -- > but my website really serves my research group, not the general public, and > there I can certainly get the users to install Waterfox+JAVA. --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol Keyboard Interaction
On Wed, Mar 29, 2017 at 2:14 PM, David Hibbitts wrote: > Thanks for the input everyone. The keyboard input will control jmol/jsmol > but also do other things, but I do like using arrow keys to rotate the > structure, for example. Other features can be added later to allow jmol to > more easily *modify* rather than merely view structures. It's hard to > imagine these features without a fuller keyboard interface (features > similar to the structure-editing capabilities of avogadro or materials > studio). > set modelkitmode allows substantial editing, but perhaps not up to those programs in terms of interface. Still, you can do a lot. Have you experimented with it? > > The javascript version already works perfectly, as keyed events are > captured by the website (even if jsmol previously has focus) and I'm just > using javascript to do whatever I want to do (including interacting with > jsmol via JmolScript calls). > > For the java version, the best I've been able to do is: use a function > which restores focus to the website (so they keyboard commands aren't > trapped by jmol) whenever 1) a script is executed by jmol using > ScriptCallback or 2) the users mouse leaves the jmol div (using a > standard mouseout event in the DOM). This means the user doesn't have to > "click" off of jmol to restore focus and re-enable the keyboard > interactions. It doesn't help if the user, for example, uses the mouse to > rotate the structure and leaves the mouse on jmol the entire time. In > that instance, jmolnever loses focus and so the keyboard events aren't > passed to the website. > That's clever. > > I could use the callbacks more aggressively, for example by using > pickcallback and hovercallback -- but those are uncommon cases -- what I > really need is something more encompassing like a "MouseUpCallback" so that > any time the clicks on jmol I can redirect focus back to the website. > Unfortunately, that callback doesn't exist in the jmol scripting > environment. > > > It's hard to know how much any of us should invest in these java-specific > issues given the aggressive nature of browsers toward javascript -- but my > website really serves my research group, not the general public, and there > I can certainly get the users to install Waterfox+JAVA. > > Ah, that is very good to hear. I have been trying to promote the idea that browser-based Jmol can be very much for local use such as that. Bob -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Java support in browsers
(I'm following another thread started by David Hibbitts but this is a different topic, so I changed the subject) David, May I ask what is the information you have regarding future support of Java by Waterfox? On 29 Mar 2017 at 15:14, David Hibbitts wrote: > It's hard to know how much any of us should invest in these java-specific > issues given the aggressive nature of browsers toward javascript -- > but my website really serves my research group, not the general public, and > there I can certainly get the users to install Waterfox+JAVA. --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol Keyboard Interaction
Thanks for the input everyone. The keyboard input will control jmol/jsmol but also do other things, but I do like using arrow keys to rotate the structure, for example. Other features can be added later to allow jmol to more easily *modify* rather than merely view structures. It's hard to imagine these features without a fuller keyboard interface (features similar to the structure-editing capabilities of avogadro or materials studio). The javascript version already works perfectly, as keyed events are captured by the website (even if jsmol previously has focus) and I'm just using javascript to do whatever I want to do (including interacting with jsmol via JmolScript calls). For the java version, the best I've been able to do is: use a function which restores focus to the website (so they keyboard commands aren't trapped by jmol) whenever 1) a script is executed by jmol using ScriptCallback or 2) the users mouse leaves the jmol div (using a standard mouseout event in the DOM). This means the user doesn't have to "click" off of jmol to restore focus and re-enable the keyboard interactions. It doesn't help if the user, for example, uses the mouse to rotate the structure and leaves the mouse on jmol the entire time. In that instance, jmolnever loses focus and so the keyboard events aren't passed to the website. I could use the callbacks more aggressively, for example by using pickcallback and hovercallback -- but those are uncommon cases -- what I really need is something more encompassing like a "MouseUpCallback" so that any time the clicks on jmol I can redirect focus back to the website. Unfortunately, that callback doesn't exist in the jmol scripting environment. It's hard to know how much any of us should invest in these java-specific issues given the aggressive nature of browsers toward javascript -- but my website really serves my research group, not the general public, and there I can certainly get the users to install Waterfox+JAVA. Thanks On Wed, Mar 29, 2017 at 2:43 PM, Robert Hanson wrote: > (sorry, I missed that nuance) > > > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol opened from command line behaves different
I was trying to have Jmol open via the command line on a Mac and ran into a roadblock. The Jmol application launches but if I try `load $ethane` in the console it gives me an error, `script ERROR: javax.net.ssl.SSLHandshakeException: java.security.cert.CertificateException: No subject alternative DNS name matching cactus.nci.nih.gov found`. That same command works as expected when I launch by clicking `Jmol.jar` the typical way. I checked and what launches from the command line is the same version of Jmol as launches when I click on it. Still what launches looks slightly different if you look at the top-most menubar. I see that when I click on Jmol.jar to open it that there is "Jmol" up next to the Apple on the menubar, but I note that when you open it from the command line you see "org.openscience.jmol.app.Jmol" in upper left next to Apple symbol on menubar I even tried it with the `jmol.sh` script and while it opens, it doesn't connect to NCI or RCSB. Do I have to somehow point the command at some security preference that I allowed the first time I ran the `Jmol.jar` when I said I acknowledged it is from the internet but I want to run it? I see at http://wiki.jmol.org/index.php/Java_Web_Start#Signing_the_JAR_File that the Jmol.jar is now signed since I am using the latest jmol-14.10.0. Or do I need to instead do a self-signed test certificate because when called from command line, the certificate isn't accessible to the Jmol application? Of course, you are asking why can't he just stick with clicking on Jmol.jar to open Jmol? The reason is that I was trying to implement a rudimentary Python wrapper for some Jmol commands. Thanks, Wayne -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol Keyboard Interaction
(sorry, I missed that nuance) -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol Keyboard Interaction
Only the JavaScript version.
On Wed, Mar 29, 2017 at 11:32 AM, Rolf Huehne
wrote:
> Am 29.03.17 um 18:21 schrieb Robert Hanson:
> > David,
> >
> > OK, so the beauty of this system is that you can implement any sort of
> > additional functionality you want using readily available methods that
> > have nothing to do with Jmol or JSmol. It's one of the bonuses of
> > working in JavaScript and jQuery.
> >
> > So, for example, if you want to implement a key listener that
> > implements + and - to actuate zooming, you can do it this way:
> >
> > c = $("#jmolApplet0_canvas2d")
> > c.attr("tabindex", 1)
> > c.mouseover(function(){c.focus()})
> > c.keypress(function(e){
> > if (e.key == "+")Jmol.script(jmolApplet0, "zoom *1.2")
> > else if (e.key == "-")Jmol.script(jmolApplet0, "zoom /1.2")
> > })
> >
> > Notice that to accept key events, we must (a) provide a tabindex to the
> > canvas and (b) make sure the canvas has focus when we are looking for
> > key events.
> >
> > I would only say that hidden specialized features like this, though
> > potentially useful, are not necessarily recommended.
> >
> It looks like the example would only work for the Javascript version. Or
> could it also work for the Java version (with some adjustment)?
>
> Regards,
> Rolf
>
>
> --
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> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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Northfield, MN
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If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Re: [Jmol-users] Jmol Keyboard Interaction
Am 29.03.17 um 18:21 schrieb Robert Hanson:
> David,
>
> OK, so the beauty of this system is that you can implement any sort of
> additional functionality you want using readily available methods that
> have nothing to do with Jmol or JSmol. It's one of the bonuses of
> working in JavaScript and jQuery.
>
> So, for example, if you want to implement a key listener that
> implements + and - to actuate zooming, you can do it this way:
>
> c = $("#jmolApplet0_canvas2d")
> c.attr("tabindex", 1)
> c.mouseover(function(){c.focus()})
> c.keypress(function(e){
> if (e.key == "+")Jmol.script(jmolApplet0, "zoom *1.2")
> else if (e.key == "-")Jmol.script(jmolApplet0, "zoom /1.2")
> })
>
> Notice that to accept key events, we must (a) provide a tabindex to the
> canvas and (b) make sure the canvas has focus when we are looking for
> key events.
>
> I would only say that hidden specialized features like this, though
> potentially useful, are not necessarily recommended.
>
It looks like the example would only work for the Javascript version. Or
could it also work for the Java version (with some adjustment)?
Regards,
Rolf
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Re: [Jmol-users] Jmol Keyboard Interaction
David,
OK, so the beauty of this system is that you can implement any sort of
additional functionality you want using readily available methods that have
nothing to do with Jmol or JSmol. It's one of the bonuses of working in
JavaScript and jQuery.
So, for example, if you want to implement a key listener that implements +
and - to actuate zooming, you can do it this way:
c = $("#jmolApplet0_canvas2d")
c.attr("tabindex", 1)
c.mouseover(function(){c.focus()})
c.keypress(function(e){
if (e.key == "+")Jmol.script(jmolApplet0, "zoom *1.2")
else if (e.key == "-")Jmol.script(jmolApplet0, "zoom /1.2")
})
Notice that to accept key events, we must (a) provide a tabindex to the
canvas and (b) make sure the canvas has focus when we are looking for key
events.
I would only say that hidden specialized features like this, though
potentially useful, are not necessarily recommended.
Bob
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Re: [Jmol-users] Jmol Keyboard Interaction
Am 29.03.17 um 17:37 schrieb Angel Herráez: > Have you checked Jmol's "navigation mode" ? > As far as I remember, it used the keyboard. > But maybe it is only applicable to the Jmol application. > > http://chemapps.stolaf.edu/jmol/docs/#navigate > http://chemapps.stolaf.edu/jmol/docs/#setnavigation > I don't find the navigation mode very suitable as a standard method for exploring a structure. In some cases it might be useful but my own experiences were rather unsatisfying. Regards, Rolf -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol Keyboard Interaction
Have you checked Jmol's "navigation mode" ? As far as I remember, it used the keyboard. But maybe it is only applicable to the Jmol application. http://chemapps.stolaf.edu/jmol/docs/#navigate http://chemapps.stolaf.edu/jmol/docs/#setnavigation -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol Keyboard Interaction
Am 28.03.17 um 22:26 schrieb David Hibbitts: > So the "allowkeystrokes" feature simply lets you send commands to the > console? > > No, that's not useful for me -- I'm sure someone has tried to implement > navigation-by-keyboard on their jmol-including website before. > It would be great if this would be possible. Especially because mouse control of Jmol-Java on MacOS became problematic in browsers. For example could '+/-' for zoom in/out be very handy. The zoom "slider" near the right applet border is quite inconvenient. And the only mouse binding that does work is on the left mouse button without any modifiers. So keyboard commands for translation and Z-rotation could also be very helpful. Regards, Rolf -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
