Difference between revisions of "Jmol JavaScript Object/Info"
AngelHerraez (talk | contribs) (some more parameters for the "Info" variable; TOC position) |
AngelHerraez (talk | contribs) (update on the use of arguments array) |
||
(61 intermediate revisions by the same user not shown) | |||
Line 1: | Line 1: | ||
+ | <div style="float:right;"> | ||
+ | __TOC__ | ||
+ | </div> | ||
= Documentation of parameters of the Info variable = | = Documentation of parameters of the Info variable = | ||
Line 5: | Line 8: | ||
''Note that, although this is usually designated as <code>Info</code> in the documentation, it is a regular JavaScript variable that you can name as you wish.'' | ''Note that, although this is usually designated as <code>Info</code> in the documentation, it is a regular JavaScript variable that you can name as you wish.'' | ||
− | <tt>Info</tt> is an associative array (a set of key/value pairs) indicating all the desired characteristics of the Jmol object (Jmol applet or JSmol) | + | <tt>Info</tt> is an associative array (a set of key/value pairs) indicating all the desired characteristics of the Jmol object (Jmol applet or JSmol). |
Values may be defined | Values may be defined | ||
Line 21: | Line 24: | ||
</pre> | </pre> | ||
− | + | An alphabetic listing of all parameters, along with a comparative view of which modalities of Jmol Object they may be applied to, may be checked in [[Jmol JavaScript_Object/InfoTable]]. | |
== Jmol object definition == | == Jmol object definition == | ||
Line 40: | Line 43: | ||
=== Files and paths === | === Files and paths === | ||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
* '''j2sPath''' <code>"j2s"</code> | * '''j2sPath''' <code>"j2s"</code> | ||
:''(HTML5 modality)'' The path to {{folder|j2s}} including its own name; the contents of this folder are essential for JSmol to work. | :''(HTML5 modality)'' The path to {{folder|j2s}} including its own name; the contents of this folder are essential for JSmol to work. | ||
+ | * '''serverURL''' <code>"<nowiki>http://your.server.here/jsmol.php</nowiki>"</code> | ||
+ | :The URL of {{file|jsmol.php}} to be used for getting file data into non-Java modalities. For better performance and to avoid cross-domain issues, '''you should set this''' to a url in the same server your pages are. In the scheme of the standard JSmol distribution, that will be <code>"<nowiki>php/jsmol.php</nowiki>"</code>. | ||
+ | :If you cannot have PHP working in your server, you may use <code>"<nowiki>https://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php</nowiki>"</code>, since that is a public site accessible to cross-domain AJAX calls. | ||
+ | :'''Setting this properly is essential''', among other situations, | ||
+ | :* when loading into JSmol models in binary files, at least in some browsers | ||
+ | :* for cross-domain loading JSmol components (<code>.js</code> files), i.e. when <code>Info.j2sPath</code> points to a server different to the one that hosts the page | ||
=== Modality === | === Modality === | ||
− | * '''use''' <code>"HTML5 | + | * '''use''' <code>"HTML5"</code> This string determines the mode to be used (either Java applet or a surrogates). |
− | ** The default setting is | + | ** The default setting is <code>HTML5</code> and indicates to use JSmol in html5-only mode. |
− | ** The value <code> | + | ** The value <code>WebGL</code> will force the [[Jmol_JavaScript_Object/WebGL|WebGL modality]] (combined with html5). ''Note that the WebGL version of JSmol does not implement the full set of functionalities of Jmol.'' |
− | ** The value <code>Java | + | ** The value <code>Java</code> forces use of the Jmol Applet (and it may display a message if Java is not enabled). ''Note that Java applets are no longer supported by the majority of web browsers.'' |
− | |||
− | |||
− | Note that | ||
== Startup period == | == Startup period == | ||
(The values shown in the listing below are the defaults) | (The values shown in the listing below are the defaults) | ||
+ | * '''appletLoadingImage''' <code>j2sPath + "/img/JSmol_spinner.gif"</code> | ||
+ | :Set the path and filename of an image that is displayed in place of the Jmol object while this is loading. | ||
+ | :It may be disabled using <code>Info.appletLoadingImage = "none"</code> | ||
* '''coverImage''' <code>""</code> | * '''coverImage''' <code>""</code> | ||
− | :Set the path and filename of an image that will be displayed on top of the Jmol object (usually as an initial | + | :Set the path and filename of an image that will be displayed on top of the Jmol object (usually as an initial replacement or during loading, see <code>deferApplet</code> and <code>deferUncover</code> parameters below). |
+ | * '''makeLiveImage''' <code>j2sPath + "/img/play_make_live.jpg"</code> | ||
+ | :Set the path and filename of a small image (icon) that is displayed over the bottom-left corner of the cover image to give a visual hint that clicking will uncover the model. The default icon, [[File:Play make live.jpg]], is included in the JSmol distribution; you may specify your own using this parameter. | ||
* '''coverTitle''' <code>""</code> | * '''coverTitle''' <code>""</code> | ||
:Set a tip that is displayed before model starts to load. | :Set a tip that is displayed before model starts to load. | ||
− | * ''' | + | * '''coverScript''' <code>""</code> |
:Set a Jmol command or script that will be executed upon clicking the cover image. | :Set a Jmol command or script that will be executed upon clicking the cover image. | ||
* '''deferApplet''' <code>false</code> | * '''deferApplet''' <code>false</code> | ||
Line 71: | Line 76: | ||
* '''deferUncover''' <code>false</code> | * '''deferUncover''' <code>false</code> | ||
:If set <code>true</code>, the cover image will remain until command execution is complete. | :If set <code>true</code>, the cover image will remain until command execution is complete. | ||
− | * '''disableInitialConsole''' <code> | + | * '''disableInitialConsole''' <code>true</code> |
− | :If set <code> | + | :If set <code>false</code>, displays messages ('console') in the Jmol panel while the Jmol object is being built initially. Note: the default used to be <code>false</code> but was changed since version 14.5.2_2016.02.14, given the implementation of <code>appletLoadingImage</code> |
* '''disableJ2SLoadMonitor''' <code>false</code> | * '''disableJ2SLoadMonitor''' <code>false</code> | ||
:If set <code>true</code>, avoids the display of messages in a single line, colored, at bottom-left of the page while code loads (both initially and every time a new module is requested by a running script). | :If set <code>true</code>, avoids the display of messages in a single line, colored, at bottom-left of the page while code loads (both initially and every time a new module is requested by a running script). | ||
− | * '''readyFunction''' <code> | + | * '''readyFunction''' <code>null</code> |
− | :The name of a JavaScript function to call when the Jmol object has been created and is ready to receive commands (and also called when the object is destroyed e.g. when the page is closed). | + | :The name (''without quotes'') of a JavaScript function to call when the Jmol object has been created and is ready to receive commands (and also called when the object is destroyed e.g. when the page is closed). |
: For example, with <code>readyFunction: jmolIsReady</code> any of the following JavaScript function definitions could be used: | : For example, with <code>readyFunction: jmolIsReady</code> any of the following JavaScript function definitions could be used: | ||
+ | :: <code>function jmolIsReady() { alert('Welcome to Jmol!'); }</code> | ||
+ | :: <code>jmolIsReady = function() { alert('Welcome to Jmol!'); }</code> | ||
:: <code>jmolIsReady = function(theJmol) { document.title = theJmol._id + " is ready"; }</code> | :: <code>jmolIsReady = function(theJmol) { document.title = theJmol._id + " is ready"; }</code> | ||
− | :: | + | :''Note:'' The JavaScript function will receive as argument a pointer to the particular Jmol object that invoked it (as exemplified in the third example above). |
− | |||
== Model loading == | == Model loading == | ||
(The values shown in the listing below are the defaults) | (The values shown in the listing below are the defaults) | ||
+ | * '''src''' <code>""</code> | ||
+ | :A filename to load once the Jmol object has finished loading. It may be a model in a supported format, or a script file. | ||
+ | * '''script''' <code>""</code> | ||
+ | :A script to run when the Jmol object has finished loading. Note that indicating a script here is not necessary; with Jmol-JSO, unlike with Jmol.js, you can start making script calls to Jmol as soon as the Jmol wrapper object has been created in JavaScript; there is no need to wait for Jmol object initialization to have completed. | ||
+ | : Note that using <code>script</code> will cancel whatever <code>src</code> specifies (but it is easy to include a <code>load</code> command as part of the script) | ||
* '''defaultModel''' <code>""</code> | * '''defaultModel''' <code>""</code> | ||
− | : | + | :The name or id of a model to be retrieved from a public database, and displayed when the Jmol object has finished loading. |
:Examples: | :Examples: | ||
− | ::<code>defaultModel: " | + | ::<code>defaultModel: "=1crn"</code> gets it from RCSB PDB |
− | ::<code>defaultModel: " | + | ::<code>defaultModel: "$caffeine"</code> gets it from NCI CACTUS |
− | + | ::<code>defaultModel: ":caffeine"</code> gets it from PubChem | |
− | : | + | ::<code>defaultModel: "caffeine"</code> gets it from NCI CACTUS |
− | |||
− | |||
== Customization or extras == | == Customization or extras == | ||
Line 100: | Line 109: | ||
* '''addSelectionOptions''' <code>false</code> | * '''addSelectionOptions''' <code>false</code> | ||
:Set this value to <code>true</code> if you want to display, below the Jmol object, a menu with options for loading structures from public databases. | :Set this value to <code>true</code> if you want to display, below the Jmol object, a menu with options for loading structures from public databases. | ||
+ | * '''allowJavaScript''' <code>true</code> | ||
+ | :Set this value to <code>false</code> if you want to prevent any JavaScript command being run from JSmol (using the [{{ScriptingDoc}}#javascript javascript] command or [{{ScriptingDoc}}#set_evalcallback_top EvalCallback]). Note: this feature is offered because allowing any arbitrary javascript may be considered a security risk in some environments. | ||
* '''console''' <code>"***_infodiv"</code> | * '''console''' <code>"***_infodiv"</code> | ||
− | :The ID in html of the container or div that will receive output from | + | :The ID in html of the container or div that will receive output from JSmol. Default value is the JSmol Object name/id (represented here by ***) followed by <code>_infodiv</code>, and it is contained in the info panel that may be displayed alternatively to the JSmol viewer. |
* '''debug''' <code>false</code> | * '''debug''' <code>false</code> | ||
:Set this value to <code>true</code> if you are having problems getting your page to show the Jmol object, buttons or ther controls. | :Set this value to <code>true</code> if you are having problems getting your page to show the Jmol object, buttons or ther controls. | ||
− | * '''language''' ''2-letter or 2+2-letter code'' | + | * '''language''' "''2-letter or 2+2-letter code''" |
:This setting can be used to specify a language to be used in the Jmol Object interface (mainly the pop-up menu). The existing choices may be checked in the pop-up menu. If not specified, the default language is automatically detected from the system settings of the user's browser. | :This setting can be used to specify a language to be used in the Jmol Object interface (mainly the pop-up menu). The existing choices may be checked in the pop-up menu. If not specified, the default language is automatically detected from the system settings of the user's browser. | ||
:Examples: | :Examples: | ||
::<code>language: "es"</code> for Spanish | ::<code>language: "es"</code> for Spanish | ||
::<code>language: "pt_BR"</code> for Brazilian Portuguese | ::<code>language: "pt_BR"</code> for Brazilian Portuguese | ||
− | * ''' | + | * '''menuFile''' "''fileName''" |
− | |||
− | |||
:Loads a [[Custom Menus|custom pop-up menu]]. | :Loads a [[Custom Menus|custom pop-up menu]]. | ||
− | |||
− | |||
− | |||
− | |||
− | |||
* '''zIndexBase''' <code>9000</code> | * '''zIndexBase''' <code>9000</code> | ||
− | : | + | :Defines the z-index property in CSS of the Jmol Object and its associated div's. This is set by default to a very high value, so the object will be laid on top of any other page elements, but it may be useful to change it when you are integrating Jmol with other components. In addition to setting for the particular applet, it also sets the default for all other applets on the page, in case it is not defined for those applets. |
+ | * '''z''' <code>{9000, 9001, 9002, 9003, 9004, 9005, 9006, 9007, 99008, 100008, 109007}</code> | ||
+ | :Defines, in a more fine-grained way, the z-index property in CSS of all div's forming the Jmol Object. | ||
+ | : It is an associative array that includes (some of these are more relevant to JmolSpecViewer): | ||
+ | <pre>Info.z = { | ||
+ | header: , | ||
+ | rear: , | ||
+ | main: , | ||
+ | image: , | ||
+ | front: , | ||
+ | fileOpener: , | ||
+ | coverImage: , | ||
+ | dialog: , | ||
+ | menu: , | ||
+ | console: , | ||
+ | monitorZIndex: | ||
+ | }</pre> | ||
+ | : When just <code>zIndexBase</code> is provided, it will set all components of <code>z</code> in this way: | ||
+ | <pre> | ||
+ | header: zIndexBase, | ||
+ | rear: zIndexBase + 1, | ||
+ | main: zIndexBase + 2, | ||
+ | image: zIndexBase + 3, | ||
+ | front: zIndexBase + 4, | ||
+ | fileOpener: zIndexBase + 5, | ||
+ | coverImage: zIndexBase + 6, | ||
+ | dialog: zIndexBase + 7, | ||
+ | menu: zIndexBase + 90000, | ||
+ | console: zIndexBase + 91000, | ||
+ | monitorZIndex: zIndexBase + 99999 | ||
+ | </pre> | ||
+ | |||
+ | == Callbacks == | ||
+ | |||
+ | These callbacks, given in the '''Info''' variable, allow the page designer to get information about what is happening within the Jmol object. The name of a function, wrapped in single- or double-quotes, should be given as value. This may be: | ||
+ | * A JavaScript function. Do not use <code>function() {....}</code> syntax. | ||
+ | * A Jmol script (preceded by the token <code>jmolscript:</code> ) | ||
+ | |||
+ | :(In the former method, Jmol.js, these could be set using either <code>jmolSetParameter()</code> or <code>jmolSetCallback()</code> functions.) | ||
+ | |||
+ | Example 1: | ||
+ | Info.pickCallback = "myPick"; | ||
+ | function myPick() { | ||
+ | alert('you clicked on atom with index=' + arguments[2]); | ||
+ | } | ||
+ | |||
+ | In each case, several parameters are returned and passed to the function (its <code>arguments</code> array): | ||
+ | # the first parameter returned (argument zero) is always the Jmol Object name; | ||
+ | # the 2nd and later parameters hold the information; not all are used by all callbacks (see below). | ||
+ | Note that the array of arguments is zero-based in JavaScript but 1-based in JmolScript. | ||
+ | |||
+ | A [http://biomodel.uah.es/Jmol/callbacks/ test page] where the output of some of the callbacks may be examined is available. | ||
+ | |||
+ | |||
+ | As an alternative, the callbacks may also be defined from a script using the [{{ScriptingDoc}}#setcallback<code>set</code>] command. | ||
+ | In this case, the parameters will be available in an <code>_arguments</code> array and an <code>_argumentCount</code> variable is also available. <code>_args()</code> and <code>_args(n)</code> are synonyms for <code>_arguments</code> and <code>_arguments[n]</code> to be used in functions, scripts, and callbacks. | ||
+ | |||
+ | Example 2: | ||
+ | Info.pickCallback = "jmolscript:print 'atom is ' + _arguments[2]"; | ||
+ | |||
+ | |||
+ | In the descriptions below, it is assumed that we are using a JavaScript function for the callback. | ||
+ | |||
+ | === animFrameCallback === | ||
+ | Called: when a change in frame/model happens. When a file is loaded, the function is called once o twice before the loading starts (returning frame index zero) and once more after it finishes (returning frame index one). | ||
+ | : arguments[1]: frame index (zero-based). | ||
+ | : arguments[2]: file number (1-based). | ||
+ | : arguments[3]: frame number within the file (1-based). | ||
+ | : arguments[4-5]: first and last frame numbers within the current animation range (1-based added to one million). | ||
+ | : arguments[6]: animation state: 0 (stopped) or 1 (animating) | ||
+ | : arguments[7]: the value of <code>animation direction</code>: +1 or -1 | ||
+ | : arguments[8]: the current direction the animation is going: 1 (forward) or -1 (reverse) | ||
+ | : arguments[9]: the name or title of the model, taken from the file contents (same that is displayed at the top of the window in the Jmol application) | ||
+ | : arguments[10]: when a morph has been calculated, a floating point number corresponding to some intermediate value between two frames | ||
+ | |||
+ | === appletReadyCallback === | ||
+ | Please, do not use this. Instead, use the <code>readyFunction</code> parameter described above. | ||
+ | <!--Called: when creation of the Jmol Object in the page has finished. | ||
+ | : arguments[1]: the Jmol Object name, followed by two underscores, the unique ID of that particular object (a 16-digit random number) and two underscores. | ||
+ | : arguments[2]: a boolean value (true/false, presumably indicating successful creation of the Jmol Object). | ||
+ | : arguments[3]: a JavaScript object of the Jmol type. | ||
+ | ''See also'' the <code>readyFunction</code> parameter above, as an alternative solution. | ||
+ | --> | ||
+ | |||
+ | === atomMovedCallback === | ||
+ | Called: when the position of one or more atoms is modified; this usually requires <code>set picking dragatom</code> + mouse action, or <code>rotateSelected</code> or similar command. | ||
+ | : arguments[1]: the affected atom set (as a Jmol atomset object - possibly in JSON construction; this will need parsing) | ||
+ | |||
+ | === dragDropCallback === | ||
+ | Called: when a file is dropped into the Jmol panel | ||
+ | : arguments[1]: a number ''(this needs explanation)'' | ||
+ | : arguments[2]: x (coordinate within the Jmol panel where the pointer was released at dropping) | ||
+ | : arguments[3]: y (coordinate) | ||
+ | : arguments[4]: the file name (preceded by "cache://DROP_") | ||
+ | : arguments[5]: an array (with a single null) | ||
+ | In addition (Jmol version 14.32.58 or later), when a file is dropped this global user variables will be set: | ||
+ | * <code>dropFileType</code> which can be read and also changed within the callback handler function | ||
+ | * <code>dropFileName</code> (preceded by "cache://DROP_") | ||
+ | * <code>doDrop</code>, initially TRUE; if set to FALSE within the callback handler function, it will prevent the file from being loaded. | ||
+ | |||
+ | === echoCallback === | ||
+ | Called: when Jmol produces some output from an <code>echo</code> command, or a <code>show</code> command (also if launched from the popup menu), or when a model is loaded (echoes the file header)... | ||
+ | : arguments[1]: a text string with the output; it may include several lines | ||
+ | |||
+ | === evalCallback === | ||
+ | ''(This is rather specialized and you will normally not need it)''. | ||
+ | |||
+ | If the Jmol [{{ScriptingDoc}}#javascript<code>javascript</code>] command is used (and is not forbidden by a setting of <code>Info.allowJavaScript = false</code>), this callback sends the JavaScript back to the web page for evaluation rather than initiating that evaluation within Jmol. For more details, see [{{ScriptingDoc}}#setcallback<code>set EvalCallback</code>] | ||
− | == | + | === hoverCallback === |
+ | Called: when the mouse or pointer is positioned (hovers) over an atom. | ||
+ | : arguments[1]: a text string with the current hover label (either the default or user-defined through <code>set hoverLabel</code>), followed by X, Y, Z coordinates of the atom. | ||
+ | :: Example for a MOL file: <code>O14 #14 -0.438 -2.4279 -0.0068</code> | ||
+ | :: Example for a PDB file: <code>[ASN]46:A.ND2 #326 13.407 3.298 15.015</code> | ||
+ | : arguments[2]: the atom index (zero-based) | ||
− | + | === loadStructCallback === | |
+ | Called: upon file loading (successful or not). | ||
+ | : arguments[1]: the URL of the loaded file (full path+filename). | ||
+ | : arguments[2]: the filename of the loaded file (without the path). | ||
+ | : arguments[3]: the internal title of the model in the loaded file. | ||
+ | : arguments[4]: any error messages generated. | ||
+ | : arguments[5]: a numeric code: 3 when the file loaded successfully, 0 when the model was zapped, -1 when the loading failed. | ||
+ | : arguments[6]: a text string with the frame number prior to loading the current model, in file.model syntax (for example, "3.1" or "1.1 - 3.31" if a whole range of models was framed). | ||
+ | : arguments[7]: a text string with the last frame number after loading the current model, in file.model syntax. | ||
+ | Note: When multiple files are loaded with the same load command, only data for the last-loaded file is returned | ||
− | + | === measureCallback === | |
+ | Called: after a measurement is started (double click on an atom) the callback runs while the measurement is in process: hovering over another atom, single-clicking or double-clicking on another atom | ||
+ | : arguments[1]: a text string with data from the atoms involved in the measurement (from one up to 4); for each one of them, atom name (space) atom number. Starts and ends with square brackets and has a comma as delimiter. For example: | ||
+ | :: <code>[H18 #18, O4 #4]</code> for a distance (MOL file) | ||
+ | :: <code>[H18 #18, O4 #4, H16 #16]</code> for an angle (MOL file) | ||
+ | :: <code>[[ILE]7:A.CD1 #47, [ASN]46:A.ND2 #326]</code> for a distance (PDB file) | ||
+ | :: <code>[[ILE]34:A.CD1 #245, [ILE]34:A.CG1 #243, [ILE]34:A.CB #242]</code> for an angle (PDB file) | ||
− | + | : arguments[2]: during the measurement, the number of atoms involved so far; when measurement is finished, the index (zero-based) of this measurement in the list of measurements. | |
− | : | + | : arguments[3]: during the measurement, the text string <code>measurePending</code>; when measurement is finished, <code>measureCompleted</code> |
− | + | : arguments[4]: the value of the measurement --angstroms or degrees--, either provisional or definitive. | |
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | : | ||
− | |||
− | |||
− | |||
− | + | === messageCallback === | |
+ | Called: every time Jmol issues some message (which will go to the scripting console). | ||
− | + | You will need to parse the arguments output by this callback, searching for whatever text you are interested on detecting. | |
− | + | === minimizationCallback === | |
+ | Called: during a 3D structure optimization (energy minimization) initiated by the <code>minimize</code> command or the pop-up menu entry under <code>calculation</code>, at every reporting stage (usually every 10 steps). Also, extra calls at the beginning and end of the process. | ||
+ | : arguments[1]: a text string declaring the status: either 'starting', 'running' or 'done'. | ||
+ | : arguments[2]: a one-element array with sequential number of the reporting stage (0 for starting, repeat the last when done). | ||
+ | : arguments[3]: a one-element array with the current value of energy (E). | ||
+ | : arguments[4]: a one-element array with the current increment/decrement of energy between stages (dE). | ||
+ | : arguments[5]: a text string indicating the kind of force field used (UFF or MMFF). | ||
− | : | + | === pickCallback === |
+ | Called: when the user clicks an atom -- or a bond (see below). | ||
− | + | Note that for this to work, <code>set atomPicking</code> must be set true (it is by default). | |
− | |||
− | |||
− | |||
− | |||
− | + | Also, note that this description applies to the standard <code>set picking ident</code>; if another variety of picking has been issued, the output of the callback will be different. | |
− | |||
− | |||
− | |||
− | * ''' | + | * '''Clicking on an atom:''' |
− | + | : arguments[1]: a text string with atom id, atom number, and xyz coordinates in the form: | |
− | + | :: (MOL file) <code>C6 #6 -0.307 -1.684 -0.717</code> | |
− | + | :: (PDB file) <code>[TYR]29:A.CE2 #210 -0.801 7.705 5.156</code> | |
− | + | : arguments[2]: an object with the single property <code>valueOf()</code>, whose result is the atom index (zero-based). Alternatively, the index as a JavaScript string may be obtained using <code>"" + arguments[2]</code>. | |
− | + | : arguments[3]: a null or empty object. | |
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | : | ||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | :: <code>C6 #6 -0. | ||
− | : | ||
− | : | ||
+ | * '''Clicking on a bond:''' | ||
:If <code>set bondPicking true</code> has been issued, bonds will become clickable and also invoke the callback function, but the return from the function will be different: | :If <code>set bondPicking true</code> has been issued, bonds will become clickable and also invoke the callback function, but the return from the function will be different: | ||
− | : | + | : arguments[1]: a text string in the form: |
− | :: <code>["bond","3 1 C2 #2 -- C4 #4 1. | + | :: (MOL file) <code>["bond","3 1 C2 #2 -- C4 #4 1.361",-0.0,0.906,-0.306]</code> |
− | :: meaning | + | :: meaning bond number (indexed by order, 1-based), bond type (single, double...), 1st atom id, 1st atom number, 2nd atom id, 2nd atom number, bond length (distance), and xyz coordinates of the bond's midpoint. |
− | : | + | :: (PDB file) <code>["bond","329 1 [ASN]46:A.N #319 -- [ALA]45:A.C #316 1.32",14.57,6.52,14.01]</code> |
− | : | + | : arguments[2]: ?. |
− | :: <code> | + | : arguments[3]: an object with these properties: |
− | + | ::: <code>model</code> e.g. 1.1 | |
− | + | ::: <code>index</code> e.g. 328 | |
− | + | ::: <code>type</code> 'bond' | |
− | + | ::: <code>info</code> a text string* with (space-delimited): bond number, bond type, 1st atom id, 1st atom number, --, 2nd atom id, 2nd atom number, bond length (*same as middle element of arguments[1] displayed above) | |
+ | ::: <code>pt</code> xyz coordinates of the bond's midpoint, e.g. {14.57, 6.52, 14.01} | ||
+ | ::: <code>modelIndex</code> (e.g. 0 ) | ||
+ | |||
+ | === resizeCallback === | ||
+ | Called: when the JSmol object div size is changed. If the resizing is done with <code>Jmol.resizeApplet()</code>, the callback is immediate. When other methods are used for resizing (e.g. dragging the corner, changing CSS via Javascript...), this callback may be delayed until the JSmol panel is refreshed, e.g. by clicking on it. | ||
+ | : arguments[1]: number of horizontal pixels (width) after the size change. | ||
+ | : arguments[2]: number of vertical pixels (height). | ||
+ | |||
+ | === scriptCallback === | ||
+ | Called: during execution of a Jmol script. | ||
+ | |||
+ | This will receive messages indicating the status of script execution. If it is not set, those messages go to the messageCallback instead. | ||
+ | |||
+ | === structureModifiedCallback === | ||
+ | Called: each time the structure is modified (e.g. by the user in the ModelKit mode, or via some commands). | ||
+ | |||
+ | See [{{ScriptingDoc}}#setcallback<code>set StructureModifiedCallback</code>]. | ||
+ | |||
+ | === syncCallback === | ||
+ | Called: when the Jmol object issues/receives (?) a synchronization message to/from (?) another Jmol object (see the [{{ScriptingDoc}}#sync <code>sync</code> command]). | ||
+ | : Within this callback function the message is intercepted and may be accepted, modified or cancelled before being transmitted to the Jmol objects affected by synchronization. | ||
+ | |||
+ | == Lightweight version == | ||
+ | |||
+ | A special alternative version of JSmol may be invoked, with a very small file size and high responsiveness, particularly adequate for a quick startup and for systems with limited resources and power, like phones. | ||
+ | It accepts a subset of the parameters described here, plus some additional, unique parameters. | ||
+ | See [[Lightweight JSmol]] for details. | ||
+ | |||
== Misc. == | == Misc. == | ||
Line 207: | Line 338: | ||
* '''progresscolor''' | * '''progresscolor''' | ||
:These five values generally should not be adjusted. | :These five values generally should not be adjusted. | ||
+ | |||
+ | The following are deprecated since they only applied to the Java modality (Jmol Java applet): | ||
+ | |||
+ | * '''jarFile''' <code>"JmolApplet0.jar"</code> | ||
+ | :''The file to be used, usually either <code>JmolApplet0.jar</code> (for faster incremental loading) or <code>JmolApplet.jar</code> (a single 2.5+ MB download), or the signed versions <code>JmolAppletSigned0.jar</code> and <code>JmolAppletSigned.jar</code>. Be careful that the setting here should match that of '''isSigned'''. | ||
+ | * '''isSigned''' <code>false</code> | ||
+ | :Make sure to change this to <code>true</code> if the file indicated for '''jarFile''' is the signed applet. | ||
+ | * '''jarPath''' <code>"java"</code> | ||
+ | :''The path to the applet files. Note that if the unsigned applet is used and the page is tested locally, then all model files must be in or under the folder indicated by this value, to satisfy Java security policy. | ||
+ | * '''memoryLimit''' <code>512</code> | ||
+ | :The maximum amount of memory allowed for the Java applet, in MB. | ||
+ | * '''usecommandthread''' <code>false</code> | ||
+ | :The signed Jmol Java applet generally runs commands by passing them to a command thread that is established when the applet is created, while the unsigned applet does not. You can change this behavior if you are observing Java security issues. Otherwise, it should not be adjusted. |
Latest revision as of 09:36, 1 August 2023
Contents
- 1 Documentation of parameters of the Info variable
- 1.1 Jmol object definition
- 1.2 Startup period
- 1.3 Model loading
- 1.4 Customization or extras
- 1.5 Callbacks
- 1.5.1 animFrameCallback
- 1.5.2 appletReadyCallback
- 1.5.3 atomMovedCallback
- 1.5.4 dragDropCallback
- 1.5.5 echoCallback
- 1.5.6 evalCallback
- 1.5.7 hoverCallback
- 1.5.8 loadStructCallback
- 1.5.9 measureCallback
- 1.5.10 messageCallback
- 1.5.11 minimizationCallback
- 1.5.12 pickCallback
- 1.5.13 resizeCallback
- 1.5.14 scriptCallback
- 1.5.15 structureModifiedCallback
- 1.5.16 syncCallback
- 1.6 Lightweight version
- 1.7 Misc.
Documentation of parameters of the Info variable
This page explains the parameters of the Info
variable, an essential part of the Jmol JavaScript Object and hence of JSmol.
Note that, although this is usually designated as Info
in the documentation, it is a regular JavaScript variable that you can name as you wish.
Info is an associative array (a set of key/value pairs) indicating all the desired characteristics of the Jmol object (Jmol applet or JSmol).
Values may be defined
- either during initialization of the
Info
variable:
var Info = { color: "#E8F4FF", height: 400, width: 400 };
- or separately:
Info.color = "#E8F4FF";
An alphabetic listing of all parameters, along with a comparative view of which modalities of Jmol Object they may be applied to, may be checked in Jmol JavaScript_Object/InfoTable.
Jmol object definition
(The values shown in the listing below are the defaults)
Dimensions
- height
300
- The size of the Jmol object in pixels or expressed as percent of its container height as a string in quotes: "100%".
- width
300
- The width of the Jmol object in pixels or expressed as percent of its container width as a string in quotes: "100%".
Note that for a percent to work, all surrounding HTML elements must explicitly implement the CSS attributes style=height:...
and style=width:...
. That includes setting height to 100% for body
and html
.
Note also that, despite that, non-Java JSmol uses the canvas
element, which will not resize correctly.
Background color
- color
"white"
- The background color of the Jmol object, as a quoted text string in any JmolScript-supported format: color name, decimal triplet
[r,g,b]
or hexadecimal[xRRGGBB]
, or in html-style format:#RRGGBB
. Note that default is now white, in contrast to black in the classic Jmol.js method.
Files and paths
- j2sPath
"j2s"
- (HTML5 modality) The path to j2s including its own name; the contents of this folder are essential for JSmol to work.
- serverURL
"http://your.server.here/jsmol.php"
- The URL of jsmol.php to be used for getting file data into non-Java modalities. For better performance and to avoid cross-domain issues, you should set this to a url in the same server your pages are. In the scheme of the standard JSmol distribution, that will be
"php/jsmol.php"
. - If you cannot have PHP working in your server, you may use
"https://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php"
, since that is a public site accessible to cross-domain AJAX calls. - Setting this properly is essential, among other situations,
- when loading into JSmol models in binary files, at least in some browsers
- for cross-domain loading JSmol components (
.js
files), i.e. whenInfo.j2sPath
points to a server different to the one that hosts the page
Modality
- use
"HTML5"
This string determines the mode to be used (either Java applet or a surrogates).- The default setting is
HTML5
and indicates to use JSmol in html5-only mode. - The value
WebGL
will force the WebGL modality (combined with html5). Note that the WebGL version of JSmol does not implement the full set of functionalities of Jmol. - The value
Java
forces use of the Jmol Applet (and it may display a message if Java is not enabled). Note that Java applets are no longer supported by the majority of web browsers.
- The default setting is
Startup period
(The values shown in the listing below are the defaults)
- appletLoadingImage
j2sPath + "/img/JSmol_spinner.gif"
- Set the path and filename of an image that is displayed in place of the Jmol object while this is loading.
- It may be disabled using
Info.appletLoadingImage = "none"
- coverImage
""
- Set the path and filename of an image that will be displayed on top of the Jmol object (usually as an initial replacement or during loading, see
deferApplet
anddeferUncover
parameters below).
- makeLiveImage
j2sPath + "/img/play_make_live.jpg"
- Set the path and filename of a small image (icon) that is displayed over the bottom-left corner of the cover image to give a visual hint that clicking will uncover the model. The default icon, , is included in the JSmol distribution; you may specify your own using this parameter.
- coverTitle
""
- Set a tip that is displayed before model starts to load.
- coverScript
""
- Set a Jmol command or script that will be executed upon clicking the cover image.
- deferApplet
false
- If set
true
, the model will not be loaded until the user clicks on the cover image (seecoverImage
parameter above).
- deferUncover
false
- If set
true
, the cover image will remain until command execution is complete.
- disableInitialConsole
true
- If set
false
, displays messages ('console') in the Jmol panel while the Jmol object is being built initially. Note: the default used to befalse
but was changed since version 14.5.2_2016.02.14, given the implementation ofappletLoadingImage
- disableJ2SLoadMonitor
false
- If set
true
, avoids the display of messages in a single line, colored, at bottom-left of the page while code loads (both initially and every time a new module is requested by a running script).
- readyFunction
null
- The name (without quotes) of a JavaScript function to call when the Jmol object has been created and is ready to receive commands (and also called when the object is destroyed e.g. when the page is closed).
- For example, with
readyFunction: jmolIsReady
any of the following JavaScript function definitions could be used:function jmolIsReady() { alert('Welcome to Jmol!'); }
jmolIsReady = function() { alert('Welcome to Jmol!'); }
jmolIsReady = function(theJmol) { document.title = theJmol._id + " is ready"; }
- Note: The JavaScript function will receive as argument a pointer to the particular Jmol object that invoked it (as exemplified in the third example above).
Model loading
(The values shown in the listing below are the defaults)
- src
""
- A filename to load once the Jmol object has finished loading. It may be a model in a supported format, or a script file.
- script
""
- A script to run when the Jmol object has finished loading. Note that indicating a script here is not necessary; with Jmol-JSO, unlike with Jmol.js, you can start making script calls to Jmol as soon as the Jmol wrapper object has been created in JavaScript; there is no need to wait for Jmol object initialization to have completed.
- Note that using
script
will cancel whateversrc
specifies (but it is easy to include aload
command as part of the script)
- defaultModel
""
- The name or id of a model to be retrieved from a public database, and displayed when the Jmol object has finished loading.
- Examples:
defaultModel: "=1crn"
gets it from RCSB PDBdefaultModel: "$caffeine"
gets it from NCI CACTUSdefaultModel: ":caffeine"
gets it from PubChemdefaultModel: "caffeine"
gets it from NCI CACTUS
Customization or extras
(The values shown in the listing below are the defaults)
- addSelectionOptions
false
- Set this value to
true
if you want to display, below the Jmol object, a menu with options for loading structures from public databases.
- allowJavaScript
true
- Set this value to
false
if you want to prevent any JavaScript command being run from JSmol (using the javascript command or EvalCallback). Note: this feature is offered because allowing any arbitrary javascript may be considered a security risk in some environments.
- console
"***_infodiv"
- The ID in html of the container or div that will receive output from JSmol. Default value is the JSmol Object name/id (represented here by ***) followed by
_infodiv
, and it is contained in the info panel that may be displayed alternatively to the JSmol viewer.
- debug
false
- Set this value to
true
if you are having problems getting your page to show the Jmol object, buttons or ther controls.
- language "2-letter or 2+2-letter code"
- This setting can be used to specify a language to be used in the Jmol Object interface (mainly the pop-up menu). The existing choices may be checked in the pop-up menu. If not specified, the default language is automatically detected from the system settings of the user's browser.
- Examples:
language: "es"
for Spanishlanguage: "pt_BR"
for Brazilian Portuguese
- menuFile "fileName"
- Loads a custom pop-up menu.
- zIndexBase
9000
- Defines the z-index property in CSS of the Jmol Object and its associated div's. This is set by default to a very high value, so the object will be laid on top of any other page elements, but it may be useful to change it when you are integrating Jmol with other components. In addition to setting for the particular applet, it also sets the default for all other applets on the page, in case it is not defined for those applets.
- z
{9000, 9001, 9002, 9003, 9004, 9005, 9006, 9007, 99008, 100008, 109007}
- Defines, in a more fine-grained way, the z-index property in CSS of all div's forming the Jmol Object.
- It is an associative array that includes (some of these are more relevant to JmolSpecViewer):
Info.z = { header: , rear: , main: , image: , front: , fileOpener: , coverImage: , dialog: , menu: , console: , monitorZIndex: }
- When just
zIndexBase
is provided, it will set all components ofz
in this way:
header: zIndexBase, rear: zIndexBase + 1, main: zIndexBase + 2, image: zIndexBase + 3, front: zIndexBase + 4, fileOpener: zIndexBase + 5, coverImage: zIndexBase + 6, dialog: zIndexBase + 7, menu: zIndexBase + 90000, console: zIndexBase + 91000, monitorZIndex: zIndexBase + 99999
Callbacks
These callbacks, given in the Info variable, allow the page designer to get information about what is happening within the Jmol object. The name of a function, wrapped in single- or double-quotes, should be given as value. This may be:
- A JavaScript function. Do not use
function() {....}
syntax. - A Jmol script (preceded by the token
jmolscript:
)
- (In the former method, Jmol.js, these could be set using either
jmolSetParameter()
orjmolSetCallback()
functions.)
Example 1:
Info.pickCallback = "myPick"; function myPick() { alert('you clicked on atom with index=' + arguments[2]); }
In each case, several parameters are returned and passed to the function (its arguments
array):
- the first parameter returned (argument zero) is always the Jmol Object name;
- the 2nd and later parameters hold the information; not all are used by all callbacks (see below).
Note that the array of arguments is zero-based in JavaScript but 1-based in JmolScript.
A test page where the output of some of the callbacks may be examined is available.
As an alternative, the callbacks may also be defined from a script using the set
command.
In this case, the parameters will be available in an _arguments
array and an _argumentCount
variable is also available. _args()
and _args(n)
are synonyms for _arguments
and _arguments[n]
to be used in functions, scripts, and callbacks.
Example 2:
Info.pickCallback = "jmolscript:print 'atom is ' + _arguments[2]";
In the descriptions below, it is assumed that we are using a JavaScript function for the callback.
animFrameCallback
Called: when a change in frame/model happens. When a file is loaded, the function is called once o twice before the loading starts (returning frame index zero) and once more after it finishes (returning frame index one).
- arguments[1]: frame index (zero-based).
- arguments[2]: file number (1-based).
- arguments[3]: frame number within the file (1-based).
- arguments[4-5]: first and last frame numbers within the current animation range (1-based added to one million).
- arguments[6]: animation state: 0 (stopped) or 1 (animating)
- arguments[7]: the value of
animation direction
: +1 or -1 - arguments[8]: the current direction the animation is going: 1 (forward) or -1 (reverse)
- arguments[9]: the name or title of the model, taken from the file contents (same that is displayed at the top of the window in the Jmol application)
- arguments[10]: when a morph has been calculated, a floating point number corresponding to some intermediate value between two frames
appletReadyCallback
Please, do not use this. Instead, use the readyFunction
parameter described above.
atomMovedCallback
Called: when the position of one or more atoms is modified; this usually requires set picking dragatom
+ mouse action, or rotateSelected
or similar command.
- arguments[1]: the affected atom set (as a Jmol atomset object - possibly in JSON construction; this will need parsing)
dragDropCallback
Called: when a file is dropped into the Jmol panel
- arguments[1]: a number (this needs explanation)
- arguments[2]: x (coordinate within the Jmol panel where the pointer was released at dropping)
- arguments[3]: y (coordinate)
- arguments[4]: the file name (preceded by "cache://DROP_")
- arguments[5]: an array (with a single null)
In addition (Jmol version 14.32.58 or later), when a file is dropped this global user variables will be set:
dropFileType
which can be read and also changed within the callback handler functiondropFileName
(preceded by "cache://DROP_")doDrop
, initially TRUE; if set to FALSE within the callback handler function, it will prevent the file from being loaded.
echoCallback
Called: when Jmol produces some output from an echo
command, or a show
command (also if launched from the popup menu), or when a model is loaded (echoes the file header)...
- arguments[1]: a text string with the output; it may include several lines
evalCallback
(This is rather specialized and you will normally not need it).
If the Jmol javascript
command is used (and is not forbidden by a setting of Info.allowJavaScript = false
), this callback sends the JavaScript back to the web page for evaluation rather than initiating that evaluation within Jmol. For more details, see set EvalCallback
hoverCallback
Called: when the mouse or pointer is positioned (hovers) over an atom.
- arguments[1]: a text string with the current hover label (either the default or user-defined through
set hoverLabel
), followed by X, Y, Z coordinates of the atom.- Example for a MOL file:
O14 #14 -0.438 -2.4279 -0.0068
- Example for a PDB file:
[ASN]46:A.ND2 #326 13.407 3.298 15.015
- Example for a MOL file:
- arguments[2]: the atom index (zero-based)
loadStructCallback
Called: upon file loading (successful or not).
- arguments[1]: the URL of the loaded file (full path+filename).
- arguments[2]: the filename of the loaded file (without the path).
- arguments[3]: the internal title of the model in the loaded file.
- arguments[4]: any error messages generated.
- arguments[5]: a numeric code: 3 when the file loaded successfully, 0 when the model was zapped, -1 when the loading failed.
- arguments[6]: a text string with the frame number prior to loading the current model, in file.model syntax (for example, "3.1" or "1.1 - 3.31" if a whole range of models was framed).
- arguments[7]: a text string with the last frame number after loading the current model, in file.model syntax.
Note: When multiple files are loaded with the same load command, only data for the last-loaded file is returned
measureCallback
Called: after a measurement is started (double click on an atom) the callback runs while the measurement is in process: hovering over another atom, single-clicking or double-clicking on another atom
- arguments[1]: a text string with data from the atoms involved in the measurement (from one up to 4); for each one of them, atom name (space) atom number. Starts and ends with square brackets and has a comma as delimiter. For example:
[H18 #18, O4 #4]
for a distance (MOL file)[H18 #18, O4 #4, H16 #16]
for an angle (MOL file)[[ILE]7:A.CD1 #47, [ASN]46:A.ND2 #326]
for a distance (PDB file)[[ILE]34:A.CD1 #245, [ILE]34:A.CG1 #243, [ILE]34:A.CB #242]
for an angle (PDB file)
- arguments[2]: during the measurement, the number of atoms involved so far; when measurement is finished, the index (zero-based) of this measurement in the list of measurements.
- arguments[3]: during the measurement, the text string
measurePending
; when measurement is finished,measureCompleted
- arguments[4]: the value of the measurement --angstroms or degrees--, either provisional or definitive.
messageCallback
Called: every time Jmol issues some message (which will go to the scripting console).
You will need to parse the arguments output by this callback, searching for whatever text you are interested on detecting.
minimizationCallback
Called: during a 3D structure optimization (energy minimization) initiated by the minimize
command or the pop-up menu entry under calculation
, at every reporting stage (usually every 10 steps). Also, extra calls at the beginning and end of the process.
- arguments[1]: a text string declaring the status: either 'starting', 'running' or 'done'.
- arguments[2]: a one-element array with sequential number of the reporting stage (0 for starting, repeat the last when done).
- arguments[3]: a one-element array with the current value of energy (E).
- arguments[4]: a one-element array with the current increment/decrement of energy between stages (dE).
- arguments[5]: a text string indicating the kind of force field used (UFF or MMFF).
pickCallback
Called: when the user clicks an atom -- or a bond (see below).
Note that for this to work, set atomPicking
must be set true (it is by default).
Also, note that this description applies to the standard set picking ident
; if another variety of picking has been issued, the output of the callback will be different.
- Clicking on an atom:
- arguments[1]: a text string with atom id, atom number, and xyz coordinates in the form:
- (MOL file)
C6 #6 -0.307 -1.684 -0.717
- (PDB file)
[TYR]29:A.CE2 #210 -0.801 7.705 5.156
- (MOL file)
- arguments[2]: an object with the single property
valueOf()
, whose result is the atom index (zero-based). Alternatively, the index as a JavaScript string may be obtained using"" + arguments[2]
. - arguments[3]: a null or empty object.
- Clicking on a bond:
- If
set bondPicking true
has been issued, bonds will become clickable and also invoke the callback function, but the return from the function will be different: - arguments[1]: a text string in the form:
- (MOL file)
["bond","3 1 C2 #2 -- C4 #4 1.361",-0.0,0.906,-0.306]
- meaning bond number (indexed by order, 1-based), bond type (single, double...), 1st atom id, 1st atom number, 2nd atom id, 2nd atom number, bond length (distance), and xyz coordinates of the bond's midpoint.
- (PDB file)
["bond","329 1 [ASN]46:A.N #319 -- [ALA]45:A.C #316 1.32",14.57,6.52,14.01]
- (MOL file)
- arguments[2]: ?.
- arguments[3]: an object with these properties:
model
e.g. 1.1index
e.g. 328type
'bond'info
a text string* with (space-delimited): bond number, bond type, 1st atom id, 1st atom number, --, 2nd atom id, 2nd atom number, bond length (*same as middle element of arguments[1] displayed above)pt
xyz coordinates of the bond's midpoint, e.g. {14.57, 6.52, 14.01}modelIndex
(e.g. 0 )
resizeCallback
Called: when the JSmol object div size is changed. If the resizing is done with Jmol.resizeApplet()
, the callback is immediate. When other methods are used for resizing (e.g. dragging the corner, changing CSS via Javascript...), this callback may be delayed until the JSmol panel is refreshed, e.g. by clicking on it.
- arguments[1]: number of horizontal pixels (width) after the size change.
- arguments[2]: number of vertical pixels (height).
scriptCallback
Called: during execution of a Jmol script.
This will receive messages indicating the status of script execution. If it is not set, those messages go to the messageCallback instead.
structureModifiedCallback
Called: each time the structure is modified (e.g. by the user in the ModelKit mode, or via some commands).
See set StructureModifiedCallback
.
syncCallback
Called: when the Jmol object issues/receives (?) a synchronization message to/from (?) another Jmol object (see the sync
command).
- Within this callback function the message is intercepted and may be accepted, modified or cancelled before being transmitted to the Jmol objects affected by synchronization.
Lightweight version
A special alternative version of JSmol may be invoked, with a very small file size and high responsiveness, particularly adequate for a quick startup and for systems with limited resources and power, like phones. It accepts a subset of the parameters described here, plus some additional, unique parameters. See Lightweight JSmol for details.
Misc.
- boxbgcolor
- boxfgcolor
- boxmessage
- progressbar
- progresscolor
- These five values generally should not be adjusted.
The following are deprecated since they only applied to the Java modality (Jmol Java applet):
- jarFile
"JmolApplet0.jar"
- The file to be used, usually either
JmolApplet0.jar
(for faster incremental loading) orJmolApplet.jar
(a single 2.5+ MB download), or the signed versionsJmolAppletSigned0.jar
andJmolAppletSigned.jar
. Be careful that the setting here should match that of isSigned.
- isSigned
false
- Make sure to change this to
true
if the file indicated for jarFile is the signed applet.
- jarPath
"java"
- The path to the applet files. Note that if the unsigned applet is used and the page is tested locally, then all model files must be in or under the folder indicated by this value, to satisfy Java security policy.
- memoryLimit
512
- The maximum amount of memory allowed for the Java applet, in MB.
- usecommandthread
false
- The signed Jmol Java applet generally runs commands by passing them to a command thread that is established when the applet is created, while the unsigned applet does not. You can change this behavior if you are observing Java security issues. Otherwise, it should not be adjusted.