Menu
▾
▴
[Jmol-commits] SF.net SVN: jmol:[17290] trunk/Jmol/appletweb
|
From: <ha...@us...> - 2012-06-12 23:32:05
|
Revision: 17290
http://jmol.svn.sourceforge.net/jmol/?rev=17290&view=rev
Author: hansonr
Date: 2012-06-12 23:31:58 +0000 (Tue, 12 Jun 2012)
Log Message:
-----------
JmolCore upgrade; includes JmolGLmol.js
Modified Paths:
--------------
trunk/Jmol/appletweb/JmolApi.js
trunk/Jmol/appletweb/JmolApplet.jar
trunk/Jmol/appletweb/JmolAppletSigned.jar
trunk/Jmol/appletweb/JmolCD.js
trunk/Jmol/appletweb/JmolCore.js
Added Paths:
-----------
trunk/Jmol/appletweb/JmolGLmol.js
Modified: trunk/Jmol/appletweb/JmolApi.js
===================================================================
--- trunk/Jmol/appletweb/JmolApi.js 2012-06-12 18:54:58 UTC (rev 17289)
+++ trunk/Jmol/appletweb/JmolApi.js 2012-06-12 23:31:58 UTC (rev 17290)
@@ -11,16 +11,16 @@
addSelectionOptions: false,
serverURL: "http://chemapps.stolaf.edu/jmol/jmolcd.php",
defaultModel: "",
+ script: null,
+ src: null,
+ readyFunction: null,
useNoApplet: false,
useJmolOnly: true,
useWebGlIfAvailable: true,
useImageOnly: false,
- isSigned: false,
jarPath: ".",
jarFile: "JmolApplet0.jar",
- readyFunction: null,
- script: null,
- src: null,
+ isSigned: false,
debug: false
};
Modified: trunk/Jmol/appletweb/JmolApplet.jar
===================================================================
(Binary files differ)
Modified: trunk/Jmol/appletweb/JmolAppletSigned.jar
===================================================================
(Binary files differ)
Modified: trunk/Jmol/appletweb/JmolCD.js
===================================================================
--- trunk/Jmol/appletweb/JmolCD.js 2012-06-12 18:54:58 UTC (rev 17289)
+++ trunk/Jmol/appletweb/JmolCD.js 2012-06-12 23:31:58 UTC (rev 17290)
@@ -24,7 +24,7 @@
// overrides the function in JmolCore.js
// ChemDoodle: first try with WebGL unless that doesn't work or we have indicated NOWEBGL
var canvas = null;
- if (Info.useWebGlIfAvailable && ChemDoodle.featureDetection.supports_webgl())
+ if (Info.useWebGlIfAvailable && Jmol.featureDetection.supportsWebGL())
canvas = new Jmol._Canvas3D(id, Info, null, checkOnly);
if (canvas == null)
canvas = new Jmol._Canvas(id, Info, null, checkOnly);
@@ -35,7 +35,7 @@
Jmol._Canvas3D = function(id, Info, caption, checkOnly){
this._is2D = false;
- this._jmolType = "Jmol._Canvas3D";
+ this._jmolType = "Jmol._Canvas3D (ChemDoodle)";
if (checkOnly)
return this;
this._dataMultiplier=1;
@@ -45,7 +45,7 @@
Jmol._Canvas = function(id, Info, caption, checkOnly){
this._is2D = true;
- this._jmolType = "Jmol._Canvas";
+ this._jmolType = "Jmol._Canvas (ChemDoodle)";
if (checkOnly)
return this;
this._dataMultiplier=20;
@@ -69,10 +69,6 @@
Jmol._documentWrite(t);
this.create(id, Info.width, Info.height);
this._setDefaults();
- if (this.defaultModel)
- this._search(this._defaultModel);
- if (this._readyScript)
- this._script(this._readyScript);
t = "";
} else {
t += '<script type="text/javascript">'
@@ -133,15 +129,8 @@
}
proto._searchDatabase = function(query, database, script){
- this._showInfo(false);
- if (query.indexOf("?") >= 0) {
- Jmol._getInfoFromDatabase(this, database, query.split("?")[0]);
+ if (Jmol._searchDatabase(this, query, database, script))
return;
- }
- if (Jmol.db._DirectDatabaseCalls[database]) {
- this._loadFile(database + query);
- return;
- }
this.emptyMessage="Searching...";
this.molecule=null;
this.repaint();
@@ -163,7 +152,7 @@
this.emptyMessage="Retrieving data...";
this.molecule=null;
this.repaint();
- this._jmolFileType = Jmol._cdGetFileType(fileName);
+ this._jmolFileType = Jmol._getFileType(fileName);
var cdcanvas = this;
Jmol._loadFileData(this, fileName, function(data){Jmol._cdProcessFileData(cdcanvas, data)});
}
@@ -190,20 +179,9 @@
this.specs.bonds_clearOverlaps_2D = true;
}
- Jmol._cdGetFileType = function(name) {
- var database = name.substring(0, 1);
- if (database == "$" || database == ":")
- return "MOL";
- if (database == "=")
- return (name.substring(1,2) == "=" ? "LCIF" : "PDB");
- // just the extension, which must be PDB, XYZ..., CIF, or MOL
- name = name.split('.').pop().toUpperCase();
- return name.substring(0, Math.min(name.length, 3));
- }
-
Jmol._cdProcessFileData = function(cdcanvas, data) {
var factor = cdcanvas._dataMultiplier;
- data = Jmol._cdCleanFileData(data);
+ data = Jmol._cleanFileData(data);
var molecule;
switch(cdcanvas._jmolFileType) {
case "PDB":
@@ -232,16 +210,6 @@
cdcanvas.loadMolecule(Jmol._cdScaleMolecule(molecule, factor));
}
- Jmol._cdCleanFileData = function(data) {
- if (data.indexOf("\r") >= 0 && data.indexOf("\n") >= 0) {
- return data.replace(/\r\n/g,"\n");
- }
- if (data.indexOf("\r") >= 0) {
- return data.replace(/\r/g,"\n");
- }
- return data;
- }
-
Jmol._cdScaleMolecule = function(molecule, multiplier) {
if (multiplier != 0 && multiplier != 1) {
var atoms = molecule.atoms;
Modified: trunk/Jmol/appletweb/JmolCore.js
===================================================================
--- trunk/Jmol/appletweb/JmolCore.js 2012-06-12 18:54:58 UTC (rev 17289)
+++ trunk/Jmol/appletweb/JmolCore.js 2012-06-12 23:31:58 UTC (rev 17290)
@@ -358,6 +358,19 @@
features.supportsXhr2 = function() {return jQuery && jQuery.support.cors}
+ features._webGLtest = 0;
+
+ features.supportsWebGL = function() {
+ if (!Jmol.featureDetection._webGLtest) {
+ var canvas;
+ Jmol.featureDetection._webGLtest = (
+ window.WebGLRenderingContext
+ && ((canvas = document.createElement("canvas")).getContext("webgl")
+ || canvas.getContext("experimental-webgl")) ? 1 : -1);
+ }
+ return (Jmol.featureDetection._webGLtest > 0);
+ };
+
features.compliantBrowser = function() {
var a = !!document.getElementById;
var os = features.os()
@@ -578,4 +591,37 @@
obj._src = Info.src;
}
+ Jmol._cleanFileData = function(data) {
+ if (data.indexOf("\r") >= 0 && data.indexOf("\n") >= 0) {
+ return data.replace(/\r\n/g,"\n");
+ }
+ if (data.indexOf("\r") >= 0) {
+ return data.replace(/\r/g,"\n");
+ }
+ return data;
+ };
+
+ Jmol._getFileType = function(name) {
+ var database = name.substring(0, 1);
+ if (database == "$" || database == ":")
+ return "MOL";
+ if (database == "=")
+ return (name.substring(1,2) == "=" ? "LCIF" : "PDB");
+ // just the extension, which must be PDB, XYZ..., CIF, or MOL
+ name = name.split('.').pop().toUpperCase();
+ return name.substring(0, Math.min(name.length, 3));
+ };
+
+ Jmol._searchDatabase = function(applet, query, database, script) {
+ applet._showInfo(false);
+ if (query.indexOf("?") >= 0) {
+ Jmol._getInfoFromDatabase(applet, database, query.split("?")[0]);
+ return true;
+ }
+ if (Jmol.db._DirectDatabaseCalls[database]) {
+ applet._loadFile(database + query, script);
+ return true;
+ }
+ return false;
+ }
})(Jmol);
\ No newline at end of file
Added: trunk/Jmol/appletweb/JmolGLmol.js
===================================================================
--- trunk/Jmol/appletweb/JmolGLmol.js (rev 0)
+++ trunk/Jmol/appletweb/JmolGLmol.js 2012-06-12 23:31:58 UTC (rev 17290)
@@ -0,0 +1,230 @@
+// JmolGLmol.js -- Jmol GLmol extension author: Bob Hanson, ha...@st... 4/16/2012
+// biochem_fan 6/12/2012
+
+// This library requires
+//
+// json2.js
+// JmolCore.js
+// jQuery.min.js
+// Three49cusom.js
+// GLmol.js
+//
+// prior to JmolGlmol.js
+
+if(typeof(GLmol)=="undefined") GLmol = null;
+
+(function (Jmol) {
+
+ if (!GLmol)
+ return;
+
+ Jmol._getCanvas = function(id, Info, checkOnly) {
+ // overrides the function in JmolCore.js
+ var canvas = null;
+ if (Info.useWebGlIfAvailable && Jmol.featureDetection.supportsWebGL())
+ canvas = new Jmol._Canvas3D(id, Info, null, checkOnly);
+ else
+ return null;
+ if (Jmol._document)
+ canvas._readyCallback(id, id, true, null);
+ return canvas;
+ }
+
+ Jmol._Canvas3D = function(id, Info, caption, checkOnly){
+ this._is2D = false;
+ this._jmolType = "Jmol._Canvas3D (GLmol)";
+ if (checkOnly)
+ return this;
+ this._dataMultiplier=1;
+ this._create(id, Info, caption);
+ return this;
+ };
+
+ var _glSetPrototype = function(proto) {
+ Jmol._setCommonMethods(proto);
+
+ proto._create = function(id, Info, caption) {
+ Jmol._setObject(this, id, Info);
+ var t = Jmol._getWrapper(this, true);
+ //console.log(this);
+ if (Jmol._document) {
+ Jmol._documentWrite(t);
+ this.glmol = new GLmol(id + "_appletdiv", true);
+ this.glmol.defineRepresentation = Jmol._glmol_DefineRep;
+ this.glmol.wrapper = this;
+ this._setDefaults();
+ t = "";
+ } else {
+ t += '<script type="text/javascript">'
+ + id + '.create("'+id+'",'+Info.width+','+Info.height+');'
+ + id + '._setDefaults();'
+ if (Info.defaultModel)
+ t += id + "._search(" + id + "._defaultModel);";
+ if (this._readyScript)
+ t += id + '._script(' + id + '._readyScript);'
+ t += '</script>';
+ }
+ t += Jmol._getWrapper(this, false);
+ if (Info.addSelectionOptions)
+ t += Jmol._getGrabberOptions(this, caption);
+ if (Jmol._debugAlert && !Jmol._document)
+ alert(t);
+ this._code = Jmol._documentWrite(t);
+ };
+
+ proto._canScript = function(script) {return (script.indexOf("#alt") >= 0);};
+
+ proto._script = function(script) {
+ if (!this._canScript(script))
+ return;
+ var Cmd = jQuery.trim(script.split("#alt:")[1]);
+ var pt = Cmd.indexOf(" ");
+ var what = jQuery.trim(Cmd.substring(pt + 1));
+ switch (Cmd.substring(0, pt)) {
+ case "SETTING":
+ switch (what) {
+ case "Ball and Stick": this.hetatmMode = 'ballAndStick2'; break;
+ case "Line": this.hetatmMode = 'line'; break;
+ case "van der Waals Spheres": this.hetatmMode = 'sphere'; break;
+ }
+ this.glmol.rebuildScene();
+ this.glmol.show();
+ return;
+ case "LOAD":
+ if (what.indexOf("??") >= 0) {
+ var db = what.split("??")[0];
+ what = prompt(what.split("??")[1], "");
+ if (!what)
+ return;
+ if (!Jmol.db._DirectDatabaseCalls[what.substring(0,1)])
+ what = db + what;
+ }
+ Jmol.loadFile(this, what);
+ return;
+ }
+ };
+
+ proto._searchDatabase = function(query, database, script){
+ if (Jmol._searchDatabase(this, query, database, script))
+ return;
+ this.emptyMessage="Searching...";
+ var glcanvas = this;
+ Jmol._getRawDataFromServer(
+ database,
+ query,
+ function(data){Jmol._glProcessFileData(glcanvas, data, script)}
+ );
+ };
+
+ proto._show = function(tf) {
+ document.getElementById(this._id + "_appletdiv").style.display = (tf ? "block" : "none");
+ };
+
+ proto._loadFile = function(fileName, script){
+ this._showInfo(false);
+ this._thisJmolModel = "" + Math.random();
+ this.emptyMessage="Retrieving data...";
+ this._jmolFileType = Jmol._getFileType(fileName);
+ var glcanvas = this;
+ Jmol._loadFileData(glcanvas, fileName, function(data){Jmol._glProcessFileData(glcanvas, data, script)});
+ };
+
+ return proto;
+ };
+
+ Jmol._Canvas3D.prototype = _glSetPrototype({});
+
+ Jmol._Canvas3D.prototype._setDefaults = function() {
+ this.backgroundColor = 0x000000;
+ this.hetatmMode = 'ballAndStick2';
+ this.mainchainMode = 'thickRibbon';
+ this.colorMode = 'chainbow';
+ };
+
+ Jmol._glProcessFileData = function(glcanvas, data, script) {
+ glcanvas.glmol.loadMoleculeStr(false, Jmol._cleanFileData(data));
+ script && Jmol.script(glcanvas, script);
+ };
+
+ Jmol._glmol_DefineRep = function() {
+ // "this" is glcanvas.glmol
+ var all = this.getAllAtoms();
+ var allHet = this.getHetatms(all);
+ var hetatm = this.removeSolvents(allHet);
+ this.colorByAtom(all, {});
+ switch (this.wrapper.colorMode) {
+ case 'ss': this.colorByStructure(all, 0xcc00cc, 0x00cccc); break;
+ case 'chain': this.colorByChain(all); break;
+ case 'chainbow': this.colorChainbow(all); break;
+ case 'b': this.colorByBFactor(all); break;
+ case 'polarity': this.colorByPolarity(all, 0xcc0000, 0xcccccc); break;
+ }
+
+ var asu = new THREE.Object3D();
+ switch (this.wrapper.mainchainMode) {
+ case 'ribbon':
+ this.drawCartoon(asu, all, this.wraper.doNotSmoothen);
+ this.drawCartoonNucleicAcid(asu, all);
+ break;
+ case 'thickRibbon':
+ this.drawCartoon(asu, all, this.wrapper.doNotSmoothen, this.thickness);
+ this.drawCartoonNucleicAcid(asu, all, null, this.thickness);
+ break;
+ case 'strand':
+ this.drawStrand(asu, all, null, null, null, null, null, doNotSmoothen);
+ this.drawStrandNucleicAcid(asu, all);
+ break;
+ case 'chain':
+ this.drawMainchainCurve(asu, all, this.curveWidth, 'CA', 1);
+ this.drawMainchainCurve(asu, all, this.curveWidth, 'O3\'', 1);
+ break;
+ case 'tube':
+ this.drawMainchainTube(asu, all, 'CA');
+ this.drawMainchainTube(asu, all, 'O3\'');
+ break;
+ case 'bonds':
+ this.drawBondsAsLine(asu, all, this.lineWidth);
+ break;
+ }
+
+ if (this.wrapper.drawSidechains)
+ this.drawBondsAsLine(this.modelGroup, this.getSidechains(all), this.lineWidth);
+
+ switch (this.wrapper.baseMode) {
+ case 'nuclStick': this.drawNucleicAcidStick(this.modelGroup, all); break;
+ case 'nuclLine': this.drawNucleicAcidLine(this.modelGroup, all); break;
+ case 'nuclPolygon': this.drawNucleicAcidLadder(this.modelGroup, all); break;
+ }
+
+ var target = this.wrapper.symopAtoms ? asu : this.modelGroup;
+ if (this.wrapper.showNonbonded) {
+ var nonBonded = this.getNonbonded(allHet);
+ if (this.wrapper.nbMode == 'nb_sphere') {
+ this.drawAtomsAsIcosahedron(target, nonBonded, 0.3, true);
+ } else if (this.wrapper.nbMode == 'nb_cross') {
+ this.drawAsCross(target, nonBonded, 0.3, true);
+ }
+ }
+
+ switch (this.wrapper.hetatmMode) {
+ case 'stick': this.drawBondsAsStick(target, hetatm, this.cylinderRadius, this.cylinderRadius, true); break;
+ case 'sphere': this.drawAtomsAsSphere(target, hetatm, this.sphereRadius); break;
+ case 'line': this.drawBondsAsLine(target, hetatm, this.curveWidth); break;
+ case 'ballAndStick': this.drawBondsAsStick(target, hetatm, this.cylinderRadius / 2.0, this.cylinderRadius, true, false, 0.3); break;
+ case 'ballAndStick2': this.drawBondsAsStick(target, hetatm, this.cylinderRadius / 2.0, this.cylinderRadius, true, true, 0.3); break;
+ }
+
+ this.setBackground(this.wrapper.backgroundColor);
+
+ if (this.wrapper.showCell)
+ this.drawUnitcell(this.modelGroup);
+
+ if (this.wrapper.drawBiomt)
+ this.drawSymmetryMates2(this.modelGroup, asu, this.protein.biomtMatrices);
+
+ if (this.wrapper.drawPacking)
+ this.drawSymmetryMatesWithTranslation2(this.modelGroup, asu, this.protein.symMat);
+ this.modelGroup.add(asu);
+ };
+
+})(Jmol);
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|