-
Notifications
You must be signed in to change notification settings - Fork 0
/
test2.htm
295 lines (263 loc) · 16.2 KB
/
test2.htm
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
<!DOCTYPE html>
<html>
<title>HTML5-only and WebGL Jmol Demo</title>
<head>
<meta charset="utf-8">
<!-- breaking out the library for debugging -->
<script type="text/javascript" src="jquery/jquery.js"></script>
<script type="text/javascript" src="js/JSmoljQueryExt.js"></script>
<script type="text/javascript" src="js/JSmolCore.js"></script>
<script type="text/javascript" src="js/JSmolApplet.js"></script>
<script type="text/javascript" src="js/JSmolApi.js"></script>
<script type="text/javascript" src="js/JSmolControls.js"></script>
<script type="text/javascript" src="js/j2sjmol.js"></script>
<script type="text/javascript" src="js/JSmol.js"></script>
<script type="text/javascript" src="js/JSmolConsole.js"></script>
<script type="text/javascript" src="js/JSmolMenu.js"></script>
<!-- // following two only necessary for WebGL version:
-->
<script type="text/javascript" src="js/JSmolThree.js"></script>
<script type="text/javascript" src="js/JSmolGLmol.js"></script>
<script type="text/javascript">
Jmol._isAsync = false;
Jmol.getProfile() // records repeat calls to overridden or overloaded Java methods
var jmolApplet0; // set up in HTML table, below
// use ?_USE=JAVA or _USE=SIGNED or _USE=HTML5
jmol_isReady = function(applet) {
document.title = (applet._id + " is ready")
Jmol._getElement(applet, "appletdiv").style.border="1px solid blue"
}
Info = {
width: 420,
height: 300,
debug: false,
color: "#F0F0F0",
zIndexBase: 20000,
z:{monitorZIndex:100},
addSelectionOptions: true,
serverURL: "http://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php",
use: "HTML5",
//language: "fr", // NOTE: LOCALIZATION REQUIRES <meta charset="utf-8"> (see JSmolCore Jmol.featureDetection.supportsLocalization)
jarPath: "java",
j2sPath: "j2s",
jarFile: "JmolApplet.jar",
isSigned: false,
disableJ2SLoadMonitor: false,
disableInitialConsole: false, // default now is true
readyFunction: jmol_isReady,
allowjavascript: true,
// appletLoadingImage: "none",
script: "set zoomlarge false;set antialiasdisplay;load async data/caffeine.mol;"
// script: "set antialiasDisplay;set showtiming;load async data/caffeine.mol;"
//,defaultModel: ":dopamine"
//,noscript: true
//console: "none", // default will be jmolApplet0_infodiv
//script: "set antialiasDisplay;background white;load data/caffeine.mol;"
//delay 3;background yellow;delay 0.1;background white;for (var i = 0; i < 10; i+=1){rotate y 3;delay 0.01}"
}
</script>
</head>
<body>
<table width=1000 cellpadding=10>
<tr><td colspan=2 style="font-size:8pt">
For a zip file containing all the files in this directory,
see <a href=http://chemapps.stolaf.edu/jmol/zip/Jmol.zip>http://chemapps.stolaf.edu/jmol/zip/Jmol.zip</a>.
This test page uses unminified files and can implement the signed Jmol applet, the unsigned Jmol applet, or just JavaScript and HTML5 with or without WebGL.
Credits:
WebGL interface written by <b>Takanori Nakane</b>.
Java2Script written by <b>Zhou Renjian, et al.</b>
Jzlib written by <b>Atsuhiko Yamanaka</b>.
Jmol code conversion to JavaScript by <b>Bob Hanson</b>.
</td></tr>
<tr><td valign=top>
<script>
// note that the variable name MUST match the first parameter in quotes
jmolApplet0 = Jmol.getApplet("jmolApplet0", Info)
// note that now scripts can be sent immediately after the _Applet object is created
//Jmol.script(jmolApplet0,"background gray;delay 0.5;background black")
var lastPrompt=0;
</script>
<br>
<a href="javascript:Jmol.script(jmolApplet0,'console')">console</a>
<a href="javascript:Jmol.script(jmolApplet0,'image')">image</a>
display
<a href="javascript:Jmol.script(jmolApplet0,'set antialiasDisplay false')">faster</a>
<a href="javascript:Jmol.script(jmolApplet0,'set antialiasDisplay true')">sharper</a>
<br>
platformSpeed:
<a href="javascript:Jmol.script(jmolApplet0,'set platformSpeed 8')" title='all features'>8</a>
<a href="javascript:Jmol.script(jmolApplet0,'set platformSpeed 7')" title='no antialiasing'>7</a>
<a href="javascript:Jmol.script(jmolApplet0,'set platformSpeed 6')" title='no translucency'>6</a>
<a href="javascript:Jmol.script(jmolApplet0,'set platformSpeed 5')" title='surfaces dotted'>5</a>
<a href="javascript:Jmol.script(jmolApplet0,'set platformSpeed 4')" title='cartoons as trace'>4</a>
<a href="javascript:Jmol.script(jmolApplet0,'set platformSpeed 3')" title='geosurfaces as dots'>3</a>
<a href="javascript:Jmol.script(jmolApplet0,'set platformSpeed 2')" title='ellipsoids as dots'>2</a>
<a href="javascript:Jmol.script(jmolApplet0,'set platformSpeed 1')" title='wireframe only'>1</a>
<br>
info <a href="javascript:Jmol.showInfo(jmolApplet0, true)">show</a>
<a href="javascript:Jmol.clearConsole(jmolApplet0)">clear</a>
<a href="javascript:Jmol.showInfo(jmolApplet0, false)">hide</a>
<br><a href="javascript:Jmol.script(jmolApplet0,'select *;cartoons off;spacefill only')">spacefill</a>
<a href="javascript:Jmol.script(jmolApplet0,'select *;cartoons off;wireframe -0.1')">wire</a>
<a href="javascript:Jmol.script(jmolApplet0,'select *;cartoons off;spacefill 23%;wireframe 0.15')">ball&stick</a>
<a href="javascript:Jmol.script(jmolApplet0,'select protein or nucleic;cartoons only')">cartoons</a>
<a href="javascript:Jmol.script(jmolApplet0,'set cartoonFancy true')">fancy</a>
<a href="javascript:Jmol.script(jmolApplet0,'set cartoonFancy false')">not</a>
<a href="javascript:Jmol.script(jmolApplet0,'set cartoonFancy false;set hermitelevel 0')">flat</a>
<br><a href="javascript:Jmol.script(jmolApplet0,'color property atomno')">color atomno</a>
<a href="javascript:Jmol.script(jmolApplet0,'color cpk')">color cpk</a>
<a href="javascript:Jmol.script(jmolApplet0,'color structure')">color structure</a>
<br>
<a href="javascript:Jmol.script(jmolApplet0,'select *;isosurface vdw')">isosurface vdw</a>
<a href="javascript:Jmol.script(jmolApplet0,'isosurface delete')">off</a>
<a href="javascript:Jmol.script(jmolApplet0,'if ({atomno < 10}.partialcharge == 0){calculate partialcharge};isosurface vdw map mep')">mep</a>
<a href="javascript:Jmol.script(jmolApplet0,'isosurface translucent')">translucent</a>
<a href="javascript:Jmol.script(jmolApplet0,'isosurface opaque')">opaque</a>
<br>
labels <a href="javascript:Jmol.script(jmolApplet0,'if (_fileType == "Pdb"){select *.CA;label %n%r}else{select *;label %a};select *;')">on</a>
<a href="javascript:Jmol.script(jmolApplet0,'select *;labels off')">off</a>
<a href="javascript:Jmol.script(jmolApplet0,'font echo 20 serif;fsize=20;set echo top center;echo echo test')">echo</a>
<a href="javascript:Jmol.script(jmolApplet0,'if (!fsize){fsize=20};fsize += 4;font echo @fsize serif;')">larger</a>
<a href="javascript:Jmol.script(jmolApplet0,'if (!fsize){fsize=20};fsize -= 4;if (fsize < 10){fsize = 10};font echo @fsize serif')">smaller</a>
</td><td valign=top>
<b>Try various buttons. If anything doesn't work please <a href=mailto:hansonr@stolaf.edu>let me know</a>.</b>
<br><br>
<span style="font-size:8pt">
Current status: 7 SEP 2013 -
<b>Jmol is working completely Java-free, requiring only HTML5.</b>
The <b>platformSpeed</b> option (set 1 to 10) allows for rapid rotation of models for platforms that have limited JavaScript capability (iPad/iPhone, tablets).
Popup menu, script queuing, animation, spin, vibration, move, moveto, hover, and (guided) navigation, pause/resume are all working;
echos/labels working; antialiasDisplay working;
synchronous binary and XML file reading working;
cartoons, translucency, surfaces -- all are working in a simple HTML5 2D canvas. WebGL is less developed, with just basic shapes and no text.
Enter "!" and a command into the search box and press ENTER to execute a <a target=_blank href=http://chemapps.stolaf.edu/jmol/docs>script command</a>.
</span>
<br><br>
<table cellpadding=5><tr><td valign=top>
<b>rendering options:</b>
<br>
<a href=test2.htm?_USE=JAVA>unsigned Jmol applet</a>
<br>
<a href=test2.htm?_USE=SIGNED>signed Jmol applet</a>
<br>
<a href=test2.htm?_USE=HTML5>JSmol (HTML5 only)</a>
<br>
<a href=test2.htm?_USE=WEBGL>JSmol (WebGL)</a>
<br>
<b>keyword searches</b>
<br>
<a href="javascript:Jmol.search(jmolApplet0,'=caffeine?')">=caffeine? (RCSB)</a>
<br>
<a href="javascript:Jmol.search(jmolApplet0,'=1blu?')">=1blu? (RCSB)</a>
<br>
<a href="javascript:Jmol.search(jmolApplet0,'=1crn?')">=1crn? (RCSB)</a>
</td><td valign=top>
<b>this-domain calls</b>
<br>
<a href="javascript:Jmol.script(jmolApplet0,'load =1blu; set echo top left;echo loading map file...;refresh;isosurface "=1blu" mesh nofill;echo')">EDS map test</a>
<br>
<a href="javascript:Jmol.script(jmolApplet0,'load data/1cbs.cif; set echo top left;echo loading map file...;refresh;isosurface downsample 2 cutoff 0.5 boundbox "data/1cbs_2fofc.map" mesh nofill;isosurface display within 2.0 {*};echo')">2.2MB EDM test</a>
<br>
<a href="javascript:Jmol.script(jmolApplet0,'load ?')">local file reading</a>
<br>
<a href="javascript:Jmol.script(jmolApplet0,'minimize')">minimize</a>
<a href="javascript:Jmol.script(jmolApplet0,'set modelkitmode;set picking dragMinimize')">drag-minimize</a>
<a href="javascript:Jmol.script(jmolApplet0,'!quit;set modelkitmode false;set picking ident;')">!quit</a>
<br>
<a href="javascript:Jmol.script(jmolApplet0,'script data/flexfit.spt')">flexible fit</a>
<br>
<a href="javascript:Jmol.script(jmolApplet0,'load data/dna.pse')">PyMOL session - dna</a>
<br>
<a href="javascript:Jmol.script(jmolApplet0,'load data/estron.cml;delete molecule!=1;moveto /* time, axisAngle */ 0.0 { -569 -266 778 170.22} /* zoom, translation */ 210.8 0.0 0.0 /* center, rotationRadius */ {1.612277686904762 3.7877332476190473 1.6109263519047616} 16.399569513870535 /* navigation center, translation, depth */ {0 0 0} 9.485930041021248 -20.361702729557265 0;')">estron.cml</a>
<a href="javascript:Jmol.script(jmolApplet0,'load data/vasp.xml')">vasp.xml</a>
<a href="javascript:Jmol.script(jmolApplet0,'load data/water.xodydata')">water.xodydata</a>
<br>
<a href="javascript:Jmol.script(jmolApplet0,'script data/test.spt;background black')">thread test</a>
<br>
<a href="javascript:Jmol.script(jmolApplet0,'pause')">pause</a>
<a href="javascript:Jmol.script(jmolApplet0,'resume')">resume</a>
<br>
<a href="javascript:Jmol.script(jmolApplet0,'!quit')">!quit</a>
<a href="javascript:Jmol.script(jmolApplet0,'!exit')">!exit</a>
<br>
<a href="javascript:Jmol.script(jmolApplet0,'load data/caffeine.mol;if (random() > 0.3){moveto 1 left}else if (random() > 0.7) {moveto 1 right} else {moveto 1 top};background black;delay 0.1;background white')">moveto</a>
<br>
<a href="javascript:Jmol.script(jmolApplet0,'load data/caffeine.mol;set echo top center;delay 1.0;echo caffeine;delay 1.0;set selectionhalos on;select _O;echo oxygen;delay 1.0;select _N;echo nitrogen;delay 1.0; select none;echo hover over an atom')">delay/hover</a>
<br>
<a href="javascript:Jmol.script(jmolApplet0,'var x=antialiasDisplay;load data/cyclohexaneFlip.jmol;antialiasdisplay = x;animation mode palindrome;animation on')">animation</a>
<br>
<a href="javascript:Jmol.script(jmolApplet0,'load data/c6h6.smol -3;rotate x 30;spin on;vibration on')">spin/vibration</a>
<br>
<a href="javascript:Jmol.script(jmolApplet0,'load data/co2.smol;mo homo SQUARED')">mo homo SQUARED</a>
<br>
<a href="javascript:Jmol.script(jmolApplet0,'load data/1hxw.png')">load data/1hxw.png</a> (<a target=_blank href=data/1hxw.png>image</a>)
<br>
<a href="javascript:Jmol.script(jmolApplet0,'load data/square_planar.spartan')">load data/square_planar.spartan</a>
<br>
<a href="javascript:Jmol.script(jmolApplet0,'load data/water.xyz.gz')">load data/water.xyz.gz</a>
<br>
<a href="javascript:Jmol.script(jmolApplet0,'zap;pmesh "data/sage.pmesh" fullylit;')">pmesh "data/sage.pmesh"</a>
<br>
<a href="javascript:Jmol.loadFile(jmolApplet0,'data/caffeine.mol')">load data/caffeine.mol</a>
<br>
<a href="javascript:Jmol.loadFile(jmolApplet0,'data/caffeine.mol',';isosurface "data/caffeine.jvxl"')">isosurface "caffeine.jvxl"</a>
<br>
<a href="javascript:Jmol.loadFile(jmolApplet0,'data/1crn.pdb',';if (_is2D) {set hermitelevel 0} else {set hermitelevel 6;set ribbonAspectRatio 4};cartoons only;color structure;')">load data/1crn.pdb</a>
<br>
<a href="javascript:Jmol.loadFile(jmolApplet0,'data/k04041.cif','load "" {1 1 1}')">load data/k04041.cif {1 1 1}</a>
<br>
<a href="javascript:Jmol.loadFile(jmolApplet0,'data/cl2o.gamess')">load data/cl2o.gamess</a>
<br>
<a href="javascript:Jmol.loadFile(jmolApplet0,'data/cl2o.gamess',';model 1.2;if (_is2D){mo mesh nofill} else {mo fill nomesh};mo homo')">(load +) mo homo</a>
<br>
<a href="javascript:Jmol.script(jmolApplet0,'model 1.2;mo fill nomesh; mo lumo')">mo lumo</a>
<a href="javascript:Jmol.script(jmolApplet0,'mo mesh nofill')">mesh</a>
<a href="javascript:Jmol.script(jmolApplet0,'mo fill nomesh')">fill</a>
<br>
<br>
<a href="javascript:Jmol.script(jmolApplet0,'set echo myimage [0 0];set echo myimage depth 50; set echo myimage image "data/bob.png"')">image</a>
<a href="javascript:Jmol.script(jmolApplet0,'set echo myimage scale 0.5')">x 0.5</a>
<a href="javascript:Jmol.script(jmolApplet0,'set echo myimage scale 1.0')">x 1.0</a>
<a href="javascript:Jmol.script(jmolApplet0,'set echo myimage scale 2.0')">x 2.0</a>
<a href="javascript:Jmol.script(jmolApplet0,'set echo myimage off')">off</a>
<a href="javascript:Jmol.script(jmolApplet0,'set echo myimage image "data/bob.png";set echo myimage depth 50')">on</a>
<a href="javascript:Jmol.script(jmolApplet0,'set echo myimage depth 100')">front</a>
<a href="javascript:Jmol.script(jmolApplet0,'set echo myimage depth 50')">mid</a>
<a href="javascript:Jmol.script(jmolApplet0,'set echo myimage depth 0')">back</a>
<br>
<br>
<a href="javascript:Jmol.script(jmolApplet0,'script data/cyclflip2.spt')">cyclflip2.spt</a>
<a href="javascript:Jmol.script(jmolApplet0,'!quit')">!quit</a>
<br>
<br>
</td><td valign=top>
<b>direct database calls(<a href="javascript:alert('MSIE cannot do synchronous cross-domain file transfer, so if you want to do that, you must put jsmol.php on your OWN server and point to it using Info.serverURL, which for this page is ' + Info.serverURL + '\nA text version of this php file is at http://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php.txt')">unless MSIE</a>)</b>
<br>
<a href="javascript:Jmol.loadFile(jmolApplet0,'$caffeine')">load $caffeine (from NCI)</a>
<br>
<a href="javascript:Jmol.loadFile(jmolApplet0,'=1blu',';display not water;select protein or nucleic;cartoons only;color structure;select *')">load =1blu (from RCSB)</a>
<br>
<a href="javascript:Jmol.loadFile(jmolApplet0,'=1d66',';display not water;select protein or nucleic;cartoons only;color structure;select *')">load =1d66 (from RCSB)</a>
<br>
<a href="javascript:Jmol.loadFile(jmolApplet0,'=4tra',';display not water;select protein or nucleic;cartoons only;color structure;select *')">load =4tra (from RCSB)</a>
<br>
<a href="javascript:Jmol.loadFile(jmolApplet0,':1983')">load :1983 (PubChem CID)</a>
<br>
<a href="javascript:Jmol.loadFile(jmolApplet0,':aspirin')">load :aspirin (PubChem name)</a>
<br>
<a href="javascript:Jmol.loadFile(jmolApplet0,':smiles:CC/C=C/CC')">load :smiles:CC/C=C/CC (PubChem SMILES)</a>
<br>
<a href="javascript:Jmol.loadFile(jmolApplet0,'$CC/C=C/CC')">load $CC/C=C/CC (NCI SMILES)</a>
<br>
<a href="javascript:Jmol.search(jmolApplet0,':caffeine',';isosurface vdw map mep translucent')">load :caffeine (PubChem, with mep)</a>
<br>
<a href="javascript:Jmol.search(jmolApplet0,'$caffeine',';moveto /* time, axisAngle */ 0.0 { -18 -17 1000 179.69} /* zoom, translation */ 100.0 0.0 0.0 /* center, rotationRadius */ {-0.44874999999999954 0.18930000000000002 -0.06529999999999997} 5.536731293601459 /* navigation center, translation, depth */ {0 0 0} -4.041090898432742 -1.7041175988342825 0;calculate partialCharge;isosurface vdw map mep translucent')">load $caffeine (NCI, with MMFF94 mep)</a>
<br>
<a href="javascript:Jmol.loadFile(jmolApplet0,'==HEM')">load ==HEM (RCSB ligand)</a>
<div id=xjmolApplet0_Image_app_holder></div>
<div id=xjmolApplet0_Image_holder></div>
</td></tr></table>
</td>
</tr></table>
</body>
</html>