Revision: 20354
http://sourceforge.net/p/jmol/code/20354
Author: hansonr
Date: 2015-03-04 23:48:32 +0000 (Wed, 04 Mar 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.2.13_2015.03.05"
synchronized with 14.3.12
released
bug fix: (14.3 only) write VRML|MAYA|OBJ|POVRAY broken
JmolVersion="14.3.12_2015.03.01"
bug fix: late discovery of mmCIF format does not load secondary structure
bug fix: reading PNGJ file saved after load with /dssr or /rna3d annotations
ignores annotations
bug fix: {*}.find("~d~G:C") broken (find with bioSMARTS)
new feature: image # the current view as an image
new feature: image 300 400 # adjustable size
new feature: image "c:/temp/t.bmp" # image from a file
new feature: image "" close # close the current view image
new feature: image "c:/temp/t.bmp" close # close image from a file
new feature: image CLOSE # close all
new feature: image ID ...
-- id for IMAGE CLOSE;
-- displayed in title of frame
-- examples:
image ID "test"
image ID "test" 400 500
image ID "test" "bob.png"
image ID "test" close
new feature: write IMAGE
-- same as IMAGE
new feature: write IMAGE 500 500
-- same as IMAGE 500 500
new feature: (JavaScript/HTML5; see JSmol_Console.java)
// page designer may indicate one of three divs for images on the page:
// <appletID>_Image_app_holder for IMAGE command by itself (current app image)
// <appletID>_Image_<cleaned id or filename>_holder for IMAGE ID "xxx" ...
or IMAGE "xxx"
// where cleaning is with .replace(/\W/g,"_")
// <appletID>_Image_holder for all images not identified as above
// if a page div is not identified, then the image will be placed in a new
floating div
note: experimental SHOW IMAGE now replaced by new command IMAGE
JmolVersion="14.3.12_2015.02.26"
bug fix: imageFontScaling integer instead of float; does not scale
appropriately on resize
bug fix: writing image of MO fails to write info (Jmol 12 or before)
JmolVersion="14.3.12_2015.02.25c"
bug fix: legacy non-XML JVXL files with color mapping should default to RGB
color scheme
bug fix: Jmol 14.1.2_2013.12.13 disabled some mmCIF file reading for non-wwPDB
mmCIF files
JmolVersion="14.3.12_2015.02.25b"
new feature: random(low,high,seed)
-- provides a new seed for the random() function
-- seed may be any 48-bit integer.
-- x = random(0.0,1.0,121231223)
-- low and high are simply placeholders
-- does return the first number from this seed
-- note that Java and JavaScript will have DIFFERENT seedings
-- utilizes https://github.com/davidbau/seedrandom/blob/released/seedrandom.js
(appended to java.util.Random.js)
JmolVersion="14.3.12_2015.02.25"
new feature: show chemical drawing
new feature: show drawing
-- pops up window with drawing of model
-- service is from NCI
-- uses SMILES if structure was not loaded using $... (NCI) or :... (PubChem)
JmolVersion="14.3.12_2015.02.24"
// 02.28 removes "show " from these
new feature: show IMAGE
-- pops up a frame with the current image
-- allows "Save As..."
new feature: show IMAGE "filename"
-- pops up a frame with the image loaded from a file
-- allows "Save As..."
new feature: show image 300 400 # adjustable size
new feature: show image none # closes all image panels
new feature: show image CLOSE # "all" presumed
new feature: show image CLOSE "" # the model image
new feature: show image CLOSE "c:/temp/t.bmp" # the image for this file
new feature: write IMAGE
-- same as SHOW IMAGE
new feature: write IMAGE 500 500
-- same as SHOW IMAGE 500 500; allows customization of width and height
new feature: Windows BMP image reading
-- reads 24-bit (full color) as well as 16-, 8-, 4-, 2-, and 1-bit color
palette modes
-- 14-byte and 40-byte headers only
-- does not read compressed modes
bug fix: restriction against getting SMILES string for biomolecule lifted
bug fix: end-on bonds may appear to disappear
bug fix: JavaScript -2.format("%8.3") gives 2.000 not -2.000
bug fix: minimizer treats hydrogen bonds as covalent single bonds
code: javajs.img.BMPDecoder
code: org.openscience.jmol.app.jmolpanel.ImageDialog
JmolVersion="14.3.12_2015.02.19"
bug fix: CML reader does not show proper atom names for crystal structures
bug fix: POV-Ray renderer does not show proper backbone width (since forever)
bug fix: POV-Ray renderer with a translucent surface shows bonds that should be
hidden (since 13.1)
bug fix: unitcell info for PDB file biomolecule does not show "biomolecule 1"
JmolVersion="14.3.12_2015.02.18"
bug fix: load filter "biomolecule 1" broken in 14.3.12_2015.02.14
JmolVersion="14.3.12_2015.02.17b"
bug fix: writing to PNGJ data to .ZIP file should create a standard ZIP file.
-- especially useful now that some zip readers will not open PNGJ files as
zip files
(with newer 7zip you can right-click file, then select 7zip...open
archive...zip)
var x = load("t.png", true)
write var x "t.zip"
bug fix: VASP POSCAR fix for atom symbols in header line
JmolVersion="14.3.12_2015.02.17"
new feature: set zshadePower 0
-- allows examination of depth buffer and writing to image for external
processing
set zShadePower 0
set zSlab 100
set zDepth 0
set zShade true
write z.jpg
set zShade false
write rgb.jpg
JmolVersion="14.3.12_2015.02.16"
new feature: x.dot(y) for planes and points -- was present but undocumented
and not working correctly
new feature: (undocumented) x.distance.all(y)
new feature: load MUTATE "==LYS"
-- loads using set appendNew false
-- bypasses regeneration of secondary structure
-- not to be documented
-- issued by MUTATE command only
bug fix: write isosurface "./xxx.jvxl" broken -- concatenates "isosurface"
with filename
bug fix: write ISOSURFACE by itself broken (similarly for write POINTGROUP and
others)
bug fix: MUTATE command adjustments for saving state
bug fix: MUTATE command should not force recreation of shapes
bug fix: MUTATE command should not change backbone atoms
bug fix: x = measure(a,b) where b is {none} crashes Jmol
bug fix: compare({atomA},{atomsB}) should return standard 4x4 matrix, not one
involving a rotation
about an atom center
-- (not adjusted when ROTATESELECTED was fixed in 14.3.11_2014.12.17; Angel
Herraez)
code: org.jmol.modelsetbio.BioExt
-- extracts struts, quaternion plots, polymerInfo, mutate into optional module
-- saves 15K in corebio.js
JmolVersion="14.3.12_2015.02.11"
bug fix: 14.3.12_2015.02.09 breaks MODEL "someTitle" syntax
bug fix: MUTATE not properly saved in state
bug fix: "USER MOD" not accepted at beginning of PDB file (MolProbity breaking
PDB format here)
bug fix: 02.10 may break loading ligand files
JmolVersion="14.3.12_2015.02.10"
bug fix: color $contact1 "roygb" range -0.5 1.0; broken (in state after using
CONTACT)
bug fix: mmCIF reader does not flag first model of a multimodel set as type PDB
JmolVersion="14.3.12_2015.02.09"
new feature: frame align {atoms} FIXED
-- shifts atom positions in each frame to match first atom in {atoms}
-- unlike just frame align {atoms}, frame * will still show alignment
-- objects such as DRAW and ISOSURFACE will NOT be shifted
-- needs testing
new feature: frame align [modelNo] [pt]
-- FIXED is assumed
-- used in state; shifts a model by a specific amount after removing any
current frame alignment
Modified Paths:
--------------
branches/v14_2/Jmol/srcjsv/jspecview/java/AwtPlatform.java
branches/v14_2/Jmol/srcjsv/jspecview/js2d/JsPlatform.java
Added Paths:
-----------
branches/v14_2/Jmol/srcjs/java/util/Random.js
Added: branches/v14_2/Jmol/srcjs/java/util/Random.js
===================================================================
--- branches/v14_2/Jmol/srcjs/java/util/Random.js
(rev 0)
+++ branches/v14_2/Jmol/srcjs/java/util/Random.js 2015-03-04 23:48:32 UTC
(rev 20354)
@@ -0,0 +1,355 @@
+Clazz.load(null,"java.util.Random",["java.lang.IllegalArgumentException"],function(){
+c$=Clazz.decorateAsClass(function(){
+this.haveNextNextGaussian=false;
+this.seed=0;
+this.nextNextGaussian=0;
+Clazz.instantialize(this,arguments);
+},java.util,"Random",null,java.io.Serializable);
+Clazz.makeConstructor(c$,
+function(){
+this.setSeed(System.currentTimeMillis());
+});
+Clazz.makeConstructor(c$,
+function(seed){
+this.setSeed(seed);
+},"~N");
+Clazz.defineMethod(c$,"next",
+function(bits){
+this.seed=(this.seed*25214903917+0xb)&(281474976710655);
+return(this.seed>>>(48-bits));
+},"~N");
+Clazz.defineMethod(c$,"nextBoolean",
+function(){
+return Math.random()>0.5;
+});
+Clazz.defineMethod(c$,"nextBytes",
+function(buf){
+for(var i=0;i<bytes.length;i++){
+bytes[i]=Math.round(0x100*Math.random());
+}
+},"~A");
+Clazz.defineMethod(c$,"nextDouble",
+function(){
+return Math.random();
+});
+Clazz.defineMethod(c$,"nextFloat",
+function(){
+return Math.random();
+});
+Clazz.defineMethod(c$,"nextGaussian",
+function(){
+if(this.haveNextNextGaussian){
+this.haveNextNextGaussian=false;
+return this.nextNextGaussian;
+}var v1;
+var v2;
+var s;
+do{
+v1=2*this.nextDouble()-1;
+v2=2*this.nextDouble()-1;
+s=v1*v1+v2*v2;
+}while(s>=1);
+var norm=Math.sqrt(-2*Math.log(s)/s);
+this.nextNextGaussian=v2*norm;
+this.haveNextNextGaussian=true;
+return v1*norm;
+});
+Clazz.defineMethod(c$,"nextInt",
+function(){
+return Math.ceil(0xffff*Math.random())-0x8000;
+});
+Clazz.defineMethod(c$,"nextInt",
+function(n){
+if(n>0){
+if((n&-n)==n){
+return((n*this.next(31))>>31);
+}var bits;
+var val;
+do{
+bits=this.next(31);
+val=bits%n;
+}while(bits-val+(n-1)<0);
+return val;
+}throw new IllegalArgumentException();
+},"~N");
+Clazz.defineMethod(c$,"nextLong",
+function(){
+return Math.ceil(0xffffffff*Math.random())-0x80000000;
+});
+Clazz.defineMethod(c$,"setSeed",
+function(seed){
+Math.seedrandom(seed);
+//this.seed=(seed^25214903917)&(281474976710655);
+//this.haveNextNextGaussian=false;
+},"~N");
+Clazz.defineStatics(c$,
+"multiplier",0x5deece66d);
+});
+
+// seedrandom.js
+// Author: David Bau 3/11/2010
+//
+// Defines a method Math.seedrandom() that, when called, substitutes
+// an explicitly seeded RC4-based algorithm for Math.random(). Also
+// supports automatic seeding from local or network sources of entropy.
+//
+// Usage:
+//
+// <script src=http://davidbau.com/encode/seedrandom-min.js></script>
+//
+// Math.seedrandom('yipee'); Sets Math.random to a function that is
+// initialized using the given explicit seed.
+//
+// Math.seedrandom(); Sets Math.random to a function that is
+// seeded using the current time, dom state,
+// and other accumulated local entropy.
+// The generated seed string is returned.
+//
+// Math.seedrandom('yowza', true);
+// Seeds using the given explicit seed mixed
+// together with accumulated entropy.
+//
+// <script src="http://bit.ly/srandom-512";></script>
+// Seeds using physical random bits downloaded
+// from random.org.
+//
+// Examples:
+//
+// Math.seedrandom("hello"); // Use "hello" as the seed.
+// document.write(Math.random()); // Always 0.5463663768140734
+// document.write(Math.random()); // Always 0.43973793770592234
+// var rng1 = Math.random; // Remember the current prng.
+//
+// var autoseed = Math.seedrandom(); // New prng with an automatic seed.
+// document.write(Math.random()); // Pretty much unpredictable.
+//
+// Math.random = rng1; // Continue "hello" prng sequence.
+// document.write(Math.random()); // Always 0.554769432473455
+//
+// Math.seedrandom(autoseed); // Restart at the previous seed.
+// document.write(Math.random()); // Repeat the 'unpredictable' value.
+//
+// Notes:
+//
+// Each time seedrandom('arg') is called, entropy from the passed seed
+// is accumulated in a pool to help generate future seeds for the
+// zero-argument form of Math.seedrandom, so entropy can be injected over
+// time by calling seedrandom with explicit data repeatedly.
+//
+// On speed - This javascript implementation of Math.random() is about
+// 3-10x slower than the built-in Math.random() because it is not native
+// code, but this is typically fast enough anyway. Seeding is more expensive,
+// especially if you use auto-seeding. Some details (timings on Chrome 4):
+//
+// Our Math.random() - avg less than 0.002 milliseconds per call
+// seedrandom('explicit') - avg less than 0.5 milliseconds per call
+// seedrandom('explicit', true) - avg less than 2 milliseconds per call
+// seedrandom() - avg about 38 milliseconds per call
+//
+// LICENSE (BSD):
+//
+// Copyright 2010 David Bau, all rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+// 1. Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// 2. Redistributions in binary form must reproduce the above copyright
+// notice, this list of conditions and the following disclaimer in the
+// documentation and/or other materials provided with the distribution.
+//
+// 3. Neither the name of this module nor the names of its contributors may
+// be used to endorse or promote products derived from this software
+// without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+/**
+ * All code is in an anonymous closure to keep the global namespace clean.
+ *
+ * @param {number=} overflow
+ * @param {number=} startdenom
+ */
+(function (pool, math, width, chunks, significance, overflow, startdenom) {
+
+var copyright = "Copyright 2010 David Bau, all rights reserved. (BSD)"
+//
+// seedrandom()
+// This is the seedrandom function described above.
+//
+math['seedrandom'] = function seedrandom(seed, use_entropy) {
+ var key = [];
+ var arc4;
+
+ // Flatten the seed string or build one from local entropy if needed.
+ seed = mixkey(flatten(
+ use_entropy ? [seed, pool] :
+ arguments.length ? seed :
+ [new Date().getTime(), pool, window], 3), key);
+
+ // Use the seed to initialize an ARC4 generator.
+ arc4 = new ARC4(key);
+
+ // Mix the randomness into accumulated entropy.
+ mixkey(arc4.S, pool);
+
+ // Override Math.random
+
+ // This function returns a random double in [0, 1) that contains
+ // randomness in every bit of the mantissa of the IEEE 754 value.
+
+ math['random'] = function random() { // Closure to return a random double:
+ var n = arc4.g(chunks); // Start with a numerator n < 2 ^ 48
+ var d = startdenom; // and denominator d = 2 ^ 48.
+ var x = 0; // and no 'extra last byte'.
+ while (n < significance) { // Fill up all significant digits by
+ n = (n + x) * width; // shifting numerator and
+ d *= width; // denominator and generating a
+ x = arc4.g(1); // new least-significant-byte.
+ }
+ while (n >= overflow) { // To avoid rounding up, before adding
+ n /= 2; // last byte, shift everything
+ d /= 2; // right using integer math until
+ x >>>= 1; // we have exactly the desired bits.
+ }
+ return (n + x) / d; // Form the number within [0, 1).
+ };
+
+ // Return the seed that was used
+ return seed;
+};
+
+//
+// ARC4
+//
+// An ARC4 implementation. The constructor takes a key in the form of
+// an array of at most (width) integers that should be 0 <= x < (width).
+//
+// The g(count) method returns a pseudorandom integer that concatenates
+// the next (count) outputs from ARC4. Its return value is a number x
+// that is in the range 0 <= x < (width ^ count).
+//
+/** @constructor */
+function ARC4(key) {
+ var t, u, me = this, keylen = key.length;
+ var i = 0, j = me.i = me.j = me.m = 0;
+ me.S = [];
+ me.c = [];
+
+ // The empty key [] is treated as [0].
+ if (!keylen) { key = [keylen++]; }
+
+ // Set up S using the standard key scheduling algorithm.
+ while (i < width) { me.S[i] = i++; }
+ for (i = 0; i < width; i++) {
+ t = me.S[i];
+ j = lowbits(j + t + key[i % keylen]);
+ u = me.S[j];
+ me.S[i] = u;
+ me.S[j] = t;
+ }
+
+ // The "g" method returns the next (count) outputs as one number.
+ me.g = function getnext(count) {
+ var s = me.S;
+ var i = lowbits(me.i + 1); var t = s[i];
+ var j = lowbits(me.j + t); var u = s[j];
+ s[i] = u;
+ s[j] = t;
+ var r = s[lowbits(t + u)];
+ while (--count) {
+ i = lowbits(i + 1); t = s[i];
+ j = lowbits(j + t); u = s[j];
+ s[i] = u;
+ s[j] = t;
+ r = r * width + s[lowbits(t + u)];
+ }
+ me.i = i;
+ me.j = j;
+ return r;
+ };
+ // For robust unpredictability discard an initial batch of values.
+ // See http://www.rsa.com/rsalabs/node.asp?id=2009
+ me.g(width);
+}
+
+//
+// flatten()
+// Converts an object tree to nested arrays of strings.
+//
+/** @param {Object=} result
+ * @param {string=} prop */
+function flatten(obj, depth, result, prop) {
+ result = [];
+ if (depth && typeof(obj) == 'object') {
+ for (prop in obj) {
+ if (prop.indexOf('S') < 5) { // Avoid FF3 bug (local/sessionStorage)
+ try { result.push(flatten(obj[prop], depth - 1)); } catch (e) {}
+ }
+ }
+ }
+ return result.length ? result : '' + obj;
+}
+
+//
+// mixkey()
+// Mixes a string seed into a key that is an array of integers, and
+// returns a shortened string seed that is equivalent to the result key.
+//
+/** @param {number=} smear
+ * @param {number=} j */
+function mixkey(seed, key, smear, j) {
+ seed += ''; // Ensure the seed is a string
+ smear = 0;
+ for (j = 0; j < seed.length; j++) {
+ key[lowbits(j)] =
+ lowbits((smear ^= key[lowbits(j)] * 19) + seed.charCodeAt(j));
+ }
+ seed = '';
+ for (j in key) { seed += String.fromCharCode(key[j]); }
+ return seed;
+}
+
+//
+// lowbits()
+// A quick "n mod width" for width a power of 2.
+//
+function lowbits(n) { return n & (width - 1); }
+
+//
+// The following constants are related to IEEE 754 limits.
+//
+startdenom = math.pow(width, chunks);
+significance = math.pow(2, significance);
+overflow = significance * 2;
+
+//
+// When seedrandom.js is loaded, we immediately mix a few bits
+// from the built-in RNG into the entropy pool. Because we do
+// not want to intefere with determinstic PRNG state later,
+// seedrandom will not call math.random on its own again after
+// initialization.
+//
+mixkey(math.random(), pool);
+
+// End anonymous scope, and pass initial values.
+})(
+ [], // pool: entropy pool starts empty
+ Math, // math: package containing random, pow, and seedrandom
+ 256, // width: each RC4 output is 0 <= x < 256
+ 6, // chunks: at least six RC4 outputs for each double
+ 52 // significance: there are 52 significant digits in a double
+);
+
Modified: branches/v14_2/Jmol/srcjsv/jspecview/java/AwtPlatform.java
===================================================================
--- branches/v14_2/Jmol/srcjsv/jspecview/java/AwtPlatform.java 2015-03-04
23:47:18 UTC (rev 20353)
+++ branches/v14_2/Jmol/srcjsv/jspecview/java/AwtPlatform.java 2015-03-04
23:48:32 UTC (rev 20354)
@@ -9,8 +9,10 @@
import java.net.URL;
import java.text.SimpleDateFormat;
import java.util.Date;
+import java.util.Map;
import javajs.api.GenericFileInterface;
+import javajs.api.GenericImageDialog;
import javajs.api.GenericMenuInterface;
import javajs.api.GenericMouseInterface;
import javajs.api.GenericPlatform;
@@ -304,5 +306,12 @@
return null;
}
+ @Override
+ public GenericImageDialog getImageDialog(String title,
+ Map<String, GenericImageDialog> imageMap) {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
}
Modified: branches/v14_2/Jmol/srcjsv/jspecview/js2d/JsPlatform.java
===================================================================
--- branches/v14_2/Jmol/srcjsv/jspecview/js2d/JsPlatform.java 2015-03-04
23:47:18 UTC (rev 20353)
+++ branches/v14_2/Jmol/srcjsv/jspecview/js2d/JsPlatform.java 2015-03-04
23:48:32 UTC (rev 20354)
@@ -2,11 +2,13 @@
import java.io.BufferedInputStream;
import java.net.URL;
+import java.util.Map;
import javajs.api.GenericFileInterface;
import javajs.api.GenericMenuInterface;
import javajs.api.GenericMouseInterface;
import javajs.api.GenericPlatform;
+import javajs.api.GenericImageDialog;
import javajs.api.PlatformViewer;
import javajs.awt.Font;
import javajs.util.P3;
@@ -377,4 +379,11 @@
return null;
}
+ @Override
+ public GenericImageDialog getImageDialog(String title,
+ Map<String, GenericImageDialog> imageMap) {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
}
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