From: <ha...@us...> - 2013-12-04 19:32:15
|
Revision: 19060 http://sourceforge.net/p/jmol/code/19060 Author: hansonr Date: 2013-12-04 19:32:06 +0000 (Wed, 04 Dec 2013) Log Message: ----------- Modified Paths: -------------- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-12-04 19:23:09 UTC (rev 19059) +++ branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-12-04 19:32:06 UTC (rev 19060) @@ -2,12 +2,10 @@ ___fullJmolProperties="src/org/jmol/viewer/Jmol.properties" -# THIS IS THE DEVELOPMENT TRUNK +# THIS IS THE RELEASE BRANCH -# Developers: to add a description of changes you have made, -# add it on a line below the "___JmolVersion=..." line. -# Don't use ___ in your text, as that is the key for stripping out -# the information saved in the JAR version of this file. +# Bug fixes only, please. +# # The quotes above look odd for a parameter file, but they are # important for the JavaScript version of Jmol. This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-12-13 23:36:22
|
Revision: 19099 http://sourceforge.net/p/jmol/code/19099 Author: hansonr Date: 2013-12-13 23:36:19 +0000 (Fri, 13 Dec 2013) Log Message: ----------- ___JmolVersion="14.0.2" JmolVersion="14.0.2_2013.12.13" (note that 14.0 and 14.1 are identical except for version number at this time) new feature: JavaScript: JSmol api Jmol.evaluateVar(applet, expression) -- better than Jmol.evaluate because result is a JavaScript variable, not a string. -- DEPRECATING JSmol api Jmol.evaluate(applet, expression) new feature: getProperty("JSON", ....) -- returns JSON code for property -- allows JavaScript: x = Jmol.getPropertyAsArray("variableInfo","some expression") new feature: getProperty variableInfo <expression> -- allows retrieval of variables in Java or JSON format -- evaluates expression -- defaults to "all" new feature: modulation adjustable by q and t, up to d=3 // modulation on/off (all atoms) // moduation {atom set} on/off // modulation int q-offset // modulation x.x t-offset // modulation {t1 t2 t3} // modulation {q1 q2 q3} TRUE new feature: pickedList -- ordered array of recently picked atoms -- can be used the same as the PICKED variable, but that is ordered sequentially, not temporally -- twice clicking off structure clears the list -- @{pickedList}[0] last-picked atom -- @{pickedList}[-1] next-to-last-picked atom -- @{pickedList}[-1][0] last two picked atoms new feature: array.pop(), array.push() -- similar to JavaScript -- for example: // create a distance t-plot at = [] // t points am = [] // distance measurements var p1 = a.modulation(1e10)[1] var p2 = a2.modulation(1e10)[1] for (var i = 0; i <= 50; i++) { var t = i / 50.0; at.push(t); var b1 = a.modulation(t)[1]; var b2 = b.modulation(t)[1]; var m = distance((p1 + b1).xyz, (p2 + b2).xyz); am.push(m); } d = at.add("\t", am) new feature: modulation scale x.x new feature: caption "xxxxx" x.x -- number of seconds to run new feature: modulation 0.2 // sets t-value new feature: array.pop(), array.push(x) a=[];a.push("testing");print a.pop() new feature: select ON/OFF atom-set -- turns selection halos on or off as well as doing the selection -- convenience only -- for example: select on _O2 select off * new feature: pt1.mul3(pt2) -- returns {pt1.x*pt2.x, pt1.y*pt2.y, pt1.z*pt2.z} -- if both are not points, reverts to simple multiplication new reature: array.mul3(pt2) -- applies mul3 to all elements of array new feature: {atomset}.modulation(type, t) -- delivers P3 (displacement modulation) -- implemented only for type="D" (optional) -- optional t is 0 by default bug fix: modulation not distinguishing between q and t; bug fix: modulated measurements not working bug fix: not skipping set defaultLattice "{NaN NaN NaN}" bug fix: isosurface map atomic orbital fails bug fix: vibrational display of modulation with distances doesn't update bug fix: vibration off causes unnecessary warning in console bug fix: draw symop broken bug fix: array.mul(matrix3f) crashes Jmol bug fix: select symop=1555 broken bug fix: set picking dragSelected not working code: refactored CifReader, separating out MMCifReader and MSCifReader code: minor renaming/refactoring of methods in SV code: adds javajs.api.JSONEncodable interface -- super-simple implementation in org.jmol.script.SV -- allows implementations of javajs to deliver custom JSON results Modified Paths: -------------- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-12-13 23:34:45 UTC (rev 19098) +++ branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-12-13 23:36:19 UTC (rev 19099) @@ -113,7 +113,7 @@ -- allows implementations of javajs to deliver custom JSON results -JmolVersion="14.1.1_2013.12.04" +JmolVersion="14.0.1_2013.12.04" JmolVersion="13.3.9_dev_2013.12.04" This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-12-14 17:45:02
|
Revision: 19102 http://sourceforge.net/p/jmol/code/19102 Author: hansonr Date: 2013-12-14 17:44:58 +0000 (Sat, 14 Dec 2013) Log Message: ----------- ___JmolVersion="14.0.2" JmolVersion="14.0.2_2013.12.13" (note that 14.0 and 14.1 are identical except for version number at this time) bug fix: modulation not distinguishing between q and t; bug fix: modulated measurements not working bug fix: not skipping set defaultLattice "{NaN NaN NaN}" bug fix: isosurface map atomic orbital fails bug fix: vibrational display of modulation with distances doesn't update bug fix: vibration off causes unnecessary warning in console bug fix: draw symop broken bug fix: array.mul(matrix3f) crashes Jmol bug fix: select symop=1555 broken bug fix: set picking dragSelected not working code: refactored CifReader, separating out MMCifReader and MSCifReader code: minor renaming/refactoring of methods in SV code: adds javajs.api.JSONEncodable interface -- super-simple implementation in org.jmol.script.SV -- allows implementations of javajs to deliver custom JSON results Modified Paths: -------------- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-12-14 17:43:42 UTC (rev 19101) +++ branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-12-14 17:44:58 UTC (rev 19102) @@ -14,105 +14,23 @@ (note that 14.0 and 14.1 are identical except for version number at this time) -new feature: JavaScript: JSmol api Jmol.evaluateVar(applet, expression) - -- better than Jmol.evaluate because result is a JavaScript variable, not a string. - -- DEPRECATING JSmol api Jmol.evaluate(applet, expression) - -new feature: getProperty("JSON", ....) - -- returns JSON code for property - -- allows JavaScript: x = Jmol.getPropertyAsArray("variableInfo","some expression") - -new feature: getProperty variableInfo <expression> - -- allows retrieval of variables in Java or JSON format - -- evaluates expression - -- defaults to "all" - -new feature: modulation adjustable by q and t, up to d=3 - // modulation on/off (all atoms) - // moduation {atom set} on/off - // modulation int q-offset - // modulation x.x t-offset - // modulation {t1 t2 t3} - // modulation {q1 q2 q3} TRUE - -new feature: pickedList -- ordered array of recently picked atoms - -- can be used the same as the PICKED variable, - but that is ordered sequentially, not temporally - -- twice clicking off structure clears the list - -- @{pickedList}[0] last-picked atom - -- @{pickedList}[-1] next-to-last-picked atom - -- @{pickedList}[-1][0] last two picked atoms - -new feature: array.pop(), array.push() - -- similar to JavaScript - -- for example: - - // create a distance t-plot - - at = [] // t points - am = [] // distance measurements - - var p1 = a.modulation(1e10)[1] - var p2 = a2.modulation(1e10)[1] - for (var i = 0; i <= 50; i++) { - var t = i / 50.0; - at.push(t); - var b1 = a.modulation(t)[1]; - var b2 = b.modulation(t)[1]; - var m = distance((p1 + b1).xyz, (p2 + b2).xyz); - am.push(m); - } - d = at.add("\t", am) - -new feature: modulation scale x.x -new feature: caption "xxxxx" x.x -- number of seconds to run -new feature: modulation 0.2 // sets t-value - -new feature: array.pop(), array.push(x) - a=[];a.push("testing");print a.pop() -new feature: select ON/OFF atom-set - -- turns selection halos on or off as well as doing the selection - -- convenience only - -- for example: - - select on _O2 - select off * - -new feature: pt1.mul3(pt2) - -- returns {pt1.x*pt2.x, pt1.y*pt2.y, pt1.z*pt2.z} - -- if both are not points, reverts to simple multiplication -new reature: array.mul3(pt2) - -- applies mul3 to all elements of array - -new feature: {atomset}.modulation(type, t) - -- delivers P3 (displacement modulation) - -- implemented only for type="D" (optional) - -- optional t is 0 by default - bug fix: modulation not distinguishing between q and t; bug fix: modulated measurements not working - bug fix: not skipping set defaultLattice "{NaN NaN NaN}" bug fix: isosurface map atomic orbital fails - bug fix: vibrational display of modulation with distances doesn't update bug fix: vibration off causes unnecessary warning in console bug fix: draw symop broken - bug fix: array.mul(matrix3f) crashes Jmol - bug fix: select symop=1555 broken bug fix: set picking dragSelected not working code: refactored CifReader, separating out MMCifReader and MSCifReader - code: minor renaming/refactoring of methods in SV - code: adds javajs.api.JSONEncodable interface -- super-simple implementation in org.jmol.script.SV -- allows implementations of javajs to deliver custom JSON results - JmolVersion="14.0.1_2013.12.04" JmolVersion="13.3.9_dev_2013.12.04" This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-12-30 04:02:27
|
Revision: 19141 http://sourceforge.net/p/jmol/code/19141 Author: hansonr Date: 2013-12-30 04:01:56 +0000 (Mon, 30 Dec 2013) Log Message: ----------- Modified Paths: -------------- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-12-30 01:25:00 UTC (rev 19140) +++ branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-12-30 04:01:56 UTC (rev 19141) @@ -2,17 +2,17 @@ ___fullJmolProperties="src/org/jmol/viewer/Jmol.properties" -# THIS IS THE DEVELOPMENT TRUNK +# THIS IS THE RELEASE BRANCH -# Developers: to add a description of changes you have made, -# add it on a line below the "___JmolVersion=..." line. -# Don't use ___ in your text, as that is the key for stripping out -# the information saved in the JAR version of this file. +# Bug fixes only, please. +# # The quotes above look odd for a parameter file, but they are # important for the JavaScript version of Jmol. -___JmolVersion="14.0.3" +___JmolVersion="14.0.4_dev" +JmolVersion="14.0.3" + (synced with 14.1.3 2013.12.29) new feature: filter "MODCELL=x" This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2014-01-05 22:16:23
|
Revision: 19152 http://sourceforge.net/p/jmol/code/19152 Author: hansonr Date: 2014-01-05 22:16:19 +0000 (Sun, 05 Jan 2014) Log Message: ----------- Modified Paths: -------------- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2014-01-05 21:45:34 UTC (rev 19151) +++ branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2014-01-05 22:16:19 UTC (rev 19152) @@ -9,7 +9,7 @@ # The quotes above look odd for a parameter file, but they are # important for the JavaScript version of Jmol. -JmolVersion="14.0.4" +___JmolVersion="14.0.4" bug fix: rockets broken bug fix: PDB byChain, bySymop not supported. This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2014-01-09 20:50:18
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Revision: 19160 http://sourceforge.net/p/jmol/code/19160 Author: hansonr Date: 2014-01-09 20:50:12 +0000 (Thu, 09 Jan 2014) Log Message: ----------- ___JmolVersion="14.0.5" JmolVersion="14.0.5_dev_2014.01.09" bug fix: LCAOCartoon translucency broken bug fix: translucent backbone broken bug fix: pqr,p2n readers broken bug fix: isosurface map property xxx can fail if surface is a fragment that (somehow) has a point not associated with an underlying atom. Modified Paths: -------------- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2014-01-09 13:50:48 UTC (rev 19159) +++ branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2014-01-09 20:50:12 UTC (rev 19160) @@ -9,7 +9,8 @@ # The quotes above look odd for a parameter file, but they are # important for the JavaScript version of Jmol. -___JmolVersion="14.0.5_dev_2014.01.08" +___JmolVersion="14.0.5" +JmolVersion="14.0.5_dev_2014.01.09" bug fix: LCAOCartoon translucency broken bug fix: translucent backbone broken This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2014-01-19 21:58:36
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Revision: 19200 http://sourceforge.net/p/jmol/code/19200 Author: hansonr Date: 2014-01-19 21:58:34 +0000 (Sun, 19 Jan 2014) Log Message: ----------- Modified Paths: -------------- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2014-01-19 21:58:00 UTC (rev 19199) +++ branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2014-01-19 21:58:34 UTC (rev 19200) @@ -11,15 +11,16 @@ # The quotes above look odd for a parameter file, but they are # important for the JavaScript version of Jmol. +JmolVersion="14.0.7_dev_2014.01.19" ___JmolVersion="14.0.6" -JmolVersion="14.1.6_dev_2014.01.19" - bug fix: translucent geosurface was turned off; - recommend set TRANSLUCENT FALSE to remove inner translucent sections +JmolVersion="14.0.6_dev_2014.01.19" + bug fix: Jmol2.js should have commented lines in Jmol.Info but does not bug fix: JSpecView cannot close "Options...Show Header" panel in HTML5 bug fix: select visible not right after this sequence: This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2014-02-07 04:09:59
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Revision: 19282 http://sourceforge.net/p/jmol/code/19282 Author: hansonr Date: 2014-02-07 04:09:55 +0000 (Fri, 07 Feb 2014) Log Message: ----------- Modified Paths: -------------- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2014-02-07 03:32:34 UTC (rev 19281) +++ branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2014-02-07 04:09:55 UTC (rev 19282) @@ -2,13 +2,11 @@ ___JmolDate="$Date$" ___fullJmolProperties="src/org/jmol/viewer/Jmol.properties" - -# THIS IS THE DEVELOPMENT TRUNK -# Developers: to add a description of changes you have made, -# add it on a line below the "___JmolVersion=..." line. -# Don't use ___ in your text, as that is the key for stripping out -# the info rmation saved in the JAR version of this file. +# THIS IS THE RELEASE BRANCH + +# Bug fixes only, please. +# # The quotes above look odd for a parameter file, but they are # important for the JavaScript version of Jmol. This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2014-02-14 19:23:04
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Revision: 19322 http://sourceforge.net/p/jmol/code/19322 Author: hansonr Date: 2014-02-14 19:23:01 +0000 (Fri, 14 Feb 2014) Log Message: ----------- Modified Paths: -------------- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2014-02-14 19:17:34 UTC (rev 19321) +++ branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2014-02-14 19:23:01 UTC (rev 19322) @@ -12,10 +12,8 @@ # important for the JavaScript version of Jmol. -___JmolVersion="14.0.8" +___JmolVersion="14.1.8" -synced with Jmol 14.1.8 on Feb 24, 2014 - bug fix: set defaultLoadScript "{0 0 0}" actually sets that to {1 1 1} -- goes way way back to early Jmol math where there were no point-type variables bug fix: PyMOL reader update for Version 1700 lacking setting 83. This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2014-02-14 19:28:46
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Revision: 19323 http://sourceforge.net/p/jmol/code/19323 Author: hansonr Date: 2014-02-14 19:28:43 +0000 (Fri, 14 Feb 2014) Log Message: ----------- ___JmolVersion="14.0.8" JmolVersion="14.0.8_2014.02.14" feature change: IDTF exporter now calling media9 rather than movie15 in accompanying TeX file new feature: JSmol Info.z, Info.zIndexBase new feature: set cartoonRibose -- draws in ribose rings, with facets showing puckering -- connects via C4'-C5'-O5'-P explicitly -- shows C3'-O3' for reference. -- disables cartoonBaseEdges (Leontis-Westhof Edges) -- disabled by SET cartoonBaseEdges ON -- suggested by Rick Spinney, Ohio State new feature: anim frame [a,b,c,d] works with negative numbers to indicate ranges: -- anim frame [1, -5, 10, -6] --> [1,2,3,4,5,10,9,8,7,6] -- read as "1 through 5 and then 10 through 6" new feature: Tinker file reader (and FoldingXYZ reader upgrade) -- Can use Tinker:: but this is only required if first line is JUST an atomCount -- accommodates older Tinker format with n-1 atoms for atomCount -- allows for trajectories and desired model number new feature: (actually 13.1 but undocumented) animation frame [ 51 50 49 48 47 46 45 (etc) 27 1 2 3 4 5 6 7 (etc)....] new feature: x = compare({atomset1}, {atomset2}, "MAP") new feature: x = compare({atomset1}, {atomset2}, "MAP", "all") new feature: x = compare({atomset1}, {atomset2}, "MAP", "best") new feature: x = compare({atomset1}, {atomset2}, "MAP", "H") new feature: x = compare({atomset1}, {atomset2}, "MAP", "allH") new feature: x = compare({atomset1}, {atomset2}, "MAP", "bestH") -- generates one or more correlations lists based on non-aromatic SMILES -- optionally includes H atoms -- optionally generates all possible atom mappings -- returns int[][] = [ [a1 b1],[a2 b2],[a3 b3],... ] where an and bn are integer atom indices or list<int[][]> when "all" option is chosen. -- the following will generate one atom correlation map for two structures including hydrogen atoms: load files "a.mol" "b.mol" x = compare({1.1} {2.1} "MAP" "H") (useful for 2D/3D model atom matching) -- the following compares the model of caffeine from NCI to that from PubChem: load $caffeine;load append :caffeine;frame * select 2.1; label %[atomIndex] compare {1.1} {2.1} SMILES rotate translate x = compare({1.1}, {2.1}, "MAP" "bestH") for (a in x) {a1 = a[1];a2=a[2];select atomindex=a1;label @a2} new feature: compare {model1} {model2} SMILES -- no need to give SMILES; Jmol can generate it from {model1} new feature: x = {*}.find("SMILES", "H") -- generates SMILES with explicit H atoms bug fix: set defaultLoadScript "{0 0 0}" actually sets that to {1 1 1} -- goes way way back to early Jmol math where there were no point-type variables bug fix: PyMOL reader update for Version 1700 lacking setting 83. bug fix: -m option not working with Jmol.jar bug fix: PNGJ files within ZIP collections not being read. -- full PNGJ models can be extracted from MS Word .docx files. -- for example: show file "t.docx" [Content_Types].xml _rels/.rels word/_rels/document.xml.rels word/document.xml word/media/image1.png word/theme/theme1.xml word/settings.xml word/webSettings.xml docProps/core.xml word/styles.xml word/fontTable.xml docProps/app.xml load t.docx|word/media/image1.png bug fix: tensor("efg", "value") should return sparce array, not dense for missing tensors bug fix: JSmol now allows writing POVRAY, MAYA, IDTF, VRML, etc. both from Java and from HTML5 code: reworking of export classes bug fix: label @{math expression...} not working bug fix: interpretation of x and @x in select commands and {...} phrases -- Variable substitution has been unintuitive and inconsistent. For instance: x = "C or T" select @x -- works fine print {@x} -- fails The problem is the use of @ to reference the variable NAMED BY another variable within a math expression (print context) but not a select context. For instance: y = 3 x = "y" print x --> "y" print @x --> 3 Such referencing is important for math expressions, but the extension of this to atom expressions is not necessary and not generally useful. -- The current situation is as follows: x = "A or T" select @x --> all A and T groups print {@x} --> nothing (because @x is "the contents of the variable 'A or T'") -- This fix simplifies the situation by not allowing variable-variable referencing within atom expressions bounded by braces, just like within implicit atom expression commands (select, display, hide, delete, etc.). -- The result is much more consistent. The following do exactly what you think they would do: x = "A or T" select @x print {@x} -- The current way of doing this, by defining a temporary atom expression using the DEFINE (or @) command still works: x = "A or T" @y @x select y same as select @x -- Note that the difference between "select x" and "select @x" may be significant: ala = "cys" select ala --> selects all alanines select @ala --> selects all cysteines bug fix: for(i in ...) does not exit when i is assigned a value, as per documentation bug fix: for(x in ...) command broken and also quite inefficient. bug fix: substructure() function using SMILES instead of SMARTS, so only full structures; bug fix: better error trapping and messages in SMILES-related methods bug fix: make webexport discovery of path to Jmol.jar and jsmol.zip more robust. bug fix: getProperty extractModel not honoring subset bug fix: set pdbGetHeader TRUE does not capture REMARK3 REMARK290 REMARK350 bug fix: getProperty("JSON",....) should wrap value in {value:...} bug fix: MO persistent translucency broken in 11.x bug fix: show MENU write MENU load MENU all broken in 12.2 bug fix: {*}[n] should be empty if nAtoms <=n bug fix: abinit reader was nonfunctional bug fix: assign atom into into PDB file loses atom names bug fix: y = ([3])[1][1] should be [3] not 3 bug fix: break n nonfunctional bug fix: format() and label() functions limited to 4 arguments; should be unlimited bug fix: errors in paths to js code in web export templates. code: way more efficient for loop -- loop overhead decreased by > 80% code: JSmol: applying atom mapping between mol2D and mol3D for viewSets code: refactoring to enable SWING in JavaScript for all menus code: methods from jcampdxReader extracted to org.jmol.jsv.JDXMOLParser code: reader overhaul for setting atom coordinates in a consistent fashion Modified Paths: -------------- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2014-02-14 19:23:01 UTC (rev 19322) +++ branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2014-02-14 19:28:43 UTC (rev 19323) @@ -2,24 +2,77 @@ ___fullJmolProperties="src/org/jmol/viewer/Jmol.properties" -# THIS IS THE DEVELOPMENT TRUNK -# Developers: to add a description of changes you have made, -# add it on a line below the "___JmolVersion=..." line. -# Don't use ___ in your text, as that is the key for stripping out -# the information saved in the JAR version of this file. +# THIS IS THE RELEASE BRANCH + +# Bug fixes only, please. +# # The quotes above look odd for a parameter file, but they are # important for the JavaScript version of Jmol. -___JmolVersion="14.1.8" +___JmolVersion="14.0.8" + +JmolVersion="14.0.8_2014.02.14" + +feature change: IDTF exporter now calling media9 rather than movie15 in accompanying TeX file + +new feature: JSmol Info.z, Info.zIndexBase + +new feature: set cartoonRibose + -- draws in ribose rings, with facets showing puckering + -- connects via C4'-C5'-O5'-P explicitly + -- shows C3'-O3' for reference. + -- disables cartoonBaseEdges (Leontis-Westhof Edges) + -- disabled by SET cartoonBaseEdges ON + -- suggested by Rick Spinney, Ohio State + +new feature: anim frame [a,b,c,d] works with negative numbers to indicate ranges: + -- anim frame [1, -5, 10, -6] --> [1,2,3,4,5,10,9,8,7,6] + -- read as "1 through 5 and then 10 through 6" + +new feature: Tinker file reader (and FoldingXYZ reader upgrade) + -- Can use Tinker:: but this is only required if first line is JUST an atomCount + -- accommodates older Tinker format with n-1 atoms for atomCount + -- allows for trajectories and desired model number + +new feature: (actually 13.1 but undocumented) animation frame [ 51 50 49 48 47 46 45 (etc) 27 1 2 3 4 5 6 7 (etc)....] + +new feature: x = compare({atomset1}, {atomset2}, "MAP") +new feature: x = compare({atomset1}, {atomset2}, "MAP", "all") +new feature: x = compare({atomset1}, {atomset2}, "MAP", "best") +new feature: x = compare({atomset1}, {atomset2}, "MAP", "H") +new feature: x = compare({atomset1}, {atomset2}, "MAP", "allH") +new feature: x = compare({atomset1}, {atomset2}, "MAP", "bestH") + -- generates one or more correlations lists based on non-aromatic SMILES + -- optionally includes H atoms + -- optionally generates all possible atom mappings + -- returns int[][] = [ [a1 b1],[a2 b2],[a3 b3],... ] + where an and bn are integer atom indices + or list<int[][]> when "all" option is chosen. + -- the following will generate one atom correlation + map for two structures including hydrogen atoms: + load files "a.mol" "b.mol" + x = compare({1.1} {2.1} "MAP" "H") + (useful for 2D/3D model atom matching) + -- the following compares the model of caffeine from NCI to that from PubChem: + load $caffeine;load append :caffeine;frame * + select 2.1; label %[atomIndex] + compare {1.1} {2.1} SMILES rotate translate + x = compare({1.1}, {2.1}, "MAP" "bestH") + for (a in x) {a1 = a[1];a2=a[2];select atomindex=a1;label @a2} + +new feature: compare {model1} {model2} SMILES + -- no need to give SMILES; Jmol can generate it from {model1} + +new feature: x = {*}.find("SMILES", "H") + -- generates SMILES with explicit H atoms + bug fix: set defaultLoadScript "{0 0 0}" actually sets that to {1 1 1} -- goes way way back to early Jmol math where there were no point-type variables bug fix: PyMOL reader update for Version 1700 lacking setting 83. bug fix: -m option not working with Jmol.jar -feature change: IDTF exporter now calling media9 rather than movie15 in accompanying TeX file - bug fix: PNGJ files within ZIP collections not being read. -- full PNGJ models can be extracted from MS Word .docx files. -- for example: @@ -38,7 +91,7 @@ docProps/app.xml load t.docx|word/media/image1.png -new feature: JSmol Info.z, Info.zIndexBase + bug fix: tensor("efg", "value") should return sparce array, not dense for missing tensors bug fix: JSmol now allows writing POVRAY, MAYA, IDTF, VRML, etc. both from Java and from HTML5 @@ -97,63 +150,9 @@ select @ala --> selects all cysteines - -code: way more efficient for loop -- loop overhead decreased by > 80% bug fix: for(i in ...) does not exit when i is assigned a value, as per documentation bug fix: for(x in ...) command broken and also quite inefficient. - -JmolVersion="14.1.8_dev_2014.02.06" - -new feature: set cartoonRibose - -- draws in ribose rings, with facets showing puckering - -- connects via C4'-C5'-O5'-P explicitly - -- shows C3'-O3' for reference. - -- disables cartoonBaseEdges (Leontis-Westhof Edges) - -- disabled by SET cartoonBaseEdges ON - -- suggested by Rick Spinney, Ohio State - -new feature: anim frame [a,b,c,d] works with negative numbers to indicate ranges: - -- anim frame [1, -5, 10, -6] --> [1,2,3,4,5,10,9,8,7,6] - -- read as "1 through 5 and then 10 through 6" - -new feature: Tinker file reader (and FoldingXYZ reader upgrade) - -- Can use Tinker:: but this is only required if first line is JUST an atomCount - -- accommodates older Tinker format with n-1 atoms for atomCount - -- allows for trajectories and desired model number - -new feature: (actually 13.1 but undocumented) animation frame [ 51 50 49 48 47 46 45 (etc) 27 1 2 3 4 5 6 7 (etc)....] - -new feature: x = compare({atomset1}, {atomset2}, "MAP") -new feature: x = compare({atomset1}, {atomset2}, "MAP", "all") -new feature: x = compare({atomset1}, {atomset2}, "MAP", "best") -new feature: x = compare({atomset1}, {atomset2}, "MAP", "H") -new feature: x = compare({atomset1}, {atomset2}, "MAP", "allH") -new feature: x = compare({atomset1}, {atomset2}, "MAP", "bestH") - -- generates one or more correlations lists based on non-aromatic SMILES - -- optionally includes H atoms - -- optionally generates all possible atom mappings - -- returns int[][] = [ [a1 b1],[a2 b2],[a3 b3],... ] - where an and bn are integer atom indices - or list<int[][]> when "all" option is chosen. - -- the following will generate one atom correlation - map for two structures including hydrogen atoms: - load files "a.mol" "b.mol" - x = compare({1.1} {2.1} "MAP" "H") - (useful for 2D/3D model atom matching) - -- the following compares the model of caffeine from NCI to that from PubChem: - load $caffeine;load append :caffeine;frame * - select 2.1; label %[atomIndex] - compare {1.1} {2.1} SMILES rotate translate - x = compare({1.1}, {2.1}, "MAP" "bestH") - for (a in x) {a1 = a[1];a2=a[2];select atomindex=a1;label @a2} - -new feature: compare {model1} {model2} SMILES - -- no need to give SMILES; Jmol can generate it from {model1} - -new feature: x = {*}.find("SMILES", "H") - -- generates SMILES with explicit H atoms - bug fix: substructure() function using SMILES instead of SMARTS, so only full structures; bug fix: better error trapping and messages in SMILES-related methods bug fix: make webexport discovery of path to Jmol.jar and jsmol.zip more robust. @@ -169,7 +168,8 @@ bug fix: break n nonfunctional bug fix: format() and label() functions limited to 4 arguments; should be unlimited bug fix: errors in paths to js code in web export templates. - + +code: way more efficient for loop -- loop overhead decreased by > 80% code: JSmol: applying atom mapping between mol2D and mol3D for viewSets code: refactoring to enable SWING in JavaScript for all menus code: methods from jcampdxReader extracted to org.jmol.jsv.JDXMOLParser This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2014-02-16 00:12:55
|
Revision: 19330 http://sourceforge.net/p/jmol/code/19330 Author: hansonr Date: 2014-02-16 00:12:52 +0000 (Sun, 16 Feb 2014) Log Message: ----------- ___JmolVersion="14.0.8" JmolVersion="14.0.8_2014.02.15" -- note I am leaving version as 14.0.8 here but updating the date bug fix: bond/draw/isosurface picking broken bug fix: [1 -5 6 -2] gives [1 (-5+6-2)] instead of [(1-5) (6-2)] Modified Paths: -------------- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2014-02-16 00:11:54 UTC (rev 19329) +++ branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2014-02-16 00:12:52 UTC (rev 19330) @@ -12,7 +12,8 @@ -___JmolVersion="14.0.8_2014.02.15" +___JmolVersion="14.0.8" +JmolVersion="14.0.8_2014.02.15" -- note I am leaving version as 14.0.8 here but updating the date bug fix: bond/draw/isosurface picking broken This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2014-02-17 03:09:07
|
Revision: 19340 http://sourceforge.net/p/jmol/code/19340 Author: hansonr Date: 2014-02-17 03:09:01 +0000 (Mon, 17 Feb 2014) Log Message: ----------- Modified Paths: -------------- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2014-02-17 01:28:47 UTC (rev 19339) +++ branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2014-02-17 03:09:01 UTC (rev 19340) @@ -10,7 +10,8 @@ # important for the JavaScript version of Jmol. -___JmolVersion="14.0.8_2014.02.16" +___JmolVersion="14.0.8" +JmolVersion="14.0.8_2014.02.16" -- note I am leaving version as 14.0.8 here but updating the date bug fix: PyMOL reader multiple bond view This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2014-03-31 00:16:30
|
Revision: 19546 http://sourceforge.net/p/jmol/code/19546 Author: hansonr Date: 2014-03-31 00:16:24 +0000 (Mon, 31 Mar 2014) Log Message: ----------- ___JmolVersion="14.0.12" JmolVersion="14.1.12_2014.03.30" changes since 14.0.11: new feature: JSpecView getSolutionColor fill/all/none/false -- any combination of these four flags -- fill: fill area under a VIS spectrum with color -- none: remove fill -- all: do this for all spectra, not just the selected spectrum -- false: use interpolation method rather than curve fitting (see jspecview.common.Visible.java for details) new feature: JSpecView PEAK command -- adds PEAK GC/MS "#1" -- #1 here indicates "MS for first GC peak" summary: We now have general ZIP and image file (including PDF) creation in JavaScript independent of Jmol itself. new feature: x= format("JSON", data) -- simple way to generate JSON code. new feature: x = format("base64", data) -- creates base64-encoding of the data -- prepends the string with ";base64," new feature; binary byte array -- from array(s) where s starts with ";base64," -- from binary associative arrays new feature: binary associative arrays -- Any array containing "$_BINARY_$" as a key. -- Values may contain raw byte array data, but need not. -- Can be expanded or changed, just like any associative array. -- Seen in string form when in a string context. -- .type of elements will report "byteArray" new feature: x = write("PNGJ") -- Creates a binary associative array equivalent to writing a PNGJ file -- Contains keys "_IMAGE_", "JmolManifest.txt", "state.spt" and all associated files. new feature: write VAR x "filename" or write @x "filename" -- Where x is a binary array or a binary associative array. -- When x is a binary array, writes binary data to a file. -- When x is an array, creates a ZIP file (or PNGJ file, if _IMAGE_ is present and is PNG format), automatically converting strings starting with ";base64," to byte arrays in the ZIP file. To do the same with x a binary array, just use @{array(x)} instead of @x. new feature: x = load("myfile",true) -- Creates a binary associative array variable x that contains the contents of the file file. -- data are stored as raw bytes. -- If the file is a standard file, the key "_DATA_" will hold the file data. -- If the file is a PNGJ file, the key "_IMAGE_" will hold the image data, and additional files are keyed by file name. -- If the file is a zip file, the files are keyed by file name. -- Note that x = load("myfile") without "true" loads the contents of the file into x and, if the file is a PNGJ or ZIP file, just loads the list of files in the collection, not the actual data. new feature: filter "ATOM" opposite of filter "HETATM" new feature: load ASYNC .... new feature: script ASYNC .... -- load and script ASYNC start a new asynchronous thread to load the file and then continue after that. -- JSmol/HTML5 only; others ignore new feature: Mol3D reader new feature: show CHEMICAL STDINCHIKEY new feature: show CHEMICAL STDINCHI new feature: load ":inchikey:xxxxx" -- requires STANDARD InChIKey (as from {*}.find("chemical", "stdinchikey") new feature: x = {*}.find("chemical",type) -- type is "smiles", "inchi", "stdinchi", "inchikey", "stdinchikey" -- uses NCI/CADD CIR -- Note that unlike SHOW CHEMICAL, "InChIKey=" and "InChI=" are dropped -- Note that unlike SHOW CHEMICAL, trailing new line char is removed new feature: x = smilesString.find("chemical",type) -- type is "smiles", "inchi", "stdinchi", "inchikey", "stdinchikey" -- allows going directly from SMILES to other quantities -- uses NCI/CADD CIR -- Note that unlike SHOW CHEMICAL, "InChIKey=" and "InChI=" are dropped -- Note that unlike SHOW CHEMICAL, trailing new line char is removed bug fix: NWChem reader broken bug fix: JSpecView GC/MS issues bug fix: JSmol callbacks should refer to "jmolApplet0" not "jmolApplet0_object" bug fix: set cameraDepth not working -- note that loading of PyMOL files affects this setting, which is reset only using the INITIALIZE command bug fix: getProperty() function does not recognize a list as a variable and returns it as a string bug fix: Dsn6Reader.java misnamed, causing EDS map file load error in JavaScript only. (I did not know that was even possible!) bug fix: java.io.dataStreamReader.readShort() does not take into account JavaScript equivalence of short and int, causing "-1" to be read as 65535. bug fix: minimum modulationScale set to 1; should be 0.1. bug fix: translucent echo backgrounds broken bug fix: filter "HETATM" does not work bug fix: write XYZ broken by changes to the way arrays are shown with the PRINT command bug fix: x = adfjladj(3) crashes Jmol bug fix: x[0] = "tst" "here" "now" should cause script exception bug fix: isosurface MOLECULAR delivers wrong surface bug fix: spacefill ionic not working bug fix: set cameraDepth disabled bug fix: some translations not being carried out. bug fix: msCIF reader not accepting normalized commensurate Fourier vectors bug fix: JSmol/HTML MSIE local installation AJAX working again (still no binary files) code: variable compression issues in Jmol and JSV code: org.jmol.io and org.jmol.io2 consolidated code: select water hard-coded for speed (2 x faster) code: careful attention to loading of biomolecules results in 160K core bio load savings code: JavaScript core load reduced by 2% (30KB) by changing high-frequency global name "viewer" to "vwr" code: refactoring of image writing code to javajs.img for general use code: refactoring of zip code into javajs.util for general use code: refactoring of minimization code saves 10KB code: isosurface MOLECULAR speed-up by a factor of 10. -- better handling of constants during iteration -- better identification of unnecessary edges and faces Modified Paths: -------------- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2014-03-30 21:04:51 UTC (rev 19545) +++ branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2014-03-31 00:16:24 UTC (rev 19546) @@ -143,7 +143,6 @@ -- better handling of constants during iteration -- better identification of unnecessary edges and faces - JmolVersion="14.1.12_2014.03.27b" bug fix: NWChem reader broken This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2014-04-01 14:28:29
|
Revision: 19563 http://sourceforge.net/p/jmol/code/19563 Author: hansonr Date: 2014-04-01 14:28:24 +0000 (Tue, 01 Apr 2014) Log Message: ----------- re-release due to missing class files in Java version Modified Paths: -------------- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2014-04-01 14:04:26 UTC (rev 19562) +++ branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2014-04-01 14:28:24 UTC (rev 19563) @@ -11,8 +11,10 @@ # The quotes above look odd for a parameter file, but they are # important for the JavaScript version of Jmol. -___JmolVersion="14.0.13_2014.03.31" +JmolVersion="14.1.13_2014.03.31" +new feature: Gaussian fchk file reader + bug fix: A=[]; A[3] = 5 not working new feature: var x,y,z; @@ -20,10 +22,11 @@ -- similar to JavaScript -- initializes the variable to "" + bug fix: var x not isolated to script context bug fix: ellipsoid command broken -JmolVersion="14.0.12" +__JmolVersion="14.1.12b" JmolVersion="14.1.12_2014.03.30" changes since 14.1.11: This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2014-04-01 14:40:58
|
Revision: 19565 http://sourceforge.net/p/jmol/code/19565 Author: hansonr Date: 2014-04-01 14:40:55 +0000 (Tue, 01 Apr 2014) Log Message: ----------- Modified Paths: -------------- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2014-04-01 14:35:29 UTC (rev 19564) +++ branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2014-04-01 14:40:55 UTC (rev 19565) @@ -26,7 +26,7 @@ bug fix: var x not isolated to script context bug fix: ellipsoid command broken -__JmolVersion="14.1.12b" +___JmolVersion="14.0.12b" JmolVersion="14.1.12_2014.03.30" changes since 14.1.11: This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2014-04-02 03:18:32
|
Revision: 19573 http://sourceforge.net/p/jmol/code/19573 Author: hansonr Date: 2014-04-02 03:18:27 +0000 (Wed, 02 Apr 2014) Log Message: ----------- ___JmolVersion="14.0.13" JmolVersion="14.0.13_2014.04.01c" bug fix: changes to var incomplete bug fix: JmolAppletSigned0.jar missing export classes (POV-Ray, VRML, for example) bug fix: Mac Spartan spardir reading -- for web, use zipped up version of spardir Modified Paths: -------------- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2014-04-02 03:15:13 UTC (rev 19572) +++ branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2014-04-02 03:18:27 UTC (rev 19573) @@ -11,8 +11,14 @@ # The quotes above look odd for a parameter file, but they are # important for the JavaScript version of Jmol. -JmolVersion="14.1.13_2014.03.31" +___JmolVersion="14.0.13" +JmolVersion="14.0.13_2014.04.01c" +bug fix: changes to var incomplete +bug fix: JmolAppletSigned0.jar missing export classes (POV-Ray, VRML, for example) +bug fix: Mac Spartan spardir reading + -- for web, use zipped up version of spardir + new feature: Gaussian fchk file reader bug fix: A=[]; A[3] = 5 not working @@ -26,7 +32,7 @@ bug fix: var x not isolated to script context bug fix: ellipsoid command broken -___JmolVersion="14.0.12b" +JmolVersion="14.1.12" JmolVersion="14.1.12_2014.03.30" changes since 14.1.11: This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2014-04-02 04:18:29
|
Revision: 19575 http://sourceforge.net/p/jmol/code/19575 Author: hansonr Date: 2014-04-02 04:18:18 +0000 (Wed, 02 Apr 2014) Log Message: ----------- Modified Paths: -------------- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2014-04-02 03:19:12 UTC (rev 19574) +++ branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2014-04-02 04:18:18 UTC (rev 19575) @@ -2,12 +2,10 @@ ___fullJmolProperties="src/org/jmol/viewer/Jmol.properties" -# THIS IS THE DEVELOPMENT TRUNK +# THIS IS THE RELEASE BRANCH -# Developers: to add a description of changes you have made, -# add it on a line below the "___JmolVersion=..." line. -# Don't use ___ in your text, as that is the key for stripping out -# the information saved in the JAR version of this file. +# Bug fixes only, please. +# # The quotes above look odd for a parameter file, but they are # important for the JavaScript version of Jmol. This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2014-04-02 04:19:35
|
Revision: 19577 http://sourceforge.net/p/jmol/code/19577 Author: hansonr Date: 2014-04-02 04:19:32 +0000 (Wed, 02 Apr 2014) Log Message: ----------- Modified Paths: -------------- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2014-04-02 04:19:08 UTC (rev 19576) +++ branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2014-04-02 04:19:32 UTC (rev 19577) @@ -10,7 +10,7 @@ # important for the JavaScript version of Jmol. ___JmolVersion="14.0.13" -JmolVersion="14.0.13_2014.04.01c" +JmolVersion="14.0.13_2014.04.01d" bug fix: changes to var incomplete bug fix: JmolAppletSigned0.jar missing export classes (POV-Ray, VRML, for example) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2014-06-09 17:41:17
|
Revision: 19793 http://sourceforge.net/p/jmol/code/19793 Author: hansonr Date: 2014-06-09 17:41:11 +0000 (Mon, 09 Jun 2014) Log Message: ----------- Modified Paths: -------------- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2014-06-09 17:16:40 UTC (rev 19792) +++ branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2014-06-09 17:41:11 UTC (rev 19793) @@ -758,7 +758,7 @@ summary: We now have general ZIP and image file (including PDF) creation in JavaScript independent of Jmol itself. -new feature; byteArray type +new feature: byteArray type -- from format("byteArray", x) where x is an integer array, or x is a string starting with ";base64," This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2014-06-10 00:19:51
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Revision: 19800 http://sourceforge.net/p/jmol/code/19800 Author: hansonr Date: 2014-06-10 00:19:46 +0000 (Tue, 10 Jun 2014) Log Message: ----------- ___JmolVersion="14.0.17_2014.06.09" synchonized with Jmol 14.1.17 June 9, 2014 bug fix: zoomto broken bug fix: atoms turned off with restrict still clickable Modified Paths: -------------- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2014-06-10 00:12:47 UTC (rev 19799) +++ branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2014-06-10 00:19:46 UTC (rev 19800) @@ -9,15 +9,13 @@ # The quotes above look odd for a parameter file, but they are # important for the JavaScript version of Jmol. -___JmolVersion="14.0.18_2014.06.09" +___JmolVersion="14.0.17_2014.06.09" +synchonized with Jmol 14.1.17 June 9, 2014 + bug fix: zoomto broken bug fix: atoms turned off with restrict still clickable -JmolVersion="14.0.17" - -synchonized with Jmol 14.1.17 June 9, 2014 - JmolVersion="14.1.17_2014.06.07" FEATURE CHANGE: jmolCommandInput 6th parameter added is default value This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2014-06-10 14:25:35
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Revision: 19811 http://sourceforge.net/p/jmol/code/19811 Author: hansonr Date: 2014-06-10 14:25:22 +0000 (Tue, 10 Jun 2014) Log Message: ----------- ___JmolVersion="14.0.17_2014.06.10" bug fix: 06.09 broke unitcell display Modified Paths: -------------- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2014-06-10 14:23:42 UTC (rev 19810) +++ branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2014-06-10 14:25:22 UTC (rev 19811) @@ -10,7 +10,7 @@ # important for the JavaScript version of Jmol. -___JmolVersion="14.0.17_2014.06.09b" +___JmolVersion="14.0.17_2014.06.10" bug fix: 06.09 broke unitcell display bug fix: WebPanel error trapping problem; too long file name for tar file This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2014-06-13 14:12:15
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Revision: 19827 http://sourceforge.net/p/jmol/code/19827 Author: hansonr Date: 2014-06-13 14:12:04 +0000 (Fri, 13 Jun 2014) Log Message: ----------- Modified Paths: -------------- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2014-06-13 13:03:52 UTC (rev 19826) +++ branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2014-06-13 14:12:04 UTC (rev 19827) @@ -1,15 +1,10 @@ ___JmolDate="$Date$" ___fullJmolProperties="src/org/jmol/viewer/Jmol.properties" - -# THIS IS THE RELEASE BRANCH +# ALL WORK ON THIS BRANCH IS COMPLETE. +# NO MORE REVISIONS, PLEASE. +# SEE JMOL 14.2.0/14.2.1 -# Bug fixes only, please. -# -# The quotes above look odd for a parameter file, but they are -# important for the JavaScript version of Jmol. - - ___JmolVersion="14.0.17_2014.06.11" bug fix: set pdbAddHydrogens fails for structures with ANISOU records This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |