From: <ha...@us...> - 2008-07-17 05:11:07
|
Revision: 9606 http://jmol.svn.sourceforge.net/jmol/?rev=9606&view=rev Author: hansonr Date: 2008-07-17 05:11:05 +0000 (Thu, 17 Jul 2008) Log Message: ----------- new Quaternion algorithm uses double precision Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-07-17 05:10:21 UTC (rev 9605) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-07-17 05:11:05 UTC (rev 9606) @@ -3,10 +3,10 @@ version=11.5.48_dev +# code: simpler matrix-->quaternion code # bug fix: 11.5.47 shows oddly sized arrow for very first rendering # bug fix: quaternion frame "n" after rotationSelected does not reset NH hydrogen positions # new feature: // at beginning of a line marks comments - # ----------------------------------------------------------------------------- #version=11.5.47 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2008-07-19 14:09:35
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Revision: 9617 http://jmol.svn.sourceforge.net/jmol/?rev=9617&view=rev Author: hansonr Date: 2008-07-19 14:09:23 +0000 (Sat, 19 Jul 2008) Log Message: ----------- 11.5.48 VERSION # new feature: mol file bond type 8 as partial # code: compiler error reporting improved # bug fix: PDB site definition does not ignore empty site definitions # bug fix: DEFINE can cause compiling error, e.g. "[2MO]" in 1tmo # bug fix: quaternion derivative DRAW arrows placed on residue i+1 instead of residue i # bug fix: connect aromatic auto; select connected([bond type],...) # bug fix: queue thread termination when applets are off screen # bug fix : sheetsmoothing not consistent among structures in multi-chain systems # bug fix: messages not sent to messageCallback # code: simpler matrix-->quaternion code # bug fix: 11.5.47 shows oddly sized arrow for very first rendering # bug fix: quaternion frame "n" after rotationSelected does not reset NH hydrogen positions # new feature: // at beginning of a line marks comments Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-07-19 14:04:07 UTC (rev 9616) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-07-19 14:09:23 UTC (rev 9617) @@ -1,7 +1,7 @@ # Developers: to add a description of changes you have made, # add it on line starting with # below the "version=..." line -version=11.5.48_dev +version=11.5.48 # new feature: mol file bond type 8 as partial # code: compiler error reporting improved @@ -16,6 +16,7 @@ # bug fix: 11.5.47 shows oddly sized arrow for very first rendering # bug fix: quaternion frame "n" after rotationSelected does not reset NH hydrogen positions # new feature: // at beginning of a line marks comments + # ----------------------------------------------------------------------------- #version=11.5.47 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2008-07-19 14:50:09
|
Revision: 9618 http://jmol.svn.sourceforge.net/jmol/?rev=9618&view=rev Author: nicove Date: 2008-07-19 14:49:33 +0000 (Sat, 19 Jul 2008) Log Message: ----------- Version Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-07-19 14:09:23 UTC (rev 9617) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-07-19 14:49:33 UTC (rev 9618) @@ -1,8 +1,12 @@ # Developers: to add a description of changes you have made, # add it on line starting with # below the "version=..." line -version=11.5.48 +version=11.5.49_dev +# ----------------------------------------------------------------------------- + +#version=11.5.48 + # new feature: mol file bond type 8 as partial # code: compiler error reporting improved # bug fix: PDB site definition does not ignore empty site definitions This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2008-07-21 17:20:51
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Revision: 9624 http://jmol.svn.sourceforge.net/jmol/?rev=9624&view=rev Author: nicove Date: 2008-07-21 17:20:47 +0000 (Mon, 21 Jul 2008) Log Message: ----------- Version Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-07-21 15:12:30 UTC (rev 9623) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-07-21 17:20:47 UTC (rev 9624) @@ -1,8 +1,12 @@ # Developers: to add a description of changes you have made, # add it on line starting with # below the "version=..." line -version=11.5.49 +version=11.5.50_dev +# ----------------------------------------------------------------------------- + +#version=11.5.49 + # bug fix: strange "scripted: ?" message with measurements removed # bug fix: extra values in measure reporting, and wrong format # bug fix: 11.5.48 is broken for scripts with array definitions such as This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2008-10-26 23:26:31
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Revision: 10152 http://jmol.svn.sourceforge.net/jmol/?rev=10152&view=rev Author: hansonr Date: 2008-10-26 23:26:27 +0000 (Sun, 26 Oct 2008) Log Message: ----------- version=11.7.6_dev # code: ScriptWindow public: sendConsoleEcho,sendConsoleMessage,notifyScriptStart,notifyScriptTermination,PdbReader Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-10-26 23:25:56 UTC (rev 10151) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-10-26 23:26:27 UTC (rev 10152) @@ -3,7 +3,7 @@ version=11.7.6_dev -# code: ScriptWindow public: sendConsoleEcho,sendConsoleMessage,notifyScriptStart,notifyScriptTermination +# code: ScriptWindow public: sendConsoleEcho,sendConsoleMessage,notifyScriptStart,notifyScriptTermination,PdbReader # ----------------------------------------------------------------------------- This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2009-03-22 16:00:09
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Revision: 10736 http://jmol.svn.sourceforge.net/jmol/?rev=10736&view=rev Author: nicove Date: 2009-03-22 15:59:59 +0000 (Sun, 22 Mar 2009) Log Message: ----------- Version Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2009-03-22 09:04:31 UTC (rev 10735) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2009-03-22 15:59:59 UTC (rev 10736) @@ -1,8 +1,12 @@ # Developers: to add a description of changes you have made, # add it on a line starting with # below the "version=..." line -version=11.7.30 +version=11.7.31_dev +# ----------------------------------------------------------------------------- + +#version=11.7.30 + # bug fix: signed applet does not use CD to set dialog default directory # bug fix: errorCallback not functional # new feature: set autoLoadOrientation (default: FALSE) automatically sets "reset" orientation to that in file, if present @@ -10,6 +14,7 @@ # code: generalized setTransform() in JmolAdapter readers CSF and SpartanSmol (.spardir) # bug fix: Spartan .spardir /input files not being read # bug fix: draw arrow/vector slightly overshoots end point + # ----------------------------------------------------------------------------- #version=11.7.29 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-04-08 21:16:07
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Revision: 10780 http://jmol.svn.sourceforge.net/jmol/?rev=10780&view=rev Author: hansonr Date: 2009-04-08 21:15:31 +0000 (Wed, 08 Apr 2009) Log Message: ----------- version=11.7.32_dev # bug fix: Spartan SMOL file reader failure (coded & instead of && in if statement!) Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2009-04-08 18:55:41 UTC (rev 10779) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2009-04-08 21:15:31 UTC (rev 10780) @@ -3,6 +3,7 @@ version=11.7.32_dev +# bug fix: Spartan SMOL file reader failure (coded & instead of && in if statement!) # new feature: CML "isotope" and CML "partial12" bond order. # new feature: GAMESS reader reads NBOs using # load "xxx.gamess" filter "!EIGEN" # to only load NBOs; by default ALL MOs are loaded. This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-05-11 03:57:55
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Revision: 10852 http://jmol.svn.sourceforge.net/jmol/?rev=10852&view=rev Author: hansonr Date: 2009-05-11 03:57:46 +0000 (Mon, 11 May 2009) Log Message: ----------- 11.7.35 VERSION # bug fix: (applet) jmolGetPropertyAsString("image") not functional # new feature: label %G -- group index, like atom index, 0-based for entire collection # new feature: ramachandran DRAW -- draws dihedral planes and angles # bug fix: draw/isosurface *name* # bug fix: data "append" does not set model the way load "append" does # bug fix: application frame arrows do not work after loading multiple models Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2009-05-11 03:54:11 UTC (rev 10851) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2009-05-11 03:57:46 UTC (rev 10852) @@ -1,7 +1,7 @@ # Developers: to add a description of changes you have made, # add it on a line starting with # below the "version=..." line -version=11.7.35_dev +version=11.7.35 # bug fix: (applet) jmolGetPropertyAsString("image") not functional # new feature: label %G -- group index, like atom index, 0-based for entire collection This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-07-12 04:53:59
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Revision: 11204 http://jmol.svn.sourceforge.net/jmol/?rev=11204&view=rev Author: hansonr Date: 2009-07-12 04:53:56 +0000 (Sun, 12 Jul 2009) Log Message: ----------- version=11.7.47 # new feature: navigation now does continuous motion with arrow keys; # SPACE to stop # LEFT/RIGHT to pan left or right # UP/DN to move forward/back # ALT UP/DN to pitch up/down # CNTL UP/DN to increase/decrease speed in larger amounts Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2009-07-12 04:50:34 UTC (rev 11203) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2009-07-12 04:53:56 UTC (rev 11204) @@ -4,7 +4,13 @@ version=11.7.47 # code: more efficient labelGroup calculatiion -# new feature: navigation now does continuous motion with arrow keys; space to stop +# new feature: navigation now does continuous motion with arrow keys; +# SPACE to stop +# LEFT/RIGHT to pan left or right +# UP/DN to move forward/back +# ALT UP/DN to pitch up/down +# CNTL UP/DN to increase/decrease speed in larger amounts + # bug fix: navigationmode not properly adapting with window resize or antialiasdisplay # new feature: draw HELIX AXIS or quaternion HELIX AXIS, also for DNA/RNA # code: cleaned up navigation business; an attempt at navigating a surface...Maybe not... This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-10-26 04:59:27
|
Revision: 11627 http://jmol.svn.sourceforge.net/jmol/?rev=11627&view=rev Author: hansonr Date: 2009-10-26 04:59:20 +0000 (Mon, 26 Oct 2009) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2009-10-26 04:57:16 UTC (rev 11626) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2009-10-26 04:59:20 UTC (rev 11627) @@ -3,18 +3,15 @@ version=11.9.7_dev -# code: reworking of JVXL reader classes, creation of JvxlCoder.java -# code: reworking of ASimpleJvxlWriter to utilize standard classes -# code: reworking of Parser, TextFormat, ArrayUtil, and Escape -# to not utilize any nonstandard Java classes (such as -# Graphics3D or BondSet or Token), thus making these -# classes generic and not Jmol-dependent. -# # new feature: isosurface/pmesh commands accept unquoted file names. # new feature: Jvxl 2.0 -- XML format for JVXL files # here, initially, only being used for writing contour or triangle data # NOTE -- Jvxl-XML is not backward-compatible with previous versions of Jmol. # for now use SET testflag4 ON to enable full XML writing of JVXL files +# new feature: Jmol frank hover provides menu tip +# new feature: getproperty shapeinfo better reports contour levels +# new feature: isosurface ... map CONTOUR DISCRETE [0.5, 1.0, 1.5, 2.0] +# new feature: isosurface ... map CONTOUR INCREMENT {0.0, 1.0, 0.2} # # bug fix: isosurface does not clear data after functionXY or functionXYZ # bug fix: label %vx giving x coord, not vibration x component @@ -23,13 +20,16 @@ # bug fix: PQR reader not adaptive # bug fix: zshade now working correctly -- not tied to slab on # bug fix: setting spacefill to a large user-defined VDW radius incorrect -# new feature: Jmol frank hover provides menu tip -# new feature: getproperty shapeinfo better reports contour levels -# new feature: isosurface ... map CONTOUR DISCRETE [0.5, 1.0, 1.5, 2.0] -# new feature: isosurface ... map CONTOUR INCREMENT {0.0, 1.0, 0.2} -# code: StatusListener refactored as individual class # bug fix: Gaussian 09 LOG file reader upgrade for MOs # bug fix: unitcell offset {1 1 1}; select UNITCELL +# +# code: reworking of JVXL reader classes, creation of JvxlCoder.java +# code: reworking of ASimpleJvxlWriter to utilize standard classes +# code: reworking of Parser, TextFormat, ArrayUtil, and Escape +# to not utilize any nonstandard Java classes (such as +# Graphics3D or BondSet or Token), thus making these +# classes generic and not Jmol-dependent. +# code: StatusListener refactored as individual class -------------------------------------------------------------- This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-01-28 16:15:42
|
Revision: 12256 http://jmol.svn.sourceforge.net/jmol/?rev=12256&view=rev Author: hansonr Date: 2010-01-28 16:15:27 +0000 (Thu, 28 Jan 2010) Log Message: ----------- 11.9.23 VERSION # new feature: set preserveState FALSE (default TRUE) -- # for some applications it can be helpful to turn off the # feature of preserving the state in order to save memory # * This flag if set FALSE: # * # * 1) turns UNDO off for the application # * 2) turns history off # * 3) prevents saving of inlinedata for later LOAD "" commands # * 4) turns off the saving of changed atom properties # * 5) does not guarantee accurate state representation # * # * It is useful in situations such as web sites where # * memory is an issue and there is no need for such. # * # * # new feature: set strutsMultiple (default FALSE) allows multiple struts on a given atom # new feature: set LOGFILE "name" -- log file will be "JmolLog_" + name # in the Jar file directory -- note that this is not # ever possible with the web-based version, even with the # signed applet, but signed applet or application running # locally can write to this file # # set logFile "test" # # new feature: LOG command -- same as print but to the log file # can be prepended with nicely formatted date with "NOW" as the # first three characters # # log "NOW\n" + getProperty("modelInfo") # # new feature: show state [name] # new feature: all saved orientations now saved in state # bug fix: isosurface ID @{xxxx} .... #ID .. #ID not overriding # new feature: write MESH t.mesh JVXL "vertex-only" very compact style mesh surface # new feature: isosurface SLAB {plane definition} [optional offset] # new feature: -{plane definition} refers to opposite-facing plane as {plane definition} # bug fix: frame *;draw {atomno=1} {atomno=5} not working properly # bug fix: frame ALIGN for trajectories # bug fix: isosurface vdw broken # new feature: PDB trajectory for concatenated PDB files (no "MODEL" line) # bug fix: pdb reader trajectory error # bug fix: multitouch applet activation via display.hasFocus() # working properly except you can't just jump from one # page to another if applets are producing the SparshUI server # be sure to go through an intermediary page, like a MAIN page # -------------------------------------------------------------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2010-01-28 15:57:43 UTC (rev 12255) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2010-01-28 16:15:27 UTC (rev 12256) @@ -1,7 +1,7 @@ # Developers: to add a description of changes you have made, # add it on a line starting with # below the "version=..." line -version=11.9.23_dev +version=11.9.23 # new feature: set preserveState FALSE (default TRUE) -- # for some applications it can be helpful to turn off the This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-04-18 11:04:04
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Revision: 12887 http://jmol.svn.sourceforge.net/jmol/?rev=12887&view=rev Author: hansonr Date: 2010-04-18 11:03:57 +0000 (Sun, 18 Apr 2010) Log Message: ----------- version=12.0.RC7_dev # bug fix for parallel processing and isosurface Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2010-04-18 11:02:58 UTC (rev 12886) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2010-04-18 11:03:57 UTC (rev 12887) @@ -3,6 +3,8 @@ version=12.0.RC7_dev +# bug fix for parallel processing and isosurface + # -------------------------------------------------------------- #version=12.0.RC6 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-09-16 03:36:12
|
Revision: 14306 http://jmol.svn.sourceforge.net/jmol/?rev=14306&view=rev Author: hansonr Date: 2010-09-16 03:36:06 +0000 (Thu, 16 Sep 2010) Log Message: ----------- version=12.1.11 # test: set testFlag3 -- reports mouse action and mode (for Eric Martz) # new feature: set multipleBondRadiusFactor 0.75 # new feature: set isosurfacePropertySmoothingPower # 0 (no property smoothing) # 10 (very strong smoothing) # 7 (default, same as Jmol 11.8) # new feature: AppletConsole allows embedding in larger applications # new feature: smooth on-the-fly language changes in applet and application # new feature: integrated AppConsole for embedded Jmol -- see Integration.java # new feature: multipleBondSpacing # set multipleBondSpacing = -1 (default, varies with viewing angle) # set multipleBondSpacing = -0.5 (half that distance; varies with viewing angle) # set multipleBondSpacing = 0.35 (positive ==> fixed multiple bond spacing) # bug fix: SmarterJmolAdapter should not read zip bytes it doesn't have to # bug fix: spacefill JMOL does not work # bug fix: Jmol 12 does not read old 11.1 isosurface commands from states # bug fix: load {i j k} RANGE x.x not expanding load box by 1 in each direction # bug fix: applet console does not display startup message # bug fix: console buttons do not change with new language # bug fix: undo/redo problems in AppConsole # bug fix: crystal reader can't read selected model # bug fix: 3.5E+0.0 read as "3.5 0.0" # bug fix: navY/navy color issue # bug fix: write PDB for nonPDB files incorrect # code: streamlined AppConsole and AppletConsole # code: GuiMap/JmolConsole AbstractButton methods merged # code: AppConsole now implements JmolStatusListener, called by JmolPanel.notifyCallback Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2010-09-16 03:35:30 UTC (rev 14305) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2010-09-16 03:36:06 UTC (rev 14306) @@ -32,7 +32,7 @@ # code: streamlined AppConsole and AppletConsole # code: GuiMap/JmolConsole AbstractButton methods merged -# code: AppConsole now implements JmolStatusListener, called by JmolPanel.notifyCallback +# code: AppConsole now implements JmolCallbackListener, called by JmolPanel.notifyCallback # -------------------------------------------------------------- This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2010-11-29 19:23:11
|
Revision: 14729 http://jmol.svn.sourceforge.net/jmol/?rev=14729&view=rev Author: nicove Date: 2010-11-29 19:23:04 +0000 (Mon, 29 Nov 2010) Log Message: ----------- Version Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2010-11-29 17:17:47 UTC (rev 14728) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2010-11-29 19:23:04 UTC (rev 14729) @@ -1,8 +1,12 @@ # Developers: to add a description of changes you have made, # add it on a line starting with # below the "version=..." line -version=12.1.24 +version=12.1.25_dev +# -------------------------------------------------------------- + +#version=12.1.24 + # new feature: isosurface solvent [optionalRadius default:1.2] FULL # FULL option does full triples-test, about 3 times slower than # standard Jmol solvent/MOLECULAR surface, which only checks pairs. This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-02-06 23:55:27
|
Revision: 15132 http://jmol.svn.sourceforge.net/jmol/?rev=15132&view=rev Author: hansonr Date: 2011-02-06 23:55:21 +0000 (Sun, 06 Feb 2011) Log Message: ----------- version=12.1.34_dev # bug fix: JavaScript getPropertyAsArray("auxiliaryInfo.models") will fail for crystal structures Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-02-06 23:54:32 UTC (rev 15131) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-02-06 23:55:21 UTC (rev 15132) @@ -4,6 +4,7 @@ version=12.1.34_dev +# bug fix: JavaScript getPropertyAsArray("auxiliaryInfo.models") will fail for crystal structures # bug fix: undocumented select within(hkl,...) and select within(plane,...) missing # bug fix: message @x should replace x with a variable; "message @x is the value of x" should not # bug fix: older syntax MESSAGE %{x} for variable value missing This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2011-04-26 21:25:50
|
Revision: 15407 http://jmol.svn.sourceforge.net/jmol/?rev=15407&view=rev Author: nicove Date: 2011-04-26 21:25:44 +0000 (Tue, 26 Apr 2011) Log Message: ----------- Version Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-04-26 20:33:35 UTC (rev 15406) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-04-26 21:25:44 UTC (rev 15407) @@ -1,8 +1,12 @@ # Developers: to add a description of changes you have made, # add it on a line starting with # below the "version=..." line -version=12.1.44 +version=12.1.45_dev +# -------------------------------------------------------------- + +#version=12.1.44 + # bug fix: MOs broken in 12.1.43 # bug fix: drawpicking fails for drawn polyhedra. (turned off for now) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-05-09 02:19:55
|
Revision: 15442 http://jmol.svn.sourceforge.net/jmol/?rev=15442&view=rev Author: hansonr Date: 2011-05-09 02:19:49 +0000 (Mon, 09 May 2011) Log Message: ----------- version=12.1.46_dev # bug fix: molecules incorrectly assigned for covalently attached cofactors, such as HEM (1gzx) # TODO: This is still not quite right. It's possible that a cofactor will connect two biopolymers, # or that two biopolymers will be connected with an S-S bond. # In that case, we will have already created a set of independent but connected molecules # What about hydrogen bonding? # And we are not checking for that. Must find a way around this! Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-05-09 02:13:33 UTC (rev 15441) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-05-09 02:19:49 UTC (rev 15442) @@ -4,6 +4,12 @@ version=12.1.46_dev # bug fix: molecules incorrectly assigned for covalently attached cofactors, such as HEM (1gzx) +# TODO: This is still not quite right. It's possible that a cofactor will connect two biopolymers, +# or that two biopolymers will be connected with an S-S bond. +# In that case, we will have already created a set of independent but connected molecules +# What about hydrogen bonding? +# And we are not checking for that. Must find a way around this! + # bug fix: set picking dragMolecule then use of SHIFT after rotate COMPARE will result in unwanted translation # -------------------------------------------------------------- This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-07-02 16:45:12
|
Revision: 15686 http://jmol.svn.sourceforge.net/jmol/?rev=15686&view=rev Author: hansonr Date: 2011-07-02 16:45:05 +0000 (Sat, 02 Jul 2011) Log Message: ----------- version=12.1.51 # new feature: set ligandLoadFormat # new feature: set pdbAddHydrogens # -- for file loading # -- adds hydrogens to ALL groups, including HET groups # -- unlike PDB2PQR, then, ligands are properly shown # -- also adds all multiple bonds to PDB files # -- for altlocs you should use load option FILTER "CONF 1" (or some other specific configuration) # -- atom numbers are appended to maximum number in file # todo: single-element metals? -- no need to get CIF file? # new feature: CIF reader for Ligand CIF files (e.g. http://www.rcsb.org/pdb/files/ligand/AMU.cif) # # new feature: calculate HYDROGEN now works for standard amino acids and nucleic acids # -- adds "GROUP" option to connect -- puts new atoms in group of previous # -- saves connection in state with negative first atom -- indicating that we need to assign the group # new feature: CONTACT {xxx} MISC, and redefinition of HYDROPHOBIC # new feature: CONTACT {xxx} VDW # -- just maps a VDW isosurface with distances to another VDW isosurface # new feature: LOAD command reports header/title for PDB files # -- specifically when scriptLevel = 0 (typed entry) # new feature: isosurface SLAB OFF -- for SLAB n, this turns that slabbing off. # new feature: isosurface FUNCTIONXY = "x * y" and isosurface FUNCTIONXYZ = "x * x + y + z" # -- default is from -10 to 10 every 0.25 Angstroms # new feature: CONTACT command (Erik Wyatt/Bob Hanson 6/22/2011) # -- creates an object of a variety of forms that # indicates nonbonding interactions # -- can be a planar disk perpendicular to the interaction, # or a cigar-shaped connector # -- HBOND (just between O and/or N) # -- HYDROPHOBIC (not between O and/or N) # -- percent of van der Waals distance # # -- works by doing a sum or difference of two complementary # van der Waals surfaces (PLANAR) or by showing the # intersection of the two surfaces (FULL) or by doing an NCI # (noncovalent interaction) PROMOLECULAR calculation. # # -- DENSITY x.x (spot size) option does rough volume rendering. # # # contact # # -- parameters # # required: # {setA} # optional: # ID aaaa (if present, must be the very FIRST parameter # ON/OFF/DELETE/LIST (if present must be the only parameter other than ID # {setB} # DENSITY x.x # COLOR DENSITY # IGNORE {ignoreSet} # DISTANCE x.x # PARAMETERS [....] # FULL|PLANAR|CONNECT|NCI (FULL not implemented yet) # HYDROPHOBIC|HBOND # INTRAMOLECULAR|INTERMOLECULAR # nnn% # COLOR ... # TRANSLUCENT/OPAQUE/MESH/NOMESH, etc... (must be last parameters) # # new feature: show LIGHTING # bug fix: set defaultVDW user not working # bug fix: _smilesString variable not being cleared when a PDB file is loaded # code: much more efficient plane creation and mapping # code: work on isosurface, JVXL, plane mapping # bug fix: isosurface VDW mapping onto plane now has somewhat different coloration, # and properly slabs to the VDW radius. This is just a SLAB option that can # be removed like all others using isosurface SLAB NONE # TODO: contours from saved JVXL planar isosurfaces does not seem to be correct. # bug fix: WebMO reader fails to read HOMO/LUMO business. # bug fix: AMU added (NAM-NAG sequences) # bug fix: NDG added (epimer of NAG) # bug fix: definition of CARBOHYDRATE was updated: # -- [A2G],[NGA],[SIA],[SLB],[LBT] added (GalNAc, NeuNAc, lactose) # -- [ASF],[NAM] removed, they are not carbohydrates # -- a few existing ones are deprecated by PDB; they are left for compatibility # but are now listed as such (maybe remove them in future). # obscure bug fix: This fix: http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java?r1=13502&r2=13525 # broke Jmol reading of the Epcot hemoglobin file. Only relevant to sequential or trajectory PDB files that do not have MODEL statements. # So then any version starting with 12.0.RC_24 (7/8/2010) through now (7/2/2011) will read the files # correctly -- not missing the first atom -- but that messes up earlier scripts. Unfortunately the Epcot business # (Touch-A-Molecule) was written using 12.9.23 (1/24/2010), so that is affected. # This fix only affects states written prior to 12.0.RC_1 and just makes it so that they display correctly (though missing that one atom) # when they involve PDB trajectories of file without MODEL records separating models. Pretty sure this is just that one file. # # code: Viewer passes stateScriptVersionInt on to file readers # Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-07-02 16:41:43 UTC (rev 15685) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-07-02 16:45:05 UTC (rev 15686) @@ -3,6 +3,7 @@ version=12.1.51 +# new feature: set ligandLoadFormat # new feature: set pdbAddHydrogens # -- for file loading # -- adds hydrogens to ALL groups, including HET groups This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-07-24 18:34:11
|
Revision: 15832 http://jmol.svn.sourceforge.net/jmol/?rev=15832&view=rev Author: hansonr Date: 2011-07-24 18:34:05 +0000 (Sun, 24 Jul 2011) Log Message: ----------- version=12.2.RC1 # RELEASE CANDIDATE 1 for Jmol 12.2 # new feature: Surface Tool GUI -- just slicing so far and does all surfaces rather # then selected. (Jonathan Gutow) # new feature: select within(x.x, VDW, aaaa) # -- selects atoms that have overlapping VDW surfaces with set aaaa # -- if x.x is present, BOTH interacting atom radii are adjusted: # -- if x.x > 10, then this is assumed to be a percent, such as 110%, 100%, 90% # -- if x.x <= 10, then this is assumed to be a distance to be added to the VDW radii # -- so, for example, select within(1.4, VDW, aaaa) selects groups with overlapping solvent-accessible surfaces # new feature: getProperty isosurfaceInfo # -- includes vertexCount, polygonCount, vertices, vertexValues, and polygons # new feature: isosurface atomicOrbital <n> <l> <m> <z> POINTS <radius> <seed> # -- new default cutoff of 0.04 corresponds to factoring in 1/2sqrtPI # -- <radius> is new # -- must be a decimal number to distinguish it from the seed. # -- specifies a given radius # bug fix: isosurface slab of isosurface MO causes null pointer exception # bug fix: isosurface slab translucent of translucent isosurfaces causes problems # -- isosurface slab translucent ---> will now turn isosurface opaque first # -- isosurface slab translucent without a color ---> will now take on current color of isosurface rather than white # -- color isosurface translucent of translucent-slabbed isosurface will remove ALL slabbing # bug fix: WebExport not getting Jmol Icon for title bar. # bug fix: PDB reader may read bfactors off by 0.01 # bug fix: NWChem reader without input deck but with frequencies fails to load # bug fix: 12.1.51 breaks isosurface... colorscheme... # bug fix: isosurface slab -@xxxx... will negate variable xxxx if it is a plane # bug fix: contact {setA} {setB} should not allow overall of setA and setB unless NCI. # bug fix: contact FULL set to minimum resolution 10 (pairwise) # bug fix: isosurface intersection .... function "..." ignores function and just does "a-b" # code: super-fast "micro-isosurface" merging for CONTACT. Wow! # -- set pdbAddHydrogens; load =2bxa; contact {:A} {:A} # -- merges 2341 microisosurfaces in 325 ms on BH laptop! # code: fast pointilist atomic orbitals. THANK YOU, Pshemak Maslak, Brian Hardock, Rob Caldwell, and Tom Stitt! Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-07-24 18:29:24 UTC (rev 15831) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-07-24 18:34:05 UTC (rev 15832) @@ -1,31 +1,18 @@ # Developers: to add a description of changes you have made, # add it on a line starting with # below the "version=..." line -version=12.1.52_dev +version=12.2.RC1 -# code: super-fast "micro-isosurface" merging for CONTACT. Wow! -# -- set pdbAddHydrogens; load =2bxa; contact {:A} {:A} -# -- merges 2341 microisosurfaces in 325 ms on BH laptop! -# bug fix: isosurface slab of isosurface MO causes null pointer exception -# bug fix: isosurface slab translucent of translucent isosurfaces causes problems -# -- isosurface slab translucent ---> will now turn isosurface opaque first -# -- isosurface slab translucent without a color ---> will now take on current color of isosurface rather than white -# -- color isosurface translucent of translucent-slabbed isosurface will remove ALL slabbing +# RELEASE CANDIDATE 1 for Jmol 12.2 + # new feature: Surface Tool GUI -- just slicing so far and does all surfaces rather -# then selected. -# bug fix: WebExport not getting Jmol Icon for title bar. -# bug fix: PDB reader may read bfactors off by 0.01 -# bug fix: NWChem reader without input deck but with frequencies fails to load -# bug fix: 12.1.51 breaks isosurface... colorscheme... +# then selected. (Jonathan Gutow) # new feature: select within(x.x, VDW, aaaa) # -- selects atoms that have overlapping VDW surfaces with set aaaa # -- if x.x is present, BOTH interacting atom radii are adjusted: # -- if x.x > 10, then this is assumed to be a percent, such as 110%, 100%, 90% # -- if x.x <= 10, then this is assumed to be a distance to be added to the VDW radii # -- so, for example, select within(1.4, VDW, aaaa) selects groups with overlapping solvent-accessible surfaces -# bug fix: isosurface slab -@xxxx... will negate variable xxxx if it is a plane -# bug fix: contact {setA} {setB} should not allow overall of setA and setB unless NCI. -# bug fix: contact FULL set to minimum resolution 10 (pairwise) # new feature: getProperty isosurfaceInfo # -- includes vertexCount, polygonCount, vertices, vertexValues, and polygons # new feature: isosurface atomicOrbital <n> <l> <m> <z> POINTS <radius> <seed> @@ -33,9 +20,26 @@ # -- <radius> is new # -- must be a decimal number to distinguish it from the seed. # -- specifies a given radius -# code: superfast atomic orbitals. THANK YOU, Pshemak Maslak, Brian Hardock, Rob Caldwell, and Tom Stitt! + +# bug fix: isosurface slab of isosurface MO causes null pointer exception +# bug fix: isosurface slab translucent of translucent isosurfaces causes problems +# -- isosurface slab translucent ---> will now turn isosurface opaque first +# -- isosurface slab translucent without a color ---> will now take on current color of isosurface rather than white +# -- color isosurface translucent of translucent-slabbed isosurface will remove ALL slabbing +# bug fix: WebExport not getting Jmol Icon for title bar. +# bug fix: PDB reader may read bfactors off by 0.01 +# bug fix: NWChem reader without input deck but with frequencies fails to load +# bug fix: 12.1.51 breaks isosurface... colorscheme... +# bug fix: isosurface slab -@xxxx... will negate variable xxxx if it is a plane +# bug fix: contact {setA} {setB} should not allow overall of setA and setB unless NCI. +# bug fix: contact FULL set to minimum resolution 10 (pairwise) # bug fix: isosurface intersection .... function "..." ignores function and just does "a-b" +# code: super-fast "micro-isosurface" merging for CONTACT. Wow! +# -- set pdbAddHydrogens; load =2bxa; contact {:A} {:A} +# -- merges 2341 microisosurfaces in 325 ms on BH laptop! +# code: fast pointilist atomic orbitals. THANK YOU, Pshemak Maslak, Brian Hardock, Rob Caldwell, and Tom Stitt! + # -------------------------------------------------------------- #version=12.1.51 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-08-09 18:15:33
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Revision: 15959 http://jmol.svn.sourceforge.net/jmol/?rev=15959&view=rev Author: hansonr Date: 2011-08-09 18:15:27 +0000 (Tue, 09 Aug 2011) Log Message: ----------- it's fine -- do release, please Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-08-09 18:13:33 UTC (rev 15958) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-08-09 18:15:27 UTC (rev 15959) @@ -1,7 +1,7 @@ # Developers: to add a description of changes you have made, # add it on a line starting with # below the "version=..." line -version=12.2.RC3_HOLD +version=12.2.RC3 # new feature: selection of surfaces in SurfaceTool # bug fix: color broken in 12.2.RC2 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2011-11-15 03:23:32
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Revision: 16470 http://jmol.svn.sourceforge.net/jmol/?rev=16470&view=rev Author: nicove Date: 2011-11-15 03:23:26 +0000 (Tue, 15 Nov 2011) Log Message: ----------- Version Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-11-14 20:45:09 UTC (rev 16469) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-11-15 03:23:26 UTC (rev 16470) @@ -1,8 +1,12 @@ # Developers: to add a description of changes you have made, # add it on a line starting with # below the "version=..." line -version=12.3.5 +version=12.3.6_dev +# ============================================================================= + +#version=12.3.5 + # new feature: color isosurface PHASE color1 color2 # -- allows post-isosurface creation coloring by phase (atomicOrbitals) # bug fix: isosurface scale 0.5 plane... broken if no atoms present This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2012-03-05 19:15:11
|
Revision: 16862 http://jmol.svn.sourceforge.net/jmol/?rev=16862&view=rev Author: nicove Date: 2012-03-05 19:15:04 +0000 (Mon, 05 Mar 2012) Log Message: ----------- Version Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2012-03-05 12:01:58 UTC (rev 16861) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2012-03-05 19:15:04 UTC (rev 16862) @@ -1,8 +1,12 @@ # Developers: to add a description of changes you have made, # add it on a line starting with # below the "version=..." line -version=12.3.17 +version=12.3.18_dev +# ============================================================================= + +#version=12.3.17 + # new feature: (JspecView 2.0.10033) new script commands (indicated with *) # UNKNOWN("?"), # APPLETID("APPLETID"), This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2012-08-09 17:39:02
|
Revision: 17442 http://jmol.svn.sourceforge.net/jmol/?rev=17442&view=rev Author: nicove Date: 2012-08-09 17:38:55 +0000 (Thu, 09 Aug 2012) Log Message: ----------- Version Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2012-08-09 16:37:04 UTC (rev 17441) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2012-08-09 17:38:55 UTC (rev 17442) @@ -7,8 +7,12 @@ # Don't use ___ in your text, as that is the key for stripping out # the information saved in the JAR version of this file. -___version=13.0.RC4 +___version=13.0.RC5_dev +============================================================================= + +version=13.0.RC4 + new feature: write SCENE PNG|PNGJ "xxxx.spt" option to create PNG or PNGJ files (same file, just different extension) new feature: "menu" as sole contents of a script pops up the context menu -- joins category of special commands, including "exit" "pause" and "quit" This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2012-08-14 17:34:38
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Revision: 17455 http://jmol.svn.sourceforge.net/jmol/?rev=17455&view=rev Author: nicove Date: 2012-08-14 17:34:32 +0000 (Tue, 14 Aug 2012) Log Message: ----------- Version Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2012-08-13 23:19:11 UTC (rev 17454) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2012-08-14 17:34:32 UTC (rev 17455) @@ -7,8 +7,12 @@ # Don't use ___ in your text, as that is the key for stripping out # the information saved in the JAR version of this file. -___version=13.0.RC6 +___version=13.0.RC7_dev +============================================================================= + +version=13.0.RC6 + bug fix: Gaussian reader not reading "AO basis set in the form of general basis input" properly ("Gen" keyword) bug fix: Gaussian reader not reading "7D 0" correctly bug fix: Trajectories still broken for PDB files This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2012-10-17 16:36:58
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Revision: 17668 http://jmol.svn.sourceforge.net/jmol/?rev=17668&view=rev Author: nicove Date: 2012-10-17 16:36:48 +0000 (Wed, 17 Oct 2012) Log Message: ----------- Version Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2012-10-17 15:22:58 UTC (rev 17667) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2012-10-17 16:36:48 UTC (rev 17668) @@ -7,8 +7,12 @@ # Don't use ___ in your text, as that is the key for stripping out # the information saved in the JAR version of this file. -___version=13.1.7 +___version=13.1.8_dev +============================================================================= + +version=13.1.7 + FEATURE CHANGE: getProperty isosurfaceInfo no longer returns vertex data new feature: getProperty isosurfaceData returns vertex data new feature: set cartoonFancy -- creates elliptical ribbon for cartoons This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |