[Jmol-commits] SF.net SVN: jmol:[12336] trunk/Jmol/src/org/jmol/util/FastBitSet.java

Revision: 12336 http://jmol.svn.sourceforge.net/jmol/?rev=12336&view=rev Author: migueljmol Date: 2010-02-08 15:10:57 + (Mon, 08 Feb 2010) Log Message: --- added comment. deleted unused copyFast Modified Paths: -- trunk/Jmol/src/org/jmol/

[Jmol-commits] SF.net SVN: jmol:[12334] trunk/Jmol

Revision: 12334 http://jmol.svn.sourceforge.net/jmol/?rev=12334&view=rev Author: migueljmol Date: 2010-02-08 13:24:10 + (Mon, 08 Feb 2010) Log Message: --- additional int[] bitmap functionality Modified Paths: -- trunk/Jmol/jmol trunk/Jmol/src

[Jmol-commits] SF.net SVN: jmol:[12335] trunk/Jmol/src/org/jmol

Revision: 12335 http://jmol.svn.sourceforge.net/jmol/?rev=12335&view=rev Author: migueljmol Date: 2010-02-08 14:56:14 + (Mon, 08 Feb 2010) Log Message: --- removed deprecated code from FastBitSet implementation Modified Paths: -- trunk/Jmol/src

[Jmol-commits] SF.net SVN: jmol: [5103] trunk/Jmol/build.xml

Revision: 5103 Author: migueljmol Date: 2006-05-12 07:38:08 -0700 (Fri, 12 May 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=5103&view=rev Log Message: --- prerelease 10.3.1 Modified Paths: -- trunk/Jmol/build.xml Modified: trunk/Jmol/build

[Jmol-commits] SF.net SVN: jmol: [5104] tags/pre10.3.1/

Revision: 5104 Author: migueljmol Date: 2006-05-12 07:41:34 -0700 (Fri, 12 May 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=5104&view=rev Log Message: --- prerelease 10.3.1 Added Paths: --- tags/pre10.3.1/ Copied: tags/pre10.3.1 (from rev 5103, trunk) This

[Jmol-commits] SF.net SVN: jmol: [5099] trunk/Jmol/src/org/jmol/popup

Revision: 5099 Author: migueljmol Date: 2006-05-11 11:08:11 -0700 (Thu, 11 May 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=5099&view=rev Log Message: --- restored top menu items in About menu which were accidentally removed ... oops Modified Paths: -- t

[Jmol-commits] SF.net SVN: jmol: [5098] trunk/Jmol/src/org/jmol/popup

Revision: 5098 Author: migueljmol Date: 2006-05-11 08:45:04 -0700 (Thu, 11 May 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=5098&view=rev Log Message: --- popup now shows memory statistics & cpu count + bumped version number to 10.3.1 Modifi

[Jmol-commits] SF.net SVN: jmol: [5095] trunk/Jmol

Revision: 5095 Author: migueljmol Date: 2006-05-10 08:22:48 -0700 (Wed, 10 May 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=5095&view=rev Log Message: --- added org.jmol.vecmath.* to applet.classes and put it in JmolApplet5.jar also moved org.jmol.smiles from JmolApplet

[Jmol-commits] SF.net SVN: jmol: [5092] trunk/Jmol/src/org/jmol/g3d/Graphics3D.java

Revision: 5092 Author: migueljmol Date: 2006-05-09 18:46:46 -0700 (Tue, 09 May 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=5092&view=rev Log Message: --- more javadoc comments for g3d package Modified Paths: -- trunk/Jmol/src/org/jmol/g3d/Graphics3D.

[Jmol-commits] SF.net SVN: jmol: [5091] trunk/Jmol/src/org/jmol/g3d

Revision: 5091 Author: migueljmol Date: 2006-05-09 18:26:26 -0700 (Tue, 09 May 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=5091&view=rev Log Message: --- No more javax.vecmath.Point3f in g3d shape drawing routines. There were some cases where screen coordinates were b

[Jmol-commits] SF.net SVN: jmol: [5081] trunk/Jmol/src/org/jmol/g3d/Graphics3D.java

Revision: 5081 Author: migueljmol Date: 2006-05-07 13:58:45 -0700 (Sun, 07 May 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=5081&view=rev Log Message: --- javadoc for triangle routines Modified Paths: -- trunk/Jmol/src/org/jmol/g3d/Graphics3D.java Modi

[Jmol-commits] SF.net SVN: jmol: [5080] trunk/Jmol/src/org/jmol/g3d/Graphics3D.java

Revision: 5080 Author: migueljmol Date: 2006-05-07 13:18:36 -0700 (Sun, 07 May 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=5080&view=rev Log Message: --- javadoc for g3d line drawing routines Modified Paths: -- trunk/Jmol/src/org/jmol/g3d/Graphics3D.

[Jmol-commits] SF.net SVN: jmol: [5079] trunk/Jmol/src/org/jmol/g3d

Revision: 5079 Author: migueljmol Date: 2006-05-07 13:01:53 -0700 (Sun, 07 May 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=5079&view=rev Log Message: --- introduced initial changes to Graphics3D API to use Point3fi Modified Paths: -- trunk/Jmol/src/org/

[Jmol-commits] SF.net SVN: jmol: [5072] trunk/Jmol/src/org/jmol

Revision: 5072 Author: migueljmol Date: 2006-05-06 13:15:11 -0700 (Sat, 06 May 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=5072&view=rev Log Message: --- Introduced Point3fi class which includeds members for screen coordinates. Atom derives from Point3fi. At atom can

[Jmol-commits] SF.net SVN: jmol: [5058] tags/r4818/

Revision: 5058 Author: migueljmol Date: 2006-05-03 12:41:05 -0700 (Wed, 03 May 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=5058&view=rev Log Message: --- r4818 after rollback Added Paths: --- tags/r4818/ Copied: tags/r4818 (from rev 4818, trunk) This was

[Jmol-commits] SF.net SVN: jmol: [5057] tags/r4649/

Revision: 5057 Author: migueljmol Date: 2006-05-03 12:40:31 -0700 (Wed, 03 May 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=5057&view=rev Log Message: --- r4649 before sluggishness Added Paths: --- tags/r4649/ Copied: tags/r4649 (from rev 4649, trunk) This

[Jmol-commits] SF.net SVN: jmol: [5056] branches/pauldana200605/

Revision: 5056 Author: migueljmol Date: 2006-05-03 09:27:34 -0700 (Wed, 03 May 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=5056&view=rev Log Message: --- private branch for pfaat integration Added Paths: --- branches/pauldana200605/ Copied: bran

[Jmol-commits] SF.net SVN: jmol: [5052] trunk/Jmol/src/org/jmol/g3d

Revision: 5052 Author: migueljmol Date: 2006-05-02 16:56:23 -0700 (Tue, 02 May 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=5052&view=rev Log Message: --- rollback of zbuffer to int[] Modified Paths: -- trunk/Jmol/src/org/jmol/g3d/Graphics3D.java t

[Jmol-commits] SF.net SVN: jmol: [5051] trunk/Jmol/src/org/jmol/g3d

Revision: 5051 Author: migueljmol Date: 2006-05-02 16:52:58 -0700 (Tue, 02 May 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=5051&view=rev Log Message: --- temporarily check in of 'revert z-buffer from ints back to shorts' Modified Paths: --

[Jmol-commits] SF.net SVN: jmol: [4919] trunk/Jmol

Revision: 4919 Author: migueljmol Date: 2006-04-05 17:06:01 -0700 (Wed, 05 Apr 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4919&view=rev Log Message: --- prerelease 10.00.58 Modified Paths: -- trunk/Jmol/build.xml trunk/Jmol/src/org/jmol/transla

[Jmol-commits] SF.net SVN: jmol: [4920] tags/pre10_00_58/

Revision: 4920 Author: migueljmol Date: 2006-04-05 17:07:51 -0700 (Wed, 05 Apr 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4920&view=rev Log Message: --- prerelease 10.00.58 Added Paths: --- tags/pre10_00_58/ Copied: tags/pre10_00_58 (from rev 4919, t

[Jmol-commits] SF.net SVN: jmol: [4911] tags/pre10_00_57/

Revision: 4911 Author: migueljmol Date: 2006-04-04 13:35:42 -0700 (Tue, 04 Apr 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4911&view=rev Log Message: --- prerelease 10.00.57 Added Paths: --- tags/pre10_00_57/ Copied: tags/pre10_00_57 (from rev 4910, t

[Jmol-commits] SF.net SVN: jmol: [4910] trunk/Jmol

Revision: 4910 Author: migueljmol Date: 2006-04-04 13:25:52 -0700 (Tue, 04 Apr 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4910&view=rev Log Message: --- prerelease 10.00.57 Modified Paths: -- trunk/Jmol/build.xml trunk/Jmol/src/org/jmol/vi

[Jmol-commits] SF.net SVN: jmol: [4909] trunk/Jmol/src/org/jmol/viewer

Revision: 4909 Author: migueljmol Date: 2006-04-04 12:56:22 -0700 (Tue, 04 Apr 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4909&view=rev Log Message: --- reintroduced implementation of connected() operator a different implementation than before Modified P

[Jmol-commits] SF.net SVN: jmol: [4905] trunk/Jmol/src/org/jmol/viewer

Revision: 4905 Author: migueljmol Date: 2006-04-04 09:50:58 -0700 (Tue, 04 Apr 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4905&view=rev Log Message: --- reintroduction of 'connected' compiler code. Note that the parentheses() are now *required*

[Jmol-commits] SF.net SVN: jmol: [4904] trunk/Jmol/src/org/jmol/viewer/JmolConstants.java

Revision: 4904 Author: migueljmol Date: 2006-04-04 08:02:38 -0700 (Tue, 04 Apr 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4904&view=rev Log Message: --- properly 'quote' unrecognized element symbols Modified Paths: -- trunk/Jmol/src/o

[Jmol-commits] SF.net SVN: jmol: [4902] tags/pre10_00_56/trunk/

Revision: 4902 Author: migueljmol Date: 2006-04-04 07:34:05 -0700 (Tue, 04 Apr 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4902&view=rev Log Message: --- prerelease 10.00.56 Added Paths: --- tags/pre10_00_56/trunk/ Copied: tags/pre10_00_56/trunk (from rev

[Jmol-commits] SF.net SVN: jmol: [4901] trunk/Jmol

Revision: 4901 Author: migueljmol Date: 2006-04-04 07:33:19 -0700 (Tue, 04 Apr 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4901&view=rev Log Message: --- prerelease 10.00.56 Modified Paths: -- trunk/Jmol/build.xml trunk/Jmol/src/org/jmol/vi

[Jmol-commits] SF.net SVN: jmol: [4900] trunk/Jmol/src/org/jmol/g3d/Graphics3D.java

Revision: 4900 Author: migueljmol Date: 2006-04-04 07:23:42 -0700 (Tue, 04 Apr 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4900&view=rev Log Message: --- Fixed ArrayIndexOutOfBoundsException in plotPixelsClipped as reported by Jan Problem was boundary condition invol

[Jmol-commits] SF.net SVN: jmol: [4899] tags/pre10_00_56/

Revision: 4899 Author: migueljmol Date: 2006-04-04 07:10:37 -0700 (Tue, 04 Apr 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4899&view=rev Log Message: --- prerelease 10.00.55 - but I failed to commit the changes, so Bob's polyhedra changes were not actually pa

[Jmol-commits] SF.net SVN: jmol: [4898] trunk/Jmol

Revision: 4898 Author: migueljmol Date: 2006-04-04 07:09:21 -0700 (Tue, 04 Apr 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4898&view=rev Log Message: --- prerelease 10.00.55 -- somewhat messed up. I forgot to commit prerelease 10.00.55. Bob checked in polyhedra cha

[Jmol-commits] SF.net SVN: jmol: [4895] trunk/Jmol/src/org/jmol/viewer

Revision: 4895 Author: migueljmol Date: 2006-04-03 19:13:20 -0700 (Mon, 03 Apr 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4895&view=rev Log Message: --- Provisional checking of polyhedra code with collapsed. Has significant bugs with face identification. The '

[Jmol-commits] SF.net SVN: jmol: [4894] trunk/Jmol-datafiles/crystals/znqukrod.mol

Revision: 4894 Author: migueljmol Date: 2006-04-03 17:32:53 -0700 (Mon, 03 Apr 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4894&view=rev Log Message: --- decahedron around zinc with 7 vertices Added Paths: --- trunk/Jmol-datafiles/crystals/znqukrod.mol A

[Jmol-commits] SF.net SVN: jmol: [4893] trunk/Jmol/src/org/jmol/viewer

Revision: 4893 Author: migueljmol Date: 2006-04-03 12:06:33 -0700 (Mon, 03 Apr 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4893&view=rev Log Message: --- intermediate checkin of attempted polyhedra integration Modified Paths: -- trunk/Jmol/src/org/

[Jmol-commits] SF.net SVN: jmol: [4892] trunk/Jmol/src/org/jmol/g3d/Hermite3D.java

Revision: 4892 Author: migueljmol Date: 2006-04-03 06:05:16 -0700 (Mon, 03 Apr 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4892&view=rev Log Message: --- Fixed meshribbon crosshatch coloring bug reported by Jan. Bug was introduced a long time ago, but post V10.00 This

[Jmol-commits] SF.net SVN: jmol: [4890] tags/pre10_00_54/

Revision: 4890 Author: migueljmol Date: 2006-04-02 18:53:44 -0700 (Sun, 02 Apr 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4890&view=rev Log Message: --- prerelease 10.00.54 Added Paths: --- tags/pre10_00_54/ Copied: tags/pre10_00_54 (from rev 4889, t

[Jmol-commits] SF.net SVN: jmol: [4889] trunk/Jmol

Revision: 4889 Author: migueljmol Date: 2006-04-02 18:53:05 -0700 (Sun, 02 Apr 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4889&view=rev Log Message: --- prerelease 10.00.54 Modified Paths: -- trunk/Jmol/build.xml trunk/Jmol/src/org/jmol/vi

[Jmol-commits] SF.net SVN: jmol: [4888] trunk/Jmol/src/org/jmol/viewer

Revision: 4888 Author: migueljmol Date: 2006-04-02 18:50:45 -0700 (Sun, 02 Apr 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4888&view=rev Log Message: --- removed extraneous System.out.println() output Modified Paths: -- trunk/Jmol/src/org/jmol/vi

[Jmol-commits] SF.net SVN: jmol: [4887] trunk/Jmol/src/org/jmol/viewer

Revision: 4887 Author: migueljmol Date: 2006-04-02 18:47:47 -0700 (Sun, 02 Apr 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4887&view=rev Log Message: --- introduced 'hbondcount' atom property and 'hbonded' predefined set Modified Paths: -

[Jmol-commits] SF.net SVN: jmol: [4886] trunk/Jmol/src/org/jmol/viewer

Revision: 4886 Author: migueljmol Date: 2006-04-02 18:41:12 -0700 (Sun, 02 Apr 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4886&view=rev Log Message: --- exposed _bondedcount atom property as 'bondcount' for count of covalent bonds. replaces experimen

[Jmol-commits] SF.net SVN: jmol: [4885] trunk/Jmol/src/org/jmol/adapter/smarter

Revision: 4885 Author: migueljmol Date: 2006-04-02 18:17:20 -0700 (Sun, 02 Apr 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4885&view=rev Log Message: --- org.jmol.adapter.smarter brought back up to 10.00.49 level This includes changes made in this package from r4624,r

[Jmol-commits] SF.net SVN: jmol: [4884] trunk/Jmol/src/org/jmol/viewer/Sticks.java

Revision: 4884 Author: migueljmol Date: 2006-04-02 17:15:00 -0700 (Sun, 02 Apr 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4884&view=rev Log Message: --- 'connect delete single' was not deleting sulfur bonds because of the BOND_SULFUR_MASK bit. Perhaps t

[Jmol-commits] SF.net SVN: jmol: [4881] trunk/Jmol/src/org/jmol/viewer

Revision: 4881 Author: migueljmol Date: 2006-04-02 12:10:27 -0700 (Sun, 02 Apr 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4881&view=rev Log Message: --- full implementation of connect auto hbond with bitset restrictions Modified Paths: -- trunk/Jmol

[Jmol-commits] SF.net SVN: jmol: [4882] trunk/Jmol

Revision: 4882 Author: migueljmol Date: 2006-04-02 12:11:43 -0700 (Sun, 02 Apr 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4882&view=rev Log Message: --- prerelease 10.00.53 Modified Paths: -- trunk/Jmol/build.xml trunk/Jmol/src/org/jmol/vi

[Jmol-commits] SF.net SVN: jmol: [4883] tags/pre10_00_53/

Revision: 4883 Author: migueljmol Date: 2006-04-02 12:12:24 -0700 (Sun, 02 Apr 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4883&view=rev Log Message: --- prerelease 10.00.53 Added Paths: --- tags/pre10_00_53/ Copied: tags/pre10_00_53 (from rev 4882, t

[Jmol-commits] SF.net SVN: jmol: [4880] trunk/Jmol/src/org/jmol/viewer/Sticks.java

Revision: 4880 Author: migueljmol Date: 2006-04-02 11:46:48 -0700 (Sun, 02 Apr 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4880&view=rev Log Message: --- extend order when deleting so that different flavors of hbond get deleted Modified Paths: -- trunk/

[Jmol-commits] SF.net SVN: jmol: [4878] trunk/Jmol/src/org/jmol/viewer/Frame.java

Revision: 4878 Author: migueljmol Date: 2006-04-02 09:07:26 -0700 (Sun, 02 Apr 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4878&view=rev Log Message: --- replaced older global rebond() code with autoBond(null, null) upon file load Modified Paths: -- t

[Jmol-commits] SF.net SVN: jmol: [4877] trunk/Jmol/src/org/jmol/viewer

Revision: 4877 Author: migueljmol Date: 2006-04-02 09:00:39 -0700 (Sun, 02 Apr 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4877&view=rev Log Message: --- checkin before removing rebond() code Modified Paths: -- trunk/Jmol/src/org/jmol/viewer/Frame.

[Jmol-commits] SF.net SVN: jmol: [4875] trunk/Jmol/src/org/jmol/viewer

Revision: 4875 Author: migueljmol Date: 2006-04-02 07:46:54 -0700 (Sun, 02 Apr 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4875&view=rev Log Message: --- simplified rebonding a wee bit Modified Paths: -- trunk/Jmol/src/org/jmol/viewer/Frame.java t

[Jmol-commits] SF.net SVN: jmol: [4873] trunk/Jmol/src/org/jmol/viewer/Viewer.java

Revision: 4873 Author: migueljmol Date: 2006-04-02 07:16:03 -0700 (Sun, 02 Apr 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4873&view=rev Log Message: --- minBondDistance and bondTolerance methods in Viewer are no longer public Modified Paths: -- trunk/

[Jmol-commits] SF.net SVN: jmol: [4874] trunk/Jmol/src/org/jmol/viewer/Frame.java

Revision: 4874 Author: migueljmol Date: 2006-04-02 07:22:21 -0700 (Sun, 02 Apr 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4874&view=rev Log Message: --- changed inappropriate references from Integer.MIN_VALUE -> Float.MIN_VALUE Modified Paths: --

[Jmol-commits] SF.net SVN: jmol: [4871] trunk/Jmol/src/org/jmol/api

Revision: 4871 Author: migueljmol Date: 2006-04-02 07:06:20 -0700 (Sun, 02 Apr 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4871&view=rev Log Message: --- remove api and app references to rebond() as well as minimumBondingDistance and bondTolerance values Modified P

[Jmol-commits] SF.net SVN: jmol: [4870] trunk/Jmol/src/org/jmol/viewer

Revision: 4870 Author: migueljmol Date: 2006-04-02 06:56:46 -0700 (Sun, 02 Apr 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4870&view=rev Log Message: --- removed script references to viewer.rebond() Modified Paths: -- trunk/Jmol/src/org/jmol/vi

[Jmol-commits] SF.net SVN: jmol: [4869] trunk/Jmol/src/org/jmol/viewer

Revision: 4869 Author: migueljmol Date: 2006-04-02 06:29:42 -0700 (Sun, 02 Apr 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4869&view=rev Log Message: --- framework for 'connect auto', including 'connect auto hbond' Modified Paths: --

[Jmol-commits] SF.net SVN: jmol: [4868] trunk/Jmol/src/org/jmol/viewer

Revision: 4868 Author: migueljmol Date: 2006-04-02 06:12:47 -0700 (Sun, 02 Apr 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4868&view=rev Log Message: --- no longer autocalc hydrogen bonds up 'hbond on' or for secondary structure identification. Explicit calcu

[Jmol-commits] SF.net SVN: jmol: [4862] trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java

Revision: 4862 Author: migueljmol Date: 2006-03-31 03:35:35 -0800 (Fri, 31 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4862&view=rev Log Message: --- remove logging of "short input buffer" from Resolver when the inptu file is less than N lines ... wh

[Jmol-commits] SF.net SVN: jmol: [4861] tags/pre10_00_52/

Revision: 4861 Author: migueljmol Date: 2006-03-30 16:42:45 -0800 (Thu, 30 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4861&view=rev Log Message: --- prerelease 10.00.52 Added Paths: --- tags/pre10_00_52/ Copied: tags/pre10_00_52 (from rev 4860, t

[Jmol-commits] SF.net SVN: jmol: [4860] trunk/Jmol

Revision: 4860 Author: migueljmol Date: 2006-03-30 16:41:14 -0800 (Thu, 30 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4860&view=rev Log Message: --- prerelease 10.00.52 Modified Paths: -- trunk/Jmol/build.xml trunk/Jmol/src/org/jmol/vi

[Jmol-commits] SF.net SVN: jmol: [4859] trunk/Jmol/src/org/jmol/viewer/Viewer.java

Revision: 4859 Author: migueljmol Date: 2006-03-30 16:32:06 -0800 (Thu, 30 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4859&view=rev Log Message: --- reenable running System.gc() after a file open Modified Paths: -- trunk/Jmol/src/org/jmol/vi

[Jmol-commits] SF.net SVN: jmol: [4858] trunk/Jmol/src/org/jmol/viewer/Bond.java

Revision: 4858 Author: migueljmol Date: 2006-03-30 16:27:49 -0800 (Thu, 30 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4858&view=rev Log Message: --- hbond defaults to 1 pixel Modified Paths: -- trunk/Jmol/src/org/jmol/viewer/Bond.java Modified: t

[Jmol-commits] SF.net SVN: jmol: [4857] trunk/Jmol/src/org/jmol/viewer

Revision: 4857 Author: migueljmol Date: 2006-03-30 14:16:58 -0800 (Thu, 30 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4857&view=rev Log Message: --- hbonds are created with default bond diameter. Affects both files that contain hbonds and hbonds that are created

[Jmol-commits] SF.net SVN: jmol: [4856] trunk/Jmol/src/org/jmol/viewer/Atom.java

Revision: 4856 Author: migueljmol Date: 2006-03-30 12:16:44 -0800 (Thu, 30 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4856&view=rev Log Message: --- %M shows modelTagNumber, not modelTag ... originally part of r4501 Modified Paths: -- trunk/Jmol

[Jmol-commits] SF.net SVN: jmol: [4855] trunk/Jmol/src/org/jmol/adapter/smarter/SpartanSmolReader.java

Revision: 4855 Author: migueljmol Date: 2006-03-30 11:20:18 -0800 (Thu, 30 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4855&view=rev Log Message: --- reintroduced r4623 ... SpartanSmol tests now succeed Modified Paths: -- trunk/Jmol/src/org/jmol/ada

[Jmol-commits] SF.net SVN: jmol: [4854] trunk/Jmol/src/org/jmol/adapter/smarter

Revision: 4854 Author: migueljmol Date: 2006-03-30 10:45:04 -0800 (Thu, 30 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4854&view=rev Log Message: --- reintroduced r4657 - extended Gaussian 94 support Modified Paths: -- trunk/Jmol/src/org/jmol/ada

[Jmol-commits] SF.net SVN: jmol: [4853] trunk/Jmol/src/org/jmol/viewer/Sticks.java

Revision: 4853 Author: migueljmol Date: 2006-03-30 10:32:10 -0800 (Thu, 30 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4853&view=rev Log Message: --- removed old code that was commented out in r4850 Modified Paths: -- trunk/Jmol/src/org/jmol/vi

[Jmol-commits] SF.net SVN: jmol: [4852] trunk/Jmol/src/org/jmol/viewer/Eval.java

Revision: 4852 Author: migueljmol Date: 2006-03-30 10:11:13 -0800 (Thu, 30 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4852&view=rev Log Message: --- reintroduced r4686 - statementLength checks in script interpreter Modified Paths: -- trunk/Jmol/src

[Jmol-commits] SF.net SVN: jmol: [4851] trunk/Jmol/src/org/jmol/viewer/Eval.java

Revision: 4851 Author: migueljmol Date: 2006-03-30 10:04:50 -0800 (Thu, 30 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4851&view=rev Log Message: --- reintroduced restrict() bug fix from r4557 Modified Paths: -- trunk/Jmol/src/org/jmol/viewer/Eval.

[Jmol-commits] SF.net SVN: jmol: [4849] trunk/Jmol/src/org/jmol/viewer/MouseManager.java

Revision: 4849 Author: migueljmol Date: 2006-03-30 10:00:29 -0800 (Thu, 30 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4849&view=rev Log Message: --- reintroduced MouseManager change from r4527 Viewer gets notified 'atomPicked' while measurements

[Jmol-commits] SF.net SVN: jmol: [4848] trunk/Jmol/src/org/jmol/viewer/AminoPolymer.java

Revision: 4848 Author: migueljmol Date: 2006-03-30 09:45:45 -0800 (Thu, 30 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4848&view=rev Log Message: --- reintroduced hbond calculation fixes done by Bob in r4456 & r4457 Note that these patches contained other chan

[Jmol-commits] SF.net SVN: jmol: [4847] trunk/Jmol-datafiles/pdb/readme.txt

Revision: 4847 Author: migueljmol Date: 2006-03-30 07:07:49 -0800 (Thu, 30 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4847&view=rev Log Message: --- identified that 1JGQ has insertion codes Modified Paths: -- trunk/Jmol-datafiles/pdb/readme

[Jmol-commits] SF.net SVN: jmol: [4846] tags/pre10_00_51/

Revision: 4846 Author: migueljmol Date: 2006-03-29 20:34:05 -0800 (Wed, 29 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4846&view=rev Log Message: --- prerelesae 10.00.51 Added Paths: --- tags/pre10_00_51/ Copied: tags/pre10_00_51 (from rev 4845, t

[Jmol-commits] SF.net SVN: jmol: [4845] trunk/Jmol

Revision: 4845 Author: migueljmol Date: 2006-03-29 20:27:48 -0800 (Wed, 29 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4845&view=rev Log Message: --- prerelease 10.00.51 Modified Paths: -- trunk/Jmol/build.xml trunk/Jmol/src/org/jmol/vi

[Jmol-commits] SF.net SVN: jmol: [4844] trunk/Jmol/src/org/jmol/g3d/Cylinder3D.java

Revision: 4844 Author: migueljmol Date: 2006-03-29 20:23:25 -0800 (Wed, 29 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4844&view=rev Log Message: --- fixed problem with cylinders of diameter == 1 ... backbone 1 using member variables dx/dy/dz before calculating

[Jmol-commits] SF.net SVN: jmol: [4843] trunk/Jmol/src/org/jmol/viewer

Revision: 4843 Author: migueljmol Date: 2006-03-29 18:49:30 -0800 (Wed, 29 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4843&view=rev Log Message: --- eliminated bondorder command ... connect does a better job Modified Paths: -- trunk/Jmol/src/org/

[Jmol-commits] SF.net SVN: jmol: [4842] trunk/Jmol/src/org/jmol/viewer

Revision: 4842 Author: migueljmol Date: 2006-03-29 15:59:14 -0800 (Wed, 29 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4842&view=rev Log Message: --- reintroduction of 'connect' functionality prior to deleting bondorder Modified Paths: --

[Jmol-commits] SF.net SVN: jmol: [4838] trunk/Jmol/src/org/jmol/viewer

Revision: 4838 Author: migueljmol Date: 2006-03-29 07:32:26 -0800 (Wed, 29 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4838&view=rev Log Message: --- reintroduce compiler support for multiple embedded expressions Modified Paths: -- trunk/Jmol/src

[Jmol-commits] SF.net SVN: jmol: [4837] trunk/Jmol/doc/source/JmolDevelopersGuide.docbook.xml

Revision: 4837 Author: migueljmol Date: 2006-03-28 13:00:35 -0800 (Tue, 28 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4837&view=rev Log Message: --- change some doc references from CVS to SVN Modified Paths: -- trunk/Jmol/doc/so

[Jmol-commits] SF.net SVN: jmol: [4835] tags/pre10_00_50/

Revision: 4835 Author: migueljmol Date: 2006-03-28 07:06:12 -0800 (Tue, 28 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4835&view=rev Log Message: --- prerelease 10.00.50 ... rollback to 10.00.48 and apply patches Added Paths: --- tags/pre10_00_50/ Co

[Jmol-commits] SF.net SVN: jmol: [4834] trunk/Jmol

Revision: 4834 Author: migueljmol Date: 2006-03-28 06:29:32 -0800 (Tue, 28 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4834&view=rev Log Message: --- prerelease 10.00.50 - rollback to 10.00.48 and selectively apply patches Modified Paths: -- trunk/

[Jmol-commits] SF.net SVN: jmol: [4833] trunk/Jmol/appletweb/Jmol.js

Revision: 4833 Author: migueljmol Date: 2006-03-28 05:40:55 -0800 (Tue, 28 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4833&view=rev Log Message: --- remove restriction for docroot relative URL + extend warning message Modified Paths: -- trunk/

[Jmol-commits] SF.net SVN: jmol: [4831] trunk/Jmol/src/org/openscience/jmol/app/Jmol.java

Revision: 4831 Author: migueljmol Date: 2006-03-28 05:08:27 -0800 (Tue, 28 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4831&view=rev Log Message: --- r4788 private -> protected for jmol-pfaat Modified Paths: -- trunk/Jmol/src/org/openscience/j

[Jmol-commits] SF.net SVN: jmol: [4832] branches/pauldana200603/

Revision: 4832 Author: migueljmol Date: 2006-03-28 05:09:53 -0800 (Tue, 28 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4832&view=rev Log Message: --- branch made for pauldata pfaat work Added Paths: --- branches/pauldana200603/ Copied: bran

[Jmol-commits] SF.net SVN: jmol: [4830] trunk/Jmol/src/org/jmol/viewer/Viewer.java

Revision: 4830 Author: migueljmol Date: 2006-03-28 04:58:56 -0800 (Tue, 28 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4830&view=rev Log Message: --- r4710 removed dead wood references to oversampling Modified Paths: -- trunk/Jmol/src/org/jmol/vi

[Jmol-commits] SF.net SVN: jmol: [4829] trunk/Jmol/src/org/jmol/viewer

Revision: 4829 Author: migueljmol Date: 2006-03-28 04:55:21 -0800 (Tue, 28 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4829&view=rev Log Message: --- r4709 preliminary work on getPublicProperties Modified Paths: -- trunk/Jmol/src/org/jmol/vi

[Jmol-commits] SF.net SVN: jmol: [4827] trunk/Jmol/src/org/jmol/viewer

Revision: 4827 Author: migueljmol Date: 2006-03-28 04:06:47 -0800 (Tue, 28 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4827&view=rev Log Message: --- r4706 r4707 eclipse warnings + JUnit for V3000 Modified Paths: -- trunk/Jmol/src/org/jmol/ada

[Jmol-commits] SF.net SVN: jmol: [4826] trunk/Jmol-web/

Revision: 4826 Author: migueljmol Date: 2006-03-28 03:18:58 -0800 (Tue, 28 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4826&view=rev Log Message: --- restoring Jmol-web to trunk Added Paths: --- trunk/Jmol-web/ Copied: trunk/Jmol-web (from rev

[Jmol-commits] SF.net SVN: jmol: [4825] trunk/JmolScriptDocumentation/

Revision: 4825 Author: migueljmol Date: 2006-03-28 03:17:52 -0800 (Tue, 28 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4825&view=rev Log Message: --- restoring JmolScriptDocumentation to trunk Added Paths: --- trunk/JmolScriptDocumentation/ Copied: t

[Jmol-commits] SF.net SVN: jmol: [4824] trunk/JmolScriptDocumentation/

Revision: 4824 Author: migueljmol Date: 2006-03-28 02:52:07 -0800 (Tue, 28 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4824&view=rev Log Message: --- deleting JmolScriptDocumentation in order to restore trunk Removed Paths: - t

[Jmol-commits] SF.net SVN: jmol: [4823] trunk/Jmol-web/

Revision: 4823 Author: migueljmol Date: 2006-03-28 02:49:41 -0800 (Tue, 28 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4823&view=rev Log Message: --- deleting Jmol-web in order to restore trunk Removed Paths: - trunk/Jmol-web/ This was sent by

[Jmol-commits] SF.net SVN: jmol: [4822] trunk/Jmol-FAH/

Revision: 4822 Author: migueljmol Date: 2006-03-28 02:48:39 -0800 (Tue, 28 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4822&view=rev Log Message: --- restoring Jmol-FAH to trunk Added Paths: --- trunk/Jmol-FAH/ Copied: trunk/Jmol-FAH (from rev

[Jmol-commits] SF.net SVN: jmol: [4821] trunk/Jmol-FAH/

Revision: 4821 Author: migueljmol Date: 2006-03-28 02:48:09 -0800 (Tue, 28 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4821&view=rev Log Message: --- deleting Jmol-FAH to restore trunk Removed Paths: - trunk/Jmol-FAH/ This was sent by

[Jmol-commits] SF.net SVN: jmol: [4820] trunk/Jmol-datafiles/

Revision: 4820 Author: migueljmol Date: 2006-03-28 02:46:36 -0800 (Tue, 28 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4820&view=rev Log Message: --- restoring clean datafiles to trunk Added Paths: --- trunk/Jmol-datafiles/ Copied: trunk/Jmol-dataf

[Jmol-commits] SF.net SVN: jmol: [4819] trunk/Jmol-datafiles/

Revision: 4819 Author: migueljmol Date: 2006-03-28 02:45:29 -0800 (Tue, 28 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4819&view=rev Log Message: --- deleting datafiles to grab current trunk Removed Paths: - trunk/Jmol-datafiles/ This was sent by

[Jmol-commits] SF.net SVN: jmol: [4818]

Revision: 4818 Author: migueljmol Date: 2006-03-28 02:42:40 -0800 (Tue, 28 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4818&view=rev Log Message: --- move rolled-back branch to trunk Added Paths: --- trunk/ Removed Paths: - bran

[Jmol-commits] SF.net SVN: jmol: [4817]

Revision: 4817 Author: migueljmol Date: 2006-03-28 02:40:55 -0800 (Tue, 28 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4817&view=rev Log Message: --- moving trunk to a branch Added Paths: --- branches/trunk200603/ Removed Paths: - t

[Jmol-commits] SF.net SVN: jmol: [4816] branches/bob200603/

Revision: 4816 Author: migueljmol Date: 2006-03-28 02:34:07 -0800 (Tue, 28 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4816&view=rev Log Message: --- former trunk against which 10.00.49 was released Added Paths: --- branches/bob200603/ Copied: bran

[Jmol-commits] SF.net SVN: jmol: [4815] branches/r4453rollback/Jmol/src/org/jmol/translation/Jmol

Revision: 4815 Author: migueljmol Date: 2006-03-27 20:31:32 -0800 (Mon, 27 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4815&view=rev Log Message: --- translations from trunk Modified Paths: -- branches/r4453rollback/Jmol/src/org/jmol/translation/

[Jmol-commits] SF.net SVN: jmol: [4812] branches/r4453rollback/Jmol

Revision: 4812 Author: migueljmol Date: 2006-03-27 18:52:02 -0800 (Mon, 27 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4812&view=rev Log Message: --- r4696 r4697 r4698 r4699 r4700 r4701 r4702 r4703 r4704 to approx 10.00.49 Modified Paths: -- bran

[Jmol-commits] SF.net SVN: jmol: [4811] branches/r4453rollback/Jmol/src/org/jmol/g3d/Graphics3D.java

Revision: 4811 Author: migueljmol Date: 2006-03-27 17:27:10 -0800 (Mon, 27 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4811&view=rev Log Message: --- r4695 step in eliminating Xyzd Modified Paths: -- branches/r4453rollback/Jmol/src/org/jmol

[Jmol-commits] SF.net SVN: jmol: [4810] branches/r4453rollback/Jmol/src/org/jmol/adapter/smarter/V3000Reader.java

Revision: 4810 Author: migueljmol Date: 2006-03-27 17:24:32 -0800 (Mon, 27 Mar 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=4810&view=rev Log Message: --- r4691 v3000 related -- only read first model of .sdf file Modified Paths: -- branches/r4453roll

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