From: <ha...@us...> - 2014-03-21 19:12:42
|
Revision: 19510 http://sourceforge.net/p/jmol/code/19510 Author: hansonr Date: 2014-03-21 19:12:39 +0000 (Fri, 21 Mar 2014) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2014-03-21 19:10:38 UTC (rev 19509) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2014-03-21 19:12:39 UTC (rev 19510) @@ -4365,9 +4365,9 @@ /** * @j2sNative * - * if (this.stm.jmolStatusListener.isStereoSlave) return; + * if (this.sm.jmolStatusListener.isStereoSlave) return; * g = this.apiPlatform.context; - * gright = this.stm.jmolStatusListener.gright; + * gright = this.sm.jmolStatusListener.gright; * * */ This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2014-03-30 15:11:26
|
Revision: 19539 http://sourceforge.net/p/jmol/code/19539 Author: hansonr Date: 2014-03-30 15:11:23 +0000 (Sun, 30 Mar 2014) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2014-03-30 15:10:52 UTC (rev 19538) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2014-03-30 15:11:23 UTC (rev 19539) @@ -4806,6 +4806,8 @@ if (name.startsWith("$$")) { // 2D version f = f.substring(1); + + //http://cactus.nci.nih.gov/chemical/structure/C%28O%29CCC/file?format=sdf format = PT.rep(g.smilesUrlFormat, "&get3d=True", ""); return Txt.formatStringS(format, "FILE", PT.escapeUrl(f)); @@ -8775,6 +8777,10 @@ break; default: info = SV.sValue(t); + // the following should not be necessary + // but an NCI server fault on 3/29/2014 required this + //if (info.equals("sdf")) + //info = "file?format=sdf"; } String s = (String) setLoadFormat("_" + smiles, type, false); if (type == '/') This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2014-09-16 23:58:40
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Revision: 20002 http://sourceforge.net/p/jmol/code/20002 Author: hansonr Date: 2014-09-16 23:58:38 +0000 (Tue, 16 Sep 2014) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2014-09-16 23:14:01 UTC (rev 20001) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2014-09-16 23:58:38 UTC (rev 20002) @@ -8764,6 +8764,7 @@ /** * + * @param eval * @param steps * Integer.MAX_VALUE --> use defaults * @param crit @@ -9316,7 +9317,7 @@ } public ScriptContext getEvalContextAndHoldQueue(JmolScriptEvaluator eval) { - if (false && (eval == null || !isJS)) + if (eval == null || !isJS && !testAsync) return null; eval.pushContextDown("getEvalContextAndHoldQueue"); ScriptContext sc = eval.getThisContext(); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2015-01-22 23:21:51
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Revision: 20234 http://sourceforge.net/p/jmol/code/20234 Author: hansonr Date: 2015-01-22 23:21:48 +0000 (Thu, 22 Jan 2015) Log Message: ----------- removing unwanted forcing of chain case Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-01-22 22:43:01 UTC (rev 20233) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-01-22 23:21:48 UTC (rev 20234) @@ -2457,6 +2457,7 @@ tempArray.clear(); chainMap.clear(); chainList.clear(); + chainCaseSpecified = false; //cm.clear(); definedAtomSets.clear(); lastData = null; @@ -4973,7 +4974,7 @@ case T.cartoonrockets: return g.cartoonRockets; case T.chaincasesensitive: - return g.chainCaseSensitive || chainList.size() > 0; + return g.chainCaseSensitive || chainCaseSpecified; case T.debugscript: return g.debugScript; case T.defaultstructuredssp: @@ -8943,6 +8944,8 @@ ms.setDihedrals(dihedralList, bsBranches, rate); } + private boolean chainCaseSpecified; + /** * Create a unique integer for any chain string. Note that if there are any * chains that are more than a single character, chainCaseSensitive is @@ -8974,6 +8977,7 @@ } if (i >= 256) { //this will force chainCaseSensitive when it is necessary + chainCaseSpecified |= isAssign; chainList.addLast(id); } // if select :a and there is NO chain "a" in the structure, This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2015-02-12 12:51:34
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Revision: 20289 http://sourceforge.net/p/jmol/code/20289 Author: hansonr Date: 2015-02-12 12:51:26 +0000 (Thu, 12 Feb 2015) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-02-12 12:48:51 UTC (rev 20288) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-02-12 12:51:26 UTC (rev 20289) @@ -1747,10 +1747,7 @@ return null; } boolean isLigand = prefix.equals("ligand_"); - if (isLigand) - id = id.toUpperCase(); - else - id = id.substring(id.lastIndexOf("/") + 1); + id = (isLigand ? id.toUpperCase() : id.substring(id.lastIndexOf("/") + 1)); if (ligandModelSet == null) ligandModelSet = new Hashtable<String, Boolean>(); ligandModelSet.put(id, Boolean.TRUE); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2016-07-13 19:40:34
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Revision: 21174 http://sourceforge.net/p/jmol/code/21174 Author: hansonr Date: 2016-07-13 19:40:30 +0000 (Wed, 13 Jul 2016) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2016-07-12 03:28:38 UTC (rev 21173) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2016-07-13 19:40:30 UTC (rev 21174) @@ -3,6 +3,7 @@ * $Date: 2014-02-02 22:24:37 -0600 (Sun, 02 Feb 2014) $ * $Revision: 19253 $ * + * * Copyright (C) 2002-2006 Miguel, Jmol Development, www.jmol.org * * Contact: jmo...@li... This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2016-07-13 19:45:20
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Revision: 21175 http://sourceforge.net/p/jmol/code/21175 Author: hansonr Date: 2016-07-13 19:45:16 +0000 (Wed, 13 Jul 2016) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2016-07-13 19:40:30 UTC (rev 21174) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2016-07-13 19:45:16 UTC (rev 21175) @@ -3,7 +3,6 @@ * $Date: 2014-02-02 22:24:37 -0600 (Sun, 02 Feb 2014) $ * $Revision: 19253 $ * - * * Copyright (C) 2002-2006 Miguel, Jmol Development, www.jmol.org * * Contact: jmo...@li... This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2016-07-13 19:48:58
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Revision: 21177 http://sourceforge.net/p/jmol/code/21177 Author: hansonr Date: 2016-07-13 19:48:56 +0000 (Wed, 13 Jul 2016) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Property Changed: ---------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2016-07-13 19:47:30 UTC (rev 21176) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2016-07-13 19:48:56 UTC (rev 21177) @@ -1,6 +1,6 @@ /* $RCSfile$ * $Author: hansonr $ - * $Date$ + * $LastChangedDate$ * $Revision: 19253 $ * * Copyright (C) 2002-2006 Miguel, Jmol Development, www.jmol.org Property changes on: trunk/Jmol/src/org/jmol/viewer/Viewer.java ___________________________________________________________________ Added: svn:keywords ## -0,0 +1 ## +LastChangedDate \ No newline at end of property This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2016-07-13 19:51:51
|
Revision: 21179 http://sourceforge.net/p/jmol/code/21179 Author: hansonr Date: 2016-07-13 19:51:46 +0000 (Wed, 13 Jul 2016) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2016-07-13 19:49:54 UTC (rev 21178) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2016-07-13 19:51:46 UTC (rev 21179) @@ -1,6 +1,6 @@ /* $RCSfile$ * $Author: hansonr $ - * $LastChangedDate$ + * $Date$ * $Revision: 19253 $ * * Copyright (C) 2002-2006 Miguel, Jmol Development, www.jmol.org This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2016-07-13 19:52:40
|
Revision: 21180 http://sourceforge.net/p/jmol/code/21180 Author: hansonr Date: 2016-07-13 19:52:37 +0000 (Wed, 13 Jul 2016) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Property Changed: ---------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2016-07-13 19:51:46 UTC (rev 21179) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2016-07-13 19:52:37 UTC (rev 21180) @@ -1,6 +1,6 @@ /* $RCSfile$ * $Author: hansonr $ - * $Date$ + * $Date: 2016-07-13 14:51:46 -0500 (Wed, 13 Jul 2016) $ * $Revision: 19253 $ * * Copyright (C) 2002-2006 Miguel, Jmol Development, www.jmol.org Property changes on: trunk/Jmol/src/org/jmol/viewer/Viewer.java ___________________________________________________________________ Deleted: svn:keywords ## -1 +0,0 ## -LastChangedDate \ No newline at end of property This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2017-02-07 03:19:57
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Revision: 21402 http://sourceforge.net/p/jmol/code/21402 Author: hansonr Date: 2017-02-07 03:19:54 +0000 (Tue, 07 Feb 2017) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2017-02-07 03:17:24 UTC (rev 21401) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2017-02-07 03:19:54 UTC (rev 21402) @@ -8924,9 +8924,14 @@ null); } + /** + * Run a script using the script function script("xxxxxx") using + * direct script tokens for script ( "xxxxxxx" ) + * + */ @Override public String runScript(String script) { - return "" + evaluateExpression(new T[][] { new T[] {T.t(T.script), T.t(T.leftparen), SV.newS(script), T.t(T.rightparen)}, null }); + return "" + evaluateExpression(new T[][] { new T[] {T.t(T.script), T.t(T.leftparen), SV.newS(script), T.t(T.rightparen)}}); } /** This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2021-08-12 02:59:18
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Revision: 22217 http://sourceforge.net/p/jmol/code/22217 Author: hansonr Date: 2021-08-12 02:59:16 +0000 (Thu, 12 Aug 2021) Log Message: ----------- Jmol.___JmolVersion="14.31.51" also 15.1.51 new feature: ISOSURFACE DENSITY option - checks for cryo-EM data from EBI/EMDB and, if that exists, uses it; otherwise uses x-ray diffraction data bug fix: problems with ISOSURFACE in 14.31.50 Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2021-08-12 02:41:28 UTC (rev 22216) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2021-08-12 02:59:16 UTC (rev 22217) @@ -5046,8 +5046,6 @@ if ("cif".equals(ciftype)) { id = id.replace("bcif", "cif"); } - if (type != '?') - showString("retrieving " + id, false); break; } return id; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2022-02-20 23:20:43
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Revision: 22344 http://sourceforge.net/p/jmol/code/22344 Author: hansonr Date: 2022-02-20 23:20:40 +0000 (Sun, 20 Feb 2022) Log Message: ----------- Jmol.___JmolVersion="14.32.24" also 15.2.24 bug fix: ChemDraw CDXML reader was not tested in 15.2.23 -- now loads proper compounds with (common) protecting groups. -- 2D -> 3D enabled; adds "Nickname" nodes (minimized as fluorine) undocumented feature: filter "*.ca;/=3"; bug fix: bonds to transparent atoms should be flat ends, not open new feature: SET UNDOAUTO FALSE|TRUE -- default value TRUE, enabling automatic saving of the state only in the Java application -- setting false turns off Java application console automatic undo/redo and allows user-defined undo/redo states -- disabled by SET PRESERVESTATE FALSE new feature: SET UNDO -- saves the current state on the UNDO stack. -- clears the REDO stack -- sets undoAuto FALSE new feature SET UNDOMAX n -- sets the maximum number of saved states (default 20) with SET defaultAuto FALSE -- setting this value to 0 clears both the UNDO and the REDO stacks new feature UNDO -- when undoAuto is true, in the Jmol application console only, carries out an undo action -- when undoAuto is false, or not in the Java application, restores the most recent state saved using SET UNDO new feature REDO -- when undoAuto is true, in the Jmol application console only, carries out a redo action -- when undoAuto is false, or not in the Java application, restores the most recent state prior to an UNDO operation new feature: SHOW UNDO -- reports if undoAuto is true or false, and if it is false, reports the sizes of the user UNDO and REDO stacks. new feature: MODELKIT UNDO/REDO -- a separate undo/redo stack specifically for the ModelKit -- undoes or redoes a ModelKit action -- disabled by SET PRESERVESTATE FALSE new feature: UNITCELL SURFACE {h k l} [height | scale%] [offset or offset%] [TOP] -- operates on current unit cell, so for repeat use, use unitcell reset -- allows creating a unit cell based on a Miller plane -- perpendicular to plane, with u = b/k - a/h, v = c/l - b/k (generally) -- optional height in Angstroms or scaled relative to hkl distance to origin -- optional offset in Angstroms or percent of unit cell height -- default offset sets bottom of unit cell at origin -- optional TOP parameter measure from the top of the new unit cell -- examples: load =ams/halite 1 packed unitcell reset;unitcell surface {1 1 1} 100% // between {0 0 0} and Miller plane unitcell reset;unitcell surface {1 1 1} 100% // between {0 0 0} and Miller plane unitcell reset;unitcell surface {1 1 1} 100% 50% // centers unit cell on Miller plane unitcell reset;unitcell surface {1 1 1} 50% 150% // half-height cell centered on Miller plane unitcell reset;unitcell surface {1 1 1} 100% -100% // top on {0 0 0} unitcell reset;unitcell surface {1 1 1} 100% @{hkl(1 1 1).w} // same as 100% -100% unitcell reset;unitcell surface {1 1 1} TOP // same as 100% -100% unitcell reset;unitcell surface {1 1 1} 10 TOP // same as 50% -100% Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2022-02-20 23:14:32 UTC (rev 22343) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2022-02-20 23:20:40 UTC (rev 22344) @@ -340,8 +340,6 @@ } int screenWidth, screenHeight; - final Lst<String> actionStates; - final Lst<String> actionStatesRedo; VDW defaultVdw; public RadiusData rd; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2022-08-20 23:36:14
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Revision: 22463 http://sourceforge.net/p/jmol/code/22463 Author: hansonr Date: 2022-08-20 23:36:12 +0000 (Sat, 20 Aug 2022) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2022-08-20 23:35:24 UTC (rev 22462) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2022-08-20 23:36:12 UTC (rev 22463) @@ -10574,18 +10574,28 @@ } } - public Object findSpaceGroup(BS bsAtoms, String opXYZ, boolean asString) { + /** + * + * @param bsAtoms + * @param xyzList if present, a semicolon-separated list of operators + * @param unitCell + * @param asString + * @param isAssign from ModelKit + * @return either an array of space group identifiers or, if asString, "", or null + * + */ + public Object findSpaceGroup(BS bsAtoms, String xyzList, float[] unitCell, boolean asString, boolean isAssign) { Object ret = null; - if (opXYZ == null) { - if (bsAtoms == null) + if (bsAtoms == null && xyzList == null || isAssign) bsAtoms = getThisModelAtoms(); + if (xyzList == null) { if (!bsAtoms.isEmpty()) { SymmetryInterface uc = getCurrentUnitCell(); ret = (uc == null ? null - : uc.findSpaceGroup(this, bsAtoms, opXYZ, asString)); + : uc.findSpaceGroup(this, bsAtoms, null, unitCell, asString, isAssign)); } } else { - ret = getSymTemp().findSpaceGroup(this, null, opXYZ, asString); + ret = getSymTemp().findSpaceGroup(this, bsAtoms, xyzList, unitCell, asString, isAssign); } return (ret == null && asString ? "" : ret); } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |