From: <ha...@us...> - 2012-12-18 21:47:13
|
Revision: 17820 http://jmol.svn.sourceforge.net/jmol/?rev=17820&view=rev Author: hansonr Date: 2012-12-18 21:47:06 +0000 (Tue, 18 Dec 2012) Log Message: ----------- ___version=13.0.11_dev bug fix: MOPAC2012 files not recognized Modified Paths: -------------- branches/v13_0/Jmol/src/org/jmol/adapter/readers/simple/MopacReader.java branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v13_0/Jmol/src/org/jmol/adapter/readers/simple/MopacReader.java =================================================================== --- branches/v13_0/Jmol/src/org/jmol/adapter/readers/simple/MopacReader.java 2012-12-18 21:46:42 UTC (rev 17819) +++ branches/v13_0/Jmol/src/org/jmol/adapter/readers/simple/MopacReader.java 2012-12-18 21:47:06 UTC (rev 17820) @@ -56,6 +56,8 @@ mopacVersion = 93; else if (line.indexOf("2002") >= 0) mopacVersion = 2002; + else if (line.indexOf("MOPAC2") >= 0) + mopacVersion = Parser.parseInt(line.substring(line.indexOf("MOPAC2") + 5)); } Logger.info("MOPAC version " + mopacVersion); } Modified: branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2012-12-18 21:46:42 UTC (rev 17819) +++ branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2012-12-18 21:47:06 UTC (rev 17820) @@ -11,6 +11,8 @@ ___version=13.0.11_dev +bug fix: MOPAC2012 files not recognized + ============================================================================= version=13.0.10 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-01-23 20:56:07
|
Revision: 17875 http://jmol.svn.sourceforge.net/jmol/?rev=17875&view=rev Author: hansonr Date: 2013-01-23 20:55:57 +0000 (Wed, 23 Jan 2013) Log Message: ----------- ___version=13.0.12 bug fix: PDB file reading of remediated 1A7Y and 1E9W error due to too many CONECT bonds -- now reads HEADER columns 63-66 for 4-digit PDB ID. -- only if this ID is absent will the number of CONECT bonds be checked in decision to autobond Modified Paths: -------------- branches/v13_0/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java branches/v13_0/Jmol/src/org/jmol/modelset/ModelLoader.java branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v13_0/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java =================================================================== --- branches/v13_0/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java 2013-01-19 22:14:05 UTC (rev 17874) +++ branches/v13_0/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java 2013-01-23 20:55:57 UTC (rev 17875) @@ -387,8 +387,11 @@ if (lineLength < 8) return; appendLoadNote(line.substring(7).trim()); - if (lineLength >= 66) - atomSetCollection.setCollectionName(line.substring(62, 66)); + String pdbID = (lineLength >= 66 ? line.substring(62, 66).trim() : ""); + if (pdbID.length() == 4) { + atomSetCollection.setCollectionName(pdbID); + atomSetCollection.setAtomSetCollectionAuxiliaryInfo("havePDBHeaderName", Boolean.TRUE); + } if (lineLength > 50) line = line.substring(0, 50); atomSetCollection.setAtomSetCollectionAuxiliaryInfo("CLASSIFICATION", line.substring(7).trim()); Modified: branches/v13_0/Jmol/src/org/jmol/modelset/ModelLoader.java =================================================================== --- branches/v13_0/Jmol/src/org/jmol/modelset/ModelLoader.java 2013-01-19 22:14:05 UTC (rev 17874) +++ branches/v13_0/Jmol/src/org/jmol/modelset/ModelLoader.java 2013-01-23 20:55:57 UTC (rev 17875) @@ -1127,12 +1127,14 @@ // use ATOM, so that's a problem. Those atoms would not be excluded from // the // automatic bonding, and additional bonds might be made. - boolean doBond = (forceAutoBond || doAutoBond - && (modelBondCount == 0 || modelIsPDB && jmolData == null - && modelBondCount < modelAtomCount / 2 || modelHasSymmetry - && !symmetryAlreadyAppliedToBonds - && !modelSet.getModelAuxiliaryInfoBoolean(i, "hasBonds") - )); + boolean doBond = (forceAutoBond || doAutoBond && ( + modelBondCount == 0 + || modelIsPDB + && (modelSet.getModelSetAuxiliaryInfoBoolean("havePDBHeaderName") + || modelIsPDB && jmolData == null && modelBondCount < modelAtomCount / 2) + || modelHasSymmetry && !symmetryAlreadyAppliedToBonds + && !modelSet.getModelAuxiliaryInfoBoolean(i, "hasBonds") + )); if (!doBond) continue; autoBonding = true; Modified: branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-01-19 22:14:05 UTC (rev 17874) +++ branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-01-23 20:55:57 UTC (rev 17875) @@ -11,6 +11,10 @@ ___version=13.0.12 +bug fix: PDB file reading of remediated 1A7Y and 1E9W error due to too many CONECT bonds + -- now reads HEADER columns 63-66 for 4-digit PDB ID. + -- only if this ID is absent will the number of CONECT bonds be checked in decision to autobond + version=13.0.11 bug fix: MOPAC2012 files not recognized This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-01-27 21:09:19
|
Revision: 17886 http://jmol.svn.sourceforge.net/jmol/?rev=17886&view=rev Author: hansonr Date: 2013-01-27 21:09:12 +0000 (Sun, 27 Jan 2013) Log Message: ----------- ___version=13.0.13_dev bug fix: The "show history" command is supposed to clear out the "show history" command itself, but only if it is a top-level command (from the console), but it does more than that if it is part of script("show history"). Probably true with all recent versions of Jmol. Modified Paths: -------------- branches/v13_0/Jmol/src/org/jmol/script/ScriptEvaluator.java branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v13_0/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- branches/v13_0/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-01-27 21:08:07 UTC (rev 17885) +++ branches/v13_0/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-01-27 21:09:12 UTC (rev 17886) @@ -14910,6 +14910,7 @@ if (n < 1) error(ERROR_invalidArgument); if (!isSyntaxCheck) { + if (scriptLevel == 0) viewer.removeCommand(); msg = viewer.getSetHistory(n); } Modified: branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-01-27 21:08:07 UTC (rev 17885) +++ branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-01-27 21:09:12 UTC (rev 17886) @@ -11,6 +11,11 @@ ___version=13.0.13_dev +bug fix: The "show history" command is supposed to clear out the "show history" command + itself, but only if it is a top-level command (from the console), + but it does more than that if it is part of script("show history"). + Probably true with all recent versions of Jmol. + ============================================================================= version=13.0.12 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-02-05 18:00:23
|
Revision: 17906 http://jmol.svn.sourceforge.net/jmol/?rev=17906&view=rev Author: hansonr Date: 2013-02-05 18:00:16 +0000 (Tue, 05 Feb 2013) Log Message: ----------- ___version=13.0.13_dev bug fix: load CENTROID does not always work -- wrong implicit normalization flag (was -1 instead of 1) Modified Paths: -------------- branches/v13_0/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v13_0/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java =================================================================== --- branches/v13_0/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2013-02-05 17:58:22 UTC (rev 17905) +++ branches/v13_0/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2013-02-05 18:00:16 UTC (rev 17906) @@ -466,6 +466,8 @@ latticeCells[1] = (int) pt.y; latticeCells[2] = (int) pt.z; doCentroidUnitCell = (htParams.containsKey("centroid")); + if (doCentroidUnitCell && (latticeCells[2] == -1 || latticeCells[2] == 0)) + latticeCells[2] = 1; centroidPacked = doCentroidUnitCell && htParams.containsKey("packed"); doPackUnitCell = !doCentroidUnitCell && (htParams.containsKey("packed") || latticeCells[2] < 0); Modified: branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-02-05 17:58:22 UTC (rev 17905) +++ branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-02-05 18:00:16 UTC (rev 17906) @@ -11,6 +11,8 @@ ___version=13.0.13_dev +bug fix: load CENTROID does not always work -- wrong implicit normalization flag (was -1 instead of 1) + bug fix: The "show history" command is supposed to clear out the "show history" command itself, but only if it is a top-level command (from the console), but it does more than that if it is part of script("show history"). This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-02-06 14:13:49
|
Revision: 17909 http://jmol.svn.sourceforge.net/jmol/?rev=17909&view=rev Author: hansonr Date: 2013-02-06 14:13:41 +0000 (Wed, 06 Feb 2013) Log Message: ----------- ___version=13.0.13_dev bug fix: labels within fog should be hidden Modified Paths: -------------- branches/v13_0/Jmol/src/org/jmol/shape/LabelsRenderer.java branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties branches/v13_0/Jmol/src/org/jmol/viewer/TransformManager.java branches/v13_0/Jmol/src/org/jmol/viewer/Viewer.java Modified: branches/v13_0/Jmol/src/org/jmol/shape/LabelsRenderer.java =================================================================== --- branches/v13_0/Jmol/src/org/jmol/shape/LabelsRenderer.java 2013-02-05 20:11:02 UTC (rev 17908) +++ branches/v13_0/Jmol/src/org/jmol/shape/LabelsRenderer.java 2013-02-06 14:13:41 UTC (rev 17909) @@ -38,9 +38,12 @@ protected int descent; final int[] minZ = new int[1]; + private int zCutoff; + @Override protected void render() { fidPrevious = 0; + zCutoff = viewer.getZShadeStart(); Labels labels = (Labels) shape; @@ -91,6 +94,8 @@ int textAlign = Labels.getAlignment(offsetFull); int pointer = offsetFull & Labels.POINTER_FLAGS; int zSlab = atom.screenZ - atom.screenDiameter / 2 - 3; + if (zCutoff > 0 && zSlab > zCutoff) + continue; if (zSlab < 1) zSlab = 1; int zBox = zSlab; Modified: branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-02-05 20:11:02 UTC (rev 17908) +++ branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-02-06 14:13:41 UTC (rev 17909) @@ -11,6 +11,7 @@ ___version=13.0.13_dev +bug fix: labels within fog should be hidden bug fix: load CENTROID does not always work -- wrong implicit normalization flag (was -1 instead of 1) bug fix: The "show history" command is supposed to clear out the "show history" command Modified: branches/v13_0/Jmol/src/org/jmol/viewer/TransformManager.java =================================================================== --- branches/v13_0/Jmol/src/org/jmol/viewer/TransformManager.java 2013-02-05 20:11:02 UTC (rev 17908) +++ branches/v13_0/Jmol/src/org/jmol/viewer/TransformManager.java 2013-02-06 14:13:41 UTC (rev 17909) @@ -900,6 +900,10 @@ int zSlabValue; int zDepthValue; + int getZShadeStart() { + return (zShadeEnabled ? zSlabValue : 0); + } + float slabRange = 0f; public void setSlabRange(float value) { Modified: branches/v13_0/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- branches/v13_0/Jmol/src/org/jmol/viewer/Viewer.java 2013-02-05 20:11:02 UTC (rev 17908) +++ branches/v13_0/Jmol/src/org/jmol/viewer/Viewer.java 2013-02-06 14:13:41 UTC (rev 17909) @@ -1101,6 +1101,10 @@ return transformManager.getTranslationScript(); } + public int getZShadeStart() { + return transformManager.getZShadeStart(); + } + @Override public int getZoomPercent() { // deprecated This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-02-11 15:35:58
|
Revision: 17920 http://jmol.svn.sourceforge.net/jmol/?rev=17920&view=rev Author: hansonr Date: 2013-02-11 15:35:48 +0000 (Mon, 11 Feb 2013) Log Message: ----------- ___version=13.0.13_dev bug fix: signed applet file open dialog does not work Modified Paths: -------------- branches/v13_0/Jmol/src/org/jmol/export/dialog/Dialog.java branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v13_0/Jmol/src/org/jmol/export/dialog/Dialog.java =================================================================== --- branches/v13_0/Jmol/src/org/jmol/export/dialog/Dialog.java 2013-02-10 00:08:44 UTC (rev 17919) +++ branches/v13_0/Jmol/src/org/jmol/export/dialog/Dialog.java 2013-02-11 15:35:48 UTC (rev 17920) @@ -153,7 +153,7 @@ closePreview(); if (fileName.startsWith("/")) fileName = "file://" + fileName; // for Macs - return (doCartoons ? "" : "#NOC#;") + (doAppend ? "load append " + Escape.escape(fileName) : fileName); + return (!allowAppend || doCartoons ? "" : "#NOC#;") + (doAppend ? "load append " + Escape.escape(fileName) : fileName); } String closePreview() { Modified: branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-02-10 00:08:44 UTC (rev 17919) +++ branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-02-11 15:35:48 UTC (rev 17920) @@ -11,6 +11,7 @@ ___version=13.0.13_dev +bug fix: signed applet file open dialog does not work bug fix: labels within fog should be hidden bug fix: load CENTROID does not always work -- wrong implicit normalization flag (was -1 instead of 1) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-02-13 20:40:54
|
Revision: 17925 http://jmol.svn.sourceforge.net/jmol/?rev=17925&view=rev Author: hansonr Date: 2013-02-13 20:40:42 +0000 (Wed, 13 Feb 2013) Log Message: ----------- ___version=13.0.13_dev bug fix: set ellipsoid FILL does not exclude bonds leading into the empty quadrant Modified Paths: -------------- branches/v13_0/Jmol/src/org/jmol/g3d/Graphics3D.java branches/v13_0/Jmol/src/org/jmol/g3d/Sphere3D.java branches/v13_0/Jmol/src/org/jmol/modelset/ModelLoader.java branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v13_0/Jmol/src/org/jmol/g3d/Graphics3D.java =================================================================== --- branches/v13_0/Jmol/src/org/jmol/g3d/Graphics3D.java 2013-02-12 13:16:30 UTC (rev 17924) +++ branches/v13_0/Jmol/src/org/jmol/g3d/Graphics3D.java 2013-02-13 20:40:42 UTC (rev 17925) @@ -773,7 +773,17 @@ pixel.addPixel(offset, z, p); } + void clearPixel(int offset, int z) { + pixel.clearPixel(offset, z); + } + class Pixel { + + void clearPixel(int offset, int z) { + if (!isPass2 && zbuf[offset] > z) + zbuf[offset] = Integer.MAX_VALUE; + } + void addPixel(int offset, int z, int p) { if (!isPass2) { zbuf[offset] = z; Modified: branches/v13_0/Jmol/src/org/jmol/g3d/Sphere3D.java =================================================================== --- branches/v13_0/Jmol/src/org/jmol/g3d/Sphere3D.java 2013-02-12 13:16:30 UTC (rev 17924) +++ branches/v13_0/Jmol/src/org/jmol/g3d/Sphere3D.java 2013-02-13 20:40:42 UTC (rev 17925) @@ -458,6 +458,7 @@ private final Point3f ptTemp = new Point3f(); private final int[] planeShades = new int[3]; private final float[][] dxyz = new float[3][3]; + private int z0; private void renderQuadrantClipped(int radius, int xSign, int ySign) { boolean isEllipsoid = (mat != null); @@ -526,27 +527,35 @@ if (checkOctant) { ptTemp.set(xCurrent - x, yCurrent - y, zPixel - z); mat.transform(ptTemp); - int thisOctant = Quadric.getOctant(ptTemp); + int thisOctant = Quadric.getOctant(ptTemp); + z0 = zPixel; if (thisOctant == selectedOctant) { - iShade = getPlaneShade(xCurrent, yCurrent, zroot); + iShade = getPlaneShade(xCurrent, yCurrent, zroot); zPixel = (int) zroot[0]; mode = 3; // another option: show back only //iRoot = 1; //zPixel = (int) zroot[iRoot]; } + boolean isCore = (z < slab ? zPixel >= slab : zPixel < slab); + if (isCore) { + z0 = zPixel = slab; + mode = 0; + } + if (zPixel < slab || zPixel > depth || zbuf[offset] <= z0) + continue; } } else { int zOffset = (int)Math.sqrt(s2 - j2); zPixel = z + (z < slab ? zOffset : -zOffset); + boolean isCore = (z < slab ? zPixel >= slab : zPixel < slab); + if (isCore) { + zPixel = slab; + mode = 0; + } + if (zPixel < slab || zPixel > depth || zbuf[offset] <= zPixel) + continue; } - boolean isCore = (z < slab ? zPixel >= slab : zPixel < slab); - if (isCore) { - zPixel = slab; - mode = 0; - } - if (zPixel < slab || zPixel > depth || zbuf[offset] <= zPixel) - continue; switch(mode) { case 0: //core iShade = (SHADE_SLAB_CLIPPED - 3 + ((randu >> 8) & 0x07)); @@ -557,6 +566,7 @@ iShade = getEllipsoidShade(xCurrent, yCurrent, (float) zroot[iRoot], radius, mDeriv); break; case 3: //ellipsoid fill + g3d.clearPixel(offset, z0); break; default: //sphere int x8 = ((j * xSign + radius) << 8) / dDivisor; Modified: branches/v13_0/Jmol/src/org/jmol/modelset/ModelLoader.java =================================================================== --- branches/v13_0/Jmol/src/org/jmol/modelset/ModelLoader.java 2013-02-12 13:16:30 UTC (rev 17924) +++ branches/v13_0/Jmol/src/org/jmol/modelset/ModelLoader.java 2013-02-13 20:40:42 UTC (rev 17925) @@ -1172,6 +1172,9 @@ if (modelSet.modelSetAuxiliaryInfo != null) { modelSet.modelSetAuxiliaryInfo.put("group3Lists", group3Lists); modelSet.modelSetAuxiliaryInfo.put("group3Counts", group3Counts); + for (int i = 0; i < group3Counts.length; i++) + if (group3Counts[i] == null) + group3Counts[i] = new int[0]; } } Modified: branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-02-12 13:16:30 UTC (rev 17924) +++ branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-02-13 20:40:42 UTC (rev 17925) @@ -11,6 +11,7 @@ ___version=13.0.13_dev +bug fix: set ellipsoid FILL does not exclude bonds leading into the empty quadrant bug fix: set picking IDENT when picking is already ident can cancel a pending measurement bug fix: applet does not refresh when mouse exits with pending measurement bug fix: signed applet file open dialog does not work This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-02-18 18:51:13
|
Revision: 17935 http://jmol.svn.sourceforge.net/jmol/?rev=17935&view=rev Author: hansonr Date: 2013-02-18 18:51:03 +0000 (Mon, 18 Feb 2013) Log Message: ----------- ___version=13.0.13_dev bug fix: MOPAC reader not reading recent MOPAC files Modified Paths: -------------- branches/v13_0/Jmol/src/org/jmol/adapter/smarter/Resolver.java branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v13_0/Jmol/src/org/jmol/adapter/smarter/Resolver.java =================================================================== --- branches/v13_0/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2013-02-16 19:59:32 UTC (rev 17934) +++ branches/v13_0/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2013-02-18 18:51:03 UTC (rev 17935) @@ -1008,9 +1008,9 @@ { "Ampac", "AMPAC Version" }; private final static String[] mopacContainsRecords = - { "Mopac", "MOPAC 93 (c) Fujitsu", "MOPAC2002 (c) Fujitsu", + { "Mopac", "MOPAC 93 (c) Fujitsu", "MOPAC FOR LINUX (PUBLIC DOMAIN VERSION)", - "MOPAC: VERSION 6", "MOPAC 7", "MOPAC2009", "MOPAC (PUBLIC" }; + "MOPAC: VERSION 6", "MOPAC 7", "MOPAC2", "MOPAC (PUBLIC" }; private final static String[] qchemContainsRecords = { "Qchem", "Welcome to Q-Chem", "A Quantum Leap Into The Future Of Chemistry" }; Modified: branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-02-16 19:59:32 UTC (rev 17934) +++ branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-02-18 18:51:03 UTC (rev 17935) @@ -11,6 +11,7 @@ ___version=13.0.13_dev +bug fix: MOPAC reader not reading recent MOPAC files bug fix: set ellipsoid FILL does not exclude bonds leading into the empty quadrant bug fix: set picking IDENT when picking is already ident can cancel a pending measurement bug fix: applet does not refresh when mouse exits with pending measurement This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-02-27 19:10:18
|
Revision: 17953 http://jmol.svn.sourceforge.net/jmol/?rev=17953&view=rev Author: hansonr Date: 2013-02-27 19:10:09 +0000 (Wed, 27 Feb 2013) Log Message: ----------- ___version=13.0.14_dev bug fix: ModelKit menu "SHIFT to rotate" should read "ALT to rotate" Modified Paths: -------------- branches/v13_0/Jmol/src/org/jmol/modelkit/ModelKitPopupResourceBundle.java branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v13_0/Jmol/src/org/jmol/modelkit/ModelKitPopupResourceBundle.java =================================================================== --- branches/v13_0/Jmol/src/org/jmol/modelkit/ModelKitPopupResourceBundle.java 2013-02-27 19:04:34 UTC (rev 17952) +++ branches/v13_0/Jmol/src/org/jmol/modelkit/ModelKitPopupResourceBundle.java 2013-02-27 19:10:09 UTC (rev 17953) @@ -97,7 +97,7 @@ "assignAtom_XxP!CB" , GT._("drag to bond"), "dragAtomP!CB" , GT._("drag atom"), "dragMinimizeP!CB" , GT._("drag atom (and minimize)"), - "dragMoleculeP!CB" , GT._("drag molecule (SHIFT to rotate)"), + "dragMoleculeP!CB" , GT._("drag molecule (ALT to rotate)"), "dragMinimizeMoleculeP!CB" , GT._("drag and minimize molecule (docking)"), "assignAtom_CP!CB" , "C", "assignAtom_HP!CB" , "H", Modified: branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-02-27 19:04:34 UTC (rev 17952) +++ branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-02-27 19:10:09 UTC (rev 17953) @@ -11,6 +11,8 @@ ___version=13.0.14_dev +bug fix: ModelKit menu "SHIFT to rotate" should read "ALT to rotate" + ============================================================================= ___version=13.0.13 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-03-01 04:36:19
|
Revision: 17956 http://jmol.svn.sourceforge.net/jmol/?rev=17956&view=rev Author: hansonr Date: 2013-03-01 04:36:12 +0000 (Fri, 01 Mar 2013) Log Message: ----------- ___version=13.0.14_dev bug fix: incorrect calculation of RMSD for COMPARE and SMILES Modified Paths: -------------- branches/v13_0/Jmol/src/org/jmol/util/Measure.java branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v13_0/Jmol/src/org/jmol/util/Measure.java =================================================================== --- branches/v13_0/Jmol/src/org/jmol/util/Measure.java 2013-03-01 04:35:41 UTC (rev 17955) +++ branches/v13_0/Jmol/src/org/jmol/util/Measure.java 2013-03-01 04:36:12 UTC (rev 17956) @@ -567,22 +567,25 @@ } public static float getRmsd(Point3f[][] centerAndPoints, Quaternion q) { - double sum = 0; double sum2 = 0; - int n = centerAndPoints[0].length - 1; + Point3f[] ptsA = centerAndPoints[0]; + Point3f[] ptsB = centerAndPoints[1]; + Point3f cA = ptsA[0]; + Point3f cB = ptsB[0]; + int n = ptsA.length - 1; Point3f ptAnew = new Point3f(); + for (int i = n + 1; --i >= 1;) { - ptAnew.set(centerAndPoints[0][i]); - ptAnew.sub(centerAndPoints[0][0]); + ptAnew.set(ptsA[i]); + ptAnew.sub(cA); q.transform(ptAnew, ptAnew); - ptAnew.add(centerAndPoints[1][0]); - double d = ptAnew.distance(centerAndPoints[1][i]); - sum += d; - sum2 += d * d; + ptAnew.add(cB); + sum2 += ptAnew.distanceSquared(ptsB[i]); } - return (float) Math.sqrt((sum2 - sum * sum / n) / (n - 1)); + return (float) Math.sqrt(sum2 / n); } + public static List<Point3f> transformPoints(List<Point3f> vPts, Matrix4f m4, Point3f center) { List<Point3f> v = new ArrayList<Point3f>(); for (int i = 0; i < vPts.size(); i++) { Modified: branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-03-01 04:35:41 UTC (rev 17955) +++ branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-03-01 04:36:12 UTC (rev 17956) @@ -11,6 +11,7 @@ ___version=13.0.14_dev +bug fix: incorrect calculation of RMSD for COMPARE and SMILES bug fix: ModelKit menu "SHIFT to rotate" should read "ALT to rotate" ============================================================================= This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-03-11 16:18:31
|
Revision: 17968 http://sourceforge.net/p/jmol/code/17968 Author: hansonr Date: 2013-03-11 16:18:28 +0000 (Mon, 11 Mar 2013) Log Message: ----------- ___version=13.0.14_dev bug fix: LcaoCartoon "-sp3d" not working Modified Paths: -------------- branches/v13_0/Jmol/src/org/jmol/modelset/AtomCollection.java branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v13_0/Jmol/src/org/jmol/modelset/AtomCollection.java =================================================================== --- branches/v13_0/Jmol/src/org/jmol/modelset/AtomCollection.java 2013-03-11 16:17:10 UTC (rev 17967) +++ branches/v13_0/Jmol/src/org/jmol/modelset/AtomCollection.java 2013-03-11 16:18:28 UTC (rev 17968) @@ -1488,7 +1488,7 @@ .substring(1) : lcaoTypeRaw); - if (lcaoTypeRaw.indexOf("d") >= 0 && !lcaoTypeRaw.equals("sp3d")) + if (lcaoTypeRaw.indexOf("d") >= 0 && !lcaoTypeRaw.endsWith("sp3d")) return getHybridizationAndAxesD(atomIndex, z, x, lcaoType); Atom atom = atoms[atomIndex]; Modified: branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-03-11 16:17:10 UTC (rev 17967) +++ branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-03-11 16:18:28 UTC (rev 17968) @@ -11,6 +11,7 @@ ___version=13.0.14_dev +bug fix: LcaoCartoon "-sp3d" not working bug fix: incorrect calculation of RMSD for COMPARE and SMILES bug fix: ModelKit menu "SHIFT to rotate" should read "ALT to rotate" This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-03-13 18:34:39
|
Revision: 17971 http://sourceforge.net/p/jmol/code/17971 Author: hansonr Date: 2013-03-13 18:34:34 +0000 (Wed, 13 Mar 2013) Log Message: ----------- ___version=13.0.14_dev bug fix: assign atom does not update selections for elements Modified Paths: -------------- branches/v13_0/Jmol/src/org/jmol/script/ScriptEvaluator.java branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v13_0/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- branches/v13_0/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-03-12 12:10:55 UTC (rev 17970) +++ branches/v13_0/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-03-13 18:34:34 UTC (rev 17971) @@ -12152,7 +12152,7 @@ int index2 = -1; String type = null; if (index < 0) - error(ERROR_invalidArgument); + return; if (atomsOrBonds == Token.connect) { index2 = atomExpression(++iToken).nextSetBit(0); } else { @@ -12163,6 +12163,7 @@ return; switch (atomsOrBonds) { case Token.atoms: + clearDefinedVariableAtomSets(); viewer.assignAtom(index, pt, type); break; case Token.bonds: Modified: branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-03-12 12:10:55 UTC (rev 17970) +++ branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-03-13 18:34:34 UTC (rev 17971) @@ -11,6 +11,7 @@ ___version=13.0.14_dev +bug fix: assign atom does not update selections for elements bug fix: LcaoCartoon "-sp3d" not working bug fix: incorrect calculation of RMSD for COMPARE and SMILES bug fix: ModelKit menu "SHIFT to rotate" should read "ALT to rotate" This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-03-17 17:13:39
|
Revision: 17994 http://sourceforge.net/p/jmol/code/17994 Author: hansonr Date: 2013-03-17 17:13:36 +0000 (Sun, 17 Mar 2013) Log Message: ----------- ___version=13.0.14_dev bug fix: WRITE PNGJ does not allow sizing of image Modified Paths: -------------- branches/v13_0/Jmol/src/org/jmol/script/ScriptEvaluator.java branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v13_0/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- branches/v13_0/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-03-16 20:23:34 UTC (rev 17993) +++ branches/v13_0/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-03-17 17:13:36 UTC (rev 17994) @@ -14262,9 +14262,14 @@ // evalError(GT._("The {0} command is not available for the applet.", // "WRITE CLIPBOARD")); } else if (Parser.isOneOf(val.toLowerCase(), - "png;pngj;pngt;jpg;jpeg;jpg64;jpeg64") - && tokAt(pt + 1, args) == Token.integer) { - quality = ScriptVariable.iValue(tokenAt(++pt, args)); + "png;pngj;pngt;jpg;jpeg;jpg64;jpeg64")) { + if (tokAt(pt + 1, args) == Token.integer + && tokAt(pt + 2, args) == Token.integer) { + width = ScriptVariable.iValue(tokenAt(++pt, args)); + height = ScriptVariable.iValue(tokenAt(++pt, args)); + } + if (tokAt(pt + 1, args) == Token.integer) + quality = ScriptVariable.iValue(tokenAt(++pt, args)); } else if (Parser.isOneOf(val.toLowerCase(), "xyz;xyzrn;xyzvib;mol;sdf;v2000;v3000;cd;pdb;pqr;cml")) { type = val.toUpperCase(); Modified: branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-03-16 20:23:34 UTC (rev 17993) +++ branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-03-17 17:13:36 UTC (rev 17994) @@ -11,6 +11,7 @@ ___version=13.0.14_dev +bug fix: WRITE PNGJ does not allow sizing of image bug fix: backbone/spine defs do not take into account phosphorylated proteins. Better: "@backbone protein&(_a>=1&_a<6|_a>=64&_a<72)|nucleic&(_a>=6&_a<14|_a>=72)", "@spine protein&_a>=1&_a<4|nucleic&_a>=6&_a<14&_a!=12", This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-03-28 16:08:50
|
Revision: 18018 http://sourceforge.net/p/jmol/code/18018 Author: hansonr Date: 2013-03-28 16:08:43 +0000 (Thu, 28 Mar 2013) Log Message: ----------- ___version=13.0.14_dev28 bug fix: isosurface slab translucent broken when saved in state bug fix: isosurface slab translucent mesh broken when saved in state Modified Paths: -------------- branches/v13_0/Jmol/src/org/jmol/shape/MeshCollection.java branches/v13_0/Jmol/src/org/jmol/shape/MeshRenderer.java branches/v13_0/Jmol/src/org/jmol/shapesurface/IsosurfaceRenderer.java branches/v13_0/Jmol/src/org/jmol/util/MeshSurface.java branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v13_0/Jmol/src/org/jmol/shape/MeshCollection.java =================================================================== --- branches/v13_0/Jmol/src/org/jmol/shape/MeshCollection.java 2013-03-28 16:07:08 UTC (rev 18017) +++ branches/v13_0/Jmol/src/org/jmol/shape/MeshCollection.java 2013-03-28 16:08:43 UTC (rev 18018) @@ -351,7 +351,7 @@ return; case Token.translucent: m.setTranslucent(bProp, translucentLevel); - if (m.bsSlabGhost != null) + if (bProp && m.bsSlabGhost != null) m.resetSlab(); return; default: Modified: branches/v13_0/Jmol/src/org/jmol/shape/MeshRenderer.java =================================================================== --- branches/v13_0/Jmol/src/org/jmol/shape/MeshRenderer.java 2013-03-28 16:07:08 UTC (rev 18017) +++ branches/v13_0/Jmol/src/org/jmol/shape/MeshRenderer.java 2013-03-28 16:08:43 UTC (rev 18018) @@ -130,8 +130,9 @@ return false; if (mesh.bsSlabGhost != null) g3d.setColix(mesh.slabColix); // forces a second pass + System.out.println(mesh + " " + mesh.bsSlabGhost); haveBsSlabGhost = (mesh.bsSlabGhost != null && (isExport ? exportPass == 2 - : g3d.isPass2())); + : g3d.isPass2())); isTranslucent = haveBsSlabGhost || Graphics3D.isColixTranslucent(mesh.colix); doRender = (setColix(mesh.colix) || mesh.showContourLines); @@ -151,6 +152,7 @@ haveBsDisplay = (mesh.bsDisplay != null); haveBsSlabDisplay = (haveBsSlabGhost || mesh.bsSlabDisplay != null); + System.out.println(haveBsSlabGhost + " ghost | disp " + haveBsSlabDisplay); bsSlab = (haveBsSlabGhost ? mesh.bsSlabGhost : haveBsSlabDisplay ? mesh.bsSlabDisplay : null); frontOnly = !viewer.getSlabEnabled() && mesh.frontOnly Modified: branches/v13_0/Jmol/src/org/jmol/shapesurface/IsosurfaceRenderer.java =================================================================== --- branches/v13_0/Jmol/src/org/jmol/shapesurface/IsosurfaceRenderer.java 2013-03-28 16:07:08 UTC (rev 18017) +++ branches/v13_0/Jmol/src/org/jmol/shapesurface/IsosurfaceRenderer.java 2013-03-28 16:08:43 UTC (rev 18018) @@ -74,7 +74,6 @@ continue; hasColorRange = false; if (renderMesh(mySlabValue, slabValue)) { - //System.out.println("render isossurface " + i + " " + isosurface.meshCount); if (!isExport) renderInfo(); if (isExport && haveBsSlabGhost) { @@ -334,8 +333,6 @@ @Override protected void renderTriangles(boolean fill, boolean iShowTriangles, boolean isExport) { - //System.out.println("isorend mvc=" + imesh.mergeVertexCount0 + " mpc=" + imesh.mergePolygonCount0 + " vc=" + imesh.vertexCount + " pc=" + imesh.polygonCount + " " + imesh); - //if (bsSlab != null) System.out.println("isorend bsSlab=" + bsSlab.cardinality() + " " + bsSlab); int[][] polygonIndexes = imesh.polygonIndexes; colix = (haveBsSlabGhost ? imesh.slabColix : !fill && imesh.meshColix != 0 ? imesh.meshColix : imesh.colix); @@ -382,11 +379,6 @@ int iA = polygon[0]; int iB = polygon[1]; int iC = polygon[2]; -/* - int iTest = 6596; - if (iA == iTest|| iB == iTest || iC == iTest) - System.out.println(iA + " " + iB + " " + iC); -*/ if (imesh.jvxlData.thisSet >= 0 && imesh.vertexSets != null && imesh.vertexSets[iA] != imesh.jvxlData.thisSet) continue; Modified: branches/v13_0/Jmol/src/org/jmol/util/MeshSurface.java =================================================================== --- branches/v13_0/Jmol/src/org/jmol/util/MeshSurface.java 2013-03-28 16:07:08 UTC (rev 18017) +++ branches/v13_0/Jmol/src/org/jmol/util/MeshSurface.java 2013-03-28 16:08:43 UTC (rev 18018) @@ -344,10 +344,14 @@ StringBuffer sb = new StringBuffer(); sb.append(andCap ? " cap " : " slab "); - if (isGhost) + if (isGhost) { sb.append("translucent ").append( Graphics3D.getColixTranslucencyFractional(slabColix)).append(" ") .append(Graphics3D.getHexCode(slabColix)).append(" "); + if (slabMeshType == Token.mesh) + sb.append("mesh "); + } + switch (slabType) { case Token.brillouin: sb.append("brillouin"); Modified: branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-03-28 16:07:08 UTC (rev 18017) +++ branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-03-28 16:08:43 UTC (rev 18018) @@ -9,8 +9,11 @@ # 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=13.0.14_dev22 +___version=13.0.14_dev28 +bug fix: isosurface slab translucent broken when saved in state +bug fix: isosurface slab translucent mesh broken when saved in state + bug fix: sync socket connections not working bug fix: WRITE PNGJ does not allow sizing of image bug fix: backbone/spine defs do not take into account phosphorylated proteins. Better: This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-03-31 21:26:07
|
Revision: 18028 http://sourceforge.net/p/jmol/code/18028 Author: hansonr Date: 2013-03-31 21:26:01 +0000 (Sun, 31 Mar 2013) Log Message: ----------- ___version=13.0.14_dev31 bug fix: MOL2 reader not properly assigning element symbols Modified Paths: -------------- branches/v13_0/Jmol/src/org/jmol/adapter/readers/more/Mol2Reader.java branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v13_0/Jmol/src/org/jmol/adapter/readers/more/Mol2Reader.java =================================================================== --- branches/v13_0/Jmol/src/org/jmol/adapter/readers/more/Mol2Reader.java 2013-03-31 20:24:08 UTC (rev 18027) +++ branches/v13_0/Jmol/src/org/jmol/adapter/readers/more/Mol2Reader.java 2013-03-31 21:26:01 UTC (rev 18028) @@ -169,9 +169,11 @@ for (int i = 0; i < atomCount; ++i) { Atom atom = atomSetCollection.addNewAtom(); String[] tokens = getTokens(readLine()); - //Logger.debug(tokens.length + " -" + tokens[5] + "- " + line); String atomType = tokens[5]; atom.atomName = tokens[1] + '\0' + atomType; + int pt = atomType.indexOf("."); + // accepts "." for "no atom type" + atom.elementSymbol = (pt == 0 ? atom.atomName : pt > 0 ? atomType.substring(0, pt) : atomType); atom.set(parseFloat(tokens[2]), parseFloat(tokens[3]), parseFloat(tokens[4])); // apparently "NO_CHARGES" is not strictly enforced @@ -194,44 +196,46 @@ atom.formalCharge = (int) atom.partialCharge; } } + + // trying to guess if this is a PDB-type file + Atom[] atoms = atomSetCollection.getAtoms(); + + // 1. Does the very first atom have a group name? + String g3 = atoms[i0].group3; if (g3 == null) return; - isPDB = false; + + boolean isPDB = false; + + // 2. If so, is there more than one kind of group? + for (int i = atomSetCollection.getAtomCount(); --i >= i0;) if (!g3.equals(atoms[atomSetCollection.getAtomCount() - 1].group3)) { isPDB = true; break; } + + // 3. If so, is there an identifiable group name? + if (isPDB) { isPDB = false; for (int i = atomSetCollection.getAtomCount(); --i >= i0;) { Atom atom = atoms[i]; if (atom.group3.length() <= 3 && JmolAdapter.lookupGroupID(atom.group3) >= 0) { - isPDB = true; + isPDB = this.isPDB = true; break; } } - if (isPDB) { - for (int i = atomSetCollection.getAtomCount(); --i >= i0;) { - Atom atom = atoms[i]; - atom.isHetero = JmolAdapter.isHetero(atom.group3); - String atomType = atom.atomName - .substring(atom.atomName.indexOf('\0') + 1); - boolean deduceSymbol = !getElementSymbol(atom, atomType); - if (deduceSymbol) - atom.elementSymbol = deducePdbElementSymbol(atom.isHetero, - atomType, atom.group3); - } //System.out.print(atom.atomName + "/" + atom.elementSymbol + " " ); - return; - } } - if (!isPDB) { - for (int i = atomSetCollection.getAtomCount(); --i >= i0;) - atoms[i].group3 = null; - } + + for (int i = atomSetCollection.getAtomCount(); --i >= i0;) + if (isPDB) + atoms[i].isHetero = isPDB && JmolAdapter.isHetero(atoms[i].group3); + else + atoms[i].group3 = null; } private void readBonds(int bondCount) throws Exception { Modified: branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-03-31 20:24:08 UTC (rev 18027) +++ branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-03-31 21:26:01 UTC (rev 18028) @@ -9,8 +9,9 @@ # 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=13.0.14_dev28 +___version=13.0.14_dev31 +bug fix: MOL2 reader not properly assigning element symbols bug fix: isosurface slab translucent broken when saved in state bug fix: isosurface slab translucent mesh broken when saved in state This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-03-31 22:53:20
|
Revision: 18037 http://sourceforge.net/p/jmol/code/18037 Author: hansonr Date: 2013-03-31 22:53:17 +0000 (Sun, 31 Mar 2013) Log Message: ----------- ___version=13.0.14 bug fix: JVXL 1.0 format reading broken bug fix: MOL2 reader not properly assigning element symbols bug fix: isosurface slab translucent broken when saved in state bug fix: isosurface slab translucent mesh broken when saved in state bug fix: sync socket connections not working bug fix: WRITE PNGJ does not allow sizing of image bug fix: backbone/spine defs do not take into account phosphorylated proteins. Better: "@backbone protein&(_a>=1&_a<6|_a>=64&_a<72)|nucleic&(_a>=6&_a<14|_a>=72)", "@spine protein&_a>=1&_a<4|nucleic&_a>=6&_a<14&_a!=12", bug fix: getProperty fileInfo fixed and documented bug fix: assign atom does not update selections for elements bug fix: LcaoCartoon "-sp3d" not working bug fix: incorrect calculation of RMSD for COMPARE and SMILES bug fix: ModelKit menu "SHIFT to rotate" should read "ALT to rotate" Modified Paths: -------------- branches/v13_0/Jmol/src/org/jmol/jvxl/readers/JvxlReader.java branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v13_0/Jmol/src/org/jmol/jvxl/readers/JvxlReader.java =================================================================== --- branches/v13_0/Jmol/src/org/jmol/jvxl/readers/JvxlReader.java 2013-03-31 22:43:11 UTC (rev 18036) +++ branches/v13_0/Jmol/src/org/jmol/jvxl/readers/JvxlReader.java 2013-03-31 22:53:17 UTC (rev 18037) @@ -82,9 +82,9 @@ readVoxelVector(0); readVoxelVector(1); readVoxelVector(2); - skipComments(true); for (int i = 0; i < atomCount; ++i) jvxlFileHeaderBuffer.append(readLine() + "\n"); + skipComments(true); Logger.info("Reading extra JVXL information line: " + line); nSurfaces = parseInt(line); if (!(isJvxl = (nSurfaces < 0))) Modified: branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-03-31 22:43:11 UTC (rev 18036) +++ branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-03-31 22:53:17 UTC (rev 18037) @@ -9,8 +9,9 @@ # 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=13.0.14_hold +___version=13.0.14 +bug fix: JVXL 1.0 format reading broken bug fix: MOL2 reader not properly assigning element symbols bug fix: isosurface slab translucent broken when saved in state bug fix: isosurface slab translucent mesh broken when saved in state This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-03-31 23:58:19
|
Revision: 18041 http://sourceforge.net/p/jmol/code/18041 Author: hansonr Date: 2013-03-31 23:58:16 +0000 (Sun, 31 Mar 2013) Log Message: ----------- ___version=13.0.14 bug fix: isourface boundbox plane .... bug fix: isosurface boundbox {pt1} {pt2} plane ... bug fix: JVXL 1.0 format reading broken bug fix: MOL2 reader not properly assigning element symbols bug fix: isosurface slab translucent broken when saved in state bug fix: isosurface slab translucent mesh broken when saved in state bug fix: sync socket connections not working bug fix: WRITE PNGJ does not allow sizing of image bug fix: backbone/spine defs do not take into account phosphorylated proteins. Better: "@backbone protein&(_a>=1&_a<6|_a>=64&_a<72)|nucleic&(_a>=6&_a<14|_a>=72)", "@spine protein&_a>=1&_a<4|nucleic&_a>=6&_a<14&_a!=12", bug fix: getProperty fileInfo fixed and documented bug fix: assign atom does not update selections for elements bug fix: LcaoCartoon "-sp3d" not working bug fix: incorrect calculation of RMSD for COMPARE and SMILES bug fix: ModelKit menu "SHIFT to rotate" should read "ALT to rotate" Modified Paths: -------------- branches/v13_0/Jmol/src/org/jmol/jvxl/readers/AtomDataReader.java branches/v13_0/Jmol/src/org/jmol/shapesurface/IsosurfaceRenderer.java branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v13_0/Jmol/src/org/jmol/jvxl/readers/AtomDataReader.java =================================================================== --- branches/v13_0/Jmol/src/org/jmol/jvxl/readers/AtomDataReader.java 2013-03-31 23:57:30 UTC (rev 18040) +++ branches/v13_0/Jmol/src/org/jmol/jvxl/readers/AtomDataReader.java 2013-03-31 23:58:16 UTC (rev 18041) @@ -115,12 +115,15 @@ xyzMax.x += (params.points.x - 1) * params.steps.x; xyzMax.y += (params.points.y - 1) * params.steps.y; xyzMax.z += (params.points.z - 1) * params.steps.z; - } else { + } else if (params.boundingBox == null) { getAtoms(params.bsSelected, false, true, false, false, false, false, params.mep_marginAngstroms); if (xyzMin == null) { xyzMin = new Point3f(-10,-10,-10); xyzMax = new Point3f(10, 10, 10); } + } else { + xyzMin = new Point3f(params.boundingBox[0]); + xyzMax = new Point3f(params.boundingBox[1]); } setRanges(params.plane_ptsPerAngstrom, params.plane_gridMax, 0); } Modified: branches/v13_0/Jmol/src/org/jmol/shapesurface/IsosurfaceRenderer.java =================================================================== --- branches/v13_0/Jmol/src/org/jmol/shapesurface/IsosurfaceRenderer.java 2013-03-31 23:57:30 UTC (rev 18040) +++ branches/v13_0/Jmol/src/org/jmol/shapesurface/IsosurfaceRenderer.java 2013-03-31 23:58:16 UTC (rev 18041) @@ -230,8 +230,8 @@ return; } - if (imesh.jvxlData.vertexDataOnly) - return; + //if (imesh.jvxlData.vertexDataOnly) + //return; hasColorRange = (imesh.meshColix == 0); for (int i = vContours.length; --i >= 0;) { List<Object> v = vContours[i]; Modified: branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-03-31 23:57:30 UTC (rev 18040) +++ branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-03-31 23:58:16 UTC (rev 18041) @@ -11,6 +11,8 @@ ___version=13.0.14 +bug fix: isourface boundbox plane .... +bug fix: isosurface boundbox {pt1} {pt2} plane ... bug fix: JVXL 1.0 format reading broken bug fix: MOL2 reader not properly assigning element symbols bug fix: isosurface slab translucent broken when saved in state This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-04-03 03:39:50
|
Revision: 18066 http://sourceforge.net/p/jmol/code/18066 Author: hansonr Date: 2013-04-03 03:39:45 +0000 (Wed, 03 Apr 2013) Log Message: ----------- ___version=13.0.15_dev bug fix: select dots > 0 does not work Modified Paths: -------------- branches/v13_0/Jmol/src/org/jmol/shapespecial/Dots.java branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v13_0/Jmol/src/org/jmol/shapespecial/Dots.java =================================================================== --- branches/v13_0/Jmol/src/org/jmol/shapespecial/Dots.java 2013-04-03 03:38:59 UTC (rev 18065) +++ branches/v13_0/Jmol/src/org/jmol/shapespecial/Dots.java 2013-04-03 03:39:45 UTC (rev 18066) @@ -70,7 +70,7 @@ @Override public int getSize(int atomIndex) { // mads are actually radii not diameters - return (mads == null ? (int) (ec.getRadius(atomIndex) * 2000) : mads[atomIndex]*2); + return (mads != null ? mads[atomIndex]*2 : bsOn.get(atomIndex) ? (int) Math.floor(ec.getRadius(atomIndex) * 2000) : 0); } @Override Modified: branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-04-03 03:38:59 UTC (rev 18065) +++ branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-04-03 03:39:45 UTC (rev 18066) @@ -11,6 +11,8 @@ ___version=13.0.15_dev +bug fix: select dots > 0 does not work + ============================================================================= version=13.0.14 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-04-07 15:29:16
|
Revision: 18079 http://sourceforge.net/p/jmol/code/18079 Author: hansonr Date: 2013-04-07 15:29:10 +0000 (Sun, 07 Apr 2013) Log Message: ----------- ___version=13.0.15_dev_2013.04.07a" bug fix: command f.sort() and f.reverse() fail. bug fix: select dots > 0 does not work Modified Paths: -------------- branches/v13_0/Jmol/src/org/jmol/script/ScriptCompiler.java branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v13_0/Jmol/src/org/jmol/script/ScriptCompiler.java =================================================================== --- branches/v13_0/Jmol/src/org/jmol/script/ScriptCompiler.java 2013-04-07 06:24:41 UTC (rev 18078) +++ branches/v13_0/Jmol/src/org/jmol/script/ScriptCompiler.java 2013-04-07 15:29:10 UTC (rev 18079) @@ -617,7 +617,8 @@ String s = (nTokens == 2 ? lastToken.value.toString().toUpperCase() : null); if (nTokens > 2 && !(tokAt(2) == Token.leftparen && ltoken.get(1).value.toString().endsWith(".spt")) - || s != null && (s.endsWith(".SORT") || s.endsWith(".REVERSE"))) { + || s != null && (s.endsWith(".SORT") || s.endsWith(".REVERSE") + || s.indexOf(".SORT(") >= 0 || s.indexOf(".REVERSE(") >= 0)) { // check for improperly parsed implied script command: // only two tokens: // [implied script] xxx.SORT Modified: branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-04-07 06:24:41 UTC (rev 18078) +++ branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-04-07 15:29:10 UTC (rev 18079) @@ -9,8 +9,9 @@ # 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=13.0.15_dev +___version=13.0.15_dev_2013.04.07a" +bug fix: command f.sort() and f.reverse() fail. bug fix: select dots > 0 does not work ============================================================================= This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-04-07 16:04:34
|
Revision: 18082 http://sourceforge.net/p/jmol/code/18082 Author: hansonr Date: 2013-04-07 16:04:31 +0000 (Sun, 07 Apr 2013) Log Message: ----------- ___version=13.0.15_dev_2013.04.07b" bug fix: isosurface translucent level not re-zeroed properly Modified Paths: -------------- branches/v13_0/Jmol/src/org/jmol/shapesurface/Isosurface.java branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v13_0/Jmol/src/org/jmol/shapesurface/Isosurface.java =================================================================== --- branches/v13_0/Jmol/src/org/jmol/shapesurface/Isosurface.java 2013-04-07 16:02:42 UTC (rev 18081) +++ branches/v13_0/Jmol/src/org/jmol/shapesurface/Isosurface.java 2013-04-07 16:04:31 UTC (rev 18082) @@ -995,6 +995,7 @@ explicitContours = false; atomIndex = -1; colix = Graphics3D.ORANGE; + translucentLevel = 0; defaultColix = meshColix = 0; isPhaseColored = isColorExplicit = false; //allowContourLines = true; //but not for f(x,y) or plane, which use mesh Modified: branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-04-07 16:02:42 UTC (rev 18081) +++ branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-04-07 16:04:31 UTC (rev 18082) @@ -9,8 +9,9 @@ # 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=13.0.15_dev_2013.04.07a" +___version=13.0.15_dev_2013.04.07b" +bug fix: isosurface translucent level not re-zeroed properly bug fix: command f.sort() and f.reverse() fail. bug fix: select dots > 0 does not work This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-04-08 14:40:07
|
Revision: 18086 http://sourceforge.net/p/jmol/code/18086 Author: hansonr Date: 2013-04-08 14:40:03 +0000 (Mon, 08 Apr 2013) Log Message: ----------- ___version=13.0.15_dev_2013.04.08a" bug fix: {xxx}.cartoon = {xxx}.temperature.all fails to use correct values (also backbone, trace, etc.) Modified Paths: -------------- branches/v13_0/Jmol/src/org/jmol/modelset/ModelSet.java branches/v13_0/Jmol/src/org/jmol/shapebio/Backbone.java branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v13_0/Jmol/src/org/jmol/modelset/ModelSet.java =================================================================== --- branches/v13_0/Jmol/src/org/jmol/modelset/ModelSet.java 2013-04-07 18:59:32 UTC (rev 18085) +++ branches/v13_0/Jmol/src/org/jmol/modelset/ModelSet.java 2013-04-08 14:40:03 UTC (rev 18086) @@ -799,6 +799,13 @@ case Token.trace: if (fValue > Shape.RADIUS_MAX) fValue = Shape.RADIUS_MAX; + if (values != null) { + // convert to atom indices + float[] newValues = new float[atomCount]; + for (int i = bs.nextSetBit(0), ii = 0; i >= 0; i = bs.nextSetBit(i + 1)) + newValues[i] = values[ii++]; + values = newValues; + } //$FALL-THROUGH$ case Token.halo: case Token.star: Modified: branches/v13_0/Jmol/src/org/jmol/shapebio/Backbone.java =================================================================== --- branches/v13_0/Jmol/src/org/jmol/shapebio/Backbone.java 2013-04-07 18:59:32 UTC (rev 18085) +++ branches/v13_0/Jmol/src/org/jmol/shapebio/Backbone.java 2013-04-08 14:40:03 UTC (rev 18086) @@ -84,9 +84,10 @@ bioShape.monomers[i].setShapeVisibility(myVisibilityFlag, isVisible); Atom atomA = modelSet.atoms[index1]; if (rd != null) { - if (Float.isNaN(rd.values[i])) + if (Float.isNaN(rd.values[index1]) || Float.isNaN(rd.values[index2])) continue; - mad = (short) (rd.values[i] * 2000); + mad = (short) ((rd.values[index1] + rd.values[index2]) * 1000); // average + isVisible = (mad != 0); } Atom atomB = modelSet.atoms[index2]; boolean wasVisible = (bioShape.mads[i] != 0); Modified: branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-04-07 18:59:32 UTC (rev 18085) +++ branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-04-08 14:40:03 UTC (rev 18086) @@ -9,8 +9,9 @@ # 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=13.0.15_dev_2013.04.07b" +___version=13.0.15_dev_2013.04.08a" +bug fix: {xxx}.cartoon = {xxx}.temperature.all fails to use correct values (also backbone, trace, etc.) bug fix: isosurface translucent level not re-zeroed properly bug fix: command f.sort() and f.reverse() fail. bug fix: select dots > 0 does not work This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-04-23 23:07:46
|
Revision: 18149 http://sourceforge.net/p/jmol/code/18149 Author: hansonr Date: 2013-04-23 23:07:40 +0000 (Tue, 23 Apr 2013) Log Message: ----------- ___version=13.0.15_dev_2013.04.23 bug fix: deleting atoms does not remove bioshape rendering Modified Paths: -------------- branches/v13_0/Jmol/src/org/jmol/script/ScriptEvaluator.java branches/v13_0/Jmol/src/org/jmol/shapebio/BioShapeRenderer.java branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v13_0/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- branches/v13_0/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-04-23 23:06:38 UTC (rev 18148) +++ branches/v13_0/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-04-23 23:07:40 UTC (rev 18149) @@ -17015,11 +17015,12 @@ } propertyValue = data; break; + case Token.modelindex: case Token.model: if (surfaceObjectSeen) error(ERROR_invalidArgument); - modelIndex = modelNumberParameter(++i); - sbCommand.append(" model " + modelIndex); + modelIndex = (theTok == Token.modelindex ? intParameter(++i) : modelNumberParameter(++i)); + sbCommand.append(" modelIndex " + modelIndex); if (modelIndex < 0) { propertyName = "fixed"; propertyValue = Boolean.TRUE; Modified: branches/v13_0/Jmol/src/org/jmol/shapebio/BioShapeRenderer.java =================================================================== --- branches/v13_0/Jmol/src/org/jmol/shapebio/BioShapeRenderer.java 2013-04-23 23:06:38 UTC (rev 18148) +++ branches/v13_0/Jmol/src/org/jmol/shapebio/BioShapeRenderer.java 2013-04-23 23:07:40 UTC (rev 18149) @@ -140,6 +140,7 @@ } private boolean initializePolymer(BioShape bioShape) { + BitSet bsDeleted = viewer.getDeletedAtoms(); if (viewer.isJmolDataFrame(bioShape.modelIndex)) { controlPoints = bioShape.bioPolymer.getControlPoints(true, 0, false); } else { @@ -157,7 +158,7 @@ bioShape.falsifyMesh(); for (int i = monomerCount; --i >= 0;) { if ((monomers[i].shapeVisibilityFlags & myVisibilityFlag) == 0 - || modelSet.isAtomHidden(leadAtomIndices[i])) + || modelSet.isAtomHidden(leadAtomIndices[i]) || bsDeleted != null && bsDeleted.get(leadAtomIndices[i])) continue; Atom lead = modelSet.atoms[leadAtomIndices[i]]; if (!g3d.isInDisplayRange(lead.screenX, lead.screenY)) Modified: branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-04-23 23:06:38 UTC (rev 18148) +++ branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-04-23 23:07:40 UTC (rev 18149) @@ -9,8 +9,10 @@ # 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=13.0.15_dev_2013.04.11a +___version=13.0.15_dev_2013.04.23 +bug fix: deleting atoms does not remove bioshape rendering +bug fix: isosurface in multi-model context saved in state with wrong model number bug fix: labels lost upon z-shading bug fix: {xxx}.cartoon = {xxx}.temperature.all fails to use correct values (also backbone, trace, etc.) bug fix: isosurface translucent level not re-zeroed properly This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-04-24 13:49:47
|
Revision: 18150 http://sourceforge.net/p/jmol/code/18150 Author: hansonr Date: 2013-04-24 13:49:41 +0000 (Wed, 24 Apr 2013) Log Message: ----------- ___version=13.0.15_dev_2013.04.23 bug fix: set isosurfacekey may not work with slabbing Modified Paths: -------------- branches/v13_0/Jmol/src/org/jmol/shapesurface/IsosurfaceRenderer.java branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v13_0/Jmol/src/org/jmol/shapesurface/IsosurfaceRenderer.java =================================================================== --- branches/v13_0/Jmol/src/org/jmol/shapesurface/IsosurfaceRenderer.java 2013-04-23 23:07:40 UTC (rev 18149) +++ branches/v13_0/Jmol/src/org/jmol/shapesurface/IsosurfaceRenderer.java 2013-04-24 13:49:41 UTC (rev 18150) @@ -137,7 +137,7 @@ g3d.setColor(colors[i]); break; } - g3d.fillRect(x, y, 5, 5, dx, dy); + g3d.fillRect(x, y, 5, Integer.MIN_VALUE, dx, dy); } isosurface.keyXy[1] = (y + dy) / factor; } Modified: branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-04-23 23:07:40 UTC (rev 18149) +++ branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-04-24 13:49:41 UTC (rev 18150) @@ -11,6 +11,7 @@ ___version=13.0.15_dev_2013.04.23 +bug fix: set isosurfacekey may not work with slabbing bug fix: deleting atoms does not remove bioshape rendering bug fix: isosurface in multi-model context saved in state with wrong model number bug fix: labels lost upon z-shading This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-04-24 21:58:42
|
Revision: 18159 http://sourceforge.net/p/jmol/code/18159 Author: hansonr Date: 2013-04-24 21:58:37 +0000 (Wed, 24 Apr 2013) Log Message: ----------- ___version=13.0.15_dev_2013.04.23 bug fix: isosurface map property may not reference correct atom Modified Paths: -------------- branches/v13_0/Jmol/src/org/jmol/jvxl/readers/AtomPropertyMapper.java branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v13_0/Jmol/src/org/jmol/jvxl/readers/AtomPropertyMapper.java =================================================================== --- branches/v13_0/Jmol/src/org/jmol/jvxl/readers/AtomPropertyMapper.java 2013-04-24 21:56:43 UTC (rev 18158) +++ branches/v13_0/Jmol/src/org/jmol/jvxl/readers/AtomPropertyMapper.java 2013-04-24 21:58:37 UTC (rev 18159) @@ -170,7 +170,7 @@ } } else if (d2 < dmin) { dmin = d2; - iAtomSurface = iAtom; + iAtomSurface = ia; if (!doSmoothProperty) value = p; } Modified: branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-04-24 21:56:43 UTC (rev 18158) +++ branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-04-24 21:58:37 UTC (rev 18159) @@ -11,6 +11,7 @@ ___version=13.0.15_dev_2013.04.23 +bug fix: isosurface map property may not reference correct atom bug fix: set isosurfacekey may not work with slabbing bug fix: deleting atoms does not remove bioshape rendering bug fix: isosurface in multi-model context saved in state with wrong model number This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-04-29 11:14:33
|
Revision: 18185 http://sourceforge.net/p/jmol/code/18185 Author: hansonr Date: 2013-04-29 11:14:29 +0000 (Mon, 29 Apr 2013) Log Message: ----------- ___version=13.0.16_dev_2013.04.29 bug fix: isosurface VOLUME/ARRAY SET n cannot return to full array reporting; SET -1 added. bug fix: isosurface VOLUME/ARRAY always returns an array, possibly of length 0 bug fix: isosurface molecular/solvent can give inappropriate inner surfaces bug fix: show selected includes deleted atoms Modified Paths: -------------- branches/v13_0/Jmol/src/org/jmol/jvxl/data/JvxlData.java branches/v13_0/Jmol/src/org/jmol/jvxl/data/MeshData.java branches/v13_0/Jmol/src/org/jmol/script/ScriptEvaluator.java branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties branches/v13_0/Jmol/src/org/jmol/viewer/Viewer.java Modified: branches/v13_0/Jmol/src/org/jmol/jvxl/data/JvxlData.java =================================================================== --- branches/v13_0/Jmol/src/org/jmol/jvxl/data/JvxlData.java 2013-04-28 20:35:07 UTC (rev 18184) +++ branches/v13_0/Jmol/src/org/jmol/jvxl/data/JvxlData.java 2013-04-29 11:14:29 UTC (rev 18185) @@ -98,7 +98,7 @@ public boolean jvxlDataIs2dContour; public boolean jvxlDataIsColorDensity; public boolean isColorReversed; - public int thisSet = -1; + public int thisSet = Integer.MIN_VALUE; public int edgeFractionBase = JvxlCoder.defaultEdgeFractionBase; public int edgeFractionRange = JvxlCoder.defaultEdgeFractionRange; @@ -184,7 +184,7 @@ nVertexColors = 0; slabInfo = null; slabValue = Integer.MIN_VALUE; - thisSet = -1; + thisSet = Integer.MIN_VALUE; rendering = null; translucency = 0; vContours = null; Modified: branches/v13_0/Jmol/src/org/jmol/jvxl/data/MeshData.java =================================================================== --- branches/v13_0/Jmol/src/org/jmol/jvxl/data/MeshData.java 2013-04-28 20:35:07 UTC (rev 18184) +++ branches/v13_0/Jmol/src/org/jmol/jvxl/data/MeshData.java 2013-04-29 11:14:29 UTC (rev 18185) @@ -306,10 +306,10 @@ } public Object calculateVolumeOrArea(int thisSet, boolean isArea, boolean getSets) { - if (getSets) + if (getSets || nSets == 0) getSurfaceSet(); - boolean justOne = (nSets == 0 || thisSet >= 0); - int n = (justOne ? 1 : nSets); + boolean justOne = (thisSet >= -1); + int n = (justOne || nSets == 0 ? 1 : nSets); double[] v = new double[n]; Vector3f vAB = new Vector3f(); Vector3f vAC = new Vector3f(); @@ -337,7 +337,7 @@ double factor = (isArea ? 2 : 6); for (int i = 0; i < n; i++) v[i] /= factor; - if (justOne && thisSet != Integer.MIN_VALUE) + if (justOne) return Float.valueOf((float) v[0]); return v; } Modified: branches/v13_0/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- branches/v13_0/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-04-28 20:35:07 UTC (rev 18184) +++ branches/v13_0/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-04-29 11:14:29 UTC (rev 18185) @@ -3304,7 +3304,7 @@ Object value) { if (isSyntaxCheck) return; - System.out.println("addshapeprop " + key + " " + value); + //System.out.println("addshapeprop " + key + " " + value); propertyList.add(new Object[] { key, value }); } @@ -16714,7 +16714,7 @@ boolean haveIntersection = false; float[] data = null; String cmd = null; - int thisSetNumber = -1; + int thisSetNumber = Integer.MIN_VALUE; int nFiles = 0; int nX, nY, nZ, ptX, ptY; float sigma = Float.NaN; @@ -18094,7 +18094,7 @@ addShapeProperty(propertyList, "nomap", Float.valueOf(0)); surfaceObjectSeen = true; } - if (thisSetNumber >= 0) + if (thisSetNumber >= -1) addShapeProperty(propertyList, "getSurfaceSets", Integer .valueOf(thisSetNumber - 1)); if (discreteColixes != null) { Modified: branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-04-28 20:35:07 UTC (rev 18184) +++ branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-04-29 11:14:29 UTC (rev 18185) @@ -9,8 +9,13 @@ # 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=13.0.16_dev +___version=13.0.16_dev_2013.04.29 +bug fix: isosurface VOLUME/ARRAY SET n cannot return to full array reporting; SET -1 added. +bug fix: isosurface VOLUME/ARRAY always returns an array, possibly of length 0 +bug fix: isosurface molecular/solvent can give inappropriate inner surfaces +bug fix: show selected includes deleted atoms + ============================================================================= version=13.0.15 Modified: branches/v13_0/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- branches/v13_0/Jmol/src/org/jmol/viewer/Viewer.java 2013-04-28 20:35:07 UTC (rev 18184) +++ branches/v13_0/Jmol/src/org/jmol/viewer/Viewer.java 2013-04-29 11:14:29 UTC (rev 18185) @@ -3414,7 +3414,7 @@ } public String getChimeInfo(int tok) { - return modelSet.getChimeInfo(tok, getSelectionSet(true)); + return modelSet.getChimeInfo(tok, getSelectionSet(false)); } public Map<String, List<Map<String, Object>>> getAllChainInfo( This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |