From: <ha...@us...> - 2011-05-08 19:28:38
|
Revision: 15438 http://jmol.svn.sourceforge.net/jmol/?rev=15438&view=rev Author: hansonr Date: 2011-05-08 19:28:31 +0000 (Sun, 08 May 2011) Log Message: ----------- version=12.1.46_dev # bug fix: set picking dragMolecule then use of SHIFT after rotate COMPARE will result in unwanted translation Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties trunk/Jmol/src/org/jmol/viewer/TransformManager.java trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-05-05 20:50:28 UTC (rev 15437) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-05-08 19:28:31 UTC (rev 15438) @@ -3,6 +3,8 @@ version=12.1.46_dev +# bug fix: set picking dragMolecule then use of SHIFT after rotate COMPARE will result in unwanted translation + # -------------------------------------------------------------- #version=12.1.45 Modified: trunk/Jmol/src/org/jmol/viewer/TransformManager.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2011-05-05 20:50:28 UTC (rev 15437) +++ trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2011-05-08 19:28:31 UTC (rev 15438) @@ -393,32 +393,32 @@ matrixRotate.rotZ(angleRadians); } - private void applyRotation(Matrix3f mNew, boolean isInternal, BitSet bsAtoms) { + private void applyRotation(Matrix3f mNew, boolean isInternal, BitSet bsAtoms, Vector3f translation) { if (bsAtoms == null) { matrixRotate.mul(mNew, matrixRotate); return; } viewer.rotateAtoms(mNew, matrixRotate, rotateMolecule, internalRotationCenter, isInternal, bsAtoms); - if (internalTranslation != null) { - viewer.setAtomCoordRelative(internalTranslation, bsAtoms); - internalRotationCenter.add(internalTranslation); + if (translation != null) { + viewer.setAtomCoordRelative(translation, bsAtoms); + internalRotationCenter.add(translation); } } synchronized void rotateXRadians(float angleRadians, BitSet bsAtoms) { matrixTemp3.rotX(angleRadians); - applyRotation(matrixTemp3, false, bsAtoms); + applyRotation(matrixTemp3, false, bsAtoms, null); } synchronized void rotateYRadians(float angleRadians, BitSet bsAtoms) { matrixTemp3.rotY(angleRadians); - applyRotation(matrixTemp3, false, bsAtoms); + applyRotation(matrixTemp3, false, bsAtoms, null); } synchronized void rotateZRadians(float angleRadians) { matrixTemp3.rotZ(angleRadians); - applyRotation(matrixTemp3, false, null); + applyRotation(matrixTemp3, false, null, null); } protected void rotateAxisAngle(Vector3f rotAxis, float radians) { @@ -429,7 +429,7 @@ synchronized void rotateAxisAngle(AxisAngle4f axisAngle, BitSet bsAtoms) { //matrixTemp3.setIdentity(); matrixTemp3.set(axisAngle); - applyRotation(matrixTemp3, false, bsAtoms); + applyRotation(matrixTemp3, false, bsAtoms, null); } /* @@ -553,7 +553,7 @@ // NOW apply that rotation matrixTemp3.set(axisangleT); - applyRotation(matrixTemp3, true, bsAtoms); + applyRotation(matrixTemp3, true, bsAtoms, internalTranslation); if (bsAtoms == null) getNewFixedRotationCenter(); } Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2011-05-05 20:50:28 UTC (rev 15437) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2011-05-08 19:28:31 UTC (rev 15438) @@ -9373,9 +9373,9 @@ void undoAction(boolean isSave, int taintedAtom, int type) { int modelIndex = (taintedAtom >= 0 ? modelSet.atoms[taintedAtom].modelIndex : modelSet.getModelCount() - 1); - System.out.println(isSave + " " + type + " undoAction " + modelSet.getModels()[modelIndex].isModelkit()); if (!modelSet.getModels()[modelIndex].isModelkit()) return; + //System.out.println(isSave + " " + type + " undoAction " + modelSet.getModels()[modelIndex].isModelkit()); if (!isSave) { stopMinimization(); String s; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-05-12 19:23:08
|
Revision: 15459 http://jmol.svn.sourceforge.net/jmol/?rev=15459&view=rev Author: hansonr Date: 2011-05-12 19:23:01 +0000 (Thu, 12 May 2011) Log Message: ----------- version=12.1.46 # bug fix: no ALT-x menu action in application # new feature: set partialDots -- partial bonds rendered with dots rather than dashes # new feature: UNDO/REDO commands -- for atom movement or modelkit actions only # UNDO/UNDO 1 # undo last movement # UNDO n # undo last n movements # UNDO 0|ALL # undo all movements # REDO/REDO 1 # redo last movement # REDO n # redo last n movements # REDO 0|ALL # redo all movements # UNDO -1 # clear UNDO history # REDO -1 # clear REDO history # REDO -2/UNDO -2 # clear both histories # bug fix: undocumented "redo" "undo" application-only commands changed to "redocmd" "undocmd" # bug fix: FIX command not working properly # bug fix: CTRL-SHIFT-Z not working for "redo" # bug fix: select within(chain, atomno=xxx) will not select all desired atoms # if the chain is spread out over multiple regions of the file (1gzx) # # note: For dragging and rotating atoms, chains, and molecules # there are several parameters that govern the process # because there are several different ways of going about it. # # -- You can specify a set of atoms to FIX in place and not allow movement: FIX # -- You can specify whether or not to allow rotation of atoms when dragging: set allowRotateSelected # -- You can specify to move preselected atoms only, and you can specify the atoms # either with SELECT commands using set picking dragSelected # or by clicking on them (using set picking SELECT...) # # set dragSelected (12.0) # Allows dragging of selected atoms but, by itself, no rotation. # pressing ALT shows selected atoms that will be moved # ALT-SHIFT-LEFT moves, CTRL-Z undos, CTRL-SHIFT-Z or CTRL-Y redos # along with set picking SELECT x # where x is one of: atom, group, chain, molecule, polymer, structure, model # You can also use set picking extendedSelect for Rasmol-style picking, where # you get one group at a time only; the default is to toggle selections on and off # # set dragSelected; set allowRotateSelected (12.0) # AllowRotateSelected by itself does nothing, but with set dragSelected # also allows rotation. # Rotations, though allowed, are carried out on FULL MOLECULES ONLY. # pressing ALT shows selected atoms that will be moved # ALT-LEFT rotates, ALT-SHIFT-LEFT moves, CTRL-Z undos, CTRL-SHIFT-Z or CTRL-Y redos # # set allowMoveAtoms TRUE (12.2) # A setting that enables/disables dragSelected and allowRotateSelected # and also allows rotation of atoms within molecules. # pressing ALT shows selected atoms that will be moved # ALT-LEFT rotates, ALT-SHIFT-LEFT moves, CTRL-Z undos, CTRL-SHIFT-Z or CTRL-Y redos # # set allowMoveAtoms FALSE (12.2) # turns off dragSelected, allowRotateSelected, and itself, forcing selected rotations # to act on complete molecules # # set picking dragSelected (12.2, new) # Based on those currently selected atoms, simple access to drag/rotate: # LEFT (on those atoms) rotates, SHIFT-LEFT (on those atoms) moves, # CTRL-Z undos, CTRL-SHIFT-Z or CTRL-Y redos # # bug fix: undo (CTRL-Z) and redo (CTRL-Y) not implemented for dragSelected # bug fix: set dragselected may not turn off transient selection halos # new feature: set PICKING dragSelected # -- like dragMolecule; must be over an atom (any atom) # -- use SHIFT to rotate selected atoms # bug fix: molecules incorrectly assigned for covalently attached cofactors, such as HEM (1gzx) # What about hydrogen bonding? # bug fix: set picking dragMolecule then use of SHIFT after rotate COMPARE will result in unwanted translation Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/ActionManager.java trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/ActionManager.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/ActionManager.java 2011-05-12 12:14:19 UTC (rev 15458) +++ trunk/Jmol/src/org/jmol/viewer/ActionManager.java 2011-05-12 19:23:01 UTC (rev 15459) @@ -561,7 +561,8 @@ * @param ke */ public void keyPressed(KeyEvent ke) { - ke.consume(); + if (viewer.isApplet()) + ke.consume(); if (keyProcessing) return; hoverOff(); Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-05-12 12:14:19 UTC (rev 15458) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-05-12 19:23:01 UTC (rev 15459) @@ -1,8 +1,9 @@ # Developers: to add a description of changes you have made, # add it on a line starting with # below the "version=..." line -version=12.1.46_dev +version=12.1.46 +# bug fix: no ALT-x menu action in application # new feature: set partialDots -- partial bonds rendered with dots rather than dashes # new feature: UNDO/REDO commands -- for atom movement or modelkit actions only # UNDO/UNDO 1 # undo last movement This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-06-09 20:35:20
|
Revision: 15562 http://jmol.svn.sourceforge.net/jmol/?rev=15562&view=rev Author: hansonr Date: 2011-06-09 20:35:13 +0000 (Thu, 09 Jun 2011) Log Message: ----------- version=12.1.49 # new feature: set zSlab {atom expression or point}; set zShade ON Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties trunk/Jmol/src/org/jmol/viewer/TransformManager.java Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-06-09 20:18:47 UTC (rev 15561) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-06-09 20:35:13 UTC (rev 15562) @@ -1,7 +1,7 @@ # Developers: to add a description of changes you have made, # add it on a line starting with # below the "version=..." line -version=12.1.49_HOLD +version=12.1.49 # new feature: set zSlab {atom expression or point}; set zShade ON # -- sets the front of the shading to be at a position in space Modified: trunk/Jmol/src/org/jmol/viewer/TransformManager.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2011-06-09 20:18:47 UTC (rev 15561) +++ trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2011-06-09 20:35:13 UTC (rev 15562) @@ -203,9 +203,13 @@ commands.append(" set slabRange ").append(slabRange).append(";\n"); if (zShadeEnabled) commands.append(" set zShade;\n"); + try { if (zSlabPoint != null) commands.append(" set zSlab ").append(Escape.escape(zSlabPoint)).append( ";\n"); + } catch (Exception e) { + // don't care + } if (slabPlane != null) commands.append(" slab plane ").append(Escape.escape(slabPlane)).append( ";\n"); @@ -873,7 +877,7 @@ Point3f zSlabPoint; void setZslabPoint(Point3f pt) { - zSlabPoint = new Point3f(pt); + zSlabPoint = (pt == null ? null : new Point3f(pt)); } int slabValue; @@ -1479,8 +1483,12 @@ zDepthValue = zValueFromPercent(zDepthPercentSetting); } if (zSlabPoint != null) { + try { transformPoint(zSlabPoint, pointT2); zSlabValue = (int) pointT2.z; + } catch (Exception e) { + // don't care + } } viewer.getGlobalSettings().setParameterValue("_slabPlane", This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-06-28 05:03:52
|
Revision: 15653 http://jmol.svn.sourceforge.net/jmol/?rev=15653&view=rev Author: hansonr Date: 2011-06-28 05:03:46 +0000 (Tue, 28 Jun 2011) Log Message: ----------- version=12.1.51_dev # bug fix: _smilesString variable not being cleared when a PDB file is loaded Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties trunk/Jmol/src/org/jmol/viewer/StateManager.java Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-06-28 05:03:15 UTC (rev 15652) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-06-28 05:03:46 UTC (rev 15653) @@ -3,6 +3,7 @@ version=12.1.51_dev +# bug fix: _smilesString variable not being cleared when a PDB file is loaded # new feature: LOAD command reports header/title for PDB files # -- specifically when scriptLevel = 0 (typed entry) # new feature: isosurface SLAB OFF -- for SLAB n, this turns that slabbing off. Modified: trunk/Jmol/src/org/jmol/viewer/StateManager.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/StateManager.java 2011-06-28 05:03:15 UTC (rev 15652) +++ trunk/Jmol/src/org/jmol/viewer/StateManager.java 2011-06-28 05:03:46 UTC (rev 15653) @@ -1376,6 +1376,7 @@ // used by setAxesModeUnitCell to remove axesMolecular // and either remove axesWindow or axesUnitCell + key = key.toLowerCase(); if (htBooleanParameterFlags.containsKey(key)) { htBooleanParameterFlags.remove(key); if (!htPropertyFlagsRemoved.containsKey(key)) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-06-28 16:01:19
|
Revision: 15658 http://jmol.svn.sourceforge.net/jmol/?rev=15658&view=rev Author: hansonr Date: 2011-06-28 16:01:12 +0000 (Tue, 28 Jun 2011) Log Message: ----------- version=12.1.51_dev # bug fix: set defaultVDW user not working Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/DataManager.java trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/DataManager.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/DataManager.java 2011-06-28 15:32:24 UTC (rev 15657) +++ trunk/Jmol/src/org/jmol/viewer/DataManager.java 2011-06-28 16:01:12 UTC (rev 15658) @@ -313,6 +313,7 @@ case JmolConstants.VDW_BABEL: case JmolConstants.VDW_RASMOL: case JmolConstants.VDW_AUTO: + case JmolConstants.VDW_USER: break; default: iType = JmolConstants.VDW_JMOL; Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-06-28 15:32:24 UTC (rev 15657) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-06-28 16:01:12 UTC (rev 15658) @@ -3,6 +3,7 @@ version=12.1.51_dev +# bug fix: set defaultVDW user not working # new feature: CONTACT {xxx} VDW # -- just maps a VDW isosurface with distances to another VDW isosurface # bug fix: _smilesString variable not being cleared when a PDB file is loaded This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ahe...@us...> - 2011-06-29 19:45:56
|
Revision: 15670 http://jmol.svn.sourceforge.net/jmol/?rev=15670&view=rev Author: aherraez Date: 2011-06-29 19:45:49 +0000 (Wed, 29 Jun 2011) Log Message: ----------- updating the definition of the 'carbohydrate' atom set Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties trunk/Jmol/src/org/jmol/viewer/JmolConstants.java Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-06-29 18:16:50 UTC (rev 15669) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-06-29 19:45:49 UTC (rev 15670) @@ -4,7 +4,7 @@ version=12.1.51_dev # bug fix: definition of CARBOHYDRATE was updated: -# -- [A2G],[NGA],[SIA],[SLB] added (GalNAc and NeuNAc) +# -- [A2G],[NGA],[SIA],[SLB],[LBT] added (GalNAc, NeuNAc, lactose) # -- [ASF],[NAM] removed, they are not carbohydrates # -- a few existing ones are deprecated by PDB; they are left for compatibility # but are now listed as such (maybe remove them in future). Modified: trunk/Jmol/src/org/jmol/viewer/JmolConstants.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/JmolConstants.java 2011-06-29 18:16:50 UTC (rev 15669) +++ trunk/Jmol/src/org/jmol/viewer/JmolConstants.java 2011-06-29 19:45:49 UTC (rev 15670) @@ -2246,7 +2246,7 @@ ",[GUP],[LXC],[MAN],[RAM],[RIB],[RIP],[XYP],[XYS]" + ",[CBI],[CT3],[CTR],[CTT],[LAT],[MAB],[MAL],[MLR],[MTT]" + ",[SUC],[TRE],[GCU],[MTL],[NAG],[RHA],[SOR]" + - ",[XYL],[A2G],[NGA],[SIA],[SLB]" + + ",[XYL],[A2G],[LBT],[NGA],[SIA],[SLB]" + ",[AFL],[AGC],[GLB],[NAN],[RAA]"; //these 4 are deprecated in PDB // from Eric Martz; revision by Angel Herraez This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-06-30 06:01:08
|
Revision: 15672 http://jmol.svn.sourceforge.net/jmol/?rev=15672&view=rev Author: hansonr Date: 2011-06-30 06:01:02 +0000 (Thu, 30 Jun 2011) Log Message: ----------- version=12.1.51_dev # -- NAM returned as obsoleted(BH) and replacement AMU added (NAM-NAG sequences) # -- NDG added (epimer of NAG) # -- I suspect ASF is also formerly a carbohydrate; we can let that go. Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties trunk/Jmol/src/org/jmol/viewer/JmolConstants.java Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-06-30 05:23:23 UTC (rev 15671) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-06-30 06:01:02 UTC (rev 15672) @@ -3,11 +3,12 @@ version=12.1.51_dev +# -- NAM returned as obsoleted(BH) and replacement AMU added (NAM-NAG sequences) +# -- NDG added (epimer of NAG) +# -- I suspect ASF is also formerly a carbohydrate; we can let that go. # bug fix: definition of CARBOHYDRATE was updated: # -- [A2G],[NGA],[SIA],[SLB],[LBT] added (GalNAc, NeuNAc, lactose) # -- [ASF],[NAM] removed, they are not carbohydrates -# -- ASF and NAM returned (BH) -- needed for NAM-NAG sequences; these are aminoglycosides - # -- a few existing ones are deprecated by PDB; they are left for compatibility # but are now listed as such (maybe remove them in future). # Modified: trunk/Jmol/src/org/jmol/viewer/JmolConstants.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/JmolConstants.java 2011-06-30 05:23:23 UTC (rev 15671) +++ trunk/Jmol/src/org/jmol/viewer/JmolConstants.java 2011-06-30 06:01:02 UTC (rev 15672) @@ -2265,11 +2265,11 @@ // this form is used for counting groups in ModelSet private final static String allCarbohydrates = - ",[AHR],[ASF],[ARA],[ARB],[BDF],[BDR],[BGC],[BMA]" + + ",[AHR],[AMU],[ARA],[ARB],[BDF],[BDR],[BGC],[BMA]" + ",[FCA],[FCB],[FRU],[FUC],[FUL],[GAL],[GLA],[GLC]" + ",[GUP],[LXC],[MAN],[RAM],[RIB],[RIP],[XYP],[XYS]" + ",[CBI],[CT3],[CTR],[CTT],[LAT],[MAB],[MAL],[MLR],[MTT]" + - ",[SUC],[TRE],[GCU],[MTL],[NAG],[NAM],[RHA],[SOR]" + // we need NAM for NAM-NAG sequences. + ",[SUC],[TRE],[GCU],[MTL],[NAG],[NDG],[NAM],[RHA],[SOR]" + // we need NAM for NAM-NAG sequences. ",[XYL],[A2G],[LBT],[NGA],[SIA],[SLB]" + ",[AFL],[AGC],[GLB],[NAN],[RAA]"; //these 4 are deprecated in PDB // from Eric Martz; revision by Angel Herraez This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ahe...@us...> - 2011-08-30 15:58:02
|
Revision: 16003 http://jmol.svn.sourceforge.net/jmol/?rev=16003&view=rev Author: aherraez Date: 2011-08-30 15:57:56 +0000 (Tue, 30 Aug 2011) Log Message: ----------- SOE added to carbohydrate list (L-sorbose in pyranose form; SOL is the open form, 3AI3.pdb) Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties trunk/Jmol/src/org/jmol/viewer/JmolConstants.java Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-08-30 14:35:23 UTC (rev 16002) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-08-30 15:57:56 UTC (rev 16003) @@ -3,6 +3,7 @@ version=12.2.RC6_dev +# bug fix: SOE added to carbohydrate list (L-sorbose in pyranose form; SOL is the open form, 3AI3.pdb) # bug fix: setting DOTS off can cause null pointer exception # bug fix: saving state of contact broken # bug fix: contact SLAB n not working Modified: trunk/Jmol/src/org/jmol/viewer/JmolConstants.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/JmolConstants.java 2011-08-30 14:35:23 UTC (rev 16002) +++ trunk/Jmol/src/org/jmol/viewer/JmolConstants.java 2011-08-30 15:57:56 UTC (rev 16003) @@ -1057,7 +1057,7 @@ ",[FCA],[FCB],[FRU],[FUC],[FUL],[GAL],[GLA],[GLC]" + ",[GUP],[LXC],[MAN],[RAM],[RIB],[RIP],[XYP],[XYS]" + ",[CBI],[CT3],[CTR],[CTT],[LAT],[MAB],[MAL],[MLR],[MTT]" + - ",[SUC],[TRE],[GCU],[MTL],[NAG],[NDG],[RHA],[SOR],[SOL]" + + ",[SUC],[TRE],[GCU],[MTL],[NAG],[NDG],[RHA],[SOR],[SOL],[SOE]" + ",[XYL],[A2G],[LBT],[NGA],[SIA],[SLB]" + ",[AFL],[AGC],[GLB],[NAN],[RAA]"; //these 4 are deprecated in PDB // from Eric Martz; revision by Angel Herraez This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-11-15 14:45:21
|
Revision: 16473 http://jmol.svn.sourceforge.net/jmol/?rev=16473&view=rev Author: hansonr Date: 2011-11-15 14:45:15 +0000 (Tue, 15 Nov 2011) Log Message: ----------- version=12.3.6_dev # bug fix: zSlab settings not stored properly in parameters; should have default zSlab = 50 Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties trunk/Jmol/src/org/jmol/viewer/StateManager.java trunk/Jmol/src/org/jmol/viewer/TransformManager.java Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-11-15 14:44:45 UTC (rev 16472) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-11-15 14:45:15 UTC (rev 16473) @@ -3,6 +3,7 @@ version=12.3.6_dev +# bug fix: zSlab settings not stored properly in parameters; should have default zSlab = 50 # new feature: load files "xxx.tlsout" "xxxx.pdb" # -- loads REFMAC-style TLS data into xxxx.pdb Modified: trunk/Jmol/src/org/jmol/viewer/StateManager.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/StateManager.java 2011-11-15 14:44:45 UTC (rev 16472) +++ trunk/Jmol/src/org/jmol/viewer/StateManager.java 2011-11-15 14:45:15 UTC (rev 16473) @@ -720,6 +720,8 @@ setParameterValue("slabEnabled", false); // maintained by TransformManager setParameterValue("depth", 0); // maintained by TransformManager setParameterValue("slab", 100); // maintained by TransformManager + setParameterValue("zDepth", 0); // maintained by TransformManager + setParameterValue("zSlab", 50); // maintained by TransformManager setParameterValue("slabrange", 0f); // maintained by TransformManager setParameterValue("spinX", 0); // maintained by TransformManager setParameterValue("spinY", TransformManager.DEFAULT_SPIN_Y); @@ -967,8 +969,8 @@ int specularPower = 40; int zDepth = 0; int zShadePower = 3; // increased to 3 from 1 for Jmol 12.1.49 - int zSlab = 0; - + int zSlab = 50; // increased to 50 from 0 in Jmol 12.3.6 and Jmol 12.2.6 + boolean slabByMolecule = false; boolean slabByAtom = false; Modified: trunk/Jmol/src/org/jmol/viewer/TransformManager.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2011-11-15 14:44:45 UTC (rev 16472) +++ trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2011-11-15 14:45:15 UTC (rev 16473) @@ -872,8 +872,8 @@ int slabPercentSetting; int depthPercentSetting; - int zSlabPercentSetting; // from global.zSlab - int zDepthPercentSetting;// from global.zDepth + int zSlabPercentSetting = 50; // new default for 12.3.6 and 12.2.6 + int zDepthPercentSetting = 0; Point3f zSlabPoint; void setZslabPoint(Point3f pt) { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-12-13 20:20:45
|
Revision: 16579 http://jmol.svn.sourceforge.net/jmol/?rev=16579&view=rev Author: hansonr Date: 2011-12-13 20:20:39 +0000 (Tue, 13 Dec 2011) Log Message: ----------- version=12.3.10_dev # bug fix: adding H atoms to mol2 file faulty Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties trunk/Jmol/src/org/jmol/viewer/JmolConstants.java Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-12-13 20:20:16 UTC (rev 16578) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-12-13 20:20:39 UTC (rev 16579) @@ -3,6 +3,7 @@ version=12.3.10_dev +# bug fix: adding H atoms to mol2 file faulty # bug fix: load xxx.png;write PNGJ xxx.png (to same file as loaded) fails # new feature: compare {from} {to} FRAME # -- aligns frames automatically Modified: trunk/Jmol/src/org/jmol/viewer/JmolConstants.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/JmolConstants.java 2011-12-13 20:20:16 UTC (rev 16578) +++ trunk/Jmol/src/org/jmol/viewer/JmolConstants.java 2011-12-13 20:20:39 UTC (rev 16579) @@ -786,14 +786,16 @@ */ public static boolean getAminoAcidValenceAndCharge(String res, String name, int[] ret) { - if (res == null || res.length() == 0 || name.equals("CA") + if (res == null || res.length() == 0 || res.length() > 3 || name.equals("CA") || name.equals("CB")) return false; char ch0 = name.charAt(0); char ch1 = (name.length() == 1 ? 0 : name.charAt(1)); boolean isSp2 = false; int bondCount = ret[3]; - if (res.length() == 3) { + switch (res.length()) { + case 3: + // protein, but also carbohydrate? if (name.length() == 1) { switch (ch0) { case 'N': @@ -819,8 +821,8 @@ ret[1] = -1; } } - - } else if (name.length() > 1) { + case 1: + case 2: // dna/rna if (name.length() > 2 && name.charAt(2) == '\'') return false; @@ -828,6 +830,7 @@ case 'C': if (ch1 == '7') // T CH3 return false; + break; case 'N': switch (ch1) { case '1': This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-12-20 14:24:05
|
Revision: 16607 http://jmol.svn.sourceforge.net/jmol/?rev=16607&view=rev Author: hansonr Date: 2011-12-20 14:23:59 +0000 (Tue, 20 Dec 2011) Log Message: ----------- version=12.3.10_dev # bug fix: after "ZAP; LOAD append" show orientation will have incorrect zyz script Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties trunk/Jmol/src/org/jmol/viewer/TransformManager.java Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-12-20 14:23:44 UTC (rev 16606) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-12-20 14:23:59 UTC (rev 16607) @@ -3,6 +3,7 @@ version=12.3.10_dev +# bug fix: after "ZAP; LOAD append" show orientation will have incorrect zyz script # bug fix: function call with @x or @1 in parameters fails # bug fix: PNGJ reading remote fails # new feature: write PDB adds CONECT records Modified: trunk/Jmol/src/org/jmol/viewer/TransformManager.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2011-12-20 14:23:44 UTC (rev 16606) +++ trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2011-12-20 14:23:59 UTC (rev 16607) @@ -2106,7 +2106,8 @@ truncate2(sb, tY); sb.append(";"); } - if (modelRadius != rotationRadiusDefault) { + if (modelRadius != rotationRadiusDefault || modelRadius == 10) { + // after ZAP;load APPEND we need modelRadius, which is 10 sb.append(" set rotationRadius"); truncate2(sb, modelRadius); sb.append(";"); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2012-01-31 13:20:19
|
Revision: 16705 http://jmol.svn.sourceforge.net/jmol/?rev=16705&view=rev Author: hansonr Date: 2012-01-31 13:20:08 +0000 (Tue, 31 Jan 2012) Log Message: ----------- version=12.3.15_dev # new feature: when picking struts or delete bond or measure, distance shows as per usual measurement Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/ActionManager.java trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/ActionManager.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/ActionManager.java 2012-01-31 02:44:48 UTC (rev 16704) +++ trunk/Jmol/src/org/jmol/viewer/ActionManager.java 2012-01-31 13:20:08 UTC (rev 16705) @@ -488,12 +488,15 @@ measuresEnabled = false; break; case PICKING_SELECT_ATOM: + measuresEnabled = false; + break; case PICKING_MEASURE_DISTANCE: case PICKING_MEASURE_SEQUENCE: case PICKING_MEASURE_ANGLE: case PICKING_MEASURE_TORSION: measuresEnabled = false; - break; + return; + //break; } exitMeasurementMode(); } @@ -586,7 +589,6 @@ if (keyProcessing) return; hoverOff(); - //System.out.println("ActionmManager keyPressed: " + ke.getKeyCode()); keyProcessing = true; switch(key) { case Event.VK_ALT: @@ -624,7 +626,6 @@ } public void keyReleased(int key) { - //System.out.println("ActionmManager keyReleased: " + ke.getKeyCode()); switch(key) { case Event.VK_ALT: if (dragSelectedMode) @@ -682,7 +683,6 @@ viewer.setCursor(JmolConstants.CURSOR_DEFAULT); return; case Binding.WHEELED: - //System.out.println("actionmanager mouseWheel " + mods); if (viewer.isApplet() && !viewer.hasFocus()) return; // sun bug? noted by Charles Xie that wheeling on a Java page @@ -714,7 +714,6 @@ if (atomPickingMode != PICKING_ASSIGN_ATOM) exitMeasurementMode(); action = Binding.getMouseAction(pressedCount, modifiers); - //System.out.println("actionmanager mouseDragged " + mods + " " + action); dragGesture.add(action, x, y, time); checkAction(action, x, y, deltaX, deltaY, time, Binding.DRAGGED); return; @@ -729,7 +728,6 @@ boolean isSelectAndDrag = isBound(Binding.getMouseAction( Integer.MIN_VALUE, modifiers), ACTION_selectAndDrag); action = Binding.getMouseAction(pressedCount, modifiers); - //System.out.println("actionmanager mousePressed " + mods + " " + action); dragGesture.setAction(action, time); if (Binding.getModifiers(action) != 0) { action = viewer.notifyMouseClicked(x, y, action, Binding.PRESSED); @@ -817,7 +815,6 @@ viewer.setInMotion(false); viewer.setCursor(JmolConstants.CURSOR_DEFAULT); action = Binding.getMouseAction(pressedCount, modifiers); - //System.out.println("actionmanager mouseReleased " + mods + " " + action); dragGesture.add(action, x, y, time); if (dragRelease) viewer.setRotateBondIndex(Integer.MIN_VALUE); @@ -1154,7 +1151,6 @@ return; } if (viewer.getSlabEnabled()) { - //System.out.println(Binding.getMouseActionName(action, false)); if (isBound(action, ACTION_depth)) { viewer.depthByPixels(deltaY); return; @@ -1439,7 +1435,7 @@ private int addToMeasurement(int atomIndex, Point3fi nearestPoint, boolean dblClick) { - if (atomIndex == -1 && nearestPoint == null) { + if (atomIndex == -1 && nearestPoint == null || measurementPending == null) { exitMeasurementMode(); return 0; } @@ -1456,6 +1452,7 @@ viewer.setCursor(JmolConstants.CURSOR_CROSSHAIR); viewer.setPendingMeasurement(measurementPending = new MeasurementPending( viewer.getModelSet())); + measurementQueued = measurementPending; } private void exitMeasurementMode() { @@ -1520,7 +1517,6 @@ return; } t = new TimeoutThread(name, mSec, script); - //System.out.println("action man new timeout " + name + " " + mSec + " " + script); timeouts.put(name, t); t.start(); } @@ -1553,7 +1549,6 @@ } void trigger() { - //System.out.println("timeout triggered " + this); triggered = (ms < 0); } @@ -1567,7 +1562,6 @@ public void run() { if (script == null || script.length() == 0 || ms == 0) return; - //System.out.println("I am the timeout thread, and my name is " + Thread.currentThread().getName()); Thread.currentThread().setName("timeout " + name); //if (true || Logger.debugging) //Logger.info(toString()); @@ -1586,10 +1580,8 @@ timeouts.remove(name); if (triggered) { triggered = false; - //System.out.println("timeout " + name + " executing " + this); viewer.evalStringQuiet(script + (looping ? ";\ntimeout ID \"" + name + "\";" : "")); } else { -// System.out.println("timeout " + name + " not triggered " + this); } if (!looping) break; @@ -1599,7 +1591,6 @@ } catch (Exception ie) { Logger.info("Timeout " + name + " Exception: " + ie); } - //System.out.println("timeout done:" + name); timeouts.remove(name); } } @@ -1655,6 +1646,7 @@ private void resetMeasurement() { // doesn't reset the measurement that is being picked using // double-click, just the one using set picking measure. + exitMeasurementMode(); measurementQueued = new MeasurementPending(viewer.getModelSet()); } @@ -1798,8 +1790,11 @@ boolean isStruts = (atomPickingMode == PICKING_STRUTS); if (!isBound(action, (isDelete ? ACTION_deleteBond : ACTION_connectAtoms))) return; - if (measurementQueued == null || measurementQueued.getCount() >= 2) + if (measurementQueued == null || measurementQueued.getCount() == 0 || measurementQueued.getCount() > 2) { resetMeasurement(); + enterMeasurementMode(atomIndex); + } + addToMeasurement(atomIndex, ptClicked, true); if (queueAtom(atomIndex, ptClicked) != 2) return; String cAction = (isDelete @@ -1807,6 +1802,7 @@ : isStruts ? "STRUTS" : ""); viewer.script("connect " + measurementQueued.getMeasurementScript(" ", true) + cAction); + resetMeasurement(); return; case PICKING_MEASURE_TORSION: n++; @@ -1819,9 +1815,13 @@ case PICKING_MEASURE_SEQUENCE: if (!isBound(action, ACTION_pickMeasure)) return; - if (measurementQueued == null || measurementQueued.getCount() >= n) + if (measurementQueued == null || measurementQueued.getCount() == 0 || measurementQueued.getCount() > n) { resetMeasurement(); - int i = queueAtom(atomIndex, ptClicked); + enterMeasurementMode(atomIndex); + } + addToMeasurement(atomIndex, ptClicked, true); + queueAtom(atomIndex, ptClicked); + int i = measurementQueued.getCount(); if (i == 1) { viewer.setPicked(-1); viewer.setPicked(atomIndex); @@ -1830,15 +1830,16 @@ return; if (atomPickingMode == PICKING_MEASURE_SEQUENCE) { getSequence(); - return; + } else { + viewer.setStatusMeasuring("measurePicked", n, measurementQueued + .getStringDetail(), measurementQueued.getValue()); + if (atomPickingMode == PICKING_MEASURE + || pickingStyleMeasure == PICKINGSTYLE_MEASURE_ON) { + viewer.script("measure " + + measurementQueued.getMeasurementScript(" ", true)); + } } - viewer.setStatusMeasuring("measurePicked", n, measurementQueued - .getStringDetail(), measurementQueued.getValue()); - if (atomPickingMode == PICKING_MEASURE - || pickingStyleMeasure == PICKINGSTYLE_MEASURE_ON) { - viewer.script("measure " - + measurementQueued.getMeasurementScript(" ", true)); - } + resetMeasurement(); return; } int mode = (measurementPending != null @@ -1974,7 +1975,8 @@ boolean isSpin = (atomPickingMode == PICKING_SPIN); if (viewer.getSpinOn() || viewer.getNavOn() || viewer.getPendingMeasurement() != null) { resetMeasurement(); - viewer.script("spin off"); + if (viewer.getSpinOn()) + viewer.script("spin off"); return; } if (measurementQueued.getCount() >= 2) @@ -2100,7 +2102,6 @@ } int add(int action, int x, int y, long time) { - //System.out.println("ActionMan gesture add " + action + " " + x + " " + y + " " + time); this.action = action; getNode(ptNext).set(ptNext, x, y, time - time0); ptNext++; @@ -2118,7 +2119,6 @@ public float getSpeedPixelsPerMillisecond(int nPoints, int nPointsPrevious) { nPoints = getPointCount(nPoints, nPointsPrevious); - //System.out.println("ActionMan getSpeed " + nPoints + " " + nPointsPrevious); if (nPoints < 2) return 0; MotionPoint mp1 = getNode(ptNext - 1 - nPointsPrevious); Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2012-01-31 02:44:48 UTC (rev 16704) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2012-01-31 13:20:08 UTC (rev 16705) @@ -3,6 +3,7 @@ version=12.3.15_dev +# new feature: when picking struts or delete bond or measure, distance shows as per usual measurement # bug fix: Popup Menu item hbond calculate should not require PDB # ============================================================================= This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2012-04-04 00:05:54
|
Revision: 16961 http://jmol.svn.sourceforge.net/jmol/?rev=16961&view=rev Author: hansonr Date: 2012-04-04 00:05:47 +0000 (Wed, 04 Apr 2012) Log Message: ----------- version=12.3.20_dev # new feature: JSpecView JCamp-MOL files can reference model="$xxxx" -- model retrieved from NCI Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2012-04-03 19:19:49 UTC (rev 16960) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2012-04-04 00:05:47 UTC (rev 16961) @@ -3,6 +3,7 @@ version=12.3.20_dev +# new feature: JSpecView JCamp-MOL files can reference model="$xxxx" -- model retrieved from NCI # note: Headless operation with image creation works perfectly using JmolData.jar # java -Djava.awt.headless=true -Xmx512m -jar "JmolData.jar" -J "load $tylenol;write image 1000 1000 t.jpg" # see also: http://leshazlewood.com/2009/08/26/linux-javaawtheadless-and-the-display-environment-variable/ Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2012-04-03 19:19:49 UTC (rev 16960) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2012-04-04 00:05:47 UTC (rev 16961) @@ -8791,10 +8791,13 @@ String atoms = Parser.getQuotedAttribute(script, "atoms"); String select = Parser.getQuotedAttribute(script, "select"); String script2 = Parser.getQuotedAttribute(script, "script"); - String id = (modelID == null ? null : (filename == null ? "" : filename + "#") + modelID); + boolean isNIH = (modelID != null && modelID.startsWith("$")); + if (isNIH) + filename = (modelID.substring(1).equals(getParameter("_smilesstring")) ? null : modelID); + String id = (isNIH || modelID == null ? null : (filename == null ? "" : filename + "#") + modelID); if ("".equals(baseModel)) id += ".baseModel"; - int modelIndex = (modelID == null ? -3 : getModelIndexFromId(id)); + int modelIndex = (id == null ? -3 : getModelIndexFromId(id)); if (modelIndex == -2) return; // file was found, or no file was indicated, but not this model -- ignore script = (modelIndex == -1 && filename != null ? script = "load " + Escape.escape(filename) @@ -8812,6 +8815,7 @@ statusManager.syncSend(fullName + "JSpecView" + script.substring(9), ">", 0); return; } + System.out.println("Jmol executing script for JSpecView: " + script); evalStringQuiet(script, true, false); return; } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2012-04-08 14:32:22
|
Revision: 16990 http://jmol.svn.sourceforge.net/jmol/?rev=16990&view=rev Author: nicove Date: 2012-04-08 14:32:16 +0000 (Sun, 08 Apr 2012) Log Message: ----------- Version date stored in Jmol.properties Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties trunk/Jmol/src/org/jmol/viewer/JmolConstants.java Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2012-04-08 09:54:40 UTC (rev 16989) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2012-04-08 14:32:16 UTC (rev 16990) @@ -1,5 +1,6 @@ # Developers: to add a description of changes you have made, # add it on a line starting with # below the "version=..." line +date=$Date: 2012-03-02 22:22:20 +0100 (ven., 02 mars 2012) $ version=12.3.22_dev Modified: trunk/Jmol/src/org/jmol/viewer/JmolConstants.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/JmolConstants.java 2012-04-08 09:54:40 UTC (rev 16989) +++ trunk/Jmol/src/org/jmol/viewer/JmolConstants.java 2012-04-08 14:32:16 UTC (rev 16990) @@ -44,22 +44,34 @@ // callback constants --> org.jmol.constant.EnumCallback // draw constants --> org.jmol.shapespecial.draw.EnumCallback - public final static String copyright = "(C) 2009 Jmol Development"; + public final static String copyright = "(C) 2012 Jmol Development"; public final static String version; + public final static String date; static { String tmpVersion = null; + String tmpDate = null; Properties props = new Properties(); // Reading version from resource inside jar - if (tmpVersion == null) { + if ((tmpVersion == null) || (tmpDate == null)) { BufferedInputStream bis = null; InputStream is = null; try { is = JmolConstants.class.getClassLoader().getResourceAsStream("org/jmol/viewer/Jmol.properties"); bis = new BufferedInputStream(is); props.load(bis); - tmpVersion = props.getProperty("version", tmpVersion); + if (tmpVersion == null) { + tmpVersion = props.getProperty("version", tmpVersion); + } + if (tmpDate == null) { + tmpDate = props.getProperty("date", tmpDate); + if (tmpDate != null) { + tmpDate = tmpDate.substring(7, 23); + // NOTE : date is update in the properties by SVN, and is in the format + // $Date$" + } + } } catch (IOException e) { // Nothing to do } finally { @@ -80,11 +92,9 @@ } } version = (tmpVersion != null ? tmpVersion : "(Unknown version)"); + date = (tmpDate != null ? tmpDate : "(Unknown date)"); } - - public final static String cvsDate = "$Date$"; // - public final static String date = cvsDate.substring(7, 23); - + public final static boolean officialRelease = false; public final static String CLASSBASE_OPTIONS = "org.jmol."; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2012-04-24 02:05:58
|
Revision: 17043 http://jmol.svn.sourceforge.net/jmol/?rev=17043&view=rev Author: hansonr Date: 2012-04-24 02:05:49 +0000 (Tue, 24 Apr 2012) Log Message: ----------- version=12.3.23_dev # new feature: PubChem search for name (which can be a CAS number), cid, or SMILES using ":" # from pubChemFormat = "http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/%FILE/SDF?record_type=3d"; # (many thanks to Evan Bolton and Paul Thiessen (NIH) for their assistance on this. # load :name:tylenol # or load :tylenol or load :103-90-2 # load :cid:1983 # or load :1983 # load :smiles:C/C=C/C Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties trunk/Jmol/src/org/jmol/viewer/StateManager.java trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2012-04-23 22:35:37 UTC (rev 17042) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2012-04-24 02:05:49 UTC (rev 17043) @@ -5,13 +5,16 @@ version=12.3.23_dev +# new feature: PubChem search for name (which can be a CAS number), cid, or SMILES using ":" +# from pubChemFormat = "http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/%FILE/SDF?record_type=3d"; +# (many thanks to Evan Bolton and Paul Thiessen (NIH) for their assistance on this. +# load :name:tylenol # or load :tylenol or load :103-90-2 +# load :cid:1983 # or load :1983 +# load :smiles:C/C=C/C +# # bug fix: callback functions for modular calls: applet0.readCallback(....) # bug fix: Molden reader problems reading frequencies # bug fix: VASP reader with {n n n} and vibration vectors problem - -# new feature: PubChem search using ":" -# load :tylenol - # bug fix: in 2bat, SIA was considered part of the carbohydrate chain because we were not checking bonding # ============================================================================= Modified: trunk/Jmol/src/org/jmol/viewer/StateManager.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/StateManager.java 2012-04-23 22:35:37 UTC (rev 17042) +++ trunk/Jmol/src/org/jmol/viewer/StateManager.java 2012-04-24 02:05:49 UTC (rev 17043) @@ -556,7 +556,7 @@ + ";_filecaching;_filecache;fontcaching;fontscaling;language" + ";legacyautobonding" + ";loglevel;logfile;loggestures;logcommands;measurestylechime" - + ";loadformat;loadligandformat;smilesurlformat;pubchemformat1;pubchemformat2;nihresolverformat;edsurlformat;edsurlcutoff;multiprocessor;navigationmode;" + + ";loadformat;loadligandformat;smilesurlformat;pubchemformat;nihresolverformat;edsurlformat;edsurlcutoff;multiprocessor;navigationmode;" + ";perspectivedepth;phongexponent;perspectivemodel;preservestate;refreshing;repaintwaitms;rotationradius" + ";showaxes;showaxis1;showaxis2;showaxis3;showboundbox;showfrank;showunitcell" + ";slabenabled;slab;slabrange;depth;zshade;zshadepower;specular;specularexponent;specularpercent;specularpower;stateversion" @@ -925,8 +925,7 @@ setParameterValue("smallMoleculeMaxAtoms", smallMoleculeMaxAtoms); setParameterValue("smilesUrlFormat", smilesUrlFormat); setParameterValue("nihResolverFormat", nihResolverFormat); - setParameterValue("pubChemFormat1", pubChemFormat1); - setParameterValue("pubChemFormat2", pubChemFormat2); + setParameterValue("pubChemFormat", pubChemFormat); setParameterValue("solventProbe", solventOn); setParameterValue("solventProbeRadius", solventProbeRadius); setParameterValue("specular", specular); @@ -1009,10 +1008,7 @@ String nmrUrlFormat = "http://www.nmrdb.org/predictor?smiles="; String smilesUrlFormat = "http://cactus.nci.nih.gov/chemical/structure/%FILE/file?format=sdf&get3d=True"; String nihResolverFormat = "http://cactus.nci.nih.gov/chemical/structure/%FILE"; - String pubChemFormat1 = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=%22%NAME%22[completesynonym]%20OR%20%22%NAME%22[iupac]%20OR%20%22%NAME%22[InChI]%20OR%20%22%NAME%22[InChIKey]"; - String pubChemFormat2 = "http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=%CID&disopt=3DDisplaySDF"; - - // "http://cheminfov.informatics.indiana.edu/rest/thread/d3.py/SMILES/%FILE"; + String pubChemFormat = "http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/%FILE/SDF?record_type=3d"; String edsUrlFormat = "http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE.omap"; String edsUrlCutoff = "load('http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE.sfdat').lines.find('MAP_SIGMA').split(' ')[2]"; String edsUrlOptions = "within 2.0 {*}"; @@ -1073,8 +1069,7 @@ appendCmd(str, "#set loadLigandFormat " + Escape.escape(loadLigandFormat)); appendCmd(str, "#set smilesUrlFormat " + Escape.escape(smilesUrlFormat)); appendCmd(str, "#set nihResolverFormat " + Escape.escape(nihResolverFormat)); - appendCmd(str, "#set pubChemFormat1 " + Escape.escape(pubChemFormat1)); - appendCmd(str, "#set pubChemFormat2 " + Escape.escape(pubChemFormat2)); + appendCmd(str, "#set pubChemFormat " + Escape.escape(pubChemFormat)); appendCmd(str, "#set edsUrlFormat " + Escape.escape(edsUrlFormat)); appendCmd(str, "#set edsUrlCutoff " + Escape.escape(edsUrlCutoff)); // if (autoLoadOrientation) Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2012-04-23 22:35:37 UTC (rev 17042) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2012-04-24 02:05:49 UTC (rev 17043) @@ -87,7 +87,6 @@ import org.jmol.util.Parser; import org.jmol.util.Rectangle; import org.jmol.util.SurfaceFileTyper; -import org.jmol.util.XmlReader; import org.jmol.util.Measure; import org.jmol.util.Quaternion; @@ -4676,6 +4675,7 @@ } public Object setLoadFormat(String name, char type, boolean withPrefix) { + String format; String f = name.substring(1); switch (type) { case '=': @@ -4688,18 +4688,26 @@ if (f.indexOf(".") > 0 && s.indexOf("%FILE.") >= 0) s = s.substring(0, s.indexOf("%FILE") + 5); return TextFormat.formatString(s, "FILE", f); - case ':': // PubChem is special - String url; + case ':': // PubChem + format = global.pubChemFormat; try { - f = String.valueOf(Integer.valueOf(f).intValue()); + f = f.toLowerCase(); + f = "cid/" + String.valueOf(Integer.valueOf(f).intValue()); } catch (Exception e) { - f = Escape.escapeUrl(f); - url = global.pubChemFormat1; - if (url.startsWith("http://")) - f = XmlReader.extractTag(getFileAsString(TextFormat.formatString(url, - "NAME", f)), "Id"); + if (f.startsWith("smiles:")) { + format += "?POST?smiles=" + f.substring(7); + f = "smiles"; + } else if (f.startsWith("cid:")) { + f = "cid/" + f.substring(4); + } else { + if (f.startsWith("name:")) + f = f.substring(5); + if (f.startsWith("cas:")) + f = f.substring(4); + f = "name/" + Escape.escapeUrl(f); + } } - return TextFormat.formatString(global.pubChemFormat2, "CID", f); + return TextFormat.formatString(format, "FILE", f); case '$': case 'N': case '2': @@ -4707,7 +4715,6 @@ case 'K': case '/': f = Escape.escapeUrl(f); - String format; switch (type) { case 'N': format = global.nihResolverFormat + "/names"; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2012-05-20 20:08:28
|
Revision: 17181 http://jmol.svn.sourceforge.net/jmol/?rev=17181&view=rev Author: hansonr Date: 2012-05-20 20:08:21 +0000 (Sun, 20 May 2012) Log Message: ----------- version=12.3.26 # bug fix: Writing file into .jmol file after reading it from another results in the whole # zip file being copied into the new .jmol file. Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/FileManager.java trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/FileManager.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/FileManager.java 2012-05-20 18:34:16 UTC (rev 17180) +++ trunk/Jmol/src/org/jmol/viewer/FileManager.java 2012-05-20 20:08:21 UTC (rev 17181) @@ -706,7 +706,7 @@ if (os != null) bytes = getStreamAsBytes(bis, os); else - bytes = (os == null || subFileList == null || subFileList.length <= 1 + bytes = (subFileList == null || subFileList.length <= 1 || !ZipUtil.isZipFile(bis) && !ZipUtil.isPngZipStream(bis) ? getStreamAsBytes( bis, os) : ZipUtil.getZipFileContentsAsBytes(bis, subFileList, 1)); Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2012-05-20 18:34:16 UTC (rev 17180) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2012-05-20 20:08:21 UTC (rev 17181) @@ -5,6 +5,8 @@ version=12.3.26 +# bug fix: Writing file into .jmol file after reading it from another results in the whole +# zip file being copied into the new .jmol file. # new feature: Jmol SMARTS searching can include full Jmol selection syntax within # an atom primitive using the "atomType" option and "select:": # This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-02-22 06:22:36
|
Revision: 17946 http://jmol.svn.sourceforge.net/jmol/?rev=17946&view=rev Author: hansonr Date: 2013-02-22 06:22:27 +0000 (Fri, 22 Feb 2013) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties trunk/Jmol/src/org/jmol/viewer/StateManager.java Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-02-22 06:00:50 UTC (rev 17945) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-02-22 06:22:27 UTC (rev 17946) @@ -9,12 +9,9 @@ # The quotes above look odd for a parameter file, but they are # important for the JavaScript version of Jmol. -___JmolVersion="13.1.14_dev" -============================================================================= +___JmolVersion="13.1.13" -Version="13.1.13" - TODO: allow PyMOL PSE files reading as part of a set of files, not just by itself (AtomSetCollection appendAtomSetCollection) Modified: trunk/Jmol/src/org/jmol/viewer/StateManager.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/StateManager.java 2013-02-22 06:00:50 UTC (rev 17945) +++ trunk/Jmol/src/org/jmol/viewer/StateManager.java 2013-02-22 06:22:27 UTC (rev 17946) @@ -614,25 +614,24 @@ useScriptQueue = g.useScriptQueue; useArcBall = g.useArcBall; databases = g.databases; - } + } if (databases == null) { databases = new Hashtable<String, String>(); getDataBaseList(JC.databases); - loadFormat = databases.get("pdb"); - loadLigandFormat = databases.get("ligand"); - nmrUrlFormat = databases.get("nmr"); - smilesUrlFormat = databases.get("nci") + "/file?format=sdf&get3d=True"; - nihResolverFormat = databases.get("nci"); - pubChemFormat = databases.get("pubchem"); - - // beyond these six, they are just in the form load =xxx/id - getDataBaseList(userDatabases); } + loadFormat = databases.get("pdb"); + loadLigandFormat = databases.get("ligand"); + nmrUrlFormat = databases.get("nmr"); + smilesUrlFormat = databases.get("nci") + "/file?format=sdf&get3d=True"; + nihResolverFormat = databases.get("nci"); + pubChemFormat = databases.get("pubchem"); - for (EnumCallback item : EnumCallback.values()) - resetValue(item.name() + "Callback", g); + // beyond these six, they are just in the form load =xxx/id + for (EnumCallback item : EnumCallback.values()) + resetValue(item.name() + "Callback", g); + setI("historyLevel", 0); //deprecated ? doesn't do anything // These next are just placeholders so that the math processor @@ -646,7 +645,7 @@ // we really just have to make sure that all these values are definitely // also initialized within the managers. - setI("depth", 0); // maintained by TransformManager + setI("depth", 0); // maintained by TransformManager setF("gestureSwipeFactor", ActionManager.DEFAULT_GESTURE_SWIPE_FACTOR); setB("hideNotSelected", false); //maintained by the selectionManager setS("hoverLabel", ""); // maintained by the Hover shape @@ -655,50 +654,49 @@ setI("logLevel", Logger.getLogLevel()); setF("mouseWheelFactor", ActionManager.DEFAULT_MOUSE_WHEEL_FACTOR); setF("mouseDragFactor", ActionManager.DEFAULT_MOUSE_DRAG_FACTOR); - setI("navFps", TransformManager.DEFAULT_NAV_FPS); - setI("navigationDepth", 0); // maintained by TransformManager - setI("navigationSlab", 0); // maintained by TransformManager - setI("navX", 0); // maintained by TransformManager - setI("navY", 0); // maintained by TransformManager - setI("navZ", 0); // maintained by TransformManager + setI("navFps", TransformManager.DEFAULT_NAV_FPS); + setI("navigationDepth", 0); // maintained by TransformManager + setI("navigationSlab", 0); // maintained by TransformManager + setI("navX", 0); // maintained by TransformManager + setI("navY", 0); // maintained by TransformManager + setI("navZ", 0); // maintained by TransformManager setS("pathForAllFiles", ""); setI("perspectiveModel", TransformManager.DEFAULT_PERSPECTIVE_MODEL); - setS("picking", "identify"); // maintained by ActionManager - setS("pickingStyle", "toggle"); // maintained by ActionManager - setB("refreshing", true); // maintained by Viewer - setI("rotationRadius", 0); // maintained by TransformManager + setS("picking", "identify"); // maintained by ActionManager + setS("pickingStyle", "toggle"); // maintained by ActionManager + setB("refreshing", true); // maintained by Viewer + setI("rotationRadius", 0); // maintained by TransformManager setI("scaleAngstromsPerInch", 0); // maintained by TransformManager - setI("scriptReportingLevel", 0); // maintained by ScriptEvaluator - setB("selectionHalos", false); // maintained by ModelSet - setB("showaxes", false); // maintained by Axes - setB("showboundbox", false); // maintained by Bbcage - setB("showfrank", false); // maintained by Viewer - setB("showUnitcell", false); // maintained by Uccage - setI("slab", 100); // maintained by TransformManager - setB("slabEnabled", false); // maintained by TransformManager - setF("slabrange", 0f); // maintained by TransformManager - setI("spinX", 0); // maintained by TransformManager + setI("scriptReportingLevel", 0); // maintained by ScriptEvaluator + setB("selectionHalos", false); // maintained by ModelSet + setB("showaxes", false); // maintained by Axes + setB("showboundbox", false); // maintained by Bbcage + setB("showfrank", false); // maintained by Viewer + setB("showUnitcell", false); // maintained by Uccage + setI("slab", 100); // maintained by TransformManager + setB("slabEnabled", false); // maintained by TransformManager + setF("slabrange", 0f); // maintained by TransformManager + setI("spinX", 0); // maintained by TransformManager setI("spinY", TransformManager.DEFAULT_SPIN_Y); - setI("spinZ", 0); // maintained by TransformManager + setI("spinZ", 0); // maintained by TransformManager setI("spinFps", TransformManager.DEFAULT_SPIN_FPS); - setI("stereoDegrees", EnumStereoMode.DEFAULT_STEREO_DEGREES); + setI("stereoDegrees", EnumStereoMode.DEFAULT_STEREO_DEGREES); setI("stateversion", 0); // only set by a saved state being recalled setB("syncScript", viewer.getStatusManager().syncingScripts); setB("syncMouse", viewer.getStatusManager().syncingMouse); setB("syncStereo", viewer.getStatusManager().stereoSync); setB("windowCentered", true); // maintained by TransformManager - setB("zoomEnabled", true); // maintained by TransformManager - setI("zDepth", 0); // maintained by TransformManager - setB("zShade", false); // maintained by TransformManager - setI("zSlab", 50); // maintained by TransformManager - + setB("zoomEnabled", true); // maintained by TransformManager + setI("zDepth", 0); // maintained by TransformManager + setB("zShade", false); // maintained by TransformManager + setI("zSlab", 50); // maintained by TransformManager // These next values have no other place than the global Hashtables. // This just means that a call to viewer.getXxxxProperty() is necessary. // Otherwise, it's the same as if they had a global variable. // It's just an issue of speed of access. Generally, these should only be // accessed by the user. - + setI("_version", getJmolVersionInt()); setB("axesWindow", true); @@ -741,7 +739,7 @@ setS("atomTypes", atomTypes); setB("autoBond", autoBond); setB("autoFps", autoFps); -// setParameterValue("autoLoadOrientation", autoLoadOrientation); + // setParameterValue("autoLoadOrientation", autoLoadOrientation); setI("axesMode", axesMode.getCode()); setF("axesScale", axesScale); setB("axesOrientationRasmol", axesOrientationRasmol); @@ -794,8 +792,8 @@ setB("ellipsoidDots", ellipsoidDots); setB("ellipsoidFill", ellipsoidFill); setS("energyUnits", energyUnits); -// setParameterValue("_fileCaching", _fileCaching); -// setParameterValue("_fileCache", _fileCache); + // setParameterValue("_fileCaching", _fileCaching); + // setParameterValue("_fileCache", _fileCache); setB("fontScaling", fontScaling); setB("fontCaching", fontCaching); setB("forceAutoBond", forceAutoBond); @@ -816,10 +814,8 @@ setF("hoverDelay", hoverDelayMs / 1000f); setB("imageState", imageState); setB("isosurfaceKey", isosurfaceKey); - setB("isosurfacePropertySmoothing", - isosurfacePropertySmoothing); - setI("isosurfacePropertySmoothingPower", - isosurfacePropertySmoothingPower); + setB("isosurfacePropertySmoothing", isosurfacePropertySmoothing); + setI("isosurfacePropertySmoothingPower", isosurfacePropertySmoothingPower); setB("justifyMeasurements", justifyMeasurements); setB("legacyAutoBonding", legacyAutoBonding); setF("loadAtomDataTolerance", loadAtomDataTolerance); @@ -923,7 +919,7 @@ setB("zeroBasedXyzRasmol", zeroBasedXyzRasmol); setB("zoomLarge", zoomLarge); setI("zShadePower", zShadePower); - setI("zSlab", zSlab); + setI("zSlab", zSlab); } //lighting (see GData.Shade3D This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-03-15 17:55:48
|
Revision: 17988 http://sourceforge.net/p/jmol/code/17988 Author: hansonr Date: 2013-03-15 17:55:45 +0000 (Fri, 15 Mar 2013) Log Message: ----------- ___JmolVersion="13.1.14_dev" 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", Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/JC.java trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/JC.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/JC.java 2013-03-15 17:55:14 UTC (rev 17987) +++ trunk/Jmol/src/org/jmol/viewer/JC.java 2013-03-15 17:55:45 UTC (rev 17988) @@ -453,7 +453,7 @@ // All entries from 64 on are backbone entries //////////////////////////////////////////////////////////////// null, // 0 - + // protein backbone // "N", // 1 - amino nitrogen SPINE @@ -668,9 +668,8 @@ public final static byte ATOMID_S4 = 48; public final static byte ATOMID_C7 = 49; - private final static int ATOMID_BACKBONE_MIN = 64; - public final static byte ATOMID_TERMINATING_OXT = 64; + public final static byte ATOMID_H5T_TERMINUS = 72; public final static byte ATOMID_O5T_TERMINUS = 73; public final static byte ATOMID_O1P = 74; @@ -1286,8 +1285,8 @@ // structure related // "@alpha _a=2", // rasmol doc says "approximately *.CA" - whatever? - "@backbone (protein,nucleic) & (_a>0 & _a<14 || _a>="+ATOMID_BACKBONE_MIN+") | _H & protein & connected(*.N)", - "@spine protein & _a>0 & _a<= 3 || nucleic & (_a >= 6 & _a <= 10 || _a=" + ATOMID_NUCLEIC_PHOSPHORUS + ")", + "@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", "@sidechain (protein,nucleic) & !backbone", "@base nucleic & !backbone", "@dynamic_flatring search('[a]')" Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-03-15 17:55:14 UTC (rev 17987) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-03-15 17:55:45 UTC (rev 17988) @@ -12,6 +12,9 @@ ___JmolVersion="13.1.14_dev" code: JavaScript optimizations +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: FileDropper broken This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-06-19 16:01:38
|
Revision: 18352 http://sourceforge.net/p/jmol/code/18352 Author: hansonr Date: 2013-06-19 16:01:34 +0000 (Wed, 19 Jun 2013) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties trunk/Jmol/src/org/jmol/viewer/PropertyManager.java trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-19 12:49:01 UTC (rev 18351) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-19 16:01:34 UTC (rev 18352) @@ -11,11 +11,13 @@ ___JmolVersion="13.1.17_dev_2013.06.19" -TODO: Problems with getproperty(bondInfo) in JavaSCript -TODO: JSmol script/scriptWait nuance with moveto. TODO: PyMOL uniqueAtomSettings for transparency -- will require by-vertex translucent option +bug fix: applet getpropertyAsArray("bondInfo") fails +bug fix: JSmol script/scriptWait nuance with moveto. + -- when using scriptWait with HTML5, there can be no threading + new feature: CIF reader upgrade to allow multicharacter chain specs. -- See 1bgl_1bgm.cif -- automatically switches to chainCaseSensitive if multi-character Modified: trunk/Jmol/src/org/jmol/viewer/PropertyManager.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2013-06-19 12:49:01 UTC (rev 18351) +++ trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2013-06-19 16:01:34 UTC (rev 18352) @@ -1220,6 +1220,9 @@ int bondCount = ms.bondCount; Bond[] bonds = ms.bonds; BS bs1; + if (bsOrArray instanceof String) { + bsOrArray = viewer.getAtomBitSet(bsOrArray); + } if (bsOrArray instanceof BS[]) { bs1 = ((BS[]) bsOrArray)[0]; BS bs2 = ((BS[]) bsOrArray)[1]; @@ -1234,7 +1237,7 @@ for (int i = bs1.nextSetBit(0); i >= 0 && i < bondCount; i = bs1 .nextSetBit(i + 1)) v.addLast(getBondInfo(i)); - } else { + } else if (bsOrArray instanceof BS){ bs1 = (BS) bsOrArray; int thisAtom = (bs1.cardinality() == 1 ? bs1.nextSetBit(0) : -1); for (int i = 0; i < bondCount; i++) { Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-06-19 12:49:01 UTC (rev 18351) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-06-19 16:01:34 UTC (rev 18352) @@ -4446,6 +4446,7 @@ * return null; * } */ + {} if (getScriptManager() == null) return null; return scriptManager.evalStringWaitStatusQueued(returnType, strScript, This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-07-02 15:26:04
|
Revision: 18408 http://sourceforge.net/p/jmol/code/18408 Author: hansonr Date: 2013-07-02 15:25:58 +0000 (Tue, 02 Jul 2013) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/ActionManager.java trunk/Jmol/src/org/jmol/viewer/binding/Binding.java Modified: trunk/Jmol/src/org/jmol/viewer/ActionManager.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/ActionManager.java 2013-07-02 14:24:19 UTC (rev 18407) +++ trunk/Jmol/src/org/jmol/viewer/ActionManager.java 2013-07-02 15:25:58 UTC (rev 18408) @@ -893,11 +893,19 @@ private boolean checkUserAction(int action, int x, int y, int deltaX, int deltaY, long time, int mode) { + if(mode == Binding.PRESSED) { + if (Binding.getClickCount(action) == 1) + action = (action & ~Binding.CLICK_MASK) + Binding.DOWN; + }else + if(mode == Binding.DRAGGED || mode == Binding.DRAGGED2) { + if (Binding.getClickCount(action) == 1) + action = (action & ~Binding.CLICK_MASK); + } if (!binding.isUserAction(action)) return false; Map<String, Object> ht = binding.getBindings(); Iterator<String> e = ht.keySet().iterator(); - boolean ret = false; + boolean passThrough = false; Object obj; while (e.hasNext()) { String key = e.next(); @@ -940,10 +948,13 @@ script = TextFormat.simpleReplace(script, "_DELTAY", "" + deltaY); script = TextFormat.simpleReplace(script, "_TIME", "" + time); script = TextFormat.simpleReplace(script, "_MODE", "" + mode); + if (script.startsWith("+:")) { + passThrough = true; + script = script.substring(2); + } viewer.evalStringQuiet(script); - ret = true; } - return ret; + return !passThrough; } /** @@ -1370,7 +1381,6 @@ exitMeasurementMode(); action = Binding.getMouseAction(pressedCount, modifiers); dragGesture.add(action, x, y, time); - action = Binding.getMouseAction(Integer.MIN_VALUE, modifiers); checkAction(action, x, y, deltaX, deltaY, time, Binding.DRAGGED); return; case Binding.PRESSED: @@ -1386,7 +1396,6 @@ Integer.MIN_VALUE, modifiers), ACTION_selectAndDrag); action = Binding.getMouseAction(pressedCount, modifiers); dragGesture.setAction(action, time); - action = Binding.getMouseAction(Integer.MIN_VALUE, modifiers); if (Binding.getModifiers(action) != 0) { action = viewer.notifyMouseClicked(x, y, action, Binding.PRESSED); if (action == 0) Modified: trunk/Jmol/src/org/jmol/viewer/binding/Binding.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/binding/Binding.java 2013-07-02 14:24:19 UTC (rev 18407) +++ trunk/Jmol/src/org/jmol/viewer/binding/Binding.java 2013-07-02 15:25:58 UTC (rev 18408) @@ -31,7 +31,7 @@ public final static int DOUBLE_CLICK = 2 << 8; public final static int SINGLE_CLICK = 1 << 8; public final static int DOWN = 4 << 8; - + public final static int CLICK_MASK = 7 << 8; // for status messages: public final static int MOVED = 0; public final static int DRAGGED = 1; @@ -128,6 +128,8 @@ } public final boolean isBound(int mouseAction, int action) { + if (mouseAction == 1040 && action == 2) + System.out.println("left-down-2" + bindings.containsKey(mouseAction + "\t" + action)); return bindings.containsKey(mouseAction + "\t" + action); } @@ -163,11 +165,12 @@ boolean isDefaultButton = (action == 0); + boolean isDown = (desc.indexOf("DOWN") >= 0); if (desc.indexOf("DOUBLE") >= 0) action |= DOUBLE_CLICK; - else if (action > 0 && (action & WHEEL) == 0 || desc.indexOf("SINGLE") >= 0) + else if (action > 0 && (action & WHEEL) == 0 && !isDown || desc.indexOf("SINGLE") >= 0) action |= SINGLE_CLICK; - else if (desc.indexOf("DOWN") >= 0) + else if (isDown) action |= DOWN; if (desc.indexOf("CTRL") >= 0) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-09-27 17:06:36
|
Revision: 18719 http://sourceforge.net/p/jmol/code/18719 Author: hansonr Date: 2013-09-27 17:06:32 +0000 (Fri, 27 Sep 2013) Log Message: ----------- ___JmolVersion="13.3.6" JmolVersion="13.3.5_dev_2013.09.27" new feature: adds remote logging for applet and app via http:// and via function for applet using jmolApplet0._applet.viewer.setLogfile(function(data) {......}) new feature compare {1.1} {2.1} BONDS "smiles" -- does flexible fit based on dihedrals. -- does internal rotation even if ROTATION TRANSLATION are not given (considered a possible bug) -- concatenation of: list = compare({1.1},{2.1},"smiles","BONDS") rotate branch @list 1 compare {1.1} {2.1} SMARTS "smiles" rotate translate so, for example: load files "$tyrosine" "$lysergamide" select 1.1; color bonds red select 2.1; color bonds yellow sm = "c1ccccc1CCN" compare {1.1} {2.1} BONDS @sm rotate translate new feature: show BEST ROTATION / show BEST VOLUME (better than undocumented show rotation best, show rotation volume) new feature: set animationMode "ONCE" "LOOP" "PALINDROME" new feature: show animationMode; x = animationMode new feature: CAPTURE command, including ROCK and SPIN -- application and signed applet only (no JS) -- creates animated GIF -- uses ANIMATION FPS to determine play-back rate. CAPTURE "filename" -- starts capturing -- uses ANIMATION MODE to determine looping -- both PALINDROME and LOOP create looping; ONCE (default) does not CAPTURE "filename" ROCK x|y|z degrees -- does a clean rocking of the molecule about one of the three major axes -- axis and degrees optional; y 5 assumed -- based on: rotate Y 10 10;delay 2.0; rotate Y -10 -10; delay 2.0;rotate Y -10 -10; delay 2.0;rotate Y 10 10;delay 2.0 -- uses LOOP mode CAPTURE "filename" SPIN x|y|z -- does a full spin of the molecule about one of the three major axes -- axis optional; y assumed -- based on: rotate Y 360 30;delay 15.0; -- uses LOOP mode CAPTURE off/on -- temporarily disables/enables capturing CAPTURE "" or just CAPTURE -- end capturing new feature: set drawFontSize // defaults to 14.0 FEATURE CHANGE: added bindings: "drag" and "up" -- may affect power users who use BIND command new: _center CTRL+SHIFT+LEFT+click new: _reset SHIFT+LEFT+double+click mouse actions include one (each) of: SINGLE DOUBLE LEFT MIDDLE RIGHT WHEEL DOWN DRAG UP CLICK for example: SINGLE-RIGHT-CLICK DOUBLE-LEFT-DRAG defaults are SINGLE, LEFT, and CLICK sequence is always: down (drag,drag,drag...) up (click) (only if no drag) Any of these actions may be tapped using bind "<some mouse action>" "<jmol action or script>" Note that adding "+:" to an action bind "<some mouse action" "+:<script...>" does not replace the Jmol action, just supplements it. $ show mouse _assignNew LEFT+click assign/new atom or bond (requires set picking assignAtom_??/assignBond_?) _center CTRL+SHIFT+LEFT+click center _clickFrank LEFT+click pop up recent context menu (click on Jmol frank) _pickConnect LEFT+click connect atoms (requires set picking CONNECT) _deleteAtom LEFT+click delete atom (requires set picking DELETE ATOM) _deleteBond LEFT+click delete bond (requires set picking DELETE BOND) _depth CTRL+SHIFT+LEFT+double+drag adjust depth (back plane; requires SLAB ON) _dragAtom LEFT+drag move atom (requires set picking DRAGATOM) _dragDrawObject SHIFT+LEFT+drag move whole DRAW object (requires set picking DRAW) _dragDrawPoint ALT+LEFT+drag move specific DRAW point (requires set picking DRAW) _dragLabel SHIFT+LEFT+drag move label (requires set picking LABEL) _dragMinimize LEFT+drag move atom and minimize molecule (requires set picking DRAGMINIMIZE) _dragMinimizeMolecule LEFT+drag move and minimize molecule (requires set picking DRAGMINIMIZEMOLECULE) _dragSelected ALT+SHIFT+LEFT+drag move selected atoms (requires set DRAGSELECTED) _dragZ SHIFT+LEFT+drag drag atoms in Z direction (requires set DRAGSELECTED) _navTranslate LEFT+drag translate navigation point (requires set NAVIGATIONMODE and set picking NAVIGATE) _pickAtom LEFT+click pick an atom _pickIsosurface LEFT+click pick an ISOSURFACE point (requires set DRAWPICKING _pickLabel LEFT+click pick a label to toggle it hidden/displayed (requires set picking LABEL) _pickMeasure LEFT+click pick an atom to include it in a measurement (after starting a measurement or after set picking DISTANCE/ANGLE/TORSION) _pickNavigate CTRL+SHIFT+LEFT+click pick a point or atom to navigate to (requires set NAVIGATIONMODE) _pickPoint LEFT+click pick a DRAW point (for measurements) (requires set DRAWPICKING _popupMenu CTRL+LEFT+down, RIGHT+down pop up the full context menu _reset SHIFT+LEFT+double+click, MIDDLE+double+click reset (when clicked off the model) _rotate LEFT+drag rotate _rotateBranch SHIFT+LEFT+drag rotate branch around bond (requires set picking ROTATEBOND) _rotateSelected ALT+LEFT+drag rotate selected atoms (requires set DRAGSELECTED) _rotateZ ALT+LEFT+drag, SHIFT+RIGHT+drag rotate Z _rotateZorZoom SHIFT+LEFT+drag, MIDDLE+drag rotate Z (horizontal motion of mouse) or zoom (vertical motion of mouse) _select LEFT+double+click select an atom (requires set pickingStyle EXTENDEDSELECT) _selectToggleOr LEFT+click if all are selected, unselect all, otherwise add this group of atoms to the set of selected atoms (requires set pickingStyle DRAG) _setMeasure LEFT+double+click pick an atom to initiate or conclude a measurement _slab CTRL+SHIFT+LEFT+drag adjust slab (front plane; requires SLAB ON) _slabAndDepth CTRL+ALT+SHIFT+LEFT+drag move slab/depth window (both planes; requires SLAB ON) _slideZoom LEFT+drag zoom (along right edge of window) _spinDrawObjectCCW LEFT+drag click on two points to spin around axis counterclockwise (requires set picking SPIN) _spinDrawObjectCW SHIFT+LEFT+drag click on two points to spin around axis clockwise (requires set picking SPIN) _stopMotion LEFT+double+click stop motion (requires set waitForMoveTo FALSE) _swipe LEFT+drag spin model (swipe and release button and stop motion simultaneously) _translate CTRL+ALT+LEFT+drag, CTRL+RIGHT+drag, SHIFT+LEFT+double+drag, MIDDLE+double+drag translate _wheelZoom WHEEL zoom bug fix: JSON NIO port SYNC broken bug fix: print getProperty("image", "width=200;height=300;type=png") not working bug fix: write IMAGE "t.png" not working bug fix: rotate -10 -10 not working bug fix: mouse bindings not distinguishing DOWN/CLICK/DRAG/UP properly bug fix: mouse bindings _center and _reset not working bug fix: show MOUSE not including user-defined mouse bindings bug fix: chains improperly selected in JSmol/HTML5 bug fix: JSmol/HTML5 not allowing drag-drop or file loading from a local drive. bug fix: JSmol/HTML5 not allowing WRITE FILE ? bug fix: JSmol/HTML5 not allowing WRITE xxx.pdb, xxx.mol, etc bug fix: platformSpeed persists but appears unreadable after loading a state bug fix: JavaScript version InputStreamReader not processing non-UTF data correctly bug fix: second reading of older PNG files with embedded script fails due to improper png file caching code: overhaul of image creation methods code: careful attention to core functions yields results in 10% reduction in core download size: -- uncompressed(former) gzipped -- JSmol.min.nojq.js 134K 38K -- core.z.js 1586K(1781K) 364K -- corescript.z.js 378K (436K) 95K -- TOTAL 2098K(2217K) 497K (9.5% reduction) -- JmolApplet0.jar 1038K 1005K -- Thus, the "real" transfer size -- based on server-side gzipping -- is half the size of Jmol/Java. code: continued refactoring of ScriptEvaluator to ScriptExt code: refactoring to isolate LabelToken and Labels from core JavaScript load code: refactoring, simplification of image output and export -- folders created: org.jmol.image, org.jmol.dialog -- JpgEncoder, Jpg64Encoder, PngEncoder brought to org.jmol.image and made subclasses of ImageEncoder -- PpmEncoder fixed -- ImageEncoder stripped of all unnecessary ImageConsumer/producer business -- org.jmol.export.image.ImageCreator and parts of org.jmol.viewer.stateCreator reorganized into org.jmol.OutputManager, org.jmol.OutputManagerAwt, and org.jmol.OutputManagerJS -- clipboard functions moved into org.jmol.awt and org.jmol.awtjs2d -- org.jmol.io.JmolOutputChannel now serves for just about all output needs. code: major simplification and consolidation of file I/O methods, including exporters, using JmolOutputChannel class. code: only FileOutputStream reference is one reference in org.jmol.awt. code: code merge between 13.2 and 13.3 18 Sept 2013 code: major clean-up of ActionManager Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties trunk/Jmol/src/org/jmol/viewer/OutputManagerAll.java trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-09-27 15:59:47 UTC (rev 18718) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-09-27 17:06:32 UTC (rev 18719) @@ -13,35 +13,11 @@ ___JmolVersion="13.3.6" -bug fix: JSON NIO port SYNC broken -code: careful attention to core functions yields results in 10% reduction in core download size: - -- uncompressed(former) gzipped - -- JSmol.min.nojq.js 134K 38K - -- core.z.js 1586K(1781K) 364K - -- corescript.z.js 378K (436K) 95K - - -- TOTAL 2098K(2217K) 497K - (9.5% reduction) - - -- JmolApplet0.jar 1038K 1005K - - -- Thus, the "real" transfer size -- based on server-side gzipping -- is half the size of Jmol/Java. - -code: continued refactoring of ScriptEvaluator to ScriptExt -code: refactoring to isolate LabelToken and Labels from core JavaScript load -code: refactoring, simplification of image output and export - -- folders created: org.jmol.image, org.jmol.dialog - -- JpgEncoder, Jpg64Encoder, PngEncoder brought to org.jmol.image - and made subclasses of ImageEncoder - -- PpmEncoder fixed - -- ImageEncoder stripped of all unnecessary ImageConsumer/producer business - -- org.jmol.export.image.ImageCreator and parts of org.jmol.viewer.stateCreator reorganized - into org.jmol.OutputManager, org.jmol.OutputManagerAwt, and org.jmol.OutputManagerJS - -- clipboard functions moved into org.jmol.awt and org.jmol.awtjs2d - -- org.jmol.io.JmolOutputChannel now serves for just about all output needs. - -bug fix: print getProperty("image", "width=200;height=300;type=png") not working +JmolVersion="13.3.5_dev_2013.09.27" +new feature: adds remote logging for applet and app via http:// and via function for applet using + jmolApplet0._applet.viewer.setLogfile(function(data) {......}) + new feature compare {1.1} {2.1} BONDS "smiles" -- does flexible fit based on dihedrals. -- does internal rotation even if ROTATION TRANSLATION are not given @@ -59,10 +35,6 @@ sm = "c1ccccc1CCN" compare {1.1} {2.1} BONDS @sm rotate translate - -code: major simplification and consolidation of file I/O methods, including exporters, using JmolOutputChannel class. -code: only FileOutputStream reference is one reference in org.jmol.awt. - new feature: show BEST ROTATION / show BEST VOLUME (better than undocumented show rotation best, show rotation volume) new feature: set animationMode "ONCE" "LOOP" "PALINDROME" @@ -91,18 +63,8 @@ CAPTURE "" or just CAPTURE -- end capturing -code: overhaul of image creation methods +new feature: set drawFontSize // defaults to 14.0 -bug fix: write IMAGE "t.png" not working -bug fix: rotate -10 -10 not working - -code: code merge between 13.2 and 13.3 18 Sept 2013 -code: major clean-up of ActionManager - -bug fix: mouse bindings not distinguishing DOWN/CLICK/DRAG/UP properly -bug fix: mouse bindings _center and _reset not working -bug fix: show MOUSE not including user-defined mouse bindings - FEATURE CHANGE: added bindings: "drag" and "up" -- may affect power users who use BIND command new: _center CTRL+SHIFT+LEFT+click new: _reset SHIFT+LEFT+double+click @@ -178,9 +140,15 @@ _translate CTRL+ALT+LEFT+drag, CTRL+RIGHT+drag, SHIFT+LEFT+double+drag, MIDDLE+double+drag translate _wheelZoom WHEEL zoom +bug fix: JSON NIO port SYNC broken +bug fix: print getProperty("image", "width=200;height=300;type=png") not working +bug fix: write IMAGE "t.png" not working +bug fix: rotate -10 -10 not working -JmolVersion="13.3.6_dev_2013.09.17" +bug fix: mouse bindings not distinguishing DOWN/CLICK/DRAG/UP properly +bug fix: mouse bindings _center and _reset not working +bug fix: show MOUSE not including user-defined mouse bindings bug fix: chains improperly selected in JSmol/HTML5 bug fix: JSmol/HTML5 not allowing drag-drop or file loading from a local drive. @@ -192,8 +160,41 @@ bug fix: second reading of older PNG files with embedded script fails due to improper png file caching -new feature: set drawFontSize // defaults to 14.0 +code: overhaul of image creation methods +code: careful attention to core functions yields results in 10% reduction in core download size: + -- uncompressed(former) gzipped + -- JSmol.min.nojq.js 134K 38K + -- core.z.js 1586K(1781K) 364K + -- corescript.z.js 378K (436K) 95K + + -- TOTAL 2098K(2217K) 497K + (9.5% reduction) + + -- JmolApplet0.jar 1038K 1005K + + -- Thus, the "real" transfer size -- based on server-side gzipping -- is half the size of Jmol/Java. + +code: continued refactoring of ScriptEvaluator to ScriptExt +code: refactoring to isolate LabelToken and Labels from core JavaScript load +code: refactoring, simplification of image output and export + -- folders created: org.jmol.image, org.jmol.dialog + -- JpgEncoder, Jpg64Encoder, PngEncoder brought to org.jmol.image + and made subclasses of ImageEncoder + -- PpmEncoder fixed + -- ImageEncoder stripped of all unnecessary ImageConsumer/producer business + -- org.jmol.export.image.ImageCreator and parts of org.jmol.viewer.stateCreator reorganized + into org.jmol.OutputManager, org.jmol.OutputManagerAwt, and org.jmol.OutputManagerJS + -- clipboard functions moved into org.jmol.awt and org.jmol.awtjs2d + -- org.jmol.io.JmolOutputChannel now serves for just about all output needs. + + +code: major simplification and consolidation of file I/O methods, including exporters, using JmolOutputChannel class. +code: only FileOutputStream reference is one reference in org.jmol.awt. + +code: code merge between 13.2 and 13.3 18 Sept 2013 +code: major clean-up of ActionManager + JmolVersion="13.3.5" JmolVersion="13.3.5_dev_2013.09.06" Modified: trunk/Jmol/src/org/jmol/viewer/OutputManagerAll.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/OutputManagerAll.java 2013-09-27 15:59:47 UTC (rev 18718) +++ trunk/Jmol/src/org/jmol/viewer/OutputManagerAll.java 2013-09-27 17:06:32 UTC (rev 18719) @@ -24,7 +24,6 @@ package org.jmol.viewer; -import java.io.BufferedWriter; import java.io.IOException; import java.util.Hashtable; import java.util.Map; @@ -742,6 +741,12 @@ String setLogFile(String value) { String path = null; String logFilePath = viewer.getLogFilePath(); + /** + * @j2sNative + * + * if (typeof value == "function") path = value; + * + */ if (logFilePath == null || value.indexOf("\\") >= 0) { value = null; } else if (value.startsWith("http://") || value.startsWith("https://")) { @@ -779,30 +784,16 @@ Logger.info(data); return; } - - // allows users to generate their own logging interface - - /** - * @j2sNative - * - * if ( if (Jmol.Logger && Jmol.Logger.logToFile) return - * Jmol.Logger.logToFile(data); - */ - - Logger.info(data); - { - BufferedWriter out = (BufferedWriter) viewer.openLogFile(privateKey, - viewer.logFileName, !doClear); - if (!doClear) { - int ptEnd = data.indexOf('\0'); - if (ptEnd >= 0) - data = data.substring(0, ptEnd); - out.write(data); - if (ptEnd < 0) - out.write("\n"); - } - out.close(); + JmolOutputChannel out = viewer.openLogFile(privateKey, !doClear); + if (!doClear) { + int ptEnd = data.indexOf('\0'); + if (ptEnd >= 0) + data = data.substring(0, ptEnd); + out.append(data); + if (ptEnd < 0) + out.append("\n"); } + Logger.info(out.closeChannel()); } catch (Exception e) { if (Logger.debugging) Logger.debug("cannot log " + data); Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-09-27 15:59:47 UTC (rev 18718) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-09-27 17:06:32 UTC (rev 18719) @@ -6077,7 +6077,7 @@ global.defaultLoadFilter = value; break; case T.logfile: - value = getOutputManager().setLogFile(value); + value = setLogFile(value); if (value == null) return; break; @@ -10370,7 +10370,7 @@ public JmolOutputChannel openOutputChannel(double privateKey, String fileName, boolean asWriter) throws IOException { return (!haveAccess(ACCESS.ALL) ? null : getFileAdapter() - .openOutputChannel(privateKey, fileManager, fileName, asWriter)); + .openOutputChannel(privateKey, fileManager, fileName, asWriter, false)); } public InputStream openFileInputStream(double privateKey, String fileName) @@ -10382,18 +10382,23 @@ return getFileAdapter().getAbsolutePath(privateKey, fileName); } - public Object openLogFile(double privateKey, String logFileName, - boolean asAppend) throws IOException { - return getFileAdapter().openLogFile(privateKey, logFileName, asAppend); + public JmolOutputChannel openLogFile(double privateKey, boolean asAppend) + throws IOException { + return (!haveAccess(ACCESS.ALL) ? null : getFileAdapter() + .openOutputChannel(privateKey, fileManager, logFileName, true, asAppend)); } + + /*default*/ String logFileName; + + private String setLogFile(String value) { + return getOutputManager().setLogFile(value); + } public void log(String data) { if (data != null) getOutputManager().logToFile(data); } - /*default*/ String logFileName; - public String getLogFileName() { return (logFileName == null ? "" : logFileName); } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-10-01 04:10:40
|
Revision: 18734 http://sourceforge.net/p/jmol/code/18734 Author: hansonr Date: 2013-10-01 04:10:33 +0000 (Tue, 01 Oct 2013) Log Message: ----------- ___JmolVersion="13.3.7" bug fix: state saving of echo "bottom left" instead does "top left" Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties trunk/Jmol/src/org/jmol/viewer/StateCreator.java Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-10-01 04:09:36 UTC (rev 18733) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-10-01 04:10:33 UTC (rev 18734) @@ -13,6 +13,7 @@ ___JmolVersion="13.3.7" +bug fix: state saving of echo "bottom left" instead does "top left" bug fix: multiple-file crystal structures may fail to load if there is a lattice shift bug fix: space group not being calculated automatically for user-defined space groups bug fix: measures broken Modified: trunk/Jmol/src/org/jmol/viewer/StateCreator.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2013-10-01 04:09:36 UTC (rev 18733) +++ trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2013-10-01 04:10:33 UTC (rev 18734) @@ -1361,7 +1361,7 @@ JC.hAlignNames[t.align]); break; default: - s.append(" set echo ").append(JC.vAlignNames[t.align]).append(" ") + s.append(" set echo ").append(JC.vAlignNames[t.valign]).append(" ") .append(JC.hAlignNames[t.align]); } if (t.valign == JC.VALIGN_XY This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2014-01-13 19:16:05
|
Revision: 19167 http://sourceforge.net/p/jmol/code/19167 Author: hansonr Date: 2014-01-13 19:16:00 +0000 (Mon, 13 Jan 2014) Log Message: ----------- ___JmolVersion="14.1.6_dev_2014.01.13" bug fix: _DirectDatabaseCalls not including NMR prediction site Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-01-10 22:46:26 UTC (rev 19166) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-01-13 19:16:00 UTC (rev 19167) @@ -11,8 +11,10 @@ # The quotes above look odd for a parameter file, but they are # important for the JavaScript version of Jmol. -___JmolVersion="14.1.6_dev_2014.01.10" +___JmolVersion="14.1.6_dev_2014.01.13" +bug fix: _DirectDatabaseCalls not including NMR prediction site + code: reader refactoring isolates symmetry aspects bug fix: reading of *co*mmensurately modulated structures (e.g. Lilianite) working Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2014-01-10 22:46:26 UTC (rev 19166) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2014-01-13 19:16:00 UTC (rev 19167) @@ -4336,14 +4336,14 @@ */ @Override public void updateJS(int width, int height) { - if (this.isWebGL) { + if (isWebGL) { if (jsParams == null) { jsParams = new Hashtable<String, Object>(); jsParams.put("type", "JS"); } if (updateWindow(width, height)) - this.render(); - this.notifyViewerRepaintDone(); + render(); + notifyViewerRepaintDone(); } else { Object g = null; Object gright = null; @@ -4437,7 +4437,7 @@ transformManager.ptOffset); int[] minMax = shapeManager.transformAtoms(); transformManager.bsSelectedAtoms = null; - if (this.isWebGL) { + if (isWebGL) { repaintManager.renderExport(gdata, modelSet, jsParams); notifyViewerRepaintDone(); return; @@ -5791,9 +5791,7 @@ return global.percentVdwAtom; case T.pickingspinrate: return global.pickingSpinRate; - case T.platformspeed: - return global.platformSpeed; - case T.ribbonaspectratio: + case T.ribbonaspectratio: return global.ribbonAspectRatio; case T.showscript: return global.scriptDelay; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2014-01-27 17:15:47
|
Revision: 19217 http://sourceforge.net/p/jmol/code/19217 Author: hansonr Date: 2014-01-27 17:15:44 +0000 (Mon, 27 Jan 2014) Log Message: ----------- ___JmolVersion="14.1.8_dev_2014.01.27" bug fix: assign atom into into PDB file loses atom names Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-01-27 17:15:19 UTC (rev 19216) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-01-27 17:15:44 UTC (rev 19217) @@ -13,8 +13,9 @@ # important for the JavaScript version of Jmol. -___JmolVersion="14.1.8_dev_2014.01.23" +___JmolVersion="14.1.8_dev_2014.01.27" +bug fix: assign atom into into PDB file loses atom names bug fix: y = ([3])[1][1] should be [3] not 3 bug fix: break n nonfunctional bug fix: format() and label() functions limited to 4 arguments; should be unlimited Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2014-01-27 17:15:19 UTC (rev 19216) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2014-01-27 17:15:44 UTC (rev 19217) @@ -9682,10 +9682,10 @@ if (modelSet.atoms[atomIndex].modelIndex != modelSet.modelCount - 1) return; clearModelDependentObjects(); + int atomCount = modelSet.getAtomCount(); if (pt == null) { statusManager.modifySend(atomIndex, modelSet.atoms[atomIndex].modelIndex, 1); - int atomCount = modelSet.getAtomCount(); modelSet.assignAtom(atomIndex, type, true); if (!PT.isOneOf(type, ";Mi;Pl;X;")) modelSet.setAtomNamesAndNumbers(atomIndex, -atomCount, null); @@ -9708,7 +9708,7 @@ } catch (Exception e) { // } - modelSet.setAtomNamesAndNumbers(atomIndex, -1, null); + modelSet.setAtomNamesAndNumbers(atomIndex, -atomCount, null); statusManager.modifySend(atomIndex, modelIndex, -3); } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2014-02-01 21:03:43
|
Revision: 19245 http://sourceforge.net/p/jmol/code/19245 Author: hansonr Date: 2014-02-01 21:03:37 +0000 (Sat, 01 Feb 2014) Log Message: ----------- static variables appletCodeBase appletDocumentBase Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties trunk/Jmol/src/org/jmol/viewer/StateCreator.java trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-02-01 20:50:54 UTC (rev 19244) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-02-01 21:03:37 UTC (rev 19245) @@ -13,8 +13,10 @@ # important for the JavaScript version of Jmol. -___JmolVersion="14.1.8_dev_2014.02.01" +___JmolVersion="14.1.8_dev_2014.02.01b" +bug fix: set pdbGetHeader TRUE does not capture REMARK3 REMARK290 REMARK350 + JSmol: applying atom mapping between mol2D and mol3D for viewSets new feature: x = compare({atomset1}, {atomset2}, "MAP") Modified: trunk/Jmol/src/org/jmol/viewer/StateCreator.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2014-02-01 20:50:54 UTC (rev 19244) +++ trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2014-02-01 21:03:37 UTC (rev 19245) @@ -122,8 +122,8 @@ s.append(JC.STATE_VERSION_STAMP + Viewer.getJmolVersion() + ";\n"); if (viewer.isApplet() && isAll) { appendCmd(s, "# fullName = " + PT.esc(viewer.fullName)); - appendCmd(s, "# documentBase = " + PT.esc(viewer.appletDocumentBase)); - appendCmd(s, "# codeBase = " + PT.esc(viewer.appletCodeBase)); + appendCmd(s, "# documentBase = " + PT.esc(Viewer.appletDocumentBase)); + appendCmd(s, "# codeBase = " + PT.esc(Viewer.appletCodeBase)); s.append("\n"); } Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2014-02-01 20:50:54 UTC (rev 19244) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2014-02-01 21:03:37 UTC (rev 19245) @@ -208,9 +208,9 @@ public boolean queueOnHold = false; public String fullName = ""; - public String appletDocumentBase = ""; - public String appletCodeBase = ""; - public String appletIdiomaBase; + public static String appletDocumentBase = ""; + public static String appletCodeBase = ""; + public static String appletIdiomaBase; public static String jsDocumentBase = ""; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |