Menu
▾
▴
jmol-commits
|
From: <ha...@us...> - 2008-08-28 12:59:56
|
Revision: 9799
http://jmol.svn.sourceforge.net/jmol/?rev=9799&view=rev
Author: hansonr
Date: 2008-08-28 12:59:51 +0000 (Thu, 28 Aug 2008)
Log Message:
-----------
version=11.6.RC12_dev # cml reader fix for not applying symmetry to first model
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlCmlReader.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlCmlReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlCmlReader.java 2008-08-28 12:58:58 UTC (rev 9798)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlCmlReader.java 2008-08-28 12:59:51 UTC (rev 9799)
@@ -206,6 +206,7 @@
state = SYMMETRY;
if (atts.containsKey("spaceGroup")) {
localSpaceGroupName = (String) atts.get("spaceGroup");
+ applySymmetry();
}
} else if (name.equals("module")) {
moduleCount++;
@@ -674,8 +675,9 @@
public void applySymmetry() {
if (moduleCount > 0 || !haveMolecule)
return;
- if (localSpaceGroupName != null)
- parent.setSpaceGroupName(localSpaceGroupName);
+ if (localSpaceGroupName == null)
+ return;
+ parent.setSpaceGroupName(localSpaceGroupName);
try {
parent.applySymmetry();
} catch (Exception e) {
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-28 12:58:58 UTC (rev 9798)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-28 12:59:51 UTC (rev 9799)
@@ -3,6 +3,7 @@
version=11.6.RC12_dev
+# cml reader fix for not applying symmetry to first model
# translation: added GT._ calls for HTML templates and JS in WebExport
# -----------------------------------------------------------------------------
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-08-29 17:54:13
|
Revision: 9806
http://jmol.svn.sourceforge.net/jmol/?rev=9806&view=rev
Author: hansonr
Date: 2008-08-29 17:54:08 +0000 (Fri, 29 Aug 2008)
Log Message:
-----------
version=11.6.RC12_dev # new feature: applet parameter jmolSetCallback("maximumSize", nnn) -- sets maximum size of applet when resizing to this value
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/applet/Jmol.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/applet/Jmol.java
===================================================================
--- trunk/Jmol/src/org/jmol/applet/Jmol.java 2008-08-29 11:45:47 UTC (rev 9805)
+++ trunk/Jmol/src/org/jmol/applet/Jmol.java 2008-08-29 17:54:08 UTC (rev 9806)
@@ -77,6 +77,11 @@
* To disable ALL access to JavaScript (as, for example, in a Wiki)
* remove the MAYSCRIPT tag or set MAYSCRIPT="false"
*
+ * To set a maximum size for the applet if resizable:
+ *
+ * [param name="maximumSize" value="nnnn" /]
+ *
+ *
* You can specify that the signed or unsign applet or application should
* use an independent command thread (EXCEPT for scripts containing the "javascript" command)
*
@@ -240,9 +245,12 @@
options += "-signed";
if (getBooleanValue("useCommandThread", isSigned))
options += "-threaded";
- String appletProxy = getValue("JmolAppletProxy", null);
- if (appletProxy != null)
- options += "-appletProxy " + appletProxy;
+ String s = getValue("MaximumSize", null);
+ if (s != null)
+ options += "-maximumSize " + s;
+ s = getValue("JmolAppletProxy", null);
+ if (s != null)
+ options += "-appletProxy " + s;
System.out.println("setAppletContext: " + options);
viewer.setAppletContext(fullName, appletWrapper.getDocumentBase(),
appletWrapper.getCodeBase(), options);
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-29 11:45:47 UTC (rev 9805)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-29 17:54:08 UTC (rev 9806)
@@ -3,6 +3,7 @@
version=11.6.RC12_dev
+# new feature: applet parameter jmolSetCallback("maximumSize", nnn) -- sets maximum size of applet when resizing to this value
# cml reader fix for not applying symmetry to first model
# translation: added GT._ calls for HTML templates and JS in WebExport
# -----------------------------------------------------------------------------
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-08-29 11:45:47 UTC (rev 9805)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-08-29 17:54:08 UTC (rev 9806)
@@ -283,6 +283,10 @@
appletProxy = str.substring(i + 13);
str = str.substring(0, i);
}
+ if (isApplet && (i = str.indexOf("-maximumSize ")) >= 0) {
+ setMaximumSize(Parser.parseInt(str.substring(i + 13)));
+ str = str.substring(0, i);
+ }
if (str.indexOf("-b") >= 0)
g3d.setBackgroundTransparent(true);
useCommandThread = (str.indexOf("-t") >= 0);
@@ -3108,9 +3112,17 @@
//final Rectangle rectClip = new Rectangle();
+ private int maximumSize = Integer.MAX_VALUE;
+
+ private void setMaximumSize(int x) {
+ maximumSize = Math.max(x, 100);
+ }
+
public void setScreenDimension(Dimension dim) {
// There is a bug in Netscape 4.7*+MacOS 9 when comparing dimension objects
// so don't try dim1.equals(dim2)
+ dim.height = Math.min(dim.height, maximumSize);
+ dim.width = Math.min(dim.width, maximumSize);
int height = dim.height;
int width = dim.width;
if (getStereoMode() == JmolConstants.STEREO_DOUBLE)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-08-30 13:31:24
|
Revision: 9813
http://jmol.svn.sourceforge.net/jmol/?rev=9813&view=rev
Author: hansonr
Date: 2008-08-30 13:31:21 +0000 (Sat, 30 Aug 2008)
Log Message:
-----------
11.6.RC12 VERSION
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/minimize/forcefield/Calculations.java
trunk/Jmol/src/org/jmol/minimize/forcefield/CalculationsUFF.java
trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
Modified: trunk/Jmol/src/org/jmol/minimize/forcefield/Calculations.java
===================================================================
--- trunk/Jmol/src/org/jmol/minimize/forcefield/Calculations.java 2008-08-30 13:31:00 UTC (rev 9812)
+++ trunk/Jmol/src/org/jmol/minimize/forcefield/Calculations.java 2008-08-30 13:31:21 UTC (rev 9813)
@@ -75,7 +75,6 @@
bonds = minBonds;
this.angles = angles;
this.torsions = torsions;
- this.partialCharges = partialCharges;
this.constraints = constraints;
atomCount = atoms.length;
bondCount = bonds.length;
@@ -87,6 +86,7 @@
}
if (!havePartialCharges)
partialCharges = null;
+ this.partialCharges = partialCharges;
}
boolean haveParams() {
Modified: trunk/Jmol/src/org/jmol/minimize/forcefield/CalculationsUFF.java
===================================================================
--- trunk/Jmol/src/org/jmol/minimize/forcefield/CalculationsUFF.java 2008-08-30 13:31:00 UTC (rev 9812)
+++ trunk/Jmol/src/org/jmol/minimize/forcefield/CalculationsUFF.java 2008-08-30 13:31:21 UTC (rev 9813)
@@ -711,12 +711,16 @@
switch (elemNo) {
case 15: // P
phi *= 84.4339;
+ break;
case 33: // As
phi *= 86.9735;
+ break;
case 51: // Sb
phi *= 87.7047;
+ break;
case 83: // Bi
phi *= 90.0;
+ break;
}
double cosPhi = Math.cos(phi);
a0 = cosPhi * cosPhi;
Modified: trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2008-08-30 13:31:00 UTC (rev 9812)
+++ trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2008-08-30 13:31:21 UTC (rev 9813)
@@ -1323,6 +1323,7 @@
for (int i = atomCount; --i >= 0;)
if (atoms[i].isPurine())
bs.set(i);
+ return bs;
case Token.pyrimidine:
for (int i = atomCount; --i >= 0;)
if (atoms[i].isPyrimidine())
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-08-30 19:04:37
|
Revision: 9818
http://jmol.svn.sourceforge.net/jmol/?rev=9818&view=rev
Author: hansonr
Date: 2008-08-30 19:04:33 +0000 (Sat, 30 Aug 2008)
Log Message:
-----------
11.6.RC12 (more)
new features: set atomPicking/set bondPicking
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/modelset/ModelSet.java
trunk/Jmol/src/org/jmol/shape/Sticks.java
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/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2008-08-30 18:59:41 UTC (rev 9817)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2008-08-30 19:04:33 UTC (rev 9818)
@@ -369,14 +369,20 @@
return shape.checkObjectHovered(x, y, bsVisible);
}
- public Point3f checkObjectClicked(int x, int y, int modifiers, BitSet bsVisible) {
+ public Point3f checkObjectClicked(int x, int y, int modifiers,
+ BitSet bsVisible) {
Shape shape = shapes[JmolConstants.SHAPE_ECHO];
Point3f pt = null;
- if (shape != null && modifiers != 0
+ if (modifiers != 0 && viewer.getBondPicking()
+ && (pt = shapes[JmolConstants.SHAPE_STICKS].checkObjectClicked(x, y,
+ modifiers, bsVisible)) != null)
+ return pt;
+
+ if (shape != null && modifiers != 0
&& (pt = shape.checkObjectClicked(x, y, modifiers, bsVisible)) != null)
return pt;
- return ((shape = shapes[JmolConstants.SHAPE_DRAW]) == null ? null
- : shape.checkObjectClicked(x, y, modifiers, bsVisible));
+ return ((shape = shapes[JmolConstants.SHAPE_DRAW]) == null ? null : shape
+ .checkObjectClicked(x, y, modifiers, bsVisible));
}
public void checkObjectDragged(int prevX, int prevY, int deltaX, int deltaY,
Modified: trunk/Jmol/src/org/jmol/shape/Sticks.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/Sticks.java 2008-08-30 18:59:41 UTC (rev 9817)
+++ trunk/Jmol/src/org/jmol/shape/Sticks.java 2008-08-30 19:04:33 UTC (rev 9818)
@@ -33,7 +33,11 @@
import java.util.BitSet;
import java.util.Hashtable;
+import javax.vecmath.Point3f;
+import javax.vecmath.Point3i;
+
import org.jmol.g3d.Graphics3D;
+import org.jmol.modelset.Atom;
import org.jmol.modelset.Bond;
import org.jmol.modelset.BondIterator;
@@ -214,4 +218,55 @@
+ (haveTainted ? getShapeCommands(temp2, null, -1, "select BONDS") + "\n"
: "");
}
+
+ public Point3f checkObjectClicked(int x, int y, int modifiers,
+ BitSet bsVisible) {
+ Point3f pt = new Point3f();
+ Bond bond = findPickedBond(x, y, bsVisible, pt);
+ if (bond == null)
+ return null;
+ viewer.setStatusAtomPicked(-3, "[\"bond\",\"" + bond.getIdentity() + "\"," + pt.x + "," + pt.y + "," + pt.z + "]");
+ return pt;
+ }
+
+ private final static int MAX_BOND_CLICK_DISTANCE_SQUARED = 10 * 10;
+
+ private Bond findPickedBond(int x, int y, BitSet bsVisible, Point3f pt) {
+ int dmin2 = MAX_BOND_CLICK_DISTANCE_SQUARED;
+ if (g3d.isAntialiased()) {
+ x <<= 1;
+ y <<= 1;
+ dmin2 <<= 1;
+ }
+ Bond pickedBond = null;
+ Point3f v = new Point3f();
+ Bond[] bonds = modelSet.getBonds();
+ for (int i = modelSet.getBondCount(); --i >= 0;) {
+ Bond bond = bonds[i];
+ if (bond.getShapeVisibilityFlags() == 0)
+ continue;
+ Atom atom1 = bond.getAtom1();
+ Atom atom2 = bond.getAtom2();
+ if (!atom1.isVisible() || !atom2.isVisible())
+ continue;
+ v.set(atom1);
+ v.add(atom2);
+ v.scale(0.5f);
+ int d2 = coordinateInRange(x, y, v, dmin2);
+ if (d2 >= 0) {
+ dmin2 = d2;
+ pickedBond = bond;
+ pt.set(v);
+ }
+ }
+ return pickedBond;
+ }
+
+ private final Point3i ptXY = new Point3i();
+ private int coordinateInRange(int x, int y, Point3f vertex, int dmin2) {
+ viewer.transformPoint(vertex, ptXY);
+ int d2 = (x - ptXY.x) * (x - ptXY.x) + (y - ptXY.y) * (y - ptXY.y);
+ return (d2 < dmin2 ? d2 : -1);
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-30 18:59:41 UTC (rev 9817)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-08-30 19:04:33 UTC (rev 9818)
@@ -3,6 +3,8 @@
version=11.6.RC12
+# new feature: set atomPicking TRUE/FALSE
+# new feature: set bondPicking TRUE/FALSE
# bug fix: draw pointgroup when principalPlane == null
# bug fix: findbugs corrections in minimize.forcefield, modelset.AtomCollection, shapespecial.DrawRenderer
# new feature: applet parameter jmolSetCallback("maximumSize", nnn) -- sets maximum size of applet when resizing to this value
Modified: trunk/Jmol/src/org/jmol/viewer/StateManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StateManager.java 2008-08-30 18:59:41 UTC (rev 9817)
+++ trunk/Jmol/src/org/jmol/viewer/StateManager.java 2008-08-30 19:04:33 UTC (rev 9818)
@@ -615,6 +615,8 @@
float dipoleScale = 1.0f;
boolean disablePopupMenu = false;
boolean drawPicking = false;
+ boolean bondPicking = false;
+ boolean atomPicking = true;
String helpPath = JmolConstants.DEFAULT_HELP_PATH;
boolean fontScaling = false;
boolean hideNameInPopup = false;
@@ -1098,6 +1100,7 @@
setParameterValue("appendNew", appendNew);
setParameterValue("appletProxy", appletProxy);
setParameterValue("applySymmetryToBonds", applySymmetryToBonds);
+ setParameterValue("atomPicking", atomPicking);
setParameterValue("autoBond", autoBond);
setParameterValue("autoFps", autoFps);
setParameterValue("axesMode", axesMode);
@@ -1109,6 +1112,7 @@
setParameterValue("axesOrientationRasmol", axesOrientationRasmol);
setParameterValue("backgroundModel", 0);
setParameterValue("bondModeOr", bondModeOr);
+ setParameterValue("bondPicking", bondPicking);
setParameterValue("bondRadiusMilliAngstroms", bondRadiusMilliAngstroms);
setParameterValue("bondTolerance", bondTolerance);
setParameterValue("cameraDepth", cameraDepth);
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-08-30 18:59:41 UTC (rev 9817)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-08-30 19:04:33 UTC (rev 9818)
@@ -2331,7 +2331,7 @@
}
int findNearestAtomIndex(int x, int y) {
- return (modelSet == null ? -1 : modelSet.findNearestAtomIndex(x, y));
+ return (modelSet == null || !getAtomPicking() ? -1 : modelSet.findNearestAtomIndex(x, y));
}
void selectRectangle(Rectangle rect, int modifiers) {
@@ -3794,6 +3794,14 @@
return global.drawPicking;
}
+ public boolean getBondPicking() {
+ return global.bondPicking;
+ }
+
+ private boolean getAtomPicking() {
+ return global.atomPicking;
+ }
+
private void setPickingStyle(String style) {
int pickingStyle = JmolConstants.getPickingStyle(style);
if (pickingStyle < 0)
@@ -4600,7 +4608,19 @@
boolean notFound = false;
boolean doRepaint = true;
while (true) {
-
+
+ // 11.6.RC13
+ if (key.equalsIgnoreCase("atomPicking")) {
+ global.atomPicking = value;
+ break;
+ }
+
+ // 11.6.RC13
+ if (key.equalsIgnoreCase("bondPicking")) {
+ global.bondPicking = value;
+ break;
+ }
+
//11.5.52
if (key.equalsIgnoreCase("selectAllModels")) {
global.selectAllModels = value;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-08-31 01:38:47
|
Revision: 9825
http://jmol.svn.sourceforge.net/jmol/?rev=9825&view=rev
Author: hansonr
Date: 2008-08-31 01:38:43 +0000 (Sun, 31 Aug 2008)
Log Message:
-----------
version=11.6.RC12
# bug fix: getProperty("atominfo",{atom expression}) not working for "atominfo[0].xxx
# bug fix: getProperty("modelinfo",{atom expression}) not working
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2008-08-31 01:15:07 UTC (rev 9824)
+++ trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2008-08-31 01:38:43 UTC (rev 9825)
@@ -1127,7 +1127,7 @@
return "no header information found";
}
- public Hashtable getModelInfo() {
+ public Hashtable getModelInfo(BitSet bsModels) {
Hashtable info = new Hashtable();
info.put("modelSetName", modelSetName);
info.put("modelCount", new Integer(modelCount));
@@ -1135,8 +1135,13 @@
.valueOf(modelSetHasVibrationVectors()));
if (modelSetProperties != null)
info.put("modelSetProperties", modelSetProperties);
+ info.put("modelCountSelected", new Integer(BitSetUtil.cardinalityOf(bsModels)));
+ info.put("modelsSelected", bsModels);
Vector vModels = new Vector();
+
for (int i = 0; i < modelCount; ++i) {
+ if (!bsModels.get(i))
+ continue;
Hashtable model = new Hashtable();
model.put("_ipt", new Integer(i));
model.put("num", new Integer(getModelNumber(i)));
@@ -2453,12 +2458,14 @@
return sb.toString();
}
- public Hashtable getAuxiliaryInfo() {
+ public Hashtable getAuxiliaryInfo(BitSet bsModels) {
Hashtable info = getModelSetAuxiliaryInfo();
if (info == null)
return info;
Vector models = new Vector();
for (int i = 0; i < modelCount; ++i) {
+ if (bsModels != null && !bsModels.get(i))
+ continue;
Hashtable modelinfo = getModelAuxiliaryInfo(i);
models.addElement(modelinfo);
}
@@ -2540,9 +2547,10 @@
public Vector getAllBondInfo(BitSet bs) {
Vector V = new Vector();
+ int thisAtom = (BitSetUtil.cardinalityOf(bs) == 1 ? BitSetUtil.firstSetBit(bs) : -1);
for (int i = 0; i < bondCount; i++)
- if (bs.get(bonds[i].atom1.atomIndex)
- && bs.get(bonds[i].atom2.atomIndex))
+ if (thisAtom >= 0? (bonds[i].atom1.atomIndex == thisAtom || bonds[i].atom2.atomIndex == thisAtom)
+ : bs.get(bonds[i].atom1.atomIndex) && bs.get(bonds[i].atom2.atomIndex))
V.addElement(getBondInfo(i));
return V;
}
Modified: trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelLoader.java 2008-08-31 01:15:07 UTC (rev 9824)
+++ trunk/Jmol/src/org/jmol/modelset/ModelLoader.java 2008-08-31 01:38:43 UTC (rev 9825)
@@ -307,7 +307,7 @@
private void initializeMerge() {
merge(mergeModelSet);
bsSymmetry = mergeModelSet.bsSymmetry;
- Hashtable info = mergeModelSet.getAuxiliaryInfo();
+ Hashtable info = mergeModelSet.getAuxiliaryInfo(null);
String[] mergeGroup3Lists = (String[]) info.get("group3Lists");
int[][] mergeGroup3Counts = (int[][]) info.get("group3Counts");
if (mergeGroup3Lists != null) {
Modified: trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2008-08-31 01:15:07 UTC (rev 9824)
+++ trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2008-08-31 01:38:43 UTC (rev 9825)
@@ -72,7 +72,7 @@
"jmolStatus" , "statusNameList", "",
"jmolViewer" , "", "",
"messageQueue" , "", "",
- "auxiliaryInfo" , "", "",
+ "auxiliaryInfo" , atomExpression, "*",
"boundBoxInfo" , "", "",
"dataInfo" , "<data type>", "types",
@@ -312,7 +312,7 @@
case PROP_ATOM_INFO:
return viewer.getAllAtomInfo(myParam);
case PROP_AUXILIARY_INFO:
- return viewer.getAuxiliaryInfo();
+ return viewer.getAuxiliaryInfo(myParam);
case PROP_BOND_INFO:
return viewer.getAllBondInfo(myParam);
case PROP_BOUNDBOX_INFO:
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-08-31 01:15:07 UTC (rev 9824)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-08-31 01:38:43 UTC (rev 9825)
@@ -2462,8 +2462,8 @@
return modelSet.getModelInfo(getModelBitSet(getAtomBitSet(atomExpression)));
}
- public Hashtable getAuxiliaryInfo() {
- return modelSet.getAuxiliaryInfo();
+ public Hashtable getAuxiliaryInfo(Object atomExpression) {
+ return modelSet.getAuxiliaryInfo(getModelBitSet(getAtomBitSet(atomExpression)));
}
public Hashtable getShapeInfo() {
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-09-03 19:10:12
|
Revision: 9847
http://jmol.svn.sourceforge.net/jmol/?rev=9847&view=rev
Author: hansonr
Date: 2008-09-03 19:09:59 +0000 (Wed, 03 Sep 2008)
Log Message:
-----------
version=11.6.RC13_dev # bug fix/new feature: HIDE/DiSPLAY/DELETE/COLOR $*xxx* extended to ECHO
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/shape/Echo.java
trunk/Jmol/src/org/jmol/shape/Object2dShape.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/shape/Echo.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/Echo.java 2008-09-01 20:15:09 UTC (rev 9846)
+++ trunk/Jmol/src/org/jmol/shape/Echo.java 2008-09-03 19:09:59 UTC (rev 9847)
@@ -25,6 +25,7 @@
package org.jmol.shape;
import org.jmol.util.Logger;
+import org.jmol.util.TextFormat;
import org.jmol.g3d.*;
import java.awt.Image;
@@ -57,7 +58,7 @@
if (Logger.debugging) {
Logger.debug("Echo.setProperty(" + propertyName + "," + value + ")");
}
-
+
if ("scalereference" == propertyName) {
if (currentObject != null) {
float val = ((Float) value).floatValue();
@@ -65,10 +66,11 @@
}
return;
}
-
+
if ("xyz" == propertyName) {
if (currentObject != null && viewer.getFontScaling())
- currentObject.setScalePixelsPerMicron(viewer.getScalePixelsPerAngstrom() * 10000f);
+ currentObject.setScalePixelsPerMicron(viewer
+ .getScalePixelsPerAngstrom() * 10000f);
// continue on to Object2d setting
}
@@ -85,25 +87,37 @@
((Text) currentObject).setImage(image);
return;
}
-
+ if ("thisID" == propertyName) {
+ String target = (String) value;
+ currentObject = (Text) objects.get(target);
+ if (currentObject == null && TextFormat.isWild(target))
+ thisID = target.toUpperCase();
+ return;
+ }
+
if ("hidden" == propertyName) {
- boolean isHidden = ((Boolean)value).booleanValue();
- if (currentObject == null) {
- if (isAll) {
+ boolean isHidden = ((Boolean) value).booleanValue();
+ if (currentObject == null)
+ if (isAll || thisID != null) {
Enumeration e = objects.elements();
- while (e.hasMoreElements())
- ((Text) e.nextElement()).hidden = isHidden;
+ while (e.hasMoreElements()) {
+ Text text = (Text) e.nextElement();
+ if (isAll
+ || TextFormat.isMatch(text.target.toUpperCase(), thisID, true,
+ true))
+ text.hidden = isHidden;
+ }
+ return;
}
- return;
- }
((Text) currentObject).hidden = isHidden;
return;
}
if (Object2d.setProperty(propertyName, value, currentObject))
return;
-
+
if ("target" == propertyName) {
+ thisID = null;
String target = ((String) value).intern().toLowerCase();
if (target == "none" || target == "all") {
// process in Object2dShape
@@ -143,6 +157,20 @@
super.setProperty(propertyName, value, null);
}
+ public Object getProperty(String property, int index) {
+ if (property.startsWith("checkID:")) {
+ // returns FIRST match
+ String key = property.substring(8).toUpperCase();
+ boolean isWild = TextFormat.isWild(key);
+ Enumeration e = objects.elements();
+ while (e.hasMoreElements()) {
+ String id = ((Text) e.nextElement()).target.toUpperCase();
+ if (id.equals(key) || isWild && TextFormat.isMatch(id, key, true, true))
+ return id;
+ }
+ }
+ return null;
+ }
public String getShapeState() {
StringBuffer s = new StringBuffer("\n set echo off;\n");
Enumeration e = objects.elements();
Modified: trunk/Jmol/src/org/jmol/shape/Object2dShape.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/Object2dShape.java 2008-09-01 20:15:09 UTC (rev 9846)
+++ trunk/Jmol/src/org/jmol/shape/Object2dShape.java 2008-09-03 19:09:59 UTC (rev 9847)
@@ -8,6 +8,7 @@
import org.jmol.g3d.Font3D;
import org.jmol.util.Logger;
+import org.jmol.util.TextFormat;
import org.jmol.viewer.Viewer;
public class Object2dShape extends Shape {
@@ -21,7 +22,8 @@
Object currentBgColor;
float currentTranslucentLevel;
float currentBgTranslucentLevel;
-
+ protected String thisID;
+
boolean isHover;
boolean isAll;
@@ -38,6 +40,24 @@
return;
}
+ if ("delete" == propertyName) {
+ if (currentObject == null)
+ if (isAll || thisID != null) {
+ Enumeration e = objects.elements();
+ while (e.hasMoreElements()) {
+ Text text = (Text) e.nextElement();
+ if (isAll
+ || TextFormat.isMatch(text.target.toUpperCase(), thisID, true,
+ true))
+ objects.remove(text.target);
+ }
+ return;
+ }
+ objects.remove(currentObject.target);
+ currentObject = null;
+ return;
+ }
+
if ("off" == propertyName) {
if (isAll) {
objects = new Hashtable();
@@ -65,7 +85,7 @@
currentObject.setModel(modelIndex);
return;
}
-
+
if ("align" == propertyName) {
String align = (String) value;
if (currentObject == null) {
@@ -97,14 +117,18 @@
if ("color" == propertyName) {
currentColor = value;
- if (currentObject == null) {
- if (isAll) {
+ if (currentObject == null)
+ if (isAll || thisID != null) {
Enumeration e = objects.elements();
- while (e.hasMoreElements())
- ((Text) e.nextElement()).setColix(value);
+ while (e.hasMoreElements()) {
+ Text text = (Text) e.nextElement();
+ if (isAll
+ || TextFormat.isMatch(text.target.toUpperCase(), thisID, true,
+ true))
+ text.setColix(value);
+ }
+ return;
}
- return;
- }
currentObject.setColix(value);
return;
}
@@ -138,9 +162,9 @@
currentObject.setTranslucent(translucentLevel, isBackground);
return;
}
-
+
if (propertyName == "deleteModelAtoms") {
- int modelIndex = ((int[])((Object[])value)[2])[0];
+ int modelIndex = ((int[]) ((Object[]) value)[2])[0];
Enumeration e = objects.elements();
while (e.hasMoreElements()) {
Text text = (Text) e.nextElement();
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-09-01 20:15:09 UTC (rev 9846)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-09-03 19:09:59 UTC (rev 9847)
@@ -3,6 +3,8 @@
version=11.6.RC13_dev
+
+# bug fix/new feature: HIDE/DiSPLAY/DELETE/COLOR $*xxx* extended to ECHO
# bug fix: findbugs input stream closure
# translation: add GT.escapeHTML and stricter checking for special characters in file names
# used by web export.
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-09-06 14:32:51
|
Revision: 9848
http://jmol.svn.sourceforge.net/jmol/?rev=9848&view=rev
Author: hansonr
Date: 2008-09-06 14:32:48 +0000 (Sat, 06 Sep 2008)
Log Message:
-----------
version=11.6.RC13_dev # bug fix: y-offset for echo text and images
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/shape/Echo.java
trunk/Jmol/src/org/jmol/shape/Object2d.java
trunk/Jmol/src/org/jmol/shape/Text.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/shape/Echo.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/Echo.java 2008-09-03 19:09:59 UTC (rev 9847)
+++ trunk/Jmol/src/org/jmol/shape/Echo.java 2008-09-06 14:32:48 UTC (rev 9848)
@@ -137,7 +137,7 @@
}
text = new Text(viewer, g3d, g3d.getFont3D(FONTFACE, FONTSIZE),
target, COLOR, valign, halign, 0);
- text.setAdjustForWindow(true); // when a box is around it
+ text.setAdjustForWindow(true);
objects.put(target, text);
if (currentFont != null)
text.setFont(currentFont);
Modified: trunk/Jmol/src/org/jmol/shape/Object2d.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/Object2d.java 2008-09-03 19:09:59 UTC (rev 9847)
+++ trunk/Jmol/src/org/jmol/shape/Object2d.java 2008-09-06 14:32:48 UTC (rev 9848)
@@ -280,82 +280,6 @@
}
}
- protected void setPosition(float scale) {
- float xLeft, xCenter, xRight;
- boolean is3dEcho = (xyz != null);
- if (valign == VALIGN_XY || valign == VALIGN_XYZ) {
- float x = (movableXPercent != Integer.MAX_VALUE ? movableXPercent
- * windowWidth / 100 : is3dEcho ? movableX : movableX * scale);
- float offsetX = this.offsetX * scale;
- xLeft = xRight = xCenter = x + offsetX;
- //System.out.print("movableX = " + movableX + " offsetX = " + offsetX);
- } else {
- xLeft = 5 * scale;
- xCenter = windowWidth / 2;
- xRight = windowWidth - xLeft;
- }
-
- // set box X from alignments
-
- boxXY[0] = xLeft;
- switch (align) {
- case ALIGN_CENTER:
- boxXY[0] = xCenter - boxWidth / 2;
- break;
- case ALIGN_RIGHT:
- boxXY[0] = xRight - boxWidth;
- }
-
- // set box Y from alignments
-
- boxXY[1] = 0;
- switch (valign) {
- case VALIGN_TOP:
- break;
- case VALIGN_MIDDLE:
- boxXY[1] = windowHeight / 2;
- break;
- case VALIGN_BOTTOM:
- boxXY[1] = windowHeight;
- break;
- default:
- float y = (movableYPercent != Integer.MAX_VALUE ? movableYPercent
- * windowHeight / 100 : is3dEcho? movableY : movableY * scale);
- float offsetY = this.offsetY * scale;
- boxXY[1] = (is3dEcho ? y : (windowHeight - y)) + offsetY;
- //System.out.println(" movableY = " + movableY + " offsetY = " + offsetY + " boxXY[1]=" + boxXY[1]);
- }
- }
-
- protected static void setPosition(float boxWidth, float boxHeight,
- float xOffset, float yOffset, float[] boxXY) {
- float xBoxOffset, yBoxOffset;
-
- // these are based on a standard |_ grid, so y is reversed.
- if (xOffset > 0) {
- xBoxOffset = xOffset;
- } else {
- xBoxOffset = -boxWidth;
- if (xOffset == 0)
- xBoxOffset /= 2;
- else
- xBoxOffset += xOffset;
- }
-
- if (yOffset > 0) {
- yBoxOffset = yOffset;
- } else {
- if (yOffset == 0)
- yBoxOffset = -boxHeight / 2 - 2;
- else
- yBoxOffset = -boxHeight + yOffset;
- }
-
- boxXY[0] += xBoxOffset;
- boxXY[1] += yBoxOffset;
-
- }
-
protected void setBoxOffsetsInWindow(float margin, float vMargin, float vTop) {
// not labels
Modified: trunk/Jmol/src/org/jmol/shape/Text.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/Text.java 2008-09-03 19:09:59 UTC (rev 9847)
+++ trunk/Jmol/src/org/jmol/shape/Text.java 2008-09-06 14:32:48 UTC (rev 9848)
@@ -148,6 +148,7 @@
textWidth = textHeight = 0;
boxWidth = image.getWidth(null) * fontScale;
boxHeight = image.getHeight(null) * fontScale;
+ ascent = 0;
return;
}
if (text == null) {
@@ -193,8 +194,6 @@
* imageFontScaling, boxXY);
} else {
setPosition(fontScale);
- if (xyz != null) //3d echo
- boxXY[1] -= (align == ALIGN_CENTER ? boxHeight : ascent) / 2;
}
boxX = boxXY[0];
boxY = boxXY[1];
@@ -202,7 +201,7 @@
// adjust positions if necessary
if (adjustForWindow)
- setBoxOffsetsInWindow(image == null ? fontScale * 5 : 0, isLabelOrHover ? 16
+ setBoxOffsetsInWindow(/*image == null ? fontScale * 5 :*/ 0, isLabelOrHover ? 16
* fontScale + lineHeight : 0, boxY - textHeight);
// draw the box if necessary
@@ -250,6 +249,94 @@
drawPointer(g3d);
}
+ private void setPosition(float scale) {
+ float xLeft, xCenter, xRight;
+ boolean is3dEcho = (xyz != null);
+ if (valign == VALIGN_XY || valign == VALIGN_XYZ) {
+ float x = (movableXPercent != Integer.MAX_VALUE ? movableXPercent
+ * windowWidth / 100 : is3dEcho ? movableX : movableX * scale);
+ float offsetX = this.offsetX * scale;
+ xLeft = xRight = xCenter = x + offsetX;
+ //System.out.print("movableX = " + movableX + " offsetX = " + offsetX);
+ } else {
+ xLeft = 5 * scale;
+ xCenter = windowWidth / 2;
+ xRight = windowWidth - xLeft;
+ }
+
+ // set box X from alignments
+
+ boxXY[0] = xLeft;
+ switch (align) {
+ case ALIGN_CENTER:
+ boxXY[0] = xCenter - boxWidth / 2;
+ break;
+ case ALIGN_RIGHT:
+ boxXY[0] = xRight - boxWidth;
+ }
+
+ // set box Y from alignments
+
+ boxXY[1] = 0;
+ switch (valign) {
+ case VALIGN_TOP:
+ break;
+ case VALIGN_MIDDLE:
+ boxXY[1] = windowHeight / 2;
+ break;
+ case VALIGN_BOTTOM:
+ boxXY[1] = windowHeight;
+ break;
+ default:
+ float y = (movableYPercent != Integer.MAX_VALUE ? movableYPercent
+ * windowHeight / 100 : is3dEcho ? movableY : movableY * scale);
+ boxXY[1] = (is3dEcho ? y : (windowHeight - y)) + offsetY * scale;
+ }
+
+ System.out.print("boxXY[1]=" + boxXY[1]);
+ if (align == ALIGN_CENTER)
+ boxXY[1] -= (image != null ? boxHeight : xyz != null ? boxHeight
+ : ascent - boxHeight) / 2;
+ else if (image != null)
+ boxXY[1] -= 0;
+ else if (xyz != null)
+ boxXY[1] -= ascent / 2;
+
+ System.out.println(" movableY = " + movableY + " offsetY = " + offsetY
+ + " boxXY[1]=" + boxXY[1] + " boxHeight=" + boxHeight + " ascent="
+ + ascent + " " + text);
+
+ }
+
+ private static void setPosition(float boxWidth, float boxHeight,
+ float xOffset, float yOffset, float[] boxXY) {
+ float xBoxOffset, yBoxOffset;
+
+ // these are based on a standard |_ grid, so y is reversed.
+ if (xOffset > 0) {
+ xBoxOffset = xOffset;
+ } else {
+ xBoxOffset = -boxWidth;
+ if (xOffset == 0)
+ xBoxOffset /= 2;
+ else
+ xBoxOffset += xOffset;
+ }
+
+ if (yOffset > 0) {
+ yBoxOffset = yOffset;
+ } else {
+ if (yOffset == 0)
+ yBoxOffset = -boxHeight / 2 - 2;
+ else
+ yBoxOffset = -boxHeight + yOffset;
+ }
+
+ boxXY[0] += xBoxOffset;
+ boxXY[1] += yBoxOffset;
+
+ }
+
private static void showBox(JmolRendererInterface g3d, short colix,
short bgcolix, int x, int y, int z, int zSlab,
int boxWidth, int boxHeight,
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-09-03 19:09:59 UTC (rev 9847)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-09-06 14:32:48 UTC (rev 9848)
@@ -3,7 +3,7 @@
version=11.6.RC13_dev
-
+# bug fix: y-offset for echo text and images
# bug fix/new feature: HIDE/DiSPLAY/DELETE/COLOR $*xxx* extended to ECHO
# bug fix: findbugs input stream closure
# translation: add GT.escapeHTML and stricter checking for special characters in file names
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-09-07 04:09:35
|
Revision: 9852
http://jmol.svn.sourceforge.net/jmol/?rev=9852&view=rev
Author: hansonr
Date: 2008-09-07 04:09:32 +0000 (Sun, 07 Sep 2008)
Log Message:
-----------
version=11.6.RC14_dev # bug fix: ramachandran and quaternion derivative not indicating structure due to dropping last atom
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
trunk/Jmol/src/org/jmol/modelset/Polymer.java
trunk/Jmol/src/org/jmol/modelsetbio/AminoPolymer.java
trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java
trunk/Jmol/src/org/jmol/modelsetbio/NucleicPolymer.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2008-09-06 18:22:34 UTC (rev 9851)
+++ trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2008-09-07 04:09:32 UTC (rev 9852)
@@ -889,7 +889,7 @@
Model model = models[i];
int nPoly = model.getBioPolymerCount();
for (int p = 0; p < nPoly; p++)
- model.bioPolymers[p].getPdbData('s','p', 2, false, null, null, null, null, false);
+ model.bioPolymers[p].getPdbData('s','p', 2, false, null, null, null, null, false, new BitSet());
}
}
@@ -989,14 +989,15 @@
: type.length() > 13 && type.indexOf("ramachandran ") >= 0 ?
type.charAt(13) : 'R');
int derivType = (type.indexOf("diff") < 0 ? 0 : type.indexOf("2") < 0 ? 1 : 2);
- boolean isDraw = (type.indexOf("draw") >= 0);
+ boolean isDraw = (type.indexOf("draw") >= 0);
BitSet bsAtoms = getModelAtomBitSet(modelIndex, false);
int nPoly = model.getBioPolymerCount();
StringBuffer pdbATOM = new StringBuffer();
StringBuffer pdbCONECT = new StringBuffer();
+ BitSet bsWritten = new BitSet();
for (int p = 0; p < nPoly; p++)
model.bioPolymers[p].getPdbData(ctype, qtype, derivType, isDraw,
- bsAtoms, pdbATOM, pdbCONECT, bsSelected, p == 0);
+ bsAtoms, pdbATOM, pdbCONECT, bsSelected, p == 0, bsWritten);
pdbATOM.append(pdbCONECT);
String s = pdbATOM.toString();
if (isDraw || s.length() == 0)
@@ -1005,7 +1006,8 @@
if (ctype != 'R')
remark += " quaternionFrame = \"" + qtype + "\"";
remark += "\nREMARK 6 Jmol Version " + Viewer.getJmolVersion();
- remark += "\n\n" + getProteinStructureState(bsAtoms, false, ctype == 'R');
+ bsSelected.and(bsAtoms);
+ remark += "\n\n" + getProteinStructureState(bsWritten, false, ctype == 'R');
return remark + s;
}
Modified: trunk/Jmol/src/org/jmol/modelset/Polymer.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Polymer.java 2008-09-06 18:22:34 UTC (rev 9851)
+++ trunk/Jmol/src/org/jmol/modelset/Polymer.java 2008-09-07 04:09:32 UTC (rev 9852)
@@ -105,7 +105,8 @@
public void getPdbData(char ctype, char qtype, int derivType,
boolean isDraw, BitSet bsAtoms, StringBuffer pdbATOM,
- StringBuffer pdbCONECT, BitSet bsSelected, boolean addHeader) {
+ StringBuffer pdbCONECT, BitSet bsSelected, boolean addHeader,
+ BitSet bsWritten) {
return;
}
}
Modified: trunk/Jmol/src/org/jmol/modelsetbio/AminoPolymer.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/AminoPolymer.java 2008-09-06 18:22:34 UTC (rev 9851)
+++ trunk/Jmol/src/org/jmol/modelsetbio/AminoPolymer.java 2008-09-07 04:09:32 UTC (rev 9852)
@@ -540,9 +540,9 @@
public void getPdbData(char ctype, char qtype, int derivType,
boolean isDraw, BitSet bsAtoms,
StringBuffer pdbATOM, StringBuffer pdbCONECT,
- BitSet bsSelected, boolean addHeader) {
+ BitSet bsSelected, boolean addHeader, BitSet bsWritten) {
getPdbData(this, ctype, qtype, derivType, isDraw, bsAtoms, pdbATOM,
- pdbCONECT, bsSelected, addHeader);
+ pdbCONECT, bsSelected, addHeader, bsWritten);
}
}
Modified: trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java 2008-09-06 18:22:34 UTC (rev 9851)
+++ trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java 2008-09-07 04:09:32 UTC (rev 9852)
@@ -472,8 +472,8 @@
final public static void getPdbData(BioPolymer p, char ctype, char qtype,
int derivType, boolean isDraw,
BitSet bsAtoms, StringBuffer pdbATOM,
- StringBuffer pdbCONECT,
- BitSet bsSelected, boolean addHeader) {
+ StringBuffer pdbCONECT, BitSet bsSelected,
+ boolean addHeader, BitSet bsWritten) {
int atomno = Integer.MIN_VALUE;
boolean isRamachandran = (ctype == 'R');
if (isRamachandran && !p.calcPhiPsiAngles())
@@ -558,7 +558,6 @@
pdbATOM.append(" NHX_______ NHY_______ NHZ_______");
pdbATOM.append("\n\n");
}
-
for (int m = 0; m < p.monomerCount; m++) {
Monomer monomer = p.monomers[m];
if (bsAtoms == null || bsAtoms.get(monomer.getLeadAtomIndex())) {
@@ -575,8 +574,10 @@
if (z < -90)
z += 360;
z -= 180; // center on 0
- if (Float.isNaN(x) || Float.isNaN(y) || Float.isNaN(z))
+ if (Float.isNaN(x) || Float.isNaN(y) || Float.isNaN(z)) {
+ bsAtoms.clear(a.getAtomIndex());
continue;
+ }
if (isDraw) {
if (bsSelected != null && !bsSelected.get(a.getAtomIndex()))
continue;
@@ -785,6 +786,7 @@
pdbCONECT.append(TextFormat.formatString("%5i", "i", a
.getAtomNumber()));
pdbCONECT.append('\n');
+ bsWritten.set(((Monomer)a.getGroup()).getLeadAtomIndex());
}
atomno = a.getAtomNumber();
}
Modified: trunk/Jmol/src/org/jmol/modelsetbio/NucleicPolymer.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/NucleicPolymer.java 2008-09-06 18:22:34 UTC (rev 9851)
+++ trunk/Jmol/src/org/jmol/modelsetbio/NucleicPolymer.java 2008-09-07 04:09:32 UTC (rev 9852)
@@ -93,8 +93,8 @@
public void getPdbData(char ctype, char qtype, int derivType,
boolean isDraw, BitSet bsAtoms,
StringBuffer pdbATOM, StringBuffer pdbCONECT,
- BitSet bsSelected, boolean addHeader) {
+ BitSet bsSelected, boolean addHeader, BitSet bsWritten) {
getPdbData(this, ctype, qtype, derivType, isDraw, bsAtoms, pdbATOM,
- pdbCONECT, bsSelected, addHeader);
+ pdbCONECT, bsSelected, addHeader, bsWritten);
}
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-09-06 18:22:34 UTC (rev 9851)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-09-07 04:09:32 UTC (rev 9852)
@@ -3,6 +3,7 @@
version=11.6.RC14_dev
+# bug fix: ramachandran and quaternion derivative not indicating structure due to dropping last atom
# -----------------------------------------------------------------------------
#version=11.6.RC13
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-09-11 19:10:42
|
Revision: 9869
http://jmol.svn.sourceforge.net/jmol/?rev=9869&view=rev
Author: hansonr
Date: 2008-09-11 19:10:37 +0000 (Thu, 11 Sep 2008)
Log Message:
-----------
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/export/_Exporter.java
trunk/Jmol/src/org/jmol/shape/Text.java
Modified: trunk/Jmol/src/org/jmol/export/_Exporter.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/_Exporter.java 2008-09-11 19:10:04 UTC (rev 9868)
+++ trunk/Jmol/src/org/jmol/export/_Exporter.java 2008-09-11 19:10:37 UTC (rev 9869)
@@ -181,8 +181,7 @@
commandLineOptions = fileName.substring(pt + 3);
fileName = fileName.substring(0, pt);
}
- viewer.createImage(fileName + ".spt", viewer.getSavedState("_Export"),
- Integer.MIN_VALUE, 0, 0);
+ viewer.writeTextFile(fileName + ".spt", viewer.getSavedState("_Export"));
try {
os = new FileOutputStream(fileName);
bw = new BufferedWriter(new OutputStreamWriter(os));
Modified: trunk/Jmol/src/org/jmol/shape/Text.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/Text.java 2008-09-11 19:10:04 UTC (rev 9868)
+++ trunk/Jmol/src/org/jmol/shape/Text.java 2008-09-11 19:10:37 UTC (rev 9869)
@@ -293,7 +293,7 @@
boxXY[1] = (is3dEcho ? y : (windowHeight - y)) + offsetY * scale;
}
- System.out.print("boxXY[1]=" + boxXY[1]);
+ //System.out.print("boxXY[1]=" + boxXY[1]);
if (align == ALIGN_CENTER)
boxXY[1] -= (image != null ? boxHeight : xyz != null ? boxHeight
: ascent - boxHeight) / 2;
@@ -302,9 +302,9 @@
else if (xyz != null)
boxXY[1] -= ascent / 2;
- System.out.println(" movableY = " + movableY + " offsetY = " + offsetY
- + " boxXY[1]=" + boxXY[1] + " boxHeight=" + boxHeight + " ascent="
- + ascent + " " + text);
+ //System.out.println(" movableY = " + movableY + " offsetY = " + offsetY
+ // + " boxXY[1]=" + boxXY[1] + " boxHeight=" + boxHeight + " ascent="
+ //+ ascent + " " + text);
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-09-15 03:55:34
|
Revision: 9893
http://jmol.svn.sourceforge.net/jmol/?rev=9893&view=rev
Author: hansonr
Date: 2008-09-15 03:55:18 +0000 (Mon, 15 Sep 2008)
Log Message:
-----------
11.6.RC15 VERSION
# new feature: load menu items for signed applet
# new feature: save menu items for signed applet
# bug fix: applet -- setting a jmolScript callback prevents menu updates
# new feature: minimize menu item
# new feature: signed applet allows "load ?" and includes previewer
# bug fix: H-M spacegroup designations specifying nonstandard Hall symbols by default
# new feature: signed applet/application load ?xxx uses load dialog
# webexport help updated to reflect ability to handle files opened with "load append"
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/export/dialog/Dialog.java
trunk/Jmol/src/org/jmol/export/dialog/FilePreview.java
trunk/Jmol/src/org/jmol/popup/PopupResourceBundle.java
trunk/Jmol/src/org/jmol/viewer/FileManager.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/export/dialog/Dialog.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/dialog/Dialog.java 2008-09-14 23:54:12 UTC (rev 9892)
+++ trunk/Jmol/src/org/jmol/export/dialog/Dialog.java 2008-09-15 03:55:18 UTC (rev 9893)
@@ -47,6 +47,7 @@
import org.jmol.api.JmolViewer;
import org.jmol.i18n.GT;
import org.jmol.util.Escape;
+import org.jmol.util.TextFormat;
import org.jmol.viewer.FileManager;
public class Dialog extends JPanel implements JmolDialogInterface {
@@ -87,11 +88,20 @@
openChooser.setDialogSize(historyFile.getWindowSize(windowName));
openChooser.setDialogLocation(historyFile.getWindowPosition(windowName));
}
+
- if (fileName != null && fileName.length() > 0)
- openChooser.setSelectedFile(new File(fileName));
- if (fileName != null && fileName.indexOf(":") < 0)
- openChooser.setCurrentDirectory(FileManager.getLocalDirectory(viewer));
+ if (fileName != null) {
+ int pt = fileName.lastIndexOf(".");
+ String sType = fileName.substring(pt + 1);
+ if (pt >= 0 && sType.length() > 0)
+ openChooser.addChoosableFileFilter(new TypeFilter(sType));
+ if (fileName.indexOf(".") == 0)
+ fileName = "Jmol" + fileName;
+ if (fileName.length() > 0)
+ openChooser.setSelectedFile(new File(fileName));
+ if ( fileName.indexOf(":") < 0)
+ openChooser.setCurrentDirectory(FileManager.getLocalDirectory(viewer));
+ }
File file = null;
if (openChooser.showOpenDialog(this) == JFileChooser.APPROVE_OPTION)
file = openChooser.getSelectedFile();
@@ -101,7 +111,7 @@
if (historyFile != null)
historyFile.addWindowInfo(windowName, openChooser.getDialog(), null);
- String url = FileManager.getLocalUrl(file.getAbsolutePath());
+ String url = getLocalUrl(file);
if (url != null) {
fileName = url;
} else {
@@ -113,6 +123,33 @@
return (doAppend ? "load append " + Escape.escape(fileName) : fileName);
}
+ private final static String[] urlPrefixes = {
+ "http:", "http://",
+ "www.", "http://www.",
+ "https:", "https://",
+ "ftp:", "ftp://",
+ "file:", "file:///"};
+
+ private static String getLocalUrl(File file) {
+ // entering a url on a file input box will be accepted,
+ // but cause an error later. We can fix that...
+ // return null if there is no problem, the real url if there is
+ if (file.getName().startsWith("="))
+ return file.getName();
+ String path = file.getAbsolutePath().replace('\\', '/');
+ for (int i = 0; i < urlPrefixes.length; i++)
+ if (path.indexOf(urlPrefixes[i]) == 0)
+ return null;
+ for (int i = 0; i < urlPrefixes.length; i += 2)
+ if (path.indexOf(urlPrefixes[i]) > 0)
+ return urlPrefixes[i + 1]
+ + TextFormat.trim(path.substring(
+ path.indexOf(urlPrefixes[i]) + urlPrefixes[i].length())
+ , "/");
+ return null;
+ }
+
+
public String getSaveFileNameFromDialog(JmolViewer viewer, String fileName,
String type) {
if (saveChooser == null)
Modified: trunk/Jmol/src/org/jmol/export/dialog/FilePreview.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/dialog/FilePreview.java 2008-09-14 23:54:12 UTC (rev 9892)
+++ trunk/Jmol/src/org/jmol/export/dialog/FilePreview.java 2008-09-15 03:55:18 UTC (rev 9893)
@@ -125,6 +125,7 @@
*/
void updatePreview(File file) {
if (file != null) {
+ //doesn't update from use input?
display.getViewer().evalStringQuiet("load \"" + file.getAbsolutePath() + "\"");
display.repaint();
} else {
Modified: trunk/Jmol/src/org/jmol/popup/PopupResourceBundle.java
===================================================================
--- trunk/Jmol/src/org/jmol/popup/PopupResourceBundle.java 2008-09-14 23:54:12 UTC (rev 9892)
+++ trunk/Jmol/src/org/jmol/popup/PopupResourceBundle.java 2008-09-15 03:55:18 UTC (rev 9893)
@@ -75,10 +75,10 @@
{ "@AXESCOLOR", "gray salmon maroon olive slateblue gold orchid"},
{ "popupMenu",
- "modelSetMenu FRAMESbyModelComputedMenu configurationComputedMenu - selectMenuText viewMenu renderMenu colorMenu - surfaceMenu SYMMETRYUNITCELLMenu - "
+ "modelSetMenu SIGNEDloadMenu SIGNEDwriteMenu FRAMESbyModelComputedMenu configurationComputedMenu - selectMenuText viewMenu renderMenu colorMenu - surfaceMenu SYMMETRYUNITCELLMenu - "
+ "zoomMenu spinMenu VIBRATIONMenu "
+ "FRAMESanimateMenu - "
- + "measureMenu pickingMenu - JVM12showConsole JVM12showMenu SIGNEDwriteMenu - "
+ + "measureMenu pickingMenu - JVM12showConsole JVM12showMenu - "
+ "languageComputedMenu aboutComputedMenu" },
{ "selectMenuText",
@@ -212,8 +212,11 @@
+ "showSpacegroup showState SYMMETRYshowSymmetry UNITCELLshow - showIsosurface showMo - extractMOL" },
+ { "SIGNEDloadMenu",
+ "loadPdb loadFileOrURL loadFileUnitCell - loadScript" },
+
{ "SIGNEDwriteMenu",
- "writeFileTextVARIABLE writeState writeHistory writeIsosurface - writeJpg writePng - writePovray writeVrml writeMaya" },
+ "writeFileTextVARIABLE writeState writeHistory - writeJpg writePng writePovray - writeIsosurface writeVrml writeMaya" },
{ "[set_spin_X]Menu", "s0 s5 s10 s20 s30 s40 s50" },
@@ -476,6 +479,12 @@
{ "showOrient", "console on;show orientation" },
{ "showSpacegroup", "console on;show spacegroup" },
{ "showState", "console on;show state" },
+
+ { "loadPdb", "load ?=1crn" },
+ { "loadFileOrURL", "load ?" },
+ { "loadFileUnitCell", "load ? {1 1 1}" },
+ { "loadScript", "script ?.spt" },
+
{ "writeFileTextVARIABLE", "write file \"?FILE?\"" },
{ "writeState", "write state \"?FILEROOT?.spt\"" },
{ "writeHistory", "write history \"?FILEROOT?.his\"" },
@@ -860,16 +869,22 @@
"SYMMETRYshowSymmetry", GT._("Symmetry"),
"showState", GT._("Current state"),
- "SIGNEDwriteMenu", GT._("Write"),
+ "SIGNEDloadMenu", GT._("Load"),
+ "loadPdb", GT._("Load PDB"),
+ "loadFileOrURL", GT._("Load file or URL"),
+ "loadFileUnitCell", GT._("Load full unit cell"),
+ "loadScript", GT._("Script"),
+
+ "SIGNEDwriteMenu", GT._("Save"),
"writeFileTextVARIABLE", GT._("File {0}"),
- "writeState", GT._("State"),
- "writeHistory", GT._("History"),
- "writeIsosurface", GT._("Isosurface"),
- "writeJpg", GT._("Image - JPG"),
- "writePng", GT._("Image - PNG"),
- "writePovray", "POV-Ray",
- "writeVrml", GT._("VRML"),
- "writeMaya", GT._("Maya"),
+ "writeState", GT._("SPT State"),
+ "writeHistory", GT._("SPT History"),
+ "writeJpg", GT._("{0} Image", "JPG"),
+ "writePng", GT._("{0} Image", "PNG"),
+ "writePovray", GT._("{0} Image", "POV-Ray"),
+ "writeIsosurface", GT._("JVXL Isosurface"),
+ "writeVrml", GT._("{0} 3D Model", "VRML"),
+ "writeMaya", GT._("{0} 3D Model", "Maya"),
"UNITCELLshow", GT._("Unit cell"),
Modified: trunk/Jmol/src/org/jmol/viewer/FileManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/FileManager.java 2008-09-14 23:54:12 UTC (rev 9892)
+++ trunk/Jmol/src/org/jmol/viewer/FileManager.java 2008-09-15 03:55:18 UTC (rev 9893)
@@ -515,18 +515,6 @@
return -1;
}
- public static String getLocalUrl(String path) {
- // entering a url on a file input box will be accepted,
- // but cause an error later. We can fix that...
- // return null if there is no problem, the real url if there is
- if (urlTypeIndex(path) < 0)
- for (int i = 0; i < urlPrefixes.length; ++i)
- if (path.indexOf(urlPrefixes[i]) >= 0)
- return TextFormat.simpleReplace(path.substring(path.indexOf(urlPrefixes[i]))
- .replace('\\', '/'), ":", ":/");
- return null;
- }
-
private void setNames(String[] names) {
if (names == null)
return;
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-09-14 23:54:12 UTC (rev 9892)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-09-15 03:55:18 UTC (rev 9893)
@@ -1,16 +1,18 @@
# Developers: to add a description of changes you have made,
# add it on a line starting with # below the "version=..." line
-version=11.6.RC15_dev
+version=11.6.RC15
+# new feature: load menu items for signed applet
+# new feature: save menu items for signed applet
# bug fix: applet -- setting a jmolScript callback prevents menu updates
-# new feature: write menu items for signed applet
# new feature: minimize menu item
# new feature: signed applet allows "load ?" and includes previewer
# bug fix: H-M spacegroup designations specifying nonstandard Hall symbols by default
# new feature: signed applet/application load ?xxx uses load dialog
# webexport help updated to reflect ability to handle files opened with "load append"
+
# -----------------------------------------------------------------------------
#version=11.6.RC14
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-09-15 10:59:30
|
Revision: 9895
http://jmol.svn.sourceforge.net/jmol/?rev=9895&view=rev
Author: hansonr
Date: 2008-09-15 10:59:26 +0000 (Mon, 15 Sep 2008)
Log Message:
-----------
threads
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/applet/Jmol.java
trunk/Jmol/src/org/jmol/applet/Jvm12.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/applet/Jmol.java
===================================================================
--- trunk/Jmol/src/org/jmol/applet/Jmol.java 2008-09-15 05:51:23 UTC (rev 9894)
+++ trunk/Jmol/src/org/jmol/applet/Jmol.java 2008-09-15 10:59:26 UTC (rev 9895)
@@ -1239,7 +1239,7 @@
public String dialogAsk(String type, String data) {
if (!isSigned || jvm12 == null)
return null;
- return jvm12.dialogAsk(null, type, data);
+ return jvm12.dialogAsk(type, data);
}
}
Modified: trunk/Jmol/src/org/jmol/applet/Jvm12.java
===================================================================
--- trunk/Jmol/src/org/jmol/applet/Jvm12.java 2008-09-15 05:51:23 UTC (rev 9894)
+++ trunk/Jmol/src/org/jmol/applet/Jvm12.java 2008-09-15 10:59:26 UTC (rev 9895)
@@ -24,13 +24,16 @@
package org.jmol.applet;
import java.awt.*;
+import java.lang.reflect.InvocationTargetException;
+import javax.swing.SwingUtilities;
+
import org.jmol.api.*;
import org.jmol.util.Logger;
class Jvm12 {
- private JmolViewer viewer;
+ protected JmolViewer viewer;
JmolAdapter modelAdapter;
private Component awtComponent;
Console console;
@@ -94,8 +97,8 @@
return console.getText();
}
- final private static String[] imageChoices = { "JPEG", "PNG", "GIF", "PPM" };
- final private static String[] imageExtensions = { "jpg", "png", "gif", "PPM" };
+ final protected static String[] imageChoices = { "JPEG", "PNG", "GIF", "PPM" };
+ final protected static String[] imageExtensions = { "jpg", "png", "gif", "PPM" };
static JmolDialogInterface newDialog(boolean forceNewTranslation) {
JmolDialogInterface sd = (JmolDialogInterface) Interface
@@ -104,56 +107,74 @@
return sd;
}
- public String dialogAsk(JmolDialogInterface sd, String type,
- String fileName) {
- if (type.equals("load"))
- return getOpenFileNameFromDialog(fileName);
- if (sd == null)
- sd = newDialog(false);
- if (type.equals("save")) {
- return sd.getSaveFileNameFromDialog(viewer, fileName, null);
+ String inputFileName;
+ String outputFileName;
+ String dialogType;
+
+ public String dialogAsk(String type, String fileName) {
+ inputFileName = fileName;
+ dialogType = type;
+ System.out.println(Thread.currentThread().getName());
+ try {
+ SwingUtilities.invokeAndWait(new Runnable() {
+ public void run() {
+ if (dialogType.equals("load")) {
+ outputFileName = newDialog(false).getOpenFileNameFromDialog(
+ modelAdapter, viewer, inputFileName, null, null, false);
+ return;
+ }
+ JmolDialogInterface sd = newDialog(false);
+ if (dialogType.equals("save")) {
+ outputFileName = sd.getSaveFileNameFromDialog(viewer,
+ inputFileName, null);
+ return;
+ }
+ if (dialogType.startsWith("saveImage")) {
+ outputFileName = sd.getImageFileNameFromDialog(viewer,
+ inputFileName, imageType, imageChoices, imageExtensions,
+ qualityJPG, qualityPNG);
+ qualityJPG = sd.getQuality("JPG");
+ qualityPNG = sd.getQuality("PNG");
+ String sType = sd.getType();
+ if (sType != null)
+ imageType = sType;
+ int iQuality = sd.getQuality(sType);
+ if (iQuality > 0)
+ imageQuality = iQuality;
+ return;
+ }
+ outputFileName = null;
+ }
+ });
+ } catch (InterruptedException e) {
+ System.out.println(e.getMessage());
+ } catch (InvocationTargetException e) {
+ System.out.println(e.getMessage());
}
- if (type.startsWith("saveImage")) {
- return sd.getImageFileNameFromDialog(viewer, fileName,
- imageType, imageChoices, imageExtensions, qualityJPG, qualityPNG);
- }
- return null;
+ return outputFileName;
}
- public String getOpenFileNameFromDialog(String fileName) {
- return newDialog(false).getOpenFileNameFromDialog(modelAdapter, viewer, fileName, null, null, false);
- }
-
int qualityJPG = -1;
int qualityPNG = -1;
String imageType;
+ int imageQuality;
String createImage(String fileName, String type, Object text_or_bytes,
int quality) {
- String sType = null;
- int iQuality = quality;
if (quality == Integer.MIN_VALUE) {
// text or bytes
- fileName = dialogAsk(null, "save", fileName);
+ fileName = dialogAsk("save", fileName);
} else {
- // image
- JmolDialogInterface sd = newDialog(false);
- fileName = dialogAsk(sd, "saveImage+" + type, fileName);
- qualityJPG = sd.getQuality("JPG");
- qualityPNG = sd.getQuality("PNG");
- sType = imageType = sd.getType();
- if (sType == null)
- sType = type.toUpperCase();
- iQuality = sd.getQuality(sType);
- if (iQuality < 0)
- iQuality = quality;
+ imageType = type.toUpperCase();
+ imageQuality = quality;
+ fileName = dialogAsk("saveImage+" + type, fileName);
}
if (fileName == null)
return null;
JmolImageCreatorInterface c = (JmolImageCreatorInterface) Interface
.getOptionInterface("export.image.ImageCreator");
c.setViewer(viewer);
- return c.createImage(fileName, sType, text_or_bytes, iQuality);
+ return c.createImage(fileName, imageType, text_or_bytes, imageQuality);
}
void clipImage() {
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-09-15 05:51:23 UTC (rev 9894)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-09-15 10:59:26 UTC (rev 9895)
@@ -1,7 +1,7 @@
# Developers: to add a description of changes you have made,
# add it on a line starting with # below the "version=..." line
-version=11.6.RC15
+version=11.6.RC15_b
# new feature: load menu items for signed applet
# new feature: save menu items for signed applet
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-09-15 12:00:48
|
Revision: 9897
http://jmol.svn.sourceforge.net/jmol/?rev=9897&view=rev
Author: hansonr
Date: 2008-09-15 12:00:35 +0000 (Mon, 15 Sep 2008)
Log Message:
-----------
threading, debug comments
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/applet/Jmol.java
trunk/Jmol/src/org/jmol/applet/Jvm12.java
trunk/Jmol/src/org/jmol/export/dialog/Dialog.java
trunk/Jmol/src/org/jmol/export/dialog/FilePreview.java
trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
trunk/Jmol/src/org/jmol/symmetry/SymmetryOperation.java
trunk/Jmol/src/org/jmol/symmetry/UnitCell.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/applet/Jmol.java
===================================================================
--- trunk/Jmol/src/org/jmol/applet/Jmol.java 2008-09-15 11:16:04 UTC (rev 9896)
+++ trunk/Jmol/src/org/jmol/applet/Jmol.java 2008-09-15 12:00:35 UTC (rev 9897)
@@ -244,7 +244,7 @@
// viewer = new JmolViewer(this, new CdkJmolAdapter(null));
viewer = JmolViewer.allocateViewer(appletWrapper,
modelAdapter = new SmarterJmolAdapter());
- String options = "";
+ String options = "-applet";
isSigned = getBooleanValue("signed", false) || appletWrapper.isSigned();
if (isSigned)
options += "-signed";
Modified: trunk/Jmol/src/org/jmol/applet/Jvm12.java
===================================================================
--- trunk/Jmol/src/org/jmol/applet/Jvm12.java 2008-09-15 11:16:04 UTC (rev 9896)
+++ trunk/Jmol/src/org/jmol/applet/Jvm12.java 2008-09-15 12:00:35 UTC (rev 9897)
@@ -116,7 +116,7 @@
public String dialogAsk(String type, String fileName) {
inputFileName = fileName;
dialogType = type;
- System.out.println(Thread.currentThread().getName());
+ System.out.println("Jvm12 thread: " + Thread.currentThread().getName());
try {
SwingUtilities.invokeAndWait(new Runnable() {
public void run() {
Modified: trunk/Jmol/src/org/jmol/export/dialog/Dialog.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/dialog/Dialog.java 2008-09-15 11:16:04 UTC (rev 9896)
+++ trunk/Jmol/src/org/jmol/export/dialog/Dialog.java 2008-09-15 12:00:35 UTC (rev 9897)
@@ -130,7 +130,7 @@
"http://www.", "https:", "https://", "ftp:", "ftp://", "file:",
"file:///" };
- private static String getLocalUrl(File file) {
+ static String getLocalUrl(File file) {
// entering a url on a file input box will be accepted,
// but cause an error later. We can fix that...
// return null if there is no problem, the real url if there is
Modified: trunk/Jmol/src/org/jmol/export/dialog/FilePreview.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/dialog/FilePreview.java 2008-09-15 11:16:04 UTC (rev 9896)
+++ trunk/Jmol/src/org/jmol/export/dialog/FilePreview.java 2008-09-15 12:00:35 UTC (rev 9897)
@@ -126,9 +126,13 @@
*/
void updatePreview(File file) {
if (file != null) {
+ String fileName = file.getAbsolutePath();
+ String url = Dialog.getLocalUrl(file);
+ if (url != null)
+ fileName = url;
//doesn't update from use input?
display.getViewer().evalStringQuiet(
- "load \"" + file.getAbsolutePath() + "\"");
+ "zap;set echo top left;echo loading...;refresh;load \"" + fileName + "\"");
display.repaint();
} else {
display.getViewer().evalStringQuiet("zap");
Modified: trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2008-09-15 11:16:04 UTC (rev 9896)
+++ trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2008-09-15 12:00:35 UTC (rev 9897)
@@ -1350,10 +1350,10 @@
atoms[i].add(center);
} else {
ptTemp.add(atoms[i]);
- System.out.println((Point3f)atoms[i]);
+ //System.out.println((Point3f)atoms[i]);
matTemp.transform(atoms[i]);
ptTemp.sub(atoms[i]);
- System.out.println((Point3f)atoms[i]);
+ //System.out.println((Point3f)atoms[i]);
}
taint(i, TAINT_COORD);
n++;
Modified: trunk/Jmol/src/org/jmol/symmetry/SymmetryOperation.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/SymmetryOperation.java 2008-09-15 11:16:04 UTC (rev 9896)
+++ trunk/Jmol/src/org/jmol/symmetry/SymmetryOperation.java 2008-09-15 12:00:35 UTC (rev 9897)
@@ -164,9 +164,9 @@
if (i % 4 == 3)
v = normalizeTwelfths((v < 0 ? -1 : 1) * (int)(Math.abs(v) * 12.001f));
temp[i] = v;
- System.out.print(v + " ");
+ //System.out.print(v + " ");
}
- System.out.println();
+ //System.out.println();
return true;
}
Modified: trunk/Jmol/src/org/jmol/symmetry/UnitCell.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/UnitCell.java 2008-09-15 11:16:04 UTC (rev 9896)
+++ trunk/Jmol/src/org/jmol/symmetry/UnitCell.java 2008-09-15 12:00:35 UTC (rev 9897)
@@ -280,7 +280,7 @@
: 1 );
// types 6 and 7 not supported
- System.out.println("ortep type " + ortepType + " isFractional=" + isFractional + " D = " + dd + " C=" + cc);
+ //System.out.println("ortep type " + ortepType + " isFractional=" + isFractional + " D = " + dd + " C=" + cc);
double B11 = parBorU[0] * dd * (isFractional ? a_ * a_ : 1);
double B22 = parBorU[1] * dd * (isFractional ? b_ * b_ : 1);
double B33 = parBorU[2] * dd * (isFractional ? c_ * c_ : 1);
@@ -307,7 +307,7 @@
* c * cB_ * B13;
Bcart[5] = 2 * c * c * cA_ * cB_ * B33 + b * c * cB_ * sinGamma * B23;
- System.out.println("UnitCell Bcart="+Bcart[0] + " " + Bcart[1] + " " + Bcart[2] + " " + Bcart[3] + " " + Bcart[4] + " " + Bcart[5]);
+ //System.out.println("UnitCell Bcart="+Bcart[0] + " " + Bcart[1] + " " + Bcart[2] + " " + Bcart[3] + " " + Bcart[4] + " " + Bcart[5]);
Vector3f unitVectors[] = new Vector3f[3];
for (int i = 0; i < 3; i++)
unitVectors[i] = new Vector3f();
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-09-15 11:16:04 UTC (rev 9896)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-09-15 12:00:35 UTC (rev 9897)
@@ -273,9 +273,9 @@
htmlName = (i < 0 ? fullName : fullName.substring(0, i));
syncId = (i < 0 ? "" : fullName
.substring(i + 1, fullName.length() - 1));
- isApplet = (documentBase != null);
String str = "" + commandOptions;
+ isApplet = (commandOptions.indexOf("-applet") >= 0);
if (isApplet) {
Logger.info("applet context: " + commandOptions);
String appletProxy = null;
@@ -293,7 +293,6 @@
scriptManager.startCommandWatcher(true);
} else {
// not an applet -- used to pass along command line options
- isPreviewOnly = (str.indexOf("#previewOnly") >= 0);
g3d.setBackgroundTransparent(str.indexOf("-b") >= 0);
isSilent = (str.indexOf("-i") >= 0);
if (isSilent)
@@ -314,6 +313,7 @@
}
mustRender = (haveDisplay || writeInfo != null);
}
+ isPreviewOnly = (str.indexOf("#previewOnly") >= 0);
setBooleanProperty("_applet", isApplet);
setBooleanProperty("_signedApplet", isSignedApplet);
setBooleanProperty("_useCommandThread", useCommandThread);
@@ -1989,7 +1989,7 @@
repaintManager.initializePointers(1);
setCurrentModelIndex(0);
setBackgroundModelIndex(-1);
- setFrankOn(!isPreviewOnly && getShowFrank());
+ setFrankOn(getShowFrank());
mouseManager.startHoverWatcher(!isPreviewOnly);
setTainted(true);
finalizeTransformParameters();
@@ -3420,7 +3420,7 @@
/// direct no-queue use:
public String scriptWait(String strScript) {
- System.out.println("Viewer scriptWait1 " + htmlName + " " + strScript + " ");
+ //System.out.println("Viewer scriptWait1 " + htmlName + " " + strScript + " ");
scriptManager.waitForQueue();
boolean doTranslateTemp = GT.getDoTranslate();
GT.setDoTranslate(false);
@@ -3432,7 +3432,7 @@
}
public Object scriptWaitStatus(String strScript, String statusList) {
- System.out.println("Viewer scriptWait2 " + htmlName + " " + strScript);
+ //System.out.println("Viewer scriptWait2 " + htmlName + " " + strScript);
scriptManager.waitForQueue();
boolean doTranslateTemp = GT.getDoTranslate();
GT.setDoTranslate(false);
@@ -3444,7 +3444,7 @@
public Object evalStringWaitStatus(String returnType, String strScript,
String statusList) {
- System.out.println("Viewer scriptWait3 " + htmlName + " " + strScript);
+ //System.out.println("Viewer scriptWait3 " + htmlName + " " + strScript);
scriptManager.waitForQueue();
return evalStringWaitStatus(returnType, strScript, statusList, false,
false, false);
@@ -5568,12 +5568,16 @@
boolean frankOn = true;
public void setFrankOn(boolean TF) {
- frankOn = TF && !isPreviewOnly;
+ if (isPreviewOnly)
+ TF = false;
+ frankOn = TF;
setObjectMad(JmolConstants.SHAPE_FRANK, "frank", (short) (TF ? 1 : 0));
}
public boolean getShowFrank() {
- return (!isApplet || !creatingImage) && (isSignedApplet || getObjectMad(StateManager.OBJ_FRANK) != 0);
+ if (isPreviewOnly || isApplet && creatingImage)
+ return false;
+ return (isSignedApplet || frankOn);
}
public boolean isSignedApplet() {
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-09-15 12:48:19
|
Revision: 9898
http://jmol.svn.sourceforge.net/jmol/?rev=9898&view=rev
Author: hansonr
Date: 2008-09-15 12:48:13 +0000 (Mon, 15 Sep 2008)
Log Message:
-----------
signed applet cancel dialog action
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/export/dialog/Dialog.java
trunk/Jmol/src/org/jmol/export/dialog/FilePreview.java
trunk/Jmol/src/org/jmol/viewer/FileManager.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/export/dialog/Dialog.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/dialog/Dialog.java 2008-09-15 12:00:35 UTC (rev 9897)
+++ trunk/Jmol/src/org/jmol/export/dialog/Dialog.java 2008-09-15 12:48:13 UTC (rev 9898)
@@ -108,8 +108,11 @@
File file = null;
if (openChooser.showOpenDialog(this) == JFileChooser.APPROVE_OPTION)
file = openChooser.getSelectedFile();
- if (file == null)
+ if (file == null) {
+ openChooser.setAccessory(null);
+ openPreview = null;
return null;
+ }
if (historyFile != null)
historyFile.addWindowInfo(windowName, openChooser.getDialog(), null);
@@ -122,6 +125,7 @@
fileName = file.getAbsolutePath();
}
boolean doAppend = (openPreview != null && openPreview.isAppendSelected());
+ openChooser.setAccessory(null);
openPreview = null;
return (doAppend ? "load append " + Escape.escape(fileName) : fileName);
}
Modified: trunk/Jmol/src/org/jmol/export/dialog/FilePreview.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/dialog/FilePreview.java 2008-09-15 12:00:35 UTC (rev 9897)
+++ trunk/Jmol/src/org/jmol/export/dialog/FilePreview.java 2008-09-15 12:48:13 UTC (rev 9898)
@@ -128,11 +128,14 @@
if (file != null) {
String fileName = file.getAbsolutePath();
String url = Dialog.getLocalUrl(file);
+ System.out.println("updatePreview + " + fileName + " " + url);
if (url != null)
fileName = url;
//doesn't update from use input?
display.getViewer().evalStringQuiet(
- "zap;set echo top left;echo loading...;refresh;load \"" + fileName + "\"");
+ "zap;set echo top left;echo loading...;refresh;"
+ + (fileName.indexOf(".spt") >= 0 ? "script" : "load")
+ + " \"" + fileName + "\"");
display.repaint();
} else {
display.getViewer().evalStringQuiet("zap");
Modified: trunk/Jmol/src/org/jmol/viewer/FileManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/FileManager.java 2008-09-15 12:00:35 UTC (rev 9897)
+++ trunk/Jmol/src/org/jmol/viewer/FileManager.java 2008-09-15 12:48:13 UTC (rev 9898)
@@ -526,8 +526,10 @@
if (name == null)
return null;
if (name.startsWith("?")
- && (name = viewer.dialogAsk("load", name.substring(1))) == null)
+ && (name = viewer.dialogAsk("load", name.substring(1))) == null) {
+ openErrorMessage = "#CANCELED#";
return null;
+ }
File file = null;
URL url = null;
String[] names = null;
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-09-15 12:00:35 UTC (rev 9897)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-09-15 12:48:13 UTC (rev 9898)
@@ -1543,7 +1543,7 @@
// openStringsInline(fileManager.getInlineDataArray(), htParams, false);
return;
}
- if (!isAppend)
+ if (!isAppend && name.charAt(0) != '?')
zap(false, false);
Logger.startTimer();
fileManager.openFile(name, htParams, loadScript, isAppend);
@@ -1744,7 +1744,7 @@
if (clientFile instanceof String || clientFile == null) {
String errorMsg = (String) clientFile;
setStatusFileNotLoaded(fullPathName, errorMsg);
- if (errorMsg != null && !isAppend)
+ if (errorMsg != null && !isAppend && !errorMsg.equals("#CANCELED#"))
zap(errorMsg);
return errorMsg;
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-09-15 21:39:52
|
Revision: 9902
http://jmol.svn.sourceforge.net/jmol/?rev=9902&view=rev
Author: hansonr
Date: 2008-09-16 04:39:49 +0000 (Tue, 16 Sep 2008)
Log Message:
-----------
11.6.RC15 VERSION Mac and PC signed applet load/save working
# code: thread control for Java Swing in applet context
# thread creating Swing objects MUST be event thread
# -- using SwingUtilities.invokeAndWait() from the commandWatcher thread
# new feature: load menu items for signed applet
# new feature: save menu items for signed applet
# bug fix: applet -- setting a jmolScript callback prevents menu updates
# new feature: minimize menu item
# new feature: signed applet allows "load ?" and includes previewer
# bug fix: H-M spacegroup designations specifying nonstandard Hall symbols by default
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/applet/Jvm12.java
trunk/Jmol/src/org/jmol/export/dialog/Dialog.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/applet/Jvm12.java
===================================================================
--- trunk/Jmol/src/org/jmol/applet/Jvm12.java 2008-09-15 20:03:32 UTC (rev 9901)
+++ trunk/Jmol/src/org/jmol/applet/Jvm12.java 2008-09-16 04:39:49 UTC (rev 9902)
@@ -100,7 +100,7 @@
}
final protected static String[] imageChoices = { "JPEG", "PNG", "GIF", "PPM" };
- final protected static String[] imageExtensions = { "jpg", "png", "gif", "PPM" };
+ final protected static String[] imageExtensions = { "jpg", "png", "gif", "ppm" };
static JmolDialogInterface newDialog(boolean forceNewTranslation) {
JmolDialogInterface sd = (JmolDialogInterface) Interface
@@ -141,7 +141,7 @@
if (sType != null)
imageType = sType;
int iQuality = sd.getQuality(sType);
- if (iQuality > 0)
+ if (iQuality >= 0)
imageQuality = iQuality;
return;
}
Modified: trunk/Jmol/src/org/jmol/export/dialog/Dialog.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/dialog/Dialog.java 2008-09-15 20:03:32 UTC (rev 9901)
+++ trunk/Jmol/src/org/jmol/export/dialog/Dialog.java 2008-09-16 04:39:49 UTC (rev 9902)
@@ -55,12 +55,18 @@
String[] extensions = new String[10];
String choice;
String extension;
- private int defaultChoice;
+
+ // static so that they can be shared among instances
+
+ static private int defaultChoice;
+ static int qualityJPG = 75;
+ static int qualityPNG = 2;
+
private JSlider qSliderJPEG, qSliderPNG;
private JComboBox cb;
JPanel qPanelJPEG, qPanelPNG;
- static JFileChooser exportChooser;
+ static JFileChooser imageChooser;
static JFileChooser saveChooser;
public Dialog() {
@@ -177,70 +183,76 @@
return file.getAbsolutePath();
}
+
public String getImageFileNameFromDialog(JmolViewer viewer, String fileName,
String type, String[] imageChoices,
String[] imageExtensions,
- int qualityJPG, int qualityPNG) {
- if (exportChooser == null)
- exportChooser = new JFileChooser();
- exportChooser.setCurrentDirectory(FileManager.getLocalDirectory(viewer));
- exportChooser.resetChoosableFileFilters();
+ int qualityJPG0, int qualityPNG0) {
+ if (qualityJPG0 < 0 || qualityJPG0 > 100)
+ qualityJPG0 = qualityJPG;
+ if (qualityPNG0 < 0)
+ qualityPNG0 = qualityPNG;
+ if (qualityPNG0 > 9)
+ qualityPNG0 = 2;
+ qualityJPG = qualityJPG0;
+ qualityPNG = qualityPNG0;
+
+ if (imageChooser == null)
+ imageChooser = new JFileChooser();
+ imageChooser.setCurrentDirectory(FileManager.getLocalDirectory(viewer));
+ imageChooser.resetChoosableFileFilters();
File file = null;
if (fileName == null) {
fileName = viewer.getModelSetFileName();
- String pathName = exportChooser.getCurrentDirectory().getPath();
- createPanel(exportChooser, imageChoices, imageExtensions, type,
- qualityJPG, qualityPNG);
+ String pathName = imageChooser.getCurrentDirectory().getPath();
if (fileName != null && pathName != null) {
int extensionStart = fileName.lastIndexOf('.');
if (extensionStart != -1) {
fileName = fileName.substring(0, extensionStart) + "."
- + getExtension();
+ + extension;
}
file = new File(pathName, fileName);
}
} else {
if (fileName.indexOf(".") == 0)
fileName = "Jmol" + fileName;
- String sType = fileName.substring(fileName.lastIndexOf(".") + 1);
+ file = new File(fileName);
+ type = fileName.substring(fileName.lastIndexOf(".") + 1);
for (int i = 0; i < imageExtensions.length; i++)
- if (sType.equals(imageChoices[i])
- || sType.toLowerCase().equals(imageExtensions[i])) {
- sType = imageChoices[i];
+ if (type.equals(imageChoices[i])
+ || type.toLowerCase().equals(imageExtensions[i])) {
+ type = imageChoices[i];
break;
}
- createPanel(exportChooser, imageChoices, imageExtensions, sType,
- qualityJPG, qualityPNG);
- file = new File(fileName);
}
- exportChooser.setSelectedFile(initialFile = file);
- if ((file = showSaveDialog(this, this, exportChooser, file)) == null)
+ createExportPanel(imageChoices, imageExtensions, type);
+ imageChooser.setSelectedFile(initialFile = file);
+ if ((file = showSaveDialog(this, this, imageChooser, file)) == null)
return null;
+ qualityJPG = qSliderJPEG.getValue();
+ qualityPNG = qSliderPNG.getValue();
+ if (cb.getSelectedIndex() >= 0)
+ defaultChoice = cb.getSelectedIndex();
viewer.setStringProperty("currentLocalPath", file.getParent());
return file.getAbsolutePath();
}
File initialFile;
- /* (non-Javadoc)
- * @see org.jmol.export.JmolImageTyperInterface#createPanel(javax.swing.JFileChooser, java.lang.String[], java.lang.String[], int)
- */
- public void createPanel(JFileChooser fc, String[] choices,
- String[] extensions, String type, int qualityJPEG,
- int qualityPNG) {
- exportChooser = fc;
- fc.setAccessory(this);
+ private void createExportPanel(String[] choices,
+ String[] extensions, String type) {
+ imageChooser.setAccessory(this);
setLayout(new BorderLayout());
- choice = null;
if (type.equals("JPG"))
type = "JPEG";
for (defaultChoice = choices.length; --defaultChoice >= 1;)
if (choices[defaultChoice].equals(type))
break;
extension = extensions[defaultChoice];
+ choice = choices[defaultChoice];
this.extensions = extensions;
- exportChooser.resetChoosableFileFilters();
- exportChooser.addChoosableFileFilter(new TypeFilter(extension));
+ imageChooser.resetChoosableFileFilters();
+ imageChooser.addChoosableFileFilter(new TypeFilter(extension));
JPanel cbPanel = new JPanel();
cbPanel.setLayout(new FlowLayout());
cbPanel.setBorder(new TitledBorder(GT._("Image Type")));
@@ -250,24 +262,17 @@
}
cbPanel.add(cb);
cb.setSelectedIndex(defaultChoice);
- cb.addItemListener(new ChoiceListener());
+ cb.addItemListener(new ExportChoiceListener());
add(cbPanel, BorderLayout.NORTH);
JPanel qPanel2 = new JPanel();
qPanel2.setLayout(new BorderLayout());
- if (qualityJPEG < 0)
- qualityJPEG = 75;
- if (qualityPNG < 0)
- qualityPNG = 2;
- if (qualityPNG > 9)
- qualityPNG = 9;
-
qPanelJPEG = new JPanel();
qPanelJPEG.setLayout(new BorderLayout());
qPanelJPEG.setBorder(new TitledBorder(GT._("JPEG Quality ({0})",
- qualityJPEG)));
- qSliderJPEG = new JSlider(SwingConstants.HORIZONTAL, 50, 100, qualityJPEG);
+ qualityJPG)));
+ qSliderJPEG = new JSlider(SwingConstants.HORIZONTAL, 50, 100, qualityJPG);
qSliderJPEG.putClientProperty("JSlider.isFilled", Boolean.TRUE);
qSliderJPEG.setPaintTicks(true);
qSliderJPEG.setMajorTickSpacing(10);
@@ -279,7 +284,7 @@
qPanelPNG = new JPanel();
qPanelPNG.setLayout(new BorderLayout());
qPanelPNG
- .setBorder(new TitledBorder(GT._("PNG Quality ({0})", qualityPNG)));
+ .setBorder(new TitledBorder(GT._("PNG Compression ({0})", qualityPNG)));
qSliderPNG = new JSlider(SwingConstants.HORIZONTAL, 0, 9, qualityPNG);
qSliderPNG.putClientProperty("JSlider.isFilled", Boolean.TRUE);
qSliderPNG.setPaintTicks(true);
@@ -304,50 +309,42 @@
public void stateChanged(ChangeEvent arg0) {
int value = slider.getValue();
if (isJPEG) {
+ qualityJPG = value;
qPanelJPEG
.setBorder(new TitledBorder(GT._("JPEG Quality ({0})", value)));
} else {
+ qualityPNG = value;
qPanelPNG.setBorder(new TitledBorder(GT._("PNG Quality ({0})", value)));
}
}
-
}
- public class ChoiceListener implements ItemListener {
+ public class ExportChoiceListener implements ItemListener {
public void itemStateChanged(ItemEvent e) {
JComboBox source = (JComboBox) e.getSource();
- choice = (String) source.getSelectedItem();
- String ext = extensions[source.getSelectedIndex()];
- File selectedFile = exportChooser.getSelectedFile();
+ File selectedFile = imageChooser.getSelectedFile();
if (selectedFile == null)
selectedFile = initialFile;
File newFile = null;
String name;
+ String newExt = extensions[source.getSelectedIndex()];
if ((name = selectedFile.getName()) != null
&& name.endsWith("." + extension)) {
name = name.substring(0, name.length() - extension.length());
- name += ext;
- newFile = new File(selectedFile.getPath(), name);
+ name += newExt;
+ initialFile = newFile = new File(selectedFile.getParent(), name);
}
- exportChooser.resetChoosableFileFilters();
- exportChooser.addChoosableFileFilter(new TypeFilter(ext));
+ extension = newExt;
+ imageChooser.resetChoosableFileFilters();
+ imageChooser.addChoosableFileFilter(new TypeFilter(extension));
if (newFile != null)
- exportChooser.setSelectedFile(newFile);
- extension = extensions[source.getSelectedIndex()];
+ imageChooser.setSelectedFile(newFile);
+ choice = (String) source.getSelectedItem();
}
}
/* (non-Javadoc)
- * @see org.jmol.export.JmolImageTyperInterface#memorizeDefaultType()
- */
- public void memorizeDefaultType() {
- if ((cb != null) && (cb.getSelectedIndex() >= 0)) {
- defaultChoice = cb.getSelectedIndex();
- }
- }
-
- /* (non-Javadoc)
* @see org.jmol.export.JmolImageTyperInterface#getType()
*/
public String getType() {
@@ -355,18 +352,11 @@
}
/* (non-Javadoc)
- * @see org.jmol.export.JmolImageTyperInterface#getExtension()
- */
- public String getExtension() {
- return extension;
- }
-
- /* (non-Javadoc)
* @see org.jmol.export.JmolImageTyperInterface#getQuality(java.lang.String)
*/
public int getQuality(String sType) {
- return (sType.equals("JPEG") || sType.equals("JPG") ? qSliderJPEG
- .getValue() : sType.equals("PNG") ? qSliderPNG.getValue() : -1);
+ return (sType.equals("JPEG") || sType.equals("JPG") ? qualityJPG : sType
+ .equals("PNG") ? qualityPNG : -1);
}
private static boolean doOverWrite(JFileChooser chooser, File file) {
@@ -378,13 +368,13 @@
return (opt == 0);
}
- private static File showSaveDialog(Dialog it, Component c,
+ private File showSaveDialog(Dialog sd, Component c,
JFileChooser chooser, File file) {
while (true) {
if (chooser.showSaveDialog(c) != JFileChooser.APPROVE_OPTION)
return null;
- if (it != null)
- it.memorizeDefaultType();
+ if (cb != null && cb.getSelectedIndex() >= 0)
+ defaultChoice = cb.getSelectedIndex();
if ((file = chooser.getSelectedFile()) == null || !file.exists()
|| doOverWrite(chooser, file))
return file;
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-09-15 20:03:32 UTC (rev 9901)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-09-16 04:39:49 UTC (rev 9902)
@@ -1,8 +1,11 @@
# Developers: to add a description of changes you have made,
# add it on a line starting with # below the "version=..." line
-version=11.6.RC15_dev
+version=11.6.RC15
+# code: thread control for Java Swing in applet context
+# thread creating Swing objects MUST be event thread
+# -- using SwingUtilities.invokeAndWait() from the commandWatcher thread
# new feature: load menu items for signed applet
# new feature: save menu items for signed applet
# bug fix: applet -- setting a jmolScript callback prevents menu updates
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-09-15 20:03:32 UTC (rev 9901)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-09-16 04:39:49 UTC (rev 9902)
@@ -3191,6 +3191,9 @@
}
public void renderScreenImage(Graphics g, Dimension size, Rectangle clip) {
+ // from paint/update event
+ if (creatingImage)
+ return;
if (isTainted || getSlabEnabled())
setModelVisibility();
isTainted = false;
@@ -6346,6 +6349,7 @@
public String createImage(String file, String type, Object text_or_bytes,
int quality, int width, int height) {
+ //pushHoldRepaint();
int saveWidth = dimScreen.width;
int saveHeight = dimScreen.height;
if (quality != Integer.MIN_VALUE) {
@@ -6363,6 +6367,7 @@
if (quality != Integer.MIN_VALUE) {
resizeImage(saveWidth, saveHeight, true, false, true);
}
+ //popHoldRepaint();
return err;
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-09-16 05:22:47
|
Revision: 9904
http://jmol.svn.sourceforge.net/jmol/?rev=9904&view=rev
Author: hansonr
Date: 2008-09-16 12:22:42 +0000 (Tue, 16 Sep 2008)
Log Message:
-----------
11.6.RC15_devb still working on file open dialogs
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/export/dialog/Dialog.java
trunk/Jmol/src/org/jmol/export/dialog/FilePreview.java
trunk/Jmol/src/org/jmol/viewer/FileManager.java
trunk/Jmol/src/org/jmol/viewer/MouseManager.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/export/dialog/Dialog.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/dialog/Dialog.java 2008-09-16 11:08:21 UTC (rev 9903)
+++ trunk/Jmol/src/org/jmol/export/dialog/Dialog.java 2008-09-16 12:22:42 UTC (rev 9904)
@@ -83,13 +83,13 @@
HistoryFile historyFile = (HistoryFile) historyFileObject;
- if (openChooser == null) {
+ if (openChooser == null)
openChooser = new FileChooser();
- String previewProperty = System.getProperty("openFilePreview", "true");
- if (Boolean.valueOf(previewProperty).booleanValue()) {
- openPreview = new FilePreview(openChooser, modelAdapter, allowAppend,
- appletContext);
- }
+ if (openPreview == null
+ && (viewer.isApplet() || Boolean.valueOf(
+ System.getProperty("openFilePreview", "true")).booleanValue())) {
+ openPreview = new FilePreview(openChooser, modelAdapter, allowAppend,
+ appletContext);
}
if (historyFile != null) {
@@ -114,12 +114,8 @@
File file = null;
if (openChooser.showOpenDialog(this) == JFileChooser.APPROVE_OPTION)
file = openChooser.getSelectedFile();
- if (file == null) {
- openChooser.setAccessory(null);
- openPreview = null;
- return null;
- }
-
+ if (file == null)
+ return closePreview();
if (historyFile != null)
historyFile.addWindowInfo(windowName, openChooser.getDialog(), null);
@@ -131,11 +127,16 @@
fileName = file.getAbsolutePath();
}
boolean doAppend = (openPreview != null && openPreview.isAppendSelected());
- openChooser.setAccessory(null);
- openPreview = null;
+ closePreview();
return (doAppend ? "load append " + Escape.escape(fileName) : fileName);
}
+ String closePreview() {
+ if (openPreview != null)
+ openPreview.updatePreview(null);
+ return null;
+ }
+
private final static String[] urlPrefixes = { "http:", "http://", "www.",
"http://www.", "https:", "https://", "ftp:", "ftp://", "file:",
"file:///" };
Modified: trunk/Jmol/src/org/jmol/export/dialog/FilePreview.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/dialog/FilePreview.java 2008-09-16 11:08:21 UTC (rev 9903)
+++ trunk/Jmol/src/org/jmol/export/dialog/FilePreview.java 2008-09-16 12:22:42 UTC (rev 9904)
@@ -125,21 +125,25 @@
* @param file File selected
*/
void updatePreview(File file) {
- if (file != null) {
+ String script;
+ if (file == null) {
+ script = "zap";
+ } else {
String fileName = file.getAbsolutePath();
String url = Dialog.getLocalUrl(file);
System.out.println("updatePreview + " + fileName + " " + url);
if (url != null)
fileName = url;
//doesn't update from use input?
- display.getViewer().evalStringQuiet(
- "zap;set echo top left;echo loading...;refresh;"
- + (fileName.indexOf(".spt") >= 0 ? "script" : "load")
- + " \"" + fileName + "\"");
- display.repaint();
- } else {
- display.getViewer().evalStringQuiet("zap");
+ script = " \"" + fileName + "\"";
+ if (fileName.indexOf(".spt") >= 0)
+ script = "script " + script;
+ else
+ script = "zap;set echo top left;echo loading...;refresh; load " + script
+ + ";if({1}.size);cartoons only;color structure;endif";
}
+ display.getViewer().evalStringQuiet(script);
+ //display.repaint();
}
private class JmolPanel extends JPanel {
Modified: trunk/Jmol/src/org/jmol/viewer/FileManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/FileManager.java 2008-09-16 11:08:21 UTC (rev 9903)
+++ trunk/Jmol/src/org/jmol/viewer/FileManager.java 2008-09-16 12:22:42 UTC (rev 9904)
@@ -537,13 +537,15 @@
name = TextFormat.formatString(viewer.getLoadFormat(), "FILE", name
.substring(1));
String defaultDirectory = viewer.getDefaultDirectory();
- if (name.indexOf(":") < 0)
+ if (name.indexOf(":") < 0 && name.indexOf("/") != 0)
name = addDirectory(defaultDirectory, name);
if (appletDocumentBase != null) {
// This code is only for the applet
try {
if (name.indexOf(":\\") == 1 || name.indexOf(":/") == 1)
- name = "file:///" + name;
+ name = "file:/" + name;
+ else if (name.indexOf("/") == 0)
+ name = "file:" + name;
url = new URL(appletDocumentBase, name);
} catch (MalformedURLException e) {
openErrorMessage = e.getMessage();
Modified: trunk/Jmol/src/org/jmol/viewer/MouseManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/MouseManager.java 2008-09-16 11:08:21 UTC (rev 9903)
+++ trunk/Jmol/src/org/jmol/viewer/MouseManager.java 2008-09-16 12:22:42 UTC (rev 9904)
@@ -68,6 +68,8 @@
}
synchronized void startHoverWatcher(boolean isStart) {
+ if (viewer.isPreviewOnly())
+ return;
try {
if (isStart) {
if (hoverWatcherThread != null)
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-09-16 11:08:21 UTC (rev 9903)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-09-16 12:22:42 UTC (rev 9904)
@@ -1990,7 +1990,7 @@
setCurrentModelIndex(0);
setBackgroundModelIndex(-1);
setFrankOn(getShowFrank());
- mouseManager.startHoverWatcher(!isPreviewOnly);
+ mouseManager.startHoverWatcher(true);
setTainted(true);
finalizeTransformParameters();
}
@@ -3892,6 +3892,10 @@
return statusManager.getStatusChanged(statusNameList);
}
+ boolean isPreviewOnly() {
+ return isPreviewOnly;
+ }
+
void popupMenu(int x, int y) {
if (isPreviewOnly || global.disablePopupMenu)
return;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-09-16 20:40:02
|
Revision: 9905
http://jmol.svn.sourceforge.net/jmol/?rev=9905&view=rev
Author: hansonr
Date: 2008-09-17 03:39:58 +0000 (Wed, 17 Sep 2008)
Log Message:
-----------
version=11.6.RC15 VERSION
# bug fix: CML files not properly loading symmetry
# bug fix: O- radius MUCH too large.
# code: thread control for Java Swing in applet context
# thread creating Swing objects MUST be event thread
# -- using SwingUtilities.invokeAndWait() from the commandWatcher thread
# new feature: load menu items for signed applet
# new feature: save menu items for signed applet
# bug fix: applet -- setting a jmolScript callback prevents menu updates
# new feature: minimize menu item
# new feature: signed applet allows "load ?" and includes previewer
# bug fix: H-M spacegroup designations specifying nonstandard Hall symbols by default
# new feature: signed applet/application load ?xxx uses load dialog
# webexport help updated to reflect ability to handle files opened with "load append"
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlCmlReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
trunk/Jmol/src/org/jmol/export/dialog/FilePreview.java
trunk/Jmol/src/org/jmol/modelset/Atom.java
trunk/Jmol/src/org/jmol/modelset/Bond.java
trunk/Jmol/src/org/jmol/modelset/BondCollection.java
trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/JmolConstants.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlCmlReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlCmlReader.java 2008-09-16 12:22:42 UTC (rev 9904)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlCmlReader.java 2008-09-17 03:39:58 UTC (rev 9905)
@@ -184,13 +184,13 @@
HashMap atts) {
//if (!uri.equals(NAMESPACE_URI))
//return;
-/*
+
try {
- System.out.println(name + "::"+atts.get("name"));
+ System.out.println(name + "::" + atts.get("name"));
} catch (Exception e) {
System.out.println(name);
}
-*/
+
switch (state) {
case START:
if (name.equals("molecule")) {
@@ -204,9 +204,10 @@
state = CRYSTAL;
} else if (name.equals("symmetry")) {
state = SYMMETRY;
- localSpaceGroupName = (atts.containsKey("spaceGroup") ? (String) atts.get("spaceGroup") : "P1");
+ localSpaceGroupName = (atts.containsKey("spaceGroup") ? (String) atts
+ .get("spaceGroup") : "P1");
} else if (name.equals("module")) {
- moduleCount++;
+ moduleCount++;
}
break;
@@ -220,7 +221,7 @@
int iColon = scalarDictRef.indexOf(":");
scalarDictValue = scalarDictRef.substring(iColon + 1);
//scalarDictKey = scalarDictRef
- // .substring(0, (iColon >= 0 ? iColon : 0));
+ // .substring(0, (iColon >= 0 ? iColon : 0));
}
} else if (name.equals("symmetry")) {
state = CRYSTAL_SYMMETRY;
@@ -346,8 +347,6 @@
if (name.equals("atom")) {
state = MOLECULE_ATOM;
atom = new Atom();
- boolean coords3D = false;
- boolean coordsFractional = false;
parent.setFractionalCoordinates(false);
if (atts.containsKey("label"))
atom.atomName = (String) atts.get("label");
@@ -355,24 +354,18 @@
atom.atomName = (String) atts.get("id");
if (atts.containsKey("xFract")
&& (parent.iHaveUnitCell || !atts.containsKey("x3"))) {
- coords3D = coordsFractional = true;
parent.setFractionalCoordinates(true);
parent.setAtomCoord(atom, parseFloat((String) atts.get("xFract")),
parseFloat((String) atts.get("yFract")), parseFloat((String) atts
.get("zFract")));
+ } else if (atts.containsKey("x3")) {
+ parent.setAtomCoord(atom, parseFloat((String) atts.get("x3")),
+ parseFloat((String) atts.get("y3")), parseFloat((String) atts
+ .get("z3")));
+ } else if (atts.containsKey("x2")) {
+ parent.setAtomCoord(atom, parseFloat((String) atts.get("x2")),
+ parseFloat((String) atts.get("y2")), 0);
}
- if (atts.containsKey("x3") && !coordsFractional) {
- coords3D = true;
- atom.x = parseFloat((String) atts.get("x3"));
- atom.y = parseFloat((String) atts.get("y3"));
- atom.z = parseFloat((String) atts.get("z3"));
- }
- if (atts.containsKey("x2") && !coords3D ) {
- atom.x = parseFloat((String) atts.get("x2"));
- atom.y = parseFloat((String) atts.get("y2"));
- atom.z = 0;
- }
- parent.setAtomCoord(atom);
if (atts.containsKey("elementType"))
atom.elementSymbol = (String) atts.get("elementType");
if (atts.containsKey("formalCharge"))
@@ -384,7 +377,7 @@
if (atts.containsKey("builtin")) {
setKeepChars(true);
state = MOLECULE_BOND_BUILTIN;
- scalarDictValue = (String) atts.get("builtin");
+ scalarDictValue = (String) atts.get("builtin");
}
break;
case MOLECULE_ATOM:
@@ -397,12 +390,12 @@
int iColon = scalarDictRef.indexOf(":");
scalarDictValue = scalarDictRef.substring(iColon + 1);
//scalarDictKey = scalarDictRef
- // .substring(0, (iColon >= 0 ? iColon : 0));
+ // .substring(0, (iColon >= 0 ? iColon : 0));
}
} else if (atts.containsKey("builtin")) {
setKeepChars(true);
state = MOLECULE_ATOM_BUILTIN;
- scalarDictValue = (String) atts.get("builtin");
+ scalarDictValue = (String) atts.get("builtin");
}
break;
case MOLECULE_ATOM_SCALAR:
@@ -424,7 +417,8 @@
case START:
if (name.equals("module")) {
moduleCount--;
- applySymmetry();
+ if (iHaveUnitCell)
+ applySymmetry();
}
break;
case CRYSTAL:
@@ -440,14 +434,12 @@
setKeepChars(false);
if (tokens.length != 3 || cellParameterType == null) {
} else if (cellParameterType.equals("length")) {
- parent.needToApplySymmetry = true;
for (int i = 0; i < 3; i++)
parent.setUnitCellItem(i, parseFloat(tokens[i]));
break;
} else if (cellParameterType.equals("angle")) {
for (int i = 0; i < 3; i++)
parent.setUnitCellItem(i + 3, parseFloat(tokens[i]));
- applySymmetry();
break;
}
//if here, then something is wrong
@@ -491,14 +483,13 @@
case CRYSTAL_SYMMETRY:
case SYMMETRY:
if (name.equals("symmetry")) {
- applySymmetry();
state = (state == CRYSTAL_SYMMETRY ? CRYSTAL : START);
}
break;
case MOLECULE:
if (name.equals("molecule")) {
if (--moleculeNesting == 0) {
- // if <molecule> is within <module>, then
+ // if <molecule> is within <molecule>, then
// we have to wait until the end of <module> to
// apply symmetry.
applySymmetry();
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2008-09-16 12:22:42 UTC (rev 9904)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2008-09-17 03:39:58 UTC (rev 9905)
@@ -1026,7 +1026,6 @@
////////////////////////////////////////////////////////////////
void addTrajectory() {
- //System.out.println(atomCount);
if (trajectory.length == 0 || trajectory.length < atomCount) {
trajectory = new Point3f[atomCount];
}
Modified: trunk/Jmol/src/org/jmol/export/dialog/FilePreview.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/dialog/FilePreview.java 2008-09-16 12:22:42 UTC (rev 9904)
+++ trunk/Jmol/src/org/jmol/export/dialog/FilePreview.java 2008-09-17 03:39:58 UTC (rev 9905)
@@ -130,6 +130,7 @@
script = "zap";
} else {
String fileName = file.getAbsolutePath();
+ System.out.println("updatePreview "+ fileName + " " + chooser.getSelectedFile());
String url = Dialog.getLocalUrl(file);
System.out.println("updatePreview + " + fileName + " " + url);
if (url != null)
@@ -139,8 +140,8 @@
if (fileName.indexOf(".spt") >= 0)
script = "script " + script;
else
- script = "zap;set echo top left;echo loading...;refresh; load " + script
- + ";if({1}.size);cartoons only;color structure;endif";
+ script = "zap;set echo top left;echo loading...;refresh;load " + script
+ + ";if({1-10000}.size);cartoons only;color structure;endif";
}
display.getViewer().evalStringQuiet(script);
//display.repaint();
Modified: trunk/Jmol/src/org/jmol/modelset/Atom.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Atom.java 2008-09-16 12:22:42 UTC (rev 9904)
+++ trunk/Jmol/src/org/jmol/modelset/Atom.java 2008-09-17 03:39:58 UTC (rev 9905)
@@ -274,7 +274,7 @@
}
public int getRasMolRadius() {
- return Math.abs(madAtom / (4 * 2));
+ return Math.abs(madAtom / 8); // 1000r = 1000d / 2; rr = (1000r / 4);
}
public int getCovalentBondCount() {
Modified: trunk/Jmol/src/org/jmol/modelset/Bond.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Bond.java 2008-09-16 12:22:42 UTC (rev 9904)
+++ trunk/Jmol/src/org/jmol/modelset/Bond.java 2008-09-17 03:39:58 UTC (rev 9905)
@@ -79,10 +79,8 @@
Bond(Atom atom1, Atom atom2, short order,
short mad, short colix) {
- if (atom1 == null)
+ if (atom1 == null || atom2 == null)
throw new NullPointerException();
- if (atom2 == null)
- throw new NullPointerException();
this.atom1 = atom1;
this.atom2 = atom2;
if (atom1.getElementNumber() == 16 && atom2.getElementNumber() == 16)
Modified: trunk/Jmol/src/org/jmol/modelset/BondCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/BondCollection.java 2008-09-16 12:22:42 UTC (rev 9904)
+++ trunk/Jmol/src/org/jmol/modelset/BondCollection.java 2008-09-17 03:39:58 UTC (rev 9905)
@@ -245,41 +245,36 @@
protected short getBondOrder(Atom atomA, float bondingRadiusA, Atom atomB,
float bondingRadiusB, float distance2,
float minBondDistance2, float bondTolerance) {
- if (bondingRadiusA == 0 || bondingRadiusB == 0)
+ if (bondingRadiusA == 0 || bondingRadiusB == 0 || distance2 < minBondDistance2)
return 0;
float maxAcceptable = bondingRadiusA + bondingRadiusB + bondTolerance;
float maxAcceptable2 = maxAcceptable * maxAcceptable;
- if (distance2 < minBondDistance2) {
- return 0;
- }
- if (distance2 <= maxAcceptable2) {
- return 1;
- }
- return 0;
+ return (distance2 > maxAcceptable2 ? (short) 0 : (short) 1);
}
private boolean haveWarned = false;
- void checkValencesAndBond(Atom atomA, Atom atomB, short order, short mad,
+ boolean checkValencesAndBond(Atom atomA, Atom atomB, short order, short mad,
BitSet bsBonds) {
if (atomA.getCurrentBondCount() > JmolConstants.MAXIMUM_AUTO_BOND_COUNT
|| atomB.getCurrentBondCount() > JmolConstants.MAXIMUM_AUTO_BOND_COUNT) {
if (!haveWarned)
Logger.warn("maximum auto bond count reached");
haveWarned = true;
- return;
+ return false;
}
int formalChargeA = atomA.getFormalCharge();
if (formalChargeA != 0) {
int formalChargeB = atomB.getFormalCharge();
if ((formalChargeA < 0 && formalChargeB < 0)
|| (formalChargeA > 0 && formalChargeB > 0))
- return;
+ return false;
}
if (atomA.alternateLocationID != atomB.alternateLocationID
&& atomA.alternateLocationID != '\0' && atomB.alternateLocationID != '\0')
- return;
+ return false;
getOrAddBond(atomA, atomB, order, mad, bsBonds);
+ return true;
}
protected void deleteAllBonds() {
Modified: trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2008-09-16 12:22:42 UTC (rev 9904)
+++ trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2008-09-17 03:39:58 UTC (rev 9905)
@@ -2094,8 +2094,8 @@
.getBondingRadiusFloat(), iter.foundDistance2(), minBondDistance2,
bondTolerance);
if (order > 0) {
- checkValencesAndBond(atom, atomNear, order, mad, bsBonds);
- nNew++;
+ if (checkValencesAndBond(atom, atomNear, order, mad, bsBonds))
+ nNew++;
}
}
iter.release();
Modified: trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java 2008-09-16 12:22:42 UTC (rev 9904)
+++ trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java 2008-09-17 03:39:58 UTC (rev 9905)
@@ -453,10 +453,10 @@
name = name.substring(0, i).trim();
}
- // generate spaceless abbreviation "P m m m" --> "Pmmm"
+ // generate spaceless abbreviation "P m m m" --> "Pmmm" "P 2(1)/c" --> "P21/c"
String abbr = "";
for (i = 0; i < name.length(); i++) {
- if (name.charAt(i) != ' ')
+ if (" ()".indexOf(name.charAt(i)) < 0)
abbr += name.charAt(i);
}
SpaceGroup s;
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-09-16 12:22:42 UTC (rev 9904)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-09-17 03:39:58 UTC (rev 9905)
@@ -1,8 +1,10 @@
# Developers: to add a description of changes you have made,
# add it on a line starting with # below the "version=..." line
-version=11.6.RC15_dev2
+version=11.6.RC15
+# bug fix: CML files not properly loading symmetry
+# bug fix: O- radius MUCH too large.
# code: thread control for Java Swing in applet context
# thread creating Swing objects MUST be event thread
# -- using SwingUtilities.invokeAndWait() from the commandWatcher thread
Modified: trunk/Jmol/src/org/jmol/viewer/JmolConstants.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/JmolConstants.java 2008-09-16 12:22:42 UTC (rev 9904)
+++ trunk/Jmol/src/org/jmol/viewer/JmolConstants.java 2008-09-17 03:39:58 UTC (rev 9905)
@@ -1395,28 +1395,30 @@
(95 << 4) + (4 + 4), 920, // "Am+4"
};
+ // Q: What does it mean that X(-1) radius >> X(-2) radius?
+
private final static short[] anionLookupTable = {
(1 << 4) + (-1 + 4), 1540, // "H-1"
(6 << 4) + (-4 + 4), 2600, // "C-4"
(7 << 4) + (-3 + 4), 1710, // "N-3"
(8 << 4) + (-2 + 4), 1320, // "O-2"
- (8 << 4) + (-1 + 4), 1760, // "O-1"
+ (8 << 4) + (-1 + 4), 1000, // "O-1" // this was 1760! But then RC(=0)O- is rediculously bonded
(9 << 4) + (-1 + 4), 1330, // "F-1"
(14 << 4) + (-4 + 4), 2710, // "Si-4"
- (14 << 4) + (-1 + 4), 3840, // "Si-1"
+ (14 << 4) + (-1 + 4), 3840, // "Si-1" // same problem here?
(15 << 4) + (-3 + 4), 2120, // "P-3"
(16 << 4) + (-2 + 4), 1840, // "S-2"
(17 << 4) + (-1 + 4), 1810, // "Cl-1"
(32 << 4) + (-4 + 4), 2720, // "Ge-4"
(33 << 4) + (-3 + 4), 2220, // "As-3"
(34 << 4) + (-2 + 4), 1910, // "Se-2"
- (34 << 4) + (-1 + 4), 2320, // "Se-1"
+ (34 << 4) + (-1 + 4), 2320, // "Se-1" // same problem here?
(35 << 4) + (-1 + 4), 1960, // "Br-1"
(50 << 4) + (-4 + 4), 2940, // "Sn-4"
- (50 << 4) + (-1 + 4), 3700, // "Sn-1"
+ (50 << 4) + (-1 + 4), 3700, // "Sn-1" // same problem here?
(51 << 4) + (-3 + 4), 2450, // "Sb-3"
(52 << 4) + (-2 + 4), 2110, // "Te-2"
- (52 << 4) + (-1 + 4), 2500, // "Te-1"
+ (52 << 4) + (-1 + 4), 2500, // "Te-1" // same problem here?
(53 << 4) + (-1 + 4), 2200, // "I-1"
};
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-09-18 04:38:09
|
Revision: 9906
http://jmol.svn.sourceforge.net/jmol/?rev=9906&view=rev
Author: hansonr
Date: 2008-09-18 11:38:04 +0000 (Thu, 18 Sep 2008)
Log Message:
-----------
11.6.RC15 VERSION
# note: CML reader only reads the first structure of a file
# bug fix: CML reader not assigning atom labels
# bug fix: CML files not properly loading symmetry
# bug fix: O- formal charge radius MUCH too large; N+ MUCH too small. -- REMOVED
# code: thread control for Java Swing in applet context
# thread creating Swing objects MUST be event thread
# -- using SwingUtilities.invokeAndWait() from the commandWatcher thread
# new feature: load menu items for signed applet
# new feature: save menu items for signed applet
# bug fix: applet -- setting a jmolScript callback prevents menu updates
# new feature: minimize menu item
# new feature: signed applet allows "load ?" and includes previewer
# bug fix: H-M spacegroup designations specifying nonstandard Hall symbols by default
# new feature: signed applet/application load ?xxx uses load dialog
# webexport help updated to reflect ability to handle files opened with "load append"
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlCmlReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
trunk/Jmol/src/org/jmol/applet/Jvm12.java
trunk/Jmol/src/org/jmol/export/dialog/Dialog.java
trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
trunk/Jmol/src/org/jmol/popup/JmolPopup.java
trunk/Jmol/src/org/jmol/popup/PopupResourceBundle.java
trunk/Jmol/src/org/jmol/viewer/FileManager.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/JmolConstants.java
trunk/Jmol/src/org/jmol/viewer/ScriptManager.java
trunk/Jmol/src/org/jmol/viewer/StatusManager.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlCmlReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlCmlReader.java 2008-09-17 03:39:58 UTC (rev 9905)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlCmlReader.java 2008-09-18 11:38:04 UTC (rev 9906)
@@ -29,6 +29,7 @@
import java.io.BufferedReader;
import java.util.HashMap;
import java.util.NoSuchElementException;
+import java.util.Properties;
import java.util.StringTokenizer;
import netscape.javascript.JSObject;
@@ -106,9 +107,11 @@
int tokenCount;
String[] tokens = new String[16];
- int moduleCount = 0;
+ int nModules = 0;
+ int moduleNestingLevel = 0;
boolean haveMolecule = false;
String localSpaceGroupName;
+ boolean processing = true;
/**
* state constants
*/
@@ -179,18 +182,21 @@
// parent molecule that exists.
int moleculeNesting = 0;
boolean embeddedCrystal = false;
+ Properties atomIdNames;
public void processStartElement(String uri, String name, String qName,
HashMap atts) {
//if (!uri.equals(NAMESPACE_URI))
//return;
- try {
+/* try {
System.out.println(name + "::" + atts.get("name"));
} catch (Exception e) {
System.out.println(name);
}
-
+*/
+ if (!processing)
+ return;
switch (state) {
case START:
if (name.equals("molecule")) {
@@ -207,7 +213,8 @@
localSpaceGroupName = (atts.containsKey("spaceGroup") ? (String) atts
.get("spaceGroup") : "P1");
} else if (name.equals("module")) {
- moduleCount++;
+ moduleNestingLevel++;
+ nModules++;
}
break;
@@ -216,13 +223,7 @@
state = CRYSTAL_SCALAR;
setKeepChars(true);
scalarTitle = (String) atts.get("title");
- scalarDictRef = (String) atts.get("dictRef");
- if (scalarDictRef != null) {
- int iColon = scalarDictRef.indexOf(":");
- scalarDictValue = scalarDictRef.substring(iColon + 1);
- //scalarDictKey = scalarDictRef
- // .substring(0, (iColon >= 0 ? iColon : 0));
- }
+ getDictRefValue(atts);
} else if (name.equals("symmetry")) {
state = CRYSTAL_SYMMETRY;
if (atts.containsKey("spaceGroup")) {
@@ -385,13 +386,7 @@
state = MOLECULE_ATOM_SCALAR;
setKeepChars(true);
scalarTitle = (String) atts.get("title");
- scalarDictRef = (String) atts.get("dictRef");
- if (scalarDictRef != null) {
- int iColon = scalarDictRef.indexOf(":");
- scalarDictValue = scalarDictRef.substring(iColon + 1);
- //scalarDictKey = scalarDictRef
- // .substring(0, (iColon >= 0 ? iColon : 0));
- }
+ getDictRefValue(atts);
} else if (atts.containsKey("builtin")) {
setKeepChars(true);
state = MOLECULE_ATOM_BUILTIN;
@@ -409,16 +404,28 @@
}
}
+ private void getDictRefValue(HashMap atts) {
+ scalarDictRef = (String) atts.get("dictRef");
+ if (scalarDictRef != null) {
+ int iColon = scalarDictRef.indexOf(":");
+ scalarDictValue = scalarDictRef.substring(iColon + 1);
+ }
+ }
+
public void processEndElement(String uri, String name, String qName) {
//if (!uri.equals(NAMESPACE_URI))
//return;
//System.out.println("END: " + name);
+ if (!processing)
+ return;
switch (state) {
case START:
if (name.equals("module")) {
- moduleCount--;
- if (iHaveUnitCell)
- applySymmetry();
+ if (--moduleNestingLevel == 0) {
+ if (parent.iHaveUnitCell)
+ applySymmetry();
+ atomIdNames = atomSetCollection.setAtomNames(atomIdNames);
+ }
}
break;
case CRYSTAL:
@@ -485,14 +492,17 @@
if (name.equals("symmetry")) {
state = (state == CRYSTAL_SYMMETRY ? CRYSTAL : START);
}
+ if (moduleNestingLevel == 0 && parent.iHaveUnitCell)
+ applySymmetry();
break;
case MOLECULE:
if (name.equals("molecule")) {
if (--moleculeNesting == 0) {
// if <molecule> is within <molecule>, then
- // we have to wait until the end of <module> to
+ // we have to wait until the end of all <molecule>s to
// apply symmetry.
- applySymmetry();
+ applySymmetry();
+ atomIdNames = atomSetCollection.setAtomNames(atomIdNames);
state = START;
} else {
state = MOLECULE;
@@ -536,6 +546,10 @@
state = MOLECULE_ATOM;
if ("jmol:charge".equals(scalarDictRef)) {
atom.partialCharge = parseFloat(chars);
+ } else if (scalarDictRef != null && "_atom_site_label".equals(scalarDictValue)) {
+ if (atomIdNames == null)
+ atomIdNames = new Properties();
+ atomIdNames.put(atom.atomName, chars);
}
}
setKeepChars(false);
@@ -662,7 +676,7 @@
}
public void applySymmetry() {
- if (moduleCount > 0 || !haveMolecule)
+ if (moduleNestingLevel > 0 || !haveMolecule)
return;
if (localSpaceGroupName == null)
return;
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2008-09-17 03:39:58 UTC (rev 9905)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2008-09-18 11:38:04 UTC (rev 9906)
@@ -1333,4 +1333,15 @@
return v;
}
+ public Properties setAtomNames(Properties atomIdNames) {
+ // for CML reader "a3" --> "N3"
+ if (atomIdNames == null)
+ return null;
+ String s;
+ for (int i = 0; i < atomCount; i++)
+ if ((s = atomIdNames.getProperty(atoms[i].atomName)) != null)
+ atoms[i].atomName = s;
+ return null;
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2008-09-17 03:39:58 UTC (rev 9905)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2008-09-18 11:38:04 UTC (rev 9906)
@@ -372,6 +372,7 @@
if (Logger.debugging) {
Logger.debug("setunitcellitem " + i + " " + x);
}
+ System.out.println("atomSetCollection unitcell item " + i + " = " + x);
if (i < 6)
iHaveUnitCell = checkUnitCell(6);
else if(++nMatrixElements == 12)
Modified: trunk/Jmol/src/org/jmol/applet/Jvm12.java
===================================================================
--- trunk/Jmol/src/org/jmol/applet/Jvm12.java 2008-09-17 03:39:58 UTC (rev 9905)
+++ trunk/Jmol/src/org/jmol/applet/Jvm12.java 2008-09-18 11:38:04 UTC (rev 9906)
@@ -27,6 +27,7 @@
import java.lang.reflect.InvocationTargetException;
import javax.swing.SwingUtilities;
+import javax.swing.UIManager;
import org.jmol.api.*;
import org.jmol.util.Logger;
@@ -44,6 +45,12 @@
this.viewer = viewer;
this.modelAdapter = modelAdapter;
this.appletContext = appletContext;
+ try {
+ UIManager
+ .setLookAndFeel(UIManager.getCrossPlatformLookAndFeelClassName());
+ } catch (Exception exc) {
+ System.err.println("Error loading L&F: " + exc);
+ }
}
private final Rectangle rectClip = new Rectangle();
Modified: trunk/Jmol/src/org/jmol/export/dialog/Dialog.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/dialog/Dialog.java 2008-09-17 03:39:58 UTC (rev 9905)
+++ trunk/Jmol/src/org/jmol/export/dialog/Dialog.java 2008-09-18 11:38:04 UTC (rev 9906)
@@ -111,11 +111,18 @@
if (fileName.indexOf(":") < 0)
openChooser.setCurrentDirectory(FileManager.getLocalDirectory(viewer));
}
+
+ UIManager.put("FileChooser.fileNameLabelText", GT._("File or URL:"));
+
File file = null;
if (openChooser.showOpenDialog(this) == JFileChooser.APPROVE_OPTION)
file = openChooser.getSelectedFile();
+
+ UIManager.put("FileChooser.fileNameLabelText", GT._("File Name:"));
+
if (file == null)
return closePreview();
+
if (historyFile != null)
historyFile.addWindowInfo(windowName, openChooser.getDialog(), null);
@@ -126,7 +133,7 @@
viewer.setStringProperty("currentLocalPath", file.getParent());
fileName = file.getAbsolutePath();
}
- boolean doAppend = (openPreview != null && openPreview.isAppendSelected());
+ boolean doAppend = (allowAppend && openPreview != null && openPreview.isAppendSelected());
closePreview();
return (doAppend ? "load append " + Escape.escape(fileName) : fileName);
}
@@ -171,6 +178,8 @@
String sType = fileName.substring(pt + 1);
if (pt >= 0 && sType.length() > 0)
saveChooser.addChoosableFileFilter(new TypeFilter(sType));
+ if (fileName.equals("*"))
+ fileName = viewer.getModelSetFileName();
if (fileName.indexOf(".") == 0)
fileName = "Jmol" + fileName;
file = new File(fileName);
@@ -435,7 +444,7 @@
UIManager.put("FileChooser.fileDateHeaderText", GT._("Modified"));
UIManager.put("FileChooser.fileDescriptionText", GT._("Generic File"));
UIManager.put("FileChooser.fileNameHeaderText", GT._("Name"));
- UIManager.put("FileChooser.fileNameLabelText", GT._("File or URL:"));
+ UIManager.put("FileChooser.fileNameLabelText", GT._("File Name:"));
UIManager.put("FileChooser.fileSizeHeaderText", GT._("Size"));
UIManager.put("FileChooser.filesOfTypeLabelText", GT._("Files of Type:"));
UIManager.put("FileChooser.fileTypeHeaderText", GT._("Type"));
Modified: trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelLoader.java 2008-09-17 03:39:58 UTC (rev 9905)
+++ trunk/Jmol/src/org/jmol/modelset/ModelLoader.java 2008-09-18 11:38:04 UTC (rev 9906)
@@ -706,11 +706,17 @@
if (iterBond == null)
return;
short mad = viewer.getMadBond();
+ short order;
defaultCovalentMad = (jmolData == null ? mad : 0);
+ boolean haveMultipleBonds = false;
while (iterBond.hasNext()) {
- bondAtoms(iterBond.getAtomUniqueID1(), iterBond.getAtomUniqueID2(),
- (short) iterBond.getEncodedOrder());
+ order = (short) iterBond.getEncodedOrder();
+ bondAtoms(iterBond.getAtomUniqueID1(), iterBond.getAtomUniqueID2(), order);
+ if (order > 1)
+ haveMultipleBonds = true;
}
+ if (haveMultipleBonds && someModelsHaveSymmetry && !viewer.getApplySymmetryToBonds())
+ Logger.info("ModelSet: use \"set appletSymmetryToBonds TRUE \" to apply the file-based multiple bonds to symmetry-generated atoms.");
defaultCovalentMad = mad;
}
Modified: trunk/Jmol/src/org/jmol/popup/JmolPopup.java
===================================================================
--- trunk/Jmol/src/org/jmol/popup/JmolPopup.java 2008-09-17 03:39:58 UTC (rev 9905)
+++ trunk/Jmol/src/org/jmol/popup/JmolPopup.java 2008-09-18 11:38:04 UTC (rev 9906)
@@ -856,8 +856,8 @@
if (script.indexOf("SELECT") == 0) {
return "select thisModel and (" + script.substring(6) + ")";
}
-
- if ((pt = id.lastIndexOf("[")) >= 0) {
+
+ if ((pt = id.lastIndexOf("[")) >= 0) {
// setSpin
id = id.substring(pt + 1);
if ((pt = id.indexOf("]")) >= 0)
@@ -865,11 +865,15 @@
id = id.replace('_', ' ');
if (script.indexOf("[]") < 0)
script = "[] " + script;
- return TextFormat.simpleReplace(script, "[]", id);
- } else if (script.indexOf("?FILEROOT?") >= 0)
+ return TextFormat.simpleReplace(script, "[]", id);
+ } else if (script.indexOf("?FILEROOT?") >= 0) {
script = TextFormat.simpleReplace(script, "FILEROOT?", modelSetRoot);
- else if (script.indexOf("?FILE?") >= 0)
+ } else if (script.indexOf("?FILE?") >= 0) {
script = TextFormat.simpleReplace(script, "FILE?", modelSetFileName);
+ } else if (script.indexOf("?PdbId?") >= 0) {
+ script = TextFormat.simpleReplace(script, "PdbId?",
+ "=" + (modelSetRoot.length() == 4 && modelSetRoot.indexOf(".") < 0 ? modelSetRoot : "1crn"));
+ }
return script;
}
Modified: trunk/Jmol/src/org/jmol/popup/PopupResourceBundle.java
===================================================================
--- trunk/Jmol/src/org/jmol/popup/PopupResourceBundle.java 2008-09-17 03:39:58 UTC (rev 9905)
+++ trunk/Jmol/src/org/jmol/popup/PopupResourceBundle.java 2008-09-18 11:38:04 UTC (rev 9906)
@@ -480,7 +480,7 @@
{ "showSpacegroup", "console on;show spacegroup" },
{ "showState", "console on;show state" },
- { "loadPdb", "load ?=1crn" },
+ { "loadPdb", "load ?PdbId?" },
{ "loadFileOrURL", "load ?" },
{ "loadFileUnitCell", "load ? {1 1 1}" },
{ "loadScript", "script ?.spt" },
Modified: trunk/Jmol/src/org/jmol/viewer/FileManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/FileManager.java 2008-09-17 03:39:58 UTC (rev 9905)
+++ trunk/Jmol/src/org/jmol/viewer/FileManager.java 2008-09-18 11:38:04 UTC (rev 9906)
@@ -613,7 +613,7 @@
break;
boolean isURL = (iurlPrefix >= 0);
boolean isApplet = (appletDocumentBase != null);
- InputStream in;
+ InputStream in = null;
int length;
try {
if (isApplet || isURL) {
@@ -635,6 +635,12 @@
}
return new MonitorInputStream(in, length);
} catch (Exception e) {
+ try {
+ if (in != null)
+ in.close();
+ } catch (IOException e1) {
+ // TODO
+ }
errorMessage = "" + e;
}
return errorMessage;
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-09-17 03:39:58 UTC (rev 9905)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-09-18 11:38:04 UTC (rev 9906)
@@ -3,8 +3,10 @@
version=11.6.RC15
+# note: CML reader only reads the first structure of a file
+# bug fix: CML reader not assigning atom labels
# bug fix: CML files not properly loading symmetry
-# bug fix: O- radius MUCH too large.
+# bug fix: O- formal charge radius MUCH too large; N+ MUCH too small. -- REMOVED
# code: thread control for Java Swing in applet context
# thread creating Swing objects MUST be event thread
# -- using SwingUtilities.invokeAndWait() from the commandWatcher thread
Modified: trunk/Jmol/src/org/jmol/viewer/JmolConstants.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/JmolConstants.java 2008-09-17 03:39:58 UTC (rev 9905)
+++ trunk/Jmol/src/org/jmol/viewer/JmolConstants.java 2008-09-18 11:38:04 UTC (rev 9906)
@@ -1223,7 +1223,19 @@
* At the same time, the table was split into cations and anions for easier
* retrieval.
*
- * Bob Hanson is suspicious of Sn(-IV)
+ * O- and N+ removed 9/2008 - BH. The problem is that
+ * the formal charge is used to determine bonding radius.
+ * But these formal charges are different than the charges used in
+ * compilation of HCP data (which is crystal ionic radii).
+ * Specifically, because O- and N+ are very common in organic
+ * compounds, I have removed their radii from the table FOR OUR PURPOSES HERE.
+ *
+ * I suppose there are some ionic compounds that have O- and N+ as
+ * isolated ions, but what they would be I have no clue. Better to
+ * be safe and go with somewhat more reasonable values.
+ *
+ * Argh. Changed for Jmol 11.6.RC15
+ *
*
****************************************************************/
@@ -1237,7 +1249,7 @@
(5 << 4) + (1 + 4), 350, // "B+1"
(5 << 4) + (3 + 4), 230, // "B+3"
(6 << 4) + (4 + 4), 160, // "C+4"
- (7 << 4) + (1 + 4), 250, // "N+1"
+ (7 << 4) + (1 + 4), 680, // "N+1" // covalent radius -- 250 way too small for organic charges
(7 << 4) + (3 + 4), 160, // "N+3"
(7 << 4) + (5 + 4), 130, // "N+5"
(8 << 4) + (1 + 4), 220, // "O+1"
@@ -1401,24 +1413,24 @@
(1 << 4) + (-1 + 4), 1540, // "H-1"
(6 << 4) + (-4 + 4), 2600, // "C-4"
(7 << 4) + (-3 + 4), 1710, // "N-3"
- (8 << 4) + (-2 + 4), 1320, // "O-2"
- (8 << 4) + (-1 + 4), 1000, // "O-1" // this was 1760! But then RC(=0)O- is rediculously bonded
+ (8 << 4) + (-2 + 4), 1360, // "O-2" *Shannon (1976)
+ (8 << 4) + (-1 + 4), 680, // "O-1" *necessary for CO2-, NO2, etc.
(9 << 4) + (-1 + 4), 1330, // "F-1"
- (14 << 4) + (-4 + 4), 2710, // "Si-4"
- (14 << 4) + (-1 + 4), 3840, // "Si-1" // same problem here?
+ //(14 << 4) + (-4 + 4), 2710, // "Si-4" *not in 77th
+ //(14 << 4) + (-1 + 4), 3840, // "Si-1" *not in 77th
(15 << 4) + (-3 + 4), 2120, // "P-3"
(16 << 4) + (-2 + 4), 1840, // "S-2"
(17 << 4) + (-1 + 4), 1810, // "Cl-1"
(32 << 4) + (-4 + 4), 2720, // "Ge-4"
(33 << 4) + (-3 + 4), 2220, // "As-3"
- (34 << 4) + (-2 + 4), 1910, // "Se-2"
- (34 << 4) + (-1 + 4), 2320, // "Se-1" // same problem here?
+ (34 << 4) + (-2 + 4), 1980, // "Se-2" *Shannon (1976)
+ //(34 << 4) + (-1 + 4), 2320, // "Se-1" *not in 77th
(35 << 4) + (-1 + 4), 1960, // "Br-1"
(50 << 4) + (-4 + 4), 2940, // "Sn-4"
- (50 << 4) + (-1 + 4), 3700, // "Sn-1" // same problem here?
+ (50 << 4) + (-1 + 4), 3700, // "Sn-1"
(51 << 4) + (-3 + 4), 2450, // "Sb-3"
(52 << 4) + (-2 + 4), 2110, // "Te-2"
- (52 << 4) + (-1 + 4), 2500, // "Te-1" // same problem here?
+ (52 << 4) + (-1 + 4), 2500, // "Te-1"
(53 << 4) + (-1 + 4), 2200, // "I-1"
};
Modified: trunk/Jmol/src/org/jmol/viewer/ScriptManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/ScriptManager.java 2008-09-17 03:39:58 UTC (rev 9905)
+++ trunk/Jmol/src/org/jmol/viewer/ScriptManager.java 2008-09-18 11:38:04 UTC (rev 9906)
@@ -87,7 +87,7 @@
scriptItem.addElement(isQuiet ? Boolean.TRUE : Boolean.FALSE);
scriptItem.addElement(new Integer(useCommandThread ? -1 : 1));
scriptQueue.addElement(scriptItem);
- if (Logger.debugging)
+ if (true || Logger.debugging)
Logger.info(scriptQueue.size() + " scripts; added: " + strScript);
startScriptQueue(false);
return "pending";
@@ -143,9 +143,10 @@
Vector getScriptItem(boolean watching, boolean isByCommandWatcher) {
Vector scriptItem = (Vector) scriptQueue.elementAt(0);
int flag = (((Integer) scriptItem.elementAt(5)).intValue());
- boolean isOK = (watching ? flag < 0 : isByCommandWatcher ? flag == 0
+ boolean isOK = (watching ? flag < 0
+ : isByCommandWatcher ? flag == 0
: flag == 1);
- //System.out.println("checking queue for thread " + (watching ? 1 : 0) + "watching = " + watching + " flag=" + flag + " isOK = " + isOK + " " + scriptItem.get(0));
+ //System.out.println("checking queue for thread " + (watching ? 1 : 0) + "watching = " + watching + " isbycommandthread=" + isByCommandWatcher + " flag=" + flag + " isOK = " + isOK + " " + scriptItem.get(0));
return (isOK ? scriptItem : null);
}
@@ -157,23 +158,34 @@
public ScriptQueueRunnable(boolean startedByCommandThread, int pt) {
this.startedByCommandThread = startedByCommandThread;
this.pt = pt;
+ //System.out.println("scriptqueurunnable " + startedByCommandThread + " " + pt + " " + this);
}
public void run() {
while (scriptQueue.size() != 0) {
+ /* System.out.println("run while size != 0: " + this + " pt=" + this.pt + " size=" + scriptQueue.size());
+ for (int i = 0; i < scriptQueue.size(); i++)
+ System.out.println("queue: " + i + " " + scriptQueue.get(i));
+ System.out.println("running: " + scriptQueueRunning[0] + " " + queueThreads[0]);
+ System.out.println("running: " + scriptQueueRunning[1] + " " + queueThreads[1]);
+ */
+
if (!runNextScript())
try {
Thread.sleep(100); //cycle for the command watcher thread
} catch (Exception e) {
+ System.out.println(this + " Exception " + e.getMessage());
break; //-- interrupt?
}
}
- queueThreads[pt] = null;
+ //System.out.println("scriptquenerunnable " + pt + " done " + this);
+ queueThreads[pt].interrupt();
stop();
}
public void stop() {
scriptQueueRunning[pt] = false;
+ queueThreads[pt] = null;
viewer.setSyncDriver(StatusManager.SYNC_ENABLE);
}
@@ -193,7 +205,9 @@
Logger.info("Queue[" + pt + "][" + scriptQueue.size()
+ "] scripts; running: " + script);
}
- scriptQueue.removeElement(scriptItem);
+ //System.out.println("removing: " + scriptItem);
+ scriptQueue.removeElementAt(0);
+ //System.out.println("removed: " + scriptItem);
runScript(returnType, script, statusList, isScriptFile, isQuiet);
if (scriptQueue.size() == 0) {// might have been cleared with an exit
//Logger.info("SCRIPT QUEUE READY", 0);
@@ -205,8 +219,10 @@
private void runScript(String returnType, String strScript,
String statusList, boolean isScriptFile,
boolean isQuiet) {
+ //System.out.println("runScript evalstrngwait " + strScript);
viewer.evalStringWaitStatus(returnType, strScript, statusList,
isScriptFile, isQuiet, true);
+ //System.out.println("runScript evalstrngwait DONE");
}
}
@@ -250,7 +266,7 @@
* The 5th vector position is an Integer flag.
*
* -1 -- Owned by CommandWatcher; ready for thread assignment
- * 0 -- Owned by CommmadWatcher; running
+ * 0 -- Owned by CommandWatcher; running
* 1 -- Owned by the JavaScript-enabled/browser-limited thread
*
* If the command is to be ignored by the CommandWatcher, the flag is set
@@ -283,7 +299,7 @@
}
}
} catch (InterruptedException ie) {
- Logger.info("CommandWatcher InterruptedException!");
+ Logger.info("CommandWatcher InterruptedException! " + this);
break;
} catch (Exception ie) {
String s = "script processing ERROR:\n\n" + ie.toString();
Modified: trunk/Jmol/src/org/jmol/viewer/StatusManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StatusManager.java 2008-09-17 03:39:58 UTC (rev 9905)
+++ trunk/Jmol/src/org/jmol/viewer/StatusManager.java 2008-09-18 11:38:04 UTC (rev 9906)
@@ -267,7 +267,7 @@
&& viewer.getDebugScript()) {
jmolStatusListener.notifyCallback(JmolConstants.CALLBACK_SCRIPT,
new Object[] { null, "script <exiting>", statusMessage, new Integer(-1) });
- strStatus = "Chime script completed.";
+ strStatus = "Jmol script completed.";
}
jmolStatusListener.notifyCallback(JmolConstants.CALLBACK_SCRIPT,
new Object[] { null, strStatus, statusMessage,
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-09-17 03:39:58 UTC (rev 9905)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-09-18 11:38:04 UTC (rev 9906)
@@ -425,7 +425,7 @@
stateManager.setCrystallographicDefaults();//modelSet.someModelsHavePeriodicOrigin);
else
setAxesModeMolecular(false);
-
+ prevFrame = Integer.MIN_VALUE;
refresh(1, "Viewer:homePosition()");
}
@@ -3423,7 +3423,6 @@
/// direct no-queue use:
public String scriptWait(String strScript) {
- //System.out.println("Viewer scriptWait1 " + htmlName + " " + strScript + " ");
scriptManager.waitForQueue();
boolean doTranslateTemp = GT.getDoTranslate();
GT.setDoTranslate(false);
@@ -3435,7 +3434,6 @@
}
public Object scriptWaitStatus(String strScript, String statusList) {
- //System.out.println("Viewer scriptWait2 " + htmlName + " " + strScript);
scriptManager.waitForQueue();
boolean doTranslateTemp = GT.getDoTranslate();
GT.setDoTranslate(false);
@@ -3447,7 +3445,6 @@
public Object evalStringWaitStatus(String returnType, String strScript,
String statusList) {
- //System.out.println("Viewer scriptWait3 " + htmlName + " " + strScript);
scriptManager.waitForQueue();
return evalStringWaitStatus(returnType, strScript, statusList, false,
false, false);
@@ -3461,6 +3458,8 @@
boolean isScriptFile,
boolean isQuiet, boolean isQueued) {
// from the scriptManager or scriptWait()
+ System.out.println("DEBUG: evalStringWaitStatus " + Thread.currentThread().getName()
+ + " " + Thread.currentThread().getId());
if (checkResume(strScript))
return "script processing resumed"; //be very odd if this fired
if (checkHalt(strScript))
@@ -3907,9 +3906,12 @@
statusManager.setJmolStatusListener(jmolStatusListener);
}
+ int prevFrame = Integer.MIN_VALUE;
+
void setStatusFrameChanged(int frameNo) {
transformManager.setVibrationPeriod(Float.NaN);
int modelIndex = repaintManager.currentModelIndex;
+
int firstIndex = repaintManager.firstModelIndex;
int lastIndex = repaintManager.lastModelIndex;
@@ -3944,6 +3946,11 @@
global.setParameterValue("_modelFile", (modelIndex < 0 ? ""
: getModelFileName(modelIndex)));
+ if (modelIndex == prevFrame) {
+ return;
+ }
+ prevFrame = modelIndex;
+
s = statusManager.getCallbackScript("animframecallback");
if (s != null)
evalStringQuiet(s, true, false);
@@ -3966,7 +3973,7 @@
String fileName, String modelName,
String strError) {
String s = statusManager.getCallbackScript("loadstructcallback");
- if (s != null)
+ if (s != null && ptLoad >= 0 && strError == null)
evalStringQuiet(s, true, false);
statusManager.setStatusFileLoaded(s, fullPathName, fileName, modelName,
strError, ptLoad);
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-09-20 15:29:30
|
Revision: 9910
http://jmol.svn.sourceforge.net/jmol/?rev=9910&view=rev
Author: hansonr
Date: 2008-09-20 15:29:23 +0000 (Sat, 20 Sep 2008)
Log Message:
-----------
11.6.RC15 VERSION
# new feature: data() and DATA expanded to allow fixed-column entry
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
trunk/Jmol/src/org/jmol/util/Parser.java
trunk/Jmol/src/org/jmol/viewer/DataManager.java
trunk/Jmol/src/org/jmol/viewer/Eval.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/StateManager.java
trunk/Jmol/src/org/jmol/viewer/Token.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2008-09-20 01:51:41 UTC (rev 9909)
+++ trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2008-09-20 15:29:23 UTC (rev 9910)
@@ -656,7 +656,7 @@
taint(atomIndex, (byte) type);
}
if (type == TAINT_MAX && n > 0)
- viewer.setData(name, new Object[] {name, fData, bs}, 0, 0, 0);
+ viewer.setData(name, new Object[] {name, fData, bs}, 0, 0, 0, 0, 0);
} catch (Exception e) {
Logger.error("AtomCollection.loadData error: " + e);
Modified: trunk/Jmol/src/org/jmol/util/Parser.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Parser.java 2008-09-20 01:51:41 UTC (rev 9909)
+++ trunk/Jmol/src/org/jmol/util/Parser.java 2008-09-20 15:29:23 UTC (rev 9910)
@@ -74,55 +74,102 @@
}
return data;
}
+
+ /**
+ *
+ * @param f
+ * @param bs
+ * @param data
+ */
+ public static void setSelectedFloats(float f, BitSet bs, float[] data) {
+ for (int i = 0; i < data.length; i++)
+ if (bs == null || bs.get(i))
+ data[i] = f;
+ }
- public static void parseFloatArrayFromMatchAndField(String str, BitSet bs,
- int fieldMatch,
- int[] matchData,
- int field, float[] data) {
+ public static float[] extractData(String data, int field, int nBytes,
+ int firstLine) {
+ return parseFloatArrayFromMatchAndField(data, null, 0, 0, null, field,
+ nBytes, null, firstLine);
+ }
+
+ /**
+ * the major lifter here.
+ *
+ * @param str string containing the data
+ * @param bs selects specific rows of the data
+ * @param fieldMatch a free-format field pointer, or a column pointer
+ * @param fieldMatchColumnCount specifies a column count -- not free-format
+ * @param matchData an array of data to match (atom numbers)
+ * @param field a free-format field pointer, or a column pointer
+ * @param fieldColumnCount specifies a column count -- not free-format
+ * @param data float array to modify or null if size unknown
+ * @param firstLine first line to parse (1 indicates all)
+ * @return data
+ */
+ public static float[] parseFloatArrayFromMatchAndField(
+ String str,
+ BitSet bs,
+ int fieldMatch,
+ int fieldMatchColumnCount,
+ int[] matchData,
+ int field,
+ int fieldColumnCount,
+ float[] data, int firstLine) {
float f;
- if (field == Integer.MIN_VALUE) { //just one value
- f = parseFloat(str);
- for (int i = 0; i < data.length; i++)
- if (bs == null || bs.get(i))
- data[i] = f;
- return;
- }
- if (field <= 0) {
- parseFloatArray(str, bs, data);
- return;
- }
- int len = data.length;
int i = -1;
boolean isMatch = (matchData != null);
int[] lines = markLines(str, (str.indexOf('\n') >= 0 ? '\n' : ';'));
+ int iLine = (firstLine <= 1 || firstLine >= lines.length ? 0 : firstLine - 1);
+ int pt = (iLine == 0 ? 0 : lines[iLine - 1]);
int nLines = lines.length;
- int pt = 0;
- for (int iLine = 0; iLine < nLines; iLine++) {
- String[] tokens = getTokens(str.substring(pt, lines[iLine]));
+ if (data == null)
+ data = new float[nLines - iLine];
+ int len = data.length;
+ int minLen = (fieldColumnCount <= 0 ? Math.max(field, fieldMatch) : Math
+ .max(field + fieldColumnCount, fieldMatch + fieldMatchColumnCount) - 1);
+
+ for (; iLine < nLines; iLine++) {
+ String line = str.substring(pt, lines[iLine]).trim();
pt = lines[iLine];
- if (tokens.length < field || tokens.length < fieldMatch
- || Float.isNaN(f = parseFloat(tokens[field - 1])))
- continue;
+ String[] tokens = (fieldColumnCount <= 0 ? getTokens(line) : null);
+ // check for inappropriate data -- line too short or too few tokens or NaN for data
+ // and parse data
+ if (fieldColumnCount <= 0) {
+ if (tokens.length < minLen
+ || Float.isNaN(f = parseFloat(tokens[field - 1])))
+ continue;
+ } else {
+ if (line.length() < minLen
+ || Float.isNaN(f = parseFloat(line.substring(field - 1, field
+ + fieldColumnCount - 1))))
+ continue;
+ }
int iData;
if (isMatch) {
- iData = parseInt(tokens[fieldMatch - 1]);
- //in the fieldMatch column we have an integer pointing into matchData
- //we replace that number then with the corresponding number in matchData
+ iData = parseInt(tokens == null ? line.substring(fieldMatch - 1,
+ fieldMatch + fieldMatchColumnCount - 1) : tokens[fieldMatch - 1]);
+ // in the fieldMatch column we have an integer pointing into matchData
+ // we replace that number then with the corresponding number in matchData
if (iData == Integer.MIN_VALUE || iData < 0 || iData >= len
|| (iData = matchData[iData]) < 0)
continue;
+ // and we set bs to indicate we are updating that value
if (bs != null)
bs.set(iData);
} else {
+ // no match data
+ // bs here indicates the specific data elements that need filling
while (++i < len && bs != null && !bs.get(i)) {
}
if (i >= len)
- return;
+ return data;
iData = i;
}
data[iData] = f;
- //System.out.println("assigning " + data[iData] + " to " + iData);
+ //System.out.println("data[" + iData + "] = " + data[iData]);
}
+ return data;
}
/**
Modified: trunk/Jmol/src/org/jmol/viewer/DataManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/DataManager.java 2008-09-20 01:51:41 UTC (rev 9909)
+++ trunk/Jmol/src/org/jmol/viewer/DataManager.java 2008-09-20 15:29:23 UTC (rev 9910)
@@ -51,7 +51,8 @@
}
void setData(Viewer viewer, String type, Object[] data, int atomCount,
- int matchField, int field) {
+ int matchField, int matchFieldColumnCount, int field,
+ int fieldColumnCount) {
//Eval
/*
* data[0] -- label
@@ -78,41 +79,56 @@
}
if (bsUserVdws == null)
setUserVdw(defaultVdw);
- Parser.parseFloatArrayFromMatchAndField(stringData, bsUserVdws, 1, (int[]) data[2], 2, userVdws);
- for (int i = userVdws.length; --i >= 0; )
- userVdwMars[i] = (int)(userVdws[i] * 1000);
+ Parser.parseFloatArrayFromMatchAndField(stringData, bsUserVdws, 1, 0,
+ (int[]) data[2], 2, 0, userVdws, 1);
+ for (int i = userVdws.length; --i >= 0;)
+ userVdwMars[i] = (int) (userVdws[i] * 1000);
return;
- }
+ }
if (data[2] != null && atomCount > 0) {
String stringData = (String) data[1];
- boolean createNew = (matchField != 0
- || field != Integer.MIN_VALUE && field != Integer.MAX_VALUE);
+ boolean createNew = (matchField != 0 || field != Integer.MIN_VALUE
+ && field != Integer.MAX_VALUE);
Object[] oldData = (Object[]) dataValues.get(type);
BitSet bs;
- float[] f = (oldData == null || createNew ? new float[atomCount]
+ float[] f = (oldData == null || createNew ? new float[atomCount]
: ArrayUtil.ensureLength(((float[]) oldData[1]), atomCount));
+
+ // check to see if the data COULD be interpreted as a string of float values
+ // and if so, do that. This pre-fetches the tokens in that case.
+
String[] strData = null;
- if (field == Integer.MIN_VALUE &&
- (strData = Parser.getTokens(stringData)).length > 1)
+ if (field == Integer.MIN_VALUE
+ && (strData = Parser.getTokens(stringData)).length > 1)
field = 0;
- if (field == 0 || field == Integer.MAX_VALUE) {
+
+ if (field == Integer.MIN_VALUE) {
+ // set the selected data elements to a single value
bs = (BitSet) data[2];
- if (strData == null)
- strData = Parser.getTokens(stringData);
- Parser.parseFloatArray(strData, bs, f);
- } else if (matchField == 0) {
+ Parser.setSelectedFloats(Parser.parseFloat(stringData), bs, f);
+ } else if (field == 0 || field == Integer.MAX_VALUE) {
+ // just get the selected token values
bs = (BitSet) data[2];
- Parser.parseFloatArrayFromMatchAndField(stringData, bs, 0, null, field, f);
+ Parser.parseFloatArray(strData == null ? Parser.getTokens(stringData)
+ : strData, bs, f);
+ } else if (matchField <= 0) {
+ // get the specified field >= 1 for the selected atoms
+ bs = (BitSet) data[2];
+ Parser.parseFloatArrayFromMatchAndField(stringData, bs, 0, 0, null,
+ field, fieldColumnCount, f, 1);
} else {
- int[] iData = (int[]) data[2];
+ // get the selected field, with an integer match in a specified field
+ // in this case, bs is created and indicates which data points were set
+ int[] iData = (int[]) data[2];
+ Parser.parseFloatArrayFromMatchAndField(stringData, null, matchField,
+ matchFieldColumnCount, iData, field, fieldColumnCount, f, 1);
bs = new BitSet();
- Parser.parseFloatArrayFromMatchAndField(stringData, null, matchField, iData, field, f);
- for (int i = iData.length; --i >= 0; )
+ for (int i = iData.length; --i >= 0;)
if (iData[i] >= 0)
bs.set(iData[i]);
}
if (oldData != null && oldData[2] instanceof BitSet && !createNew)
- bs.or((BitSet)(oldData[2]));
+ bs.or((BitSet) (oldData[2]));
data[2] = bs;
data[1] = f;
if (type.indexOf("property_") == 0) {
@@ -125,7 +141,7 @@
fValues[n++] = f[i];
viewer.setAtomProperty(bs, tok, 0, 0, fValues);
}
- }
+ }
}
dataValues.put(type, data);
}
@@ -281,5 +297,5 @@
return (bs == null ? sb.toString() :
"\n DATA \"element_vdw\"\n" + sb.append(" end \"element_vdw\";\n\n").toString());
}
-
+
}
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-09-20 01:51:41 UTC (rev 9909)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-09-20 15:29:23 UTC (rev 9910)
@@ -4003,7 +4003,7 @@
dataLabel = parameterAsString(1);
if (dataLabel.equalsIgnoreCase("clear")) {
if (!isSyntaxCheck)
- viewer.setData(null, null, 0, 0, 0);
+ viewer.setData(null, null, 0, 0, 0, 0, 0);
return;
}
if ((i = dataLabel.indexOf("@")) >= 0) {
@@ -4039,13 +4039,14 @@
for (int ie = 1; ie <= n; ie++)
eArray[ie] = ie;
data[2] = eArray;
- viewer.setData("element_vdw", data, n, 0, 0);
+ viewer.setData("element_vdw", data, n, 0, 0, 0, 0);
return;
- } else if (dataType.indexOf("data2d_") == 0) {
+ }
+ if (dataType.indexOf("data2d_") == 0) {
//data2d someName
data[0] = dataLabel;
data[1] = Parser.parseFloatArray2d(dataString);
- viewer.setData(dataLabel, data, 0, 0, 0);
+ viewer.setData(dataLabel, data, 0, 0, 0, 0, 0);
return;
}
String[] tokens = Parser.getTokens(dataLabel);
@@ -4053,22 +4054,34 @@
&& !(tokens.length == 2 && tokens[1].equals("set"))) {
BitSet bs = viewer.getSelectionSet();
data[0] = dataType;
- int atomNumberField = isOneValue ? 0 : ((Integer) viewer
- .getParameter("propertyAtomNumberField")).intValue();
- int propertyField = isOneValue ? Integer.MIN_VALUE : ((Integer) viewer
- .getParameter("propertyDataField")).intValue();
+ int atomNumberField = (isOneValue ? 0 : ((Integer) viewer
+ .getParameter("propertyAtomNumberField")).intValue());
+ int atomNumberFieldColumnCount = (isOneValue ? 0 : ((Integer) viewer
+ .getParameter("propertyAtomNumberColumnCount")).intValue());
+ int propertyField = (isOneValue ? Integer.MIN_VALUE : ((Integer) viewer
+ .getParameter("propertyDataField")).intValue());
+ int propertyFieldColumnCount = (isOneValue ? 0 : ((Integer) viewer
+ .getParameter("propertyDataColumnCount")).intValue());
if (!isOneValue && dataLabel.indexOf(" ") >= 0) {
- // DATA "property_whatever [atomField] [propertyField]"
if (tokens.length == 3) {
+ // DATA "property_whatever [atomField] [propertyField]"
dataLabel = tokens[0];
atomNumberField = Parser.parseInt(tokens[1]);
propertyField = Parser.parseInt(tokens[2]);
- if (atomNumberField < 0)
- atomNumberField = 0;
- if (propertyField < 0)
- propertyField = 0;
}
+ if (tokens.length == 5) {
+ // DATA "property_whatever [atomField] [atomFieldColumnCount] [propertyField] [propertyDataColumnCount]"
+ dataLabel = tokens[0];
+ atomNumberField = Parser.parseInt(tokens[1]);
+ atomNumberFieldColumnCount = Parser.parseInt(tokens[2]);
+ propertyField = Parser.parseInt(tokens[3]);
+ propertyFieldColumnCount = Parser.parseInt(tokens[4]);
+ }
}
+ if (atomNumberField < 0)
+ atomNumberField = 0;
+ if (propertyField < 0)
+ propertyField = 0;
int atomCount = viewer.getAtomCount();
int[] atomMap = null;
BitSet bsAtoms = new BitSet(atomCount);
@@ -4091,12 +4104,12 @@
}
data[1] = dataString;
viewer.setData(dataType, data, atomCount, atomNumberField,
- propertyField);
+ atomNumberFieldColumnCount, propertyField, propertyFieldColumnCount);
userType = Integer.MAX_VALUE; //we're done
} else {
data[0] = dataLabel;
data[1] = dataString;
- viewer.setData(dataType, data, 0, 0, 0);
+ viewer.setData(dataType, data, 0, 0, 0, 0, 0);
}
}
if (processModel) {
@@ -4771,7 +4784,7 @@
return;
}
if (tokAt(1) == Token.vanderwaals) {
- viewer.setData("element_vdw", new Object[] {null, ""}, 0, 0, 0);
+ viewer.setData("element_vdw", new Object[] {null, ""}, 0, 0, 0, 0, 0);
return;
}
String var = parameterAsString(1);
@@ -7164,7 +7177,7 @@
if (propertyName.startsWith("property_")) {
viewer.setData(propertyName, new Object[] { propertyName,
Token.sValue(tv), bs }, viewer.getAtomCount(), 0,
- tv.tok == Token.list ? Integer.MAX_VALUE : Integer.MIN_VALUE);
+ 0, tv.tok == Token.list ? Integer.MAX_VALUE : Integer.MIN_VALUE, 0);
return;
}
setBitsetProperty(bs, tokProperty, Token.iValue(tv), Token.fValue(tv), tv);
@@ -7180,7 +7193,7 @@
int n = viewer.getAtomCount();
viewer.setData(key,
new Object[] { key, "" + v, viewer.getSelectionSet() }, n, 0,
- Integer.MIN_VALUE);
+ 0, Integer.MIN_VALUE, 0);
return;
}
if (v == null)
@@ -11420,7 +11433,7 @@
boolean useBraces = true;//(!Compiler.tokAttr(tok, Token.atomExpressionCommand));
boolean inBrace = false;
boolean inClauseDefine = false;
- boolean setEquals = (tok == Token.set && ((String) statement[0].value) == "");
+ boolean setEquals = (tok == Token.set && ((String) statement[0].value) == "" && tokAt(1) != Token.expressionBegin);
for (int i = 0; i < statementLength; ++i) {
if (iToken == i - 1)
sb.append(" <<");
@@ -11608,9 +11621,10 @@
else if (message.indexOf("file recognized as a script file:") >= 0)
isOK = true;
if (!isOK) {
- this.message += contextTrace();
- if (!isSyntaxCheck)
+ if (!isSyntaxCheck) {
+ this.message += contextTrace();
Logger.error("eval ERROR: " + toString());
+ }
}
}
@@ -12611,12 +12625,43 @@
}
private boolean evaluateData(Token[] args) {
- if (args.length == 0 || args.length > 2)
+
+ // x = data("somedataname") # the data
+ // x = data("data2d_xxxx") # 2D data (x,y paired values)
+ // x = data("data2d_xxxx", iSelected) # selected row of 2D data, with <=0 meaning "relative to the last row"
+ // x = data("property_x", "property_y") # array addition of two property sets
+ // x = data({atomno < 10},"xyz") # (or "pdb" or "mol") coordinate data in xyz, pdb, or mol format
+ // x = data(someData,ptrFieldOrColumn,nBytes,firstLine) # extraction of a column of data based on a field (nBytes = 0) or column range (nBytes > 0)
+ if (args.length != 1 && args.length != 2 && args.length != 4)
return false;
if (isSyntaxCheck)
return addX("");
String selected = Token.sValue(args[0]);
String type = (args.length == 2 ? Token.sValue(args[1]) : "");
+
+ if (args.length == 4) {
+ int iField = Token.iValue(args[1]);
+ int nBytes = Token.iValue(args[2]);
+ int firstLine = Token.iValue(args[3]);
+ float[] f = Parser.extractData(selected, iField, nBytes, firstLine);
+ return addX(Escape.escape(f));
+ }
+
+ if (selected.indexOf("data2d_") == 0) {
+ // tab, newline separated data
+ float[][] f1 = viewer.getDataFloat2D(selected);
+ if (f1 == null)
+ return addX("");
+ if (args.length == 2 && args[1].tok == Token.integer) {
+ int pt = args[1].intValue;
+ if (pt < 0)
+ pt += f1.length;
+ if (pt >= 0 && pt < f1.length)
+ return addX(Escape.escape(f1[pt]));
+ return addX("");
+ }
+ return addX(Escape.escape(f1, false));
+ }
// parallel addition of float property data sets
@@ -12633,20 +12678,6 @@
}
return addX(Escape.escape(f1));
}
- if (selected.indexOf("data2d_") == 0) {
- float[][] f1 = viewer.getDataFloat2D(selected);
- if (f1 == null)
- return addX("");
- if (args.length == 2 && args[1].tok == Token.integer) {
- int pt = args[1].intValue;
- if (pt < 0)
- pt += f1.length;
- if (pt >= 0 && pt < f1.length)
- return addX(Escape.escape(f1[pt]));
- return addX("");
- }
- return addX(Escape.escape(f1, false));
- }
// some other data type -- just return it
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-09-20 01:51:41 UTC (rev 9909)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-09-20 15:29:23 UTC (rev 9910)
@@ -3,6 +3,7 @@
version=11.6.RC15
+# new feature: data() and DATA expanded to allow fixed-column entry
# bug fix: data property_partialcharge does not update atomic partialCharge data itself for MEP
# but instead just creates a data type "property_partialcharge"
# bug fix: CML reader failst to load primitive lattice parameters when no symmetry
Modified: trunk/Jmol/src/org/jmol/viewer/StateManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StateManager.java 2008-09-20 01:51:41 UTC (rev 9909)
+++ trunk/Jmol/src/org/jmol/viewer/StateManager.java 2008-09-20 15:29:23 UTC (rev 9910)
@@ -1195,8 +1195,10 @@
setParameterValue("pointGroupLinearTolerance", pointGroupLinearTolerance);
setParameterValue("pointGroupDistanceTolerance", pointGroupDistanceTolerance);
setParameterValue("propertyColorScheme", propertyColorScheme);
+ setParameterValue("propertyAtomNumberColumnCount", 0);
+ setParameterValue("propertyAtomNumberField", 0);
+ setParameterValue("propertyDataColumnCount", 0);
setParameterValue("propertyDataField", 0);
- setParameterValue("propertyAtomNumberField", 0);
setParameterValue("quaternionFrame", quaternionFrame);
setParameterValue("rangeSelected", rangeSelected);
setParameterValue("refreshing", true);
Modified: trunk/Jmol/src/org/jmol/viewer/Token.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Token.java 2008-09-20 01:51:41 UTC (rev 9909)
+++ trunk/Jmol/src/org/jmol/viewer/Token.java 2008-09-20 15:29:23 UTC (rev 9910)
@@ -540,9 +540,8 @@
// xxx(a,b)
final static int random = 1 | 2 << 9 | mathfunc;
- final static int data = 2 | 2 << 9 | mathfunc | command;
- final static int cross = 3 | 2 << 9 | mathfunc;
- final static int script = 4 | 2 << 9 | mathfunc | command;
+ final static int cross = 2 | 2 << 9 | mathfunc;
+ final static int script = 3 | 2 << 9 | mathfunc | command;
// ___.xxx(a,b)
@@ -562,10 +561,11 @@
// xxx(a,b,c,d)
final static int angle = 1 | 4 << 9 | mathfunc;
- final static int plane = 2 | 4 << 9 | mathfunc;
- final static int point = 3 | 4 << 9 | mathfunc;
- final static int quaternion = 4 | 4 << 9 | mathfunc | command;
- final static int axisangle = 5 | 4 << 9 | mathfunc;
+ final static int data = 2 | 4 << 9 | mathfunc | command;
+ final static int plane = 3 | 4 << 9 | mathfunc;
+ final static int point = 4 | 4 << 9 | mathfunc;
+ final static int quaternion = 5 | 4 << 9 | mathfunc | command;
+ final static int axisangle = 6 | 4 << 9 | mathfunc;
// xxx(a,b,c,d,e)
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-09-20 01:51:41 UTC (rev 9909)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-09-20 15:29:23 UTC (rev 9910)
@@ -2597,8 +2597,10 @@
}
public void setData(String type, Object[] data, int atomCount,
- int matchField, int field) {
- dataManager.setData(this, type, data, atomCount, matchField, field);
+ int matchField, int matchFieldColumnCount, int field,
+ int fieldColumnCount) {
+ dataManager.setData(this, type, data, atomCount, matchField,
+ matchFieldColumnCount, field, fieldColumnCount);
}
public static Object testData; // for isosurface
@@ -4454,6 +4456,15 @@
boolean notFound = false;
while (true) {
+ //11.6.RC16//
+ if (key.equalsIgnoreCase("propertyDataColumnCount")) {
+ break;
+ }
+
+ if (key.equalsIgnoreCase("propertyAtomNumberColumnCount")) {
+ break;
+ }
+
//11.6.RC2//
if (key.equalsIgnoreCase("dotDensity")) {
global.dotDensity = value;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-09-20 20:06:12
|
Revision: 9911
http://jmol.svn.sourceforge.net/jmol/?rev=9911&view=rev
Author: hansonr
Date: 2008-09-20 20:06:04 +0000 (Sat, 20 Sep 2008)
Log Message:
-----------
11.6.RC15 VERSION
# new feature: MOL2 reader is PDB-enabled.
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/more/Mol2Reader.java
trunk/Jmol/src/org/jmol/adapter/smarter/SmarterJmolAdapter.java
trunk/Jmol/src/org/jmol/api/JmolAdapter.java
trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
trunk/Jmol/src/org/jmol/quantum/MOCalculation.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/JmolConstants.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/more/Mol2Reader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/more/Mol2Reader.java 2008-09-20 15:29:23 UTC (rev 9910)
+++ trunk/Jmol/src/org/jmol/adapter/readers/more/Mol2Reader.java 2008-09-20 20:06:04 UTC (rev 9911)
@@ -55,6 +55,7 @@
int nAtoms = 0;
int atomCount = 0;
+ boolean isPDB = false;
public AtomSetCollection readAtomSetCollection(BufferedReader reader) {
this.reader = reader;
@@ -97,6 +98,7 @@
*/
+ isPDB = false;
String thisDataSetName = readLineTrimmed();
readLine();
line += " 0 0 0 0 0 0";
@@ -128,11 +130,15 @@
readLine();
}
nAtoms += atomCount;
+ if (isPDB) {
+ atomSetCollection.setAtomSetCollectionAuxiliaryInfo("isPDB",
+ Boolean.TRUE);
+ atomSetCollection.setAtomSetAuxiliaryInfo("isPDB", Boolean.TRUE);
+ }
applySymmetry();
}
- void readAtoms(int atomCount, boolean iHaveCharges)
- throws Exception {
+ void readAtoms(int atomCount, boolean iHaveCharges) throws Exception {
// 1 Cs 0.0000 4.1230 0.0000 Cs 1 RES1 0.0000
// 1 C1 7.0053 11.3096 -1.5429 C.3 1 <0> -0.1912
// free format, but no blank lines
@@ -149,13 +155,47 @@
if (elementSymbol.length() > 2)
elementSymbol = elementSymbol.substring(0, 2);
atom.elementSymbol = elementSymbol;
- // apparently "NO_CHARGES" is not strictly enforced
- // if (iHaveCharges)
+ // apparently "NO_CHARGES" is not strictly enforced
+ // if (iHaveCharges)
+ if (tokens.length > 6)
+ atom.sequenceNumber = parseInt(tokens[6]);
+ if (tokens.length > 7) {
+ atom.group3 = tokens[7];
+ atom.isHetero = JmolAdapter.isHetero(atom.group3);
+ if (atom.group3.length() == 3
+ && JmolAdapter.lookupGroupID(atom.group3) >= 0) {
+ isPDB = true;
+ }
+ if (isPDB)
+ atom.elementSymbol = deduceElementSymbol(atom.isHetero, tokens[5], atom.group3);
+ }
if (tokens.length > 8)
atom.partialCharge = parseFloat(tokens[8]);
}
}
+ String deduceElementSymbol(boolean isHetero, String XX, String group3) {
+ // short of having an entire table,
+ if (XX.equalsIgnoreCase(group3))
+ return XX; // Cd Mg etc.
+ char ch1 = XX.charAt(0);
+ char ch2 = (XX.length() > 1 ? XX.charAt(1) : ' ');
+ String full = group3 + "." + ch1 + ch2;
+ // Cd Nd Ne are not in complex hetero; Ca is in these:
+ if (("OEC.CA ICA.CA OC1.CA OC2.CA OC4.CA").indexOf(full)>=0)
+ return "Ca";
+ if ("NA NB NC ND NE NF NG NH CA CB CC CD CE CF CG CH OA OB OC OD OE OF OG OH".indexOf(XX) >= 0)
+ return "" + ch1;
+ if (isHetero && Atom.isValidElementSymbolNoCaseSecondChar(ch1, ch2))
+ return (isHetero || ch1 != 'H' ? XX.trim() : "H");
+ if (Atom.isValidElementSymbol(ch1))
+ return "" + ch1;
+ if (Atom.isValidElementSymbol(ch2))
+ return "" + ch2;
+ return "Xx";
+ }
+
+
void readBonds(int bondCount) throws Exception {
// 6 1 42 1
// free format, but no blank lines
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/SmarterJmolAdapter.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/SmarterJmolAdapter.java 2008-09-20 15:29:23 UTC (rev 9910)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/SmarterJmolAdapter.java 2008-09-20 20:06:04 UTC (rev 9911)
@@ -401,7 +401,6 @@
.getAtomSetAuxiliaryInfo(atomSetIndex);
}
-
/* **************************************************************
* The frame related methods
* **************************************************************/
@@ -512,6 +511,7 @@
public int getSequenceNumber() { return atom.sequenceNumber; }
public char getInsertionCode()
{ return canonizeInsertionCode(atom.insertionCode); }
+
}
class BondIterator extends JmolAdapter.BondIterator {
@@ -597,6 +597,7 @@
return structure.endInsertionCode;
}
}
+
}
Modified: trunk/Jmol/src/org/jmol/api/JmolAdapter.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/JmolAdapter.java 2008-09-20 15:29:23 UTC (rev 9910)
+++ trunk/Jmol/src/org/jmol/api/JmolAdapter.java 2008-09-20 20:06:04 UTC (rev 9911)
@@ -30,7 +30,7 @@
import java.util.Hashtable;
import java.util.BitSet;
-import org.jmol.quantum.MOCalculation;
+import org.jmol.modelset.Group;
import org.jmol.viewer.JmolConstants;
/****************************************************************
@@ -68,14 +68,14 @@
public final static short ORDER_PARTIAL32 = JmolConstants.BOND_PARTIAL32;
public final static short ORDER_UNSPECIFIED = JmolConstants.BOND_ORDER_UNSPECIFIED;
- public final static int SHELL_S = MOCalculation.SHELL_S;
- public final static int SHELL_P = MOCalculation.SHELL_P;
- public final static int SHELL_SP = MOCalculation.SHELL_SP;
- public final static int SHELL_L = MOCalculation.SHELL_L;
- public final static int SHELL_D_CARTESIAN = MOCalculation.SHELL_D_CARTESIAN;
- public final static int SHELL_D_SPHERICAL = MOCalculation.SHELL_D_SPHERICAL;
- public final static int SHELL_F_CARTESIAN = MOCalculation.SHELL_F_CARTESIAN;
- public final static int SHELL_F_SPHERICAL = MOCalculation.SHELL_F_SPHERICAL;
+ public final static int SHELL_S = JmolConstants.SHELL_S;
+ public final static int SHELL_P = JmolConstants.SHELL_P;
+ public final static int SHELL_SP = JmolConstants.SHELL_SP;
+ public final static int SHELL_L = JmolConstants.SHELL_L;
+ public final static int SHELL_D_CARTESIAN = JmolConstants.SHELL_D_CARTESIAN;
+ public final static int SHELL_D_SPHERICAL = JmolConstants.SHELL_D_SPHERICAL;
+ public final static int SHELL_F_CARTESIAN = JmolConstants.SHELL_F_CARTESIAN;
+ public final static int SHELL_F_SPHERICAL = JmolConstants.SHELL_F_SPHERICAL;
public static String getElementSymbol(int elementNumber) {
return JmolConstants.elementSymbolFromNumber(elementNumber);
@@ -90,25 +90,30 @@
}
public static int getQuantumShellTagID(String tag) {
- return MOCalculation.getQuantumShellTagID(tag);
+ return JmolConstants.getQuantumShellTagID(tag);
}
public static int getQuantumShellTagIDSpherical(String tag) {
- return MOCalculation.getQuantumShellTagIDSpherical(tag);
+ return JmolConstants.getQuantumShellTagIDSpherical(tag);
}
final public static int getQuantumSubshellTagID(int shell, String tag) {
- return MOCalculation.getQuantumSubshellTagID(shell, tag);
+ return JmolConstants.getQuantumSubshellTagID(shell, tag);
}
final public static String getQuantumSubshellTag(int shell, int subshell) {
- return MOCalculation.getQuantumSubshellTag(shell, subshell);
+ return JmolConstants.getQuantumSubshellTag(shell, subshell);
}
final public static String canonicalizeQuantumSubshellTag(String tag) {
- return MOCalculation.canonicalizeQuantumSubshellTag(tag);
+ return JmolConstants.canonicalizeQuantumSubshellTag(tag);
}
-
+
+ final public static short lookupGroupID(String group3) {
+ return Group.lookupGroupID(group3);
+ }
+
+
//////////////////////////////////////////////////////////////////
// file related
//////////////////////////////////////////////////////////////////
Modified: trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2008-09-20 15:29:23 UTC (rev 9910)
+++ trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2008-09-20 20:06:04 UTC (rev 9911)
@@ -964,9 +964,9 @@
sb.append("MODEL " + (iModelLast + 1) + "\n");
}
if (a.isHetero())
- sb.append(a.formatLabel("HETATM%5i %-4a%1A%3n %1c%4R%1E %8.3x%8.3y%8.3z%6.2Q%6.2b %2e \n", '\0', null));
+ sb.append(a.formatLabel("HETATM%5i %-4a%1A%3.3n %1c%4R%1E %8.3x%8.3y%8.3z%6.2Q%6.2b %2e \n", '\0', null));
else
- sb.append(a.formatLabel("ATOM %5i %-4a%1A%3n %1c%4R%1E %8.3x%8.3y%8.3z%6.2Q%6.2b %2e \n", '\0', null));
+ sb.append(a.formatLabel("ATOM %5i %-4a%1A%3.3n %1c%4R%1E %8.3x%8.3y%8.3z%6.2Q%6.2b %2e \n", '\0', null));
}
if (showModels)
sb.append("ENDMDL\n");
Modified: trunk/Jmol/src/org/jmol/quantum/MOCalculation.java
===================================================================
--- trunk/Jmol/src/org/jmol/quantum/MOCalculation.java 2008-09-20 15:29:23 UTC (rev 9910)
+++ trunk/Jmol/src/org/jmol/quantum/MOCalculation.java 2008-09-20 20:06:04 UTC (rev 9911)
@@ -27,11 +27,12 @@
import org.jmol.api.VolumeDataInterface;
import org.jmol.jvxl.readers.Parameters;
import org.jmol.util.Logger;
+import org.jmol.viewer.JmolConstants;
+
import javax.vecmath.Point3f;
import java.util.Vector;
import java.util.Hashtable;
import java.util.BitSet;
-import java.util.Arrays;
/*
* See J. Computational Chemistry, vol 7, p 359, 1986.
@@ -118,77 +119,6 @@
int gaussianPtr;
int firstAtomOffset;
- private final static String[][] shellOrder = {
- {"S"},
- {"X", "Y", "Z"},
- {"S", "X", "Y", "Z"},
- {"XX", "YY", "ZZ", "XY", "XZ", "YZ"},
- {"d0", "d1+", "d1-", "d2+", "d2-"},
- {"XXX", "YYY", "ZZZ", "XYY", "XXY", "XXZ", "XZZ", "YZZ", "YYZ", "XYZ"},
- {"f0", "f1+", "f1-", "f2+", "f2-", "f3+", "f3-"}
- };
-
- final public static int SHELL_S = 0;
- final public static int SHELL_P = 1;
- final public static int SHELL_SP = 2;
- final public static int SHELL_L = 2;
-
- // these next in cartesian/spherical pairs:
-
- final public static int SHELL_D_CARTESIAN = 3;
- final public static int SHELL_D_SPHERICAL = 4;
- final public static int SHELL_F_CARTESIAN = 5;
- final public static int SHELL_F_SPHERICAL = 6;
-
- final private static String[] quantumShellTags = {"S", "P", "SP", "L",
- "D", "5D", "F", "7F"};
-
- final private static int[] quantumShellIDs = {
- SHELL_S, SHELL_P, SHELL_SP, SHELL_L,
- SHELL_D_CARTESIAN, SHELL_D_SPHERICAL,
- SHELL_F_CARTESIAN, SHELL_F_SPHERICAL
- };
-
- final public static int getQuantumShellTagID(String tag) {
- for (int i = quantumShellTags.length; --i >= 0;)
- if (tag.equals(quantumShellTags[i]))
- return quantumShellIDs[i];
- return -1;
- }
-
- final public static int getQuantumShellTagIDSpherical(String tag) {
- final int tagID = getQuantumShellTagID(tag);
- return tagID + (tagID < SHELL_D_CARTESIAN ? 0 : tagID % 2);
- }
-
- final public static String getQuantumShellTag(int shell) {
- for (int i = quantumShellTags.length; --i >= 0;)
- if (shell == quantumShellIDs[i])
- return quantumShellTags[i];
- return "" + shell;
- }
-
- final public static String canonicalizeQuantumSubshellTag(String tag) {
- char firstChar = tag.charAt(0);
- if (firstChar == 'X' || firstChar == 'Y' || firstChar == 'Z') {
- char[] sorted = tag.toCharArray();
- Arrays.sort(sorted);
- return new String(sorted);
- }
- return tag;
- }
-
- final public static int getQuantumSubshellTagID(int shell, String tag) {
- for (int iSubshell = shellOrder[shell].length; --iSubshell >= 0; )
- if (shellOrder[shell][iSubshell].equals(tag))
- return iSubshell;
- return -1;
- }
-
- final public static String getQuantumSubshellTag(int shell, int subshell) {
- return shellOrder[shell][subshell];
- }
-
public MOCalculation() {
}
@@ -273,7 +203,7 @@
if (doDebug)
Logger.debug( "processShell: " + iShell
- + " type=" + getQuantumShellTag(basisType)
+ + " type=" + JmolConstants.getQuantumShellTag(basisType)
+ " nGaussians=" + nGaussians
+ " atom=" + atomIndex
);
@@ -296,25 +226,25 @@
}
}
switch(basisType) {
- case SHELL_S:
+ case JmolConstants.SHELL_S:
addDataS(nGaussians);
break;
- case SHELL_P:
+ case JmolConstants.SHELL_P:
addDataP(nGaussians);
break;
- case SHELL_SP:
+ case JmolConstants.SHELL_SP:
addDataSP(nGaussians);
break;
- case SHELL_D_CARTESIAN:
+ case JmolConstants.SHELL_D_CARTESIAN:
addData6D(nGaussians);
break;
- case SHELL_D_SPHERICAL:
+ case JmolConstants.SHELL_D_SPHERICAL:
addData5D(nGaussians);
break;
- case SHELL_F_CARTESIAN:
+ case JmolConstants.SHELL_F_CARTESIAN:
addData10F(nGaussians);
break;
- case SHELL_F_SPHERICAL:
+ case JmolConstants.SHELL_F_SPHERICAL:
addData7F(nGaussians);
break;
default:
@@ -492,7 +422,7 @@
return;
}
if (doDebug)
- dumpInfo(nGaussians, SHELL_F_CARTESIAN);
+ dumpInfo(nGaussians, JmolConstants.SHELL_F_CARTESIAN);
setMinMax();
float alpha;
@@ -596,7 +526,7 @@
return;
}
if (doDebug)
- dumpInfo(nGaussians, SHELL_D_SPHERICAL);
+ dumpInfo(nGaussians, JmolConstants.SHELL_D_SPHERICAL);
setMinMax();
@@ -678,7 +608,7 @@
}
if (doDebug)
- dumpInfo(nGaussians, SHELL_F_SPHERICAL);
+ dumpInfo(nGaussians, JmolConstants.SHELL_F_SPHERICAL);
setMinMax();
@@ -894,18 +824,14 @@
for (int ig = 0; ig < nGaussians; ig++) {
float alpha = gaussians[gaussianPtr + ig][0];
float c1 = gaussians[gaussianPtr + ig][1];
- if (Logger.debugging) {
- Logger.debug("Gaussian " + (ig + 1) + " alpha=" + alpha + " c=" + c1);
- }
+ Logger.debug("Gaussian " + (ig + 1) + " alpha=" + alpha + " c=" + c1);
}
- if (shell >= 0 && Logger.debugging){
- for (int i = 0; i < shellOrder[shell].length; i++) {
- Logger.debug(
- "MO coeff " + shellOrder[shell][i] + " " +
- (moCoeff + i + 1) + " " + moCoefficients[moCoeff + i]);
- }
+ if (shell >= 0 && Logger.debugging) {
+ String[] so = JmolConstants.getShellOrder(shell);
+ for (int i = 0; i < so.length; i++)
+ Logger.debug("MO coeff " + so[i] + " " + (moCoeff + i + 1) + " "
+ + moCoefficients[moCoeff + i]);
}
-
}
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-09-20 15:29:23 UTC (rev 9910)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-09-20 20:06:04 UTC (rev 9911)
@@ -3,6 +3,7 @@
version=11.6.RC15
+# new feature: MOL2 reader is PDB-enabled.
# new feature: data() and DATA expanded to allow fixed-column entry
# bug fix: data property_partialcharge does not update atomic partialCharge data itself for MEP
# but instead just creates a data type "property_partialcharge"
Modified: trunk/Jmol/src/org/jmol/viewer/JmolConstants.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/JmolConstants.java 2008-09-20 15:29:23 UTC (rev 9910)
+++ trunk/Jmol/src/org/jmol/viewer/JmolConstants.java 2008-09-20 20:06:04 UTC (rev 9911)
@@ -29,6 +29,7 @@
import java.io.BufferedInputStream;
import java.io.IOException;
import java.io.InputStream;
+import java.util.Arrays;
import java.util.Hashtable;
import java.util.BitSet;
import java.util.Properties;
@@ -2883,4 +2884,81 @@
throw new NullPointerException();
}
}
+
+ // quantum MO calculation constants need to be here so quantum class is not opened
+
+ private final static String[][] shellOrder = {
+ {"S"},
+ {"X", "Y", "Z"},
+ {"S", "X", "Y", "Z"},
+ {"XX", "YY", "ZZ", "XY", "XZ", "YZ"},
+ {"d0", "d1+", "d1-", "d2+", "d2-"},
+ {"XXX", "YYY", "ZZZ", "XYY", "XXY", "XXZ", "XZZ", "YZZ", "YYZ", "XYZ"},
+ {"f0", "f1+", "f1-", "f2+", "f2-", "f3+", "f3-"}
+ };
+
+ final public static String[] getShellOrder(int i) {
+ return shellOrder[i];
+ }
+
+ final public static int SHELL_S = 0;
+ final public static int SHELL_P = 1;
+ final public static int SHELL_SP = 2;
+ final public static int SHELL_L = 2;
+
+ // these next in cartesian/spherical pairs:
+
+ final public static int SHELL_D_CARTESIAN = 3;
+ final public static int SHELL_D_SPHERICAL = 4;
+ final public static int SHELL_F_CARTESIAN = 5;
+ final public static int SHELL_F_SPHERICAL = 6;
+
+ final private static String[] quantumShellTags = {"S", "P", "SP", "L",
+ "D", "5D", "F", "7F"};
+
+ final private static int[] quantumShellIDs = {
+ SHELL_S, SHELL_P, SHELL_SP, SHELL_L,
+ SHELL_D_CARTESIAN, SHELL_D_SPHERICAL,
+ SHELL_F_CARTESIAN, SHELL_F_SPHERICAL
+ };
+
+ final public static int getQuantumShellTagID(String tag) {
+ for (int i = quantumShellTags.length; --i >= 0;)
+ if (tag.equals(quantumShellTags[i]))
+ return quantumShellIDs[i];
+ return -1;
+ }
+
+ final public static int getQuantumShellTagIDSpherical(String tag) {
+ final int tagID = getQuantumShellTagID(tag);
+ return tagID + (tagID < SHELL_D_CARTESIAN ? 0 : tagID % 2);
+ }
+
+ final public static String getQuantumShellTag(int shell) {
+ for (int i = quantumShellTags.length; --i >= 0;)
+ if (shell == quantumShellIDs[i])
+ return quantumShellTags[i];
+ return "" + shell;
+ }
+
+ final public static String canonicalizeQuantumSubshellTag(String tag) {
+ char firstChar = tag.charAt(0);
+ if (firstChar == 'X' || firstChar == 'Y' || firstChar == 'Z') {
+ char[] sorted = tag.toCharArray();
+ Arrays.sort(sorted);
+ return new String(sorted);
+ }
+ return tag;
+ }
+
+ final public static int getQuantumSubshellTagID(int shell, String tag) {
+ for (int iSubshell = shellOrder[shell].length; --iSubshell >= 0; )
+ if (shellOrder[shell][iSubshell].equals(tag))
+ return iSubshell;
+ return -1;
+ }
+
+ final public static String getQuantumSubshellTag(int shell, int subshell) {
+ return shellOrder[shell][subshell];
+ }
}
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-09-20 15:29:23 UTC (rev 9910)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-09-20 20:06:04 UTC (rev 9911)
@@ -6077,8 +6077,8 @@
exp = "{selected}.label(\"%{" + type + "}\")";
else if (type.equalsIgnoreCase("PDB"))
//old crude
- exp = "{selected and not hetero}.label(\"ATOM %5i %-4a%1A%3n %1c%4R%1E %8.3x%8.3y%8.3z%6.2Q%6.2b %2e \").lines"
- + "+{selected and hetero}.label(\"HETATM%5i %-4a%1A%3n %1c%4R%1E %8.3x%8.3y%8.3z%6.2Q%6.2b %2e \").lines";
+ exp = "{selected and not hetero}.label(\"ATOM %5i %-4a%1A%3.3n %1c%4R%1E %8.3x%8.3y%8.3z%6.2Q%6.2b %2e \").lines"
+ + "+{selected and hetero}.label(\"HETATM%5i %-4a%1A%3.3n %1c%4R%1E %8.3x%8.3y%8.3z%6.2Q%6.2b %2e \").lines";
else if (type.equalsIgnoreCase("MOL"))
exp = "\"line1\nline2\nline3\n\"+(\"\"+{selected}.size)%-3+(\"\"+{selected}.bonds.size)%-3+\" 0 0 0\n\""
+ "+{selected}.labels(\"%10.4x%10.4y%10.4z %-2e 0 0 0 0 0\").lines"
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-09-22 04:11:45
|
Revision: 9918
http://jmol.svn.sourceforge.net/jmol/?rev=9918&view=rev
Author: hansonr
Date: 2008-09-22 04:11:38 +0000 (Mon, 22 Sep 2008)
Log Message:
-----------
version=11.6.RC16_dev # bug fix: mol2 PDB format better handling of chains and derived element types
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/more/Mol2Reader.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/adapter/readers/more/Mol2Reader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/more/Mol2Reader.java 2008-09-21 18:33:52 UTC (rev 9917)
+++ trunk/Jmol/src/org/jmol/adapter/readers/more/Mol2Reader.java 2008-09-22 04:11:38 UTC (rev 9918)
@@ -26,7 +26,6 @@
import org.jmol.adapter.smarter.*;
-
import java.io.BufferedReader;
import org.jmol.api.JmolAdapter;
@@ -37,6 +36,19 @@
* <a href='http://www.tripos.com/data/support/mol2.pdf '>
* http://www.tripos.com/data/support/mol2.pdf
* </a>
+ *
+ * PDB note:
+ *
+ * Note that mol2 format of PDB files is quite minimal. All we
+ * get is the PDB atom name, coordinates, residue number, and residue name
+ * No chain terminator, not chain designator, no element symbol.
+ *
+ * Chains based on numbering reset just labeled A B C D .... Z a b c d .... z
+ * Element symbols based on reasoned guess and properties of hetero groups
+ *
+ * So this is just a hack -- trying to guess at all of these.
+ *
+ *
*<p>
*/
@@ -53,11 +65,11 @@
public class Mol2Reader extends AtomSetCollectionReader {
- int nAtoms = 0;
- int atomCount = 0;
- boolean isPDB = false;
-
- public AtomSetCollection readAtomSetCollection(BufferedReader reader) {
+ private int nAtoms = 0;
+ private int atomCount = 0;
+ private boolean isPDB = false;
+
+ public AtomSetCollection readAtomSetCollection(BufferedReader reader) {
this.reader = reader;
atomSetCollection = new AtomSetCollection("mol2");
try {
@@ -81,7 +93,7 @@
return atomSetCollection;
}
- void processMolecule() throws Exception {
+ private void processMolecule() throws Exception {
/* 4-6 lines:
ZINC02211856
55 58 0 0 0
@@ -100,6 +112,8 @@
isPDB = false;
String thisDataSetName = readLineTrimmed();
+ lastSequenceNumber = Integer.MAX_VALUE;
+ chainID = 'A' - 1;
readLine();
line += " 0 0 0 0 0 0";
atomCount = parseInt(line);
@@ -131,14 +145,17 @@
}
nAtoms += atomCount;
if (isPDB) {
- atomSetCollection.setAtomSetCollectionAuxiliaryInfo("isPDB",
- Boolean.TRUE);
+ atomSetCollection
+ .setAtomSetCollectionAuxiliaryInfo("isPDB", Boolean.TRUE);
atomSetCollection.setAtomSetAuxiliaryInfo("isPDB", Boolean.TRUE);
}
applySymmetry();
}
- void readAtoms(int atomCount, boolean iHaveCharges) throws Exception {
+ private int lastSequenceNumber = Integer.MAX_VALUE;
+ private char chainID = 'A' - 1;
+
+ private void readAtoms(int atomCount, boolean iHaveCharges) throws Exception {
// 1 Cs 0.0000 4.1230 0.0000 Cs 1 RES1 0.0000
// 1 C1 7.0053 11.3096 -1.5429 C.3 1 <0> -0.1912
// free format, but no blank lines
@@ -157,37 +174,56 @@
atom.elementSymbol = elementSymbol;
// apparently "NO_CHARGES" is not strictly enforced
// if (iHaveCharges)
- if (tokens.length > 6)
+ if (tokens.length > 6) {
atom.sequenceNumber = parseInt(tokens[6]);
+ if (atom.sequenceNumber < lastSequenceNumber) {
+ if (chainID == 'Z')
+ chainID = 'a' - 1;
+ chainID++;
+ }
+ lastSequenceNumber = atom.sequenceNumber;
+ atom.chainID = chainID;
+ }
if (tokens.length > 7) {
atom.group3 = tokens[7];
atom.isHetero = JmolAdapter.isHetero(atom.group3);
- if (atom.group3.length() == 3
+ if (!isPDB && atom.group3.length() <= 3
&& JmolAdapter.lookupGroupID(atom.group3) >= 0) {
isPDB = true;
- }
+ }
if (isPDB)
- atom.elementSymbol = deduceElementSymbol(atom.isHetero, tokens[5], atom.group3);
+ atom.elementSymbol = deduceElementSymbol(atom.isHetero, tokens[5],
+ atom.group3);
+ //System.out.print(atom.atomName + "/" + atom.elementSymbol + " " );
}
if (tokens.length > 8)
atom.partialCharge = parseFloat(tokens[8]);
}
}
- String deduceElementSymbol(boolean isHetero, String XX, String group3) {
+ private static String deduceElementSymbol(boolean isHetero, String XX,
+ String group3) {
// short of having an entire table,
- if (XX.equalsIgnoreCase(group3))
- return XX; // Cd Mg etc.
- char ch1 = XX.charAt(0);
- char ch2 = (XX.length() > 1 ? XX.charAt(1) : ' ');
+ if (XX.equalsIgnoreCase(group3))
+ return XX; // Cd Mg etc.
+ int i = 0;
+ int len = XX.length();
+ char ch1 = ' ';
+ while (i < len && (ch1 = XX.charAt(i++)) <= '9') {
+ // find first nonnumeric letter
+ }
+
+ char ch2 = (i < len ? XX.charAt(i) : ' ');
String full = group3 + "." + ch1 + ch2;
// Cd Nd Ne are not in complex hetero; Ca is in these:
- if (("OEC.CA ICA.CA OC1.CA OC2.CA OC4.CA").indexOf(full)>=0)
+ if (("OEC.CA ICA.CA OC1.CA OC2.CA OC4.CA").indexOf(full) >= 0)
return "Ca";
- if ("NA NB NC ND NE NF NG NH CA CB CC CD CE CF CG CH OA OB OC OD OE OF OG OH".indexOf(XX) >= 0)
+ if (XX.indexOf("'") > 0 || XX.indexOf("*") >= 0
+ || "NCO".indexOf(ch1) >= 0 && ch2 <= 'H'
+ || XX.startsWith("CM"))
return "" + ch1;
if (isHetero && Atom.isValidElementSymbolNoCaseSecondChar(ch1, ch2))
- return (isHetero || ch1 != 'H' ? XX.trim() : "H");
+ return (isHetero || ch1 != 'H' ? ("" + ch1 + ch2).trim() : "H");
if (Atom.isValidElementSymbol(ch1))
return "" + ch1;
if (Atom.isValidElementSymbol(ch2))
@@ -195,8 +231,7 @@
return "Xx";
}
-
- void readBonds(int bondCount) throws Exception {
+ private void readBonds(int bondCount) throws Exception {
// 6 1 42 1
// free format, but no blank lines
for (int i = 0; i < bondCount; ++i) {
@@ -205,13 +240,14 @@
int atomIndex2 = parseInt(tokens[2]);
int order = parseInt(tokens[3]);
if (order == Integer.MIN_VALUE)
- order = (tokens[3].equals("ar") ? JmolAdapter.ORDER_AROMATIC : JmolAdapter.ORDER_UNSPECIFIED);
- atomSetCollection
- .addBond(new Bond(nAtoms + atomIndex1 - 1, nAtoms + atomIndex2 - 1, order));
+ order = (tokens[3].equals("ar") ? JmolAdapter.ORDER_AROMATIC
+ : JmolAdapter.ORDER_UNSPECIFIED);
+ atomSetCollection.addBond(new Bond(nAtoms + atomIndex1 - 1, nAtoms
+ + atomIndex2 - 1, order));
}
}
- void readResInfo(int resCount) throws Exception {
+ private void readResInfo(int resCount) throws Exception {
// free format, but no blank lines
for (int i = 0; i < resCount; ++i) {
readLine();
@@ -219,7 +255,7 @@
}
}
- void readCrystalInfo() throws Exception {
+ private void readCrystalInfo() throws Exception {
// 4.1230 4.1230 4.1230 90.0000 90.0000 90.0000 221 1
readLine();
String[] tokens = getTokens();
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-09-21 18:33:52 UTC (rev 9917)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-09-22 04:11:38 UTC (rev 9918)
@@ -3,6 +3,7 @@
version=11.6.RC16_dev
+# bug fix: mol2 PDB format better handling of chains and derived element types
# bug fix: save image button/menu interface broken in 11.6.RC15
# -----------------------------------------------------------------------------
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-09-23 05:25:21
|
Revision: 9926
http://jmol.svn.sourceforge.net/jmol/?rev=9926&view=rev
Author: hansonr
Date: 2008-09-23 05:23:47 +0000 (Tue, 23 Sep 2008)
Log Message:
-----------
version=11.6.RC17_dev # bug fix: select model=0.0 causes infinite loop
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2008-09-22 22:00:33 UTC (rev 9925)
+++ trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2008-09-23 05:23:47 UTC (rev 9926)
@@ -776,7 +776,7 @@
int file = (int) (fDotM);
int model = (int) ((fDotM - file + 0.00001) * 10000);
- while (model % 10 == 0)
+ while (model != 0 && model % 10 == 0)
model /= 10;
return file * 1000000 + model;
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-09-22 22:00:33 UTC (rev 9925)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-09-23 05:23:47 UTC (rev 9926)
@@ -3,6 +3,8 @@
version=11.6.RC17_dev
+# bug fix: select model=0.0 causes infinite loop
+
# -----------------------------------------------------------------------------
#version=11.6.RC16
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-09-22 22:00:33 UTC (rev 9925)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-09-23 05:23:47 UTC (rev 9926)
@@ -3460,8 +3460,8 @@
boolean isScriptFile,
boolean isQuiet, boolean isQueued) {
// from the scriptManager or scriptWait()
- System.out.println("DEBUG: evalStringWaitStatus " + Thread.currentThread().getName()
- + " " + Thread.currentThread().getId());
+ //System.out.println("DEBUG: evalStringWaitStatus " + Thread.currentThread().getName()
+ // + " " + Thread.currentThread().getId());
if (checkResume(strScript))
return "script processing resumed"; //be very odd if this fired
if (checkHalt(strScript))
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-09-23 13:29:38
|
Revision: 9927
http://jmol.svn.sourceforge.net/jmol/?rev=9927&view=rev
Author: hansonr
Date: 2008-09-23 13:29:34 +0000 (Tue, 23 Sep 2008)
Log Message:
-----------
version=11.6.RC17_dev
# code: if (true...)/ if (false...) code cleanup
# bug fix: select model=_modelNumber didn't differentiate between 2.10 and 2.1
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/more/JaguarReader.java
trunk/Jmol/src/org/jmol/export/_PovrayExporter.java
trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceRenderer.java
trunk/Jmol/src/org/jmol/viewer/Eval.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/ScriptManager.java
trunk/Jmol/src/org/jmol/viewer/TransformManager.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/more/JaguarReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/more/JaguarReader.java 2008-09-23 05:23:47 UTC (rev 9926)
+++ trunk/Jmol/src/org/jmol/adapter/readers/more/JaguarReader.java 2008-09-23 13:29:34 UTC (rev 9927)
@@ -247,8 +247,8 @@
*/
void readBasisNormalized() throws Exception {
- //don't know what this is about yet -- asking Jimmy Stewart
-
+ //TODO don't know what this is about yet -- Bob Hanson
+/*
if (true)
return;
String lastAtom = "";
@@ -271,6 +271,7 @@
rCoef = parseFloat(tokens[5]);
}
}
+*/
}
/*
Modified: trunk/Jmol/src/org/jmol/export/_PovrayExporter.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/_PovrayExporter.java 2008-09-23 05:23:47 UTC (rev 9926)
+++ trunk/Jmol/src/org/jmol/export/_PovrayExporter.java 2008-09-23 13:29:34 UTC (rev 9927)
@@ -669,11 +669,12 @@
String s = coef[0] + "," + coef[1] + "," + coef[2] + "," + coef[3] + ","
+ coef[4] + "," + coef[5] + "," + coef[6] + "," + coef[7] + ","
+ coef[8] + "," + coef[9] + "," + color4(colix);
- if (true || selectedPoints == null) {
+ //if (true || selectedPoints == null) {
output("q(" + s + ")\n");
- return;
- }
+ // return;
+ //}
//TODO: The following does not work.
+ /*
tempP1.set(ix, iy, iz);
for (int i = 0; i < 3; i++) {
tempP1.x += selectedPoints[i].x - ix;
@@ -682,6 +683,7 @@
}
output("qf(" + s + "," + ix + "," + iy + "," + iz
+ "," + tempP1.x + "," + tempP1.y + "," + tempP1.z + ")\n");
+ */
}
public void renderBackground() {
Modified: trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceRenderer.java 2008-09-23 05:23:47 UTC (rev 9926)
+++ trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceRenderer.java 2008-09-23 13:29:34 UTC (rev 9927)
@@ -174,7 +174,7 @@
return;
for (int i = vertexCount; --i >= 0;) {
if (vertexValues != null && !Float.isNaN(vertexValues[i]))
- if (true || (i % 3) == 0) { //investigate vertex normixes
+ //if ((i % 3) == 0) { //investigate vertex normixes
ptTemp.set(mesh.vertices[i]);
short n = mesh.normixes[i];
// -n is an intensity2sided and does not correspond to a true normal index
@@ -184,7 +184,7 @@
g3d.fillCylinder(Graphics3D.ENDCAPS_SPHERICAL, 1,
screens[i], ptTempi);
}
- }
+ //}
}
}
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-09-23 05:23:47 UTC (rev 9926)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-09-23 13:29:34 UTC (rev 9927)
@@ -159,6 +159,10 @@
}
private Object getNumericParameter(String var) {
+ if (var.equalsIgnoreCase("_modelNumber")) {
+ int modelIndex = viewer.getCurrentModelIndex();
+ return new Integer(modelIndex < 0 ? 0 : viewer.getModelFileNumber(modelIndex));
+ }
Token token = getContextVariableAsToken(var);
if (token == null) {
Object val = viewer.getParameter(var);
@@ -1375,7 +1379,8 @@
private BitSet expression(Token[] code, int pcStart, int pcStop,
boolean allowRefresh, boolean allowUnderflow,
- boolean mustBeBitSet, boolean andNotDeleted) throws ScriptException {
+ boolean mustBeBitSet, boolean andNotDeleted)
+ throws ScriptException {
//note that this is general -- NOT just statement[]
//errors reported would improperly access statement/line context
//there should be no errors anyway, because this is for
@@ -1528,8 +1533,8 @@
rpn.addX(getAtomBits(instruction.tok, (String) value));
break;
case Token.spec_model:
- // from select */1002 or */1000002 or */1.2
- // */1002 is equivalent to 1.2 when more than one file is present
+ // from select */1002 or */1000002 or */1.2
+ // */1002 is equivalent to 1.2 when more than one file is present
case Token.spec_model2:
// from just using the number 1.2
int iModel = instruction.intValue;
@@ -1549,14 +1554,17 @@
break;
case Token.spec_resid:
case Token.spec_chain:
- rpn.addX(getAtomBits(instruction.tok, new Integer(instruction.intValue)));
+ rpn
+ .addX(getAtomBits(instruction.tok,
+ new Integer(instruction.intValue)));
break;
case Token.spec_seqcode:
if (isInMath) {
rpn.addX(instruction.intValue);
break;
}
- rpn.addX(getAtomBits(Token.spec_seqcode, new Integer(getSeqCode(instruction))));
+ rpn.addX(getAtomBits(Token.spec_seqcode, new Integer(
+ getSeqCode(instruction))));
break;
case Token.spec_seqcode_range:
if (isInMath) {
@@ -1565,8 +1573,9 @@
rpn.addX(code[++pc].intValue);
break;
}
- int chainID = (pc + 3 < code.length && code[pc + 2].tok == Token.opAnd
- && code[pc + 3].tok == Token.spec_chain ? code[pc + 3].intValue : '\t');
+ int chainID = (pc + 3 < code.length && code[pc + 2].tok == Token.opAnd
+ && code[pc + 3].tok == Token.spec_chain ? code[pc + 3].intValue
+ : '\t');
rpn.addX(getAtomBits(Token.spec_seqcode_range, new int[] {
getSeqCode(instruction), getSeqCode(code[++pc]), chainID }));
if (chainID != '\t')
@@ -1622,15 +1631,15 @@
.modelFileNumberFromFloat(((Float) val).floatValue());
}
if (val instanceof Integer || tokValue == Token.integer) {
- comparisonValue *= (Compiler
- .tokAttr(tokWhat, Token.comparefloatx100) ? 100 : 1);
+ comparisonValue *= (Compiler.tokAttr(tokWhat, Token.comparefloatx100) ? 100
+ : 1);
comparisonFloat = comparisonValue;
- if (isModel && viewer.haveFileSet()) {
- if (comparisonValue >= 1000 && comparisonValue < 1000000) {
+ if (isModel) {
+ tokWhat = -Token.model;
+ if (viewer.haveFileSet() && comparisonValue >= 1000
+ && comparisonValue < 1000000)
comparisonValue = (comparisonValue / 1000) * 1000000
+ comparisonValue % 1000;
- tokWhat = -Token.model;
- }
}
} else if (val instanceof Float) {
if (isModel) {
@@ -1689,10 +1698,11 @@
error(ERROR_endOfStatementUnexpected);
}
expressionResult = ((Token) expressionResult).value;
- if (expressionResult instanceof String &&
- (mustBeBitSet || ((String) expressionResult).startsWith("({"))) {
+ if (expressionResult instanceof String
+ && (mustBeBitSet || ((String) expressionResult).startsWith("({"))) {
// allow for select @{x} where x is a string that can evaluate to a bitset
- expressionResult = (isScriptCheck ? new BitSet() : getAtomBitSet(this, viewer, (String) expressionResult));
+ expressionResult = (isScriptCheck ? new BitSet() : getAtomBitSet(this,
+ viewer, (String) expressionResult));
}
if (!mustBeBitSet && !(expressionResult instanceof BitSet))
return null; // because result is in expressionResult in that case
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-09-23 05:23:47 UTC (rev 9926)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-09-23 13:29:34 UTC (rev 9927)
@@ -3,7 +3,9 @@
version=11.6.RC17_dev
-# bug fix: select model=0.0 causes infinite loop
+# code: if (true...)/ if (false...) code cleanup
+# bug fix: select model=_modelNumber didn't differentiate between 2.10 and 2.1
+# bug fix: select model=0.0 caused infinite loop
# -----------------------------------------------------------------------------
Modified: trunk/Jmol/src/org/jmol/viewer/ScriptManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/ScriptManager.java 2008-09-23 05:23:47 UTC (rev 9926)
+++ trunk/Jmol/src/org/jmol/viewer/ScriptManager.java 2008-09-23 13:29:34 UTC (rev 9927)
@@ -87,7 +87,7 @@
scriptItem.addElement(isQuiet ? Boolean.TRUE : Boolean.FALSE);
scriptItem.addElement(new Integer(useCommandThread ? -1 : 1));
scriptQueue.addElement(scriptItem);
- if (true || Logger.debugging)
+ if (Logger.debugging)
Logger.info(scriptQueue.size() + " scripts; added: " + strScript);
startScriptQueue(false);
return "pending";
Modified: trunk/Jmol/src/org/jmol/viewer/TransformManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2008-09-23 05:23:47 UTC (rev 9926)
+++ trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2008-09-23 13:29:34 UTC (rev 9927)
@@ -32,7 +32,6 @@
import javax.vecmath.AxisAngle4f;
import org.jmol.util.Escape;
-import org.jmol.util.Logger;
import org.jmol.util.Quaternion;
import java.util.BitSet;
@@ -1212,9 +1211,8 @@
// note that the image is still centered at 0, 0 in the xy plane
- if (false && Logger.debugging)
- Logger.debug("modelCenterOffset + matrixTransform: " + modelCenterOffset
- + matrixTransform);
+ // System.out.println("modelCenterOffset + matrixTransform: " + modelCenterOffset
+ // + matrixTransform);
}
@@ -1300,7 +1298,7 @@
void transformPoint(Point3f pointAngstroms, Point3f screen) {
- //used solely by RocketsRenderer
+ //used solely by RocketsRendr
matrixTransform.transform(pointAngstroms, point3fScreenTemp);
adjustTemporaryScreenPoint();
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-09-23 16:44:44
|
Revision: 9928
http://jmol.svn.sourceforge.net/jmol/?rev=9928&view=rev
Author: hansonr
Date: 2008-09-23 16:43:46 +0000 (Tue, 23 Sep 2008)
Log Message:
-----------
version=11.6.RC17_dev # bug fix: trajectories not enabled
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2008-09-23 13:29:34 UTC (rev 9927)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2008-09-23 16:43:46 UTC (rev 9928)
@@ -277,7 +277,7 @@
// desiredSpaceGroupIndex,
// a*10000, b*10000, c*10000, alpha*10000, beta*10000, gamma*10000]
- isTrajectory = params[0] == -1;
+ isTrajectory = params[0] == Integer.MIN_VALUE;
if (!isTrajectory)
desiredModelNumber = params[0];
latticeCells[0] = params[1];
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-09-23 13:29:34 UTC (rev 9927)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-09-23 16:43:46 UTC (rev 9928)
@@ -3,6 +3,7 @@
version=11.6.RC17_dev
+# bug fix: trajectories not enabled
# code: if (true...)/ if (false...) code cleanup
# bug fix: select model=_modelNumber didn't differentiate between 2.10 and 2.1
# bug fix: select model=0.0 caused infinite loop
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-09-24 12:11:12
|
Revision: 9933
http://jmol.svn.sourceforge.net/jmol/?rev=9933&view=rev
Author: hansonr
Date: 2008-09-24 12:11:01 +0000 (Wed, 24 Sep 2008)
Log Message:
-----------
version=11.6.RC17_dev # bug fix: trajectories not enabled
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
trunk/Jmol/src/org/jmol/viewer/Eval.java
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2008-09-24 12:07:23 UTC (rev 9932)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2008-09-24 12:11:01 UTC (rev 9933)
@@ -277,7 +277,7 @@
// desiredSpaceGroupIndex,
// a*10000, b*10000, c*10000, alpha*10000, beta*10000, gamma*10000]
- isTrajectory = params[0] == Integer.MIN_VALUE;
+ isTrajectory = (params[0] == -1);
if (!isTrajectory)
desiredModelNumber = params[0];
latticeCells[0] = params[1];
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-09-24 12:07:23 UTC (rev 9932)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-09-24 12:11:01 UTC (rev 9933)
@@ -4295,7 +4295,7 @@
loadScript.append(" " + modelName);
isAppend = (modelName.equalsIgnoreCase("append"));
if (modelName.equalsIgnoreCase("trajectory"))
- params[0] = Integer.MIN_VALUE;
+ params[0] = -1;
} else {
modelName = "fileset";
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-09-25 20:57:15
|
Revision: 9938
http://jmol.svn.sourceforge.net/jmol/?rev=9938&view=rev
Author: hansonr
Date: 2008-09-25 20:57:09 +0000 (Thu, 25 Sep 2008)
Log Message:
-----------
version=11.6.RC17_dev # bug fix: Swing antialiasDisplay broken due to setTransparentBackground debugging
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/g3d/Swing3D.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/g3d/Swing3D.java
===================================================================
--- trunk/Jmol/src/org/jmol/g3d/Swing3D.java 2008-09-25 20:51:02 UTC (rev 9937)
+++ trunk/Jmol/src/org/jmol/g3d/Swing3D.java 2008-09-25 20:57:09 UTC (rev 9938)
@@ -69,7 +69,8 @@
Image allocateImage() {
- if (backgroundTransparent)
+ //backgroundTransparent not working with antialiasDisplay. I have no idea why. BH 9/24/08
+ if (false && backgroundTransparent)
return new BufferedImage(
rgbColorModelT,
Raster.createWritableRaster(
@@ -99,7 +100,7 @@
private static boolean backgroundTransparent = false;
void setBackgroundTransparent(boolean tf) {
- backgroundTransparent = true;
+ backgroundTransparent = tf;
}
Image allocateOffscreenImage(int width, int height) {
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-09-25 20:51:02 UTC (rev 9937)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-09-25 20:57:09 UTC (rev 9938)
@@ -3,6 +3,7 @@
version=11.6.RC17_dev
+# bug fix: Swing antialiasDisplay broken due to setTransparentBackground debugging
# bug fix: trajectories not enabled
# code: if (true...)/ if (false...) code cleanup
# bug fix: select model=_modelNumber didn't differentiate between 2.10 and 2.1
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
Thanks for helping keep SourceForge clean.
X