Revision: 21033
http://sourceforge.net/p/jmol/code/21033
Author: hansonr
Date: 2016-03-30 00:39:48 +0000 (Wed, 30 Mar 2016)
Log Message:
-----------
Jmol.___JmolVersion="14.4.4_2016.03.29"
new feature: Polyhedra command allows for min and max radius
-- polyhedra 2.8 3.0 @3
bug fix: unitcell PRIMITIVE for rhombohedral groups not implemented
bug fix: unitcell("primitive","R") not implemented
bug fix: WRITE IMAGE with negative width or height should throw a Jmol
ScriptException
bug fix: draw ... [x y] does not position properly with antialias true
bug fix: allow AXES TYPE "" or non-recognized to be same as "abc"
bug fix: AXES TYPE "ab" should also be allowed when offset or center is set
bug fix: labels should not change size when creating images of
different size than screen when angstromsPerInch != 0.
bug fix: if...BREAK|CONTINUE in unbracketed context does not properly
place implicit END IF when TRUE clause is on next line
AND next statement after that is another IF command:
if (xxxx)
break;
if (yyyy)
zzzz;
becomes
if (xxxx) {
break;
if (yyyy) {
zzzz;
}
}
instead of
if (xxxx) {
break;
}
if (yyyy) {
zzzz;
}
Modified Paths:
--------------
branches/v14_4/Jmol/src/org/jmol/modelset/Text.java
branches/v14_4/Jmol/src/org/jmol/render/TextRenderer.java
branches/v14_4/Jmol/src/org/jmol/renderspecial/DrawRenderer.java
branches/v14_4/Jmol/src/org/jmol/scriptext/CmdExt.java
branches/v14_4/Jmol/src/org/jmol/scriptext/IsoExt.java
branches/v14_4/Jmol/src/org/jmol/shapespecial/Polyhedra.java
branches/v14_4/Jmol/src/org/jmol/symmetry/SpaceGroup.java
branches/v14_4/Jmol/src/org/jmol/symmetry/UnitCell.java
branches/v14_4/Jmol/src/org/jmol/util/ColorEncoder.java
branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
branches/v14_4/Jmol/src/org/jmol/viewer/Viewer.java
trunk/Jmol/src/org/jmol/modelset/Text.java
trunk/Jmol/src/org/jmol/render/TextRenderer.java
trunk/Jmol/src/org/jmol/renderspecial/DrawRenderer.java
trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
trunk/Jmol/src/org/jmol/scriptext/IsoExt.java
trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java
trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java
trunk/Jmol/src/org/jmol/symmetry/UnitCell.java
trunk/Jmol/src/org/jmol/util/ColorEncoder.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: branches/v14_4/Jmol/src/org/jmol/modelset/Text.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/modelset/Text.java 2016-03-28 02:27:04 UTC
(rev 21032)
+++ branches/v14_4/Jmol/src/org/jmol/modelset/Text.java 2016-03-30 00:39:48 UTC
(rev 21033)
@@ -349,7 +349,7 @@
float y = (movableYPercent != Integer.MAX_VALUE ? movableYPercent
* windowHeight / 100 : is3dEcho ? movableY : movableY * scale);
boxXY[1] = (is3dEcho ? y : (windowHeight - y)) + offsetY * scale;
- }
+ }
if (align == JC.TEXT_ALIGN_CENTER)
boxXY[1] -= (image != null ? boxHeight : xyz != null ? boxHeight
Modified: branches/v14_4/Jmol/src/org/jmol/render/TextRenderer.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/render/TextRenderer.java 2016-03-28
02:27:04 UTC (rev 21032)
+++ branches/v14_4/Jmol/src/org/jmol/render/TextRenderer.java 2016-03-30
00:39:48 UTC (rev 21033)
@@ -59,7 +59,7 @@
// now write properly aligned text
for (int i = 0; i < text.lines.length; i++) {
text.setXYA(temp, i);
-
+ System.out.println("textrend x y " + temp[0] + " " + temp[1] + " " +
text.lines[i]);
g3d.drawString(text.lines[i], text.font, (int) temp[0], (int) temp[1],
text.z, text.zSlab, text.bgcolix);
}
Modified: branches/v14_4/Jmol/src/org/jmol/renderspecial/DrawRenderer.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/renderspecial/DrawRenderer.java
2016-03-28 02:27:04 UTC (rev 21032)
+++ branches/v14_4/Jmol/src/org/jmol/renderspecial/DrawRenderer.java
2016-03-30 00:39:48 UTC (rev 21033)
@@ -359,6 +359,7 @@
private void renderXyPoint() {
// new in Jmol 14.5
+ int f = (g3d.isAntialiased() ? 2 : 1);
pt0.setT(vertices[0]);
if (diameter == 0)
diameter = (int) width;
@@ -367,11 +368,8 @@
pt0.y *= vwr.tm.height / 100f;
diameter = (int) (diameter * vwr.getScreenDim() / 100f);
}
- if (g3d.isAntialiased())
- diameter *= 2;
- pt0.y = vwr.tm.height - pt0.y;
- pt0.z = vwr.tm.cameraDistance;
- pt1i.set((int) pt0.x, (int) pt0.y, (int) pt0.z);
+ diameter *= f;
+ pt1i.set((int) (pt0.x * f), (int) (vwr.tm.height - pt0.y * f), (int)
vwr.tm.cameraDistance);
g3d.fillSphereI(diameter, pt1i);
}
Modified: branches/v14_4/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/scriptext/CmdExt.java 2016-03-28
02:27:04 UTC (rev 21032)
+++ branches/v14_4/Jmol/src/org/jmol/scriptext/CmdExt.java 2016-03-30
00:39:48 UTC (rev 21033)
@@ -3202,6 +3202,7 @@
eval.sm.loadShape(JC.SHAPE_POLYHEDRA);
setShapeProperty(JC.SHAPE_POLYHEDRA, "init", Boolean.TRUE);
float translucentLevel = Float.MAX_VALUE;
+ float radius = -1;
int[] colorArgb = new int[] { Integer.MIN_VALUE };
P3 offset = null;
String id = null;
@@ -3273,8 +3274,8 @@
invArg();
if (nAtomSets > 0)
invPO();
- propertyName = "radius";
- propertyValue = Float.valueOf(floatParameter(i));
+ propertyName = (radius != 0 ? "radius1" : "radius");
+ propertyValue = Float.valueOf(radius = floatParameter(i));
needsGenerating = true;
break;
case T.offset:
@@ -3650,7 +3651,11 @@
}
if (tokAtArray(pt, args) == T.integer) {
width = SV.iValue(tokenAt(pt++, args));
+ if (width <= 0)
+ invArg();
height = SV.iValue(tokenAt(pt++, args));
+ if (height <= 0)
+ invArg();
}
break;
}
@@ -3669,7 +3674,11 @@
if (tokAtArray(pt + 1, args) == T.integer
&& tokAtArray(pt + 2, args) == T.integer) {
width = SV.iValue(tokenAt(++pt, args));
+ if (width <= 0)
+ invArg();
height = SV.iValue(tokenAt(++pt, args));
+ if (height <= 0)
+ invArg();
}
if (tokAtArray(pt + 1, args) == T.integer)
quality = SV.iValue(tokenAt(++pt, args));
Modified: branches/v14_4/Jmol/src/org/jmol/scriptext/IsoExt.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/scriptext/IsoExt.java 2016-03-28
02:27:04 UTC (rev 21032)
+++ branches/v14_4/Jmol/src/org/jmol/scriptext/IsoExt.java 2016-03-30
00:39:48 UTC (rev 21033)
@@ -393,8 +393,8 @@
points = new P3[nVertices];
for (int j = 0; j < nVertices; j++)
points[j] = centerParameter(++eval.iToken);
- i = eval.iToken;
}
+ i = eval.iToken;
int[][] polygons = null;
switch (tokAt(i + 1)) {
case T.matrix3f:
Modified: branches/v14_4/Jmol/src/org/jmol/shapespecial/Polyhedra.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/shapespecial/Polyhedra.java
2016-03-28 02:27:04 UTC (rev 21032)
+++ branches/v14_4/Jmol/src/org/jmol/shapespecial/Polyhedra.java
2016-03-30 00:39:48 UTC (rev 21033)
@@ -84,7 +84,7 @@
public Polyhedron[] polyhedrons = new Polyhedron[32];
public int drawEdges;
- private float radius, pointScale;
+ private float radius, radiusMin, pointScale;
private int nVertices;
float faceCenterOffset;
@@ -118,7 +118,7 @@
faceCenterOffset = DEFAULT_FACECENTEROFFSET;
//distanceFactor =
planarParam = Float.NaN;
- radius = pointScale = 0.0f;
+ radius = radiusMin = pointScale = 0.0f;
nVertices = 0;
nPoints = 0;
modelIndex = -1;
@@ -357,6 +357,12 @@
return;
}
+ if ("radius1" == propertyName) {
+ radiusMin = radius;
+ radius = ((Float) value).floatValue();
+ return;
+ }
+
if ("points" == propertyName) {
pointScale = ((Float) value).floatValue();
pointsPolyhedra(bs, pointScale);
@@ -652,13 +658,15 @@
if (bonds == null)
return null;
float r2 = radius * radius;
+ float r1 = radiusMin * radiusMin;
+ float r;
for (int i = bonds.length; --i >= 0;) {
Bond bond = bonds[i];
if (!bond.isCovalent())
continue;
Atom other = bond.getOtherAtom(atom);
if (bsVertices != null && !bsVertices.get(other.i) || radius > 0
- && other.distanceSquared(atom) > r2)
+ && ((r = other.distanceSquared(atom)) > r2 || r < r1))
continue;
otherAtoms[otherAtomCount++] = other;
if (otherAtomCount >= MAX_VERTICES)
@@ -688,7 +696,7 @@
if (myBondingRadius == 0)
return null;
float bondTolerance = vwr.getFloat(T.bondtolerance);
- float minBondDistance = vwr.getFloat(T.minbonddistance);
+ float minBondDistance = (radiusMin == 0 ? vwr.getFloat(T.minbonddistance)
: radiusMin);
float minBondDistance2 = minBondDistance * minBondDistance;
int otherAtomCount = 0;
outer: while (iter.hasNext()) {
@@ -725,21 +733,23 @@
int otherAtomCount = 0;
distanceRef = radius;
float r2 = radius * radius;
+ float r2min = radiusMin * radiusMin;
outer: while (iter.hasNext()) {
Atom other = atoms[iter.next()];
P3 pt = iter.getPosition();
if (pt == null) {
// this will happen with standard radius atom iterator
pt = other;
- if (bsVertices != null && !bsVertices.get(other.i)
- || atom.distanceSquared(pt) > r2)
+ if (bsVertices != null && !bsVertices.get(other.i))
continue;
}
- if (other.altloc != atom.altloc && other.altloc != 0 && atom.altloc != 0)
+ float r = atom.distanceSquared(pt);
+ if (other.altloc != atom.altloc && other.altloc != 0 && atom.altloc != 0
+ || r > r2 || r < r2min)
continue;
if (otherAtomCount == MAX_VERTICES)
break;
- for (int i = 0; i < otherAtomCount; i++)
+ for (int i = 0; i < otherAtomCount; i++)
if (otherAtoms[i].distanceSquared(pt) < 0.01f)
continue outer;
Modified: branches/v14_4/Jmol/src/org/jmol/symmetry/SpaceGroup.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/symmetry/SpaceGroup.java 2016-03-28
02:27:04 UTC (rev 21032)
+++ branches/v14_4/Jmol/src/org/jmol/symmetry/SpaceGroup.java 2016-03-30
00:39:48 UTC (rev 21033)
@@ -555,7 +555,6 @@
}
switch (h.latticeCode) {
case '\0':
- case 'R':
case 'S':
case 'T':
case 'P':
Modified: branches/v14_4/Jmol/src/org/jmol/symmetry/UnitCell.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/symmetry/UnitCell.java 2016-03-28
02:27:04 UTC (rev 21032)
+++ branches/v14_4/Jmol/src/org/jmol/symmetry/UnitCell.java 2016-03-30
00:39:48 UTC (rev 21033)
@@ -684,7 +684,7 @@
/**
*
* @param toPrimitive or assumed conventional
- * @param type P, A, B, C, I(BCC), or F(FCC)
+ * @param type P, R, A, B, C, I(BCC), or F(FCC)
* @param uc either [origin, va, vb, vc] or just [va, vb, vc]
* @return true if successful
*/
@@ -703,24 +703,37 @@
toPrimitive = true;
break;
case 'A':
- mf = M3.newA9(new float[] { 1, 0, 0, 0, 0.5f, -0.5f, 0, 0.5f, 0.5f});
+ mf = M3.newA9(new float[] { 1, 0, 0,
+ 0, 0.5f, -0.5f,
+ 0, 0.5f, 0.5f});
break;
case 'B':
- mf = M3.newA9(new float[] { 0.5f, 0, -0.5f, 0, 1, 0, 0.5f, 0, 0.5f});
+ mf = M3.newA9(new float[] { 0.5f, 0, -0.5f,
+ 0, 1, 0,
+ 0.5f, 0, 0.5f});
break;
case 'C':
- mf = M3.newA9(new float[] { 0.5f, -0.5f, 0, 0.5f, 0.5f, 0, 0, 0, 1});
+ mf = M3.newA9(new float[] { 0.5f, -0.5f, 0,
+ 0.5f, 0.5f, 0,
+ 0, 0, 1});
break;
+ case 'R':
+ mf = M3.newA9(new float[] { 1/3f, 1/3f, -2/3f,
+ -1/3f, 2/3f, -1/3f,
+ 1/3f, 1/3f, 1/3f});
+ break;
case 'I':
// f = new float[] { .5f, .5f, -.5f, -.5f, .5f, .5f, .5f, -.5f, .5f };
mf = M3.newA9(new float[] { -.5f, .5f, .5f, // was y
- .5f, -.5f, .5f, // was z
- .5f, .5f, -.5f });// was x
+ .5f, -.5f, .5f, // was z
+ .5f, .5f, -.5f });// was x
// : new float[] { 1, 0, 1, 1, 1, 0, 0, 1, 1 })
break;
case 'F':
// WAS f = new float[] { .5f, .5f, 0, 0, .5f, .5f, .5f, 0, .5f };
- mf = M3.newA9(new float[] { 0, 0.5f, 0.5f, 0.5f, 0, 0.5f, 0.5f, 0.5f, 0
});
+ mf = M3.newA9(new float[] { 0, 0.5f, 0.5f,
+ 0.5f, 0, 0.5f,
+ 0.5f, 0.5f, 0 });
// : new float[] { 1, -1, 1, 1, 1, -1, -1, 1, 1 }) : null);
break;
}
Modified: branches/v14_4/Jmol/src/org/jmol/util/ColorEncoder.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/util/ColorEncoder.java 2016-03-28
02:27:04 UTC (rev 21032)
+++ branches/v14_4/Jmol/src/org/jmol/util/ColorEncoder.java 2016-03-30
00:39:48 UTC (rev 21033)
@@ -425,7 +425,7 @@
return colix;
}
- public int getPaletteColorCount(int palette) {
+ private int getPaletteColorCount(int palette) {
switch (palette) {
case CUSTOM:
return thisScale.length;
@@ -445,7 +445,7 @@
case RESU:
return ce.userScale.length;
case JMOL:
- return argbsCpk.length;
+ return ce.argbsCpk.length;
case RASMOL:
return getRasmolScale().length;
case SHAPELY:
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2016-03-28
02:27:04 UTC (rev 21032)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2016-03-30
00:39:48 UTC (rev 21033)
@@ -7,8 +7,16 @@
# see also http://chemapps.stolaf.edu/jmol/zip for daily updates
-Jmol.___JmolVersion="14.4.4_2016.03.27"
+Jmol.___JmolVersion="14.4.4_2016.03.29"
+new feature: Polyhedra command allows for min and max radius
+ -- polyhedra 2.8 3.0 @3
+
+bug fix: unitcell PRIMITIVE for rhombohedral groups not implemented
+bug fix: unitcell("primitive","R") not implemented
+
+bug fix: WRITE IMAGE with negative width or height should throw a Jmol
ScriptException
+bug fix: draw ... [x y] does not position properly with antialias true
bug fix: allow AXES TYPE "" or non-recognized to be same as "abc"
bug fix: AXES TYPE "ab" should also be allowed when offset or center is set
bug fix: labels should not change size when creating images of
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/Viewer.java 2016-03-28 02:27:04 UTC
(rev 21032)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/Viewer.java 2016-03-30 00:39:48 UTC
(rev 21033)
@@ -3431,12 +3431,6 @@
setShapeProperty(JC.SHAPE_LABELS, "clearBoxes", null);
imageFontScaling = (antialiased ? 2f : 1f) * (isReset || tm.scale3D ||
width <= 0 ? 1
: (g.zoomLarge == (height > width) ? height : width) * 1f /
getScreenDim());
- System.out.println(dimScreen.width + " " + dimScreen.height
- + " " + (antialiased ? 2f : 1f)
- + " " + width + " " + height + " " + (isReset || width <= 0 ? 1
- : (g.zoomLarge == (height > width) ? height : width) * 1.0f /
getScreenDim()));
- if (imageFontScaling == 0)
- System.out.println("??? viewer");
if (width > 0) {
dimScreen.width = width;
dimScreen.height = height;
Modified: trunk/Jmol/src/org/jmol/modelset/Text.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Text.java 2016-03-28 02:27:04 UTC (rev
21032)
+++ trunk/Jmol/src/org/jmol/modelset/Text.java 2016-03-30 00:39:48 UTC (rev
21033)
@@ -349,7 +349,7 @@
float y = (movableYPercent != Integer.MAX_VALUE ? movableYPercent
* windowHeight / 100 : is3dEcho ? movableY : movableY * scale);
boxXY[1] = (is3dEcho ? y : (windowHeight - y)) + offsetY * scale;
- }
+ }
if (align == JC.TEXT_ALIGN_CENTER)
boxXY[1] -= (image != null ? boxHeight : xyz != null ? boxHeight
Modified: trunk/Jmol/src/org/jmol/render/TextRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/render/TextRenderer.java 2016-03-28 02:27:04 UTC
(rev 21032)
+++ trunk/Jmol/src/org/jmol/render/TextRenderer.java 2016-03-30 00:39:48 UTC
(rev 21033)
@@ -59,7 +59,7 @@
// now write properly aligned text
for (int i = 0; i < text.lines.length; i++) {
text.setXYA(temp, i);
-
+ System.out.println("textrend x y " + temp[0] + " " + temp[1] + " " +
text.lines[i]);
g3d.drawString(text.lines[i], text.font, (int) temp[0], (int) temp[1],
text.z, text.zSlab, text.bgcolix);
}
Modified: trunk/Jmol/src/org/jmol/renderspecial/DrawRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/renderspecial/DrawRenderer.java 2016-03-28
02:27:04 UTC (rev 21032)
+++ trunk/Jmol/src/org/jmol/renderspecial/DrawRenderer.java 2016-03-30
00:39:48 UTC (rev 21033)
@@ -359,6 +359,7 @@
private void renderXyPoint() {
// new in Jmol 14.5
+ int f = (g3d.isAntialiased() ? 2 : 1);
pt0.setT(vertices[0]);
if (diameter == 0)
diameter = (int) width;
@@ -367,11 +368,8 @@
pt0.y *= vwr.tm.height / 100f;
diameter = (int) (diameter * vwr.getScreenDim() / 100f);
}
- if (g3d.isAntialiased())
- diameter *= 2;
- pt0.y = vwr.tm.height - pt0.y;
- pt0.z = vwr.tm.cameraDistance;
- pt1i.set((int) pt0.x, (int) pt0.y, (int) pt0.z);
+ diameter *= f;
+ pt1i.set((int) (pt0.x * f), (int) (vwr.tm.height - pt0.y * f), (int)
vwr.tm.cameraDistance);
g3d.fillSphereI(diameter, pt1i);
}
Modified: trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2016-03-28 02:27:04 UTC
(rev 21032)
+++ trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2016-03-30 00:39:48 UTC
(rev 21033)
@@ -3275,7 +3275,7 @@
if (nAtomSets > 0)
invPO();
propertyName = (radius != 0 ? "radius1" : "radius");
- propertyValue = Float.valueOf(floatParameter(i));
+ propertyValue = Float.valueOf(radius = floatParameter(i));
needsGenerating = true;
break;
case T.offset:
@@ -3651,7 +3651,11 @@
}
if (tokAtArray(pt, args) == T.integer) {
width = SV.iValue(tokenAt(pt++, args));
+ if (width <= 0)
+ invArg();
height = SV.iValue(tokenAt(pt++, args));
+ if (height <= 0)
+ invArg();
}
break;
}
@@ -3670,7 +3674,11 @@
if (tokAtArray(pt + 1, args) == T.integer
&& tokAtArray(pt + 2, args) == T.integer) {
width = SV.iValue(tokenAt(++pt, args));
+ if (width <= 0)
+ invArg();
height = SV.iValue(tokenAt(++pt, args));
+ if (height <= 0)
+ invArg();
}
if (tokAtArray(pt + 1, args) == T.integer)
quality = SV.iValue(tokenAt(++pt, args));
Modified: trunk/Jmol/src/org/jmol/scriptext/IsoExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/IsoExt.java 2016-03-28 02:27:04 UTC
(rev 21032)
+++ trunk/Jmol/src/org/jmol/scriptext/IsoExt.java 2016-03-30 00:39:48 UTC
(rev 21033)
@@ -393,8 +393,8 @@
points = new P3[nVertices];
for (int j = 0; j < nVertices; j++)
points[j] = centerParameter(++eval.iToken);
- i = eval.iToken;
}
+ i = eval.iToken;
int[][] polygons = null;
switch (tokAt(i + 1)) {
case T.matrix3f:
Modified: trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java 2016-03-28 02:27:04 UTC
(rev 21032)
+++ trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java 2016-03-30 00:39:48 UTC
(rev 21033)
@@ -696,7 +696,7 @@
if (myBondingRadius == 0)
return null;
float bondTolerance = vwr.getFloat(T.bondtolerance);
- float minBondDistance = vwr.getFloat(T.minbonddistance);
+ float minBondDistance = (radiusMin == 0 ? vwr.getFloat(T.minbonddistance)
: radiusMin);
float minBondDistance2 = minBondDistance * minBondDistance;
int otherAtomCount = 0;
outer: while (iter.hasNext()) {
@@ -734,22 +734,22 @@
distanceRef = radius;
float r2 = radius * radius;
float r2min = radiusMin * radiusMin;
- float r;
outer: while (iter.hasNext()) {
Atom other = atoms[iter.next()];
P3 pt = iter.getPosition();
if (pt == null) {
// this will happen with standard radius atom iterator
pt = other;
- if (bsVertices != null && !bsVertices.get(other.i)
- || (r = atom.distanceSquared(pt)) > r2 || r < r2min)
+ if (bsVertices != null && !bsVertices.get(other.i))
continue;
}
- if (other.altloc != atom.altloc && other.altloc != 0 && atom.altloc != 0)
+ float r = atom.distanceSquared(pt);
+ if (other.altloc != atom.altloc && other.altloc != 0 && atom.altloc != 0
+ || r > r2 || r < r2min)
continue;
if (otherAtomCount == MAX_VERTICES)
break;
- for (int i = 0; i < otherAtomCount; i++)
+ for (int i = 0; i < otherAtomCount; i++)
if (otherAtoms[i].distanceSquared(pt) < 0.01f)
continue outer;
Modified: trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java 2016-03-28 02:27:04 UTC
(rev 21032)
+++ trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java 2016-03-30 00:39:48 UTC
(rev 21033)
@@ -555,7 +555,6 @@
}
switch (h.latticeCode) {
case '\0':
- case 'R':
case 'S':
case 'T':
case 'P':
Modified: trunk/Jmol/src/org/jmol/symmetry/UnitCell.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/UnitCell.java 2016-03-28 02:27:04 UTC
(rev 21032)
+++ trunk/Jmol/src/org/jmol/symmetry/UnitCell.java 2016-03-30 00:39:48 UTC
(rev 21033)
@@ -684,7 +684,7 @@
/**
*
* @param toPrimitive or assumed conventional
- * @param type P, A, B, C, I(BCC), or F(FCC)
+ * @param type P, R, A, B, C, I(BCC), or F(FCC)
* @param uc either [origin, va, vb, vc] or just [va, vb, vc]
* @return true if successful
*/
@@ -703,24 +703,37 @@
toPrimitive = true;
break;
case 'A':
- mf = M3.newA9(new float[] { 1, 0, 0, 0, 0.5f, -0.5f, 0, 0.5f, 0.5f});
+ mf = M3.newA9(new float[] { 1, 0, 0,
+ 0, 0.5f, -0.5f,
+ 0, 0.5f, 0.5f});
break;
case 'B':
- mf = M3.newA9(new float[] { 0.5f, 0, -0.5f, 0, 1, 0, 0.5f, 0, 0.5f});
+ mf = M3.newA9(new float[] { 0.5f, 0, -0.5f,
+ 0, 1, 0,
+ 0.5f, 0, 0.5f});
break;
case 'C':
- mf = M3.newA9(new float[] { 0.5f, -0.5f, 0, 0.5f, 0.5f, 0, 0, 0, 1});
+ mf = M3.newA9(new float[] { 0.5f, -0.5f, 0,
+ 0.5f, 0.5f, 0,
+ 0, 0, 1});
break;
+ case 'R':
+ mf = M3.newA9(new float[] { 1/3f, 1/3f, -2/3f,
+ -1/3f, 2/3f, -1/3f,
+ 1/3f, 1/3f, 1/3f});
+ break;
case 'I':
// f = new float[] { .5f, .5f, -.5f, -.5f, .5f, .5f, .5f, -.5f, .5f };
mf = M3.newA9(new float[] { -.5f, .5f, .5f, // was y
- .5f, -.5f, .5f, // was z
- .5f, .5f, -.5f });// was x
+ .5f, -.5f, .5f, // was z
+ .5f, .5f, -.5f });// was x
// : new float[] { 1, 0, 1, 1, 1, 0, 0, 1, 1 })
break;
case 'F':
// WAS f = new float[] { .5f, .5f, 0, 0, .5f, .5f, .5f, 0, .5f };
- mf = M3.newA9(new float[] { 0, 0.5f, 0.5f, 0.5f, 0, 0.5f, 0.5f, 0.5f, 0
});
+ mf = M3.newA9(new float[] { 0, 0.5f, 0.5f,
+ 0.5f, 0, 0.5f,
+ 0.5f, 0.5f, 0 });
// : new float[] { 1, -1, 1, 1, 1, -1, -1, 1, 1 }) : null);
break;
}
Modified: trunk/Jmol/src/org/jmol/util/ColorEncoder.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/ColorEncoder.java 2016-03-28 02:27:04 UTC
(rev 21032)
+++ trunk/Jmol/src/org/jmol/util/ColorEncoder.java 2016-03-30 00:39:48 UTC
(rev 21033)
@@ -425,7 +425,7 @@
return colix;
}
- public int getPaletteColorCount(int palette) {
+ private int getPaletteColorCount(int palette) {
switch (palette) {
case CUSTOM:
return thisScale.length;
@@ -445,7 +445,7 @@
case RESU:
return ce.userScale.length;
case JMOL:
- return argbsCpk.length;
+ return ce.argbsCpk.length;
case RASMOL:
return getRasmolScale().length;
case SHAPELY:
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-03-28 02:27:04 UTC
(rev 21032)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-03-30 00:39:48 UTC
(rev 21033)
@@ -72,8 +72,16 @@
TODO: vector traces saved in state?
TODO: slightly stronger unitcell lines for near point?
-Jmol.___JmolVersion="14.5.4_2016.03.27"
+Jmol.___JmolVersion="14.5.4_2016.03.29"
+new feature: Polyhedra command allows for min and max radius
+ -- polyhedra 2.8 3.0 @3
+
+bug fix: unitcell PRIMITIVE for rhombohedral groups not implemented
+bug fix: unitcell("primitive","R") not implemented
+
+bug fix: WRITE IMAGE with negative width or height should throw a Jmol
ScriptException
+bug fix: draw ... [x y] does not position properly with antialias true
bug fix: allow AXES TYPE "" or non-recognized to be same as "abc"
bug fix: AXES TYPE "ab" should also be allowed when offset or center is set
bug fix: labels should not change size when creating images of
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2016-03-28 02:27:04 UTC (rev
21032)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2016-03-30 00:39:48 UTC (rev
21033)
@@ -3431,12 +3431,6 @@
setShapeProperty(JC.SHAPE_LABELS, "clearBoxes", null);
imageFontScaling = (antialiased ? 2f : 1f) * (isReset || tm.scale3D ||
width <= 0 ? 1
: (g.zoomLarge == (height > width) ? height : width) * 1f /
getScreenDim());
- System.out.println(dimScreen.width + " " + dimScreen.height
- + " " + (antialiased ? 2f : 1f)
- + " " + width + " " + height + " " + (isReset || width <= 0 ? 1
- : (g.zoomLarge == (height > width) ? height : width) * 1.0f /
getScreenDim()));
- if (imageFontScaling == 0)
- System.out.println("??? viewer");
if (width > 0) {
dimScreen.width = width;
dimScreen.height = height;
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