Revision: 20668
http://sourceforge.net/p/jmol/code/20668
Author: hansonr
Date: 2015-07-31 12:56:05 +0000 (Fri, 31 Jul 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.2.15_2015.07.30b"
bug fix: JavaScript deletion of array elements fails for int[] arrays.
JmolVersion="14.3.15_2015.07.30"
new feature: set multipleBondBananas TRUE
-- displays multiple bonds as banana bonds
-- does not carry over after model loading
new feature: set multipleBondSpacing 0.15; set multipleBondRadiusFactor -1.0
-- positive number for spacing but negative for radiusFactor rotates fixed
multiple bonds 90 degrees.
bug fix: magnetic spin vectors do not render properly (broken in
14.3.13_2015.05.12)
Modified Paths:
--------------
trunk/Jmol/src/javajs/util/AU.java
trunk/Jmol/src/org/jmol/render/SticksRenderer.java
trunk/Jmol/src/org/jmol/renderspecial/DrawRenderer.java
trunk/Jmol/src/org/jmol/renderspecial/VectorsRenderer.java
trunk/Jmol/src/org/jmol/script/T.java
trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/javajs/util/AU.java
===================================================================
--- trunk/Jmol/src/javajs/util/AU.java 2015-07-30 13:50:57 UTC (rev 20667)
+++ trunk/Jmol/src/javajs/util/AU.java 2015-07-31 12:56:05 UTC (rev 20668)
@@ -163,16 +163,18 @@
* @return array
*/
private static Object newInstanceO(Object array, int n) {
+ if (isAI(array))
+ return new int[n];
/**
* @j2sNative
*
- * if (!array.getClass().getComponentType)
+ * if (!array.getClass || !array.getClass().getComponentType)
* return new Array(n);
*
*/
{
- return Array.newInstance(array.getClass().getComponentType(), n);
}
+ return Array.newInstance(array.getClass().getComponentType(), n);
}
public static int getLength(Object array) {
Modified: trunk/Jmol/src/org/jmol/render/SticksRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/render/SticksRenderer.java 2015-07-30 13:50:57 UTC
(rev 20667)
+++ trunk/Jmol/src/org/jmol/render/SticksRenderer.java 2015-07-31 12:56:05 UTC
(rev 20668)
@@ -34,6 +34,9 @@
import org.jmol.util.C;
import org.jmol.util.GData;
import org.jmol.util.Edge;
+
+import javajs.util.A4;
+import javajs.util.M3;
import javajs.util.P3;
import javajs.util.V3;
import org.jmol.viewer.JC;
@@ -43,6 +46,8 @@
private boolean showMultipleBonds;
private float multipleBondSpacing;
private float multipleBondRadiusFactor;
+ private boolean bondsPerp;
+ private boolean useBananas;
private byte modeMultipleBond;
private boolean isCartesian;
//boolean showHydrogens;
@@ -113,14 +118,17 @@
return needTranslucent;
}
-// if (haveMultipleBonds) {
-// vwr.setFloatProperty("multipleBondSpacing", 0.15f);
-// vwr.setFloatProperty("multipleBondRadiusFactor", 0.4f);
-// }
-
private void getMultipleBondSettings(boolean isPymol) {
+ useBananas = (vwr.getBoolean(T.multiplebondbananas) && !isPymol);
+ // negative spacing is relative, depending upon atom-atom distance;
+ // positive spacing is absolute, for fixed in-plane (radiusFactor > 0) or
perp-plane (radiusFactor < 0)
multipleBondSpacing = (isPymol ? 0.15f
:vwr.getFloat(T.multiplebondspacing));
- multipleBondRadiusFactor = (isPymol ? 0.4f :
vwr.getFloat(T.multiplebondradiusfactor));
+ // negative radius factor indicates perpendicular fixed double bond
+ multipleBondRadiusFactor = (isPymol ? 0.4f :
vwr.getFloat(T.multiplebondradiusfactor));
+ bondsPerp = (useBananas || multipleBondSpacing > 0 &&
multipleBondRadiusFactor < 0);
+ if (useBananas)
+ multipleBondSpacing = (multipleBondSpacing < 0 ? -multipleBondSpacing *
0.4f : multipleBondSpacing);
+ multipleBondRadiusFactor = Math.abs(multipleBondRadiusFactor);
if (multipleBondSpacing == 0 && isCartesian)
multipleBondSpacing = 0.2f;
modeMultipleBond = vwr.g.modeMultipleBond;
@@ -335,9 +343,29 @@
y.cross(y, x);
y.normalize();
}
+ if (bondsPerp)
+ y.cross(y, x);
y.scale(multipleBondSpacing);
x.setT(y);
x.scale((bondOrder - 1) / 2f);
+ if (useBananas) {
+ drawBanana(a, b, x, 0);
+ switch (bondOrder) {
+ case 4:
+ drawBanana(a, b, x, 90);
+ drawBanana(a, b, x, -90);
+ //$FALL-THROUGH$
+ case 2:
+ default:
+ drawBanana(a, b, x, 180);
+ break;
+ case 3:
+ drawBanana(a, b, x, 120);
+ drawBanana(a, b, x, -120);
+ break;
+ }
+ return;
+ }
p1.sub2(a, x);
p2.sub2(b, x);
while (true) {
@@ -380,6 +408,32 @@
}
}
+ private M3 rot;
+ private A4 a4;
+ private void drawBanana(Atom a, Atom b, V3 x, int deg) {
+ g3d.addRenderer(T.hermitelevel);
+ vectorT.sub2(b, a);
+ if (rot == null) {
+ rot = new M3();
+ a4 = new A4();
+ }
+ a4.setVA(vectorT, (float) (deg * Math.PI / 180));
+ rot.setAA(a4);
+ pointT.setT(a);
+ pointT3.setT(b);
+ pointT2.ave(a, b);
+ rot.rotate2(x, vectorT);
+ pointT2.add(vectorT);
+ tm.transformPtScrT3(a, pointT);
+ tm.transformPtScrT3(pointT2, pointT2);
+ tm.transformPtScrT3(b, pointT3);
+ int w = Math.max(width, 1);
+ g3d.setC(colixA);
+ g3d.fillHermite(5, w, w, w, pointT, pointT, pointT2, pointT3);
+ g3d.setC(colixB);
+ g3d.fillHermite(5, w, w, w, pointT, pointT2, pointT3, pointT3);
+ }
+
private int xAxis1, yAxis1, xAxis2, yAxis2, dxStep, dyStep;
private void resetAxisCoordinates() {
Modified: trunk/Jmol/src/org/jmol/renderspecial/DrawRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/renderspecial/DrawRenderer.java 2015-07-30
13:50:57 UTC (rev 20667)
+++ trunk/Jmol/src/org/jmol/renderspecial/DrawRenderer.java 2015-07-31
12:56:05 UTC (rev 20668)
@@ -183,48 +183,14 @@
//renderArrowHead(controlHermites[nHermites - 2],
controlHermites[nHermites - 1], false);
//
// {pt1} {pt2} {ptref} {nDegreesOffset, theta, fractionalOffset}
+ T3 ptRef = (vertexCount > 2 ? vertices[2] : Draw.randomPoint());
float nDegreesOffset = (vertexCount > 3 ? vertices[3].x : 0);
float theta = (vertexCount > 3 ? vertices[3].y : 360);
if (theta == 0)
return;
float fractionalOffset = (vertexCount > 3 ? vertices[3].z : 0);
- vTemp.sub2(vertices[1], vertices[0]);
- // crossing point
- pt1f.scaleAdd2(fractionalOffset, vTemp, vertices[0]);
- // define rotational axis
- M3 mat = new M3().setAA(A4.newVA(vTemp,
- (float) (nDegreesOffset * Math.PI / 180)));
- // vector to rotate
- vTemp2.sub2(vertexCount > 2 ? vertices[2] : Draw.randomPoint(),
- vertices[0]);
- vTemp2.cross(vTemp, vTemp2);
- vTemp2.cross(vTemp2, vTemp);
- vTemp2.normalize();
- vTemp2.scale(dmesh.scale / 2);
- mat.rotate(vTemp2);
- //control points
- float degrees = theta / 5;
- while (Math.abs(degrees) > 5)
- degrees /= 2;
- nPoints = Math.round(theta / degrees) + 1;
- while (nPoints < 10) {
- degrees /= 2;
- nPoints = Math.round(theta / degrees) + 1;
- }
- mat.setAA(A4.newVA(vTemp, (float) (degrees * Math.PI / 180)));
- screens = vwr.allocTempScreens(nPoints);
- p3Screens = vwr.allocTempPoints(nPoints);
- int iBase = nPoints - (dmesh.scale < 2 ? 3 : 3);
- for (int i = 0; i < nPoints; i++) {
- if (i == iBase)
- pt0.setT(pt1);
- pt1.scaleAdd2(1, vTemp2, pt1f);
- if (i == 0)
- pt2.setT(pt1);
- tm.transformPtScr(pt1, screens[i]);
- tm.transformPtScrT3(pt1, p3Screens[i]);
- mat.rotate(vTemp2);
- }
+ nPoints = setArc(vertices[0], vertices[1], ptRef, nDegreesOffset, theta,
+ fractionalOffset, dmesh.scale);
if (dmesh.isVector && !dmesh.noHead) {
renderArrowHead(pt0, pt1, 0.3f, false, false, dmesh.isBarb);
tm.transformPtScr(pt1f, screens[nPoints - 1]);
@@ -267,6 +233,48 @@
}
+ private int setArc(T3 v1, T3 v2, T3 ptRef, float nDegreesOffset,
+ float theta, float fractionalOffset, float scale) {
+ vTemp.sub2(v2, v1);
+ // crossing point
+ pt1f.scaleAdd2(fractionalOffset, vTemp, v1);
+ // define rotational axis
+ M3 mat = new M3().setAA(A4.newVA(vTemp,
+ (float) (nDegreesOffset * Math.PI / 180)));
+ // vector to rotate
+ vTemp2.sub2(ptRef,
+ v1);
+ vTemp2.cross(vTemp, vTemp2);
+ vTemp2.cross(vTemp2, vTemp);
+ vTemp2.normalize();
+ vTemp2.scale(scale / 2);
+ mat.rotate(vTemp2);
+ //control points
+ float degrees = theta / 5;
+ while (Math.abs(degrees) > 5)
+ degrees /= 2;
+ int nPoints = Math.round(theta / degrees) + 1;
+ while (nPoints < 10) {
+ degrees /= 2;
+ nPoints = Math.round(theta / degrees) + 1;
+ }
+ mat.setAA(A4.newVA(vTemp, (float) (degrees * Math.PI / 180)));
+ screens = vwr.allocTempScreens(nPoints);
+ p3Screens = vwr.allocTempPoints(nPoints);
+ int iBase = nPoints - (dmesh.scale < 2 ? 3 : 3);
+ for (int i = 0; i < nPoints; i++) {
+ if (i == iBase)
+ pt0.setT(pt1);
+ pt1.scaleAdd2(1, vTemp2, pt1f);
+ if (i == 0)
+ pt2.setT(pt1);
+ tm.transformPtScr(pt1, screens[i]);
+ tm.transformPtScrT3(pt1, p3Screens[i]);
+ mat.rotate(vTemp2);
+ }
+ return nPoints;
+ }
+
private void getConnectionPoints() {
// now we screens and any adjustment to positions
// we need to set the actual control points
Modified: trunk/Jmol/src/org/jmol/renderspecial/VectorsRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/renderspecial/VectorsRenderer.java 2015-07-30
13:50:57 UTC (rev 20667)
+++ trunk/Jmol/src/org/jmol/renderspecial/VectorsRenderer.java 2015-07-31
12:56:05 UTC (rev 20668)
@@ -214,7 +214,7 @@
}
if (!standardVector) {
tm.transformPtScrT3(pointVectorEnd, screenVectorEnd);
- tm.transformPtScrT3(pointVectorStart, screenVectorEnd);
+ tm.transformPtScrT3(pointVectorStart, screenVectorStart);
if (drawCap)
pointArrowHead.add2(pointVectorEnd, headOffsetVector);
else
Modified: trunk/Jmol/src/org/jmol/script/T.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/T.java 2015-07-30 13:50:57 UTC (rev
20667)
+++ trunk/Jmol/src/org/jmol/script/T.java 2015-07-31 12:56:05 UTC (rev
20668)
@@ -1051,19 +1051,20 @@
public final static int modelkitmode = booleanparam | 107;
// 12.0.RC15
public final static int modulateoccupancy = booleanparam | 108;
// 14.3.13
public final static int monitorenergy = booleanparam | 109;
- public final static int multiprocessor = booleanparam | 110;
- public final static int navigatesurface = booleanparam | 111;
- public final static int navigationmode = booleanparam | 112;
- public final static int navigationperiodic = booleanparam | 113;
- public final static int partialdots = booleanparam | 114;
// 12.1.46
- public final static int pdbaddhydrogens = booleanparam | 115;
- public final static int pdbgetheader = booleanparam | 116;
- public final static int pdbsequential = booleanparam | 117;
- public final static int perspectivedepth = booleanparam | 118;
- public final static int preservestate = booleanparam | 119;
- public final static int rangeselected = booleanparam | 120;
- public final static int refreshing = booleanparam | 121;
- public final static int ribbonborder = booleanparam | 122;
+ public final static int multiplebondbananas = booleanparam | 110;
+ public final static int multiprocessor = booleanparam | 111;
+ public final static int navigatesurface = booleanparam | 112;
+ public final static int navigationmode = booleanparam | 113;
+ public final static int navigationperiodic = booleanparam | 114;
+ public final static int partialdots = booleanparam | 115;
// 12.1.46
+ public final static int pdbaddhydrogens = booleanparam | 116;
+ public final static int pdbgetheader = booleanparam | 117;
+ public final static int pdbsequential = booleanparam | 118;
+ public final static int perspectivedepth = booleanparam | 119;
+ public final static int preservestate = booleanparam | 120;
+ public final static int rangeselected = booleanparam | 121;
+ public final static int refreshing = booleanparam | 122;
+ public final static int ribbonborder = booleanparam | 123;
public final static int rocketbarrels = booleanparam | 124;
public final static int saveproteinstructurestate = booleanparam | 126;
public final static int scriptqueue = booleanparam | 128;
@@ -2578,6 +2579,7 @@
"modelkitMode",
"modulateOccupancy",
"monitorEnergy",
+ "multiplebondbananas",
"multipleBondRadiusFactor",
"multipleBondSpacing",
"multiProcessor",
@@ -3609,6 +3611,7 @@
modelkitmode, // "modelkitMode"
modulateoccupancy,
monitorenergy, // "monitorEnergy"
+ multiplebondbananas,
multiplebondradiusfactor, //
"multipleBondRadiusFactor"
multiplebondspacing, // "multipleBondSpacing"
multiprocessor, // "multiProcessor"
Modified: trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java 2015-07-30 13:50:57 UTC
(rev 20667)
+++ trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java 2015-07-31 12:56:05 UTC
(rev 20668)
@@ -301,6 +301,7 @@
setF("modulationScale", modulationScale);
setB("monitorEnergy", monitorEnergy);
setF("multipleBondRadiusFactor", multipleBondRadiusFactor);
+ setB("multipleBondBananas", multipleBondBananas);
setF("multipleBondSpacing", multipleBondSpacing);
setB("multiProcessor", multiProcessor && (Viewer.nProcessors > 1));
setB("navigationMode", navigationMode);
@@ -525,6 +526,7 @@
boolean ssbondsBackbone = false;
float multipleBondSpacing = -1; // 0.35?
float multipleBondRadiusFactor = 0; // 0.75?
+ boolean multipleBondBananas = false;
//secondary structure + Rasmol
@@ -1034,6 +1036,8 @@
// these next two might be part of a 2D->3D operation
app(str, "set minimizationCriterion " + minimizationCriterion);
app(str, "set minimizationSteps " + minimizationSteps);
+ // Jmol 14.3.15 introduces bananas, but this setting should not carry
through from one model to the next
+ app(str, "set multipleBondBananas false");
app(
str,
"set pdbAddHydrogens "
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-07-30 13:50:57 UTC
(rev 20667)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-07-31 12:56:05 UTC
(rev 20668)
@@ -48,8 +48,26 @@
TODO: there is something wrong with JSmol and zoneDemo. Just slow? or what?
-Jmol.___JmolVersion="14.3.15_2015.07.29"
+TODO: curved arrows overextend and with width settings do not truncate shaft
properly
+
+Jmol.___JmolVersion="14.2.15_2015.07.30b"
+
+bug fix: JavaScript deletion of array elements fails for int[] arrays.
+
+JmolVersion="14.3.15_2015.07.30"
+
+new feature: set multipleBondBananas TRUE
+ -- displays multiple bonds as banana bonds
+ -- does not carry over after model loading
+
+new feature: set multipleBondSpacing 0.15; set multipleBondRadiusFactor -1.0
+ -- positive number for spacing but negative for radiusFactor rotates fixed
multiple bonds 90 degrees.
+
+bug fix: magnetic spin vectors do not render properly (broken in
14.3.13_2015.05.12)
+
+JmolVersion="14.3.15_2015.07.29"
+
new feature: [Font] button added to ScriptEditor
bug fix: config 2 and select config=2 may not work properly (still)
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-07-30 13:50:57 UTC (rev
20667)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-07-31 12:56:05 UTC (rev
20668)
@@ -2531,6 +2531,7 @@
setSelectionHalosEnabled(false);
tm.setCenter();
am.initializePointers(1);
+ setBooleanProperty("multipleBondBananas", false);
if (!ms.getMSInfoB("isPyMOL")) {
clearAtomSets();
setCurrentModelIndex(0);
@@ -5040,6 +5041,8 @@
return g.messageStyleChime;
case T.modelkitmode:
return g.modelKitMode;
+ case T.multiplebondbananas:
+ return g.multipleBondBananas;
case T.navigationmode:
return g.navigationMode;
case T.navigationperiodic:
@@ -5857,6 +5860,10 @@
private void setBooleanPropertyTok(String key, int tok, boolean value) {
boolean doRepaint = true;
switch (tok) {
+ case T.multiplebondbananas:
+ // 14.3.15
+ g.multipleBondBananas = value;
+ break;
case T.modulateoccupancy:
// 12.0.RC6
g.modulateOccupancy = value;
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