Revision: 21517
http://sourceforge.net/p/jmol/code/21517
Author: hansonr
Date: 2017-04-13 16:27:44 +0000 (Thu, 13 Apr 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.14.1"
new feature: set jmolInJSpecView
-- allows Jmol window to NOT be embedded in JSpecView when JSpecView is
opened in Jmol
-- default TRUE
bug fix: mesh capper producing gaps
bug fix: CIP chirality fixed for rule ordering; validated for IUPAC Rules 1, 2,
and 3 (though still some questions about Rule 3)
bug fix: print getProperty("cifinfo") without file name fails
Modified Paths:
--------------
trunk/Jmol/jars/JSpecView.jar
trunk/Jmol/src/org/jmol/render/MeshRenderer.java
trunk/Jmol/src/org/jmol/rendersurface/PmeshRenderer.java
trunk/Jmol/src/org/jmol/script/T.java
trunk/Jmol/src/org/jmol/util/MeshCapper.java
trunk/Jmol/src/org/jmol/util/MeshSlicer.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
trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/StatusListener.java
Modified: trunk/Jmol/jars/JSpecView.jar
===================================================================
(Binary files differ)
Modified: trunk/Jmol/src/org/jmol/render/MeshRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/render/MeshRenderer.java 2017-04-13 04:13:56 UTC
(rev 21516)
+++ trunk/Jmol/src/org/jmol/render/MeshRenderer.java 2017-04-13 16:27:44 UTC
(rev 21517)
@@ -181,6 +181,7 @@
private boolean setVariables() {
if (mesh.visibilityFlags == 0)
return false;
+ forceShowTriangles = vwr.getBoolean(T.testflag3);
showTriangles = forceShowTriangles || mesh.showTriangles;
if (mesh.bsSlabGhost != null)
g3d.setC(mesh.slabColix); // forces a second pass
Modified: trunk/Jmol/src/org/jmol/rendersurface/PmeshRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/rendersurface/PmeshRenderer.java 2017-04-13
04:13:56 UTC (rev 21516)
+++ trunk/Jmol/src/org/jmol/rendersurface/PmeshRenderer.java 2017-04-13
16:27:44 UTC (rev 21517)
@@ -30,7 +30,6 @@
@Override
protected boolean render() {
- forceShowTriangles = vwr.getBoolean(T.testflag3);
return renderIso();
}
Modified: trunk/Jmol/src/org/jmol/script/T.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/T.java 2017-04-13 04:13:56 UTC (rev
21516)
+++ trunk/Jmol/src/org/jmol/script/T.java 2017-04-13 16:27:44 UTC (rev
21517)
@@ -1011,10 +1011,11 @@
public final static int hidenotselected = booleanparam | 86;
public final static int highresolution = booleanparam | 88;
// see predefinedset public final static int hydrogen =
booleanparam | 90;
- public final static int imagestate = booleanparam | 91;
- public static final int iskiosk = booleanparam | 92;
// 11.9.29
- public final static int isosurfacekey = booleanparam | 93;
- public final static int isosurfacepropertysmoothing = booleanparam | 94;
+ public final static int imagestate = booleanparam | 89;
+ public static final int iskiosk = booleanparam | 90;
// 11.9.29
+ public final static int isosurfacekey = booleanparam | 91;
+ public final static int isosurfacepropertysmoothing = booleanparam | 92;
+ public final static int jmolinjspecview = booleanparam | 93;
// 14.13.1
public final static int justifymeasurements = booleanparam | 95;
public final static int languagetranslation = booleanparam | 96;
public final static int legacyautobonding = booleanparam | 97;
@@ -2585,6 +2586,7 @@
"isosurfaceKey",
"isosurfacePropertySmoothing",
"isosurfacePropertySmoothingPower",
+ "jmolInJSpecView",
"justifyMeasurements",
"languageTranslation",
"leadAtom",
@@ -3632,6 +3634,7 @@
isosurfacekey, // "isosurfaceKey"
isosurfacepropertysmoothing, //
"isosurfacePropertySmoothing"
isosurfacepropertysmoothingpower, //
"isosurfacePropertySmoothingPower"
+ jmolinjspecview,
justifymeasurements, // "justifyMeasurements"
languagetranslation, // "languageTranslation"
leadatom, // "leadAtom"
Modified: trunk/Jmol/src/org/jmol/util/MeshCapper.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/MeshCapper.java 2017-04-13 04:13:56 UTC
(rev 21516)
+++ trunk/Jmol/src/org/jmol/util/MeshCapper.java 2017-04-13 16:27:44 UTC
(rev 21517)
@@ -87,7 +87,7 @@
private int nPoints;
- private M4 m4;
+ M4 m4, m4inv;
/////////////// initialization //////////////////
@@ -317,7 +317,7 @@
Quat q = Quat.getQuaternionFrameV(vab, vac, null, false);
M3 m3 = q.getMatrix();
m4 = M4.newMV(m3, vertices.get(0));
- M4 m4inv = M4.newM4(m4).invert();
+ m4inv = M4.newM4(m4).invert();
vertices.toArray(vs);
vertices = null;
@@ -331,7 +331,7 @@
if (Logger.debugging)
Logger.info("MeshCapper using " + vs.length + " vertices");
- CapVertex v0 = vs[0].sort(vs);
+ CapVertex v0 = sort(vs);
if (v0 == null) {
Logger.error("two identical points -- aborting");
return;
@@ -359,6 +359,104 @@
}
/**
+ * Generate qnext links based on scanning Y large to Y small and if Y1==Y2,
+ * then X small to large
+ *
+ * @param vs
+ * @return null if there are two identical points (edge crossings)
+ */
+ public CapVertex sort(CapVertex[] vs) {
+ Lst<CapVertex> v0s = new Lst<CapVertex>();
+ Lst<CapVertex> v1s = new Lst<CapVertex>();
+ int n = vs.length;
+// for (int i = n; --i >= 0;)
+// System.out.println(vs[i]);
+// System.out.println("#----");
+ for (int i = n; --i >= 0;) {
+ if (vs[i].next == null) {
+ v0s.addLast(vs[i]);
+ } else if (vs[i].prev == null) {
+ v1s.addLast(vs[i]);
+ }
+ }
+ for (int i = v0s.size(); --i >= 0;) {
+ CapVertex v0 = v0s.get(i);
+ CapVertex v1 = findNearestVertex(v1s, v0);
+ if (v1 == null) {
+ System.out.println("MESHCAPPER OHOH");
+ } else {
+ v0.link(v1);
+ }
+
+ }
+ MeshCapperSorter sorter = new MeshCapperSorter();
+// for (int i = 0; i < n; i++) {
+// CapVertex v = vs[i];
+// if (vs[i].next == null || vs[i].prev == null)
+// System.out.println("null meshcapper");
+// }
+//
+
+ Arrays.sort(vs, sorter);
+ int pt = n;
+
+// int pt = 0;
+// for (int i = 0; i < n; i++) {
+// if (!vs[i].disabled)
+// vs[pt++] = vs[i];
+// }
+ if (pt > 0) {
+ for (int i = pt; --i >= 0;) {
+ CapVertex v = vs[i];
+ vs[i].qnext = vs[(i + 1) % pt];
+ }
+ vs[pt - 1].qnext = vs[0];
+ }
+ return vs[0];
+ }
+
+ private CapVertex findNearestVertex(Lst<CapVertex> v1s, CapVertex v0) {
+ float min = Float.MAX_VALUE;
+ CapVertex vmin = null;
+ int imin = -1;
+ for (int i = v1s.size(); --i >= 0;) {
+ CapVertex v1 = v1s.get(i);
+ float d = v1.distanceSquared(v0);
+ if (d < min) {
+ min = d;
+ vmin = v1;
+ imin = i;
+ }
+ }
+ if (imin >= 0)
+ v1s.removeItemAt(imin);
+ return vmin;
+ }
+
+ public class MeshCapperSorter implements
+ Comparator<CapVertex> {
+
+
+ @Override
+ public int compare(CapVertex v1, CapVertex v2) {
+ // first HIGHEST Y to LOWEST Y, then LOWEST X to HIGHEST X
+ return (v1.y < v2.y ? 1 : v1.y > v2.y || v1.x < v2.x ? -1
+ : v1.x > v2.x ? 1
+ : 0);//disable(v1, v2));
+ }
+
+
+ }
+
+ int disable(CapVertex v1, CapVertex v2) {
+ if (!v1.disabled && !v2.disabled) {
+ //v2.link(null);
+ v2.disabled = true;
+ }
+ return 0;
+ }
+
+ /**
* Handle the point; mark as processed.
*
* @param v
@@ -824,6 +922,8 @@
CapVertex[] region;
boolean disabled;
+
+ T3 cartesian;
CapVertex(T3 p, int i) {
ipt = i;
@@ -840,93 +940,6 @@
}
/**
- * Generate qnext links based on scanning Y large to Y small and if Y1==Y2,
- * then X small to large
- *
- * @param vs
- * @return null if there are two identical points (edge crossings)
- */
- public CapVertex sort(CapVertex[] vs) {
- CapVertex v0 = null;
- CapVertex v1 = null;
- int n = vs.length;
- for (int i = n; --i >= 0;)
- System.out.println(i + "/" + n + " " + vs[i]);
- System.out.println("----");
- for (int i = n; --i >= 0;) {
- if (vs[i].next == null) {
- System.out.println("fixing next " + vs[i]);
- if (v0 == null) {
- v1 = vs[i];
- System.out.println("next,v0 null; v1 is now " + v1);
- } else {
- vs[i].link(v0);
- System.out.println("next null, v0 not null;linked\n" + vs[i] +
"\n" + v0);
- v0 = null;
- }
- } else if (vs[i].prev == null) {
- System.out.println("fixing prev " + vs[i]);
- if (v1 == null) {
- v0 = vs[i];
- System.out.println("prev,v1 null; v0 is now " + v0);
- } else {
- v1.link(vs[i]);
- System.out.println("prev null, v1 not null;linked\n" + v1 + "\n" +
vs[i]);
- v1 = null;
- }
- }
- }
-
- MeshCapperSorter sorter = new MeshCapperSorter();
-// for (int i = 0; i < n; i++) {
-// CapVertex v = vs[i];
-// if (vs[i].next == null || vs[i].prev == null)
-// System.out.println("null meshcapper");
-// }
-//
-
- Arrays.sort(vs, sorter);
- int pt = n;
-
-// int pt = 0;
-// for (int i = 0; i < n; i++) {
-// if (!vs[i].disabled)
-// vs[pt++] = vs[i];
-// }
- if (pt > 0) {
- for (int i = pt; --i >= 0;) {
- CapVertex v = vs[i];
- vs[i].qnext = vs[(i + 1) % pt];
- }
- vs[pt - 1].qnext = vs[0];
- }
- return vs[0];
- }
-
- public class MeshCapperSorter implements
- Comparator<CapVertex> {
-
-
- @Override
- public int compare(CapVertex v1, CapVertex v2) {
- // first HIGHEST Y to LOWEST Y, then LOWEST X to HIGHEST X
- return (v1.y < v2.y ? 1 : v1.y > v2.y || v1.x < v2.x ? -1
- : v1.x > v2.x ? 1
- : 0);//disable(v1, v2));
- }
-
-
- }
-
- int disable(CapVertex v1, CapVertex v2) {
- if (!v1.disabled && !v2.disabled) {
- //v2.link(null);
- v2.disabled = true;
- }
- return 0;
- }
-
- /**
* Get interpolated x for the scan line intersection with an edge. This
* method is used both in finding the last point for a split and for
* checking winding on same-side addition.
@@ -991,14 +1004,18 @@
@Override
public String toString() {
+ if (cartesian == null)
+ cartesian = new P3();
+ if (m4 != null)
+ m4.rotTrans2(this, cartesian);
return "draw p"
+ id
+ " {"
- + x
+ + cartesian.x
+ " "
- + y
+ + cartesian.y
+ " "
- + z
+ + cartesian.z
+ "} # "
+ (prev == null ? "null" : prev.id)
+ (next == null ? " null" : " " + next.id)
Modified: trunk/Jmol/src/org/jmol/util/MeshSlicer.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/MeshSlicer.java 2017-04-13 04:13:56 UTC
(rev 21516)
+++ trunk/Jmol/src/org/jmol/util/MeshSlicer.java 2017-04-13 16:27:44 UTC
(rev 21517)
@@ -138,9 +138,7 @@
P3[] box = (P3[]) slabbingObject;
sb.append("within ").append(Escape.eAP(box));
P4[] faces = getBoxFacesFromCriticalPoints(box);
- System.out.println("MeshSlicer test 4");
for (int i = 0; i < faces.length; i++) {
- if (i == 1 || i == 2 || i == 4)
getIntersection(0, faces[i], null, null, null, null, null, andCap,
false, T.plane, isGhost);
}
@@ -281,9 +279,11 @@
if (m.vertexSource == null)
return;
fData = new float[m.vc];
- for (int i = 0; i < m.vc; i++)
- if ((fData[i] = m.vertexSource[i]) == -1)
+ for (int i = 0; i < m.vc; i++) {
+ fData[i] = m.vertexSource[i];
+ if (fData[i] == -1)
System.out.println("meshsurface hmm");
+ }
} else {
fData = m.vvs;
}
Modified: trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java 2017-04-13 04:13:56 UTC
(rev 21516)
+++ trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java 2017-04-13 16:27:44 UTC
(rev 21517)
@@ -283,6 +283,7 @@
setB("isosurfaceKey", isosurfaceKey);
setB("isosurfacePropertySmoothing", isosurfacePropertySmoothing);
setI("isosurfacePropertySmoothingPower", isosurfacePropertySmoothingPower);
+ setB("jmolInJSpecView", jmolInJSpecView);
setB("justifyMeasurements", justifyMeasurements);
setB("legacyAutoBonding", legacyAutoBonding);
setB("legacyHAddition", legacyHAddition);
@@ -467,6 +468,7 @@
boolean legacyAutoBonding = false;
public boolean legacyHAddition = false;
public boolean legacyJavaFloat = false; // float/double issue with
crystallographic symmetry before Jmol 14.2.5
+ boolean jmolInJSpecView = true;
boolean modulateOccupancy = true;
@@ -972,7 +974,7 @@
+
";bondingversion;contextdepthmax;debug;debugscript;defaultlatttice;defaults;defaultdropscript;diffusepercent;"
+ ";exportdrivers;exportscale"
+ ";_filecaching;_filecache;fontcaching;fontscaling;forcefield;language"
- + ";legacyautobonding;legacyhaddition;legacyjavafloat"
+ + ";jmolinjspecview;legacyautobonding;legacyhaddition;legacyjavafloat"
+ ";loglevel;logfile;loggestures;logcommands;measurestylechime"
+
";loadformat;loadligandformat;smilesurlformat;pubchemformat;nihresolverformat;edsurlformat;edsurlcutoff;multiprocessor;navigationmode;"
+
";pathforallfiles;perspectivedepth;phongexponent;perspectivemodel;platformspeed"
@@ -1061,6 +1063,7 @@
// appendCmd(str, "set autoLoadOrientation true");
app(str, "set bondingVersion " + bondingVersion);
app(str, "set legacyAutoBonding " + legacyAutoBonding);
+ app(str, "set legacyAutoBonding " + legacyAutoBonding);
app(str, "set legacyHAddition " + legacyHAddition);
app(str, "set legacyJavaFloat " + legacyJavaFloat);
app(str, "set minBondDistance " + minBondDistance);
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-04-13 04:13:56 UTC
(rev 21516)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-04-13 16:27:44 UTC
(rev 21517)
@@ -49,19 +49,17 @@
# 10. Run jmol/tools build-release.xml
#
-Jmol.___JmolVersion="14.13.2"
+Jmol.___JmolVersion="14.14.1"
-bug fix: mesh capper produces gaps; problems with disabled.link(null)
-bug fix: CIP chirality fixed for rule ordering; validated for IUPAC Rules 1,
2, and 3
+new feature: set jmolInJSpecView
+ -- allows Jmol window to NOT be embedded in JSpecView when JSpecView is
opened in Jmol
+ -- default TRUE
+
+bug fix: mesh capper producing gaps
+bug fix: CIP chirality fixed for rule ordering; validated for IUPAC Rules 1,
2, and 3 (though still some questions about Rule 3)
bug fix: print getProperty("cifinfo") without file name fails
-TODO: still incomplete fix
- see:
- load nacl.cif {1 1 1} spacegroup 225
- select @24
- spacefill ionic;lcaocartoon scale 1.0 CAP unitcell "cpk";spacefill off
-
JmolVersion="14.13.1" // 2017.04.09
new feature: MOL V2000 reader loads > <dataname> blocks into _M.molData
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2017-04-13 04:13:56 UTC (rev
21516)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2017-04-13 16:27:44 UTC (rev
21517)
@@ -5199,6 +5199,8 @@
return g.rasmolHydrogenSetting;
case T.isosurfacekey:
return g.isosurfaceKey;
+ case T.jmolinjspecview:
+ return g.jmolInJSpecView;
case T.justifymeasurements:
return g.justifyMeasurements;
case T.legacyautobonding:
@@ -6454,6 +6456,9 @@
// /11.0///
setRefreshing(value);
break;
+ case T.jmolinjspecview:
+ g.jmolInJSpecView = value;
+ break;
case T.justifymeasurements:
g.justifyMeasurements = value;
break;
Modified: trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/StatusListener.java
===================================================================
--- trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/StatusListener.java
2017-04-13 04:13:56 UTC (rev 21516)
+++ trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/StatusListener.java
2017-04-13 16:27:44 UTC (rev 21517)
@@ -42,6 +42,7 @@
import org.jmol.api.JmolSyncInterface;
import org.jmol.c.CBK;
import org.jmol.dialog.Dialog;
+import org.jmol.script.T;
import org.jmol.util.Logger;
import org.jmol.viewer.Viewer;
import org.openscience.jmol.app.JmolPlugin;
@@ -511,7 +512,7 @@
return;
}
if (jSpecViewFrame == null) {
- jSpecViewFrame = new MainFrame((Component) vwr.display, this);
+ jSpecViewFrame = new MainFrame(vwr.getBoolean(T.jmolinjspecview) ?
(Component) vwr.display : null, this);
jSpecViewFrame.setSize(Math.max(1000, jmol.frame.getWidth() + 50), 600);
jSpecViewFrame.setLocation(jmol.frame.getLocation().x + 10, jmol.frame
.getLocation().y + 100);
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