Revision: 21518
http://sourceforge.net/p/jmol/code/21518
Author: hansonr
Date: 2017-04-14 04:36:53 +0000 (Fri, 14 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
new feature: WRITE ISOMESH "t.pmesh"; WRITE ISOMESHBIN "t.pmb"
-- isosurface contour only (for now)
-- creates ASCII/BINARY .pmesh/.pmb file
-- read back into Jmol using ISOSURFACE PMESH "t.pmesh"/"t.pmb"
-- note that binary files are NOT RECOMMENDED for JSmol because some
platforms cannot read them locally
-- example:
load $methane
isosurface plane {0 0 0 1} map vdw contours 20
write ISOMESHBIN contour.pmb
isosurface PMESH contour.pmb
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/src/javajs/util/OC.java
trunk/Jmol/src/javajs/util/T3.java
trunk/Jmol/src/org/jmol/jvxl/readers/PmeshReader.java
trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java
trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java
trunk/Jmol/src/org/jmol/util/MeshSurface.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/javajs/util/OC.java
===================================================================
--- trunk/Jmol/src/javajs/util/OC.java 2017-04-13 16:27:44 UTC (rev 21517)
+++ trunk/Jmol/src/javajs/util/OC.java 2017-04-14 04:36:53 UTC (rev 21518)
@@ -440,4 +440,8 @@
}
}
+ public void writeFloat(float x) {
+ writeInt(x == 0 ? 0 : Float.floatToIntBits(x));
+ }
+
}
Modified: trunk/Jmol/src/javajs/util/T3.java
===================================================================
--- trunk/Jmol/src/javajs/util/T3.java 2017-04-13 16:27:44 UTC (rev 21517)
+++ trunk/Jmol/src/javajs/util/T3.java 2017-04-14 04:36:53 UTC (rev 21518)
@@ -304,7 +304,7 @@
return (int) (bits ^ (bits >> 32));
}
- static int floatToIntBits(float x) {
+ public static int floatToIntBits(float x) {
return (x == 0 ? 0 : Float.floatToIntBits(x));
}
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/PmeshReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/PmeshReader.java 2017-04-13
16:27:44 UTC (rev 21517)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/PmeshReader.java 2017-04-14
04:36:53 UTC (rev 21518)
@@ -41,7 +41,7 @@
3.0000 3.0000 1.0000
2.3333 3.0000 1.0000
...(98 more like this)
- 81
+ 81 <-- polygonCount may be -1
5
0
10
@@ -49,6 +49,7 @@
1
0
...(80 more sets like this)
+ <-- may be 0 if polygonCount = -1
* The first line defines the number of grid points
* defining the surface (integer, n)
@@ -58,9 +59,9 @@
* The next m sets of numbers, one number per line,
* define the polygons. In each set, the first number, p, specifies
* the number of points in each set. Currently this number must be either
- * 4 (for triangles) or 5 (for quadrilaterals). The next p numbers specify
+ * 1 (points), 2 (edges), 3 (triangles), 4 (for closed triangles) or 5 (for
closed quadrilaterals). The next p numbers specify
* indexes into the list of data points (starting with 0).
- * The first and last of these numbers must be identical in order to
+ * For p > 3, the first and last of these numbers must be identical in order
to
* "close" the polygon.
*
* If the number of points in a set is negative, it indicates that a color
follows:
@@ -81,10 +82,9 @@
* note that there is NO redundant extra vertex in this format
*
* 4 bytes: P M \1 \0
- * 4 bytes: ignored
* 4 bytes: (int) 1 -- first byte used to determine big(==0) or little(!=0)
endian
* 4 bytes: (int) nVertices
- * 4 bytes: (int) nPolygons
+ * 4 bytes: (int) nPolygons -- may be -1
* 64 bytes: reserved
* ------------------------------
* float[nVertices*3]vertices {x,y,z}
@@ -92,7 +92,7 @@
* --each polygon--
* 4 bytes: (int)nVertices (1,2,3, or 4)
* [4 bytes * nVertices] int[nVertices]
- *
+ * optional 4 bytes (int)0 -- end of file
*
*/
@@ -233,19 +233,25 @@
pmeshError = type + " ERROR: polygon count must be zero or positive";
if (!isBinary)
nPolygons = getInt();
- if (nPolygons < 0) {
- pmeshError += " (" + nPolygons + ")";
- return false;
- }
+// if (nPolygons < 0) {
+// pmeshError += " (" + nPolygons + ")";
+// return false;
+// }
if (onePerLine)
iToken = Integer.MAX_VALUE;
int[] vertices = new int[5];
+ if (nPolygons == -1)
+ nPolygons = Integer.MAX_VALUE;
+ int nread = 0;
for (int iPoly = 0; iPoly < nPolygons; iPoly++) {
int intCount = (fixedCount == 0 ? getInt() : fixedCount);
+ if (intCount == 0)
+ break;
+ nread++;
boolean haveColor = (intCount < 0);
if (haveColor)
intCount = -intCount;
- int vertexCount = intCount - (isClosedFace ? 1 : 0);
+ int vertexCount = intCount - (intCount > 3 && isClosedFace ? 1 : 0);
// (we will ignore the redundant extra vertex when not binary and not
msms)
if (vertexCount < 1 || vertexCount > 4) {
pmeshError = type + " ERROR: bad polygon (must have 1-4 vertices) at
#"
@@ -271,10 +277,14 @@
vertices[i] = vertices[i - 1];
int color = 0;
if (haveColor) {
- String c = nextToken();
- color = parseIntStr(c);
- if (color == Integer.MIN_VALUE)
- color = CU.getArgbFromString(c);
+ if (isBinary) {
+ color = getInt();
+ } else {
+ String c = nextToken();
+ color = parseIntStr(c);
+ if (color == Integer.MIN_VALUE)
+ color = CU.getArgbFromString(c);
+ }
color |= 0xFF000000;
}
// check: 1 (ab) | 2(bc) | 4(ac)
@@ -299,6 +309,7 @@
}
if (isBinary)
nBytes = binarydoc.getPosition();
+ nPolygons = nread;
return true;
}
Modified: trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2017-04-13 16:27:44 UTC
(rev 21517)
+++ trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2017-04-14 04:36:53 UTC
(rev 21518)
@@ -3754,6 +3754,7 @@
// quality|PNG|PPM|SPT] "filename"
// write script "filename"
// write isosurface t.jvxl
+ // write isosurface t.pmesh
if (type.equals("IMAGE")
&& PT.isOneOf(val.toLowerCase(), JC.IMAGE_OR_SCENE)) {
@@ -3862,7 +3863,7 @@
&& !PT
.isOneOf(
type,
-
";SCENE;JMOL;ZIP;ZIPALL;SPT;HISTORY;MO;NBO;ISOSURFACE;MESH;PMESH;VAR;FILE;FUNCTION;CIF;CML;JSON;XYZ;XYZRN;XYZVIB;MENU;MOL;MOL67;PDB;PGRP;PQR;QUAT;RAMA;SDF;V2000;V3000;INLINE;"))
+
";SCENE;JMOL;ZIP;ZIPALL;SPT;HISTORY;MO;NBO;ISOSURFACE;MESH;PMESH;PMB;ISOMESHBIN;ISOMESH;VAR;FILE;FUNCTION;CIF;CML;JSON;XYZ;XYZRN;XYZVIB;MENU;MOL;MOL67;PDB;PGRP;PQR;QUAT;RAMA;SDF;V2000;V3000;INLINE;"))
eval.errorStr2(
ScriptError.ERROR_writeWhat,
"COORDS|FILE|FUNCTIONS|HISTORY|IMAGE|INLINE|ISOSURFACE|JMOL|MENU|MO|NBO|POINTGROUP|QUATERNION
[w,x,y,z] [derivative]"
@@ -4011,11 +4012,19 @@
data = getMoJvxl(Integer.MAX_VALUE, data == "NBO");
type = "XJVXL";
} else if (data == "PMESH") {
- if ((data = getIsosurfaceJvxl(true, JC.SHAPE_PMESH)) == null)
+ if ((data = (String) getIsosurfaceJvxl(JC.SHAPE_PMESH, data)) == null)
error(ScriptError.ERROR_noData);
type = "XJVXL";
+ } else if (data == "ISOMESH") {
+ if ((data = (String) getIsosurfaceJvxl(JC.SHAPE_ISOSURFACE, data)) ==
null)
+ error(ScriptError.ERROR_noData);
+ type = "PMESH";
+ } else if (data == "ISOMESHBIN" || data == "PMB") {
+ if ((bytes = getIsosurfaceJvxl(JC.SHAPE_ISOSURFACE, "ISOMESHBIN")) ==
null)
+ error(ScriptError.ERROR_noData);
+ type = "PMB";
} else if (data == "ISOSURFACE" || data == "MESH") {
- if ((data = getIsosurfaceJvxl(data == "MESH", JC.SHAPE_ISOSURFACE)) ==
null)
+ if ((data = (String) getIsosurfaceJvxl(JC.SHAPE_ISOSURFACE, data)) ==
null)
error(ScriptError.ERROR_noData);
type = (data.indexOf("<?xml") >= 0 ? "XJVXL" : "JVXL");
if (!showOnly)
@@ -5192,9 +5201,11 @@
return sb.toString();
}
- private String getIsosurfaceJvxl(boolean asMesh, int iShape) {
- return (chk ? "" : (String) getShapeProperty(iShape, asMesh ? "jvxlMeshX"
- : "jvxlDataXml"));
+ private Object getIsosurfaceJvxl(int iShape, String type) {
+ type = (type == "PMESH" || type == "MESH" ? "jvxlMeshX" :
+ type == "ISOMESH" ? "pmesh" : type == "ISOMESHBIN" ? "pmeshbin"
+ : "jvxlDataXml");
+ return (chk ? "" : getShapeProperty(iShape, type));
}
@SuppressWarnings("unchecked")
Modified: trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java 2017-04-13
16:27:44 UTC (rev 21517)
+++ trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java 2017-04-14
04:36:53 UTC (rev 21518)
@@ -925,6 +925,8 @@
return jvxlData.jvxlPlane;
if (property == "contours")
return thisMesh.getContours();
+ if (property == "pmesh" || property == "pmeshbin")
+ return thisMesh.getPmeshData(property == "pmeshbin");
if (property == "jvxlDataXml" || property == "jvxlMeshXml") {
MeshData meshData = null;
jvxlData.slabInfo = null;
Modified: trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java 2017-04-13
16:27:44 UTC (rev 21517)
+++ trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java 2017-04-14
04:36:53 UTC (rev 21518)
@@ -43,6 +43,7 @@
import javajs.util.CU;
import javajs.util.M4;
+import javajs.util.OC;
import javajs.util.P3;
import javajs.util.P3i;
import javajs.util.PT;
@@ -292,6 +293,152 @@
return jvxlData.vContours = vContours;
}
+ public Object getPmeshData(boolean isBinary) {
+ MeshWriter mw = new MeshWriter(isBinary);
+ return mw.write();
+ }
+
+ private class MeshWriter {
+ boolean isBinary;
+ private OC oc;
+
+ MeshWriter(boolean isBinary) {
+ this.isBinary = isBinary;
+ oc = vwr.getOutputChannel(null, null);
+ if (isBinary) {
+ oc.writeByteAsInt(80);
+ oc.writeByteAsInt(77);
+ oc.writeByteAsInt(1);
+ oc.writeByteAsInt(0);
+ oc.writeInt(1);
+ oc.writeInt(vc);
+ oc.writeInt(-1);
+ for (int i = 0; i < 16; i++)
+ oc.writeInt(0);
+ }
+ }
+
+ Object write() {
+ boolean fill = false;
+ int[][] polygonIndexes = pis;
+ short cx = (!fill && meshColix != 0 ? meshColix : colix);
+ short[] vertexColixes = (!fill && meshColix != 0 ? null : vcs);
+ boolean colorSolid = (vertexColixes == null);
+ boolean noColor = (vertexColixes == null || !fill && meshColix != 0);
+ boolean colorArrayed = (colorSolid && pcs != null);
+ if (colorArrayed && !fill && fillTriangles)
+ colorArrayed = false;
+ short[] contourColixes = jvxlData.contourColixes;
+ boolean haveBsDisplay = (bsDisplay != null);
+ boolean selectedPolyOnly = (bsSlabDisplay != null);
+ BS bsPolygons = (selectedPolyOnly ? bsSlabDisplay : null);
+ int i0 = 0;
+ int color = 0;
+ if (!isBinary)
+ outputInt(vc);
+ for (int i = 0; i < vc; i++)
+ outputXYZ(vs[i]);
+ if (!isBinary)
+ outputInt(-1); // null-terminated
+ for (int i = pc; --i >= i0;) {
+ int[] polygon = polygonIndexes[i];
+ if (polygon == null || selectedPolyOnly && !bsPolygons.get(i))
+ continue;
+ int iA = polygon[0];
+ int iB = polygon[1];
+ int iC = polygon[2];
+ if (jvxlData.thisSet >= 0 && vertexSets != null
+ && vertexSets[iA] != jvxlData.thisSet)
+ continue;
+ if (haveBsDisplay
+ && (!bsDisplay.get(iA) || !bsDisplay.get(iB) ||
!bsDisplay.get(iC)))
+ continue;
+ if (colorSolid) {
+ if (colorArrayed && i < pcs.length) {
+ short c = pcs[i];
+ if (c == 0)
+ continue;
+ cx = c;
+ }
+ } else {
+ cx = vertexColixes[iA];
+ }
+ color = C.getArgb(cx);
+ if (fill) {
+ if (iB == iC) {
+ if (iA == iB)
+ outputPoint(iA, color);
+ else
+ outputEdge(iA, iB, color);
+ } else if (colorsExplicit) {
+ color = polygon[MeshSurface.P_EXPLICIT_COLOR];
+ outputTriangle(iA, iB, iC, color, 7);
+ } else {
+ outputTriangle(iA, iB, iC, color, 7);
+ }
+ } else {
+ // mesh only
+ // check: 1 (ab) | 2(bc) | 4(ac)
+ int check = 7 & polygon[MeshSurface.P_CHECK];
+ if (check == 0)
+ continue;
+ if (noColor) {
+ } else if (colorArrayed) {
+ color = C.getArgb(fillTriangles ? C.BLACK
+ : contourColixes[polygon[MeshSurface.P_CONTOUR]
+ % contourColixes.length]);
+ }
+ outputTriangle(iA, iB, iC, color, check);
+ }
+ }
+ if (isBinary)
+ oc.writeInt(0);
+ else
+ oc.append("0\n");
+ oc.closeChannel();
+ return (isBinary ? oc.toByteArray() : oc.toString());
+ }
+
+ private void outputInt(int i) {
+ if (isBinary)
+ oc.writeInt(i);
+ else
+ oc.append("" + i + "\n");
+ }
+
+ private int outputPoint(int iA, int color) {
+ outputInt(-1);
+ outputInt(iA);
+ outputInt(color);
+ return 1;
+ }
+
+ private void outputXYZ(T3 pt) {
+ if (isBinary) {
+ oc.writeFloat(pt.x);
+ oc.writeFloat(pt.y);
+ oc.writeFloat(pt.z);
+ } else {
+ oc.append(pt.x + " " + pt.y + " " + pt.z + "\n");
+ }
+ }
+
+ private void outputEdge(int iA, int iB, int color) {
+ outputInt(-2);
+ outputInt(iA);
+ outputInt(iB);
+ outputInt(color);
+ }
+
+ private void outputTriangle(int iA, int iB, int iC, int color, int check) {
+ if ((check & 1) != 0)
+ outputEdge(iA, iB, color);
+ if ((check & 2) != 0)
+ outputEdge(iB, iC, color);
+ if ((check & 4) != 0)
+ outputEdge(iC, iA, color);
+ }
+ }
private static void get3dContour(IsosurfaceMesh m, Lst<Object> v, float
value, short colix) {
BS bsContour = BS.newN(m.pc);
SB fData = new SB();
Modified: trunk/Jmol/src/org/jmol/util/MeshSurface.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/MeshSurface.java 2017-04-13 16:27:44 UTC
(rev 21517)
+++ trunk/Jmol/src/org/jmol/util/MeshSurface.java 2017-04-14 04:36:53 UTC
(rev 21518)
@@ -21,7 +21,7 @@
public static final int P_CONTOUR = 4;
public static final int P_EXPLICIT_COLOR = 4;
- protected Viewer vwr;
+ public Viewer vwr;
private MeshSlicer slicer;
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-04-13 16:27:44 UTC
(rev 21517)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-04-14 04:36:53 UTC
(rev 21518)
@@ -55,6 +55,19 @@
-- allows Jmol window to NOT be embedded in JSpecView when JSpecView is
opened in Jmol
-- default TRUE
+new feature: WRITE ISOMESH "t.pmesh"; WRITE ISOMESHBIN "t.pmb"
+ -- isosurface contour only (for now)
+ -- creates ASCII/BINARY .pmesh/.pmb file
+ -- read back into Jmol using ISOSURFACE PMESH "t.pmesh"/"t.pmb"
+ -- note that binary files are NOT RECOMMENDED for JSmol because some
platforms cannot read them locally
+ -- example:
+
+ load $methane
+ isosurface plane {0 0 0 1} map vdw contours 20
+ write ISOMESHBIN contour.pmb
+ isosurface PMESH contour.pmb
+
+
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
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