Revision: 20783
http://sourceforge.net/p/jmol/code/20783
Author: hansonr
Date: 2015-09-21 12:17:42 +0000 (Mon, 21 Sep 2015)
Log Message:
-----------
DSSR fix; Ras3D reader for DSSR
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/dssx/DSSR1.java
trunk/Jmol/src/org/jmol/jvxl/readers/PmeshReader.java
trunk/Jmol/src/org/jmol/viewer/FileManager.java
Added Paths:
-----------
trunk/Jmol/src/org/jmol/jvxl/readers/Ras3DReader.java
Modified: trunk/Jmol/src/org/jmol/dssx/DSSR1.java
===================================================================
--- trunk/Jmol/src/org/jmol/dssx/DSSR1.java 2015-09-21 02:16:07 UTC (rev
20782)
+++ trunk/Jmol/src/org/jmol/dssx/DSSR1.java 2015-09-21 12:17:42 UTC (rev
20783)
@@ -136,9 +136,9 @@
if (x != null) {
info.put("dssr", x);
setGroup1(vwr.ms, modelIndex);
+ fixDSSRJSONMap(x);
+ setBioPolymers((BioModel) vwr.ms.am[modelIndex], false);
}
- fixDSSRJSONMap(x);
-
} catch (Exception e) {
info = null;
out = "" + e;
@@ -240,13 +240,7 @@
Lst<Map<String, Object>> singles = (info == null ? null
: (Lst<Map<String, Object>>) info.get("ssSegments"));
if (pairs == null && singles == null) {
- BioModel m = (BioModel) vwr.ms.am[modelIndex];
- int n = m.getBioPolymerCount();
- for (int i = n; --i >= 0;) {
- BioPolymer bp = m.bioPolymers[i];
- if (bp.isNucleic())
- ((NucleicPolymer) bp).isDssrSet = true;
- }
+ setBioPolymers((BioModel) vwr.ms.am[modelIndex], true);
return;
}
BS bsAtoms = ms.am[modelIndex].bsAtoms;
@@ -278,6 +272,15 @@
}
+ private void setBioPolymers(BioModel m, boolean b) {
+ int n = m.getBioPolymerCount();
+ for (int i = n; --i >= 0;) {
+ BioPolymer bp = m.bioPolymers[i];
+ if (bp.isNucleic())
+ ((NucleicPolymer) bp).isDssrSet = b;
+ }
+ }
+
private NucleicMonomer setRes(Atom atom) {
NucleicMonomer m = (NucleicMonomer) atom.group;
((NucleicPolymer) m.bioPolymer).isDssrSet = true;
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/PmeshReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/PmeshReader.java 2015-09-21
02:16:07 UTC (rev 20782)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/PmeshReader.java 2015-09-21
12:17:42 UTC (rev 20783)
@@ -290,11 +290,11 @@
// 2
if (vertexCount == 4) {
nTriangles += 2;
- addTriangleCheck(vertices[0], vertices[1], vertices[3], 5, color,
false, -1);
- addTriangleCheck(vertices[1], vertices[2], vertices[3], 3, color,
false, -1);
+ addTriangleCheck(vertices[0], vertices[1], vertices[3], 5, 0, false,
color);
+ addTriangleCheck(vertices[1], vertices[2], vertices[3], 3, 0, false,
color);
} else {
nTriangles++;
- addTriangleCheck(vertices[0], vertices[1], vertices[2], 7, color,
false, -1);
+ addTriangleCheck(vertices[0], vertices[1], vertices[2], 7, 0, false,
color);
}
}
if (isBinary)
Added: trunk/Jmol/src/org/jmol/jvxl/readers/Ras3DReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/Ras3DReader.java
(rev 0)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/Ras3DReader.java 2015-09-21
12:17:42 UTC (rev 20783)
@@ -0,0 +1,150 @@
+/* $RCSfile$
+ * $Author: hansonr $
+ * $Date: 2007-03-30 11:40:16 -0500 (Fri, 30 Mar 2007) $
+ * $Revision: 7273 $
+ *
+ * Copyright (C) 2007 Miguel, Bob, Jmol Development
+ *
+ * Contact: hans...@stolaf.edu
+ *
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+package org.jmol.jvxl.readers;
+
+import java.io.BufferedReader;
+import java.util.Hashtable;
+import java.util.Map;
+
+import javajs.util.CU;
+import javajs.util.P3;
+
+import org.jmol.jvxl.data.JvxlCoder;
+import org.jmol.util.Logger;
+
+/*
+ *
+ */
+
+
+class Ras3DReader extends PolygonFileReader {
+
+ private String pmeshError;
+ private String type;
+ private boolean asQuads;
+ private int nPolygons;
+
+
+ Ras3DReader(){}
+
+ @Override
+ void init2(SurfaceGenerator sg, BufferedReader br) {
+ init2PR(sg, br);
+ }
+
+ protected void init2PR(SurfaceGenerator sg, BufferedReader br) {
+ init2PFR(sg, br);
+ String fileName = (String) ((Object[])sg.getReaderData())[0];
+ if (fileName == null)
+ return;
+ type = "ras3d";
+ setHeader();
+ }
+
+ protected void setHeader() {
+ jvxlFileHeaderBuffer.append(type
+ + " file format\nvertices and triangles only\n");
+ JvxlCoder.jvxlCreateHeaderWithoutTitleOrAtoms(volumeData,
+ jvxlFileHeaderBuffer);
+ }
+
+ @Override
+ void getSurfaceData() throws Exception {
+ if (readVerticesAndPolygons())
+ Logger.info(type + " file contains "
+ + nVertices + " vertices and " + nPolygons + " polygons for "
+ + nTriangles + " triangles");
+ else
+ Logger.error(params.fileName + ": "
+ + (pmeshError == null ? "Error reading pmesh data "
+ : pmeshError));
+ }
+
+ protected boolean readVerticesAndPolygons() {
+ try {
+ if (readVertices())
+ return true;
+ } catch (Exception e) {
+ if (pmeshError == null)
+ pmeshError = type + " ERROR: " + e;
+ }
+ return false;
+ }
+
+ Map<String, Integer> htVertices;
+
+ private boolean readVertices() throws Exception {
+ htVertices = new Hashtable<String, Integer>();
+ int[] v0 = new int[3];
+ int[] v1 = new int[3];
+ int[] v2;
+ int c0 = 0, c1 = 0, c2;
+ if (rd().indexOf("DSSR") >= 0)
+ asQuads = true;
+ while (rd() != null) {
+ while (!line.equals("1")) {
+ rd();
+ }
+ // triangles only
+ rd();
+ String[] tokens = getTokens();
+ v0[0] = getPoint(tokens, 0);
+ v0[1] = getPoint(tokens, 3);
+ v0[2] = getPoint(tokens, 6);
+ nTriangles++;
+ c0 = CU.colorTriadToFFRGB(parseFloatStr(tokens[9]),
+ parseFloatStr(tokens[10]), parseFloatStr(tokens[11]));
+ System.out.println(CU.colorPtFromInt(c0, new P3()));
+ if (asQuads) {
+ if (nTriangles % 2 == 1) {
+ v2 = v1;
+ v1 = v0;
+ v0 = v2;
+ c2 = c1;
+ c1 = c0;
+ c0 = c2;
+ continue;
+ }
+ addTriangleCheck(v0[0], v0[1], v0[2], 6, 0, false, c0);
+ addTriangleCheck(v1[0], v1[1], v1[2], 3, 0, false, c1);
+ } else {
+ addTriangleCheck(v0[0], v0[1], v0[2], 7, 0, false, c0);
+ }
+ nPolygons++;
+ }
+ return true;
+ }
+
+ private int getPoint(String[] tokens, int i) {
+ String key = tokens[i] + ";" + tokens[i+1] + ";" + tokens[i+2];
+ Integer v = htVertices.get(key);
+ if (v == null) {
+
addVertexCopy(P3.new3(parseFloatStr(tokens[i]),parseFloatStr(tokens[i+1]),parseFloatStr(tokens[i+2])),
0, nVertices, false);
+ htVertices.put(key, v = Integer.valueOf(nVertices++));
+ }
+ return v.intValue();
+ }
+
+
+}
Property changes on: trunk/Jmol/src/org/jmol/jvxl/readers/Ras3DReader.java
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Modified: trunk/Jmol/src/org/jmol/viewer/FileManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/FileManager.java 2015-09-21 02:16:07 UTC
(rev 20782)
+++ trunk/Jmol/src/org/jmol/viewer/FileManager.java 2015-09-21 12:17:42 UTC
(rev 20783)
@@ -1387,6 +1387,8 @@
return "Nff";
if (line.indexOf("BEGIN_DATAGRID_3D") >= 0 ||
line.indexOf("BEGIN_BANDGRID_3D") >= 0)
return "Xsf";
+ if (line.indexOf("tiles in x, y") >= 0)
+ return "Ras3D";
// binary formats: problem here is that the buffered reader
// may be translating byte sequences into unicode
// and thus shifting the offset
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