@Override
public String getShapeState() {
StringBuffer sb = new StringBuffer();
sb.append(" axes scale ").append(viewer.getAxesScale()).append(";\n");
if (fixedOrigin != null)
sb.append(" axes center ").append(Escape.escape(fixedOrigin)).append(";\n");
if (axisXY.z != 0)
sb.append(" axes position [")
.append((int) axisXY.x)
.append(" ")
.append((int) axisXY.y)
.append(" ")
.append(axisXY.z < 0 ? " %" : "")
.append("];\n");
if (labels != null) {
sb.append(" axes labels ");
for (int i = 0; i < labels.length; i++) sb.append(Escape.escape(labels[i])).append(" ");
sb.append(";\n");
}
return super.getShapeState() + sb;
}
private void loadFiles(List<File> fileList) {
StringBuffer sb = new StringBuffer();
for (int i = 0; i < fileList.size(); ++i) {
File f = fileList.get(i);
String fname = f.getAbsolutePath();
fname = fname.replace('\\', '/').trim();
fname = (fname.startsWith("/") ? "file://" : "file:///") + fname;
sb.append("load ").append(i == 0 ? "" : "APPEND ").append(Escape.escape(fname)).append(";\n");
}
sb.append("frame *;reset;");
viewer.script(sb.toString());
}
public String getShapeState() {
if (!isValid) return "";
StringBuffer s = new StringBuffer();
s.append("dipole ID ").append(thisID);
if (haveAtoms)
s.append(" ({")
.append(atoms[0].getAtomIndex())
.append(" ")
.append(atoms[1].getAtomIndex())
.append("})");
else if (coords[0] == null) return "";
else
s.append(" ").append(Escape.escape(coords[0])).append(" ").append(Escape.escape(coords[1]));
if (isUserValue) s.append(" value ").append(dipoleValue);
if (mad != Dipoles.DEFAULT_MAD) s.append(" width ").append(mad / 1000f);
if (offsetAngstroms != 0) s.append(" offset ").append(offsetAngstroms);
else if (offsetPercent != 0) s.append(" offset ").append(offsetPercent);
if (offsetSide != Dipoles.DEFAULT_OFFSETSIDE) s.append(" offsetSide ").append(offsetSide);
if (noCross) s.append(" nocross");
if (!visible) s.append(" off");
s.append(";\n");
return s.toString();
}
public static void main(String[] args) {
// note that -o-x are implied, but -n is not.
// in this case -n means "no GRAPHICS" for speed
JmolApp jmolApp = new JmolApp();
jmolApp.isDataOnly = true;
jmolApp.haveConsole = false;
// jmolApp.haveDisplay = false;
jmolApp.info.put("exit", Boolean.TRUE);
jmolApp.parseCommandLine(args);
if (!jmolApp.isSilent) {
System.out.println("JmolData using command options " + Escape.escape(args));
if (!jmolApp.info.containsKey("noGraphics"))
System.out.println(
"Add -n (NOGRAPHICS) for faster performance if you are not creating images.");
}
new JmolData(jmolApp);
}
boolean createIsosurface(boolean justForPlane) {
resetIsosurface();
jvxlData.cutoff = Float.NaN;
if (!readAndSetVolumeParameters(justForPlane)) return false;
if (!justForPlane && !Float.isNaN(params.sigma) && !allowSigma) {
if (params.sigma > 0)
Logger.error("Reader does not support SIGMA option -- using cutoff 1.6");
params.cutoff = 1.6f;
}
// negative sigma just ignores the error message
// and means it was inserted by Jmol as a default option
if (params.sigma < 0) params.sigma = -params.sigma;
nPointsX = voxelCounts[0];
nPointsY = voxelCounts[1];
nPointsZ = voxelCounts[2];
jvxlData.isSlabbable = ((params.dataType & Parameters.IS_SLABBABLE) != 0);
jvxlData.insideOut = params.insideOut;
jvxlData.dataXYReversed = params.dataXYReversed;
jvxlData.isBicolorMap = params.isBicolorMap;
jvxlData.nPointsX = nPointsX;
jvxlData.nPointsY = nPointsY;
jvxlData.nPointsZ = nPointsZ;
jvxlData.jvxlVolumeDataXml = volumeData.xmlData;
jvxlData.voxelVolume = volumeData.voxelVolume;
if (justForPlane) {
// float[][][] voxelDataTemp = volumeData.voxelData;
volumeData.setMappingPlane(params.thePlane);
// volumeData.setDataDistanceToPlane(params.thePlane);
if (meshDataServer != null)
meshDataServer.fillMeshData(meshData, MeshData.MODE_GET_VERTICES, null);
params.setMapRanges(this, false);
generateSurfaceData();
volumeData.setMappingPlane(null);
// if (volumeData != null)
// volumeData.voxelData = voxelDataTemp;
} else {
if (!readVolumeData(false)) return false;
generateSurfaceData();
}
if (jvxlFileHeaderBuffer != null) {
String s = jvxlFileHeaderBuffer.toString();
int i = s.indexOf('\n', s.indexOf('\n', s.indexOf('\n') + 1) + 1) + 1;
jvxlData.jvxlFileTitle = s.substring(0, i);
}
if (params.contactPair == null) setBoundingBox();
if (!params.isSilent)
Logger.info("boundbox corners " + Escape.escape(xyzMin) + " " + Escape.escape(xyzMax));
jvxlData.boundingBox = new Point3f[] {xyzMin, xyzMax};
jvxlData.dataMin = dataMin;
jvxlData.dataMax = dataMax;
jvxlData.cutoff = (isJvxl ? jvxlCutoff : params.cutoff);
jvxlData.isCutoffAbsolute = params.isCutoffAbsolute;
jvxlData.pointsPerAngstrom = 1f / volumeData.volumetricVectorLengths[0];
jvxlData.jvxlColorData = "";
jvxlData.jvxlPlane = params.thePlane;
jvxlData.jvxlEdgeData = edgeData;
jvxlData.isBicolorMap = params.isBicolorMap;
jvxlData.isContoured = params.isContoured;
jvxlData.colorDensity = params.colorDensity;
if (jvxlData.vContours != null) params.nContours = jvxlData.vContours.length;
jvxlData.nContours = (params.contourFromZero ? params.nContours : -1 - params.nContours);
jvxlData.nEdges = edgeCount;
jvxlData.edgeFractionBase = edgeFractionBase;
jvxlData.edgeFractionRange = edgeFractionRange;
jvxlData.colorFractionBase = colorFractionBase;
jvxlData.colorFractionRange = colorFractionRange;
jvxlData.jvxlDataIs2dContour = jvxlDataIs2dContour;
jvxlData.jvxlDataIsColorMapped = jvxlDataIsColorMapped;
jvxlData.jvxlDataIsColorDensity = jvxlDataIsColorDensity;
jvxlData.isXLowToHigh = isXLowToHigh;
jvxlData.vertexDataOnly = vertexDataOnly;
jvxlData.saveVertexCount = 0;
if (jvxlDataIsColorMapped || jvxlData.nVertexColors > 0) {
if (meshDataServer != null) {
meshDataServer.fillMeshData(meshData, MeshData.MODE_GET_VERTICES, null);
meshDataServer.fillMeshData(meshData, MeshData.MODE_GET_COLOR_INDEXES, null);
}
jvxlData.jvxlColorData = readColorData();
updateSurfaceData();
if (meshDataServer != null) meshDataServer.notifySurfaceMappingCompleted();
}
return true;
}