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org.jmol.shapesurface.MolecularOrbital Maven / Gradle / Ivy
Jmol: an open-source Java viewer for chemical structures in 3D
/* $RCSfile$
* $Author: hansonr $
* $Date: 2006-07-14 16:23:28 -0500 (Fri, 14 Jul 2006) $
* $Revision: 5305 $
*
* Copyright (C) 2005 Miguel, Jmol Development
*
* Contact: [email protected] ,[email protected]
* Contact: [email protected]
*
* 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 Public 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.shapesurface;
import java.util.Hashtable;
import java.util.Map;
import javajs.util.AU;
import javajs.util.Lst;
import javajs.util.P4;
import javajs.util.PT;
import javajs.util.SB;
import org.jmol.java.BS;
import org.jmol.jvxl.data.JvxlCoder;
import org.jmol.jvxl.readers.Parameters;
import org.jmol.quantum.QS;
import org.jmol.script.T;
import org.jmol.shape.MeshCollection;
import org.jmol.util.Escape;
public class MolecularOrbital extends Isosurface {
@Override
public void initShape() {
super.initShape();
myType = "mo";
setPropI("thisID", myType, null);
}
// these are globals, stored here and only passed on when the they are needed.
private String moTranslucency;
private Float moTranslucentLevel;
private P4 moPlane;
private Float moCutoff;
private Float moResolution;
private Float moScale;
private Integer moColorPos;
private Integer moColorNeg;
private Integer moMonteCarloCount;
private boolean moIsPositiveOnly;
private Boolean moSquareData;
private Boolean moSquareLinear;
private Integer moRandomSeed;
private int moFill = T.nofill;
private int moMesh = T.mesh;
private int moDots = T.nodots;
private int moFrontOnly = T.frontonly;
private int moShell = T.nobackshell;
private String moTitleFormat;
private boolean moDebug;
private int myColorPt;
private String strID;
private int moNumber;
private float[] moLinearCombination;
private Map> htModels;
private Map thisModel;
@SuppressWarnings("unchecked")
@Override
public void setProperty(String propertyName, Object value, BS bs) {
// in the case of molecular orbitals, we just cache the information and
// then send it all at once.
if ("init" == propertyName) {
myColorPt = 0;
moDebug = false;
int modelIndex = ((Integer) value).intValue();
strID = getId(modelIndex);
//Logger.info("MO init " + strID);
// overide bitset selection
setPropI("init", null, null);
setPropI("modelIndex", Integer.valueOf(modelIndex), null);
if (htModels == null)
htModels = new Hashtable>();
if (!htModels.containsKey(strID))
htModels.put(strID, new Hashtable());
thisModel = htModels.get(strID);
moNumber = (!thisModel.containsKey("moNumber") ? 0 : ((Integer) thisModel
.get("moNumber")).intValue());
moLinearCombination = (float[]) thisModel.get("moLinearCombination");
moSquareData = (moLinearCombination != null ? null : (Boolean) thisModel.get("moSquareData"));
moSquareLinear = (moLinearCombination == null ? null : (Boolean) thisModel.get("moSquareLinear"));
return;
}
if ("slab" == propertyName) {
if (value instanceof Integer) {
thisModel.put("slabValue", value);
} else {
Object[] slabInfo = (Object[]) value;
int tok = ((Integer) slabInfo[0]).intValue();
moSlab = (Lst) thisModel.get("slab");
if (moSlab == null)
thisModel.put("slab", moSlab = new Lst());
if (tok == T.none) {
moSlab = null;
thisModel.remove("slab");
return;
}
moSlab.addLast(value);
}
return;
}
if ("cutoff" == propertyName) {
thisModel.put("moCutoff", value);
thisModel.put("moIsPositiveOnly", Boolean.FALSE);
return;
}
if ("scale" == propertyName) {
thisModel.put("moScale", value);
return;
}
if ("squareData" == propertyName) {
if (value == Boolean.TRUE)
thisModel.put("moSquareData", Boolean.TRUE);
else
thisModel.remove("moSquareData");
moSquareData = (Boolean) value;
return;
}
if ("squareLinear" == propertyName) {
if (value == Boolean.TRUE)
thisModel.put("moSquareLinear", Boolean.TRUE);
else
thisModel.remove("moSquareLinear");
moSquareLinear = (Boolean) value;
return;
}
if ("cutoffPositive" == propertyName) {
thisModel.put("moCutoff", value);
thisModel.put("moIsPositiveOnly", Boolean.TRUE);
return;
}
if ("resolution" == propertyName) {
thisModel.put("moResolution", value);
return;
}
if ("titleFormat" == propertyName) {
moTitleFormat = (String) value;
return;
}
if ("color" == propertyName) {
if (!(value instanceof Integer))
return;
thisModel.remove("moTranslucency");
setPropI("color", value, bs);
propertyName = "colorRGB";
myColorPt = 0;
//fall trhough to colorRGB
}
if ("colorRGB" == propertyName) {
moColorPos = (Integer) value;
if (myColorPt++ == 0)
moColorNeg = moColorPos;
thisModel.put("moColorNeg", moColorNeg);
thisModel.put("moColorPos", moColorPos);
return;
}
if ("plane" == propertyName) {
if (value == null)
thisModel.remove("moPlane");
else
thisModel.put("moPlane", value);
return;
}
if ("monteCarloCount" == propertyName) {
thisModel.put("monteCarloCount", value);
return;
}
if ("randomSeed" == propertyName) {
if (value == null)
thisModel.remove("randomSeed");
else
thisModel.put("randomSeed", value);
return;
}
if ("molecularOrbital" == propertyName) {
if (value instanceof Integer) {
moNumber = ((Integer) value).intValue();
thisModel.put("moNumber", value);
thisModel.remove("moLinearCombination");
moLinearCombination = null;
} else {
moNumber = 0;
moLinearCombination = (float[]) value;
thisModel.put("moNumber", Integer.valueOf(0));
thisModel.put("moLinearCombination", moLinearCombination);
}
if (moSquareData == Boolean.TRUE)
thisModel.put("moSquareData", Boolean.TRUE);
else
thisModel.remove("moSquareData");
if (moSquareLinear == Boolean.TRUE)
thisModel.put("moSquareLinear", Boolean.TRUE);
else
thisModel.remove("moSquareLinear");
setOrbital(moNumber, moLinearCombination);
return;
}
if (propertyName == "deleteModelAtoms") {
int modelIndex = ((int[]) ((Object[]) value)[2])[0];
Map> htModelsNew = new Hashtable>();
for (int i = meshCount; --i >= 0;) {
if (meshes[i] == null)
continue;
if (meshes[i].modelIndex == modelIndex) {
meshCount--;
if (meshes[i] == currentMesh) {
currentMesh = null;
thisModel = null;
}
meshes = (IsosurfaceMesh[]) AU.deleteElements(meshes, i, 1);
continue;
}
Map htModel = htModels.get(meshes[i].thisID);
if (meshes[i].modelIndex > modelIndex) {
meshes[i].modelIndex--;
meshes[i].thisID = getId(meshes[i].modelIndex);
}
htModelsNew.put(meshes[i].thisID, htModel);
}
htModels = htModelsNew;
return;
}
//the rest of these pass through to Isosurface
if ("moData" == propertyName) {
Map moData = (Map) value;
nboType = (String) moData.get("nboType");
if (nboType == null)
thisModel.remove("nboType");
else
thisModel.put("nboType", nboType);
} else if ("translucentLevel" == propertyName) {
if (thisModel == null) {
if (currentMesh == null)
return;
thisModel = htModels.get(currentMesh.thisID);
}
thisModel.put("moTranslucentLevel", value);
} else if ("delete" == propertyName) {
htModels.remove(strID);
moNumber = 0;
moLinearCombination = null;
} else if ("token" == propertyName) {
int tok = ((Integer) value).intValue();
switch (tok) {
case T.dots:
case T.nodots:
moDots = tok;
break;
case T.fill:
case T.nofill:
moFill = tok;
break;
case T.mesh:
case T.nomesh:
moMesh = tok;
break;
case T.backshell:
case T.nobackshell:
moShell = tok;
break;
case T.frontonly:
case T.notfrontonly:
moFrontOnly = tok;
break;
}
} else if ("translucency" == propertyName) {
if (thisModel == null) {
if (currentMesh == null)
return;
thisModel = htModels.get(currentMesh.thisID);
}
thisModel.put("moTranslucency", value);
}
setPropI(propertyName, value, bs);
}
private String getId(int modelIndex) {
return "mo_model" + vwr.getModelNumberDotted(modelIndex);
}
@SuppressWarnings("unchecked")
@Override
public Object getProperty(String propertyName, int index) {
if (propertyName.startsWith("list")) {
String s = "";
if (propertyName.equals("list")) {
s = (String) getPropI("list", index);
if (s.length() > 1)
s += "cutoff = " + jvxlData.cutoff + "\n";
s = "\n" + s;
}
return getMoInfo(-1) + s;
}
if (propertyName == "moNumber")
return Integer.valueOf(moNumber);
if (propertyName == "moLinearCombination")
return moLinearCombination;
if (propertyName == "moSquareData")
return moSquareData;
if (propertyName == "moSquareLinear")
return moSquareLinear;
if (propertyName == "showMO") {
SB str = new SB();
Lst> mos = (Lst>) (sg.params.moData
.get("mos"));
int nOrb = (mos == null ? 0 : mos.size());
int thisMO = index;
int currentMO = moNumber;
boolean isShowCurrent = (thisMO == Integer.MIN_VALUE);
if (isShowCurrent)
thisMO = currentMO;
if (nOrb == 0 || isShowCurrent && currentMO == 0)
return "";
boolean doOneMo = (thisMO != 0);
if (currentMO == 0)
thisMO = 0;
boolean haveHeader = false;
int nTotal = (thisMO > 0 ? 1 : nOrb);
int i0 = (nTotal == 1 && currentMO > 0 ? currentMO : 1);
for (int i = i0; i <= nOrb; i++)
if (thisMO == 0 || thisMO == i || !doOneMo && i == currentMO) {
if (!doOneMo) {
setPropI("init", sg.params, null);
setOrbital(i, null);
}
jvxlData.moleculeXml = vwr.getModelCml(
vwr.getModelUndeletedAtomsBitSet(thisMesh.modelIndex), 100, true, false);
if (!haveHeader) {
str.append(JvxlCoder.jvxlGetFileVwr(vwr, jvxlData, null,
null, "HEADERONLY", true, nTotal, null, null));
haveHeader = true;
}
str.append(JvxlCoder.jvxlGetFileVwr(vwr, jvxlData, null,
jvxlData.title, null, false, 1,
thisMesh.getState(myType), (thisMesh.scriptCommand == null ? "" : thisMesh.scriptCommand)));
if (!doOneMo)
setPropI("delete", "mo_show", null);
if (nTotal == 1)
break;
}
str.append(JvxlCoder.jvxlGetFileVwr(vwr, jvxlData, null, null,
"TRAILERONLY", true, 0, null, null));
return str.toString();
}
return getPropI(propertyName, index);
}
@SuppressWarnings("unchecked")
public String getMoInfo(int modelIndex) {
SB sb = new SB();
for (int m = 0, mc = vwr.ms.mc; m < mc; m++) {
if (modelIndex >= 0 && m != modelIndex)
continue;
Map moData = (Map) vwr.ms.getInfo(m, "moData");
if (moData == null)
continue;
Lst> mos = (Lst>) (moData
.get("mos"));
int nOrb = (mos == null ? 0 : mos.size());
if (nOrb == 0)
continue;
String moType = (String) moData.get("nboType");
if (moType == null)
moType = "mo";
for (int i = nOrb; --i >= 0;) {
Map mo = mos.get(i);
String type = (String) mo.get("type");
if (type == null)
type = "";
String units = (String) mo.get("energyUnits");
if (units == null)
units = "";
Float occ = (Float) mo.get("occupancy");
if (occ != null)
type = "occupancy " + occ.floatValue() + " " + type;
String sym = (String) mo.get("symmetry");
if (sym != null)
type += sym;
String energy = "" + mo.get("energy");
if (Float.isNaN(PT.parseFloat(energy)))
sb.append(PT.sprintf("model %-2s; %s %-2i # %s\n", "ssis",
new Object[] { vwr.ms.getModelNumberDotted(m), moType, Integer.valueOf(i + 1),
type }));
else
sb.append(PT.sprintf("model %-2s; %s %-2i # energy %-8.3f %s %s\n",
"ssifss",
new Object[] { vwr.ms.getModelNumberDotted(m), moType, Integer.valueOf(i + 1),
mo.get("energy"), units, type }));
}
}
return sb.toString();
}
@Override
protected void clearSg() {
//sg = null; // not Molecular Orbitals
}
private Lst moSlab;
private Integer moSlabValue;
private String nboType;
@SuppressWarnings("unchecked")
private boolean getSettings(String strID) {
thisModel = htModels.get(strID);
if (thisModel == null || thisModel.get("moNumber") == null)
return false;
moTranslucency = (String) thisModel.get("moTranslucency");
moTranslucentLevel = (Float) thisModel.get("moTranslucentLevel");
moPlane = (P4) thisModel.get("moPlane");
moCutoff = (Float) thisModel.get("moCutoff");
if (moCutoff == null)
moCutoff = (Float) sg.params.moData.get("defaultCutoff");
if (moCutoff == null) {
moCutoff = Float.valueOf(Parameters.defaultQMOrbitalCutoff);
}
thisModel.put("moCutoff", Float.valueOf(moCutoff.floatValue()));
moResolution = (Float) thisModel.get("moResolution");
moScale = (Float) thisModel.get("moScale");
nboType = (String) thisModel.get("moType");
moColorPos = (Integer) thisModel.get("moColorPos");
moColorNeg = (Integer) thisModel.get("moColorNeg");
moSquareData = (Boolean) thisModel.get("moSquareData");
moSquareLinear = (Boolean) thisModel.get("moSquareLinear");
moMonteCarloCount = (Integer) thisModel.get("monteCarloCount");
moRandomSeed = (Integer) thisModel.get("randomSeed");
moSlabValue = (Integer) thisModel.get("slabValue");
moSlab = (Lst) thisModel.get("slab");
if (moRandomSeed == null)
thisModel.put("randomSeed", moRandomSeed = Integer.valueOf(
((int) -System.currentTimeMillis())% 10000));
moNumber = ((Integer) thisModel.get("moNumber")).intValue();
moLinearCombination = (float[]) thisModel.get("moLinearCombination");
Object b = thisModel.get("moIsPositiveOnly");
moIsPositiveOnly = (b != null && ((Boolean) (b)).booleanValue());
return true;
}
private void setOrbital(int moNumber, float[] linearCombination) {
setPropI("reset", strID, null);
if (moDebug)
setPropI("debug", Boolean.TRUE, null);
getSettings(strID);
if (moScale != null)
setPropI("scale", moScale, null);
if (moResolution != null)
setPropI("resolution", moResolution, null);
if (moPlane != null) {
setPropI("plane", moPlane, null);
if (moCutoff != null) {
float max = moCutoff.floatValue();
if (moSquareData == Boolean.TRUE || moSquareLinear == Boolean.TRUE)
max = max * max;
setPropI("red", Float.valueOf(-max), null);
setPropI("blue", Float.valueOf(max), null);
}
} else {
if (moCutoff != null)
setPropI((moIsPositiveOnly ? "cutoffPositive" : "cutoff"),
moCutoff, null);
if (moColorNeg != null)
setPropI("colorRGB", moColorNeg, null);
if (moColorPos != null)
setPropI("colorRGB", moColorPos, null);
if (moMonteCarloCount != null) {
setPropI("randomSeed", moRandomSeed, null);
setPropI("monteCarloCount", moMonteCarloCount, null);
}
}
setPropI("squareData", moSquareData, null);
setPropI("squareLinear", moSquareLinear, null);
setPropI("title", moTitleFormat, null);
setPropI("fileName", vwr.fm.getFileName(), null);
currentMesh.modelIndex = modelIndex;
setPropI("molecularOrbital", linearCombination == null ? Integer
.valueOf(moNumber) : linearCombination, null);
if (moPlane != null && moColorNeg != null)
setPropI("colorRGB", moColorNeg, null);
if (moPlane != null && moColorPos != null)
setPropI("colorRGB", moColorPos, null);
currentMesh.isColorSolid = false;
if (moSlabValue != null)
setPropI("slab", moSlabValue, null);
if (moSlab != null)
for (int i = 0; i < moSlab.size(); i++)
setPropI("slab", moSlab.get(i), null);
if (moTranslucentLevel != null)
setPropI("translucentLevel", moTranslucentLevel, null);
if (moTranslucency != null)
setPropI("translucency", moTranslucency, null);
setPropI("token", Integer.valueOf(moFill), null);
setPropI("token", Integer.valueOf(moMesh), null);
setPropI("token", Integer.valueOf(moShell), null);
setPropI("token", Integer.valueOf(moDots), null);
setPropI("token", Integer.valueOf(moFrontOnly), null);
thisModel.put("mesh", currentMesh);
return;
}
@Override
public String getShapeState() {
if (htModels == null)
return "";
SB s = new SB();
int modelCount = vwr.ms.mc;
for (int iModel = 0; iModel < modelCount; iModel++) {
if (!getSettings(getId(iModel)))
continue;
if (modelCount > 1)
appendCmd(s, "frame " + vwr.getModelNumberDotted(iModel));
if (nboType != null)
appendCmd(s, "nbo type " + nboType);
if (moCutoff != null)
appendCmd(s, myType + " cutoff " + (sg.params.isPositiveOnly ? "+" : "")
+ moCutoff);
if (moScale != null)
appendCmd(s, myType + " scale " + moScale);
if (moMonteCarloCount != null)
appendCmd(s, myType + " points " + moMonteCarloCount + " " + moRandomSeed);
if (moResolution != null)
appendCmd(s, myType + " resolution " + moResolution);
if (moPlane != null)
appendCmd(s, myType + " plane {" + moPlane.x + " " + moPlane.y + " " + moPlane.z
+ " " + moPlane.w + "}");
if (moTitleFormat != null)
appendCmd(s, myType + " titleFormat " + PT.esc(moTitleFormat));
//the following is a correct object==object test
if (moColorNeg != null)
appendCmd(s, myType + " color "
+ Escape.escapeColor(moColorNeg.intValue())
+ (moColorNeg.equals(moColorPos) ? "" : " "
+ Escape.escapeColor(moColorPos.intValue())));
if (moSlab != null) {
if (thisMesh.slabOptions != null)
appendCmd(s, thisMesh.slabOptions.toString());
if (thisMesh.jvxlData.slabValue != Integer.MIN_VALUE)
appendCmd(s, myType + " slab " + thisMesh.jvxlData.slabValue);
}
if (moLinearCombination == null) {
appendCmd(s, myType + " " + (moSquareData == Boolean.TRUE ? "squared ": "") + moNumber);
} else {
appendCmd(s, myType + " " + QS.getMOString(moLinearCombination) + (moSquareLinear == Boolean.TRUE ? " squared": ""));
}
if (moTranslucency != null)
appendCmd(s, myType + " translucent " + moTranslucentLevel);
appendCmd(s, ((IsosurfaceMesh) thisModel.get("mesh")).getState(myType));
}
return s.toString();
}
@Override
public void merge(MeshCollection shape) {
MolecularOrbital mo = (MolecularOrbital) shape;
moColorNeg = mo.moColorNeg;
moColorPos = mo.moColorPos;
moCutoff = mo.moCutoff;
moPlane = mo.moPlane;
moResolution = mo.moResolution;
moScale = mo.moScale;
moSlab = mo.moSlab;
moSlabValue = mo.moSlabValue;
moTitleFormat = mo.moTitleFormat;
moTranslucency = mo.moTranslucency;
if (htModels == null)
htModels = new Hashtable>();
Map> ht = mo.htModels;
if (ht != null) {
for (Map.Entry> entry : ht.entrySet()) {
String key = entry.getKey();
htModels.put(key, entry.getValue());
}
}
super.merge(shape);
}
}
