org.jmol.shapespecial.Dipoles Maven / Gradle / Ivy
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Jmol: an open-source Java viewer for chemical structures in 3D
/* $RCSfile$
* $Author: hansonr $
* $Date: 2006-03-12 21:37:51 -0600 (Sun, 12 Mar 2006) $
* $Revision: 4586 $
*
* Copyright (C) 2002-2005 The Jmol Development Team
*
* 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.shapespecial;
import org.jmol.shape.Shape;
import org.jmol.util.BitSetUtil;
import org.jmol.util.ArrayUtil;
import org.jmol.util.JmolEdge;
import org.jmol.util.Logger;
import org.jmol.util.TextFormat;
import org.jmol.script.Token;
import org.jmol.g3d.Graphics3D;
import org.jmol.modelset.Atom;
import org.jmol.modelset.Bond;
import org.jmol.modelset.BondIterator;
import java.util.ArrayList;
import java.util.BitSet;
import java.util.Hashtable;
import java.util.List;
import java.util.Map;
import javax.vecmath.Point3f;
import javax.vecmath.Vector3f;
public class Dipoles extends Shape {
final static short DEFAULT_MAD = 5;
final static float DEFAULT_OFFSETSIDE = 0.40f;
int dipoleCount = 0;
Dipole[] dipoles = new Dipole[4];
private Dipole currentDipole;
private Dipole tempDipole;
private Point3f startCoord = new Point3f();
private Point3f endCoord = new Point3f();
private float dipoleValue;
private boolean isUserValue;
private boolean isBond;
private boolean iHaveTwoEnds;
private int atomIndex1;
private int atomIndex2;
private short colix;
private Vector3f calculatedDipole;
private String wildID;
@Override
public void setProperty(String propertyName, Object value, BitSet bs) {
if ("init" == propertyName) {
tempDipole = new Dipole();
tempDipole.dipoleValue = 1;
tempDipole.mad = DEFAULT_MAD;
atomIndex1 = -1;
tempDipole.modelIndex = -1;
dipoleValue = 0;
calculatedDipole = null;
isUserValue = isBond = iHaveTwoEnds = false;
if (currentDipole != null)
Logger.debug("current dipole: " + currentDipole.thisID);
return;
}
if ("calculate" == propertyName) {
calculatedDipole = viewer.calculateMolecularDipole();
Logger.info("calculated molecular dipole = " + calculatedDipole + " "
+ (calculatedDipole == null ? "" : "" + calculatedDipole.length()));
return;
}
if ("thisID" == propertyName) {
wildID = null;
String thisID = (String) value;
if (thisID == null || TextFormat.isWild(thisID)) {
currentDipole = null;
if (thisID != null)
wildID = thisID.toUpperCase();
return;
}
currentDipole = findDipole(thisID);
if (currentDipole == null)
currentDipole = allocDipole(thisID, "");
Logger.debug("current dipole now " + currentDipole.thisID);
tempDipole = currentDipole;
if (thisID.equals("molecular")) {
Vector3f v = calculatedDipole;
if (v == null) {
v = viewer.getModelDipole();
Logger.info("file molecular dipole = " + v + " "
+ (v != null ? "" + v.length() : ""));
}
if (v == null)
calculatedDipole = v = viewer.calculateMolecularDipole();
if (v == null) {
Logger
.warn("No molecular dipole found for this model; setting to {0 0 0}");
v = new Vector3f();
}
tempDipole.set(new Point3f(0, 0, 0), new Vector3f(-v.x, -v.y, -v.z));
tempDipole.type = Dipole.DIPOLE_TYPE_MOLECULAR;
tempDipole.thisID = "molecular";
setDipole();
}
return;
}
if ("bonds" == propertyName) {
isBond = true;
currentDipole = null;
for (int i = dipoleCount; --i >= 0;)
if (isBondDipole(i))
return;
getBondDipoles(); // only once if any bond dipoles are defined
return;
}
if ("on" == propertyName) {
setProperty(Token.on, isBond, 0, 0);
return;
}
if ("off" == propertyName) {
setProperty(Token.off, isBond, 0, 0);
return;
}
if ("delete" == propertyName) {
if (wildID == null && currentDipole == null) {
clear(false);
return;
}
setProperty(Token.delete, isBond, 0, 0);
return;
}
if ("width" == propertyName) {
short mad = tempDipole.mad = (short) (((Float) value).floatValue() * 1000);
if (currentDipole == null)
setProperty(Token.wireframe, isBond, mad, 0); //
return;
}
if ("offset" == propertyName) {
float offset = tempDipole.offsetAngstroms = ((Float) value).floatValue();
if (currentDipole == null)
setProperty(Token.axes, isBond, 0, offset);
return;
}
if ("offsetPercent" == propertyName) {
int offsetPercent = tempDipole.offsetPercent = ((Integer) value).intValue();
if (tempDipole.dipoleValue != 0)
tempDipole.offsetAngstroms = offsetPercent / 100f
* tempDipole.dipoleValue;
if (currentDipole == null)
setProperty(Token.percent, isBond, 0, offsetPercent / 100f);
return;
}
if ("offsetSide" == propertyName) {
float offsetSide = ((Float) value).floatValue();
setProperty(Token.sidechain, isBond, 0, offsetSide);
return;
}
if ("cross" == propertyName) {
setProperty(Token.cross, isBond, (((Boolean) value).booleanValue() ? 1 : 0), 0);
return;
}
if ("color" == propertyName) {
colix = Graphics3D.getColix(value);
if (isBond) {
setColixDipole(colix, JmolEdge.BOND_COVALENT_MASK, bs);
} else if (value != null) {
setProperty(Token.color, false, 0, 0);
}
return;
}
if ("translucency" == propertyName) {
setProperty(Token.translucent, isBond, (value.equals("translucent") ? 1 : 0), 0);
return;
}
if ("clear" == propertyName) {
currentDipole = null;
clear(false);
}
if ("clearBonds" == propertyName) {
clear(true);
}
if ("startSet" == propertyName) {
BitSet atomset = (BitSet) value;
startCoord = viewer.getAtomSetCenter(atomset);
tempDipole.set(startCoord, new Point3f(0, 0, 0), dipoleValue);
if (BitSetUtil.cardinalityOf(atomset) == 1)
atomIndex1 = atomset.nextSetBit(0);
return;
}
if ("atomBitset" == propertyName) {
BitSet atomset = (BitSet) value;
atomIndex1 = atomset.nextSetBit(0);
startCoord = modelSet.atoms[atomIndex1];
atomset.clear(atomIndex1);
propertyName = "endSet";
//passes to endSet
}
if ("endSet" == propertyName) {
iHaveTwoEnds = true;
BitSet atomset = (BitSet) value;
if (atomIndex1 >= 0 && BitSetUtil.cardinalityOf(atomset) == 1) {
atomIndex2 = atomset.nextSetBit(0);
tempDipole.set(modelSet.atoms[atomIndex1], modelSet.atoms[atomIndex2],
1);
currentDipole = findDipole(tempDipole.thisID, tempDipole.dipoleInfo);
tempDipole.thisID = currentDipole.thisID;
if (isSameAtoms(currentDipole, tempDipole.dipoleInfo)) {
tempDipole = currentDipole;
if (dipoleValue > 0)
tempDipole.dipoleValue = dipoleValue;
}
} else {
tempDipole.set(startCoord, viewer.getAtomSetCenter(atomset),
dipoleValue);
}
//NOTTTTTT!!!! currentDipole = tempDipole;
return;
}
if ("startCoord" == propertyName) {
startCoord.set((Point3f) value);
tempDipole.set(startCoord, new Point3f(0, 0, 0), dipoleValue);
return;
}
if ("endCoord" == propertyName) {
iHaveTwoEnds = true;
endCoord.set((Point3f) value);
tempDipole.set(startCoord, endCoord, dipoleValue);
dumpDipoles("endCoord");
return;
}
if ("value" == propertyName) {
dipoleValue = ((Float) value).floatValue();
isUserValue = true;
tempDipole.set(dipoleValue);
if (tempDipole.offsetPercent != 0)
tempDipole.offsetAngstroms = tempDipole.offsetPercent / 100f
* tempDipole.dipoleValue;
return;
}
if ("set" == propertyName) {
if (isBond || !iHaveTwoEnds)
return;
setDipole();
setModelIndex();
return;
}
if (propertyName == "deleteModelAtoms") {
int modelIndex = ((int[])((Object[])value)[2])[0];
for (int i = dipoleCount; --i >= 0;)
if (dipoles[i].modelIndex > modelIndex) {
dipoles[i].modelIndex--;
} else if (dipoles[i].modelIndex == modelIndex) {
if (dipoles[i] == currentDipole)
currentDipole = null;
dipoles = (Dipole[]) ArrayUtil.deleteElements(dipoles, i, 1);
dipoleCount--;
}
currentDipole = null;
return;
}
}
private void setProperty(int tok, boolean bondOnly, int iValue, float fValue) {
if (currentDipole != null)
setProperty(tok, currentDipole, iValue, fValue);
else {
for (int i = dipoleCount; --i >= 0;)
if (!bondOnly || isBondDipole(i))
if (wildID == null
|| TextFormat.isMatch(dipoles[i].thisID.toUpperCase(), wildID,
true, true))
setProperty(tok, dipoles[i], iValue, fValue);
}
}
private void setProperty(int tok, Dipole dipole, int iValue, float fValue) {
switch (tok) {
case Token.on:
dipole.visible = true;
return;
case Token.off:
dipole.visible = false;
return;
case Token.delete:
deleteDipole(dipole);
return;
case Token.wireframe:
dipole.mad = tempDipole.mad = (short) iValue;
return;
case Token.axes:
dipole.offsetAngstroms = fValue;
return;
case Token.percent:
dipole.offsetAngstroms = fValue * dipole.dipoleValue;
return;
case Token.sidechain:
dipole.offsetSide = fValue;
return;
case Token.cross:
dipole.noCross = (iValue == 0);
return;
case Token.color:
dipole.colix = colix;
return;
case Token.translucent:
dipole.setTranslucent(iValue == 1, translucentLevel);
return;
}
Logger.error("Unkown dipole property! " + Token.nameOf(tok));
}
// @SuppressWarnings("unchecked")
@Override
public boolean getProperty(String property, Object[] data) {
if (property == "getNames") {
/* just implemented for MeshCollection
Map map = (Map) data[0];
boolean withDollar = ((Boolean) data[1]).booleanValue();
for (int i = dipoleCount; --i >= 0;)
map.put((withDollar ? "$" : "") + dipoles[i].thisID, Token.tokenAnd); // just a placeholder
return true;
*/
}
if (property == "checkID") {
String key = ((String) data[0]).toUpperCase();
boolean isWild = TextFormat.isWild(key);
for (int i = dipoleCount; --i >= 0;) {
String id = dipoles[i].thisID;
if (id.equalsIgnoreCase(key) || isWild
&& TextFormat.isMatch(id.toUpperCase(), key, true, true)) {
data[1] = id;
return true;
}
}
return false;
}
return false;
}
@Override
public Object getProperty(String property, int index) {
if (property.equals("list")) {
return getShapeState();
}
return null;
}
private void getBondDipoles() {
float[] partialCharges = modelSet.getPartialCharges();
if (partialCharges == null)
return;
clear(true);
Bond[] bonds = modelSet.getBonds();
for (int i = modelSet.getBondCount(); --i >= 0;) {
Bond bond = bonds[i];
if (!bond.isCovalent())
continue;
float c1 = partialCharges[bond.getAtomIndex1()];
float c2 = partialCharges[bond.getAtomIndex2()];
if (c1 != c2)
setDipole(bond.getAtom1(), bond.getAtom2(), c1, c2);
}
}
private boolean isBondDipole(int i) {
if (i >= dipoles.length || dipoles[i] == null)
return false;
return (dipoles[i].isBondType());
}
private void setColixDipole(short colix, int bondTypeMask, BitSet bs) {
if (colix == Graphics3D.USE_PALETTE)
return; // not implemented
BondIterator iter = modelSet.getBondIterator(bondTypeMask, bs);
while (iter.hasNext()) {
Dipole d = findBondDipole(iter.next());
if (d != null)
d.colix = colix;
}
}
private void setDipole() {
if (currentDipole == null)
currentDipole = allocDipole("", "");
currentDipole.set(tempDipole.thisID, tempDipole.dipoleInfo,
tempDipole.atoms, tempDipole.dipoleValue, tempDipole.mad,
tempDipole.offsetAngstroms, tempDipole.offsetPercent,
tempDipole.offsetSide, tempDipole.origin, tempDipole.vector);
currentDipole.isUserValue = isUserValue;
currentDipole.modelIndex = viewer.getCurrentModelIndex();
}
final private static float E_ANG_PER_DEBYE = 0.208194f;
private void setDipole(Atom atom1, Atom atom2, float c1, float c2) {
Dipole dipole = findDipole(atom1, atom2, true);
float value = (c1 - c2) / 2f * atom1.distance(atom2) / E_ANG_PER_DEBYE;
if (value < 0) {
dipole.set(atom2, atom1, -value);
} else {
dipole.set(atom1, atom2, value);
}
dipole.type = Dipole.DIPOLE_TYPE_BOND;
dipole.modelIndex = atom1.getModelIndex();
}
private int getDipoleIndex(String dipoleInfo, String thisID) {
if (dipoleInfo != null && dipoleInfo.length() > 0)
for (int i = dipoleCount; --i >= 0;)
if (isSameAtoms(dipoles[i], dipoleInfo))
return i;
return getIndexFromName(thisID);
}
private boolean isSameAtoms(Dipole dipole, String dipoleInfo) {
// order-independent search for two atoms:
// looking for (xyz)(x'y'z') in (xyz)(x'y'z')(xyz)(x'y'z')
return (dipole != null && dipole.isBondType() && (dipole.dipoleInfo + dipole.dipoleInfo)
.indexOf(dipoleInfo) >= 0);
}
private int getDipoleIndex(int atomIndex1, int atomIndex2) {
for (int i = dipoleCount; --i >= 0;) {
if (dipoles[i] != null
&& dipoles[i].atoms[0] != null
&& dipoles[i].atoms[1] != null
&& (dipoles[i].atoms[0].getIndex() == atomIndex1
&& dipoles[i].atoms[1].getIndex() == atomIndex2 || dipoles[i].atoms[1]
.getIndex() == atomIndex1
&& dipoles[i].atoms[0].getIndex() == atomIndex2))
return i;
}
return -1;
}
private void deleteDipole(Dipole dipole) {
if (dipole == null)
return;
if (currentDipole == dipole)
currentDipole = null;
int i;
for (i = dipoleCount; dipoles[--i] != dipole;) {
}
if (i < 0)
return;
for (int j = i + 1; j < dipoleCount; ++j)
dipoles[j - 1] = dipoles[j];
dipoles[--dipoleCount] = null;
}
private Dipole findDipole(String thisID) {
int dipoleIndex = getIndexFromName(thisID);
if (dipoleIndex >= 0) {
return dipoles[dipoleIndex];
}
return null;
}
private Dipole findDipole(Atom atom1, Atom atom2, boolean doAllocate) {
int dipoleIndex = getDipoleIndex(atom1.getIndex(), atom2.getIndex());
if (dipoleIndex >= 0) {
return dipoles[dipoleIndex];
}
return (doAllocate ? allocDipole("", "") : null);
}
private Dipole findBondDipole(Bond bond) {
Dipole d = findDipole(bond.getAtom1(), bond.getAtom2(), false);
return (d == null || d.atoms[0] == null ? null : d);
}
private Dipole findDipole(String thisID, String dipoleInfo) {
// must be able to identify a dipole from its ID only SECONDARILY,
// as we want one dipole per bond. So we look for coord ID.
int dipoleIndex = getDipoleIndex(dipoleInfo, thisID);
if (dipoleIndex >= 0) {
if (thisID.length() > 0)
dipoles[dipoleIndex].thisID = thisID;
return dipoles[dipoleIndex];
}
return allocDipole(thisID, dipoleInfo);
}
private Dipole allocDipole(String thisID, String dipoleInfo) {
dipoles = (Dipole[]) ArrayUtil.ensureLength(dipoles, dipoleCount + 1);
if (thisID == null || thisID.length() == 0)
thisID = "dipole" + (dipoleCount + 1);
Dipole d = dipoles[dipoleCount++] = new Dipole(viewer
.getCurrentModelIndex(), thisID, dipoleInfo, colix, DEFAULT_MAD, true);
return d;
}
private void dumpDipoles(String msg) {
for (int i = dipoleCount; --i >= 0;) {
Dipole dipole = dipoles[i];
Logger.info("\n\n" + msg + " dump dipole " + i + " " + dipole + " "
+ dipole.thisID + " " + dipole.dipoleInfo + " "
+ dipole.visibilityFlags + " mad=" + dipole.mad + " vis="
+ dipole.visible + "\n orig" + dipole.origin + " " + " vect"
+ dipole.vector + " val=" + dipole.dipoleValue);
}
if (currentDipole != null)
Logger.info(" current = " + currentDipole + currentDipole.origin);
if (tempDipole != null)
Logger.info(" temp = " + tempDipole + " " + tempDipole.origin);
}
private void clear(boolean clearBondDipolesOnly) {
if (clearBondDipolesOnly) {
for (int i = dipoleCount; --i >= 0;)
if (isBondDipole(i))
deleteDipole(dipoles[i]);
return;
}
for (int i = dipoleCount; --i >= 0;)
if (!isBond || isBondDipole(i))
deleteDipole(dipoles[i]);
}
@Override
public int getIndexFromName(String thisID) {
if (thisID == null)
return -1;
for (int i = dipoleCount; --i >= 0;) {
if (dipoles[i] != null && thisID.equals(dipoles[i].thisID))
return i;
}
return -1;
}
@Override
public List> getShapeDetail() {
List> V = new ArrayList>();
Map atomInfo;
for (int i = 0; i < dipoleCount; i++) {
Map info = new Hashtable();
Dipole dipole = dipoles[i];
info.put("ID", dipole.thisID);
info.put("vector", dipole.vector);
info.put("origin", dipole.origin);
if (dipole.atoms[0] != null) {
atomInfo = new Hashtable();
viewer.getAtomIdentityInfo(dipole.atoms[0].getIndex(), atomInfo);
List> atoms = new ArrayList>();
atoms.add(atomInfo);
atomInfo = new Hashtable();
viewer.getAtomIdentityInfo(dipole.atoms[1].getIndex(), atomInfo);
atoms.add(atomInfo);
info.put("atoms", atoms);
info.put("magnitude", new Float(dipole.vector.length()));
}
V.add(info);
}
return V;
}
private void setModelIndex() {
if (currentDipole == null)
return;
currentDipole.visible = true;
currentDipole.modelIndex = viewer.getCurrentModelIndex();
}
@Override
public void setVisibilityFlags(BitSet bs) {
/*
* set all fixed objects visible; others based on model being displayed
*
*/
for (int i = dipoleCount; --i >= 0;) {
Dipole dipole = dipoles[i];
dipole.visibilityFlags = ((dipole.modelIndex < 0 || bs
.get(dipole.modelIndex))
&& dipole.mad != 0
&& dipole.visible
&& dipole.origin != null
&& dipole.vector != null
&& dipole.vector.length() != 0
&& dipole.dipoleValue != 0 ? myVisibilityFlag : 0);
}
//dumpDipoles("setVis");
}
@Override
public String getShapeState() {
if (dipoleCount == 0)
return "";
StringBuffer s = new StringBuffer();
int thisModel = -1;
int modelCount = viewer.getModelCount();
for (int i = 0; i < dipoleCount; i++) {
Dipole dipole = dipoles[i];
if (dipole.isValid) {
if (modelCount > 1 && dipole.modelIndex != thisModel)
appendCmd(s, "frame "
+ viewer.getModelNumberDotted(thisModel = dipole.modelIndex));
s.append(dipole.getShapeState());
appendCmd(s, getColorCommand("dipole", dipole.colix));
}
}
return s.toString();
}
}