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Jmol: an open-source Java viewer for chemical structures in 3D
/* $RCSfile$
* $Author: hansonr $
* $Date: 2006-08-22 03:13:40 -0500 (Tue, 22 Aug 2006) $
* $Revision: 5412 $
*
* 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 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.shape;
import javajs.util.AU;
import org.jmol.atomdata.RadiusData;
import org.jmol.atomdata.RadiusData.EnumType;
import org.jmol.c.PAL;
import org.jmol.c.VDW;
import org.jmol.java.BS;
import org.jmol.modelset.Atom;
import org.jmol.util.BSUtil;
import org.jmol.util.C;
import org.jmol.viewer.JC;
public abstract class AtomShape extends Shape {
// Balls, BioShape Dots, Ellipsoids, Halos, Labels, Polyhedra, Stars, Vectors
public short mad = (short)-1;
public short[] mads;
public short[] colixes;
public byte[] paletteIDs;
public int ac;
public Atom[] atoms;
public boolean isActive;
public int monomerCount;
public BS bsSizeDefault;
@Override
public void initShape() {
// nothing to do
}
@Override
protected void initModelSet() {
atoms = ms.at;
ac = ms.ac;
// in case this is due to "load append"
if (mads != null)
mads = AU.arrayCopyShort(mads, ac);
if (colixes != null)
colixes = AU.arrayCopyShort(colixes, ac);
if (paletteIDs != null)
paletteIDs = AU.arrayCopyByte(paletteIDs, ac);
}
@Override
public int getSize(int atomIndex) {
return (mads == null ? 0 : mads[atomIndex]);
}
@Override
protected void setSize(int size, BS bsSelected) {
setSize2(size, bsSelected);
}
private RadiusData rd;
protected void setSize2(int size, BS bsSelected) {
if (size == 0) {
setSizeRD(null, bsSelected);
return;
}
if (rd == null)
rd = new RadiusData(null, size, EnumType.SCREEN, null);
else
rd.value = size;
setSizeRD(rd, bsSelected);
}
@Override
protected void setSizeRD(RadiusData rd, BS bsSelected) {
// Halos Stars Vectors
if (atoms == null) // vector values are ignored if there are none for a model
return;
isActive = true;
boolean isVisible = (rd != null && rd.value != 0);
boolean isAll = (bsSelected == null);
int i0 = (isAll ? ac - 1 : bsSelected.nextSetBit(0));
if (bsSizeSet == null)
bsSizeSet = BS.newN(ac);
if (mads == null && i0 >= 0)
mads = new short[ac];
for (int i = i0; i >= 0; i = (isAll ? i - 1 : bsSelected.nextSetBit(i + 1)))
setSizeRD2(i, rd, isVisible);
}
protected void setSizeRD2(int i, RadiusData rd, boolean isVisible) {
Atom atom = atoms[i];
mads[i] = atom.calculateMad(vwr, rd);
bsSizeSet.setBitTo(i, isVisible);
atom.setShapeVisibility(vf, isVisible);
}
protected void setPropAS(String propertyName, Object value, BS bs) {
if ("color" == propertyName) {
isActive = true;
short colix = C.getColixO(value);
byte pid = PAL.pidOf(value);
int n = checkColixLength(colix, bs.length());
for (int i = bs.nextSetBit(0); i >= 0 && i < n; i = bs.nextSetBit(i + 1))
setColixAndPalette(colix, pid, i);
return;
}
if ("params" == propertyName) {
// PyMOL only
isActive = true;
Object[] data = (Object[]) value;
short[] colixes = (short[]) data[0];
float[] atrans = (float[]) data[1];
float[] sizes = (float[]) data[2];
RadiusData rd = new RadiusData(null, 0, RadiusData.EnumType.FACTOR,
VDW.AUTO);
if (bsColixSet == null)
bsColixSet = new BS();
if (bsSizeSet == null)
bsSizeSet = new BS();
int i0 = bs.nextSetBit(0);
if (mads == null && i0 >= 0)
mads = new short[ac];
int n = checkColixLength(colixes == null ? 0 : C.BLACK, bs.length());
for (int i = i0, pt = 0; i >= 0 && i < n; i = bs.nextSetBit(i + 1), pt++) {
short colix = (colixes == null ? 0 : colixes[pt]);
//if (colix == 0)
//colix = C.INHERIT_ALL; IS 0 already
float f = (atrans == null ? 0 : atrans[pt]);
if (f > 0.01f)
colix = C.getColixTranslucent3(colix, true, f);
setColixAndPalette(colix, PAL.UNKNOWN.id, i);
if (sizes == null)
continue;
boolean isVisible = ((rd.value = sizes[pt]) > 0);
setSizeRD2(i, rd, isVisible);
}
return;
}
if ("translucency" == propertyName) {
isActive = true;
boolean isTranslucent = (value.equals("translucent"));
checkColixLength(C.BLACK, ac);
for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
colixes[i] = C.getColixTranslucent3(colixes[i], isTranslucent,
translucentLevel);
if (isTranslucent)
bsColixSet.set(i);
}
return;
}
if (propertyName == "deleteModelAtoms") {
atoms = (Atom[]) ((Object[]) value)[1];
int[] info = (int[]) ((Object[]) value)[2];
ac = ms.ac;
int firstAtomDeleted = info[1];
int nAtomsDeleted = info[2];
mads = (short[]) AU.deleteElements(mads, firstAtomDeleted,
nAtomsDeleted);
colixes = (short[]) AU.deleteElements(colixes, firstAtomDeleted,
nAtomsDeleted);
paletteIDs = (byte[]) AU.deleteElements(paletteIDs,
firstAtomDeleted, nAtomsDeleted);
BSUtil.deleteBits(bsSizeSet, bs);
BSUtil.deleteBits(bsColixSet, bs);
return;
}
setPropS(propertyName, value, bs);
}
protected int checkColixLength(short colix, int n) {
n = Math.min(ac, n);
if (colix == C.INHERIT_ALL)
return (colixes == null ? 0 : colixes.length);
if (colixes == null || n > colixes.length) {
colixes = AU.ensureLengthShort(colixes, n);
paletteIDs = AU.ensureLengthByte(paletteIDs, n);
}
if (bsColixSet == null)
bsColixSet = BS.newN(ac);
return n;
}
protected void setColixAndPalette(short colix, byte paletteID, int atomIndex) {
if (colixes == null)
System.out.println("ATOMSHAPE ERROR");
colixes[atomIndex] = colix = getColixI(colix, paletteID, atomIndex);
bsColixSet.setBitTo(atomIndex, colix != C.INHERIT_ALL || shapeID == JC.SHAPE_BALLS);
paletteIDs[atomIndex] = paletteID;
}
@Override
public void setAtomClickability() {
if (!isActive)
return;
for (int i = ac; --i >= 0;) {
Atom atom = atoms[i];
if ((atom.shapeVisibilityFlags & vf) == 0
|| ms.isAtomHidden(i))
continue;
atom.setClickable(vf);
}
}
/**
* @param i
* @return script, but only for Measures
*/
public String getInfoAsString(int i) {
// only in Measures
return null;
}
@Override
public String getShapeState() {
// implemented in StateCreator, not here
return null;
}
}
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