org.jmol.geodesic.EnvelopeCalculation Maven / Gradle / Ivy
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/* $RCSfile$
* $Author: hansonr $
* $Date: 2007-03-20 07:56:22 -0500 (Tue, 20 Mar 2007) $
* $Revision: 7182 $
*
* Copyright (C) 2003-2005 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.geodesic;
import org.jmol.util.ArrayUtil;
import org.jmol.util.BitSetUtil;
import org.jmol.util.FastBitSet;
import org.jmol.util.Geodesic;
import org.jmol.util.Normix;
//import org.jmol.util.SlowBitSet;
import org.jmol.api.AtomIndexIterator;
import org.jmol.atomdata.AtomData;
import org.jmol.atomdata.AtomDataServer;
import org.jmol.atomdata.RadiusData;
import java.util.BitSet;
import javax.vecmath.Matrix3f;
import javax.vecmath.Point3f;
import javax.vecmath.Vector3f;
/* ***************************************************************
*
* 3/20/07 -- consolidation -- Bob Hanson
*
* The two geodesic code segments in g3d.Geodesic and DotsRenderer were
* cleaned up and all put in g3d.Geodesic (no new code required!)
* Then GeoSurface was split off from Dots.
* Finally, all the dot calculations were split off as EnvelopeCalculation,
* which can be used then independently of the Dots shape.
*
*
* 7/17/06 History -- Bob Hanson
*
* Connolly surface rendering was never completed. Miguel got to the point
* where he identified the three issues -- convex single-atom areas,
* two-atom connection "toruses" or "troughs", and three-atom connection "cavities",
* and he successfully took care of each in its own way. However, he never figured
* out how to patch these together effectively, and the surface had triangular
* holes.
*
* This code was never documented, so users never worked with it.
* In July of 2006, this code was superceded by the "isosurface solvent"
* command, which does this using the marching cubes algorithm to produce
* a much cleaner surface. Of course it also takes more time.
*
* What remains is the van der Waals surface, which can be extended using
*
* dots/geosurface +1.2
*
* to provide the solvent-accessible surface.
*
* A better rendering of the solvent accessible surface is given using
*
* isosurface sasurface 1.2
*
* A discussion of molecular/solvent-accessible surfaces can be found at
* http://www.netsci.org/Science/Compchem/feature14e.html
*
* In March 2007, Bob refactored all Geodesic business that was here
* into the static class g3d.Geodesic, made GeoSurface an extension of Dots,
* and generally similified the code.
*
*/
/*
* Miguel's original comments:
*
* The Dots and DotsRenderer classes implement vanderWaals and Connolly
* dot surfaces.
* The vanderWaals surface is defined by the vanderWaals radius of each
* atom. The surface of the atom is 'peppered' with dots. Each dot is
* tested to see if it falls within the vanderWaals radius of any of
* its neighbors. If so, then the dot is not displayed.
* See g3d.Geodesic for more discussion of the implementation.
* The Connolly surface is defined by rolling a probe sphere over the
* surface of the molecule. In this way, a smooth surface is generated ...
* one that does not have crevices between atoms. Three types of shapes
* are generated: convex, saddle, and concave.
* The 'probe' is a sphere. A sphere of 1.2 angstroms representing HOH
* is commonly used.
* Convex shapes are generated on the exterior surfaces of exposed atoms.
* They are points on the sphere which are exposed. In these areas of
* the molecule they look just like the vanderWaals dot surface.
* The saddles are generated between pairs of atoms. Imagine an O2
* molecule. The probe sphere is rolled around the two oxygen spheres so
* that it stays in contact with both spheres. The probe carves out a
* torus (doughnut). The portion of the torus between the two points of
* contact with the oxygen spheres is a saddle.
* The concave shapes are defined by triples of atoms. Imagine three
* atom spheres in a close triangle. The probe sphere will sit (nicely)
* in the little cavity formed by the three spheres. In fact, there are
* two cavities, one on each side of the triangle. The probe sphere makes
* one point of contact with each of the three atoms. The shape of the
* cavity is the spherical triangle on the surface of the probe sphere
* determined by these three contact points.
* For each of these three surface shapes, the dots are painted only
* when the probe sphere does not interfere with any of the neighboring
* atoms.
* See the following scripting commands:
* set solvent on/off (on defaults to 1.2 angstroms)
* set solvent 1.5 (choose another probe size)
* dots on/off
* color dots [color]
* color dotsConvex [color]
* color dotsSaddle [color]
* color dotsConcave [color]
*
* The reference article for this implementation is:
* Analytical Molecular Surface Calculation, Michael L. Connolly,
* Journal of Applied Crystalography, (1983) 15, 548-558
*
****************************************************************/
public final class EnvelopeCalculation {
private FastBitSet geodesicMap;
private FastBitSet mapT;
//Viewer viewer;
private short[] mads;
private AtomData atomData = new AtomData();
private AtomDataServer viewer;
private int atomCount;
private FastBitSet emptySet;
/**
*
* @param viewer
* @param atomCount
* @param mads
*/
public EnvelopeCalculation(AtomDataServer viewer, int atomCount, short[] mads/*, boolean asJavaBitSet*/) {
this.viewer = viewer;
this.atomCount = atomCount; //preliminary, for setFromBits()
this.mads = mads;
// geodesicCount = Geodesic.getVertexVectorsCount();
geodesicCount = Geodesic.getVertexCount(MAX_LEVEL);
//if (asJavaBitSet) {
// geodesicMap = SlowBitSet.allocateBitmap(geodesicCount);
// mapT = SlowBitSet.allocateBitmap(geodesicCount);
// emptySet = new SlowBitSet();
//} else {
geodesicMap = FastBitSet.allocateBitmap(geodesicCount);
mapT = FastBitSet.allocateBitmap(geodesicCount);
emptySet = FastBitSet.getEmptySet();
//}
}
public final static float SURFACE_DISTANCE_FOR_CALCULATION = 3f;
public final static int MAX_LEVEL = 3;//Geodesic.standardLevel;
private float maxRadius = 0;
private boolean modelZeroBased;
private boolean disregardNeighbors = false;
private BitSet bsMySelected;
private FastBitSet[] dotsConvexMaps;
public FastBitSet[] getDotsConvexMaps() {
return dotsConvexMaps;
}
private int dotsConvexMax; // the Max == the highest atomIndex with dots + 1
public int getDotsConvexMax() {
return dotsConvexMax;
}
public void allocDotsConvexMaps(int max) {
if (dotsConvexMax >= max)
return;
dotsConvexMax = max;
dotsConvexMaps = new FastBitSet[max];
}
private int geodesicCount;
private BitSet bsSurface;
public BitSet getBsSurfaceClone() {
return BitSetUtil.copy(bsSurface);
}
public void setMads(short[] mads) {
this.mads = mads;
}
public void setFromBits(int index, BitSet bs) {
geodesicMap.set(0, geodesicCount);
for (int iDot = geodesicCount; --iDot >= 0;)
if (!bs.get(iDot))
geodesicMap.clear(iDot);
if (dotsConvexMaps == null)
dotsConvexMaps = new FastBitSet[atomCount];
FastBitSet map;
if (geodesicMap.isEmpty())
map = emptySet;
else
map = new FastBitSet(geodesicMap);
if (index >= dotsConvexMaps.length)
return;
dotsConvexMaps[index] = map;
dotsConvexMax = Math.max(dotsConvexMax, index);
}
private float radiusP, diameterP;
public void newSet() {
dotsConvexMax = 0;
dotsConvexMaps = null;
radiusP = diameterP = 0;
mads = null;
}
/**
* problem prior to 12.3.18 was that dots once on the deodesic were not being moved.
* this isn't perfect, but it's reasonably good. Mostly, you should recreate dots
* after rotateSelected. This isn't a problem until after a state is saved and
* reloaded, since only then with atomData.radiusData be null.
*
* @param bs
* @param m
*/
public void reCalculate(BitSet bs, Matrix3f m) {
if (atomData.radiusData != null) {
calculate(null, maxRadius, bs, bsIgnore, disregardNeighbors,
onlySelectedDots, isSurface, multiModel);
return;
}
if (dotsConvexMaps == null || dotsConvexMax == 0)
return;
Vector3f pt = new Vector3f();
BitSet bsTemp = new BitSet();
for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
if (i >= dotsConvexMax)
return;
FastBitSet map = dotsConvexMaps[i];
if (map == null || map.isEmpty())
continue;
FastBitSet bsNew = new FastBitSet();
for (int j = map.nextSetBit(0); j >= 0; j = map.nextSetBit(j + 1)) {
pt.set(Geodesic.getVertexVector(j));
m.transform(pt);
bsNew.set(Normix.getNormix(pt, bsTemp));
}
dotsConvexMaps[i] = bsNew;
}
}
private BitSet bsIgnore;
private boolean onlySelectedDots;
private boolean isSurface;
private boolean multiModel;
/**
* @param rd
* @param maxRadius
* @param bsSelected
* @param bsIgnore
* @param disregardNeighbors
* @param onlySelectedDots
* @param isSurface
* @param multiModel
*/
public void calculate(RadiusData rd, float maxRadius, BitSet bsSelected,
BitSet bsIgnore, boolean disregardNeighbors,
boolean onlySelectedDots, boolean isSurface,
boolean multiModel) {
// was: this.setRadius = (setRadius == Float.MAX_VALUE &&
// !useVanderwaalsRadius ? SURFACE_DISTANCE_FOR_CALCULATION : setRadius);
if (rd == null) {
rd = atomData.radiusData;
if (rd == null)
return;
} else {
atomData.radiusData = rd;
this.bsIgnore = bsIgnore;
this.onlySelectedDots = onlySelectedDots;
this.multiModel = multiModel;
this.isSurface = isSurface;
}
if (rd.value == Float.MAX_VALUE)
rd.value = SURFACE_DISTANCE_FOR_CALCULATION;
atomData.modelIndex = (multiModel ? -1 : 0);
modelZeroBased = !multiModel;
viewer.fillAtomData(atomData, AtomData.MODE_FILL_COORDS
| (mads == null ? AtomData.MODE_FILL_RADII : 0));
atomCount = atomData.atomCount;
if (mads != null)
for (int i = 0; i < atomCount; i++)
atomData.atomRadius[i] = mads[i] / 1000f;
bsMySelected = (onlySelectedDots && bsSelected != null ? BitSetUtil
.copy(bsSelected) : bsIgnore != null ? BitSetUtil.setAll(atomCount)
: null);
BitSetUtil.andNot(bsMySelected, bsIgnore);
this.disregardNeighbors = disregardNeighbors;
this.maxRadius = maxRadius;
bsSurface = new BitSet();
// now, calculate surface for selected atoms
boolean isAll = (bsSelected == null);
AtomIndexIterator iter = viewer.getSelectedAtomIterator(bsMySelected,
false, modelZeroBased, false);
//true ==> only atom index > this atom accepted
int i0 = (isAll ? atomCount - 1 : bsSelected.nextSetBit(0));
for (int i = i0; i >= 0; i = (isAll ? i - 1 : bsSelected.nextSetBit(i + 1)))
if (bsIgnore == null || !bsIgnore.get(i)) {
setAtomI(i);
getNeighbors(iter);
calcConvexMap(isSurface);
}
iter.release();
currentPoints = null;
setDotsConvexMax();
}
public float getRadius(int atomIndex) {
return atomData.atomRadius[atomIndex];
}
private Point3f[] currentPoints;
public Point3f[] getPoints() {
if (dotsConvexMaps == null) {
calculate(new RadiusData(SURFACE_DISTANCE_FOR_CALCULATION, RadiusData.EnumType.ABSOLUTE, null),
Float.MAX_VALUE, bsMySelected, null, false, false, false, false);
}
if (currentPoints != null)
return currentPoints;
int nPoints = 0;
int dotCount = 42;
for (int i = dotsConvexMax; --i >= 0;)
if (dotsConvexMaps[i] != null)
nPoints += dotsConvexMaps[i].cardinality(dotCount);
Point3f[] points = new Point3f[nPoints];
if (nPoints == 0)
return points;
nPoints = 0;
for (int i = dotsConvexMax; --i >= 0;)
if (dotsConvexMaps[i] != null) {
int iDot = dotsConvexMaps[i].size();
if (iDot > dotCount)
iDot = dotCount;
while (--iDot >= 0)
if (dotsConvexMaps[i].get(iDot)) {
Point3f pt = new Point3f();
pt.scaleAdd(atomData.atomRadius[i], Geodesic.getVertexVector(iDot), atomData.atomXyz[i]);
points[nPoints++] = pt;
}
}
currentPoints = points;
return points;
}
///////////////// private methods ///////////////////
private void setDotsConvexMax() {
if (dotsConvexMaps == null)
dotsConvexMax = 0;
else {
int i;
for (i = atomCount; --i >= 0 && dotsConvexMaps[i] == null;) {
}
dotsConvexMax = i + 1;
}
}
/*
BitSet getSurfaceAtoms() {
return bsSurface;
}
*/
public float getAppropriateRadius(int atomIndex) {
return (mads != null ? (atomIndex >= mads.length ? 0 : mads[atomIndex]/1000f)
: atomData.atomRadius[atomIndex]);
}
private int indexI;
private Point3f centerI;
private float radiusI;
private float radiiIP2;
private final Point3f pointT = new Point3f();
private void setAtomI(int indexI) {
this.indexI = indexI;
centerI = atomData.atomXyz[indexI];
radiusI = atomData.atomRadius[indexI];
radiiIP2 = radiusI + radiusP;
radiiIP2 *= radiiIP2;
}
private void calcConvexMap(boolean isSurface) {
if (dotsConvexMaps == null)
dotsConvexMaps = new FastBitSet[atomCount];
calcConvexBits();
FastBitSet map;
if (geodesicMap.isEmpty())
map = emptySet;
else {
bsSurface.set(indexI);
if (isSurface) {
addIncompleteFaces(geodesicMap);
addIncompleteFaces(geodesicMap);
}
map = new FastBitSet(geodesicMap);
}
dotsConvexMaps[indexI] = map;
}
private void addIncompleteFaces(FastBitSet points) {
mapT.clear();
short[] faces = Geodesic.getFaceVertexes(MAX_LEVEL);
int len = faces.length;
int maxPt = -1;
for (int f = 0; f < len;) {
short p1 = faces[f++];
short p2 = faces[f++];
short p3 = faces[f++];
boolean ok1 = points.get(p1);
boolean ok2 = points.get(p2);
boolean ok3 = points.get(p3);
if (! (ok1 || ok2 || ok3) || ok1 && ok2 && ok3)
continue;
// trick: DO show faces if ANY ONE vertex is missing
if (!ok1) {
mapT.set(p1);
if (maxPt < p1)
maxPt = p1;
}
if (!ok2) {
mapT.set(p2);
if (maxPt < p2)
maxPt = p2;
}
if (!ok3) {
mapT.set(p3);
if (maxPt < p3)
maxPt = p3;
}
}
for (int i=0; i <= maxPt; i++) {
if (mapT.get(i))
points.set(i);
}
}
private Point3f centerT;
//level = 3 for both
private final Point3f[] vertexTest = new Point3f[12];
{
for(int i = 0; i < 12; i++)
vertexTest[i] = new Point3f();
}
private static int[] power4 = {1, 4, 16, 64, 256};
private void calcConvexBits() {
geodesicMap.set(0, geodesicCount);
float combinedRadii = radiusI + radiusP;
if (neighborCount == 0)
return;
int faceTest;
int p1, p2, p3;
short[] faces = Geodesic.getFaceVertexes(MAX_LEVEL);
int p4 = power4[MAX_LEVEL - 1];
boolean ok1, ok2, ok3;
mapT.clear();
for (int i = 0; i < 12; i++) {
vertexTest[i].set(Geodesic.getVertexVector(i));
vertexTest[i].scaleAdd(combinedRadii, centerI);
}
for (int f = 0; f < 20; f++) {
faceTest = 0;
p1 = faces[3 * p4 * (4 * f + 0)];
p2 = faces[3 * p4 * (4 * f + 1)];
p3 = faces[3 * p4 * (4 * f + 2)];
for (int j = 0; j < neighborCount; j++) {
float maxDist = neighborPlusProbeRadii2[j];
centerT = neighborCenters[j];
ok1 = vertexTest[p1].distanceSquared(centerT) >= maxDist;
ok2 = vertexTest[p2].distanceSquared(centerT) >= maxDist;
ok3 = vertexTest[p3].distanceSquared(centerT) >= maxDist;
if (!ok1)
geodesicMap.clear(p1);
if (!ok2)
geodesicMap.clear(p2);
if (!ok3)
geodesicMap.clear(p3);
if (!ok1 && !ok2 && !ok3) {
faceTest = -1;
break;
}
}
int kFirst = f * 12 * p4;
int kLast = kFirst + 12 * p4;
for (int k = kFirst; k < kLast; k++) {
int vect = faces[k];
if (mapT.get(vect) || !geodesicMap.get(vect))
continue;
switch (faceTest) {
case -1:
//face full occluded
geodesicMap.clear(vect);
break;
case 0:
//face partially occluded
for (int j = 0; j < neighborCount; j++) {
float maxDist = neighborPlusProbeRadii2[j];
centerT = neighborCenters[j];
pointT.set(Geodesic.getVertexVector(vect));
pointT.scaleAdd(combinedRadii, centerI);
if (pointT.distanceSquared(centerT) < maxDist)
geodesicMap.clear(vect);
}
break;
case 1:
//face is fully surface
}
mapT.set(vect);
}
}
}
private int neighborCount;
private int[] neighborIndices = new int[16];
private Point3f[] neighborCenters = new Point3f[16];
private float[] neighborPlusProbeRadii2 = new float[16];
private float[] neighborRadii2 = new float[16];
private AtomIndexIterator getNeighbors(AtomIndexIterator iter) {
neighborCount = 0;
if (disregardNeighbors)
return null;
viewer.setIteratorForAtom(iter, indexI, radiusI + diameterP + maxRadius);
while (iter.hasNext()) {
int indexN = iter.next();
float neighborRadius = atomData.atomRadius[indexN];
if (centerI.distance(atomData.atomXyz[indexN]) > radiusI + radiusP + radiusP
+ neighborRadius)
continue;
if (neighborCount == neighborIndices.length) {
neighborIndices = ArrayUtil.doubleLength(neighborIndices);
neighborCenters = (Point3f[]) ArrayUtil.doubleLength(neighborCenters);
neighborPlusProbeRadii2 = ArrayUtil
.doubleLength(neighborPlusProbeRadii2);
neighborRadii2 = ArrayUtil.doubleLength(neighborRadii2);
}
neighborCenters[neighborCount] = atomData.atomXyz[indexN];
neighborIndices[neighborCount] = indexN;
float r = neighborRadius + radiusP;
neighborPlusProbeRadii2[neighborCount] = r * r;
neighborRadii2[neighborCount] = neighborRadius * neighborRadius;
++neighborCount;
}
return iter;
}
/**
*
* @param firstAtomDeleted
* @param nAtomsDeleted
*/
public void deleteAtoms(int firstAtomDeleted, int nAtomsDeleted) {
dotsConvexMaps = (FastBitSet[]) ArrayUtil.deleteElements(dotsConvexMaps, firstAtomDeleted, nAtomsDeleted);
dotsConvexMax = dotsConvexMaps.length;
if (mads != null)
mads = (short[]) ArrayUtil.deleteElements(mads, firstAtomDeleted, nAtomsDeleted);
atomData.atomRadius = (float[]) ArrayUtil.deleteElements(atomData.atomRadius, firstAtomDeleted, nAtomsDeleted);
atomData.atomXyz = (Point3f[]) ArrayUtil.deleteElements(atomData.atomXyz, firstAtomDeleted, nAtomsDeleted);
atomData.atomCount -= nAtomsDeleted;
atomCount = atomData.atomCount;
}
}