Revision: 20646
http://sourceforge.net/p/jmol/code/20646
Author: hansonr
Date: 2015-07-09 04:37:42 +0000 (Thu, 09 Jul 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.15_2015.07.08c"
bug fix: load files "xxx.png|xxxx" "xxx.png|zzzz" not read from state properly
bug fix: polyhedra not saved in state property
bug fix: moving atoms with 4x4 matrix not saved in state
bug fix: moving of an atom having a polyhedron fails to move the polyhedron as
well
new feature: smiles2.find("SMILES",smiles1, asMap, allMappings)
-- asMap = TRUE (default false) indicates you want an atom
correlation map indicating positions in smiles2 corresponding to smiles1
-- allMappings = TRUE (default false) indicates you want
all mappings, not just the first found
-- returns a number, -1, 0, n>0 when asMap is false (allMappings ignored)
-- returns int[] when allMappings is false
-- returns int[][] when allMappings is true
-- example:
var s1 = atom1.polyhedron.getProperty("SMILES")
var coords = atom2.polyhedron.getProperty("vertices")
var s2 = atom2.polyhedron.getProperty("SMILES")
var coords2 = atom2.polyhedron.getProperty("vertices")
var map12 = s2.find("SMILES", s1, true, false)
var coords2Mapped = []
for (var i in map12) coords2Mapped.push(coords2[i + 1])
coords2 = coords2Mapped
var mat = compare(coords1, coords2)
select {1.1}
rotateselected @mat
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/io/FilesReader.java
trunk/Jmol/src/org/jmol/modelset/ModelSet.java
trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
trunk/Jmol/src/org/jmol/scriptext/MathExt.java
trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java
trunk/Jmol/src/org/jmol/shapespecial/Polyhedron.java
trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/StateCreator.java
trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/console/ConsoleTextArea.java
Modified: trunk/Jmol/src/org/jmol/io/FilesReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/io/FilesReader.java 2015-07-08 16:15:03 UTC (rev
20645)
+++ trunk/Jmol/src/org/jmol/io/FilesReader.java 2015-07-09 04:37:42 UTC (rev
20646)
@@ -91,7 +91,7 @@
String name = fullPathNamesIn[i];
String[] subFileList = null;
htParams.remove("subFileList");
- if (name.indexOf("|") >= 0) {
+ if (name.indexOf("|") >= 0 && !htParams.containsKey("isStateScript")) {
subFileList = PT.split(name, "|");
name = subFileList[0];
}
Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2015-07-08 16:15:03 UTC
(rev 20645)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2015-07-09 04:37:42 UTC
(rev 20646)
@@ -3641,8 +3641,10 @@
public void moveAtoms(M4 m4, M3 mNew, M3 rotation, V3 translation, BS bs,
P3 center, boolean isInternal, boolean
translationOnly) {
if (m4 != null) {
- for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1))
+ for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
m4.rotTrans(at[i]);
+ taintAtom(i, TAINT_COORD);
+ }
mat4.setM4(m4);
translation = null;
} else if (!translationOnly) {
@@ -3689,8 +3691,10 @@
}
}
if (translation != null) {
- for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1))
+ for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
at[i].add(translation);
+ taintAtom(i, TAINT_COORD);
+ }
if (!translationOnly) {
mat4t.setIdentity();
mat4t.setTranslation(translation);
Modified: trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-07-08 16:15:03 UTC
(rev 20645)
+++ trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-07-09 04:37:42 UTC
(rev 20646)
@@ -3179,6 +3179,11 @@
String propertyName = null;
Object propertyValue = null;
switch (getToken(i).tok) {
+ case T.hash:
+ propertyName = "info";
+ propertyValue = e.theToken.value;
+ needsGenerating = true;
+ break;
case T.unitcell:
propertyName = "unitCell";
propertyValue = Boolean.TRUE;
Modified: trunk/Jmol/src/org/jmol/scriptext/MathExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-07-08 16:15:03 UTC
(rev 20645)
+++ trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-07-09 04:37:42 UTC
(rev 20646)
@@ -115,7 +115,7 @@
return evaluateList(mp, op.intValue, args);
case T.array:
case T.leftsquare:
- return evaluateArray(mp, args, tok == T.leftsquare);
+ return evaluateArray(mp, args, false);
case T.axisangle:
case T.quaternion:
return evaluateQuaternion(mp, args, tok);
Modified: trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java 2015-07-08 16:15:03 UTC
(rev 20645)
+++ trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java 2015-07-09 04:37:42 UTC
(rev 20646)
@@ -45,6 +45,7 @@
import org.jmol.java.BS;
import org.jmol.modelset.Atom;
import org.jmol.modelset.Bond;
+import org.jmol.script.SV;
import org.jmol.script.T;
import org.jmol.shape.AtomShape;
import org.jmol.util.BSUtil;
@@ -52,12 +53,10 @@
import org.jmol.util.Logger;
import org.jmol.util.Normix;
-
-
public class Polyhedra extends AtomShape {
private final static float DEFAULT_DISTANCE_FACTOR = 1.85f;
-// private final static float DEFAULT_MANY_VERTEX_DISTANCE_FACTOR = 1.5f;
+ // private final static float DEFAULT_MANY_VERTEX_DISTANCE_FACTOR = 1.5f;
private final static float DEFAULT_FACECENTEROFFSET = 0.25f;
private final static int EDGES_NONE = 0;
public final static int EDGES_ALL = 1;
@@ -68,12 +67,13 @@
private V3[] normalsT = new V3[MAX_VERTICES + 1];
private int[][] planesT = new int[MAX_VERTICES][3];
private final static P3 randomPoint = P3.new3(3141f, 2718f, 1414f);
-
+
private static final int MODE_BONDING = 1;
private static final int MODE_POINTS = 2;
private static final int MODE_ITERATE = 3;
private static final int MODE_BITSET = 4;
private static final int MODE_UNITCELL = 5;
+ private static final int MODE_INFO = 6;
/**
* a dot product comparison term
*/
@@ -89,7 +89,6 @@
float faceCenterOffset;
float distanceFactor = Float.NaN;
boolean isCollapsed;
-
private boolean iHaveCenterBitSet;
private boolean bondedOnly;
@@ -98,11 +97,13 @@
private BS centers;
private BS bsVertices;
private BS bsVertexCount;
-
+
private boolean useUnitCell;
private int nPoints;
private float planarParam;
+ private Map<String, SV> info;
+ @SuppressWarnings("unchecked")
@Override
public void setProperty(String propertyName, Object value, BS bs) {
@@ -115,6 +116,7 @@
bsVertices = null;
useUnitCell = false;
centers = null;
+ info = null;
bsVertexCount = new BS();
bondedOnly = isCollapsed = iHaveCenterBitSet = false;
haveBitSetVertices = false;
@@ -140,9 +142,9 @@
if ("nVertices" == propertyName) {
int n = ((Integer) value).intValue();
- if(n < 0) {
+ if (n < 0) {
if (-n >= nVertices) {
- bsVertexCount.setBits(nVertices, -n);
+ bsVertexCount.setBits(nVertices, 1 - n);
nVertices = -n;
}
} else {
@@ -203,6 +205,13 @@
return;
}
+ if ("info" == propertyName) {
+ info = (Map<String, SV>) value;
+ centers = BSUtil.newAndSetBit(((SV) info.get("atomIndex")).intValue);
+ iHaveCenterBitSet = true;
+ return;
+ }
+
if ("delete" == propertyName) {
if (!iHaveCenterBitSet)
centers = bs;
@@ -283,6 +292,7 @@
if (propertyName == "deleteModelAtoms") {
int modelIndex = ((int[]) ((Object[]) value)[2])[0];
for (int i = polyhedronCount; --i >= 0;) {
+ polyhedrons[i].info = null;
if (polyhedrons[i].modelIndex == modelIndex) {
polyhedronCount--;
polyhedrons = (Polyhedron[]) AU.deleteElements(polyhedrons, i, 1);
@@ -296,7 +306,6 @@
setPropAS(propertyName, value, bs);
}
-
@Override
public boolean getPropertyData(String property, Object[] data) {
int iatom;
@@ -358,7 +367,7 @@
iatom = ((Integer) data[0]).intValue();
for (int i = polyhedronCount; --i >= 0;) {
if (polyhedrons[i].centralAtom.i == iatom) {
- data[1] = polyhedrons[i].getInfo(vwr);
+ data[1] = polyhedrons[i].getInfo(vwr, true);
return true;
}
}
@@ -366,15 +375,15 @@
}
return false;
}
-
+
@Override
public Lst<Map<String, Object>> getShapeDetail() {
Lst<Map<String, Object>> lst = new Lst<Map<String, Object>>();
for (int i = 0; i < polyhedronCount; i++)
- lst.addLast(polyhedrons[i].getInfo(vwr));
+ lst.addLast(polyhedrons[i].getInfo(vwr, true));
return lst;
}
-
+
private void setLighting(boolean isFullyLit, BS bs) {
for (int i = polyhedronCount; --i >= 0;)
if (bs.get(polyhedrons[i].centralAtom.i)) {
@@ -421,13 +430,11 @@
private void buildPolyhedra() {
boolean useBondAlgorithm = radius == 0 || bondedOnly;
- int mode = (nPoints > 0 ? MODE_POINTS
- : haveBitSetVertices ? MODE_BITSET
- : useUnitCell ? MODE_UNITCELL
- : useBondAlgorithm ? MODE_BONDING
- : MODE_ITERATE);
- AtomIndexIterator iter = (mode == MODE_ITERATE ?
ms.getSelectedAtomIterator(null,
- false, false, false, false) : null);
+ int mode = (info != null ? MODE_INFO : nPoints > 0 ? MODE_POINTS
+ : haveBitSetVertices ? MODE_BITSET : useUnitCell ? MODE_UNITCELL
+ : useBondAlgorithm ? MODE_BONDING : MODE_ITERATE);
+ AtomIndexIterator iter = (mode == MODE_ITERATE ? ms
+ .getSelectedAtomIterator(null, false, false, false, false) : null);
for (int i = centers.nextSetBit(0); i >= 0; i = centers.nextSetBit(i + 1))
{
Atom atom = atoms[i];
Polyhedron p = null;
@@ -448,6 +455,9 @@
vwr.setIteratorForAtom(iter, i, radius);
p = constructRadiusPolyhedron(atom, iter);
break;
+ case MODE_INFO:
+ p = new Polyhedron().setInfo(info, vwr.ms.at);
+ break;
}
if (p != null) {
if (polyhedronCount == polyhedrons.length)
@@ -465,7 +475,8 @@
return validatePolyhedron(atom, nPoints, otherAtoms);
}
- private Polyhedron constructUnitCellPolygon(Atom atom, boolean
useBondAlgorithm) {
+ private Polyhedron constructUnitCellPolygon(Atom atom,
+ boolean useBondAlgorithm) {
SymmetryInterface unitcell = vwr.ms.getUnitCellForAtom(atom.i);
if (unitcell == null)
return null;
@@ -474,7 +485,8 @@
bsAtoms.and(bsVertices);
if (bsAtoms.isEmpty())
return null;
- AtomIndexIterator iter = unitcell.getIterator(vwr, atom, atoms, bsAtoms,
useBondAlgorithm ? 5f : radius);
+ AtomIndexIterator iter = unitcell.getIterator(vwr, atom, atoms, bsAtoms,
+ useBondAlgorithm ? 5f : radius);
if (!useBondAlgorithm)
return constructRadiusPolyhedron(atom, iter);
float myBondingRadius = atom.getBondingRadius();
@@ -489,7 +501,8 @@
float otherRadius = other.getBondingRadius();
P3 pt = iter.getPosition();
float distance2 = atom.distanceSquared(pt);
- if (!vwr.ms.isBondable(myBondingRadius, otherRadius, distance2,
minBondDistance2, bondTolerance))
+ if (!vwr.ms.isBondable(myBondingRadius, otherRadius, distance2,
+ minBondDistance2, bondTolerance))
continue;
otherAtoms[bondCount++] = pt;
if (bondCount >= MAX_VERTICES)
@@ -508,17 +521,17 @@
if (!bond.isCovalent())
continue;
Atom other = bond.getOtherAtom(atom);
- if (bsVertices != null && !bsVertices.get(i)
- || radius > 0 && other.distance(atom) > radius)
+ if (bsVertices != null && !bsVertices.get(i) || radius > 0
+ && other.distance(atom) > radius)
continue;
otherAtoms[bondCount++] = other;
if (bondCount >= MAX_VERTICES)
break;
}
}
- return (bondCount < 3 || bondCount >= MAX_VERTICES
- || nVertices > 0 && !bsVertexCount.get(bondCount) ? null
- : validatePolyhedron(atom, bondCount, otherAtoms));
+ return (bondCount < 3 || bondCount >= MAX_VERTICES || nVertices > 0
+ && !bsVertexCount.get(bondCount) ? null : validatePolyhedron(atom,
+ bondCount, otherAtoms));
}
private Polyhedron constructBitSetPolyhedron(Atom atom) {
@@ -529,8 +542,7 @@
return validatePolyhedron(atom, otherAtomCount, otherAtoms);
}
- private Polyhedron constructRadiusPolyhedron(Atom atom,
- AtomIndexIterator iter) {
+ private Polyhedron constructRadiusPolyhedron(Atom atom, AtomIndexIterator
iter) {
int otherAtomCount = 0;
while (iter.hasNext()) {
Atom other = atoms[iter.next()];
@@ -548,18 +560,19 @@
otherAtoms[otherAtomCount++] = pt;
}
return (otherAtomCount < 3 || nVertices > 0
- && !bsVertexCount.get(otherAtomCount) ? null : validatePolyhedron(
- atom, otherAtomCount, otherAtoms));
+ && !bsVertexCount.get(otherAtomCount) ? null : validatePolyhedron(atom,
+ otherAtomCount, otherAtoms));
}
private Polyhedron validatePolyhedron(Atom centralAtom, int vertexCount,
- P3[] otherAtoms) {
+ P3[] otherAtoms) {
int planeCount = 0;
int iCenter = vertexCount;
int nPoints = iCenter + 1;
float distMax = 0;
float dAverage = 0;
- float planarParam = (Float.isNaN(this.planarParam) ? DEFAULT_PLANAR_PARAM
: this.planarParam);
+ float planarParam = (Float.isNaN(this.planarParam) ? DEFAULT_PLANAR_PARAM
+ : this.planarParam);
P3[] points = new P3[MAX_VERTICES * 3];
points[iCenter] = otherAtoms[iCenter] = centralAtom;
@@ -574,8 +587,8 @@
boolean isComplex = (nother1 > 6);
// for many-vertex polygons we reduce the distance allowed to avoid
through-polyhedron faces
float factor = (!Float.isNaN(distanceFactor) ? distanceFactor
- //: isComplex ? DEFAULT_MANY_VERTEX_DISTANCE_FACTOR
- : DEFAULT_DISTANCE_FACTOR);
+ //: isComplex ? DEFAULT_MANY_VERTEX_DISTANCE_FACTOR
+ : DEFAULT_DISTANCE_FACTOR);
BS bs = BS.newN(iCenter);
boolean isOK = (dAverage == 0);
@@ -606,7 +619,7 @@
if (Logger.debugging) {
Logger.debug("Polyhedra distanceFactor for " + iCenter
+ " atoms increased to " + factor + " in order to include "
- + otherAtoms[i] );
+ + otherAtoms[i]);
}
break;
}
@@ -653,8 +666,8 @@
int vmax = MAX_VERTICES;
P3 rpt = randomPoint;
BS bsTemp = Normix.newVertexBitSet();
- V3[] normals = normalsT;
- Map<Integer,String> htNormMap = new Hashtable<Integer, String>();
+ V3[] normals = normalsT;
+ Map<Integer, String> htNormMap = new Hashtable<Integer, String>();
BS bsFlat = new BS();
boolean doCheckPlane = isComplex;
for (int i = 0; i < nother2; i++)
@@ -700,7 +713,7 @@
if (collapsed || isFlat && facetCatalog.indexOf(facet) < 0) {
facetCatalog += facet;
p[planeCount] = new int[] { isWindingOK ? i : j,
- isWindingOK ? j : i, nRef , isFlat ? -7 : -6};
+ isWindingOK ? j : i, nRef, isFlat ? -15 : -6 };
getNormalFromCenter(points[k], points[i], points[j], ptRef, false,
normal);
if (isFlat)
@@ -711,7 +724,7 @@
if (collapsed || isFlat && facetCatalog.indexOf(facet) < 0) {
facetCatalog += facet;
p[planeCount] = new int[] { isWindingOK ? i : k, nRef,
- isWindingOK ? k : i , isFlat ? -7 : -5};
+ isWindingOK ? k : i, isFlat ? -15 : -5 };
getNormalFromCenter(points[j], points[i], ptRef, points[k], false,
normal);
if (isFlat)
@@ -722,7 +735,7 @@
if (collapsed || isFlat && facetCatalog.indexOf(facet) < 0) {
facetCatalog += facet;
p[planeCount] = new int[] { nRef, isWindingOK ? j : k,
- isWindingOK ? k : j , isFlat ? -7 : -4};
+ isWindingOK ? k : j, isFlat ? -15 : -4 };
getNormalFromCenter(points[i], ptRef, points[j], points[k], false,
normal);
if (isFlat)
@@ -735,7 +748,7 @@
} else {
// finally, the standard face:
p[planeCount] = new int[] { isWindingOK ? i : j,
- isWindingOK ? j : i, k, -7};
+ isWindingOK ? j : i, k, -7 };
normals[planeCount] = normal;
if (!doCheckPlane
|| checkPlane(points, iCenter, p, normals, planeCount, plane,
@@ -746,17 +759,17 @@
}
}
nPoints--;
-
+
if (Logger.debugging) {
Logger
.info("Polyhedron planeCount=" + planeCount + " nPoints=" + nPoints);
- for (int i = 0; i < planeCount; i++)
+ for (int i = 0; i < planeCount; i++)
Logger.info("Polyhedron " + getKey(p[i], i));
}
- return new Polyhedron(centralAtom, iCenter, nPoints, planeCount,
- otherAtoms, normals, bsFlat, p, collapsed, offset, factor,
planarParam);
+ return new Polyhedron().set(centralAtom, iCenter, nPoints, planeCount,
+ otherAtoms, normals, bsFlat, p, collapsed);
}
-
+
/**
*
* @param ptCenter
@@ -765,10 +778,10 @@
* @param ptC
* @param isOutward
* @param normal
- * @return true if winding is proper; false if not
+ * @return true if winding is proper; false if not
*/
- private boolean getNormalFromCenter(P3 ptCenter, P3 ptA, P3 ptB,
- P3 ptC, boolean isOutward, V3 normal) {
+ private boolean getNormalFromCenter(P3 ptCenter, P3 ptA, P3 ptB, P3 ptC,
+ boolean isOutward, V3 normal) {
V3 vAB = new V3();
float d = Measure.getNormalThroughPoints(ptA, ptB, ptC, normal, vAB);
boolean isReversed = (Measure.distanceToPlaneV(normal, d, ptCenter) > 0);
@@ -778,7 +791,6 @@
return !isReversed;
}
-
/**
* Clean out oeverlapping triangles based on normals. For now, we use
* normixes, which are approximations of normals. It is not 100% guaranteed
@@ -792,25 +804,25 @@
* @param plane
* @param vNorm
* @param htNormMap
- * @param planarParam
- * @param bsTemp
+ * @param planarParam
+ * @param bsTemp
* @return true if valid
*/
private boolean checkPlane(P3[] points, int ptCenter, int[][] planes,
V3[] normals, int index, P4 plane, V3 vNorm,
- Map<Integer, String> htNormMap, float
planarParam, BS bsTemp) {
-
+ Map<Integer, String> htNormMap, float planarParam,
+ BS bsTemp) {
+
int[] p1 = planes[index];
-
-
+
// Check here for a 3D convex hull:
plane = Measure.getPlaneThroughPoints(points[p1[0]], points[p1[1]],
points[p1[2]], vNorm, vAB, plane);
-// P3 ptest = P3.newP(points[p1[0]]);
-// ptest.add(points[p1[1]]);
-// ptest.add(points[p1[2]]);
-// ptest.scale(1/3f);
-// System.out.println("$draw ID p" + index +" vector " + ptest + vNorm);
+ // P3 ptest = P3.newP(points[p1[0]]);
+ // ptest.add(points[p1[1]]);
+ // ptest.add(points[p1[2]]);
+ // ptest.scale(1/3f);
+ // System.out.println("$draw ID p" + index +" vector " + ptest +
vNorm);
// See if all vertices are OUTSIDE the the plane we are considering.
for (int j = 0; j < ptCenter; j++) {
@@ -826,12 +838,12 @@
if (list == null) {
// we must see if there is a close normix to this
V3[] norms = Normix.getVertexVectors();
- for (Entry<Integer, String> e: htNormMap.entrySet()) {
+ for (Entry<Integer, String> e : htNormMap.entrySet()) {
if (norms[e.getKey().intValue()].dot(norm) > planarParam) {
list = e.getValue();
break;
}
- }
+ }
}
int ipt;
String match = getKey(p1, index);
@@ -867,8 +879,8 @@
planes[ipt] = pnew;
list = PT.rep(list, getKey(p0, ipt), getKey(pnew, ipt));
htNormMap.put(normix, list);
-// System.out.println("" + normix + " " +
Normix.getVertexVectors()[normix] + " " + getKey(p0, ipt) + " + "
- // + getKey(p1, index) + " = " + getKey(pnew, ipt));
+ // System.out.println("" + normix + " " +
Normix.getVertexVectors()[normix] + " " + getKey(p0, ipt) + " + "
+ // + getKey(p1, index) + " = " + getKey(pnew, ipt));
return false;
}
}
@@ -923,25 +935,23 @@
@Override
public void setModelVisibilityFlags(BS bsModels) {
- /*
- * set all fixed objects visible; others based on model being displayed
note
- * that this is NOT done with atoms and bonds, because they have mads. When
- * you say "frame 0" it is just turning on all the mads.
- */
+ /*
+ * set all fixed objects visible; others based on model being displayed note
+ * that this is NOT done with atoms and bonds, because they have mads. When
+ * you say "frame 0" it is just turning on all the mads.
+ */
for (int i = polyhedronCount; --i >= 0;) {
Polyhedron p = polyhedrons[i];
if (ms.at[p.centralAtom.i].isDeleted())
p.isValid = false;
- p.visibilityFlags = (p.visible
- && bsModels.get(p.modelIndex)
- && !ms.isAtomHidden(p.centralAtom.i)
- && !ms.at[p.centralAtom.i].isDeleted() ? vf
- : 0);
+ p.visibilityFlags = (p.visible && bsModels.get(p.modelIndex)
+ && !ms.isAtomHidden(p.centralAtom.i)
+ && !ms.at[p.centralAtom.i].isDeleted() ? vf : 0);
if (p.visibilityFlags != 0)
setShapeVisibility(atoms[p.centralAtom.i], true);
}
}
-
+
@Override
public String getShapeState() {
if (polyhedronCount == 0)
@@ -949,7 +959,7 @@
SB s = new SB();
for (int i = 0; i < polyhedronCount; i++)
if (polyhedrons[i].isValid)
- s.append(polyhedrons[i].getState());
+ s.append(polyhedrons[i].getState(vwr));
if (drawEdges == EDGES_FRONT)
appendCmd(s, "polyhedra frontedges");
else if (drawEdges == EDGES_ALL)
@@ -957,11 +967,17 @@
s.append(vwr.getAtomShapeState(this));
for (int i = 0; i < polyhedronCount; i++) {
Polyhedron p = polyhedrons[i];
- if (p.isValid && p.colixEdge != C.INHERIT_ALL &&
bsColixSet.get(p.centralAtom.i))
- appendCmd(s, "select ({" + p.centralAtom.i + "}); color polyhedra "
- + (C.isColixTranslucent(colixes[p.centralAtom.i]) ? "translucent " : "")
- + C.getHexCode(colixes[p.centralAtom.i]) + " " +
C.getHexCode(p.colixEdge));
- }
+ if (p.isValid && p.colixEdge != C.INHERIT_ALL
+ && bsColixSet.get(p.centralAtom.i))
+ appendCmd(
+ s,
+ "select ({"
+ + p.centralAtom.i
+ + "}); color polyhedra "
+ + (C.isColixTranslucent(colixes[p.centralAtom.i]) ?
"translucent "
+ : "") + C.getHexCode(colixes[p.centralAtom.i]) + " "
+ + C.getHexCode(p.colixEdge));
+ }
return s.toString();
}
}
Modified: trunk/Jmol/src/org/jmol/shapespecial/Polyhedron.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Polyhedron.java 2015-07-08
16:15:03 UTC (rev 20645)
+++ trunk/Jmol/src/org/jmol/shapespecial/Polyhedron.java 2015-07-09
04:37:42 UTC (rev 20646)
@@ -4,7 +4,9 @@
import java.util.Map;
import javajs.util.AU;
+import javajs.util.Lst;
import javajs.util.M4;
+import javajs.util.Measure;
import javajs.util.P3;
import javajs.util.V3;
@@ -12,41 +14,47 @@
import org.jmol.api.SymmetryInterface;
import org.jmol.java.BS;
import org.jmol.modelset.Atom;
+import org.jmol.modelset.ModelSet;
+import org.jmol.script.SV;
import org.jmol.script.T;
import org.jmol.util.C;
+import org.jmol.util.Escape;
+import org.jmol.util.Node;
import org.jmol.util.Normix;
+import org.jmol.util.Point3fi;
import org.jmol.viewer.Viewer;
public class Polyhedron {
int modelIndex;
- public final Atom centralAtom;
- public final P3[] vertices;
+ public Atom centralAtom;
+ public P3[] vertices;
+ public int[][] faces;
int nVertices;
- boolean visible;
- private final V3[] normals;
+ boolean collapsed = false;
+ private BS bsFlat;
+
+ private V3[] normals;
private short[] normixes;
- public int[][] faces;
- public int visibilityFlags = 0;
- boolean collapsed = false;
- float faceCenterOffset, distanceFactor, planarParam;
+ public String smiles, smarts;
+ private SymmetryInterface pointGroup;
+ private Float volume;
+
+ boolean visible = true;
boolean isFullyLit;
public boolean isValid = true;
public short colixEdge = C.INHERIT_ALL;
- public String smiles, smarts;
- private SymmetryInterface pointGroup;
- Float volume;
- private BS bsFlat;
+ public int visibilityFlags = 0;
- Polyhedron(Atom centralAtom, int nVertices, int nPoints, int planeCount,
- P3[] otherAtoms, V3[] normals, BS bsFlat, int[][] planes,
- boolean collapsed, float faceCenterOffset, float distanceFactor,
- float planarParam) {
+ Polyhedron() {
+ }
+
+ Polyhedron set(Atom centralAtom, int nVertices, int nPoints, int planeCount,
+ P3[] otherAtoms, V3[] normals, BS bsFlat, int[][] planes, boolean
collapsed) {
this.centralAtom = centralAtom;
modelIndex = centralAtom.mi;
this.nVertices = nVertices;
this.vertices = new P3[nPoints + 1];
- this.visible = true;
this.normals = new V3[planeCount];
this.bsFlat = bsFlat;
this.faces = AU.newInt2(planeCount);
@@ -58,38 +66,98 @@
for (int i = planeCount; --i >= 0;)
this.faces[i] = planes[i];
this.collapsed = collapsed;
- this.faceCenterOffset = faceCenterOffset;
- this.distanceFactor = distanceFactor;
- this.planarParam = planarParam;
+ return this;
}
- Map<String, Object> getInfo(Viewer vwr) {
+ Map<String, Object> info;
+
+ Map<String, Object> getInfo(Viewer vwr, boolean isAll) {
+ if (isAll && this.info != null)
+ return this.info;
Map<String, Object> info = new Hashtable<String, Object>();
- Object energy = vwr.ms.getInfo(centralAtom.mi, "Energy");
- if (energy != null)
- info.put("energy", energy);
- info.put("modelIndex", Integer.valueOf(centralAtom.mi));
- info.put("modelNumber", Integer.valueOf(centralAtom.getModelNumber()));
- info.put("center", P3.newP(centralAtom));
+ if (isAll) {
+ this.info = info;
+ info.put("modelIndex", Integer.valueOf(centralAtom.mi));
+ info.put("modelNumber", Integer.valueOf(centralAtom.getModelNumber()));
+ info.put("center", P3.newP(centralAtom));
+ info.put("atomNumber", Integer.valueOf(centralAtom.getAtomNumber()));
+ info.put("atomName", centralAtom.getInfo());
+ info.put("element", centralAtom.getElementSymbol());
+ info.put("vertexCount", Integer.valueOf(nVertices));
+ info.put("faceCount", Integer.valueOf(faces.length));
+ info.put("volume", getVolume());
+ if (smarts != null)
+ info.put("smarts", smarts);
+ if (smiles != null)
+ info.put("smiles", smiles);
+ if (pointGroup != null)
+ info.put("pointGroup", pointGroup.getPointGroupName());
+ Object energy = vwr.ms.getInfo(centralAtom.mi, "Energy");
+ if (energy != null)
+ info.put("energy", energy);
+ } else {
+ info.put("bsFlat", bsFlat);
+ if (collapsed)
+ info.put("collapsed", Boolean.valueOf(collapsed));
+ info.put("ptRef", vertices[nVertices]);
+ }
info.put("atomIndex", Integer.valueOf(centralAtom.i));
- info.put("atomNumber", Integer.valueOf(centralAtom.getAtomNumber()));
- info.put("atomName", centralAtom.getInfo());
- info.put("element", centralAtom.getElementSymbol());
- info.put("vertexCount", Integer.valueOf(nVertices));
info.put("vertices", AU.arrayCopyPt(vertices, nVertices));
- info.put("faceCount", Integer.valueOf(faces.length));
info.put("faces", AU.arrayCopyII(faces, faces.length));
- info.put("volume", getVolume());
- if (smarts != null)
- info.put("smarts", smarts);
- if (smiles != null)
- info.put("smiles", smiles);
- if (pointGroup != null)
- info.put("pointGroup", pointGroup.getPointGroupName());
+ int[] elemNos = new int[nVertices];
+ for (int i = 0; i < nVertices; i++) {
+ P3 pt = vertices[i];
+ elemNos[i] = (pt instanceof Node ? ((Node) pt).getElementNumber()
+ : pt instanceof Point3fi ? ((Point3fi) pt).sD : -2);
+ }
+ info.put("elemNos", elemNos);
return info;
}
+ Polyhedron setInfo(Map<String, SV> info, Atom[] at) {
+ try {
+ centralAtom = at[info.get("atomIndex").intValue];
+ modelIndex = centralAtom.mi;
+ Lst<SV> lst = info.get("vertices").getList();
+ vertices = new P3[lst.size() + 1];
+ nVertices = vertices.length - 1;
+ for (int i = nVertices; --i >= 0;)
+ vertices[i] = SV.ptValue(lst.get(i));
+ lst = info.get("elemNos").getList();
+ for (int i = nVertices; --i >= 0;) {
+ int n = lst.get(i).intValue;
+ if (n > 0) {
+ Point3fi p = new Point3fi();
+ p.setT(vertices[i]);
+ p.sD = (short) n;
+ vertices[i] = p;
+ }
+ }
+ vertices[nVertices] = SV.ptValue(info.get("ptRef"));
+ lst = info.get("faces").getList();
+ faces = AU.newInt2(lst.size());
+ normals = new V3[faces.length];
+ V3 vAB = new V3();
+ for (int i = faces.length; --i >= 0;) {
+ Lst<SV> lst2 = lst.get(i).getList();
+ int[] a = new int[lst2.size()];
+ for (int j = a.length; --j >= 0;)
+ a[j] = lst2.get(j).intValue;
+ faces[i] = a;
+ normals[i] = new V3();
+ Measure.getNormalThroughPoints(vertices[a[0]], vertices[a[1]],
+ vertices[a[2]], normals[i], vAB);
+ }
+ bsFlat = SV.getBitSet(info.get("bsFlat"), false);
+ collapsed = info.containsKey("collapsed");
+ } catch (Exception e) {
+ return null;
+ }
+ return this;
+ }
+
void getSymmetry(Viewer vwr, boolean withPointGroup) {
+ info = null;
SmilesMatcherInterface sm = vwr.getSmilesMatcher();
try {
if (smarts == null) {
@@ -138,23 +206,14 @@
return vAC.dot(vTemp);
}
- String getState() {
- P3 ptemp = new P3();
- String s = "({" + centralAtom.i + "}) TO [";
- for (int i = 0; i < nVertices; i++) {
- ptemp.setT(vertices[i]);
- s += ptemp;
- }
- s += "]";
- return " polyhedra " + s + (collapsed ? " collapsed" : "")
- + " distanceFactor " + distanceFactor + " faceCenterOffset "
- + faceCenterOffset
- // + " planarParam " + planarParam
+ String getState(Viewer vwr) {
+ return " var p = " + Escape.e(getInfo(vwr, false)) + ";polyhedron @p"
+ (isFullyLit ? " fullyLit" : "") + ";"
- + (visible ? "" : "polyhedra off;") + "\n";
+ + (visible ? "" : "polyhedra ({"+centralAtom.i+"}) off;") + "\n";
}
public void move(M4 mat) {
+ info = null;
for (int i = 0; i < nVertices; i++) {
P3 p = vertices[i];
if (p instanceof Atom)
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java 2015-07-08 16:15:03 UTC
(rev 20645)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java 2015-07-09 04:37:42 UTC
(rev 20646)
@@ -276,8 +276,6 @@
* @param atoms
* @param ac
* @param bsSelected
- * @param isSmarts
- * @param firstMatchOnly
* @return BitSet indicating which atoms match the pattern.
*/
@@ -340,8 +338,6 @@
* @param ac
* @param bsSelected
* @param bsAromatic
- * @param isSmarts
- * @param firstMatchOnly
* @return BitSet Array indicating which atoms match the pattern.
* @throws Exception
*/
@@ -409,10 +405,7 @@
* @param pattern
* SMILES or SMARTS pattern.
* @param atoms
- * @param ac
* @param bsSelected
- * @param isSmarts
- * @param firstMatchOnly
* @return a set of atom correlations
*
*/
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-07-08 16:15:03 UTC
(rev 20645)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-07-09 04:37:42 UTC
(rev 20646)
@@ -46,10 +46,16 @@
such that any call to yyy outside of the SPT sees those variable "xxx"?
-there is something wrong with JSmol and zoneDemo. Just slow? or
+TODO: there is something wrong with JSmol and zoneDemo. Just slow? or what?
-Jmol.___JmolVersion="14.3.15_2015.07.08"
+Jmol.___JmolVersion="14.3.15_2015.07.08c"
+bug fix: load files "xxx.png|xxxx" "xxx.png|zzzz" not read from state properly
+bug fix: polyhedra not saved in state property
+bug fix: moving atoms with 4x4 matrix not saved in state
+bug fix: moving of an atom having a polyhedron fails to move the polyhedron as
well
+
+
new feature: smiles2.find("SMILES",smiles1, asMap, allMappings)
-- asMap = TRUE (default false) indicates you want an atom
correlation map indicating positions in smiles2 corresponding to smiles1
@@ -71,8 +77,6 @@
select {1.1}
rotateselected @mat
-bug fix: moving of an atom having a polyhedron fails to move the polyhedron as
well
-
JmolVersion="14.3.15_2015.07.07c"
bug fix: x.getProperty("[select name where composition[1] == 0.5]")
Modified: trunk/Jmol/src/org/jmol/viewer/StateCreator.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2015-07-08 16:15:03 UTC
(rev 20645)
+++ trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2015-07-09 04:37:42 UTC
(rev 20646)
@@ -570,23 +570,25 @@
}
commands.append("# frame state;\n");
commands.append("# modelCount ").appendI(modelCount).append(";\n# first ")
- .append(vwr.getModelNumberDotted(0)).append(";\n# last ").append(
- vwr.getModelNumberDotted(modelCount - 1)).append(";\n");
+ .append(vwr.getModelNumberDotted(0)).append(";\n# last ")
+ .append(vwr.getModelNumberDotted(modelCount - 1)).append(";\n");
if (am.backgroundModelIndex >= 0)
- app(commands, "set backgroundModel "
- + vwr.getModelNumberDotted(am.backgroundModelIndex));
+ app(commands,
+ "set backgroundModel "
+ + vwr.getModelNumberDotted(am.backgroundModelIndex));
if (vwr.tm.bsFrameOffsets != null) {
app(commands, "frame align " + Escape.eBS(vwr.tm.bsFrameOffsets));
} else if (vwr.ms.translations != null) {
for (int i = modelCount; --i >= 0;) {
P3 t = (vwr.ms.getTranslation(i));
if (t != null)
- app(commands, "frame " + vwr.ms.getModelNumberDotted(i) + " align "
+ t);
+ app(commands, "frame " + vwr.ms.getModelNumberDotted(i) + " align "
+ + t);
}
}
- app(commands, "frame RANGE "
- + am.getModelSpecial(AnimationManager.FRAME_FIRST) + " "
- + am.getModelSpecial(AnimationManager.FRAME_LAST));
+ app(commands,
+ "frame RANGE " + am.getModelSpecial(AnimationManager.FRAME_FIRST) + " "
+ + am.getModelSpecial(AnimationManager.FRAME_LAST));
app(commands, "animation DIRECTION "
+ (am.animationDirection == 1 ? "+1" : "-1"));
app(commands, "animation FPS " + am.animationFps);
@@ -601,9 +603,10 @@
app(commands, "frame " + (i + 1));
showModel = (am.cmi != am.modelIndexForFrame(i));
}
- if (showModel)
- app(commands, "model "
- + am.getModelSpecial(AnimationManager.MODEL_CURRENT));
+ if (showModel) {
+ String s = am.getModelSpecial(AnimationManager.MODEL_CURRENT);
+ app(commands, s.equals("0") ? "frame *" : "model " + s);
+ }
app(commands, "animation "
+ (!am.animationOn ? "OFF" : am.currentDirection == 1 ? "PLAY"
: "PLAYREV"));
Modified:
trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/console/ConsoleTextArea.java
===================================================================
---
trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/console/ConsoleTextArea.java
2015-07-08 16:15:03 UTC (rev 20645)
+++
trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/console/ConsoleTextArea.java
2015-07-09 04:37:42 UTC (rev 20646)
@@ -23,14 +23,15 @@
*/
package org.openscience.jmol.app.jmolpanel.console;
+import java.io.BufferedReader;
+import java.io.IOException;
import java.io.InputStream;
+import java.io.InputStreamReader;
import java.io.PrintStream;
-import java.io.InputStreamReader;
-import java.io.BufferedReader;
-import java.io.IOException;
+
+import javax.swing.JOptionPane;
import javax.swing.JTextArea;
-import javax.swing.JOptionPane;
-import javax.swing.text.Document;
+
import org.jmol.i18n.GT;
import org.openscience.jmol.app.jmolpanel.LoopedStreams;
@@ -73,16 +74,16 @@
StringBuilder sb = new StringBuilder();
try {
String s;
- Document doc = getDocument();
+ //Document doc = getDocument();
s = br.readLine();
while (s != null) {
- boolean caretAtEnd = false;
- caretAtEnd = (getCaretPosition() == doc.getLength());
+ //boolean caretAtEnd = false;
+ //caretAtEnd = (getCaretPosition() == doc.getLength());
sb.setLength(0);
append(sb.append(s).append('\n').toString());
- if (caretAtEnd) {
- setCaretPosition(doc.getLength());
- }
+ //if (caretAtEnd) {
+ //setCaretPosition(doc.getLength());
+ //}
s = br.readLine();
}
} catch (IOException e) {
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