Revision: 18356
http://sourceforge.net/p/jmol/code/18356
Author: hansonr
Date: 2013-06-23 16:34:18 +0000 (Sun, 23 Jun 2013)
Log Message:
-----------
fixing recently broken write IMAGE width height TYPE quality...
Preliminary org.jmol.util.Modulation
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/quantum/GaussianReader.java
trunk/Jmol/src/org/jmol/adapter/readers/quantum/NWChemReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
trunk/Jmol/src/org/jmol/modelset/Atom.java
trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
trunk/Jmol/src/org/jmol/renderspecial/VectorsRenderer.java
trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
trunk/Jmol/src/org/jmol/util/P3.java
trunk/Jmol/src/org/jmol/viewer/ActionManager.java
trunk/Jmol/src/org/jmol/viewer/JC.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
trunk/Jmol/src/org/jmol/viewer/ShapeManager.java
trunk/Jmol/src/org/jmol/viewer/TransformManager.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Added Paths:
-----------
trunk/Jmol/src/org/jmol/util/Modulation.java
trunk/Jmol/src/org/jmol/util/Vibration.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/quantum/GaussianReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/quantum/GaussianReader.java
2013-06-20 15:05:19 UTC (rev 18355)
+++ trunk/Jmol/src/org/jmol/adapter/readers/quantum/GaussianReader.java
2013-06-23 16:34:18 UTC (rev 18356)
@@ -38,6 +38,7 @@
import org.jmol.api.JmolAdapter;
import org.jmol.util.ArrayUtil;
+import org.jmol.util.BS;
import org.jmol.util.Escape;
import org.jmol.util.Logger;
import org.jmol.util.Parser;
@@ -78,6 +79,7 @@
private int stepNumber;
private int moModelSet = -1;
+ private BS namedSets = new BS();
/**
@@ -216,7 +218,7 @@
energyString = tokens[2] + " " + tokens[3];
// now set the names for the last equivalentAtomSets
atomSetCollection.setAtomSetNames(energyKey + " = " + energyString,
- equivalentAtomSets);
+ equivalentAtomSets, namedSets);
// also set the properties for them
atomSetCollection.setAtomSetPropertyForSets(energyKey, energyString,
equivalentAtomSets);
@@ -242,7 +244,7 @@
String tokens[] = getTokens();
energyKey = "Energy";
energyString = tokens[1];
- atomSetCollection.setAtomSetNames("Energy = "+tokens[1],
equivalentAtomSets);
+ atomSetCollection.setAtomSetNames("Energy = "+tokens[1],
equivalentAtomSets, namedSets);
atomSetCollection.setAtomSetEnergy(energyString,
parseFloatStr(energyString));
}
@@ -280,7 +282,8 @@
// this is needed for the last structure in an optimization
// if energy information is found for this structure the reader
// will overwrite this setting later.
- atomSetCollection.setAtomSetName(energyKey + " = " + energyString);
+ if (energyKey.length() != 0)
+ atomSetCollection.setAtomSetName(energyKey + " = " + energyString);
atomSetCollection.setAtomSetEnergy(energyString,
parseFloatStr(energyString));
// atomSetCollection.setAtomSetName("Last read atomset.");
String path = getTokens()[0]; // path = type of orientation
@@ -628,7 +631,9 @@
continue;
atomSetCollection.cloneLastAtomSet();
// set the properties
- atomSetCollection.setAtomSetFrequency("Calculation " +
calculationNumber, symmetries[i], frequencies[i], null);
+ String name = atomSetCollection.setAtomSetFrequency("Calculation " +
calculationNumber, symmetries[i], frequencies[i], null);
+ appendLoadNote("model " + atomSetCollection.getAtomSetCount() + ": " +
name);
+ namedSets.set(atomSetCollection.getCurrentAtomSetIndex());
atomSetCollection.setAtomSetModelProperty("ReducedMass",
red_masses[i]+" AMU");
atomSetCollection.setAtomSetModelProperty("ForceConstant",
Modified: trunk/Jmol/src/org/jmol/adapter/readers/quantum/NWChemReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/quantum/NWChemReader.java
2013-06-20 15:05:19 UTC (rev 18355)
+++ trunk/Jmol/src/org/jmol/adapter/readers/quantum/NWChemReader.java
2013-06-23 16:34:18 UTC (rev 18356)
@@ -218,7 +218,7 @@
atomSetCollection.setAtomSetPropertyForSets(energyKey, energyValue,
equivalentAtomSets);
atomSetCollection.setAtomSetNames(energyKey + " = " + energyValue,
- equivalentAtomSets);
+ equivalentAtomSets, null);
atomSetCollection.setAtomSetEnergy(value, parseFloatStr(value));
haveEnergy = true;
}
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
2013-06-20 15:05:19 UTC (rev 18355)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
2013-06-23 16:34:18 UTC (rev 18356)
@@ -1695,6 +1695,7 @@
setTrajectoryName(atomSetName);
return;
}
+ System.out.println(currentAtomSetIndex + " " + atomSetName);
setAtomSetAuxiliaryInfoForSet("name", atomSetName, currentAtomSetIndex);
// TODO -- trajectories could have different names. Need this for
vibrations?
if (!allowMultiple)
@@ -1719,10 +1720,12 @@
* The name
* @param n
* The number of last AtomSets that needs these set
+ * @param namedSets
*/
- public void setAtomSetNames(String atomSetName, int n) {
- for (int idx = currentAtomSetIndex; --n >= 0 && idx >= 0; --idx)
- setAtomSetAuxiliaryInfoForSet("name", atomSetName, idx);
+ public void setAtomSetNames(String atomSetName, int n, BS namedSets) {
+ for (int i = currentAtomSetIndex; --n >= 0 && i >= 0; --i)
+ if (namedSets == null || !namedSets.get(i))
+ setAtomSetAuxiliaryInfoForSet("name", atomSetName, i);
}
/**
@@ -1919,15 +1922,17 @@
setAtomSetModelProperty("Energy", "" + value);
}
- public void setAtomSetFrequency(String pathKey, String label, String freq,
String units) {
+ public String setAtomSetFrequency(String pathKey, String label, String freq,
String units) {
freq += " " + (units == null ? "cm^-1" : units);
- setAtomSetName((label == null ? "" : label + " ") + freq);
+ String name = (label == null ? "" : label + " ") + freq;
+ setAtomSetName(name);
setAtomSetModelProperty("Frequency", freq);
if (label != null)
setAtomSetModelProperty("FrequencyLabel", label);
setAtomSetModelProperty(SmarterJmolAdapter.PATH_KEY, (pathKey == null ? ""
: pathKey + SmarterJmolAdapter.PATH_SEPARATOR + "Frequencies")
+ "Frequencies");
+ return name;
}
void toCartesian(SymmetryInterface symmetry) {
Modified: trunk/Jmol/src/org/jmol/modelset/Atom.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Atom.java 2013-06-20 15:05:19 UTC (rev
18355)
+++ trunk/Jmol/src/org/jmol/modelset/Atom.java 2013-06-23 16:34:18 UTC (rev
18356)
@@ -1053,7 +1053,7 @@
}
public V3 getVibrationVector() {
- return group.chain.model.modelSet.getVibrationVector(index, false);
+ return group.chain.model.modelSet.getVibration(index, false);
}
public float getVibrationCoord(char ch) {
Modified: trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2013-06-20
15:05:19 UTC (rev 18355)
+++ trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2013-06-23
16:34:18 UTC (rev 18356)
@@ -56,6 +56,7 @@
import org.jmol.util.Parser;
import org.jmol.util.Rectangle;
import org.jmol.util.V3;
+import org.jmol.util.Vibration;
import org.jmol.util.Measure;
import org.jmol.util.Quaternion;
@@ -84,7 +85,7 @@
atomNames = null;
atomTypes = null;
atomSerials = null;
- vibrationVectors = null;
+ vibrations = null;
occupancies = null;
bfactor100s = null;
partialCharges = null;
@@ -97,7 +98,7 @@
atomNames = mergeModelSet.atomNames;
atomTypes = mergeModelSet.atomTypes;
atomSerials = mergeModelSet.atomSerials;
- vibrationVectors = mergeModelSet.vibrationVectors;
+ vibrations = mergeModelSet.vibrations;
occupancies = mergeModelSet.occupancies;
bfactor100s = mergeModelSet.bfactor100s;
ionicRadii = mergeModelSet.ionicRadii;
@@ -145,7 +146,7 @@
String[] atomNames;
String[] atomTypes;
int[] atomSerials;
- public V3[] vibrationVectors;
+ public Vibration[] vibrations;
byte[] occupancies;
short[] bfactor100s;
float[] partialCharges;
@@ -158,7 +159,7 @@
protected boolean haveStraightness;
public boolean modelSetHasVibrationVectors(){
- return (vibrationVectors != null);
+ return (vibrations != null);
}
public String[] getAtomTypes() {
@@ -672,39 +673,36 @@
}
public float getVibrationCoord(int atomIndex, char c) {
- if (vibrationVectors == null || vibrationVectors[atomIndex] == null)
+ if (vibrations == null || vibrations[atomIndex] == null)
return 0;
switch (c) {
case 'X':
- return vibrationVectors[atomIndex].x;
+ return vibrations[atomIndex].x;
case 'Y':
- return vibrationVectors[atomIndex].y;
+ return vibrations[atomIndex].y;
default:
- return vibrationVectors[atomIndex].z;
+ return vibrations[atomIndex].z;
}
}
- public V3 getVibrationVector(int atomIndex, boolean forceNew) {
- V3 v = (vibrationVectors == null ? null : vibrationVectors[atomIndex]);
- return (v == null && forceNew ? new V3() : v);
+ public Vibration getVibration(int atomIndex, boolean forceNew) {
+ Vibration v = (vibrations == null ? null : vibrations[atomIndex]);
+ return (v == null && forceNew ? new Vibration() : v);
}
protected void setVibrationVector(int atomIndex, float x, float y, float z) {
if (Float.isNaN(x) || Float.isNaN(y) || Float.isNaN(z))
return;
- if (vibrationVectors == null || vibrationVectors.length < atomIndex)
- vibrationVectors = new V3[atoms.length];
- if (vibrationVectors[atomIndex] == null)
- vibrationVectors[atomIndex] = V3.new3(x, y, z);
- else
- vibrationVectors[atomIndex].set(x, y, z);
+ if (vibrations == null || vibrations.length < atomIndex)
+ vibrations = new Vibration[atoms.length];
+ if (vibrations[atomIndex] == null)
+ vibrations[atomIndex] = new Vibration();
+ vibrations[atomIndex].set(x, y, z);
atoms[atomIndex].setVibrationVector();
}
private void setVibrationVector2(int atomIndex, int tok, float fValue) {
- V3 v = getVibrationVector(atomIndex, true);
- if (v == null)
- v = new V3();
+ Vibration v = getVibration(atomIndex, true);
switch(tok) {
case T.vibx:
v.x = fValue;
@@ -2519,7 +2517,7 @@
firstAtomIndex, nAtoms);
ellipsoids = (Quadric[][]) ArrayUtil.deleteElements(ellipsoids,
firstAtomIndex, nAtoms);
- vibrationVectors = (V3[]) ArrayUtil.deleteElements(vibrationVectors,
+ vibrations = (Vibration[]) ArrayUtil.deleteElements(vibrations,
firstAtomIndex, nAtoms);
nSurfaceAtoms = 0;
bsSurface = null;
Modified: trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2013-06-20
15:05:19 UTC (rev 18355)
+++ trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2013-06-23
16:34:18 UTC (rev 18356)
@@ -66,6 +66,7 @@
import org.jmol.util.TextFormat;
import org.jmol.util.TriangleData;
import org.jmol.util.V3;
+import org.jmol.util.Vibration;
import org.jmol.viewer.JC;
import org.jmol.viewer.ShapeManager;
import org.jmol.io.OutputStringBuilder;
@@ -1499,10 +1500,10 @@
}
public boolean modelHasVibrationVectors(int modelIndex) {
- if (vibrationVectors != null)
+ if (vibrations != null)
for (int i = atomCount; --i >= 0;)
if ((modelIndex < 0 || atoms[i].modelIndex == modelIndex)
- && vibrationVectors[i] != null && vibrationVectors[i].length() > 0)
+ && vibrations[i] != null && vibrations[i].length() > 0)
return true;
return false;
}
@@ -3079,9 +3080,9 @@
m.firstAtomIndex = i;
m.bsAtoms.set(i);
}
- if (vibrationVectors != null)
+ if (vibrations != null)
for (int i = i0; i < atomCount; i++)
- vibrationVectors[i] = vibrationVectors[map[i]];
+ vibrations[i] = vibrations[map[i]];
if (occupancies != null)
for (int i = i0; i < atomCount; i++)
occupancies[i] = occupancies[map[i]];
@@ -3107,8 +3108,8 @@
protected void growAtomArrays(int newLength) {
atoms = (Atom[]) ArrayUtil.arrayCopyObject(atoms, newLength);
- if (vibrationVectors != null)
- vibrationVectors = (V3[]) ArrayUtil.arrayCopyObject(vibrationVectors,
+ if (vibrations != null)
+ vibrations = (Vibration[]) ArrayUtil.arrayCopyObject(vibrations,
newLength);
if (occupancies != null)
occupancies = ArrayUtil.arrayCopyByte(occupancies, newLength);
Modified: trunk/Jmol/src/org/jmol/renderspecial/VectorsRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/renderspecial/VectorsRenderer.java 2013-06-20
15:05:19 UTC (rev 18355)
+++ trunk/Jmol/src/org/jmol/renderspecial/VectorsRenderer.java 2013-06-23
16:34:18 UTC (rev 18356)
@@ -35,11 +35,11 @@
import org.jmol.util.P3;
import org.jmol.util.P3i;
import org.jmol.util.V3;
+import org.jmol.util.Vibration;
public class VectorsRenderer extends ShapeRenderer {
private final static float arrowHeadOffset = -0.2f;
- private final V3 vector2 = new V3();
private final P3 pointVectorEnd = new P3();
private final P3 pointArrowHead = new P3();
private final P3i screenVectorEnd = new P3i();
@@ -53,6 +53,7 @@
private boolean vectorSymmetry;
private float headScale;
private boolean doShaft;
+ private Vibration vibTemp;
@Override
@@ -73,7 +74,7 @@
Atom atom = atoms[i];
if (!atom.isVisible(myVisibilityFlag))
continue;
- V3 vibrationVector = viewer.getVibrationVector(i);
+ Vibration vibrationVector = viewer.getVibration(i);
if (vibrationVector == null)
continue;
if (!transform(mads[i], atom, vibrationVector))
@@ -84,16 +85,18 @@
}
renderVector(atom);
if (vectorSymmetry) {
- vector2.setT(vibrationVector);
- vector2.scale(-1);
- transform(mads[i], atom, vector2);
+ if (vibTemp == null)
+ vibTemp = new Vibration();
+ vibTemp.setT(vibrationVector);
+ vibTemp.scale(-1);
+ transform(mads[i], atom, vibTemp);
renderVector(atom);
}
}
return needTranslucent;
}
- private boolean transform(short mad, Atom atom, V3 vibrationVector) {
+ private boolean transform(short mad, Atom atom, Vibration vibrationVector) {
float len = vibrationVector.length();
// to have the vectors move when vibration is turned on
if (Math.abs(len * vectorScale) < 0.01)
Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-06-20 15:05:19 UTC
(rev 18355)
+++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-06-23 16:34:18 UTC
(rev 18356)
@@ -11065,17 +11065,15 @@
}
private void delete() throws ScriptException {
- if (slen == 1) {
- zap(true);
- return;
- }
if (tokAt(1) == T.dollarsign) {
setObjectProperty();
return;
}
- BS bs = atomExpression(st, 1, 0, true, false, true, false);
+ BS bs = (slen == 1 ? null : atomExpression(st, 1, 0, true, false, true,
false));
if (chk)
return;
+ if (bs == null)
+ bs = viewer.getModelUndeletedAtomsBitSet(-1);
int nDeleted = viewer.deleteAtoms(bs, false);
if (!(tQuiet || scriptLevel > scriptReportingLevel))
scriptStatusOrBuffer(GT._("{0} atoms deleted", nDeleted));
@@ -14707,14 +14705,13 @@
isExport = true;
if (isCommand)
fileName = "Jmol." + type.toLowerCase();
- } else if (type.equals("ZIP")) {
+ break;
+ } else if (type.equals("ZIP") || type.equals("ZIPALL")) {
pt++;
- } else if (type.equals("ZIPALL")) {
- pt++;
+ break;
} else {
type = "(image)";
}
- break;
}
if (tokAtArray(pt, args) == T.integer) {
width = SV.iValue(tokenAt(pt++, args));
Modified: trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2013-06-20
15:05:19 UTC (rev 18355)
+++ trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2013-06-23
16:34:18 UTC (rev 18356)
@@ -1072,6 +1072,17 @@
}
+ /**
+ *
+ * {xxx}.symop()
+ *
+ * symop({xxx}
+ *
+ * @param args
+ * @param haveBitSet
+ * @return true/false
+ * @throws ScriptException
+ */
private boolean evaluateSymop(SV[] args, boolean haveBitSet)
throws ScriptException {
if (args.length == 0)
Added: trunk/Jmol/src/org/jmol/util/Modulation.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Modulation.java
(rev 0)
+++ trunk/Jmol/src/org/jmol/util/Modulation.java 2013-06-23 16:34:18 UTC
(rev 18356)
@@ -0,0 +1,44 @@
+package org.jmol.util;
+
+/**
+ * A class to allow for more complex vibrations and associated
+ * phenomena, such as modulated crystals.
+ *
+ * @author Bob Hanson hans...@stolaf.edu
+ *
+ */
+
+public class Modulation extends V3 {
+
+ private double ccos;
+ private double csin;
+ private int f; // usually f[0] = 1, f[1] = 2, etc.
+ private V3 wv; // wave vectors
+ private double twoPIx4;
+
+ public static float getPointAndOffset(Modulation[] mods, P3 pt, double t,
double scale) {
+ // f(x4) = x1 + A1 cos(2pi * x4 * t) + B1 sin(2pi * x4 * t)
+ // + A2 cos(2pi * x4 * t * 2) + B2 sin(2pi * x4 * t * 2);
+ // + A3 cos(2pi * x4 * t * 3) + B3 sin(2pi * x4 * t * 3);
+ // however, more generally, we allow any number of independent wave
+ // vectors with any number of orders.
+ // x' = x1 + sum_i[ ccos[i] cos(2pi * x4[i] * f[i] * t)
+ // +csin[i] sin(2pi * x4[i] * f[i] * t) ] * wv[i] *
scale
+ P3 pt0 = P3.newP(pt);
+ for (int i = mods.length; --i >= 0;) {
+ mods[i].addTo(pt, t, scale);
+ }
+ return pt.distance(pt0);
+ }
+
+ private void addTo(P3 pt, double t, double scale) {
+ double theta = t * twoPIx4 * f;
+ double v = 0;
+ if (ccos != 0)
+ v += ccos * Math.cos(theta);
+ if (csin != 0)
+ v += csin * Math.sin(theta);
+ pt.scaleAdd2((float) (v * scale), wv, pt);
+ }
+
+}
Modified: trunk/Jmol/src/org/jmol/util/P3.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/P3.java 2013-06-20 15:05:19 UTC (rev
18355)
+++ trunk/Jmol/src/org/jmol/util/P3.java 2013-06-23 16:34:18 UTC (rev
18356)
@@ -55,7 +55,7 @@
* the other point
* @return the square of distance between these two points as a float
*/
- public final float distanceSquared(P3 p1) {
+ public final float distanceSquared(Tuple3f p1) {
double dx = x - p1.x;
double dy = y - p1.y;
double dz = z - p1.z;
@@ -69,7 +69,7 @@
* the other point
* @return the distance between these two points
*/
- public final float distance(P3 p1) {
+ public final float distance(Tuple3f p1) {
return (float) Math.sqrt(distanceSquared(p1));
}
Added: trunk/Jmol/src/org/jmol/util/Vibration.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Vibration.java (rev 0)
+++ trunk/Jmol/src/org/jmol/util/Vibration.java 2013-06-23 16:34:18 UTC (rev
18356)
@@ -0,0 +1,19 @@
+package org.jmol.util;
+
+/**
+ * A class to allow for more complex vibrations and associated
+ * phenomena, such as modulated crystals.
+ *
+ * @author Bob Hanson hans...@stolaf.edu
+ *
+ */
+
+public class Vibration extends V3 {
+
+ protected final static double twoPI = 2 * Math.PI;
+
+ public void setTempPoint(P3 pt, double t, double scale) {
+ pt.scaleAdd2((float) (Math.cos(t * twoPI) * scale), this, pt);
+ }
+
+}
Modified: trunk/Jmol/src/org/jmol/viewer/ActionManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/ActionManager.java 2013-06-20 15:05:19 UTC
(rev 18355)
+++ trunk/Jmol/src/org/jmol/viewer/ActionManager.java 2013-06-23 16:34:18 UTC
(rev 18356)
@@ -212,6 +212,7 @@
public final static int PICKING_ASSIGN_BOND = 33;
public final static int PICKING_ROTATE_BOND = 34;
public final static int PICKING_IDENTIFY_BOND = 35;
+ public final static int PICKING_DRAG_LIGAND = 36;
@@ -224,7 +225,7 @@
"navigate",
"connect", "struts",
"dragselected", "dragmolecule", "dragatom", "dragminimize",
"dragminimizemolecule",
- "invertstereo", "assignatom", "assignbond", "rotatebond", "identifybond"
+ "invertstereo", "assignatom", "assignbond", "rotatebond", "identifybond",
"dragligand"
};
public final static String getPickingModeName(int pickingMode) {
@@ -704,7 +705,7 @@
if (!isBound(action, ACTION_rotate))
viewer.setRotateBondIndex(-1);
}
- BS bs;
+ BS bs = null;
if (dragAtomIndex >= 0) {
switch (atomPickingMode) {
case PICKING_DRAG_SELECTED:
@@ -719,26 +720,27 @@
Integer.MIN_VALUE, Integer.MIN_VALUE, null, true, false);
}
return;
+ case PICKING_DRAG_LIGAND:
case PICKING_DRAG_MOLECULE:
+ case PICKING_DRAG_MINIMIZE_MOLECULE:
+ bs = viewer.getAtomBits(T.molecule,
BSUtil.newAndSetBit(dragAtomIndex));
+ if (atomPickingMode == PICKING_DRAG_LIGAND)
+ bs.and(viewer.getAtomBitSet("ligand"));
+ //$FALL-THROUGH$
case PICKING_DRAG_ATOM:
case PICKING_DRAG_MINIMIZE:
- case PICKING_DRAG_MINIMIZE_MOLECULE:
if (dragGesture.getPointCount() == 1)
viewer.undoMoveActionClear(dragAtomIndex, AtomCollection.TAINT_COORD,
true);
checkMotion(JC.CURSOR_MOVE);
if (isBound(action, ACTION_rotateSelected)) {
- bs = viewer.getAtomBits(T.molecule, BSUtil
- .newAndSetBit(dragAtomIndex));
viewer.rotateSelected(getDegrees(deltaX, 0), getDegrees(deltaY, 1),
bs);
} else {
- bs = null;
switch (atomPickingMode) {
+ case PICKING_DRAG_LIGAND:
case PICKING_DRAG_MOLECULE:
case PICKING_DRAG_MINIMIZE_MOLECULE:
- bs = viewer.getAtomBits(T.molecule, BSUtil
- .newAndSetBit(dragAtomIndex));
viewer.select(bs, false, 0, true);
break;
}
@@ -1410,6 +1412,7 @@
|| isBound(action, ACTION_dragZ);
break;
case PICKING_DRAG_SELECTED:
+ case PICKING_DRAG_LIGAND:
case PICKING_DRAG_MOLECULE:
isBound = isBound(action, ACTION_dragAtom)
|| isBound(action, ACTION_rotateSelected)
Modified: trunk/Jmol/src/org/jmol/viewer/JC.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/JC.java 2013-06-20 15:05:19 UTC (rev
18355)
+++ trunk/Jmol/src/org/jmol/viewer/JC.java 2013-06-23 16:34:18 UTC (rev
18356)
@@ -784,6 +784,8 @@
"UREA",// 45 urea, a cosolvent
"PO4", // 46 phosphate ions -- from here on is "ligand"
"SO4", // 47 sulphate ions
+ "UNL", // 48 unknown ligand
+
};
@@ -1215,7 +1217,7 @@
"@water _g>=" + GROUPID_WATER + " & _g<" + GROUPID_SOLVENT_MIN
+ ", oxygen & connected(2) & connected(2, hydrogen), (hydrogen) &
connected(oxygen & connected(2) & connected(2, hydrogen))",
"@solvent water, (_g>=" + GROUPID_SOLVENT_MIN + " & _g<" + GROUPID_ION_MAX
+ ")", // water, other solvent or ions
- "@ligand !(_g<"+ GROUPID_ION_MIN + ",protein,nucleic,water)",
+ "@ligand _g=0|!(_g<"+ GROUPID_ION_MIN + ",protein,nucleic,water)", //
includes UNL
// structure
"@turn structure=1",
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-20 15:05:19 UTC
(rev 18355)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-23 16:34:18 UTC
(rev 18356)
@@ -9,11 +9,16 @@
# The quotes above look odd for a parameter file, but they are
# important for the JavaScript version of Jmol.
-___JmolVersion="13.1.17_dev_2013.06.20"
+___JmolVersion="13.1.17_dev_2013.06.21"
TODO: PyMOL uniqueAtomSettings for transparency
-- will require by-vertex translucent option
+new feature: set picking DRAGLIGAND
+ -- won't move the protein
+
+bug fix: "ligand" should include all _g=0 (nonPDB atoms)
+
new feature: isosurface SLAB TRANSLUCENT 0.x color
-- inherits color of isosurface when color parameter is absent
-- TODO - properly save in JVXL file
Modified: trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2013-06-20 15:05:19 UTC
(rev 18355)
+++ trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2013-06-23 16:34:18 UTC
(rev 18356)
@@ -841,7 +841,7 @@
mol.appendC('\n');
for (int j = bsTemp.nextSetBit(0); j >= 0; j = bsTemp.nextSetBit(j +
1))
mol.append(LabelToken.formatLabelAtomArray(viewer, atoms[j],
- (ms.getVibrationVector(j, false) == null ? tokens2 : tokens1),
'\0',
+ (ms.getVibration(j, false) == null ? tokens2 : tokens1), '\0',
null));
}
} else {
@@ -1166,8 +1166,8 @@
info.put("y", Float.valueOf(atom.y));
info.put("z", Float.valueOf(atom.z));
info.put("coord", P3.newP(atom));
- if (ms.vibrationVectors != null && ms.vibrationVectors[i] != null) {
- info.put("vibVector", V3.newV(ms.vibrationVectors[i]));
+ if (ms.vibrations != null && ms.vibrations[i] != null) {
+ info.put("vibVector", V3.newV(ms.vibrations[i]));
}
info.put("bondCount", Integer.valueOf(atom.getCovalentBondCount()));
info.put("radius", Float.valueOf((float) (atom.getRasMolRadius() /
120.0)));
Modified: trunk/Jmol/src/org/jmol/viewer/ShapeManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/ShapeManager.java 2013-06-20 15:05:19 UTC
(rev 18355)
+++ trunk/Jmol/src/org/jmol/viewer/ShapeManager.java 2013-06-23 16:34:18 UTC
(rev 18356)
@@ -48,7 +48,7 @@
import org.jmol.util.P3;
import org.jmol.util.P3i;
import org.jmol.util.SB;
-import org.jmol.util.V3;
+import org.jmol.util.Vibration;
public class ShapeManager {
@@ -434,7 +434,7 @@
}
public int[] transformAtoms() {
- V3[] vibrationVectors = modelSet.vibrationVectors;
+ Vibration[] vibrationVectors = modelSet.vibrations;
Atom[] atoms = modelSet.atoms;
for (int i = bsRenderableAtoms.nextSetBit(0); i >= 0; i =
bsRenderableAtoms.nextSetBit(i + 1)) {
// note that this vibration business is not compatible with
Modified: trunk/Jmol/src/org/jmol/viewer/TransformManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2013-06-20
15:05:19 UTC (rev 18355)
+++ trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2013-06-23
16:34:18 UTC (rev 18356)
@@ -45,6 +45,7 @@
import org.jmol.util.SB;
import org.jmol.util.Tuple3f;
import org.jmol.util.V3;
+import org.jmol.util.Vibration;
import org.jmol.util.Quaternion;
@@ -56,7 +57,6 @@
Viewer viewer;
- final static double twoPI = 2 * Math.PI;
public final static double degreesPerRadian = 180 / Math.PI;
static final int DEFAULT_NAV_FPS = 10;
@@ -956,14 +956,6 @@
+ (isDepth ? depthValue : slabValue));
}
- boolean checkInternalSlab(P3 pt) {
- return (slabPlane != null
- && pt.x * slabPlane.x + pt.y * slabPlane.y + pt.z * slabPlane.z
- + slabPlane.w > 0 || depthPlane != null
- && pt.x * depthPlane.x + pt.y * depthPlane.y + pt.z * depthPlane.z
- + depthPlane.w < 0);
- }
-
/* ***************************************************************
* PERSPECTIVE
****************************************************************/
@@ -1359,7 +1351,7 @@
protected final P3 point3fScreenTemp = new P3();
protected final P3i point3iScreenTemp = new P3i();
- private final P3 point3fVibrationTemp = new P3();
+ private final P3 ptVibTemp = new P3();
public boolean navigating = false;
protected final static int MODE_STANDARD = 0;
@@ -1518,9 +1510,7 @@
if (pointAngstroms.z == Float.MAX_VALUE
|| pointAngstroms.z == -Float.MAX_VALUE)
return transformScreenPoint(pointAngstroms);
- getTemporaryScreenPoint(pointAngstroms);
- if (internalSlab && checkInternalSlab(pointAngstroms))
- point3iScreenTemp.z = 1;
+ getTemporaryScreenPoint(pointAngstroms, (internalSlab ? pointAngstroms :
null));
//if (!(pointAngstroms instanceof Atom))
//System.out.println("pt=" + pointAngstroms + " " + point3iScreenTemp +
" " + Thread.currentThread());
return point3iScreenTemp;
@@ -1554,30 +1544,25 @@
* @return POINTER TO point3iScreenTemp
*/
synchronized P3 transformPointNoClip(P3 pointAngstroms) {
- getTemporaryScreenPoint(pointAngstroms);
+ getTemporaryScreenPoint(pointAngstroms, null);
return point3fScreenTemp;
}
/**
* @param pointAngstroms
- * @param vibrationVector
+ * @param v
* @return POINTER TO TEMPORARY VARIABLE (caution!) point3iScreenTemp
*/
- P3i transformPointVib(P3 pointAngstroms, V3 vibrationVector) {
- point3fVibrationTemp.setT(pointAngstroms);
- if (vibrationOn && vibrationVector != null)
- point3fVibrationTemp.scaleAdd2(vibrationAmplitude, vibrationVector,
- pointAngstroms);
- getTemporaryScreenPoint(point3fVibrationTemp);
- if (internalSlab && checkInternalSlab(pointAngstroms))
- point3iScreenTemp.z = 1;
+ P3i transformPointVib(P3 pointAngstroms, Vibration v) {
+ ptVibTemp.setT(pointAngstroms);
+ if (vibrationOn && v != null)
+ v.setTempPoint(ptVibTemp, vibrationT, vibrationScale);
+ getTemporaryScreenPoint(ptVibTemp, pointAngstroms);
return point3iScreenTemp;
}
public void transformPoint2(P3 pointAngstroms, P3 screen) {
- getTemporaryScreenPoint(pointAngstroms);
- if (internalSlab && checkInternalSlab(pointAngstroms))
- point3fScreenTemp.z = 1;
+ getTemporaryScreenPoint(pointAngstroms, pointAngstroms);
screen.setT(point3fScreenTemp);
}
@@ -2051,9 +2036,8 @@
boolean vibrationOn;
float vibrationPeriod;
public int vibrationPeriodMs;
- private float vibrationAmplitude;
- private float vibrationRadians;
private float vibrationScale;
+ private double vibrationT;
void setVibrationScale(float scale) {
vibrationScale = scale;
@@ -2086,10 +2070,9 @@
}
public void setVibrationT(float t) {
- vibrationRadians = (float) (t * twoPI);
+ vibrationT = t;
if (vibrationScale == 0)
vibrationScale = viewer.global.vibrationScale;
- vibrationAmplitude = (float) Math.cos(vibrationRadians) * vibrationScale;
}
private VibrationThread vibrationThread;
@@ -2412,10 +2395,12 @@
/**
* adjusts the temporary point for perspective and offsets
- * @param pointAngstroms
*
+ * @param pointAngstroms
+ * @param pt0
+ *
*/
- protected void getTemporaryScreenPoint(P3 pointAngstroms) {
+ protected void getTemporaryScreenPoint(P3 pointAngstroms, P3 pt0) {
matrixTransform.transform2(pointAngstroms, point3fScreenTemp);
@@ -2432,12 +2417,11 @@
if (!haveNotifiedNaN && Logger.debugging)
Logger.debug("NaN seen in TransformPoint");
haveNotifiedNaN = true;
- z = 1;
+ z = point3fScreenTemp.z = 1;
} else if (z <= 0) {
// just don't let z go past 1 BH 11/15/06
- z = 1;
+ z = point3fScreenTemp.z = 1;
}
- point3fScreenTemp.z = z;
// x and y are moved inward (generally) relative to 0, which
// is either the fixed rotation center or the navigation center
@@ -2475,7 +2459,6 @@
point3fScreenTemp.y += fixedRotationOffset.y;
break;
}
-
if (Float.isNaN(point3fScreenTemp.x) && !haveNotifiedNaN) {
if (Logger.debugging)
Logger.debug("NaN found in transformPoint ");
@@ -2484,6 +2467,16 @@
point3iScreenTemp.set((int) point3fScreenTemp.x, (int) point3fScreenTemp.y,
(int) point3fScreenTemp.z);
+
+ if (pt0 != null
+ && (slabPlane != null
+ && pt0.x * slabPlane.x + pt0.y * slabPlane.y + pt0.z * slabPlane.z
+ + slabPlane.w > 0
+ || depthPlane != null
+ && pt0.x * depthPlane.x + pt0.y * depthPlane.y + pt0.z
+ * depthPlane.z + depthPlane.w < 0))
+ point3iScreenTemp.z = 1;
+
}
public void unTransformPoint(P3 screenPt, P3 coordPt) {
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-06-20 15:05:19 UTC (rev
18355)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-06-23 16:34:18 UTC (rev
18356)
@@ -113,6 +113,7 @@
import org.jmol.util.SB;
import org.jmol.util.Tuple3f;
import org.jmol.util.V3;
+import org.jmol.util.Vibration;
import org.jmol.util.Measure;
import org.jmol.util.Quaternion;
@@ -1306,7 +1307,7 @@
return transformManager.transformPoint(pointAngstroms);
}
- public P3i transformPtVib(P3 pointAngstroms, V3 vibrationVector) {
+ public P3i transformPtVib(P3 pointAngstroms, Vibration vibrationVector) {
return transformManager.transformPointVib(pointAngstroms, vibrationVector);
}
@@ -8659,8 +8660,8 @@
return modelSet.getBondAtom2(i);
}
- public V3 getVibrationVector(int atomIndex) {
- return modelSet.getVibrationVector(atomIndex, false);
+ public Vibration getVibration(int atomIndex) {
+ return modelSet.getVibration(atomIndex, false);
}
public int getVanderwaalsMar(int i) {
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