Revision: 18391
http://sourceforge.net/p/jmol/code/18391
Author: hansonr
Date: 2013-07-01 15:45:20 +0000 (Mon, 01 Jul 2013)
Log Message:
-----------
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/modelset/Atom.java
trunk/Jmol/src/org/jmol/shapespecial/Ellipsoids.java
trunk/Jmol/src/org/jmol/util/Tensor.java
Modified: trunk/Jmol/src/org/jmol/modelset/Atom.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Atom.java 2013-07-01 15:37:13 UTC (rev
18390)
+++ trunk/Jmol/src/org/jmol/modelset/Atom.java 2013-07-01 15:45:20 UTC (rev
18391)
@@ -292,7 +292,7 @@
public float getADPMinMax(boolean isMax) {
Tensor[] tensors = getTensors();
- return (tensors == null || tensors[0] == null || tensors[0].iType !=
Tensor.TYPE_TEMP? 0 : tensors[0].getFactoredValue(isMax ? 2 : 1));
+ return (tensors == null || tensors[0] == null || tensors[0].iType !=
Tensor.TYPE_ADP? 0 : tensors[0].getFactoredValue(isMax ? 2 : 1));
}
public Tensor[] getTensors() {
Modified: trunk/Jmol/src/org/jmol/shapespecial/Ellipsoids.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Ellipsoids.java 2013-07-01
15:37:13 UTC (rev 18390)
+++ trunk/Jmol/src/org/jmol/shapespecial/Ellipsoids.java 2013-07-01
15:45:20 UTC (rev 18391)
@@ -252,50 +252,53 @@
return false;
}
-// private void setPoints(P3[] points, BS bs) {
-// return;
- // doesn't really work. Just something I was playing with.
-// if (points == null)
-// return;
-// int n = bs.cardinality();
-// if (n < 3)
-// return;
-// P3 ptCenter = new P3();
-// for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1))
-// ptCenter.add(points[i]);
-// ptCenter.scale(1.0f/n);
-// double Sxx = 0, Syy = 0, Szz = 0, Sxy = 0, Sxz = 0, Syz = 0;
-// P3 pt = new P3();
-// for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
-// pt.setT(points[i]);
-// pt.sub(ptCenter);
-// Sxx += (double) pt.x * (double) pt.x;
-// Sxy += (double) pt.x * (double) pt.y;
-// Sxz += (double) pt.x * (double) pt.z;
-// Syy += (double) pt.y * (double) pt.y;
-// Szz += (double) pt.z * (double) pt.z;
-// Syz += (double) pt.y * (double) pt.z;
-// }
-// double[][] N = new double[3][3];
-// N[0][0] = Syy + Szz;
-// N[1][1] = Sxx + Szz;
-// N[2][2] = Sxx + Syy;
-// Eigen eigen = Eigen.newM(N);
-// ellipsoid.setEigen(ptCenter, eigen, 1f / n / 3);
-// }
+ // private void setPoints(P3[] points, BS bs) {
+ // return;
+ // doesn't really work. Just something I was playing with.
+ // if (points == null)
+ // return;
+ // int n = bs.cardinality();
+ // if (n < 3)
+ // return;
+ // P3 ptCenter = new P3();
+ // for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1))
+ // ptCenter.add(points[i]);
+ // ptCenter.scale(1.0f/n);
+ // double Sxx = 0, Syy = 0, Szz = 0, Sxy = 0, Sxz = 0, Syz = 0;
+ // P3 pt = new P3();
+ // for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
+ // pt.setT(points[i]);
+ // pt.sub(ptCenter);
+ // Sxx += (double) pt.x * (double) pt.x;
+ // Sxy += (double) pt.x * (double) pt.y;
+ // Sxz += (double) pt.x * (double) pt.z;
+ // Syy += (double) pt.y * (double) pt.y;
+ // Szz += (double) pt.z * (double) pt.z;
+ // Syz += (double) pt.y * (double) pt.z;
+ // }
+ // double[][] N = new double[3][3];
+ // N[0][0] = Syy + Szz;
+ // N[1][1] = Sxx + Szz;
+ // N[2][2] = Sxx + Syy;
+ // Eigen eigen = Eigen.newM(N);
+ // ellipsoid.setEigen(ptCenter, eigen, 1f / n / 3);
+ // }
-
@Override
public String getShapeState() {
+ JmolStateCreator sc = viewer.getStateCreator();
+ if (sc == null || !isActive())
+ return "";
SB sb = new SB();
- getStateID(sb);
- getStateAtoms(sb);
+ sb.append("\n");
+ if (!simpleEllipsoids.isEmpty())
+ getStateID(sb);
+ if (!atomEllipsoids.isEmpty())
+ getStateAtoms(sb, sc);
return sb.toString();
}
private void getStateID(SB sb) {
- if (!isActive())
- return;
Iterator<Ellipsoid> e = simpleEllipsoids.values().iterator();
V3 v1 = new V3();
while (e.hasNext()) {
@@ -318,40 +321,30 @@
}
}
- private void getStateAtoms(SB sb) {
- JmolStateCreator sc = viewer.getStateCreator();
- if (sc == null)
- return;
- String keyDone = "";
+ private void getStateAtoms(SB sb, JmolStateCreator sc) {
+ BS bsDone = new BS();
+ Map<String, BS> temp = new Hashtable<String, BS>();
+ Map<String, BS> temp2 = new Hashtable<String, BS>();
for (Ellipsoid e : atomEllipsoids.values()) {
- String type = e.tensor.type;
- String key = ";" + type + ";";
- if (keyDone.indexOf(key) >= 0)
+ int iType = e.tensor.iType;
+ if (bsDone.get(iType + 1))
continue;
- Map<String, BS> temp = new Hashtable<String, BS>();
- Map<String, BS> temp2 = new Hashtable<String, BS>();
- boolean isTemp = (e.tensor.iType == Tensor.TYPE_TEMP);
- String cmd = "Ellipsoids set " + Escape.eS(type);
- if (isTemp)
- sb.append(cmd);
+ bsDone.set(iType + 1);
+ boolean isADP = (e.tensor.iType == Tensor.TYPE_ADP);
+ String cmd = (isADP ? null : "Ellipsoids set " +
Escape.eS(e.tensor.type));
for (Ellipsoid e2 : atomEllipsoids.values()) {
- if (e2.tensor.type.equals(type)) {
- int i = e2.tensor.atomIndex1;
- // YES -- "e.percent" here, not "e2.percent" because there is one
and
- // only one setting for thermal ellipsoid percent
- String script = (isTemp ? "Ellipsoids " + e.percent : cmd + " scale
" + e2.scale);
- if (!isTemp && e2.isOn)
- script += " ON";
- BSUtil.setMapBitSet(temp, i, i, script);
- if (e2.colix != C.INHERIT_ALL) {
- BSUtil.setMapBitSet(temp2, i, i, getColorCommand(cmd, e2.pid,
- e2.colix, translucentAllowed));
- }
- }
+ if (e2.tensor.iType != iType || isADP && !e2.isOn)
+ continue;
+ int i = e2.tensor.atomIndex1;
+ //
+ BSUtil.setMapBitSet(temp, i, i, (isADP ? "Ellipsoids " + e2.percent
+ : cmd + " scale " + e2.scale + (e2.isOn ? " ON" : " OFF")));
+ if (e2.colix != C.INHERIT_ALL)
+ BSUtil.setMapBitSet(temp2, i, i, getColorCommand(cmd, e2.pid,
+ e2.colix, translucentAllowed));
}
- sb.append(sc.getCommands(temp, temp2, "select"));
- keyDone += key;
}
+ sb.append(sc.getCommands(temp, temp2, "select"));
}
@Override
Modified: trunk/Jmol/src/org/jmol/util/Tensor.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Tensor.java 2013-07-01 15:37:13 UTC (rev
18390)
+++ trunk/Jmol/src/org/jmol/util/Tensor.java 2013-07-01 15:45:20 UTC (rev
18391)
@@ -35,7 +35,7 @@
// factors that give reasonable first views of ellipsoids.
- private static final float TEMPERATURE_FACTOR = (float) (Math.sqrt(0.5) /
Math.PI);
+ private static final float ADP_FACTOR = (float) (Math.sqrt(0.5) / Math.PI);
private static final float MAGNETIC_SUSCEPTIBILITY_FACTOR = 0.01f;
private static final float ELECTRIC_FIELD_GRADIENT_FACTOR = 1f;
private static final float BORN_EFFECTIVE_CHARGE_FACTOR = 1f;
@@ -50,11 +50,11 @@
// type is an identifier that the reader/creator delivers:
//
- // temp -- crystallographic displacement parameters
- // - "temperature factors"; t.forThermalEllipsoid = true
+ // adp -- crystallographic displacement parameters
+ // - "erature factors"; t.forThermalEllipsoid = true
// - either anisotropic (ADP) or isotropic (IDP)
// iso -- isotropic displacement parameters; from
org.jmol.symmetry.UnitCell
- // - changed to "temp" after setting t.isIsotropic = true
+ // - changed to "adp" after setting t.isIsotropic = true
// ms -- magnetic susceptibility
// isc -- NMR interaction tensors
// - will have both atomIndex1 and atomIndex2 defined when
@@ -63,17 +63,18 @@
// TLS-U -- Translation/Libration/Skew tensor (anisotropic)
// TLS-R -- Translation/Libration/Skew tensor (residual)
- private static final String KNOWN_TYPES =
";iso....;temp...;tls-u..;tls-r..;ms.....;efg....;isc....;charge.;";
+ private static final String KNOWN_TYPES =
";iso....;adp....;tls-u..;tls-r..;ms.....;efg....;isc....;charge.;";
private static int getType(String type) {
int pt = KNOWN_TYPES.indexOf(";" + type.toLowerCase() + ".");
return (pt < 0 ? TYPE_OTHER : pt / 8);
}
// these may be augmented, but the order should be kept the same within this
list
-
+ // no types < -1, because these are used in Ellipsoids.getAtomState() as
bs.get(iType + 1)
+
public static final int TYPE_OTHER = -1;
public static final int TYPE_ISO = 0;
- public static final int TYPE_TEMP = 1;
+ public static final int TYPE_ADP = 1;
public static final int TYPE_TLS_U = 2;
public static final int TYPE_TLS_R = 3;
public static final int TYPE_MS = 4;
@@ -325,8 +326,8 @@
mat[1][2] = mat[2][1] = coefs[5] / 2; //YZ
Eigen.getUnitVectors(mat, t.eigenVectors, t.eigenValues);
sortAndNormalize(t.eigenVectors, t.eigenValues);
- t.typeFactor = TEMPERATURE_FACTOR;
- return t.setType("temp");
+ t.typeFactor = ADP_FACTOR;
+ return t.setType("adp");
}
/**
@@ -389,7 +390,7 @@
/**
* Sets typeFactor, altType, isIsotropic, forThermalEllipsoid;
- * type "iso" changed to "temp" here.
+ * type "iso" changed to "" here.
*
*/
private void processType() {
@@ -404,11 +405,11 @@
forThermalEllipsoid = true;
isIsotropic = true;
altType = "1";
- type = "temp";
+ type = "adp";
break;
- case TYPE_TEMP:
+ case TYPE_ADP:
forThermalEllipsoid = true;
- typeFactor = TEMPERATURE_FACTOR;
+ typeFactor = ADP_FACTOR;
altType = "1";
break;
case TYPE_MS:
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