Revision: 18382
http://sourceforge.net/p/jmol/code/18382
Author: hansonr
Date: 2013-06-30 07:21:27 +0000 (Sun, 30 Jun 2013)
Log Message:
-----------
Tensor Javadoc and code clean-up
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java
trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
trunk/Jmol/src/org/jmol/shapespecial/Ellipsoids.java
trunk/Jmol/src/org/jmol/symmetry/UnitCell.java
trunk/Jmol/src/org/jmol/util/Tensor.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java
2013-06-29 23:32:44 UTC (rev 18381)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java
2013-06-30 07:21:27 UTC (rev 18382)
@@ -59,6 +59,11 @@
* see http://repo.or.cz/w/gromacs.git/blob/HEAD:/src/gmxlib/pdbio.c line 244
* see http://repo.or.cz/w/gromacs.git/blob/HEAD:/src/gmxlib/pdbio.c line 323
*
+ * TLS Motion Determination:
+ *
+ * J Painter & E A Merritt (2006) Acta Cryst. D62, 439-450
+ * http://skuld.bmsc.washington.edu/~tlsmd
+ *
* symmetry added by Bob Hanson:
*
* setFractionalCoordinates()
@@ -1602,21 +1607,19 @@
tensorType, ' ').replace(':', ' ');
//System.out.println("Tensor data = " + s);
tokens = getTokensStr(s);
- float[][] tensor = new float[3][3];
- tlsGroup.put("t" + tensorType, tensor);
+ float[][] data = new float[3][3];
+ tlsGroup.put("t" + tensorType, data);
for (int i = 0; i < tokens.length; i++) {
int ti = tokens[i].charAt(0) - '1';
int tj = tokens[i].charAt(1) - '1';
- tensor[ti][tj] = parseFloatStr(tokens[++i]);
+ data[ti][tj] = parseFloatStr(tokens[++i]);
if (ti < tj)
- tensor[tj][ti] = tensor[ti][tj];
+ data[tj][ti] = data[ti][tj];
}
for (int i = 0; i < 3; i++)
for (int j = 0; j < 3; j++)
- if (Float.isNaN(tensor[i][j])) {
- tlsAddError("invalid tensor: " + Escape.escapeFloatAA(tensor,
false));
-
- }
+ if (Float.isNaN(data[i][j]))
+ tlsAddError("invalid tensor: " + Escape.escapeFloatAA(data,
false));
//System.out.println("Tensor t" + tensorType + " = " +
Escape.escape(tensor));
if (tensorType == 'S' && ++iGroup == nGroups) {
Logger.info(nGroups + " TLS groups read");
@@ -1632,10 +1635,10 @@
}
}
if (tlsGroups != null) {
- Hashtable<String, Object> groups = new Hashtable<String, Object>();
- groups.put("groupCount", Integer.valueOf(nGroups));
- groups.put("groups", tlsGroups);
- vTlsModels.addLast(groups);
+ Hashtable<String, Object> tlsModel = new Hashtable<String, Object>();
+ tlsModel.put("groupCount", Integer.valueOf(nGroups));
+ tlsModel.put("groups", tlsGroups);
+ vTlsModels.addLast(tlsModel);
}
return (nGroups < 1);
}
@@ -1648,7 +1651,8 @@
}
/**
- * sets the atom property property_tlsGroup based on TLS group ranges
+ * Sets the atom property property_tlsGroup based on TLS group ranges
+ * and adds "TLS" key to model's auxiliaryInfo.
*
* @param iGroup
* @param iModel
@@ -1656,6 +1660,26 @@
*/
@SuppressWarnings("unchecked")
private void setTlsGroups(int iGroup, int iModel, SymmetryInterface
symmetry) {
+
+ // TLS.groupCount Integer
+ // TLS.groups JmolList of Map
+ // .id String
+ // .ranges JmolList of Map
+ // .chains String
+ // .residues int[2]
+ // .origin P3
+ // .tT float[3][3]
+ // .tL float[3][3]
+ // .tS float[3][3]
+ //
+ // ultimately, each atom gets an associated TLS-U and TLS-R
org.jmol.util.Tensor
+ // that can be visualized using
+ //
+ // ellipsoid set "TLS-R"
+ // ellipsoids ON
+ //
+ //
+
Logger.info("TLS model " + (iModel + 1) + " set " + (iGroup + 1));
Map<String, Object> tlsGroupInfo = vTlsModels.get(iGroup);
JmolList<Map<String, Object>> groups = ( JmolList<Map<String, Object>>)
tlsGroupInfo
Modified: trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2013-06-29
23:32:44 UTC (rev 18381)
+++ trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2013-06-30
07:21:27 UTC (rev 18382)
@@ -168,7 +168,6 @@
return atomTypes;
}
-
public float[] getPartialCharges() {
return partialCharges;
}
@@ -266,20 +265,13 @@
t.atomIndex2 = -1;
t.modelIndex = atoms[atomIndex].modelIndex;
addTensor(t, t.type);
- int pt = "charge temp TLS-R TLS-U".indexOf(t.type + " ");
- // 0 7 14 21
- // "1" is assigned for Born Effective Charges and temperature
- // "2" is TLS-R
- // "3" is TLS-U
- // and no more of that!
- if (pt >= 0) {
- addTensor(t, t.altType = "" + (pt >= 14 ? pt / 7: 1));
- }
+ if (t.altType != null)
+ addTensor(t, t.altType);
}
}
public JmolList<Tensor> getAllAtomTensors(String type) {
- return atomTensors.get(type);
+ return atomTensors.get(type.toLowerCase());
}
private Tensor[] getTensorList(JmolList<Tensor> list) {
@@ -290,7 +282,7 @@
Tensor t = list.get(i);
if (t.forThermalEllipsoid)
pt = i;
- else if (t.type.equals("TLS-U"))
+ else if (t.iType == Tensor.TYPE_TLS_U)
haveTLS = true;
}
Tensor[] a = new Tensor[(pt >= 0 || !haveTLS ? 0 : 1) + n];
@@ -317,6 +309,7 @@
}
private void addTensor(Tensor t, String type) {
+ type = type.toLowerCase();
JmolList<Tensor> tensors = atomTensors.get(type);
if (tensors == null)
atomTensors.put(type, tensors = new JmolList<Tensor>());
Modified: trunk/Jmol/src/org/jmol/shapespecial/Ellipsoids.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Ellipsoids.java 2013-06-29
23:32:44 UTC (rev 18381)
+++ trunk/Jmol/src/org/jmol/shapespecial/Ellipsoids.java 2013-06-30
07:21:27 UTC (rev 18382)
@@ -194,7 +194,7 @@
}
if ("select" == propertyName) {
- typeSelected = (String) value;
+ typeSelected = ((String) value).toLowerCase();
return;
}
@@ -210,7 +210,7 @@
short colix = C.getColixO(value);
byte pid = EnumPalette.pidOf(value);
for (Ellipsoid e : atomEllipsoids.values())
- if (e.tensor.type.equals(typeSelected)) {
+ if (e.tensor.type.equalsIgnoreCase(typeSelected)) {
e.colix = getColixI(colix, pid, e.tensor.atomIndex1);
e.pid = pid;
}
@@ -220,7 +220,7 @@
if ("translucency" == propertyName) {
boolean isTranslucent = (value.equals("translucent"));
for (Ellipsoid e : atomEllipsoids.values())
- if (e.tensor.type.equals(typeSelected))
+ if (e.tensor.type.equalsIgnoreCase(typeSelected))
e.colix = C.getColixTranslucent3(e.colix, isTranslucent,
translucentLevel);
return;
Modified: trunk/Jmol/src/org/jmol/symmetry/UnitCell.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/UnitCell.java 2013-06-29 23:32:44 UTC
(rev 18381)
+++ trunk/Jmol/src/org/jmol/symmetry/UnitCell.java 2013-06-30 07:21:27 UTC
(rev 18382)
@@ -263,8 +263,10 @@
* The coefficients bij (i,j = 1,2,3) of the various types are defined with
* the following constant settings.
*
- * Type 0: Base = e, c = 2, D = 1 Type 1: Base = e, c = 1, D = l Type 2:
- * Base = 2, c = 2, D = l Type 3: Base = 2, c = 1, D = l
+ * Type 0: Base = e, c = 2, D = 1
+ * Type 1: Base = e, c = 1, D = l
+ * Type 2: Base = 2, c = 2, D = l
+ * Type 3: Base = 2, c = 1, D = l
*
* Anisotropic temperature factor Types 4, 5, 8, and 9 use the following
* formula for the complete temperature factor, in which a1* , a2*, a3* are
@@ -276,7 +278,9 @@
* The coefficients Uij (i,j = 1,2,3) of the various types are defined with
* the following constant settings.
*
- * Type 4: C = 2, D = 1/4 Type 5: C = 1, D = 1/4 Type 8: C = 2, D = 2pi2
+ * Type 4: C = 2, D = 1/4
+ * Type 5: C = 1, D = 1/4
+ * Type 8: C = 2, D = 2pi2
* Type 9: C = 1, D = 2pi2
*
*
Modified: trunk/Jmol/src/org/jmol/util/Tensor.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Tensor.java 2013-06-29 23:32:44 UTC (rev
18381)
+++ trunk/Jmol/src/org/jmol/util/Tensor.java 2013-06-30 07:21:27 UTC (rev
18382)
@@ -27,55 +27,110 @@
import java.util.Arrays;
import java.util.Comparator;
+/**
+ * @author Bob Hanson hans...@stolaf.edu 6/30/2013
+ *
+ */
public class Tensor {
- private static float TEMPERATURE_FACTOR = (float) (Math.sqrt(0.5) / Math.PI);
+ // 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 MAGNETIC_SUSCEPTIBILITY_FACTOR = 0.01f;
+ private static final float ELECTRIC_FIELD_GRADIENT_FACTOR = 1f;
private static final float BORN_EFFECTIVE_CHARGE_FACTOR = 1f;
private static final float INTERACTION_FACTOR = 0.04f;
+
+ private static TensorSort tSort; // used for sorting eigenvector/values
- private static TensorSort tSort;
+ // base data:
+
+ public String type;
+ public int iType = TYPE_OTHER;
+
+ // type is an identifier that the reader/creator delivers:
+ //
+ // temp -- crystallographic displacement parameters
+ // - "temperature 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
+ // ms -- magnetic susceptibility
+ // isc -- NMR interaction tensors
+ // - will have both atomIndex1 and atomIndex2 defined when
+ // - incorporated into a model
+ // charge -- Born Effective Charge tensor
+ // 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 int getType(String type) {
+ int pt = KNOWN_TYPES.indexOf(";" + type.toLowerCase() + ".");
+ return (pt < 0 ? TYPE_OTHER : pt / 8);
+ }
- private double[][] asymmetricTensor;
-
+ // these may be augmented, but the order should be kept the same within this
list
- public String type; // iso temp ms isc charge TLS-R TLS-U...
+ 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_TLS_U = 2;
+ public static final int TYPE_TLS_R = 3;
+ public static final int TYPE_MS = 4;
+ public static final int TYPE_EFG = 5;
+ public static final int TYPE_ISC = 6;
+ public static final int TYPE_CHARGE = 7;
+
+ public double[][] asymTensor;
+ public double[][] symTensor;
+ public V3[] eigenVectors;
+ public float[] eigenValues;
+
+ // derived type-based information, Jmol-centric, for rendering:
+
public String altType; // "0" "1" "2"
- public float typeFactor = 1;
+ // altType is somewhat of a legacy - just lets you use
+
+ // ellipsoid SET 1
+ // ellipsoid SET 2
+ // etc...
+
+ public boolean isIsotropic; // just rendered as balls, not special features
+ public boolean forThermalEllipsoid;
+ public int eigenSignMask = 7; // signs of eigenvalues; bits 2,1,0 set to 1
if > 0
+ private float typeFactor = 1; // an ellipsoid scaling factor depending upon
type
+
+ // added only after passing
+ // the tensor to ModelLoader:
+
public int modelIndex;
public int atomIndex1 = -1;
public int atomIndex2 = -1;
- public V3[] eigenVectors; // possibly null (isotropic)
- public float[] eigenValues;
-
- public boolean forThermalEllipsoid = true;
- public int eigenSignMask = 7;
- public boolean isIsotropic;
-
public static Tensor copyTensor(Tensor t0) {
Tensor t = new Tensor();
+ t.setType(t0.type);
t.eigenValues = t0.eigenValues;
t.eigenVectors = t0.eigenVectors;
- t.asymmetricTensor = t0.asymmetricTensor;
- t.type = t0.type;
- t.typeFactor = t0.typeFactor;
+ t.asymTensor = t0.asymTensor;
+ t.symTensor = t0.symTensor;
+ t.eigenSignMask = t0.eigenSignMask;
+ t.modelIndex = t0.modelIndex;
+ t.atomIndex1 = t0.atomIndex1;
+ t.atomIndex2 = t0.atomIndex2;
return t;
}
-
- public double[][] getAsymmetricTensor() {
- return asymmetricTensor;
- }
-
/**
- * all instantiation must go through one of the static getTensor... methods
+ * private constructor so that all instantiation must go through one
+ * of the static getTensor... methods to set fields properly.
*
*/
private Tensor() {}
/**
+ * Standard constructor for QM tensors
*
* @param asymmetricTensor
* @param type
@@ -127,10 +182,19 @@
float[] values = new float[3];
eigen.fillArrays(vectors, values);
Tensor t = newTensorType(vectors, values, type);
- t.asymmetricTensor = asymmetricTensor;
+ t.asymTensor = asymmetricTensor;
+ t.symTensor = a;
return t;
}
+ /**
+ * Standard constructor for charge and iso
+ *
+ * @param eigenVectors
+ * @param eigenValues
+ * @param type
+ * @return Tensor
+ */
public static Tensor getTensorFromEigenVectors(V3[] eigenVectors,
float[] eigenValues, String type) {
float[] values = new float[3];
@@ -139,11 +203,15 @@
vectors[i] = V3.newV(eigenVectors[i]);
values[i] = eigenValues[i];
}
- Tensor t = newTensorType(vectors, values, type);
- t.isIsotropic = "iso".equals(type);
- return t;
+ return newTensorType(vectors, values, type);
}
+ /**
+ * Standard constructor for ellipsoids based on axes
+ *
+ * @param axes
+ * @return Tensor
+ */
public static Tensor getTensorFromAxes(V3[] axes) {
Tensor t = new Tensor();
t.eigenValues = new float[3];
@@ -160,30 +228,76 @@
|| Math.abs(t.eigenVectors[2].dot(t.eigenVectors[0])) > 0.0001f)
return null;
sort(t.eigenVectors, t.eigenValues);
- return t;
+ return t.setType("other");
}
- public static Tensor getTensorFromThermalEquation(double[] coef) {
+ /**
+ * standard constructor for thermal ellipsoids convention beta
+ * (see http://www.iucr.org/iucr-top/comm/cnom/adp/finrepone/finrepone.html)
+ *
+ * @param coefs
+ * @return Tensor
+ */
+ public static Tensor getTensorFromThermalEquation(double[] coefs) {
Tensor t = new Tensor();
t.eigenValues = new float[3];
t.eigenVectors = new V3[3];
// assumes an ellipsoid centered on 0,0,0
- // called by UnitCell for the initial creation of Object[] ellipsoid
+ // called by UnitCell for the initial creation from PDB/CIF ADP data
double[][] mat = new double[3][3];
- mat[0][0] = coef[0]; //XX
- mat[1][1] = coef[1]; //YY
- mat[2][2] = coef[2]; //ZZ
- mat[0][1] = mat[1][0] = coef[3] / 2; //XY
- mat[0][2] = mat[2][0] = coef[4] / 2; //XZ
- mat[1][2] = mat[2][1] = coef[5] / 2; //YZ
+ mat[0][0] = coefs[0]; //XX
+ mat[1][1] = coefs[1]; //YY
+ mat[2][2] = coefs[2]; //ZZ
+ mat[0][1] = mat[1][0] = coefs[3] / 2; //XY
+ mat[0][2] = mat[2][0] = coefs[4] / 2; //XZ
+ mat[1][2] = mat[2][1] = coefs[5] / 2; //YZ
Eigen.getUnitVectors(mat, t.eigenVectors, t.eigenValues);
sort(t.eigenVectors, t.eigenValues);
t.typeFactor = TEMPERATURE_FACTOR;
- t.type = "temp";
- t.setTypeFactor();
- return t;
+ return t.setType("temp");
}
+ /**
+ * Note that type may be null here to skip type initialization
+ * and allow later setting of type; this should be used with care.
+ *
+ * @param type
+ * @return "this" for convenience only
+ */
+ public Tensor setType(String type) {
+ if (this.type == null || type == null)
+ this.type = type;
+ if (type != null)
+ processType();
+ return this;
+ }
+
+ /**
+ * Returns a factored eigenvalue; thermal ellipsoids use
sqrt(abs(eigenvalue)) for
+ * ellipsoid axes; others use just use abs(eigenvalue); all cases get
factored by
+ * typeFactor
+ *
+ * @param i
+ * @return factored eigenvalue
+ */
+ public float getFactoredValue(int i) {
+ float f = Math.abs(eigenValues[i]);
+ return (forThermalEllipsoid ? (float) Math.sqrt(f) : f) * typeFactor;
+ }
+
+ public void setAtomIndexes(int index1, int index2) {
+ atomIndex1 = index1;
+ atomIndex2 = index2;
+ }
+
+ /**
+ * common processing of eigenvectors.
+ *
+ * @param vectors
+ * @param values
+ * @param type
+ * @return Tensor
+ */
private static Tensor newTensorType(V3[] vectors, float[] values, String
type) {
Tensor t = new Tensor();
t.eigenValues = values;
@@ -197,62 +311,64 @@
return t;
}
- private void setTypeFactor() {
+ /**
+ * Sets typeFactor, altType, isIsotropic, forThermalEllipsoid;
+ * type "iso" changed to "temp" here.
+ *
+ */
+ private void processType() {
+
forThermalEllipsoid = false;
- switch ("iso temp ms isc chargeTLS-UTLS-R".indexOf(type)) {
- // 0 5 10 15 20 25 30
- default: // TLS, other
- typeFactor = 1;
- break;
- case 0: // iso
+ isIsotropic = false;
+ altType = null;
+ typeFactor = 1;
+
+ switch (iType = getType(type)) {
+ case TYPE_ISO:
forThermalEllipsoid = true;
- typeFactor = 1;
+ isIsotropic = true;
+ altType = "1";
+ type = "temp";
break;
- case 5: // temp
+ case TYPE_TEMP:
forThermalEllipsoid = true;
typeFactor = TEMPERATURE_FACTOR;
+ altType = "1";
break;
- case 10: // ms
+ case TYPE_MS:
typeFactor = MAGNETIC_SUSCEPTIBILITY_FACTOR;
break;
- case 15: // isc
+ case TYPE_EFG:
+ typeFactor = ELECTRIC_FIELD_GRADIENT_FACTOR;
+ break;
+ case TYPE_ISC:
typeFactor = INTERACTION_FACTOR;
break;
- case 20: // charge
+ case TYPE_CHARGE:
typeFactor = BORN_EFFECTIVE_CHARGE_FACTOR;
break;
+ case TYPE_TLS_R:
+ altType = "2";
+ break;
+ case TYPE_TLS_U:
+ altType = "3";
+ break;
}
}
- public Tensor setType(String type) {
- if (this.type == null || type == null)
- this.type = type;
- setTypeFactor();
- return this;
- }
-
- public float getFactoredValue(int i) {
- float f = Math.abs(eigenValues[i]);
- return (forThermalEllipsoid ? (float) Math.sqrt(f) : f) * typeFactor;
- }
-
- public void setAtomIndexes(int index1, int index2) {
- atomIndex1 = index1;
- atomIndex2 = index2;
- }
-
private static int[] sortOrder = { 1, 0, 2 };
/**
- * sorts EigenVectors by
+ * sorts EigenVectors by
*
+ * |sigma_3 - sigma_iso| >= |sigma_1 - sigma_iso| >= |sigma_2 - sigma_iso|
+ *
* and normalize the eigenVectors
*
* @param eigenVectors
* @param eigenValues
*/
private static void sort(V3[] eigenVectors, float[] eigenValues) {
- // |sigma_3 - sigma_iso| >= |sigma_1 - sigma_iso| >= |sigma_2 - sigma_iso|
// first sorted 3 2 1, then 1 and 2 are switched using the sortOrder above.
Object[][] o = new Object[][] {
new Object[] { eigenVectors[0], Float.valueOf(eigenValues[0]) },
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