Revision: 20075
http://sourceforge.net/p/jmol/code/20075
Author: hansonr
Date: 2014-10-14 13:59:43 +0000 (Tue, 14 Oct 2014)
Log Message:
-----------
Jmol.___JmolVersion="14.3.8_2014.10.14"
bug fix: Legendre for U not implemented in msCIF reader - preliminary
bug fix: Legendre for D,U in Jana2006 reader not implemented - preliminary
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/cif/MSCifRdr.java
trunk/Jmol/src/org/jmol/adapter/readers/cif/MSRdr.java
trunk/Jmol/src/org/jmol/adapter/readers/xtal/JanaReader.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/MSCifRdr.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/MSCifRdr.java 2014-10-14
11:50:49 UTC (rev 20074)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/MSCifRdr.java 2014-10-14
13:59:43 UTC (rev 20075)
@@ -130,20 +130,21 @@
private final static int LEG_DISP_ORDER = 63;
private final static int LEG_DISP_COEF = 64;
- private final static int LEG_OCC_LABEL = 65;
- private final static int LEG_OCC_ORDER = 66;
- private final static int LEG_OCC_COEF = 67;
+ private final static int LEG_U_LABEL = 65;
+ private final static int LEG_U_TENS = 66;
+ private final static int LEG_U_ORDER = 67;
+ private final static int LEG_U_COEF = 68;
- private final static int LEG_U_LABEL = 68;
- private final static int LEG_U_ORDER = 69;
- private final static int LEG_U_COEF = 70;
+ private final static int LEG_OCC_LABEL = 69;
+ private final static int LEG_OCC_ORDER = 70;
+ private final static int LEG_OCC_COEF = 71;
- private final static int DEPR_FD_COS = 71;
- private final static int DEPR_FD_SIN = 72;
- private final static int DEPR_FO_COS = 73;
- private final static int DEPR_FO_SIN = 74;
- private final static int DEPR_FU_COS = 75;
- private final static int DEPR_FU_SIN = 76;
+ private final static int DEPR_FD_COS = 72;
+ private final static int DEPR_FD_SIN = 73;
+ private final static int DEPR_FO_COS = 74;
+ private final static int DEPR_FO_SIN = 75;
+ private final static int DEPR_FU_COS = 76;
+ private final static int DEPR_FU_SIN = 77;
// * will be _atom_site
final private static String[] modulationFields = {
"*_fourier_wave_vector_seq_id", // *_ must be first
@@ -219,18 +220,19 @@
"*_displace_legendre_param_order",
"*_displace_legendre_param_coeff",
"*_u_legendre_atom_site_label", // 65
+ "*_u_legendre_tens_elem",
"*_u_legendre_param_order",
"*_u_legendre_param_coeff",
"*_occ_legendre_atom_site_label",
"*_occ_legendre_param_order",
- "*_occ_legendre_param_coeff", // 70
+ "*_occ_legendre_param_coeff", // 71
// deprecated:
- "*_displace_fourier_cos", // 71
+ "*_displace_fourier_cos", // 72
"*_displace_fourier_sin",
"*_occ_fourier_cos",
"*_occ_fourier_sin",
"*_u_fourier_cos",
- "*_u_fourier_sin" //76
+ "*_u_fourier_sin" //77
};
private static final int NONE = -1;
@@ -356,6 +358,10 @@
if (type_id == null)
type_id = "D_L";
//$FALL-THROUGH$
+ case LEG_U_LABEL:
+ if (type_id == null)
+ type_id = "U_L";
+ //$FALL-THROUGH$
case LEG_OCC_LABEL:
if (type_id == null)
type_id = "O_L";
@@ -377,6 +383,7 @@
if (modAxes != null && modAxes.indexOf(axis.toUpperCase()) < 0)
ignore = true;
break;
+ case LEG_U_TENS:
case FWV_U_TENS:
axis = field.toUpperCase();
break;
@@ -497,7 +504,10 @@
continue;
}
if (type_id.indexOf("_L") == 1) {
- axis += (int) pt[1];
+ if (type_id.startsWith("U"))
+ type_id += (int) pt[1]; // axis is Utype here
+ else
+ axis += (int) pt[1];
}
type_id += "#" + axis + ";" + atomLabel;
break;
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/MSRdr.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/MSRdr.java 2014-10-14
11:50:49 UTC (rev 20074)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/MSRdr.java 2014-10-14
13:59:43 UTC (rev 20075)
@@ -310,7 +310,7 @@
map = htModulation;
if (id.indexOf("@") < 0)
id += "@" + (iModel >= 0 ? iModel : cr.asc.iSet);
- if (id.startsWith("D_L#")) {
+ if (id.startsWith("D_L#") || id.startsWith("U_L")) {
if (legendres == null)
legendres = new Lst<String>();
legendres.addLast(id);
@@ -571,7 +571,7 @@
String utens = null;
switch (type) {
case 'U':
- utens = key.substring(4, key.indexOf(";"));
+ utens = key.substring(pt_, key.indexOf(";"));
//$FALL-THROUGH$
case 'O':
case 'D':
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xtal/JanaReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xtal/JanaReader.java
2014-10-14 11:50:49 UTC (rev 20074)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xtal/JanaReader.java
2014-10-14 13:59:43 UTC (rev 20075)
@@ -313,6 +313,7 @@
private P3 rho;
private boolean firstPosition;
private V3 vR, v0Cart;
+ private boolean isLegendre;
/**
@@ -690,8 +691,8 @@
*
* @throws Exception
*/
- private float[][] readAtomRecord( Atom atom, P3 rm, P3 rp,
- boolean isPos) throws Exception {
+ private float[][] readAtomRecord(Atom atom, P3 rm, P3 rp, boolean isPos)
+ throws Exception {
String label = ";" + atom.atomName;
int tType = (isPos ? -1 : getInt(13, 14));
if (!isPos && molTtypes != null)
@@ -757,6 +758,7 @@
atom.foccupancy *= o_0;
int wv = 0;
float a1, a2;
+ isLegendre = false;
for (int j = 0; j < nOcc; j++) {
if (haveSpecialOcc) {
float[][] data = readM40FloatLines(2, 1);
@@ -782,10 +784,10 @@
float w = floats[4]; // width
for (int k = 0; k < 3; k++)
if (floats[k] != 0)
- ms.addModulation(null, "D_S#" + XYZ[k] + label,
- new double[] { c, w, floats[k] }, -1);
+ ms.addModulation(null, "D_S#" + XYZ[k] + label, new double[] { c,
+ w, floats[k] }, -1);
} else {
- // Fourier displacements
+ // Fourier or Legendre displacements
addSinCos(j, "D_", label, isPos);
}
}
@@ -797,27 +799,41 @@
// finally read Uij sines and cosines
- if (!isPos) // No TLS here
+ if (!isPos) { // No TLS here
+ if (isLegendre)
+ nUij *= 2;
for (int j = 0; j < nUij; j++) {
- ensureFourier(j);
if (tType == 1) {
- // fourier?
+ // Fourier displacements
addSinCos(j, "U_", label, false);
} else {
if (haveSpecialUij) {
//TODO
Logger.error("JanaReader -- not interpreting SpecialUij flag: "
+ line);
+ } else if (isLegendre) {
+ float[][] data = readM40FloatLines(1, 6);
+ int order = j + 1;
+ double coeff = 0;
+ for (int k = 0, p = 0; k < 6; k++, p += 3) {
+ if ((coeff = data[0][k]) != 0)
+ ms.addModulation(null,
+ "U_L" + order + "#" + U_LIST.substring(p, p + 3) + label,
+ new double[] { coeff, order, 0 }, -1);
+ }
} else {
float[][] data = readM40FloatLines(2, 6);
- for (int k = 0, p = 0; k < 6; k++, p += 3)
+ for (int k = 0, p = 0; k < 6; k++, p += 3) {
+ double csin = data[1][k];
+ double ccos = data[0][k];
ms.addModulation(null,
"U_" + (j + 1) + "#" + U_LIST.substring(p, p + 3) + label,
- new double[] { data[1][k], data[0][k], 0 }, -1);
+ new double[] { csin, ccos, 0 }, -1);
+ }
}
}
}
-
+ }
// higher order temperature factor modulation ignored
// phason ignored
@@ -825,7 +841,8 @@
}
/**
- * Add x, y, and z modulations as [ csin, ccos, 0 ]
+ * Add x, y, and z modulations as [ csin, ccos, 0 ] or, possibly Legendre [
+ * coef, order, 0 ]
*
* @param j
* @param key
@@ -835,8 +852,25 @@
*/
private void addSinCos(int j, String key, String label, boolean isPos)
throws Exception {
+ readM40Floats();
+ if (isLegendre) {
+ for (int i = 0; i < 2; i++) {
+ int order = (j * 2 + i + 1);
+ for (int k = 0; k < 3; ++k) {
+ float coeff = floats[3 * i + k];
+ if (coeff == 0) {
+ continue;
+ }
+ String axis = XYZ[k % 3];
+ if (modAxes != null && modAxes.indexOf(axis.toUpperCase()) < 0)
+ continue;
+ String id = key + "L#" + axis + order + label;
+ ms.addModulation(null, id, new double[] { coeff, order, 0 }, -1);
+ }
+ }
+ return;
+ }
ensureFourier(j);
- readM40Floats();
for (int k = 0; k < 3; ++k) {
float csin = floats[k];
float ccos = floats[k + 3];
@@ -845,7 +879,7 @@
continue;
csin = 1e-10f;
}
- String axis = XYZ[k%3];
+ String axis = XYZ[k % 3];
if (modAxes != null && modAxes.indexOf(axis.toUpperCase()) < 0)
continue;
String id = key + (j + 1) + "#" + axis + label;
@@ -890,6 +924,8 @@
float[][] data = new float[nLines][nFloats];
for (int i = 0; i < nLines; i++) {
readM40Floats();
+ if (line.indexOf("Legendre") == 19)
+ isLegendre = true;
for (int j = 0; j < nFloats; j++)
data[i][j] = floats[j];
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-10-14 11:50:49 UTC
(rev 20074)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-10-14 13:59:43 UTC
(rev 20075)
@@ -14,10 +14,14 @@
TODO: design and implement sidechain mutation -- MUTATE command ?
TODO: remove HTML5 dependency on synchronous file loading
-TODO: legendre polynomials for modulation Jana2006
-Jmol.___JmolVersion="14.3.7_2014.10.13"
+Jmol.___JmolVersion="14.3.8_2014.10.14"
+bug fix: Legendre for U not implemented in msCIF reader - preliminary
+bug fix: Legendre for D,U in Jana2006 reader not implemented - preliminary
+
+JmolVersion="14.3.7_2014.10.13"
+
new feature: modulation occupancy settable using {*}.occupancy =
{*}.modulation('O',t)
-- for example:
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