Revision: 18445
http://sourceforge.net/p/jmol/code/18445
Author: hansonr
Date: 2013-07-12 07:25:22 +0000 (Fri, 12 Jul 2013)
Log Message:
-----------
incommensurate work
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java
trunk/Jmol/src/org/jmol/symmetry/SymmetryOperation.java
trunk/Jmol/src/org/jmol/viewer/StateCreator.java
Modified: trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java 2013-07-11 07:08:31 UTC
(rev 18444)
+++ trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java 2013-07-12 07:25:22 UTC
(rev 18445)
@@ -407,7 +407,7 @@
if (xyz0.startsWith("x1,x2,x3,x4")) {
xyzList.clear();
operationCount = 0;
- modulationDimension =
Parser.parseInt(xyz0.substring(xyz0.lastIndexOf("x") + 1));
+ modulationDimension =
Parser.parseInt(xyz0.substring(xyz0.lastIndexOf("x") + 1)) - 1;
}
boolean isSpecial = (xyz0.charAt(0) == '=');
if (isSpecial) xyz0 = xyz0.substring(1);
Modified: trunk/Jmol/src/org/jmol/symmetry/SymmetryOperation.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/SymmetryOperation.java 2013-07-11
07:08:31 UTC (rev 18444)
+++ trunk/Jmol/src/org/jmol/symmetry/SymmetryOperation.java 2013-07-12
07:25:22 UTC (rev 18445)
@@ -56,8 +56,6 @@
* LATT : http://macxray.chem.upenn.edu/LATT.pdf thank you, Patrick Carroll
*
* NEVER ACCESS THESE METHODS DIRECTLY! ONLY THROUGH CLASS Symmetry
- *
- *
*/
@@ -71,6 +69,7 @@
private P3 atomTest;
private P3 temp3;
+ private String[] myLabels;
/**
@@ -156,8 +155,26 @@
return false;
xyzOriginal = xyz;
xyz = xyz.toLowerCase();
- float[] rotTransMatrix = new float[16];
- float[] modulation = (modulationDimension == 0 ? null : new float[2 *
modulationDimension]);
+ int n = 16;
+ if (modulationDimension > 0) {
+ n += 2 * modulationDimension; // +/- 1 and twelfths
+ if (modulationDimension == 1) {
+ myLabels = labelsX1234;
+ } else {
+ myLabels = new String[modulationDimension + 3];
+ for (int i = modulationDimension + 3; --i >= 0;)
+ myLabels[i] = "x" + i;
+ }
+ }
+ float[] rotTransMatrix = new float[n];
+ switch (modulationDimension) {
+ case 0:
+ break;
+ case 1:
+ break;
+ default:
+ }
+
boolean isReverse = (xyz.startsWith("!"));
if (isReverse)
xyz = xyz.substring(1);
@@ -214,7 +231,7 @@
//System.out.println("SymmetryOperation: " + xyz + "\n" + (Matrix4f)this
+ "\n" + this.xyz);
return true;
}
- String strOut = getMatrixFromString(xyz, rotTransMatrix, rotTransMatrix,
doNormalize, false);
+ String strOut = getMatrixFromString(xyz, rotTransMatrix, myLabels,
doNormalize, false);
if (strOut == null)
return false;
setA(rotTransMatrix);
@@ -229,21 +246,25 @@
return true;
}
- static String getMatrixFromString(String xyz, float[] rotTransMatrix,
float[] modulation,
- boolean doNormalize, boolean allowScaling)
{
+ static String getMatrixFromString(String xyz, float[] rotTransMatrix,
+ String[] myLabels, boolean doNormalize,
boolean allowScaling) {
boolean isDenominator = false;
boolean isDecimal = false;
boolean isNegative = false;
- boolean incommensurate = (modulation != null);
+ boolean incommensurate = (rotTransMatrix.length > 16);
+ rotTransMatrix[15] = 1; // 12ths
+ if (myLabels == null)
+ myLabels = labelsXYZ;
char ch;
int x = 0;
int y = 0;
int z = 0;
+ int w = 0;
float iValue = 0;
String strOut = "";
String strT;
int rowPt = -1;
-
+
float decimalMultiplier = 1f;
xyz += ",";
if (incommensurate) {
@@ -276,9 +297,8 @@
val *= iValue;
iValue = 0;
}
- if (incommensurate && rowPt >= 0) {
- int pt = 2 * (rowPt + 1);
- modulation[pt] = val;
+ if (incommensurate && rowPt > 0) {
+ w = val;
} else {
x = val;
}
@@ -306,26 +326,28 @@
}
// put translation into 12ths
iValue = normalizeTwelfths(iValue, doNormalize);
+ int tpt;
if (rowPt > 2 && incommensurate) {
- modulation[2 * rowPt + 1] = iValue;
+ tpt = 16 + 2 * (rowPt + -2);
+ rotTransMatrix[tpt++] = w;
+ rotTransMatrix[tpt] = iValue;
} else {
- int tpt = rowPt * 4;
- rotTransMatrix[tpt++] = x;
- rotTransMatrix[tpt++] = y;
- rotTransMatrix[tpt++] = z;
- rotTransMatrix[tpt] = iValue;
- strT = "";
- strT += (x == 0 ? "" : x < 0 ? "-x" : strT.length() == 0 ? "x" : "+x");
- strT += (y == 0 ? "" : y < 0 ? "-y" : strT.length() == 0 ? "y" : "+y");
- strT += (z == 0 ? "" : z < 0 ? "-z" : strT.length() == 0 ? "z" : "+z");
- strT += xyzFraction(iValue, false, true);
- strOut += (strOut == "" ? "" : ",") + strT;
- //note: when ptLatt[3] = -1, ptLatt[rowPt] MUST be 0.
- if (rowPt == 2) {
- rotTransMatrix[15] = 1;
- return strOut;
+ tpt = rowPt * 4;
+ rotTransMatrix[tpt++] = x;
+ rotTransMatrix[tpt++] = y;
+ rotTransMatrix[tpt++] = z;
+ rotTransMatrix[tpt] = iValue;
+ strT = "";
+ strT += plusMinus(strT, x, "x");
+ strT += plusMinus(strT, y, "y");
+ strT += plusMinus(strT, z, "z");
+ strT += xyzFraction(iValue, false, true);
+ strOut += (strOut == "" ? "" : ",") + strT;
+ //note: when ptLatt[3] = -1, ptLatt[rowPt] MUST be 0.
+ if (rowPt == 2) {
+ return strOut;
+ }
}
- }
x = y = z = 0;
iValue = 0;
break;
@@ -363,6 +385,10 @@
return null;
}
+ private static String plusMinus(String strT, float x, String sx) {
+ return (x == 0 ? "" : x < 0 ? "-" : strT.length() == 0 ? "" : "+") + sx;
+ }
+
private static float normalizeTwelfths(float iValue, boolean doNormalize) {
iValue *= 12f;
if (doNormalize) {
@@ -374,23 +400,25 @@
return iValue;
}
+ final static String[] labelsXYZ = new String[] {"x", "y", "z"};
+
+ final static String[] labelsX1234 = new String[] {"x1", "x2", "x3", "x4"};
+
final static String getXYZFromMatrix(Matrix4f mat, boolean is12ths,
boolean allPositive, boolean
halfOrLess) {
String str = "";
+ String[] thisLabels = (mat instanceof SymmetryOperation ?
((SymmetryOperation) mat).myLabels : null);
+ if (thisLabels == null)
+ thisLabels = labelsXYZ;
float[] row = new float[4];
for (int i = 0; i < 3; i++) {
mat.getRow(i, row);
String term = "";
- if (row[0] != 0)
- term += (row[0] < 0 ? "-" : "+") + "x";
- if (row[1] != 0)
- term += (row[1] < 0 ? "-" : "+") + "y";
- if (row[2] != 0)
- term += (row[2] < 0 ? "-" : "+") + "z";
+ for (int j = 0; j < 3; j++)
+ if (row[j] != 0)
+ term += plusMinus(term, row[j], thisLabels[j]);
term += xyzFraction((is12ths ? row[3] : row[3] * 12), allPositive,
halfOrLess);
- if (term.length() > 0 && term.charAt(0) == '+')
- term = term.substring(1);
str += "," + term;
}
return str.substring(1);
Modified: trunk/Jmol/src/org/jmol/viewer/StateCreator.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2013-07-11 07:08:31 UTC
(rev 18444)
+++ trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2013-07-12 07:25:22 UTC
(rev 18445)
@@ -739,6 +739,8 @@
private String getViewState(TransformManager tm, SB sfunc) {
SB commands = new SB();
+ String moveToText = tm.getMoveToText(0, false);
+ // finalizes transform parameters, in case that has not been done
if (sfunc != null) {
sfunc.append(" _setPerspectiveState;\n");
commands.append("function _setPerspectiveState() {\n");
@@ -757,7 +759,7 @@
appendCmd(commands, "center " + Escape.eP(tm.fixedRotationCenter));
commands.append(viewer.getOrientationText(T.state, null));
- appendCmd(commands, tm.getMoveToText(0, false));
+ appendCmd(commands, moveToText);
if (tm.stereoMode != EnumStereoMode.NONE)
appendCmd(commands, "stereo "
+ (tm.stereoColors == null ? tm.stereoMode.getName() : Escape
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