Revision: 18443
http://sourceforge.net/p/jmol/code/18443
Author: hansonr
Date: 2013-07-11 06:49:27 +0000 (Thu, 11 Jul 2013)
Log Message:
-----------
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/CifReader.java
trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java
trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
trunk/Jmol/src/org/jmol/symmetry/SymmetryOperation.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/CifReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/CifReader.java
2013-07-10 12:52:33 UTC (rev 18442)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/CifReader.java
2013-07-11 06:49:27 UTC (rev 18443)
@@ -220,7 +220,8 @@
} else if (key.startsWith("_cell_")) {
processCellParameter();
} else if (key.startsWith("_symmetry_space_group_name_H-M")
- || key.startsWith("_symmetry_space_group_name_Hall")) {
+ || key.startsWith("_symmetry_space_group_name_Hall")
+ || key.startsWith("_space_group_ssg_name")) {
processSymmetrySpaceGroupName();
} else if (key.startsWith("_atom_sites_fract_tran")) {
processUnitCellTransformMatrix();
@@ -287,6 +288,8 @@
private int nMolecular = 0;
+ private boolean incommensurate;
+
@Override
public void applySymmetryAndSetTrajectory() throws Exception {
// This speeds up calculation, because no crosschecking
@@ -356,7 +359,8 @@
* @throws Exception
*/
private void processSymmetrySpaceGroupName() throws Exception {
- setSpaceGroupName((key.equals("_symmetry_space_group_name_H-M") ? "HM:" :
"Hall:") + data);
+ incommensurate = (key.indexOf("_ssg_") >= 0);
+ setSpaceGroupName((key.indexOf("H-M") > 0 ? "HM:" : incommensurate ?
"SSG:" : "Hall:") + data);
}
/**
@@ -506,7 +510,6 @@
return;
}
if (str.startsWith("_symmetry_equiv_pos")
- || str.startsWith("_space_group_symop")
|| str.startsWith("_space_group_symop")) {
if (ignoreFileSymmetryOperators) {
Logger.warn("ignoring file-based symmetry operators");
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2013-07-10 12:52:33 UTC (rev 18442)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2013-07-11 06:49:27 UTC (rev 18443)
@@ -650,7 +650,7 @@
break;
case PyMOL.OBJECT_MAPMESH:
case PyMOL.OBJECT_MAPDATA:
- processMap(pymolObject, type == PyMOL.OBJECT_MAPMESH);
+ processMap(pymolObject, type == PyMOL.OBJECT_MAPMESH, false);
break;
case PyMOL.OBJECT_GADGET:
processGadget(pymolObject);
@@ -721,7 +721,7 @@
*/
private void processGadget(JmolList<Object> pymolObject) {
if (objectName.endsWith("_e_pot"))
- processMap(pymolObject, true);
+ processMap(pymolObject, true, true);
}
/**
@@ -729,12 +729,13 @@
*
* @param pymolObject
* @param isObject
+ * @param isGadget
*/
- private void processMap(JmolList<Object> pymolObject, boolean isObject) {
+ private void processMap(JmolList<Object> pymolObject, boolean isObject,
boolean isGadget) {
if (isObject) {
if (isStateScript)
return;
- if (isHidden)
+ if (isHidden && !isGadget)
return; // for now
if (mapObjects == null)
mapObjects = new JmolList<JmolList<Object>>();
Modified: trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java 2013-07-10 12:52:33 UTC
(rev 18442)
+++ trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java 2013-07-11 06:49:27 UTC
(rev 18443)
@@ -397,18 +397,25 @@
}
Map<String, Integer> xyzList = new Hashtable<String, Integer>();
+ private int modulationDimension;
+
private int addOperation(String xyz0, int opId) {
if (xyz0 == null || xyz0.length() < 3) {
xyzList = new Hashtable<String, Integer>();
return -1;
}
+ if (xyz0.startsWith("x1,x2,x3,x4")) {
+ xyzList.clear();
+ operationCount = 0;
+ modulationDimension =
Parser.parseInt(xyz0.substring(xyz0.lastIndexOf("x") + 1));
+ }
boolean isSpecial = (xyz0.charAt(0) == '=');
if (isSpecial) xyz0 = xyz0.substring(1);
if (xyzList.containsKey(xyz0))
return xyzList.get(xyz0).intValue();
SymmetryOperation symmetryOperation = new SymmetryOperation(null, null, 0,
opId, doNormalize);
- if (!symmetryOperation.setMatrixFromXYZ(xyz0)) {
+ if (!symmetryOperation.setMatrixFromXYZ(xyz0, modulationDimension)) {
Logger.error("couldn't interpret symmetry operation: " + xyz0);
return -1;
}
Modified: trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2013-07-10 12:52:33 UTC
(rev 18442)
+++ trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2013-07-11 06:49:27 UTC
(rev 18443)
@@ -211,8 +211,8 @@
return SymmetryOperation.fcoord(p);
}
- public String getMatrixFromString(String xyz, float[] temp, boolean
allowScaling) {
- return SymmetryOperation.getMatrixFromString(xyz, temp, false,
allowScaling);
+ public String getMatrixFromString(String xyz, float[] rotTransMatrix,
boolean allowScaling) {
+ return SymmetryOperation.getMatrixFromString(xyz, rotTransMatrix, null,
false, allowScaling);
}
public P3 ijkToPoint3f(int nnn) {
Modified: trunk/Jmol/src/org/jmol/symmetry/SymmetryOperation.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/SymmetryOperation.java 2013-07-10
12:52:33 UTC (rev 18442)
+++ trunk/Jmol/src/org/jmol/symmetry/SymmetryOperation.java 2013-07-11
06:49:27 UTC (rev 18443)
@@ -147,7 +147,7 @@
.append("{\t0\t0\t0\t1\t}\n").toString();
}
- boolean setMatrixFromXYZ(String xyz) {
+ boolean setMatrixFromXYZ(String xyz, int modulationDimension) {
/*
* sets symmetry based on an operator string "x,-y,z+1/2", for example
*
@@ -156,7 +156,8 @@
return false;
xyzOriginal = xyz;
xyz = xyz.toLowerCase();
- float[] temp = new float[16];
+ float[] rotTransMatrix = new float[16];
+ float[] modulation = (modulationDimension == 0 ? null : new float[2 *
modulationDimension]);
boolean isReverse = (xyz.startsWith("!"));
if (isReverse)
xyz = xyz.substring(1);
@@ -179,19 +180,19 @@
* The coordinates we are using here
*/
this.xyz = xyz;
- Parser.parseStringInfestedFloatArray(xyz, null, temp);
+ Parser.parseStringInfestedFloatArray(xyz, null, rotTransMatrix);
for (int i = 0; i < 16; i++) {
- if (Float.isNaN(temp[i]))
+ if (Float.isNaN(rotTransMatrix[i]))
return false;
- float v = temp[i];
+ float v = rotTransMatrix[i];
if (Math.abs(v) < 0.00001f)
v = 0;
if (i % 4 == 3)
v = normalizeTwelfths((v < 0 ? -1 : 1) * Math.round(Math.abs(v *
12)), doNormalize);
- temp[i] = v;
+ rotTransMatrix[i] = v;
}
- temp[15] = 1;
- setA(temp);
+ rotTransMatrix[15] = 1;
+ setA(rotTransMatrix);
isFinalized = true;
if (isReverse)
invertM(this);
@@ -200,12 +201,12 @@
}
if (xyz.indexOf("[[") == 0) {
xyz = xyz.replace('[',' ').replace(']',' ').replace(',',' ');
- Parser.parseStringInfestedFloatArray(xyz, null, temp);
+ Parser.parseStringInfestedFloatArray(xyz, null, rotTransMatrix);
for (int i = 0; i < 16; i++) {
- if (Float.isNaN(temp[i]))
+ if (Float.isNaN(rotTransMatrix[i]))
return false;
}
- setA(temp);
+ setA(rotTransMatrix);
isFinalized = true;
if (isReverse)
invertM(this);
@@ -213,10 +214,10 @@
//System.out.println("SymmetryOperation: " + xyz + "\n" + (Matrix4f)this
+ "\n" + this.xyz);
return true;
}
- String strOut = getMatrixFromString(xyz, temp, doNormalize, false);
+ String strOut = getMatrixFromString(xyz, rotTransMatrix, rotTransMatrix,
doNormalize, false);
if (strOut == null)
return false;
- setA(temp);
+ setA(rotTransMatrix);
if (isReverse) {
invertM(this);
this.xyz = getXYZFromMatrix(this, true, false, false);
@@ -228,11 +229,12 @@
return true;
}
- static String getMatrixFromString(String xyz, float[] temp,
+ static String getMatrixFromString(String xyz, float[] rotTransMatrix,
float[] modulation,
boolean doNormalize, boolean allowScaling)
{
boolean isDenominator = false;
boolean isDecimal = false;
boolean isNegative = false;
+ boolean incommensurate = (modulation != null);
char ch;
int x = 0;
int y = 0;
@@ -241,15 +243,14 @@
String strOut = "";
String strT;
int rowPt = -1;
+
float decimalMultiplier = 1f;
- while (xyz.indexOf("x4") >= 0) {
- Logger.info("ignoring last parameter in " + xyz);
- xyz = xyz.substring(0, xyz.lastIndexOf(","));
+ xyz += ",";
+ if (incommensurate) {
xyz = TextFormat.simpleReplace(xyz, "x1", "x");
xyz = TextFormat.simpleReplace(xyz, "x2", "y");
xyz = TextFormat.simpleReplace(xyz, "x3", "z");
}
- xyz += ",";
for (int i = 0; i < xyz.length(); i++) {
ch = xyz.charAt(i);
switch (ch) {
@@ -270,11 +271,17 @@
continue;
case 'X':
case 'x':
- x = (isNegative ? -1 : 1);
+ int val = (isNegative ? -1 : 1);
if (allowScaling && iValue != 0) {
- x *= iValue;
+ val *= iValue;
iValue = 0;
}
+ if (incommensurate && rowPt >= 0) {
+ int pt = 2 * (rowPt + 1);
+ modulation[pt] = val;
+ } else {
+ x = val;
+ }
break;
case 'Y':
case 'y':
@@ -293,17 +300,20 @@
}
break;
case ',':
- if (++rowPt > 2) {
+ if (++rowPt > 2 && !incommensurate) {
Logger.warn("Symmetry Operation? " + xyz);
return null;
}
- int tpt = rowPt * 4;
// put translation into 12ths
iValue = normalizeTwelfths(iValue, doNormalize);
- temp[tpt++] = x;
- temp[tpt++] = y;
- temp[tpt++] = z;
- temp[tpt] = iValue;
+ if (rowPt > 2 && incommensurate) {
+ modulation[2 * rowPt + 1] = 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");
@@ -312,9 +322,10 @@
strOut += (strOut == "" ? "" : ",") + strT;
//note: when ptLatt[3] = -1, ptLatt[rowPt] MUST be 0.
if (rowPt == 2) {
- temp[15] = 1;
+ rotTransMatrix[15] = 1;
return strOut;
}
+ }
x = y = z = 0;
iValue = 0;
break;
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-07-10 12:52:33 UTC
(rev 18442)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-07-11 06:49:27 UTC
(rev 18443)
@@ -9,7 +9,7 @@
# The quotes above look odd for a parameter file, but they are
# important for the JavaScript version of Jmol.
-___JmolVersion="13.1.19_dev_2013.07.09"
+___JmolVersion="13.1.19_dev_2013.07.11"
code: org.jmol.quantum.NMRCalculation smoothly handles J-coupling and dipolar
coupling constant display.
This was sent by the SourceForge.net collaborative development platform, the
world's largest Open Source development site.
------------------------------------------------------------------------------
See everything from the browser to the database with AppDynamics
Get end-to-end visibility with application monitoring from AppDynamics
Isolate bottlenecks and diagnose root cause in seconds.
Start your free trial of AppDynamics Pro today!
http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk
_______________________________________________
Jmol-commits mailing list
Jmol-commits@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-commits
