Revision: 5254
Author: hansonr
Date: 2006-06-29 20:14:13 -0700 (Thu, 29 Jun 2006)
ViewCVS: http://svn.sourceforge.net/jmol/?rev=5254&view=rev
Log Message:
-----------
bob200603 isosurface lcaoCartoon
Modified Paths:
--------------
branches/bob200603/Jmol/src/org/jmol/viewer/Atom.java
branches/bob200603/Jmol/src/org/jmol/viewer/Bond.java
branches/bob200603/Jmol/src/org/jmol/viewer/Eval.java
branches/bob200603/Jmol/src/org/jmol/viewer/Frame.java
branches/bob200603/Jmol/src/org/jmol/viewer/Isosurface.java
branches/bob200603/Jmol/src/org/jmol/viewer/JmolConstants.java
branches/bob200603/Jmol/src/org/jmol/viewer/MeshCollection.java
branches/bob200603/Jmol/src/org/jmol/viewer/ModelManager.java
branches/bob200603/Jmol/src/org/jmol/viewer/Viewer.java
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/Atom.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/Atom.java 2006-06-29
17:21:25 UTC (rev 5253)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Atom.java 2006-06-30
03:14:13 UTC (rev 5254)
@@ -34,14 +34,14 @@
import javax.vecmath.Vector3f;
import javax.vecmath.Point3i;
-final class Atom implements Tuple {
+final public class Atom implements Tuple {
final static byte VIBRATION_VECTOR_FLAG = 0x02;
final static byte IS_HETERO_FLAG = 0x04;
Group group;
int atomIndex;
- Point3f point3f;
+ public Point3f point3f;
int screenX;
int screenY;
int screenZ;
@@ -169,24 +169,17 @@
boolean isBonded(Atom atomOther) {
if (bonds != null)
- for (int i = bonds.length; --i >= 0; ) {
- Bond bond = bonds[i];
- if ((bond.atom1 == atomOther) ||
- (bond.atom2 == atomOther))
+ for (int i = bonds.length; --i >= 0;)
+ if (bonds[i].getOtherAtom(this) == atomOther)
return true;
- }
return false;
}
Bond getBond(Atom atomOther) {
- if (bonds != null) {
- for (int i = bonds.length; --i >= 0; ) {
- Bond bond = bonds[i];
- if ((bond.atom1 == atomOther) ||
- (bond.atom2 == atomOther))
- return bond;
- }
- }
+ if (bonds != null)
+ for (int i = bonds.length; --i >= 0;)
+ if (bonds[i].getOtherAtom(atomOther) != null)
+ return bonds[i];
return null;
}
@@ -221,15 +214,11 @@
void deleteBondedAtom(Atom atomToDelete) {
if (bonds == null)
return;
- for (int i = bonds.length; --i >= 0; ) {
- Bond bond = bonds[i];
- Atom atomBonded =
- (bond.atom1 != this) ? bond.atom1 : bond.atom2;
- if (atomBonded == atomToDelete) {
+ for (int i = bonds.length; --i >= 0;)
+ if (bonds[i].getOtherAtom(this) == atomToDelete) {
deleteBond(i);
return;
}
- }
}
void deleteAllBonds() {
@@ -273,15 +262,13 @@
}
int getBondedAtomIndex(int bondIndex) {
- Bond bond = bonds[bondIndex];
- return (((bond.atom1 == this)
- ? bond.atom2
- : bond.atom1).atomIndex & 0xFFFF);
+ return bonds[bondIndex].getOtherAtom(this).atomIndex & 0xFFFF;
+ //BH: why & 0xFFFF ?
}
/*
* What is a MAR?
- * - just a term that I made up
+ * - just a term that Miguel made up
* - an abbreviation for Milli Angstrom Radius
* that is:
* - a *radius* of either a bond or an atom
@@ -595,8 +582,7 @@
Bond bondLongest = null;
for (int i = bonds.length; --i >= 0; ) {
Bond bond = bonds[i];
- Atom atomOther = bond.atom1 != this ? bond.atom1 : bond.atom2;
- float dist2 = point3f.distanceSquared(atomOther.point3f);
+ float dist2 = point3f.distanceSquared(bond.getOtherAtom(this).point3f);
if (dist2 > dist2Longest) {
bondLongest = bond;
dist2Longest = dist2;
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/Bond.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/Bond.java 2006-06-29
17:21:25 UTC (rev 5253)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Bond.java 2006-06-30
03:14:13 UTC (rev 5254)
@@ -168,6 +168,10 @@
return atom1.group.chain.frame.viewer.getColixArgb(getColix2());
}
+ Atom getOtherAtom(Atom thisAtom) {
+ return (atom1 == thisAtom ? atom2 : atom2 == thisAtom ? atom1 : null);
+ }
+
////////////////////////////////////////////////////////////////
Hashtable getPublicProperties() {
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/Eval.java 2006-06-29
17:21:25 UTC (rev 5253)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Eval.java 2006-06-30
03:14:13 UTC (rev 5254)
@@ -726,7 +726,7 @@
}
void expressionExpected() throws ScriptException {
- evalError("(atom expression) expected");
+ evalError("valid (atom expression) expected");
}
void rotationPointsIdentical() throws ScriptException {
@@ -924,6 +924,15 @@
return floatValue;
}
+ String stringParameter(int index) throws ScriptException {
+ if (index >= statementLength)
+ badArgumentCount();
+ if (statement[index].tok == Token.string)
+ return (String) statement[index].value;
+ stringExpected();
+ return null; //impossible return
+ }
+
String objectNameParameter(int index) throws ScriptException {
if (index >= statementLength || statement[index].tok != Token.identifier)
objectNameExpected();
@@ -3109,9 +3118,7 @@
}
if (str.equalsIgnoreCase("defaultLoadScript")) {
checkLength3();
- if (statement[2].tok != Token.string)
- stringExpected();
- viewer.setDefaultLoadScript((String) statement[2].value);
+ viewer.setDefaultLoadScript(stringParameter(2));
break;
}
if (str.equalsIgnoreCase("dipoleScale")) {
@@ -4101,7 +4108,6 @@
int colorRangeStage = 0;
boolean colorByPhase = false;
String str;
-
for (int i = 1; i < statementLength; ++i) {
String propertyName = null;
Object propertyValue = null;
@@ -4117,7 +4123,7 @@
drawObjectNotDefined(id);
break;
case Token.expressionBegin:
- propertyValue = viewer.getAtomSetCenter(expression(statement, i +
1));
+ propertyValue = viewer.getAtomSetCenter(expression(statement, ++i));
i = pcLastExpressionInstruction;
break;
case Token.leftbrace:
@@ -4153,6 +4159,27 @@
break;
case Token.identifier:
str = (String) token.value;
+ if (str.equalsIgnoreCase("lcaoCartoon")) {
+ String lcaoType = stringParameter(++i);
+ viewer.setShapeProperty(JmolConstants.SHAPE_ISOSURFACE,
+ "lcaoCartoon", lcaoType);
+ switch (statement[++i].tok) {
+ case Token.expressionBegin:
+ propertyName = "lcaoAxes";
+ int atomIndex = viewer.firstAtomOf(expression(statement, ++i));
+ if (atomIndex < 0)
+ expressionExpected();
+ Vector3f[] axes = { new Vector3f(), new Vector3f(),
+ new Vector3f(viewer.getAtomPoint3f(atomIndex)) };
+ viewer.getPrincipalAxes(atomIndex, axes[0], axes[1], lcaoType);
+ i = pcLastExpressionInstruction;
+ propertyValue = axes;
+ break;
+ default:
+ expressionExpected();
+ }
+ break;
+ }
if (str.equalsIgnoreCase("sphere")) {
//sphere [radius]
propertyName = "sphere";
@@ -4177,7 +4204,7 @@
nlmZR[1] = intParameter(++i);
nlmZR[2] = intParameter(++i);
nlmZR[3] = (statement.length > i + 1
- && statement[i + 1].tok == Token.integer ? floatParameter(++i)
+ && statement[i + 1].tok == Token.integer || statement[i + 1].tok
== Token.decimal ? floatParameter(++i)
: 6f);
nlmZR[4] = (statement.length > i + 1
&& statement[i + 1].tok == Token.integer ? floatParameter(++i)
@@ -4357,6 +4384,7 @@
case Token.color:
colorSeen = true;
colorRangeStage = 1;
+ signPt = i + 1;
continue;
case Token.absolute:
colorRangeStage = 1;
@@ -4516,172 +4544,6 @@
"applyConnectParameters", null);
}
- void connect10_0_99() throws ScriptException {
- boolean haveType = false;
- int nAtomSets = 0;
- int nDistances = 0;
- /*
- * connect [<=2 distance parameters] [<=2 atom sets]
- * [<=1 bond type] [<=1 operation]
- *
- */
-
- viewer.setShapeProperty(JmolConstants.SHAPE_STICKS,
- "resetConnectParameters", null);
- if (statementLength == 1) {
- viewer.setShapeProperty(JmolConstants.SHAPE_STICKS,
- "rasmolCompatibleConnect", null);
- return;
- }
- for (int i = 1; i < statementLength; ++i) {
- String propertyName = null;
- Object propertyValue = null;
- switch_tag: switch (statement[i].tok) {
- case Token.on:
- case Token.off:
- if (statementLength != 2)
- badArgumentCount();
- viewer.setShapeProperty(JmolConstants.SHAPE_STICKS,
- "rasmolCompatibleConnect", null);
- return;
- case Token.integer:
- case Token.decimal:
- if (++nDistances > 2)
- badArgumentCount();
- if (nAtomSets > 0 || haveType)
- invalidParameterOrder();
- propertyName = "connectDistance";
- propertyValue = new Float(floatParameter(i));
- break;
- case Token.expressionBegin:
- if (++nAtomSets > 2)
- badArgumentCount();
- if (haveType)
- invalidParameterOrder();
- propertyName = "connectSet";
- propertyValue = expression(statement, i);
- // i = pcLastExpressionInstruction; // the for loop will
increment i
- i = pcLastExpressionInstruction;
-
- break;
- case Token.identifier:
- case Token.hbond:
- String cmd = (String) statement[i].value;
- for (int j = JmolConstants.bondOrderNames.length; --j >= 0;) {
- if (cmd.equalsIgnoreCase(JmolConstants.bondOrderNames[j])) {
- if (haveType)
- incompatibleArguments();
- cmd = JmolConstants.bondOrderNames[j];
- propertyName = "connectBondOrder";
- propertyValue = cmd;
- haveType = true;
- break switch_tag;
- }
- }
- if (++i != statementLength)
- invalidParameterOrder();
- if ("modify".equalsIgnoreCase(cmd))
- propertyValue = "modify";
- else if ("create".equalsIgnoreCase(cmd))
- propertyValue = "create";
- else if ("modifyOrCreate".equalsIgnoreCase(cmd))
- propertyValue = "modifyOrCreate";
- else if ("auto".equalsIgnoreCase(cmd))
- propertyValue = "auto";
- else
- unrecognizedSubcommand();
- propertyName = "connectOperation";
- break;
- case Token.none:
- case Token.delete:
- if (++i != statementLength)
- invalidParameterOrder();
- propertyName = "connectOperation";
- propertyValue = "delete";
- break;
- default:
- invalidArgument();
- }
- viewer.setShapeProperty(JmolConstants.SHAPE_STICKS, propertyName,
- propertyValue);
- }
- viewer.setShapeProperty(JmolConstants.SHAPE_STICKS,
- "applyConnectParameters", null);
- }
-
- void connectOLD() throws ScriptException {
- viewer.setShapeProperty(JmolConstants.SHAPE_STICKS, "initConnect", null);
- if (statementLength == 1) {
- viewer.rebond();
- return;
- }
- String propertyName = null;
- Object propertyValue = null;
- int nNumeric = 0;
- for (int i = 1; i < statementLength; ++i) {
- propertyName = null;
- propertyValue = null;
- Token token = statement[i];
- switch (token.tok) {
- case Token.on:
- case Token.off:
- viewer.rebond();
- return;
- case Token.integer:
- if (++nNumeric > 2) {
- propertyName = "connectMad";
- propertyValue = new Short(getMadInteger(token.intValue));
- } else {
- propertyName = "connectDistance";
- propertyValue = new Float(token.intValue);
- }
- break;
- case Token.decimal:
- if (++nNumeric > 2) {
- propertyName = "connectMad";
- propertyValue = new Short(getMadFloat(floatParameter(i)));
- } else {
- propertyName = "connectDistance";
- propertyValue = token.value;
- }
- break;
- case Token.expressionBegin:
- //System.out.println(i + " " + propertyName + " " + statementLength);
- propertyValue = expression(statement, i);
- i = pcLastExpressionInstruction;
- propertyName = (i == statementLength - 1 ? "targetSet" : "sourceSet");
- break;
- case Token.identifier:
- case Token.hbond:
- String cmd = ((String) token.value).toLowerCase();
- if (cmd.equals("single") || cmd.equals("double")
- || cmd.equals("triple") || cmd.equals("aromatic")
- || cmd.equals("hbond")) {
- propertyName = "connectBondOrder";
- propertyValue = cmd;
- nNumeric = 2;
- } else if (cmd.equals("exists")) {
- propertyName = "connectNew";
- propertyValue = Boolean.FALSE;
- } else if (cmd.equals("new")) {
- propertyName = "connectExistant";
- propertyValue = Boolean.FALSE;
- } else {
- unrecognizedSubcommand();
- }
- break;
- case Token.delete:
- propertyName = "connectBondOrder";
- propertyValue = new Short((short) 0);
- break;
- default:
- invalidArgument();
- }
- viewer.setShapeProperty(JmolConstants.SHAPE_STICKS, propertyName,
- propertyValue);
- }
- }
-
void getProperty() {
String retValue = "";
String property = (statementLength < 2 ? "" : (String) statement[1].value);
@@ -4689,4 +4551,5 @@
retValue = (String) viewer.getProperty("readable", property, param);
viewer.scriptEcho(retValue);
}
+
}
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/Frame.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/Frame.java 2006-06-29
17:21:25 UTC (rev 5253)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Frame.java 2006-06-30
03:14:13 UTC (rev 5254)
@@ -33,6 +33,7 @@
import javax.vecmath.Point3f;
import javax.vecmath.Matrix3f;
import javax.vecmath.Vector3f;
+import javax.vecmath.AxisAngle4f;
import java.util.BitSet;
import java.util.Hashtable;
import java.util.Properties;
@@ -2743,4 +2744,140 @@
atoms[atomIndex].point3f.y += y;
atoms[atomIndex].point3f.z += z;
}
+
+ void getPrincipalAxes(int atomIndex, Vector3f z, Vector3f x, String
lcaoType) {
+ Atom atom = atoms[atomIndex];
+ z.set(0, 0, 0);
+ x.set(0, 0, 0);
+ Atom atom1 = atom;
+ int nBonds = 0;
+ float cutoff = (float) Math.PI / 180f * 0.95f;
+ Vector3f n = new Vector3f();
+ Vector3f x2 = new Vector3f();
+ Vector3f x3 = new Vector3f(3.14159f, 2.71828f, 1.41421f);
+ Vector3f x4 = new Vector3f();
+ Vector3f y1 = new Vector3f();
+ Vector3f y2 = new Vector3f();
+ if (atom.bonds != null)
+ for (int i = atom.bonds.length; --i >= 0;)
+ if (atom.bonds[i].isCovalent()) {
+ ++nBonds;
+ atom1 = atom.bonds[i].getOtherAtom(atom);
+ n.sub(atom.point3f, atom1.point3f);
+ n.normalize();
+ z.add(n);
+ switch (nBonds) {
+ case 1:
+ x.set(n);
+ break;
+ case 2:
+ x2.set(n);
+ break;
+ case 3:
+ x3.set(n);
+ break;
+ case 4:
+ x4.set(n);
+ break;
+ default:
+ i = -1;
+ }
+ }
+ switch (nBonds) {
+ case 0:
+ z.set(0, 0, 1);
+ x.set(1, 0, 0);
+ break;
+ case 1:
+ if (lcaoType.indexOf("sp3") == 0) { // align z as sp3 orbital
+ x.cross(x3, z);
+ y1.cross(z, x);
+ x.normalize();
+ y1.normalize();
+ y2.set(x);
+ z.normalize();
+ x.scaleAdd(2.828f, x, z); // 2*sqrt(2)
+ if (!lcaoType.equals("sp3a") && !lcaoType.equals("sp3")) {
+ x.normalize();
+ AxisAngle4f a = new AxisAngle4f(z.x, z.y, z.z, (lcaoType
+ .equals("sp3b") ? 1 : -1) * 2.09439507f); // PI*2/3
+ Matrix3f m = new Matrix3f();
+ m.setIdentity();
+ m.set(a);
+ m.transform(x);
+ }
+ z.set(x);
+ x.cross(y1, z);
+ break;
+ }
+ if (atom1.getCovalentBondCount() == 3) {
+ //special case, for example R2C=O oxygen
+ getPrincipalAxes(atom1.atomIndex, z, x3, lcaoType);
+ x3.set(x);
+ if (lcaoType.indexOf("sp2") == 0) { // align z as sp2 orbital
+ z.scale(-1);
+ }
+ }
+ x.cross(x3, z);
+ break;
+ case 2:
+ if (z.length() < 0.1) { // linear A--X--B
+ z.set(x);
+ x.cross(x3, z);
+ break;
+ } // bent A--X--B
+ x3.cross(z, x);
+ if (lcaoType.indexOf("sp") == 0) { // align z as sp2 orbital
+ if (!lcaoType.equals("sp2")) {
+ z.set(lcaoType.indexOf("b") >= 0 ? x2 : x);
+ z.scale(-1);
+ }
+ x.cross(z, x3);
+ break;
+ }
+ if (lcaoType.indexOf("lp") == 0) { // align z as lone pair
+ x3.normalize();
+ z.normalize();
+ y1.scaleAdd(1.2f, x3, z);
+ y2.scaleAdd(-1.2f, x3, z);
+ z.set(lcaoType.indexOf("b") >= 0 ? y2 : y1);
+ x.cross(z, x3);
+ break;
+ }
+ // align z as p orbital
+ x.cross(z, x3);
+ z.set(x3);
+ break;
+ default:
+ System.out.println("getPrinc z x x2 x3 " + z + x + x2 + x3);
+ if (x.angle(x2) < cutoff)
+ y1.cross(x, x2);
+ else
+ y1.cross(x, x3);
+ y1.normalize();
+ if (x2.angle(x3) < cutoff)
+ y2.cross(x2, x3);
+ else
+ y2.cross(x, x3);
+ y2.normalize();
+ System.out.println("getPrinc y1 y2 " + x.dot(x2) + y1 + " " + x2.dot(x3)
+ + y2 + y2.dot(y1));
+ if (Math.abs(y2.dot(y1)) < 0.95f) {
+ x.cross(z, x);
+ break;
+ }
+ if (lcaoType.indexOf("sp") == 0) { // align z as sp2 orbital
+ z.set(lcaoType.indexOf("d") >= 0 ? x4 : lcaoType.indexOf("c") >= 0 ? x3
+ : lcaoType.indexOf("b") >= 0 ? x2 : x);
+ z.scale(-1);
+ x.set(y1);
+ break;
+ }
+ // align z as p orbital
+ z.set(y1);
+ }
+ x.normalize();
+ z.normalize();
+ System.out.println("principal axes: " + z + " " + x);
+ }
}
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/Isosurface.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/Isosurface.java 2006-06-29
17:21:25 UTC (rev 5253)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Isosurface.java 2006-06-30
03:14:13 UTC (rev 5254)
@@ -115,16 +115,24 @@
final static int nContourMax = 100;
final static int defaultColorNegative = Graphics3D.getArgbFromString("red");
final static int defaultColorPositive = Graphics3D.getArgbFromString("blue");
+ final static int defaultColorNegativeLCAO = Graphics3D
+ .getArgbFromString("purple");
+ final static int defaultColorPositiveLCAO = Graphics3D
+ .getArgbFromString("orange");
final static float defaultSolventRadius = 1.2f;
+ short defaultColix;
boolean colorBySign;
int colorNeg;
int colorPos;
+ int colorPosLCAO;
+ int colorNegLCAO;
int colorPtr;
boolean colorByPhase;
int colorPhase;
boolean insideOut;
boolean writePrecisionColor;
+ boolean dumpJVXL;
boolean isOrbital;
boolean isSphere;
@@ -133,6 +141,8 @@
boolean isFunctionXY;
Vector functionXYinfo;
+ String lcaoCartoon;
+
boolean isAnisotropic;
boolean isEccentric;
float eccentricityScale;
@@ -193,8 +203,8 @@
void setProperty(String propertyName, Object value, BitSet bs) {
- System.out.println("isosurface "+state+" setProperty: " + propertyName + "
= "
- + value);
+ System.out.println("isosurface " + state + " setProperty: " + propertyName
+ + " = " + value);
if ("init" == propertyName) {
fileIndex = 1;
nBytes = 0;
@@ -210,19 +220,22 @@
writePrecisionColor = false;
thisContour = -1;
iDoContourPlane = true;
+ dumpJVXL = true;
dataIsJvxl2dContour = false;
+ colorPtr = 0;
colorBySign = colorByPhase = false;
+ defaultColix = 0;
colorNeg = defaultColorNegative;
colorPos = defaultColorPositive;
+ colorNegLCAO = defaultColorNegativeLCAO;
+ colorPosLCAO = defaultColorPositiveLCAO;
isSphere = isOrbital = isLobe = isSolvent = isFunctionXY = false;
isEccentric = isAnisotropic = false;
scale = Float.NaN;
center = new Point3f(Float.MAX_VALUE, Float.MAX_VALUE, Float.MAX_VALUE);
//anisotropy[0] = anisotropy[1] = anisotropy[2] = 1f;
cutoff = Float.MAX_VALUE;
- state = STATE_INITIALIZED;
- assocGridPointMap = new Hashtable();
- assocGridPointNormals = new Hashtable();
+ initState();
super.setProperty("thisID", null, null);
return;
}
@@ -255,6 +268,7 @@
if ("eccentricity" == propertyName) {
setEccentricity((Point4f) value);
+ return;
}
/// special effects
@@ -305,10 +319,11 @@
if ("colorRGB" == propertyName) {
int rgb = ((Integer) value).intValue();
if (colorPtr++ > 0) {
- colorPos = rgb;
+ colorPos = colorPosLCAO = rgb;
} else {
- colorNeg = rgb;
+ colorNeg = colorNegLCAO = rgb;
}
+ defaultColix = Graphics3D.getColix(rgb);
return;
}
@@ -336,6 +351,24 @@
boolean isCalculation = false;
+ if ("lcaoCartoon" == propertyName) {
+ lcaoCartoon = (String) value;
+ dumpJVXL = false;
+ if (colorPtr == 1)
+ colorPosLCAO = colorNegLCAO;
+ return;
+ }
+
+ if ("lcaoAxes" == propertyName) {
+ if (++state != STATE_DATA_READ)
+ return;
+ Vector3f[] info = (Vector3f[]) value;
+ // z x center
+ if (center.x == Float.MAX_VALUE)
+ center.set(info[2]);
+ drawLcaoCartoon(lcaoCartoon, info[0], info[1]);
+ }
+
if ("plane" == propertyName) {
thePlane = (Point4f) value;
if (++state != STATE_DATA_READ)
@@ -423,7 +456,7 @@
colorIsosurface();
discardTempData(dataIsJvxl2dContour);
currentMesh.nBytes = nBytes;
- if (thePlane == null)
+ if (dumpJVXL && thePlane == null)
System.out.println("\n" + jvxlGetFile(currentMesh, jvxlFileMessage));
setModelIndex();
return;
@@ -477,6 +510,13 @@
return;
}
+ if ("delete" == propertyName) {
+ if (currentMesh == null)
+ nLCAO = 0;
+ // fall through to meshCollection
+ }
+
+ // processed by meshCollection
super.setProperty(propertyName, value, bs);
}
@@ -488,6 +528,12 @@
return super.getProperty(property, index);
}
+ void initState() {
+ state = STATE_INITIALIZED;
+ assocGridPointMap = new Hashtable();
+ assocGridPointNormals = new Hashtable();
+ }
+
void setEccentricity(Point4f info) {
Vector3f ecc = new Vector3f(info.x, info.y, info.z);
float c = (scale > 0 ? scale : info.w < 0 ? 1f : ecc.length());
@@ -660,6 +706,8 @@
int indexColorNegative;
short getDefaultColix() {
+ if (defaultColix != 0)
+ return defaultColix;
int argb;
if (cutoff >= 0) {
indexColorPositive = (indexColorPositive %
JmolConstants.argbsIsosurfacePositive.length);
@@ -3277,7 +3325,7 @@
float radius = lobe_sizeAngstroms / 2f * eccentricityScale;
setVoxelRange(0, -radius, radius, lobe_ptsPerAngstrom, lobe_gridMax);
setVoxelRange(1, -radius, radius, lobe_ptsPerAngstrom, lobe_gridMax);
- setVoxelRange(2, 0, radius * 4.4f, lobe_ptsPerAngstrom, lobe_gridMax);
+ setVoxelRange(2, 0, radius * 4.5f, lobe_ptsPerAngstrom, lobe_gridMax);
jvxlFileHeader = "lobe \nn="
+ psi_n
+ ", l="
@@ -3533,6 +3581,97 @@
return viewer.functionXY(functionName, x, y);
}
+ //// LCAO Cartoons ////
+
+ int nLCAO = 0;
+
+ void drawLcaoCartoon(String lcaoCartoon, Vector3f z, Vector3f x) {
+ Vector3f y = new Vector3f();
+ boolean isReverse = (lcaoCartoon.length() > 0 && lcaoCartoon.charAt(0) ==
'-');
+ if (isReverse) {
+ lcaoCartoon = lcaoCartoon.substring(1);
+ colorNeg = colorPosLCAO;
+ colorPos = colorNegLCAO;
+ } else {
+ colorPos = colorPosLCAO;
+ colorNeg = colorNegLCAO;
+ }
+ y.cross(z, x);
+ String id = (currentMesh == null ? "lcao" + (++nLCAO) + "_" + lcaoCartoon
+ : currentMesh.thisID);
+ if (currentMesh == null)
+ allocMesh(id);
+ defaultColix = Graphics3D.getColix(colorPos);
+
+ if (lcaoCartoon.equals("px")) {
+ currentMesh.thisID += "a";
+ createLcaoLobe(x, 1);
+ setProperty("thisID", id + "b", null);
+ createLcaoLobe(x, -1);
+ currentMesh.colix = Graphics3D.getColix(colorNeg);
+ return;
+ }
+ if (lcaoCartoon.equals("py")) {
+ currentMesh.thisID += "a";
+ createLcaoLobe(y, 1);
+ setProperty("thisID", id + "b", null);
+ createLcaoLobe(y, -1);
+ currentMesh.colix = Graphics3D.getColix(colorNeg);
+ return;
+ }
+ if (lcaoCartoon.equals("pz")) {
+ currentMesh.thisID += "a";
+ createLcaoLobe(z, 1);
+ setProperty("thisID", id + "b", null);
+ createLcaoLobe(z, -1);
+ currentMesh.colix = Graphics3D.getColix(colorNeg);
+ return;
+ }
+ if (lcaoCartoon.equals("pxa")) {
+ createLcaoLobe(x, 1);
+ return;
+ }
+ if (lcaoCartoon.equals("pxb")) {
+ createLcaoLobe(x, -1);
+ return;
+ }
+ if (lcaoCartoon.equals("pya")) {
+ createLcaoLobe(y, 1);
+ return;
+ }
+ if (lcaoCartoon.equals("pyb")) {
+ createLcaoLobe(y, -1);
+ return;
+ }
+ if (lcaoCartoon.equals("pza") || lcaoCartoon.indexOf("sp") == 0 ||
lcaoCartoon.indexOf("lp") == 0) {
+ createLcaoLobe(z, 1);
+ return;
+ }
+ if (lcaoCartoon.equals("pzb")) {
+ createLcaoLobe(z, -1);
+ return;
+ }
+ // assume s
+ createLcaoLobe(null, 1);
+ return;
+ }
+
+ Point4f lcaoDir = new Point4f();
+
+ void createLcaoLobe(Vector3f lobeAxis, float factor) {
+ initState();
+ System.out.println("creating isosurface " + currentMesh.thisID);
+ if (lobeAxis == null) {
+ setProperty("sphere", new Float(factor / 2f), null);
+ return;
+ }
+ lcaoDir.x = lobeAxis.x * factor;
+ lcaoDir.y = lobeAxis.y * factor;
+ lcaoDir.z = lobeAxis.z * factor;
+ lcaoDir.w = 0.5f;
+ setProperty("lobe", lcaoDir, null);
+ }
+
//// visibility methods
void setModelIndex() {
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/JmolConstants.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/JmolConstants.java
2006-06-29 17:21:25 UTC (rev 5253)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/JmolConstants.java
2006-06-30 03:14:13 UTC (rev 5254)
@@ -39,7 +39,7 @@
// for now, just update this by hand
// perhaps use ant filter later ... but mth doesn't like it :-(
public final static String copyright = "(C) 2006 Jmol Development";
- public final static String version = "10.x.15(branch bob200603)";
+ public final static String version = "10.x.17(branch bob200603)";
public final static String cvsDate = "$Date$";
public final static String date = cvsDate.substring(7, 23);
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/MeshCollection.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/MeshCollection.java
2006-06-29 17:21:25 UTC (rev 5253)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/MeshCollection.java
2006-06-30 03:14:13 UTC (rev 5254)
@@ -175,6 +175,7 @@
meshCount = 0;
}
}
+
int getIndexFromName(String thisID) {
for (int i = meshCount; --i >= 0; ) {
if (meshes[i] != null && thisID.equals(meshes[i].thisID))
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/ModelManager.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/ModelManager.java
2006-06-29 17:21:25 UTC (rev 5253)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/ModelManager.java
2006-06-30 03:14:13 UTC (rev 5254)
@@ -1462,4 +1462,9 @@
frame.setAtomCoordRelative(atomIndex,x,y,z);
}
+ void getPrincipalAxes(int atomIndex, Vector3f z, Vector3f x, String
lcaoType) {
+ if (frame == null)
+ return;
+ frame.getPrincipalAxes(atomIndex, z, x, lcaoType);
+ }
}
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/Viewer.java 2006-06-29
17:21:25 UTC (rev 5253)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Viewer.java 2006-06-30
03:14:13 UTC (rev 5254)
@@ -1147,6 +1147,10 @@
void clearBfactorRange(){
modelManager.clearBfactorRange();
}
+
+ void getPrincipalAxes(int atomIndex, Vector3f z, Vector3f x, String
lcaoType) {
+ modelManager.getPrincipalAxes(atomIndex, z, x, lcaoType);
+ }
BitSet getModelAtomBitSet(int modelIndex) {
return modelManager.getModelAtomBitSet(modelIndex);
@@ -1197,7 +1201,7 @@
return modelManager.getExportJmolAdapter();
}
- Frame getFrame() {
+ public Frame getFrame() {
return modelManager.getFrame();
}
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