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[Jmol-commits] CVS: Jmol/src/org/openscience/jmol Atom.java,1.55,1.56 ChemFrame.java,1.101,1.102 Convertor.java,1.1,1.2 CrystalFile.java,1.15,1.16 JmolCDO.java,1.5,1.6
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From: Egon W. <eg...@us...> - 2003-03-25 08:05:36
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Update of /cvsroot/jmol/Jmol/src/org/openscience/jmol
In directory sc8-pr-cvs1:/tmp/cvs-serv3372/src/org/openscience/jmol
Modified Files:
Atom.java ChemFrame.java Convertor.java CrystalFile.java
JmolCDO.java
Log Message:
More removal (forgot exactly what) of obsolete stuff to simplify code
Index: Atom.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/Atom.java,v
retrieving revision 1.55
retrieving revision 1.56
diff -u -r1.55 -r1.56
--- Atom.java 25 Mar 2003 07:07:51 -0000 1.55
+++ Atom.java 25 Mar 2003 08:04:46 -0000 1.56
@@ -3,7 +3,7 @@
* $Date$
* $Revision$
*
- * Copyright (C) 2002 The Jmol Development Team
+ * Copyright (C) 2002-2003 The Jmol Development Team
*
* Contact: jmo...@li...
*
@@ -42,20 +42,6 @@
*
* @param the type of this atom.
*/
- public Atom(BaseAtomType baseAtomType, int atomNumber,
- double x, double y, double z, ProteinProp pprop) {
- super(baseAtomType.getSymbol(), new Point3d(x, y, z));
- super.setID(baseAtomType.getID());
- this.baseAtomType = baseAtomType;
- this.atomNumber = atomNumber;
- this.pprop = pprop;
- }
-
- /**
- * Creates an atom with the given type.
- *
- * @param the type of this atom.
- */
public Atom(Atom atom, int atomNumber,
double x, double y, double z, ProteinProp pprop) {
super(atom.getSymbol(), new Point3d(x, y, z));
@@ -95,6 +81,10 @@
ProteinProp pprop = null;
public ProteinProp getProteinProp() {
return pprop;
+ }
+
+ public void setProteinProp(ProteinProp pprop) {
+ this.pprop = pprop;
}
/**
Index: ChemFrame.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/ChemFrame.java,v
retrieving revision 1.101
retrieving revision 1.102
diff -u -r1.101 -r1.102
--- ChemFrame.java 11 Feb 2003 12:13:02 -0000 1.101
+++ ChemFrame.java 25 Mar 2003 08:04:47 -0000 1.102
@@ -18,6 +18,7 @@
*/
package org.openscience.jmol;
+import org.openscience.jmol.Atom;
import org.openscience.cdk.AtomContainer;
import java.beans.PropertyChangeSupport;
import java.beans.PropertyChangeListener;
@@ -151,63 +152,6 @@
return info;
}
- /**
- * Adds an atom to the frame and finds all bonds between the
- * new atom and pre-existing atoms in the frame
- *
- * @param name the name of the extended atom type for the new atom
- * @param x the x coordinate of the new atom
- * @param y the y coordinate of the new atom
- * @param z the z coordinate of the new atom
- */
- public int addAtom(String name, double x, double y, double z) {
- return addAtom(BaseAtomType.get(name, name), x, y, z, null);
- }
-
- public int addAtom(String name, double x, double y, double z,
- ProteinProp pprop) {
- return addAtom(BaseAtomType.get(name, name), x, y, z, pprop);
- }
-
- public int addAtom(String name, String root, double x, double y, double z) {
- return addAtom(BaseAtomType.get(name, root), x, y, z, null);
- }
-
- /**
- * Adds an atom to the frame and finds all bonds between the
- * new atom and pre-existing atoms in the frame
- *
- * @param type atom type for the new atom
- * @param x the x coordinate of the new atom
- * @param y the y coordinate of the new atom
- * @param z the z coordinate of the new atom
- */
- public int addAtom(BaseAtomType type, double x, double y, double z) {
- return addAtom(type, x, y, z, null);
- }
-
- public int addAtom(BaseAtomType type, double x, double y, double z,
- ProteinProp pprop) {
-
- clearBounds();
- int i = numberOfAtoms;
- if (i >= atoms.length) {
- setAtomArraySize(2 * atoms.length);
- }
-
- atoms[i] = new Atom(type, numberOfAtoms, x, y, z, pprop);
- AtomTypeList.getInstance().configure(atoms[i]);
- if (DisplayControl.control.getAutoBond()) {
- for (int j = 0; j < i; j++) {
- if (Atom.closeEnoughToBond(atoms[i], atoms[j],
- DisplayControl.control.getBondFudge())) {
- addBond(i, j);
- }
- }
- }
- return numberOfAtoms++;
- }
-
public int addAtom(Atom type, double x, double y, double z) {
return addAtom(type, x, y, z, null);
}
@@ -244,11 +188,13 @@
*/
public int addAtom(int atomicNumber, double x, double y, double z) {
- BaseAtomType baseType = BaseAtomType.get(atomicNumber);
- if (baseType == null) {
- return -1;
- }
- return addAtom(baseType, x, y, z);
+ org.openscience.cdk.Atom atom = new org.openscience.cdk.Atom("");
+ atom.setAtomicNumber(atomicNumber);
+ atom.setX3D(x);
+ atom.setY3D(y);
+ atom.setZ3D(z);
+ addAtom(atom);
+ return getAtomCount();
}
/**
Index: Convertor.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/Convertor.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- Convertor.java 26 Feb 2003 17:39:45 -0000 1.1
+++ Convertor.java 25 Mar 2003 08:04:52 -0000 1.2
@@ -90,25 +90,8 @@
int NOatoms = ac.getAtomCount();
ChemFrame converted = new ChemFrame(NOatoms);
for (int i=0; i<NOatoms; i++) {
- org.openscience.cdk.Atom atom = ac.getAtomAt(i);
- javax.vecmath.Point3d xyz = atom.getPoint3D();
- if (atom.getPoint3D() != null) {
- } else if (atom.getPoint2D() != null) {
- xyz =
- new javax.vecmath.Point3d(
- atom.getX2D(),
- atom.getY2D(),
- 0.0
- );
- } else {
- xyz = new javax.vecmath.Point3d(0.0, 0.0, 0.0);
- }
- converted.addAtom(
- atom.getSymbol(),
- (float)xyz.x,
- (float)xyz.y,
- (float)xyz.z
- );
+ org.openscience.cdk.Atom atom = (org.openscience.cdk.Atom)ac.getAtomAt(i).clone();
+ converted.addAtom(atom);
}
return converted;
} else {
Index: CrystalFile.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/CrystalFile.java,v
retrieving revision 1.15
retrieving revision 1.16
diff -u -r1.15 -r1.16
--- CrystalFile.java 28 Feb 2003 09:18:39 -0000 1.15
+++ CrystalFile.java 25 Mar 2003 08:04:53 -0000 1.16
@@ -366,7 +366,8 @@
double[] newAtomCartPos = new double[3];
newAtomCartPos = MathUtil.mulVec(op, newAtomRedPos);
- crystalFrame.addAtom(unitCellBoxS.getBaseAtomType(at),
+ BaseAtomType bat = unitCellBoxS.getBaseAtomType(at);
+ crystalFrame.addAtom(bat.getAtomicNumber(),
newAtomCartPos[0], newAtomCartPos[1], newAtomCartPos[2]);
Index: JmolCDO.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/JmolCDO.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- JmolCDO.java 3 Feb 2003 15:20:35 -0000 1.5
+++ JmolCDO.java 25 Mar 2003 08:04:54 -0000 1.6
@@ -20,6 +20,7 @@
import java.util.Vector;
import java.util.Enumeration;
+import org.openscience.cdk.Atom;
import org.openscience.cdk.io.cml.cdopi.ANIMATIONCDO;
import org.openscience.cdk.io.cml.cdopi.CDOAcceptedObjects;
@@ -201,7 +202,12 @@
double z = FortranFormat.atof(atomZ.trim());
try {
- int index = currentFrame.addAtom(atomType.trim(), x, y, z, null);
+ org.openscience.cdk.Atom atom = new org.openscience.cdk.Atom(atomType.trim());
+ atom.setX3D(x);
+ atom.setY3D(y);
+ atom.setZ3D(z);
+ currentFrame.addAtom(atom);
+ int index = currentFrame.getAtomCount();
if (partialCharge.length() > 0) {
// System.out.println("Adding charge for atom " + index);
double c = FortranFormat.atof(partialCharge);
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