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[Cdk-commits] CVS: cdk/src/org/openscience/cdk LonePair.java,NONE,1.1 AtomContainer.java,1.22,1.23 Ring.java,1.7,1.8 RingSet.java,1.5,1.6
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From: Egon W. <eg...@us...> - 2002-12-21 20:55:19
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Update of /cvsroot/cdk/cdk/src/org/openscience/cdk
In directory sc8-pr-cvs1:/tmp/cvs-serv27153/src/org/openscience/cdk
Modified Files:
AtomContainer.java Ring.java RingSet.java
Added Files:
LonePair.java
Log Message:
Big step in implementing RFC #5. Not fully checked for complete implementation.
--- NEW FILE: LonePair.java ---
/* $RCSfile: LonePair.java,v $
* $Author: egonw $
* $Date: 2002/12/21 20:54:46 $
* $Revision: 1.1 $
*
* Copyright (C) 1997-2002 The Chemistry Development Kit (CDK) project
*
* Contact: ste...@ic..., gez...@ma..., eg...@sc...
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
*/
package org.openscience.cdk;
/**
* Base class for entities containing electrons, like bonds, orbitals, lone-pairs.
*
* @keyword orbital
* @keyword lone-pair
* @keyword bond
*/
public class LonePair extends ElectronContainer {
/** Number of electrons in the lone pair. */
protected final int electronCount = 2;
/** The atom with which this lone pair is associated. */
protected Atom atom;
/**
* Constructs an unconnected lone pair.
*
*/
public LonePair() {
atom = null;
}
/**
* Constructs an lone pair on an Atom.
*
*/
public LonePair(Atom a) {
this.atom = a;
}
/**
* Returns the number of electrons in this electron container.
*
* @return The number of electrons in this electron container.
*
* @see #setElectronCount
*/
public int getElectronCount() {
return this.electronCount;
}
/**
* Returns the associated Atom.
*
* @return the associated Atom.
*
* @see #setAtom
*/
public Atom getAtom() {
return this.atom;
}
/**
* Sets the associated Atom.
*
* @param atom the Atom this lone pair will be associated with
*
* @see #getAtom
*/
public void setAtom(Atom a) {
this.atom = a;
}
/**
* Returns true if the given atom participates in this lone pair.
*
* @param atom The atom to be tested if it participates in this bond
* @return true if this lone pair is associated with the atom
*/
public boolean contains(Atom atom) {
return (atom == atom) ? true : false;
}
}
Index: AtomContainer.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/AtomContainer.java,v
retrieving revision 1.22
retrieving revision 1.23
diff -C2 -r1.22 -r1.23
*** AtomContainer.java 22 Oct 2002 14:25:34 -0000 1.22
--- AtomContainer.java 21 Dec 2002 20:54:46 -0000 1.23
***************
*** 29,33 ****
/**
! * Base class for all chemical objects that maintain a list of Atoms and Bonds.
*
* @author steinbeck
--- 29,41 ----
/**
! * Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.
! *
[...1239 lines suppressed...]
! bonds = newbonds;
! }
--- 1170,1184 ----
! /**
! * Grows the ElectronContainer array by a given size.
! *
! * @see #growArraySize
! */
! protected void growElectronContainerArray() {
! growArraySize = electronContainers.length;
! ElectronContainer[] newelectronContainers = new ElectronContainer[electronContainers.length + growArraySize];
! System.arraycopy(electronContainers, 0, newelectronContainers, 0, electronContainers.length);
! electronContainers = newelectronContainers;
! }
Index: Ring.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/Ring.java,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -r1.7 -r1.8
*** Ring.java 2 Oct 2002 13:17:50 -0000 1.7
--- Ring.java 21 Dec 2002 20:54:46 -0000 1.8
***************
*** 64,70 ****
{
atoms[i] = new Atom(elementSymbol);
! super.bonds[i - 1] = new Bond(atoms[i - 1], atoms[i], 1);
}
! super.bonds[ringSize - 1] = new Bond(atoms[ringSize - 1], atoms[0], 1);
super.atoms = atoms;
}
--- 64,70 ----
{
atoms[i] = new Atom(elementSymbol);
! super.addElectronContainer(new Bond(atoms[i - 1], atoms[i], 1));
}
! super.addElectronContainer(new Bond(atoms[ringSize - 1], atoms[0], 1));
super.atoms = atoms;
}
***************
*** 107,117 ****
{
Bond tempBond;
! for (int f = 0; f < getBondCount(); f++)
! {
! tempBond = getBondAt(f);
! if (tempBond.contains(atom) && bond != tempBond)
! {
! return tempBond;
! }
}
return null;
--- 107,118 ----
{
Bond tempBond;
! for (int f = 0; f < getElectronContainerCount(); f++) {
! ElectronContainer ec = getElectronContainerAt(f);
! if (ec instanceof Bond) {
! tempBond = (Bond)ec;
! if (tempBond.contains(atom) && bond != tempBond) {
! return tempBond;
! }
! }
}
return null;
***************
*** 127,134 ****
int orderSum = 0;
Bond tempBond;
! for (int i = 0; i < getBondCount(); i++)
! {
! tempBond = getBondAt(i);
! orderSum += tempBond.getOrder();
}
return orderSum;
--- 128,137 ----
int orderSum = 0;
Bond tempBond;
! for (int i = 0; i < getElectronContainerCount(); i++) {
! ElectronContainer ec = getElectronContainerAt(i);
! if (ec instanceof Bond) {
! tempBond = (Bond)ec;
! orderSum += tempBond.getOrder();
! }
}
return orderSum;
Index: RingSet.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/RingSet.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -r1.5 -r1.6
*** RingSet.java 26 Sep 2002 14:56:11 -0000 1.5
--- RingSet.java 21 Dec 2002 20:54:46 -0000 1.6
***************
*** 62,65 ****
--- 62,66 ----
Ring ring;
Bond[] bonds;
+ Bond[] newBonds;
Bond bond;
int equalCount;
***************
*** 71,83 ****
ring = (Ring)this.elementAt(f);
bonds = ring.getBonds();
! if (bonds.length == newRing.getBonds().length)
! {
! for (int i = 0; i < bonds.length; i++)
! {
! bond = newRing.getBondAt(i);
! for (int n = 0; n < bonds.length; n++)
! {
! if (bond == bonds[n])
! {
equals = true;
equalCount++;
--- 72,81 ----
ring = (Ring)this.elementAt(f);
bonds = ring.getBonds();
! newBonds = newRing.getBonds();
! if (bonds.length == newBonds.length) {
! for (int i = 0; i < bonds.length; i++) {
! bond = newBonds[i];
! for (int n = 0; n < bonds.length; n++) {
! if (bond == bonds[n]) {
equals = true;
equalCount++;
***************
*** 88,93 ****
}
}
! if (equalCount == bonds.length)
! {
return true;
}
--- 86,90 ----
}
}
! if (equalCount == bonds.length) {
return true;
}
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