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[Cdk-commits] CVS: cdk/src/org/openscience/cdk Atom.java,1.3,1.4 AtomContainer.java,1.15,1.16 Isotope.java,1.4,1.5 Molecule.java,1.3,1.4 Monomer.java,1.2,1.3 RingSet.java,1.3,1.4
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From: Egon W. <eg...@us...> - 2002-09-23 11:16:09
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Update of /cvsroot/cdk/cdk/src/org/openscience/cdk
In directory usw-pr-cvs1:/tmp/cvs-serv14906/src/org/openscience/cdk
Modified Files:
Atom.java AtomContainer.java Isotope.java Molecule.java
Monomer.java RingSet.java
Log Message:
Removed NoSuchAtomException's from core classes
(see RFC #4, fixes bugs #590570 and #590576).
Index: Atom.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/Atom.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -r1.3 -r1.4
*** Atom.java 16 Aug 2002 20:15:38 -0000 1.3
--- Atom.java 23 Sep 2002 11:16:04 -0000 1.4
***************
*** 68,76 ****
* Constructs an Atom from a String containing an element symbol
*
! * @param element The String describing the element for the Atom
*/
public Atom(String elementSymbol)
{
! super(elementSymbol);
this.point3D = null;
this.point2D = null;
--- 68,76 ----
* Constructs an Atom from a String containing an element symbol
*
! * @param elementSymbol The String describing the element for the Atom
*/
public Atom(String elementSymbol)
{
! super(elementSymbol);
this.point3D = null;
this.point2D = null;
***************
*** 80,85 ****
* Constructs an Atom from an Element and a Point3D
*
! * @param element The Element
! * @param point3D The Point
*/
public Atom(String elementSymbol, javax.vecmath.Point3d point3D)
--- 80,85 ----
* Constructs an Atom from an Element and a Point3D
*
! * @param elementSymbol The symbol of the atom
! * @param point3D The 3D coordinates of the atom
*/
public Atom(String elementSymbol, javax.vecmath.Point3d point3D)
***************
*** 92,97 ****
* Constructs an Atom from an Element and a Point2D
*
! * @param element The Element
! * @param point2D The Point
*/
public Atom(String elementSymbol, javax.vecmath.Point2d point2D)
--- 92,97 ----
* Constructs an Atom from an Element and a Point2D
*
! * @param elementSymbol The Element
! * @param point2D The Point
*/
public Atom(String elementSymbol, javax.vecmath.Point2d point2D)
***************
*** 104,108 ****
* Sets the partial charge of this atom
*
! * @param element The partial charge
*/
public void setCharge(double charge) {
--- 104,108 ----
* Sets the partial charge of this atom
*
! * @param charge The partial charge
*/
public void setCharge(double charge) {
***************
*** 112,115 ****
--- 112,117 ----
/**
* Returns the partial charge of this atom
+ *
+ * @return the charge of this atom
*/
public double getCharge() {
***************
*** 341,349 ****
/**
! * Returns the stereo parity of this atom
*
* @return The stereo parity for this atom
* @see org.openscience.cdk.CDKConstants
- * org.openscience.cdk.CDKConstants for predefined values.
*/
public int getStereoParity() {
--- 343,351 ----
/**
! * Returns the stereo parity of this atom. It uses the predefined values
! * found in CDKConstants.
*
* @return The stereo parity for this atom
* @see org.openscience.cdk.CDKConstants
*/
public int getStereoParity() {
***************
*** 354,357 ****
--- 356,360 ----
* Compares a atom with this atom
*
+ * @param object of type Atom
* @return return true, if the atoms are equal
*/
Index: AtomContainer.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/AtomContainer.java,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -r1.15 -r1.16
*** AtomContainer.java 20 Sep 2002 09:40:45 -0000 1.15
--- AtomContainer.java 23 Sep 2002 11:16:04 -0000 1.16
***************
*** 235,239 ****
/**
! * Returns the position of a given atom in the atoms array
*
* @param atom The atom to be sought
--- 235,240 ----
/**
! * Returns the position of a given atom in the atoms array. It returns -1 if
! * the atom atom does not exist.
*
* @param atom The atom to be sought
***************
*** 241,254 ****
*/
! public int getAtomNumber(Atom atom) throws org.openscience.cdk.exception.NoSuchAtomException
! {
! for (int f = 0; f < getAtomCount(); f++)
! {
! if (getAtomAt(f) == atom)
! {
return f;
}
}
! throw new org.openscience.cdk.exception.NoSuchAtomException("No such Atom");
}
--- 242,252 ----
*/
! public int getAtomNumber(Atom atom) {
! for (int f = 0; f < getAtomCount(); f++) {
! if (getAtomAt(f) == atom) {
return f;
}
}
! return -1;
}
***************
*** 465,472 ****
/**
* Compares this AtomContainer with another given AtomContainer and returns
! * the Intersection between them Important Note: This is not a maximum common
! * substructure
! *
! * @return An AtomContainer containing the Intersection between this AtomContainer
* and another given one
*/
--- 463,473 ----
/**
* Compares this AtomContainer with another given AtomContainer and returns
! * the Intersection between them.
! *
! * <p><b>Important Note</b>: This is not a maximum common
! * substructure.
! *
! * @param ac an AtomContainer object
! * @return An AtomContainer containing the Intersection between this AtomContainer
* and another given one
*/
***************
*** 559,564 ****
*/
! public double[][] getConnectionMatrix() throws org.openscience.cdk.exception.NoSuchAtomException
! {
Bond bond = null;
int i;
--- 560,564 ----
*/
! public double[][] getConnectionMatrix() {
Bond bond = null;
int i;
***************
*** 582,585 ****
--- 582,586 ----
* 1, if the i-th and the j-th atom in the atomcontainer share a bond. Otherwise it
* is zero.
+ *
* References:
* <a href="http://cdk.sf.net/biblio.html#TRI1992">TRI1992</a>,
***************
*** 589,593 ****
* @keyword adjacency matrix
*/
! public int[][] getAdjacencyMatrix() throws org.openscience.cdk.exception.NoSuchAtomException {
Bond bond = null;
int i;
--- 590,594 ----
* @keyword adjacency matrix
*/
! public int[][] getAdjacencyMatrix() {
Bond bond = null;
int i;
***************
*** 706,713 ****
* Removes all atoms and bonds of a given atomcontainer from this container
*
! * @param atomContainer The atomcontainer to be removed
*/
! public void remove(AtomContainer atomContainer) throws org.openscience.cdk.exception.NoSuchAtomException
! {
for (int f = 0; f < atomContainer.getAtomCount(); f++)
{
--- 707,713 ----
* Removes all atoms and bonds of a given atomcontainer from this container
*
! * @param atomContainer The atomcontainer to be removed
*/
! public void remove(AtomContainer atomContainer) {
for (int f = 0; f < atomContainer.getAtomCount(); f++)
{
***************
*** 804,818 ****
*
* @param atom The atom to be removed
- * @exception org.openscience.cdk.exception.NoSuchAtomException throws if the atom is not in the container
*/
! public void removeAtomAndConnectedBonds(Atom atom) throws org.openscience.cdk.exception.NoSuchAtomException
! {
int position = getAtomNumber(atom);
! Bond[] bonds = getConnectedBonds(atom);
! for (int f = 0; f < bonds.length; f++)
! {
! removeBond(bonds[f]);
! }
! removeAtom(position);
}
--- 804,817 ----
*
* @param atom The atom to be removed
*/
! public void removeAtomAndConnectedBonds(Atom atom) {
int position = getAtomNumber(atom);
! if (position != -1) {
! Bond[] bonds = getConnectedBonds(atom);
! for (int f = 0; f < bonds.length; f++) {
! removeBond(bonds[f]);
! }
! removeAtom(position);
! }
}
***************
*** 824,833 ****
*
* @param atom The atom to be removed
- * @exception org.openscience.cdk.exception.NoSuchAtomException throws if the atom is not in the container
*/
! public void removeAtom(Atom atom) throws org.openscience.cdk.exception.NoSuchAtomException
! {
int position = getAtomNumber(atom);
! removeAtom(position);
}
--- 823,832 ----
*
* @param atom The atom to be removed
*/
! public void removeAtom(Atom atom) {
int position = getAtomNumber(atom);
! if (position != -1) {
! removeAtom(position);
! }
}
Index: Isotope.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/Isotope.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -r1.4 -r1.5
*** Isotope.java 19 Sep 2002 11:05:23 -0000 1.4
--- Isotope.java 23 Sep 2002 11:16:04 -0000 1.5
***************
*** 32,36 ****
/**
! * Isotope.java Used to store data of a particular isotope
*
* @author steinbeck
--- 32,36 ----
/**
! * Used to store and retrieve data of a particular isotope.
*
* @author steinbeck
***************
*** 42,47 ****
public class Isotope extends Element implements Cloneable {
! public double exactMass = (double) -1;
! public double naturalAbundance = (double) -1;
--- 42,49 ----
public class Isotope extends Element implements Cloneable {
! /** Exact mass of this isotope. */
! public double exactMass = (double) -1;
! /** Natural abundance of this isotope */
! public double naturalAbundance = (double) -1;
Index: Molecule.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/Molecule.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -r1.3 -r1.4
*** Molecule.java 19 Sep 2002 11:05:23 -0000 1.3
--- Molecule.java 23 Sep 2002 11:16:04 -0000 1.4
***************
*** 37,41 ****
public class Molecule extends AtomContainer
{
! public String title;
private Vector chemNames;
private String autonomName = "";
--- 37,41 ----
public class Molecule extends AtomContainer
{
! private String title;
private Vector chemNames;
private String autonomName = "";
Index: Monomer.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/Monomer.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -r1.2 -r1.3
*** Monomer.java 4 Aug 2002 12:25:46 -0000 1.2
--- Monomer.java 23 Sep 2002 11:16:04 -0000 1.3
***************
*** 44,50 ****
*/
public class Monomer extends AtomContainer {
! protected String _cMonomerName; // the name of this monomer (e.g. Trp42)
! protected String _cMonomerType; // the type of this monomer (e.g. TRP)
!
/**
*
--- 44,53 ----
*/
public class Monomer extends AtomContainer {
!
! /** The name of this monomer (e.g. Trp42). */
! protected String _cMonomerName;
! /** The type of this monomer (e.g. TRP). */
! protected String _cMonomerType;
!
/**
*
Index: RingSet.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/RingSet.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -r1.3 -r1.4
*** RingSet.java 17 Aug 2002 20:01:46 -0000 1.3
--- RingSet.java 23 Sep 2002 11:16:04 -0000 1.4
***************
*** 1,5 ****
! /* RingSet.java
! *
! * $RCSfile$
* $Author$
* $Date$
--- 1,3 ----
! /* $RCSfile$
* $Author$
* $Date$
***************
*** 38,43 ****
*/
public class RingSet extends Vector{
!
public final static int LARGE_FIRST = 1;
public final static int SMALL_FIRST = 2;
--- 36,43 ----
*/
public class RingSet extends Vector{
!
! /** Flag to denote that the set is order with the largest ring first? */
public final static int LARGE_FIRST = 1;
+ /** Flag to denote that the set is order with the smallest ring first? */
public final static int SMALL_FIRST = 2;
***************
*** 340,348 ****
}
!
! public class RingSizeComparator implements java.util.Comparator
! {
int sortOrder = SMALL_FIRST;
!
public RingSizeComparator(int so)
{
--- 340,357 ----
}
!
! /**
! * Comparator to sort Ring sets by size.
! */
! public class RingSizeComparator implements java.util.Comparator {
!
int sortOrder = SMALL_FIRST;
!
! /**
! * Constructs a new comparator to sort rings by size.
! *
! * @param so Sort order: either RingSet.SMALL_FIRST or
! * RingSet.LARGE_FIRST.
! */
public RingSizeComparator(int so)
{
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