From: <raj...@us...> - 2006-12-20 20:41:16
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Revision: 7535 http://svn.sourceforge.net/cdk/?rev=7535&view=rev Author: rajarshi Date: 2006-12-20 12:41:03 -0800 (Wed, 20 Dec 2006) Log Message: ----------- fixed some deprecated code Modified Paths: -------------- trunk/cdk/src/org/openscience/cdk/geometry/BondTools.java trunk/cdk/src/org/openscience/cdk/geometry/GeometryTools.java trunk/cdk/src/org/openscience/cdk/geometry/GeometryToolsInternalCoordinates.java Modified: trunk/cdk/src/org/openscience/cdk/geometry/BondTools.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/geometry/BondTools.java 2006-12-20 20:35:25 UTC (rev 7534) +++ trunk/cdk/src/org/openscience/cdk/geometry/BondTools.java 2006-12-20 20:41:03 UTC (rev 7535) @@ -68,7 +68,7 @@ from = conAtom; } } - boolean[] array = new boolean[container.getBonds().length]; + boolean[] array = new boolean[container.getBondCount()]; for (int i = 0; i < array.length; i++) { array[i] = true; } Modified: trunk/cdk/src/org/openscience/cdk/geometry/GeometryTools.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/geometry/GeometryTools.java 2006-12-20 20:35:25 UTC (rev 7534) +++ trunk/cdk/src/org/openscience/cdk/geometry/GeometryTools.java 2006-12-20 20:41:03 UTC (rev 7535) @@ -29,20 +29,15 @@ */ package org.openscience.cdk.geometry; -import org.openscience.cdk.CDKConstants; -import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.*; -import org.openscience.cdk.isomorphism.UniversalIsomorphismTester; -import org.openscience.cdk.isomorphism.mcss.RMap; import org.openscience.cdk.tools.LoggingTool; import org.openscience.cdk.tools.manipulator.ChemModelManipulator; import javax.vecmath.Point2d; -import javax.vecmath.Point3d; import javax.vecmath.Vector2d; -import javax.vecmath.Vector3d; import java.awt.*; -import java.util.*; +import java.util.HashMap; +import java.util.Iterator; import java.util.List; /** @@ -651,10 +646,10 @@ */ public static double getBondLengthAverage(IAtomContainer ac, HashMap renderingCoordinates) { double bondLengthSum = 0; - IBond[] bonds = ac.getBonds(); - int bondCounter = 0; - for (int f = 0; f < bonds.length; f++) { - IBond bond = bonds[f]; + Iterator bonds = ac.bonds(); + int bondCounter = 0; + while (bonds.hasNext()) { + IBond bond = (IBond) bonds.next(); org.openscience.cdk.interfaces.IAtom atom1 = bond.getAtom(0); org.openscience.cdk.interfaces.IAtom atom2 = bond.getAtom(1); if (renderingCoordinates.get(atom1) != null && @@ -752,7 +747,7 @@ /** * Determines if this model contains 3D coordinates * - *@param m Description of the Parameter + *@param ac Description of the Parameter *@return boolean indication that 3D coordinates are available */ public static boolean has3DCoordinates(IAtomContainer ac) { @@ -763,7 +758,7 @@ * Determines if this AtomContainer contains 2D coordinates for some or all molecules. * See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets * - *@param m Description of the Parameter + *@param ac Description of the Parameter *@return 0 no 2d, 1=some, 2= for each atom */ public static int has2DCoordinatesNew(IAtomContainer ac) { Modified: trunk/cdk/src/org/openscience/cdk/geometry/GeometryToolsInternalCoordinates.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/geometry/GeometryToolsInternalCoordinates.java 2006-12-20 20:35:25 UTC (rev 7534) +++ trunk/cdk/src/org/openscience/cdk/geometry/GeometryToolsInternalCoordinates.java 2006-12-20 20:41:03 UTC (rev 7535) @@ -31,11 +31,13 @@ import org.openscience.cdk.CDKConstants; import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.interfaces.*; +import org.openscience.cdk.interfaces.IAtom; +import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IBond; +import org.openscience.cdk.interfaces.IRingSet; import org.openscience.cdk.isomorphism.UniversalIsomorphismTester; import org.openscience.cdk.isomorphism.mcss.RMap; import org.openscience.cdk.tools.LoggingTool; -import org.openscience.cdk.tools.manipulator.ChemModelManipulator; import javax.vecmath.Point2d; import javax.vecmath.Point3d; @@ -669,12 +671,12 @@ public static IBond getClosestBond(int xPosition, int yPosition, IAtomContainer atomCon) { Point2d bondCenter; IBond closestBond = null; - IBond currentBond; + double smallestMouseDistance = -1; double mouseDistance; - IBond[] bonds = atomCon.getBonds(); - for (int i = 0; i < bonds.length; i++) { - currentBond = bonds[i]; + Iterator bonds = atomCon.bonds(); + while (bonds.hasNext()) { + IBond currentBond = (IBond) bonds.next(); bondCenter = get2DCenter(currentBond.atoms()); mouseDistance = Math.sqrt(Math.pow(bondCenter.x - xPosition, 2) + Math.pow(bondCenter.y - yPosition, 2)); if (mouseDistance < smallestMouseDistance || smallestMouseDistance == -1) { @@ -749,10 +751,10 @@ */ public static double getBondLengthAverage(IAtomContainer ac) { double bondLengthSum = 0; - IBond[] bonds = ac.getBonds(); - int bondCounter = 0; - for (int f = 0; f < bonds.length; f++) { - IBond bond = bonds[f]; + Iterator bonds = ac.bonds(); + int bondCounter = 0; + while (bonds.hasNext()) { + IBond bond = (IBond) bonds.next(); org.openscience.cdk.interfaces.IAtom atom1 = bond.getAtom(0); org.openscience.cdk.interfaces.IAtom atom2 = bond.getAtom(1); if (atom1.getPoint2d() != null && @@ -903,7 +905,6 @@ *@return The normalizationFactor value */ public static double getNormalizationFactor(IAtomContainer container) { - IBond[] bonds = container.getBonds(); double bondlength = 0.0; double ratio; /* @@ -913,12 +914,14 @@ double desiredBondLength = 1.5; // loop over all bonds and determine the mean bond distance int counter = 0; - for (int f = 0; f < bonds.length; f++) { + Iterator bonds = container.bonds(); + while (bonds.hasNext()) { + IBond bond = (IBond) bonds.next(); // only consider two atom bonds into account - if (bonds[f].getAtomCount() == 2) { + if (bond.getAtomCount() == 2) { counter++; - org.openscience.cdk.interfaces.IAtom atom1 = bonds[f].getAtom(0); - org.openscience.cdk.interfaces.IAtom atom2 = bonds[f].getAtom(1); + org.openscience.cdk.interfaces.IAtom atom1 = bond.getAtom(0); + org.openscience.cdk.interfaces.IAtom atom2 = bond.getAtom(1); bondlength += Math.sqrt(Math.pow(atom1.getPoint2d().x - atom2.getPoint2d().x, 2) + Math.pow(atom1.getPoint2d().y - atom2.getPoint2d().y, 2)); } @@ -1352,10 +1355,10 @@ */ public static double getBondLengthAverage3D(IAtomContainer ac) { double bondLengthSum = 0; - IBond[] bonds = ac.getBonds(); - int bondCounter = 0; - for (int f = 0; f < bonds.length; f++) { - IBond bond = bonds[f]; + Iterator bonds = ac.bonds(); + int bondCounter = 0; + while (bonds.hasNext()) { + IBond bond = (IBond) bonds.next(); org.openscience.cdk.interfaces.IAtom atom1 = bond.getAtom(0); org.openscience.cdk.interfaces.IAtom atom2 = bond.getAtom(1); if (atom1.getPoint3d() != null && This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |