From: <eg...@us...> - 2006-06-29 05:40:30
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Revision: 6528 Author: egonw Date: 2006-06-28 22:40:23 -0700 (Wed, 28 Jun 2006) ViewCVS: http://svn.sourceforge.net/cdk/?rev=6528&view=rev Log Message: ----------- Added tool to determine available features in a IMolecule. Added Paths: ----------- trunk/cdk/src/org/openscience/cdk/tools/DataFeaturesTool.java trunk/cdk/src/org/openscience/cdk/tools/features/MoleculeFeaturesTool.java Added: trunk/cdk/src/org/openscience/cdk/tools/DataFeaturesTool.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/tools/DataFeaturesTool.java (rev 0) +++ trunk/cdk/src/org/openscience/cdk/tools/DataFeaturesTool.java 2006-06-29 05:40:23 UTC (rev 6528) @@ -0,0 +1,70 @@ +/* $RCSfile: $ + * $Author: egonw $ + * $Date: 2006-05-09 21:32:32 +0200 (Tue, 09 May 2006) $ + * $Revision: 6204 $ + * + * Copyright (C) 2006 The Chemistry Development Kit (CDK) project + * + * Contact: cdk...@li... + * + * 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. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * 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., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + * + */ +package org.openscience.cdk.tools; + +import org.openscience.cdk.geometry.CrystalGeometryTools; +import org.openscience.cdk.geometry.GeometryTools; +import org.openscience.cdk.interfaces.IMolecule; +import org.openscience.cdk.tools.features.MoleculeFeaturesTool; + +/** + * Utility that helps determine which data features are present. + * + * @author egonw + * + * @see org.openscience.cdk.tools.DataFeatures + */ +public class DataFeaturesTool { + + /** + * Determines the features present in the given IMolecule. + * + * @param molecule IMolecule to determine the features off + * + * @return integer representation of the present features + */ + public int getSupportedDataFeatures(IMolecule molecule) { + int features = DataFeatures.NONE; + if (GeometryTools.has2DCoordinates(molecule)) + features = features | DataFeatures.HAS_2D_COORDINATES; + if (GeometryTools.has3DCoordinates(molecule)) + features = features | DataFeatures.HAS_3D_COORDINATES; + if (CrystalGeometryTools.hasCrystalCoordinates(molecule)) + features = features | DataFeatures.HAS_FRACTIONAL_CRYSTAL_COORDINATES; + if (MoleculeFeaturesTool.hasFormalCharges(molecule)) + features = features | DataFeatures.HAS_ATOM_FORMAL_CHARGES; + if (MoleculeFeaturesTool.hasPartialCharges(molecule)) + features = features | DataFeatures.HAS_ATOM_PARTIAL_CHARGES; + if (MoleculeFeaturesTool.hasGraphRepresentation(molecule)) + features = features | DataFeatures.HAS_GRAPH_REPRESENTATION; + return features; + } + + +} Added: trunk/cdk/src/org/openscience/cdk/tools/features/MoleculeFeaturesTool.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/tools/features/MoleculeFeaturesTool.java (rev 0) +++ trunk/cdk/src/org/openscience/cdk/tools/features/MoleculeFeaturesTool.java 2006-06-29 05:40:23 UTC (rev 6528) @@ -0,0 +1,75 @@ +/* $RCSfile: $ + * $Author: egonw $ + * $Date: 2006-05-09 21:32:32 +0200 (Tue, 09 May 2006) $ + * $Revision: 6204 $ + * + * Copyright (C) 2006 The Chemistry Development Kit (CDK) project + * + * Contact: cdk...@li... + * + * 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. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * 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., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + * + */ +package org.openscience.cdk.tools.features; + +import org.openscience.cdk.interfaces.IAtom; +import org.openscience.cdk.interfaces.IBond; +import org.openscience.cdk.interfaces.IMolecule; +import org.openscience.cdk.tools.DataFeatures; + +/** + * Utility that helps determine which data features are present. + * + * @author egonw + * + * @see DataFeatures + */ +public class MoleculeFeaturesTool { + + public static boolean hasPartialCharges(IMolecule molecule) { + IAtom[] atoms = molecule.getAtoms(); + for (int i=0; i<atoms.length; i++) { + if (atoms[i].getCharge() != 0.0000) return true; + } + return false; + } + + public static boolean hasFormalCharges(IMolecule molecule) { + IAtom[] atoms = molecule.getAtoms(); + for (int i=0; i<atoms.length; i++) { + if (atoms[i].getFormalCharge() != 0) return true; + } + return false; + } + + /** + * Checks wether all bonds have exactly two atoms. + * + * @param molecule + * @return + */ + public static boolean hasGraphRepresentation(IMolecule molecule) { + IBond[] bonds = molecule.getBonds(); + for (int i=0; i<bonds.length; i++) { + if (bonds[i].getAtomCount() != 2) return false; + } + return true; + } + +} This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |