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[Cdk-commits] SF.net SVN: cdk: [8135] trunk/cdk/src/org/openscience/cdk/test/modeling/ builder3d
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From: <eg...@us...> - 2007-03-16 15:15:29
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Revision: 8135
http://svn.sourceforge.net/cdk/?rev=8135&view=rev
Author: egonw
Date: 2007-03-16 08:14:57 -0700 (Fri, 16 Mar 2007)
Log Message:
-----------
No need to write into a CMLbased ChemFile.
Modified Paths:
--------------
trunk/cdk/src/org/openscience/cdk/test/modeling/builder3d/ModelBuilder3dTest.java
Removed Paths:
-------------
trunk/cdk/src/org/openscience/cdk/test/modeling/builder3d/CMLChemFileWrapper.java
Deleted: trunk/cdk/src/org/openscience/cdk/test/modeling/builder3d/CMLChemFileWrapper.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/test/modeling/builder3d/CMLChemFileWrapper.java 2007-03-16 15:00:43 UTC (rev 8134)
+++ trunk/cdk/src/org/openscience/cdk/test/modeling/builder3d/CMLChemFileWrapper.java 2007-03-16 15:14:57 UTC (rev 8135)
@@ -1,63 +0,0 @@
-/*
- * $RCSfile$
- * $Author: egonw $
- * $Date: 2007-01-31 18:46:38 +0100 (Wed, 31 Jan 2007) $
- *
- * Copyright (C) 1997-2007 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.
- *
- * 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.test.modeling.builder3d;
-
-import org.openscience.cdk.interfaces.IAtomContainer;
-import org.openscience.cdk.interfaces.IChemModel;
-import org.openscience.cdk.interfaces.IChemSequence;
-import org.openscience.cdk.interfaces.IMoleculeSet;
-
-/**
- * @cdk.module test-builder3d
- *
- * @author chhoppe
- * @cdk.created 2004-11-04
- */
-public class CMLChemFileWrapper {
- /**
- * Method which converts an atomContainer to a CMLChemFile
- * @param atomContainer
- * @return CMLChemFile which contains the information of the atomContainer
- */
- public static CMLChemFile wrapAtomContainerInChemModel(IAtomContainer atomContainer) {
- CMLChemFile file = new CMLChemFile();
- IChemModel model = atomContainer.getBuilder().newChemModel();
- IChemSequence sequence = atomContainer.getBuilder().newChemSequence();
- IMoleculeSet moleculeSet = atomContainer.getBuilder().newMoleculeSet();
- moleculeSet.addAtomContainer(atomContainer);
- model.setMoleculeSet(moleculeSet);
- sequence.addChemModel(model);
- file.addChemSequence(sequence);
-
- return file;
- }
-
- public static CMLChemFile[] wrapAtomContainerArrayInChemModel(IAtomContainer[] atomContainer) {
- CMLChemFile[] cmlChemfile = new CMLChemFile[atomContainer.length];
- for (int i = 0; i < atomContainer.length; i++) {
- cmlChemfile[i] = wrapAtomContainerInChemModel(atomContainer[i]);
- }
- return cmlChemfile;
- }
-}
Modified: trunk/cdk/src/org/openscience/cdk/test/modeling/builder3d/ModelBuilder3dTest.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/test/modeling/builder3d/ModelBuilder3dTest.java 2007-03-16 15:00:43 UTC (rev 8134)
+++ trunk/cdk/src/org/openscience/cdk/test/modeling/builder3d/ModelBuilder3dTest.java 2007-03-16 15:14:57 UTC (rev 8135)
@@ -1,7 +1,4 @@
-/*
- * $RCSfile$
- * $Author$
- * $Date$
+/* $Revision$ $Author$ $Date$
*
* Copyright (C) 1997-2007 The Chemistry Development Kit (CDK) project
*
@@ -23,9 +20,7 @@
*/
package org.openscience.cdk.test.modeling.builder3d;
-import java.io.ByteArrayInputStream;
import java.io.InputStream;
-import java.io.StringWriter;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
@@ -43,12 +38,8 @@
import org.openscience.cdk.geometry.GeometryToolsInternalCoordinates;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
-import org.openscience.cdk.interfaces.IChemFile;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IMolecule;
-import org.openscience.cdk.io.CMLReader;
-import org.openscience.cdk.io.CMLWriter;
-import org.openscience.cdk.io.IChemObjectWriter;
import org.openscience.cdk.io.MDLV2000Reader;
import org.openscience.cdk.layout.StructureDiagramGenerator;
import org.openscience.cdk.modeling.builder3d.ModelBuilder3D;
@@ -57,7 +48,6 @@
import org.openscience.cdk.smiles.SmilesParser;
import org.openscience.cdk.test.CDKTestCase;
import org.openscience.cdk.tools.HydrogenAdder;
-import org.openscience.cdk.tools.IDCreator;
import org.openscience.cdk.tools.manipulator.ChemFileManipulator;
/**
* Description of the Class
@@ -323,27 +313,20 @@
for (int i = 0; i < smiles.length; i++) {
atomContainer[i] = sp.parseSmiles(smiles[i]);
- inputList.add(CMLChemFileWrapper.wrapAtomContainerInChemModel(atomContainer[i]));
+ inputList.add(atomContainer[i]);
}
///////////////////////////////////////////////////////////////////////////////////////////
// Generate 2D coordinats for the input molecules with the Structure Diagram Generator
StructureDiagramGenerator str;
- CMLChemFile resultFile = null;
List resultList = new ArrayList();
for (Iterator iter = inputList.iterator(); iter.hasNext();) {
- CMLChemFile file = (CMLChemFile) iter.next();
- List moleculeList = ChemFileManipulator.getAllAtomContainers(file);
- IAtomContainer molecules;
- for (Iterator iterator = moleculeList.iterator(); iterator.hasNext();){
- molecules = (IAtomContainer)iterator.next();
- str = new StructureDiagramGenerator();
- str.setMolecule((IMolecule)molecules);
- str.generateCoordinates();
- resultFile = CMLChemFileWrapper.wrapAtomContainerInChemModel(str.getMolecule());
- resultList.add(resultFile);
- }
+ IAtomContainer molecules = (IAtomContainer) iter.next();
+ str = new StructureDiagramGenerator();
+ str.setMolecule((IMolecule)molecules);
+ str.generateCoordinates();
+ resultList.add(str.getMolecule());
}
inputList = resultList;
@@ -351,15 +334,10 @@
// Delete x and y coordinats
for (Iterator iter = inputList.iterator(); iter.hasNext();) {
- IChemFile element = (IChemFile) iter.next();
- List MoleculeList = ChemFileManipulator.getAllAtomContainers(element);
- IAtomContainer molecules;
- for (Iterator iterator = MoleculeList.iterator(); iterator.hasNext();){
- molecules = (IAtomContainer)iterator.next();
- for (Iterator atom = molecules.atoms(); atom.hasNext();){
- Atom last = (Atom) atom.next();
- last.setPoint2d(null);
- }
+ IAtomContainer molecules = (IAtomContainer) iter.next();
+ for (Iterator atom = molecules.atoms(); atom.hasNext();){
+ Atom last = (Atom) atom.next();
+ last.setPoint2d(null);
}
}
@@ -368,63 +346,16 @@
ModelBuilder3D mb3d=ModelBuilder3D.getInstance();
for (Iterator iter = inputList.iterator(); iter.hasNext();) {
- CMLChemFile file = (CMLChemFile) iter.next();
- List moleculeList = ChemFileManipulator.getAllAtomContainers(file);
- IAtomContainer molecules;
- for (Iterator iterator = moleculeList.iterator(); iterator.hasNext();){
- molecules = (IAtomContainer)iterator.next();
- IMolecule mol = file.getBuilder().newMolecule(molecules);
- /*for(int i=0;i<mol.getAtomCount();i++){
+ IAtomContainer molecules = (IAtomContainer) iter.next();
+ IMolecule mol = molecules.getBuilder().newMolecule(molecules);
+ /*for(int i=0;i<mol.getAtomCount();i++){
mol.getAtom(i).setFlag(CDKConstants.ISPLACED,false);
mol.getAtom(i).setFlag(CDKConstants.VISITED,false);
} */
- mol = mb3d.generate3DCoordinates(mol, false);
- System.out.println("Calculation done");
- }
+ mol = mb3d.generate3DCoordinates(mol, false);
+ System.out.println("Calculation done");
}
assertEquals(false, notCalculatedResults);
}
}
-
-class CMLChemFile extends ChemFile {
-
- /**
- * Constructs an empty ChemFile.
- */
- public CMLChemFile() {
- super();
- }
-
- /**
- * Constructs a ChemFile from a CML String.
- *
- * @param CMLString to deserialize the ChemFile from.
- * @throws Exception
- */
- public CMLChemFile(String CMLString) throws Exception {
- CMLReader reader = new CMLReader(
- new ByteArrayInputStream(CMLString.getBytes())
- );
- reader.read(this);
- }
-
- /**
- * Serializes this ChemFile into a CML String.
- *
- * @return The CML String serialization.
- * @throws Exception
- */
- public String toCML() throws Exception {
- IDCreator.createIDs(this);
-
- StringWriter stringWriter = new StringWriter();
- IChemObjectWriter writer = new CMLWriter(stringWriter);
- writer.write(this);
-
- return stringWriter.toString();
- }
-
- private static final long serialVersionUID = -5664142472726700883L;
-
-}
\ No newline at end of file
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