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Allow IChemModels to contain IAtomContainerSets (addresses #2784940)
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Signed-off-by: Rajarshi  Guha <rajarshi.guha@gmail.com>
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@egonw @rajarshi
egonw authored and rajarshi committed Oct 2, 2011
1 parent 6ff1f78 commit 4cc5ff8
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Showing 57 changed files with 581 additions and 525 deletions.
16 changes: 11 additions & 5 deletions src/main/org/openscience/cdk/ChemModel.java
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Expand Up @@ -24,10 +24,16 @@

package org.openscience.cdk;

import org.openscience.cdk.interfaces.*;

import java.io.Serializable;

import org.openscience.cdk.interfaces.IAtomContainerSet;
import org.openscience.cdk.interfaces.IChemModel;
import org.openscience.cdk.interfaces.IChemObjectChangeEvent;
import org.openscience.cdk.interfaces.IChemObjectListener;
import org.openscience.cdk.interfaces.ICrystal;
import org.openscience.cdk.interfaces.IReactionSet;
import org.openscience.cdk.interfaces.IRingSet;

/**
* An object containing multiple MoleculeSet and
* the other lower level concepts like rings, sequences,
Expand All @@ -52,7 +58,7 @@ public class ChemModel extends ChemObject implements Serializable, IChemModel, I
/**
* A MoleculeSet.
*/
protected IMoleculeSet setOfMolecules = null;
protected IAtomContainerSet setOfMolecules = null;

/**
* A ReactionSet.
Expand Down Expand Up @@ -81,7 +87,7 @@ public ChemModel() {}
*
* @see #setMoleculeSet
*/
public IMoleculeSet getMoleculeSet()
public IAtomContainerSet getMoleculeSet()
{
return this.setOfMolecules;
}
Expand All @@ -94,7 +100,7 @@ public IMoleculeSet getMoleculeSet()
*
* @see #getMoleculeSet
*/
public void setMoleculeSet(IMoleculeSet setOfMolecules)
public void setMoleculeSet(IAtomContainerSet setOfMolecules)
{
if (this.setOfMolecules != null)
this.setOfMolecules.removeListener(this);
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8 changes: 4 additions & 4 deletions src/main/org/openscience/cdk/debug/DebugChemModel.java
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Expand Up @@ -23,12 +23,12 @@
import java.util.Map;

import org.openscience.cdk.ChemModel;
import org.openscience.cdk.interfaces.IAtomContainerSet;
import org.openscience.cdk.interfaces.IChemModel;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IChemObjectChangeEvent;
import org.openscience.cdk.interfaces.IChemObjectListener;
import org.openscience.cdk.interfaces.ICrystal;
import org.openscience.cdk.interfaces.IMoleculeSet;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IReactionSet;
import org.openscience.cdk.interfaces.IRingSet;
import org.openscience.cdk.tools.ILoggingTool;
Expand Down Expand Up @@ -144,12 +144,12 @@ public IChemObjectBuilder getBuilder() {
return DebugChemObjectBuilder.getInstance();
}

public IMoleculeSet getMoleculeSet() {
public IAtomContainerSet getMoleculeSet() {
logger.debug("Getting setOfMolecules: ", super.getMoleculeSet());
return super.getMoleculeSet();
}

public void setMoleculeSet(IMoleculeSet setOfMolecules) {
public void setMoleculeSet(IAtomContainerSet setOfMolecules) {
logger.debug("Setting setOfMolecules: ", setOfMolecules);
super.setMoleculeSet(setOfMolecules);
}
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19 changes: 7 additions & 12 deletions src/main/org/openscience/cdk/interfaces/IChemModel.java
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@@ -1,9 +1,4 @@
/* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* Copyright (C) 2006-2007 Egon Willighagen <egonw@users.sf.net>
/* Copyright (C) 2006-2007,2011 Egon Willighagen <egonw@users.sf.net>
*
* Contact: cdk-devel@lists.sourceforge.net
*
Expand All @@ -24,7 +19,7 @@
package org.openscience.cdk.interfaces;

/**
* An object containig multiple MoleculeSet and
* An object containing multiple MoleculeSet and
* the other lower level concepts like rings, sequences,
* fragments, etc.
*
Expand All @@ -34,20 +29,20 @@
public interface IChemModel extends IChemObject {

/**
* Returns the MoleculeSet of this ChemModel.
* Returns the IAtomContainerSet of this ChemModel.
*
* @return The MoleculeSet of this ChemModel
* @return The {@link IAtomContainerSet} of this ChemModel
* @see #setMoleculeSet
*/
public IMoleculeSet getMoleculeSet();
public IAtomContainerSet getMoleculeSet();

/**
* Sets the MoleculeSet of this ChemModel.
* Sets the IAtomContainerSet of this ChemModel.
*
* @param setOfMolecules the content of this model
* @see #getMoleculeSet
*/
public void setMoleculeSet(IMoleculeSet setOfMolecules);
public void setMoleculeSet(IAtomContainerSet setOfMolecules);

/**
* Returns the RingSet of this ChemModel.
Expand Down
5 changes: 3 additions & 2 deletions src/main/org/openscience/cdk/io/Gaussian03Reader.java
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Expand Up @@ -35,6 +35,7 @@
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomContainerSet;
import org.openscience.cdk.interfaces.IChemFile;
import org.openscience.cdk.interfaces.IChemModel;
import org.openscience.cdk.interfaces.IChemObject;
Expand Down Expand Up @@ -282,8 +283,8 @@ private void readCoordinates(IChemModel model) throws CDKException, IOException
*/
private void readPartialCharges(IChemModel model) throws CDKException, IOException {
logger.info("Reading partial atomic charges");
IMoleculeSet moleculeSet = model.getMoleculeSet();
IMolecule molecule = moleculeSet.getMolecule(0);
IAtomContainerSet moleculeSet = model.getMoleculeSet();
IAtomContainer molecule = moleculeSet.getAtomContainer(0);
String line = input.readLine(); // skip first line after "Total atomic charges"
while (input.ready()) {
line = input.readLine();
Expand Down
5 changes: 3 additions & 2 deletions src/main/org/openscience/cdk/io/Gaussian98Reader.java
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Expand Up @@ -41,6 +41,7 @@
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomContainerSet;
import org.openscience.cdk.interfaces.IChemFile;
import org.openscience.cdk.interfaces.IChemModel;
import org.openscience.cdk.interfaces.IChemObject;
Expand Down Expand Up @@ -355,8 +356,8 @@ private void readCoordinates(IChemModel model) throws CDKException, IOException
*/
private void readPartialCharges(IChemModel model) throws CDKException, IOException {
logger.info("Reading partial atomic charges");
IMoleculeSet moleculeSet = model.getMoleculeSet();
IMolecule molecule = moleculeSet.getMolecule(0);
IAtomContainerSet moleculeSet = model.getMoleculeSet();
IAtomContainer molecule = moleculeSet.getAtomContainer(0);
String line = input.readLine();
// skip first line after "Total atomic charges"
while (input.ready()) {
Expand Down
8 changes: 5 additions & 3 deletions src/main/org/openscience/cdk/io/MDLReader.java
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Expand Up @@ -41,6 +41,8 @@
import org.openscience.cdk.config.IsotopeFactory;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomContainerSet;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IChemFile;
import org.openscience.cdk.interfaces.IChemModel;
Expand Down Expand Up @@ -179,13 +181,13 @@ public <T extends IChemObject> T read(T object) throws CDKException {
}

private IChemModel readChemModel(IChemModel chemModel) throws CDKException {
IMoleculeSet setOfMolecules = chemModel.getMoleculeSet();
IAtomContainerSet setOfMolecules = chemModel.getMoleculeSet();
if (setOfMolecules == null) {
setOfMolecules = chemModel.getBuilder().newInstance(IMoleculeSet.class);
}
IMolecule m = readMolecule(chemModel.getBuilder().newInstance(IMolecule.class));
IAtomContainer m = readMolecule(chemModel.getBuilder().newInstance(IMolecule.class));
if (m != null) {
setOfMolecules.addMolecule(m);
setOfMolecules.addAtomContainer(m);
}
chemModel.setMoleculeSet(setOfMolecules);
return chemModel;
Expand Down
44 changes: 22 additions & 22 deletions src/main/org/openscience/cdk/io/MDLV2000Reader.java
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Expand Up @@ -23,12 +23,30 @@
*/
package org.openscience.cdk.io;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.Reader;
import java.io.StringReader;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.StringTokenizer;

import javax.vecmath.Point2d;
import javax.vecmath.Point3d;

import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.config.IsotopeFactory;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomContainerSet;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IChemFile;
import org.openscience.cdk.interfaces.IChemModel;
Expand All @@ -43,30 +61,12 @@
import org.openscience.cdk.io.formats.MDLV2000Format;
import org.openscience.cdk.io.setting.BooleanIOSetting;
import org.openscience.cdk.io.setting.IOSetting;
import org.openscience.cdk.isomorphism.matchers.CTFileQueryBond;
import org.openscience.cdk.isomorphism.matchers.QueryAtomContainer;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;

import javax.vecmath.Point2d;
import javax.vecmath.Point3d;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.Reader;
import java.io.StringReader;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.StringTokenizer;

import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.isomorphism.matchers.CTFileQueryBond;
import org.openscience.cdk.isomorphism.matchers.QueryAtom;
import org.openscience.cdk.isomorphism.matchers.QueryAtomContainer;

/**
* Reads content from MDL molfiles and SD files.
* It can read a {@link IMolecule} or {@link IChemModel} from an MDL molfile, and
Expand Down Expand Up @@ -198,13 +198,13 @@ public <T extends IChemObject> T read(T object) throws CDKException {
}

private IChemModel readChemModel(IChemModel chemModel) throws CDKException {
IMoleculeSet setOfMolecules = chemModel.getMoleculeSet();
IAtomContainerSet setOfMolecules = chemModel.getMoleculeSet();
if (setOfMolecules == null) {
setOfMolecules = chemModel.getBuilder().newInstance(IMoleculeSet.class);
}
IAtomContainer m = readAtomContainer(chemModel.getBuilder().newInstance(IMolecule.class));
if (m != null && m instanceof IMolecule) {
setOfMolecules.addMolecule((IMolecule)m);
setOfMolecules.addAtomContainer((IMolecule)m);
}
chemModel.setMoleculeSet(setOfMolecules);
return chemModel;
Expand Down
27 changes: 15 additions & 12 deletions src/main/org/openscience/cdk/io/Mol2Reader.java
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Expand Up @@ -24,12 +24,24 @@
*/
package org.openscience.cdk.io;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.Reader;
import java.io.StringReader;
import java.util.StringTokenizer;

import javax.vecmath.Point3d;

import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.config.AtomTypeFactory;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomContainerSet;
import org.openscience.cdk.interfaces.IAtomType;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IChemFile;
Expand All @@ -45,15 +57,6 @@
import org.openscience.cdk.tools.manipulator.AtomTypeManipulator;
import org.openscience.cdk.tools.periodictable.PeriodicTable;

import javax.vecmath.Point3d;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.Reader;
import java.io.StringReader;
import java.util.StringTokenizer;

/**
* Reads a molecule from an Mol2 file, such as written by Sybyl.
* See the specs <a href="http://www.tripos.com/data/support/mol2.pdf">here</a>.
Expand Down Expand Up @@ -134,13 +137,13 @@ public <T extends IChemObject> T read(T object) throws CDKException {
}

private IChemModel readChemModel(IChemModel chemModel) throws CDKException {
IMoleculeSet setOfMolecules = chemModel.getMoleculeSet();
IAtomContainerSet setOfMolecules = chemModel.getMoleculeSet();
if (setOfMolecules == null) {
setOfMolecules = chemModel.getBuilder().newInstance(IMoleculeSet.class);
}
IMolecule m = readMolecule(chemModel.getBuilder().newInstance(IMolecule.class));
IAtomContainer m = readMolecule(chemModel.getBuilder().newInstance(IMolecule.class));
if (m != null) {
setOfMolecules.addMolecule(m);
setOfMolecules.addAtomContainer(m);
}
chemModel.setMoleculeSet(setOfMolecules);
return chemModel;
Expand Down
2 changes: 1 addition & 1 deletion src/main/org/openscience/cdk/io/random/RandomAccessSDFReader.java
View file
Expand Up @@ -90,7 +90,7 @@ protected IChemObject processContent() throws CDKException {
for (int i=0; i <c;i++) {
Iterator cm = ((IChemFile) co).getChemSequence(i).chemModels().iterator();
while (cm.hasNext()) {
Iterator sm = ((IChemModel)cm.next()).getMoleculeSet().molecules().iterator();
Iterator sm = ((IChemModel)cm.next()).getMoleculeSet().atomContainers().iterator();
while (sm.hasNext()) {

co = (IMolecule) sm.next();
Expand Down
5 changes: 3 additions & 2 deletions src/main/org/openscience/cdk/libio/cml/Convertor.java
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Expand Up @@ -38,6 +38,7 @@
import org.openscience.cdk.geometry.CrystalGeometryTools;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomContainerSet;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IChemFile;
import org.openscience.cdk.interfaces.IChemModel;
Expand Down Expand Up @@ -309,7 +310,7 @@ public CMLMoleculeList cdkMoleculeSetToCMLList(IMoleculeSet moleculeSet) {
return cdkMoleculeSetToCMLList(moleculeSet, true);
}

private CMLMoleculeList cdkMoleculeSetToCMLList(IMoleculeSet moleculeSet, boolean setIDs) {
private CMLMoleculeList cdkMoleculeSetToCMLList(IAtomContainerSet moleculeSet, boolean setIDs) {
CMLMoleculeList cmlList = new CMLMoleculeList();
cmlList.setConvention("cdk:moleculeSet");

Expand All @@ -320,7 +321,7 @@ private CMLMoleculeList cdkMoleculeSetToCMLList(IMoleculeSet moleculeSet, boolea
cmlList.setId(moleculeSet.getID());

for (int i = 0; i < moleculeSet.getAtomContainerCount(); i++) {
IAtomContainer container = moleculeSet.getMolecule(i);
IAtomContainer container = moleculeSet.getAtomContainer(i);
if (container instanceof IMolecule) {
cmlList.appendChild(
cdkMoleculeToCMLMolecule((IMolecule)container, false)
Expand Down

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