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[Cdk-commits] SF.net SVN: cdk:[11729] cdk/trunk/src
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From: <eg...@us...> - 2008-07-23 21:08:07
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Revision: 11729
http://cdk.svn.sourceforge.net/cdk/?rev=11729&view=rev
Author: egonw
Date: 2008-07-23 21:08:04 +0000 (Wed, 23 Jul 2008)
Log Message:
-----------
Added missing force3DCoords setting for the iterating MDL reader (closes #2025785)
Modified Paths:
--------------
cdk/trunk/src/main/org/openscience/cdk/io/iterator/IteratingMDLReader.java
cdk/trunk/src/test/org/openscience/cdk/io/iterator/IteratingMDLReaderTest.java
Added Paths:
-----------
cdk/trunk/src/data/mdl/no3dStructures.sdf
Copied: cdk/trunk/src/data/mdl/no3dStructures.sdf (from rev 11727, cdk/trunk/src/data/mdl/emptyStructures.sdf)
===================================================================
--- cdk/trunk/src/data/mdl/no3dStructures.sdf (rev 0)
+++ cdk/trunk/src/data/mdl/no3dStructures.sdf 2008-07-23 21:08:04 UTC (rev 11729)
@@ -0,0 +1,158 @@
+
+
+
+ 4 3 0 0 0 0 0 0 0 0 1 V2000
+ 0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.6652 -1.1508 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.9956 -1.1508 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.3260 -1.1508 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 2 0 0 0 0
+ 2 3 1 0 0 0 0
+ 3 4 3 0 0 0 0
+M END
+> <Formula>
+C3H3N
+
+> <DSSTox_ID>
+29
+
+> <DSSTox_FileName>
+CPDBAS_v2a_1451_1Mar05
+
+> <MolWeight>
+53.0634
+
+> <StructureShown>
+tested form
+
+> <ChemName>
+Acrylonitrile
+
+> <CAS>
+107-13-1
+
+> <SubstanceType>
+defined organic
+
+> <TestedForm>
+parent
+
+> <ChemCount>
+1
+
+> <ChemName_IUPAC>
+acrylonitrile
+
+> <SMILES>
+C=CC#N
+
+> <SMILES_Parent>
+C=CC#N
+
+> <INChI>
+INChI=1.12Beta/C3H3N/c1-2-3-4/h1H2,2H
+
+> <StudyType>
+carcinogenicity
+
+> <Species>
+rat
+
+> <Endpoint>
+TD50, Tumor Target Sites
+
+> <SAL CPDB>
+pos
+
+> <TD50 Rat notext>
+16.9
+
+> <TD50 Rat>
+16.9 m v
+
+> <Target Sites Rat Male>
+ezy nrv orc smi sto
+
+> <Target Sites Rat Female>
+ezy mgl nas nrv orc smi sto
+
+$$$$
+
+
+
+ 4 3 0 0 0 0 0 0 0 0 1 V2000
+ 0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.6652 -1.1508 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.9956 -1.1508 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.3260 -1.1508 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 2 0 0 0 0
+ 2 3 1 0 0 0 0
+ 3 4 3 0 0 0 0
+M END
+> <Formula>
+C3H3N
+
+> <DSSTox_ID>
+29
+
+> <DSSTox_FileName>
+CPDBAS_v2a_1451_1Mar05
+
+> <MolWeight>
+53.0634
+
+> <StructureShown>
+tested form
+
+> <ChemName>
+Acrylonitrile
+
+> <CAS>
+107-13-1
+
+> <SubstanceType>
+defined organic
+
+> <TestedForm>
+parent
+
+> <ChemCount>
+1
+
+> <ChemName_IUPAC>
+acrylonitrile
+
+> <SMILES>
+C=CC#N
+
+> <SMILES_Parent>
+C=CC#N
+
+> <INChI>
+INChI=1.12Beta/C3H3N/c1-2-3-4/h1H2,2H
+
+> <StudyType>
+carcinogenicity
+
+> <Species>
+rat
+
+> <Endpoint>
+TD50, Tumor Target Sites
+
+> <SAL CPDB>
+pos
+
+> <TD50 Rat notext>
+16.9
+
+> <TD50 Rat>
+16.9 m v
+
+> <Target Sites Rat Male>
+ezy nrv orc smi sto
+
+> <Target Sites Rat Female>
+ezy mgl nas nrv orc smi sto
+
+$$$$
\ No newline at end of file
Modified: cdk/trunk/src/main/org/openscience/cdk/io/iterator/IteratingMDLReader.java
===================================================================
--- cdk/trunk/src/main/org/openscience/cdk/io/iterator/IteratingMDLReader.java 2008-07-23 20:31:32 UTC (rev 11728)
+++ cdk/trunk/src/main/org/openscience/cdk/io/iterator/IteratingMDLReader.java 2008-07-23 21:08:04 UTC (rev 11729)
@@ -32,16 +32,21 @@
import java.io.StringReader;
import java.util.NoSuchElementException;
+import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IChemObject;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.io.ISimpleChemObjectReader;
+import org.openscience.cdk.io.MDLV2000Reader;
import org.openscience.cdk.io.ReaderFactory;
import org.openscience.cdk.io.formats.IChemFormat;
import org.openscience.cdk.io.formats.IResourceFormat;
import org.openscience.cdk.io.formats.MDLFormat;
import org.openscience.cdk.io.formats.MDLV2000Format;
import org.openscience.cdk.io.formats.MDLV3000Format;
+import org.openscience.cdk.io.listener.IChemObjectIOListener;
+import org.openscience.cdk.io.setting.BooleanIOSetting;
+import org.openscience.cdk.io.setting.IOSetting;
import org.openscience.cdk.tools.LoggingTool;
/**
@@ -75,7 +80,7 @@
* @cdk.keyword file format, MDL molfile
* @cdk.keyword file format, SDF
*/
-public class IteratingMDLReader extends DefaultIteratingChemObjectReader {
+public class IteratingMDLReader extends DefaultIteratingChemObjectReader implements IChemObjectIOListener {
private BufferedReader input;
private LoggingTool logger;
@@ -88,6 +93,8 @@
private IChemObjectBuilder builder;
private IMolecule nextMolecule;
+ private BooleanIOSetting forceReadAs3DCoords;
+
/**
* Contructs a new IteratingMDLReader that can read Molecule from a given Reader.
*
@@ -98,6 +105,7 @@
logger = new LoggingTool(this);
this.builder = builder;
setReader(in);
+ initIOSettings();
}
/**
@@ -148,6 +156,10 @@
logger.debug("MDL file part read: ", buffer);
ISimpleChemObjectReader reader = factory.createReader(currentFormat);
reader.setReader(new StringReader(buffer.toString()));
+ if (currentFormat instanceof MDLV2000Format) {
+ reader.addChemObjectIOListener(this);
+ ((MDLV2000Reader)reader).customizeJob();
+ }
nextMolecule = (IMolecule)reader.read(builder.newMolecule());
// note that a molecule may have 0 atoms, but still
@@ -248,5 +260,32 @@
public void setReader(InputStream reader) {
setReader(new InputStreamReader(reader));
}
+
+ private void initIOSettings() {
+ forceReadAs3DCoords = new BooleanIOSetting("ForceReadAs3DCoordinates", IOSetting.LOW,
+ "Should coordinates always be read as 3D?",
+ "false");
+ }
+
+ public void customizeJob() {
+ fireIOSettingQuestion(forceReadAs3DCoords);
+ }
+
+ public IOSetting[] getIOSettings() {
+ IOSetting[] settings = new IOSetting[1];
+ settings[0] = forceReadAs3DCoords;
+ return settings;
+ }
+
+ public void processIOSettingQuestion(IOSetting setting) {
+ if (setting.getName().equals(forceReadAs3DCoords.getName())) {
+ try {
+ setting.setSetting(forceReadAs3DCoords.getSetting());
+ } catch (CDKException e) {
+ logger.debug("Could not propagate forceReadAs3DCoords setting");
+ }
+ }
+ }
+
}
Modified: cdk/trunk/src/test/org/openscience/cdk/io/iterator/IteratingMDLReaderTest.java
===================================================================
--- cdk/trunk/src/test/org/openscience/cdk/io/iterator/IteratingMDLReaderTest.java 2008-07-23 20:31:32 UTC (rev 11728)
+++ cdk/trunk/src/test/org/openscience/cdk/io/iterator/IteratingMDLReaderTest.java 2008-07-23 21:08:04 UTC (rev 11729)
@@ -32,9 +32,12 @@
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.Molecule;
+import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.io.formats.MDLV2000Format;
import org.openscience.cdk.io.iterator.IteratingMDLReader;
+import org.openscience.cdk.io.listener.IChemObjectIOListener;
+import org.openscience.cdk.io.setting.IOSetting;
import org.openscience.cdk.CDKTestCase;
import org.openscience.cdk.tools.LoggingTool;
@@ -166,4 +169,60 @@
}
+ public void testNo3DCoordsButForcedAs() {
+ // First test unforced 3D coordinates
+ String filename = "data/mdl/no3dStructures.sdf";
+ logger.info("Testing: " + filename);
+ InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
+ IteratingMDLReader reader = new IteratingMDLReader(ins, DefaultChemObjectBuilder.getInstance());
+ int molCount = 0;
+ IMolecule mol = null;
+ while (reader.hasNext()) {
+ Object object = reader.next();
+ assertNotNull(object);
+ assertTrue(object instanceof IMolecule);
+ molCount++;
+ mol = (IMolecule)object;
+ }
+
+ assertEquals(2, molCount);
+ assertNotNull(mol.getAtom(0).getPoint2d());
+ assertNull(mol.getAtom(0).getPoint3d());
+
+ // Now test forced 3D coordinates
+ logger.info("Testing: " + filename);
+ ins = this.getClass().getClassLoader().getResourceAsStream(filename);
+ reader = new IteratingMDLReader(ins, DefaultChemObjectBuilder.getInstance());
+ reader.addChemObjectIOListener(new MyListener());
+ reader.customizeJob();
+ molCount = 0;
+ mol = null;
+ while (reader.hasNext()) {
+ Object object = reader.next();
+ assertNotNull(object);
+ assertTrue(object instanceof IMolecule);
+ molCount++;
+ mol = (IMolecule)object;
+ }
+
+ assertEquals(2, molCount);
+ assertNull(mol.getAtom(0).getPoint2d());
+ assertNotNull(mol.getAtom(0).getPoint3d());
+ }
+
+ class MyListener implements IChemObjectIOListener {
+
+ public void processIOSettingQuestion(IOSetting setting) {
+ if ("ForceReadAs3DCoordinates".equals(setting.getName())) {
+ try {
+ setting.setSetting("true");
+ } catch (CDKException e) {
+ logger.error("Could not set forceReadAs3DCoords setting: ", e.getMessage());
+ logger.debug(e);
+ }
+ }
+ }
+
+ }
+
}
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