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Implemented a progressbar that ticks by descr/mol calculation and add…
…ed option to cancel build. git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@7041 fcb5ba71-d80d-0410-8237-ba3920747fcc
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plugins/net.bioclipse.cdk.qsar.test/src/net/bioclipse/cdk/qsar/test/testCDKAT.java
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| @@ -0,0 +1,67 @@ | ||
| package net.bioclipse.cdk.qsar.test; | ||
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| import java.io.InputStream; | ||
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| import org.openscience.cdk.atomtype.CDKAtomTypeMatcher; | ||
| import org.openscience.cdk.exception.CDKException; | ||
| import org.openscience.cdk.interfaces.IAtom; | ||
| import org.openscience.cdk.interfaces.IAtomContainer; | ||
| import org.openscience.cdk.interfaces.IAtomType; | ||
| import org.openscience.cdk.interfaces.IChemFile; | ||
| import org.openscience.cdk.io.CMLReader; | ||
| import org.openscience.cdk.io.ReaderFactory; | ||
| import org.openscience.cdk.io.formats.CMLFormat; | ||
| import org.openscience.cdk.io.formats.IChemFormatMatcher; | ||
| import org.openscience.cdk.tools.CDKHydrogenAdder; | ||
| import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; | ||
| import org.openscience.cdk.tools.manipulator.AtomTypeManipulator; | ||
| import org.openscience.cdk.tools.manipulator.ChemFileManipulator; | ||
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| public class testCDKAT { | ||
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| /** | ||
| * @param args | ||
| */ | ||
| public static void main(String[] args) { | ||
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| InputStream ins = testCDKAT.class.getResourceAsStream("/testFiles/0037.cml"); | ||
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| CMLReader reader=new CMLReader(ins); | ||
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| IChemFile chemFile = new org.openscience.cdk.ChemFile(); | ||
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| //Read file | ||
| try { | ||
| chemFile=(IChemFile)reader.read(chemFile); | ||
| } catch (CDKException e) { | ||
| e.printStackTrace(); | ||
| } | ||
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| IAtomContainer container = ChemFileManipulator.getAllAtomContainers(chemFile).get(0); | ||
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| try { | ||
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| CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.getInstance(container.getBuilder()); | ||
| for (IAtom atom : container.atoms()) { | ||
| IAtomType matched = matcher.findMatchingAtomType(container, atom); | ||
| if (matched != null){ | ||
| AtomTypeManipulator.configure(atom, matched); | ||
| }else{ | ||
| System.out.println("Could not find matching atom type for atom: " + atom); | ||
| } | ||
| } | ||
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| CDKHydrogenAdder hAdder = CDKHydrogenAdder.getInstance(container.getBuilder()); | ||
| hAdder.addImplicitHydrogens(container); | ||
| AtomContainerManipulator.convertImplicitToExplicitHydrogens(container); | ||
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| } catch (Exception e1) { | ||
| System.out.println("Error addding hydrogens : " + e1.getMessage()); | ||
| } | ||
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| } | ||
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| } |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1 @@ | ||
| <cml xmlns="http://www.xml-cml.org/schema"><molecule title="" id="nmrshiftdb20110444"><atomArray><atom id="a1" elementType="C" x2="2.89" y2="-1.25" formalCharge="0" hydrogenCount="0" /><atom id="a2" elementType="C" x2="2.89" y2="-0.42" formalCharge="0" hydrogenCount="0" /><atom id="a3" elementType="C" x2="2.17" y2="0.0" formalCharge="0" hydrogenCount="0" /><atom id="a4" elementType="C" x2="1.44" y2="-0.42" formalCharge="0" hydrogenCount="0" /><atom id="a5" elementType="C" x2="1.44" y2="-1.25" formalCharge="0" hydrogenCount="0" /><atom id="a6" elementType="C" x2="0.72" y2="-1.67" formalCharge="0" hydrogenCount="0" /><atom id="a7" elementType="C" x2="3.61" y2="-1.67" formalCharge="0" hydrogenCount="0" /><atom id="a8" elementType="C" x2="2.17" y2="-2.5" formalCharge="0" hydrogenCount="0" /><atom id="a9" elementType="C" x2="2.89" y2="-2.92" formalCharge="0" hydrogenCount="0" /><atom id="a10" elementType="C" x2="1.44" y2="-2.92" formalCharge="0" hydrogenCount="0" /><atom id="a11" elementType="C" x2="0.0" y2="-4.58" formalCharge="0" hydrogenCount="0" /><atom id="a12" elementType="C" x2="0.72" y2="-5.0" formalCharge="0" hydrogenCount="0" /><atom id="a13" elementType="C" x2="0.0" y2="-3.75" formalCharge="0" hydrogenCount="0" /><atom id="a14" elementType="C" x2="2.89" y2="-3.75" formalCharge="0" hydrogenCount="0" /><atom id="a15" elementType="C" x2="3.61" y2="-4.17" formalCharge="0" hydrogenCount="0" /><atom id="a16" elementType="C" x2="4.33" y2="-3.75" formalCharge="0" hydrogenCount="0" /><atom id="a17" elementType="C" x2="4.33" y2="-2.92" formalCharge="0" hydrogenCount="0" /><atom id="a18" elementType="C" x2="3.61" y2="-2.5" formalCharge="0" hydrogenCount="0" /><atom id="a19" elementType="O" x2="1.44" y2="-3.75" formalCharge="0" hydrogenCount="0" /><atom id="a20" elementType="N" x2="2.17" y2="-1.67" formalCharge="0" hydrogenCount="0" /><atom id="a21" elementType="N" x2="0.0" y2="-2.08" formalCharge="0" hydrogenCount="0" /><atom id="a22" elementType="Si" x2="0.72" y2="-4.17" formalCharge="0" hydrogenCount="0" /></atomArray><bondArray><bond id="b1" atomRefs2="a1 a20" order="S" /><bond id="b2" atomRefs2="a1 a2" order="S" /><bond id="b3" atomRefs2="a1 a7" order="S" /><bond id="b4" atomRefs2="a2 a3" order="S" /><bond id="b5" atomRefs2="a3 a4" order="S" /><bond id="b6" atomRefs2="a4 a5" order="S" /><bond id="b7" atomRefs2="a5 a20" order="S" /><bond id="b8" atomRefs2="a5 a6" order="S" /><bond id="b9" atomRefs2="a6 a21" order="T" /><bond id="b10" atomRefs2="a8 a20" order="S" /><bond id="b11" atomRefs2="a8 a9" order="S" /><bond id="b12" atomRefs2="a8 a10" order="S" /><bond id="b13" atomRefs2="a9 a14" order="D" /><bond id="b14" atomRefs2="a9 a18" order="S" /><bond id="b15" atomRefs2="a10 a19" order="S" /><bond id="b16" atomRefs2="a11 a22" order="S" /><bond id="b17" atomRefs2="a12 a22" order="S" /><bond id="b18" atomRefs2="a13 a22" order="S" /><bond id="b19" atomRefs2="a14 a15" order="S" /><bond id="b20" atomRefs2="a15 a16" order="D" /><bond id="b21" atomRefs2="a16 a17" order="S" /><bond id="b22" atomRefs2="a17 a18" order="D" /><bond id="b23" atomRefs2="a19 a22" order="S" /></bondArray></molecule></cml> |