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[Cdk-commits] SF.net SVN: cdk: [10292] branches/miguelrojasch/reaction/src
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From: <mig...@us...> - 2008-03-04 13:56:37
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Revision: 10292
http://cdk.svn.sourceforge.net/cdk/?rev=10292&view=rev
Author: miguelrojasch
Date: 2008-03-04 05:56:20 -0800 (Tue, 04 Mar 2008)
Log Message:
-----------
Synchronized with trunk; merged 10272:10291
Modified Paths:
--------------
branches/miguelrojasch/reaction/src/main/org/openscience/cdk/CDKConstants.java
branches/miguelrojasch/reaction/src/main/org/openscience/cdk/config/data/html.xsl
branches/miguelrojasch/reaction/src/test/org/openscience/cdk/atomtype/AbstractAtomTypeTest.java
branches/miguelrojasch/reaction/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java
Modified: branches/miguelrojasch/reaction/src/main/org/openscience/cdk/CDKConstants.java
===================================================================
--- branches/miguelrojasch/reaction/src/main/org/openscience/cdk/CDKConstants.java 2008-03-04 13:49:43 UTC (rev 10291)
+++ branches/miguelrojasch/reaction/src/main/org/openscience/cdk/CDKConstants.java 2008-03-04 13:56:20 UTC (rev 10292)
@@ -206,22 +206,22 @@
****************************************/
/** The title for a IChemObject. */
- public static final String TITLE = "Title";
+ public static final String TITLE = "cdk:Title";
/** A remark for a IChemObject.*/
- public static final String REMARK = "Remark";
+ public static final String REMARK = "cdk:Remark";
/** A String comment. */
- public static final String COMMENT = "Comment";
+ public static final String COMMENT = "cdk:Comment";
/** A List of names. */
- public static final String NAMES = "Names";
+ public static final String NAMES = "cdk:Names";
/** A List of annotation remarks. */
- public static final String ANNOTATIONS = "Annotations";
+ public static final String ANNOTATIONS = "cdk:Annotations";
/** A description for a IChemObject. */
- public static final String DESCRIPTION = "Description";
+ public static final String DESCRIPTION = "cdk:Description";
/****************************************
@@ -230,37 +230,37 @@
****************************************/
/** The Daylight SMILES. */
- public static final String SMILES = "SMILES";
+ public static final String SMILES = "cdk:SMILES";
/** The IUPAC International Chemical Identifier. */
- public static final String INCHI = "InChI";
+ public static final String INCHI = "cdk:InChI";
/** The IUPAC compatible name generated with AutoNom. */
- public static final String AUTONOMNAME = "AutonomName";
+ public static final String AUTONOMNAME = "cdk:AutonomName";
/** The Beilstein Registry Number. */
- public static final String BEILSTEINRN = "BeilsteinRN";
+ public static final String BEILSTEINRN = "cdk:BeilsteinRN";
/** The CAS Registry Number. */
- public static final String CASRN = "CasRN";
+ public static final String CASRN = "cdk:CasRN";
/** A set of all rings computed for this molecule. */
- public static final String ALL_RINGS = "AllRings";
+ public static final String ALL_RINGS = "cdk:AllRings";
/** A smallest set of smallest rings computed for this molecule. */
- public static final String SMALLEST_RINGS = "SmallestRings";
+ public static final String SMALLEST_RINGS = "cdk:SmallestRings";
/** The essential rings computed for this molecule.
* The concept of Essential Rings is defined in
* SSSRFinder
*/
- public static final String ESSENTIAL_RINGS = "EssentialRings";
+ public static final String ESSENTIAL_RINGS = "cdk:EssentialRings";
/** The relevant rings computed for this molecule.
* The concept of relevant Rings is defined in
* SSSRFinder
*/
- public static final String RELEVANT_RINGS = "RelevantRings";
+ public static final String RELEVANT_RINGS = "cdk:RelevantRings";
/****************************************
@@ -273,24 +273,24 @@
* element of the list indicates the size of the ring the given
* atom belongs to (if it is a ring atom at all).
*/
- public static final String RING_SIZES = "RingSizes";
+ public static final String RING_SIZES = "cdk:RingSizes";
/**
* This property indicates how many ring bonds are connected to
* the given atom.
*/
- public static final String RING_CONNECTIONS = "RingConnections";
+ public static final String RING_CONNECTIONS = "cdk:RingConnections";
/*
*This property indicate how many bond are present on the atom.
*
*/
- public static final String TOTAL_CONNECTIONS = "TotalConnections";
+ public static final String TOTAL_CONNECTIONS = "cdk:TotalConnections";
/*
*Hydrogen count
*
*/
- public static final String TOTAL_H_COUNT = "TotalHydrogenCount";
+ public static final String TOTAL_H_COUNT = "cdk:TotalHydrogenCount";
/** The Isotropic Shielding, usually calculated by
* a quantum chemistry program like Gaussian.
@@ -298,7 +298,7 @@
* shifts by subtracting the value from the
* isotropic shielding value of a standard (e.g. TMS).
*/
- public static final String ISOTROPIC_SHIELDING = "IsotropicShielding";
+ public static final String ISOTROPIC_SHIELDING = "cdk:IsotropicShielding";
/****************************************
* Some predefined property names for *
@@ -306,19 +306,19 @@
****************************************/
/** Used as property key for indicating the ring size of a certain atom type. */
- public static final String PART_OF_RING_OF_SIZE = "Part of ring of size";
+ public static final String PART_OF_RING_OF_SIZE = "cdk:Part of ring of size";
/** Used as property key for indicating the chemical group of a certain atom type. */
- public static final String CHEMICAL_GROUP_CONSTANT = "Chemical Group";
+ public static final String CHEMICAL_GROUP_CONSTANT = "cdk:Chemical Group";
/** Used as property key for indicating the HOSE code for a certain atom type. */
- public static final String SPHERICAL_MATCHER = "HOSE code spherical matcher";
+ public static final String SPHERICAL_MATCHER = "cdk:HOSE code spherical matcher";
/** Used as property key for indicating the HOSE code for a certain atom type. */
- public static final String PI_BOND_COUNT = "Pi Bond Count";
+ public static final String PI_BOND_COUNT = "cdk:Pi Bond Count";
/** Used as property key for indicating the HOSE code for a certain atom type. */
- public static final String LONE_PAIR_COUNT = "Lone Pair Count";
+ public static final String LONE_PAIR_COUNT = "cdk:Lone Pair Count";
}
Modified: branches/miguelrojasch/reaction/src/main/org/openscience/cdk/config/data/html.xsl
===================================================================
--- branches/miguelrojasch/reaction/src/main/org/openscience/cdk/config/data/html.xsl 2008-03-04 13:49:43 UTC (rev 10291)
+++ branches/miguelrojasch/reaction/src/main/org/openscience/cdk/config/data/html.xsl 2008-03-04 13:56:20 UTC (rev 10292)
@@ -3,41 +3,43 @@
xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
xmlns:cml="http://www.xml-cml.org/schema"
exclude-result-prefixes="cml">
-
+
<xsl:output method="html" encoding="utf-8" indent="yes"/>
- <!-- Change this depending on where we are using the development or the production server -->
- <xsl:parameter name="serverRoot" select="'http://cb.openmolecules.net/'"/>
-
<xsl:template match="/">
<html>
<head>
<title>
<xsl:value-of select="cml:atomTypeList/@title"/>
- <style type="text/css">
+ </title>
+ <style type="text/css">
body { font-family: Verdana,Arial,Helvetica, sans-serif; font-size: 11px; }
+ th { font-weight: bold; text-align: left; }
td { font-family: Verdana,Arial,Helvetica, sans-serif; font-size: 11px; }
.header { text-align:right; font-weight:bold; color:rgb(0,0,0); }
- </style>
- </title>
+ </style>
</head>
<body>
<h2>Atom Types</h2>
- <xsl:element name="div">
- <table>
- <td><b>identifier</b></td>
- <td><b>element</b></td>
- <td><b>formal charge</b></td>
- <td><b>hybridization</b></td>
- <td><b>neighbours</b></td>
- <td><b>pi bonds</b></td>
- <td><b>lone pairs</b></td>
- <xsl:for-each select="cml:atomTypeList/cml:atomType">
- <xsl:sort select="./cml:atom/@elementType"/>
- <xsl:apply-templates select="."/>
- </xsl:for-each>
- </table>
- </xsl:element>
+ <table>
+ <thead>
+ <tr>
+ <th>identifier</th>
+ <th>element</th>
+ <th>formal charge</th>
+ <th>hybridization</th>
+ <th>neighbours</th>
+ <th>pi bonds</th>
+ <th>lone pairs</th>
+ <th>unpaired electron</th>
+ </tr>
+ </thead>
+ <tbody>
+ <xsl:apply-templates select="cml:atomTypeList/cml:atomType">
+ <xsl:sort select="cml:atom/@elementType"/>
+ </xsl:apply-templates>
+ </tbody>
+ </table>
</body>
</html>
</xsl:template>
@@ -51,6 +53,7 @@
<td><xsl:value-of select="cml:atom/cml:scalar[@dictRef='cdk:formalNeighbourCount']"/></td>
<td><xsl:value-of select="cml:atom/cml:scalar[@dictRef='cdk:piBondCount']"/></td>
<td><xsl:value-of select="cml:atom/cml:scalar[@dictRef='cdk:lonePairCount']"/></td>
+ <td><xsl:if test="cml:atom/cml:scalar[@dictRef='cdk:radicalElectronCount']"><xsl:text>yes</xsl:text></xsl:if></td>
</tr>
</xsl:template>
Modified: branches/miguelrojasch/reaction/src/test/org/openscience/cdk/atomtype/AbstractAtomTypeTest.java
===================================================================
--- branches/miguelrojasch/reaction/src/test/org/openscience/cdk/atomtype/AbstractAtomTypeTest.java 2008-03-04 13:49:43 UTC (rev 10291)
+++ branches/miguelrojasch/reaction/src/test/org/openscience/cdk/atomtype/AbstractAtomTypeTest.java 2008-03-04 13:56:20 UTC (rev 10292)
@@ -26,13 +26,15 @@
import org.junit.Assert;
import org.openscience.cdk.CDKConstants;
-import org.openscience.cdk.atomtype.CDKAtomTypeMatcher;
+import org.openscience.cdk.NewCDKTestCase;
+import org.openscience.cdk.config.AtomTypeFactory;
import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.exception.NoSuchAtomTypeException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomType;
import org.openscience.cdk.interfaces.IBond;
-import org.openscience.cdk.NewCDKTestCase;
+import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder;
import org.openscience.cdk.tools.manipulator.AtomTypeManipulator;
/**
@@ -45,6 +47,22 @@
*/
abstract public class AbstractAtomTypeTest extends NewCDKTestCase {
+ private final static String ATOMTYPE_LIST = "cdk_atomtypes.xml";
+
+ private final static AtomTypeFactory factory = AtomTypeFactory.getInstance(
+ "org/openscience/cdk/config/data/" + ATOMTYPE_LIST, NoNotificationChemObjectBuilder.getInstance()
+ );
+
+ /**
+ * Helper method to test if atom types are correctly perceived. Meanwhile, it maintains a list
+ * of atom types that have been tested so far, which allows testing afterwards that all atom
+ * types are at least tested once.
+ *
+ * @param testedAtomTypes List of atom types tested so far.
+ * @param expectedTypes Expected atom types for the atoms given in <code>mol</code>.
+ * @param mol The <code>IAtomContainer</code> with <code>IAtom</code>s for which atom types should be perceived.
+ * @throws CDKException Thrown if something went wrong during the atom type perception.
+ */
public void assertAtomTypes(Map<String, Integer> testedAtomTypes, String[] expectedTypes, IAtomContainer mol) throws CDKException {
Assert.assertEquals(
"The number of expected atom types is unequal to the number of atoms",
@@ -70,6 +88,9 @@
}
/**
+ * Method that tests if the matched <code>IAtomType</code> and the <code>IAtom</code> are
+ * consistent. For example, it tests if hybridization states and formal charges are equal.
+ *
* @cdk.bug 1897589
*/
private void assertConsistentProperties(IAtomContainer mol, IAtom atom, IAtomType matched) {
@@ -117,7 +138,19 @@
if (testedAtomTypes == null) {
testedAtomTypes = new HashMap<String, Integer>();
}
-
+
+ try {
+ IAtomType type = factory.getAtomType(expectedID);
+ Assert.assertNotNull(
+ "Attempt to test atom type which is not defined in the " + ATOMTYPE_LIST + ": " + expectedID,
+ type
+ );
+ } catch (NoSuchAtomTypeException exception) {
+ Assert.assertNotNull(
+ "Attempt to test atom type which is not defined in the " + ATOMTYPE_LIST + ": " +
+ exception.getMessage()
+ );
+ }
if (testedAtomTypes.containsKey(expectedID)) {
// increase the count, so that redundancy can be calculated
testedAtomTypes.put(expectedID,
@@ -128,4 +161,19 @@
}
}
+ public void countTestedAtomTypes(Map<String, Integer> testedAtomTypes) {
+ IAtomType[] expectedTypes = factory.getAllAtomTypes();
+ if (expectedTypes.length != testedAtomTypes.size()) {
+ String errorMessage = "Atom types not tested:";
+ for (int i=0; i<expectedTypes.length; i++) {
+ if (!testedAtomTypes.containsKey(expectedTypes[i].getAtomTypeName()))
+ errorMessage += " " + expectedTypes[i].getAtomTypeName();
+ }
+ Assert.assertEquals(errorMessage,
+ factory.getAllAtomTypes().length,
+ testedAtomTypes.size()
+ );
+ }
+ }
+
}
Modified: branches/miguelrojasch/reaction/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java
===================================================================
--- branches/miguelrojasch/reaction/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java 2008-03-04 13:49:43 UTC (rev 10291)
+++ branches/miguelrojasch/reaction/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java 2008-03-04 13:56:20 UTC (rev 10292)
@@ -1799,7 +1799,7 @@
String[] expectedTypes = {"C.sp3", "C.radical.planar", "C.sp3", "C.sp3"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}
-
+
@Test public void testEthoxyEthaneRadical() throws Exception {
IMolecule mol = new Molecule();
IAtom atom = new Atom("O");
@@ -1906,23 +1906,7 @@
}
@Test public void countTestedAtomTypes() {
- AtomTypeFactory factory = AtomTypeFactory.getInstance(
- "org/openscience/cdk/config/data/cdk_atomtypes.xml",
- NoNotificationChemObjectBuilder.getInstance()
- );
-
- IAtomType[] expectedTypes = factory.getAllAtomTypes();
- if (expectedTypes.length != testedAtomTypes.size()) {
- String errorMessage = "Atom types not tested:";
- for (int i=0; i<expectedTypes.length; i++) {
- if (!testedAtomTypes.containsKey(expectedTypes[i].getAtomTypeName()))
- errorMessage += " " + expectedTypes[i].getAtomTypeName();
- }
- Assert.assertEquals(errorMessage,
- factory.getAllAtomTypes().length,
- testedAtomTypes.size()
- );
- }
+ super.countTestedAtomTypes(testedAtomTypes);
}
}
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