Upgrade Beam version, new features include optimised and improved bon…

…d placement (kekulisation,double-bond direction) algorithms and title processing. Titles are now conveniently parsed in the SmilesParser.
cdk · Nov 20, 2015 · 6ec91cb · 6ec91cb
1 parent 8503cd5
commit 6ec91cb
Show file tree

Hide file tree

Showing 6 changed files with 46 additions and 4 deletions.
diff --git a/pom.xml b/pom.xml
@@ -371,12 +371,12 @@
             <dependency>
                 <groupId>uk.ac.ebi.beam</groupId>
                 <artifactId>beam-core</artifactId>
-                <version>0.8</version>
+                <version>0.9</version>
             </dependency>
             <dependency>
                 <groupId>uk.ac.ebi.beam</groupId>
                 <artifactId>beam-func</artifactId>
-                <version>0.8</version>
+                <version>0.9</version>
             </dependency>
             <dependency>
                 <groupId>com.google.guava</groupId>

diff --git a/storage/inchi/src/test/java/org/openscience/cdk/smiles/AbsoluteSMILESTest.java b/storage/inchi/src/test/java/org/openscience/cdk/smiles/AbsoluteSMILESTest.java
@@ -27,6 +27,7 @@
 import com.google.common.base.Joiner;
 import org.junit.Assert;
 import org.junit.Test;
+import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.silent.SilentChemObjectBuilder;
 
 import java.util.HashSet;
@@ -101,6 +102,16 @@ public void tetramethyltetraazatricyclooctane() throws Exception {
                 "N12[C@H](C)N3N([C@@H]3C)[C@H](C)N1[C@H]2C", "N12N([C@@H](C)N3N([C@H]3C)[C@H]1C)[C@H]2C");
     }
 
+    @Test
+    public void dbStereoCanonGeneration() throws Exception {
+        String in = "Oc1ccc(cc1O)C(\\C([O-])=O)=c1/cc(O)\\c(cc1O)=C(/C([O-])=O)c1ccccc1";
+        SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
+        final IAtomContainer mol = smipar.parseSmiles(in);
+        final SmilesGenerator cansmi = SmilesGenerator.absolute();
+        Assert.assertEquals(cansmi.create(mol),
+                            cansmi.create(smipar.parseSmiles(cansmi.create(mol))));
+    }
+
     static void test(String... inputs) throws Exception {
 
         SmilesParser sp = new SmilesParser(SilentChemObjectBuilder.getInstance());

diff --git a/storage/smiles/src/main/java/org/openscience/cdk/io/SMILESReader.java b/storage/smiles/src/main/java/org/openscience/cdk/io/SMILESReader.java
@@ -171,7 +171,6 @@ private IAtomContainerSet readAtomContainerSet(IAtomContainerSet som) {
                 try {
                     IAtomContainer molecule = sp.parseSmiles(line);
                     molecule.setProperty("SMIdbNAME", name);
-                    molecule.setProperty(CDKConstants.TITLE, name);
                     som.addAtomContainer(molecule);
                 } catch (CDKException exception) {
                     logger.warn("This SMILES could not be parsed: ", line);

diff --git a/storage/smiles/src/main/java/org/openscience/cdk/smiles/BeamToCDK.java b/storage/smiles/src/main/java/org/openscience/cdk/smiles/BeamToCDK.java
@@ -24,6 +24,7 @@
 
 package org.openscience.cdk.smiles;
 
+import org.openscience.cdk.CDKConstants;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IBond;
@@ -147,6 +148,9 @@ IAtomContainer toAtomContainer(Graph g) {
         // use directional bonds to assign bond-based stereo-specification
         addDoubleBondStereochemistry(g, ac);
 
+        // title suffix
+        ac.setProperty(CDKConstants.TITLE, g.getTitle());
+
         return ac;
     }
 

diff --git a/storage/smiles/src/test/java/org/openscience/cdk/smiles/BeamToCDKTest.java b/storage/smiles/src/test/java/org/openscience/cdk/smiles/BeamToCDKTest.java
@@ -49,6 +49,7 @@
 import static org.hamcrest.CoreMatchers.instanceOf;
 import static org.hamcrest.CoreMatchers.is;
 import static org.hamcrest.CoreMatchers.not;
+import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertNull;
@@ -529,9 +530,24 @@ public void extendedTetrahedral_cw() throws Exception {
                 is(new IAtom[]{ac.getAtom(0), ac.getAtom(1), ac.getAtom(3), ac.getAtom(4)}));
     }
 
+    @Test public void titleWithTab() throws Exception {
+        assertEquals(convert("CN1C=NC2=C1C(=O)N(C(=O)N2C)C\tcaffeine").getProperty(CDKConstants.TITLE),
+                     "caffeine");
+    }
+
+    @Test public void titleWithSpace() throws Exception {
+        assertEquals(convert("CN1C=NC2=C1C(=O)N(C(=O)N2C)C caffeine").getProperty(CDKConstants.TITLE),
+                     "caffeine");
+    }
+
+    @Test public void titleWithMultipleSpace() throws Exception {
+        assertEquals(convert("CN1C=NC2=C1C(=O)N(C(=O)N2C)C caffeine compound").getProperty(CDKConstants.TITLE),
+                     "caffeine compound");
+    }
+
     IAtomContainer convert(String smi) throws IOException {
         BeamToCDK g2c = new BeamToCDK(SilentChemObjectBuilder.getInstance());
-        Graph g = Functions.expand(Graph.fromSmiles(smi));
+        Graph g = Graph.fromSmiles(smi);
         return g2c.toAtomContainer(g);
     }
 

diff --git a/storage/smiles/src/test/java/org/openscience/cdk/smiles/SmilesGeneratorTest.java b/storage/smiles/src/test/java/org/openscience/cdk/smiles/SmilesGeneratorTest.java
@@ -1199,6 +1199,18 @@ public void bug328() throws Exception {
                    is(canon("Clc1ccc(Cl)c2[nH]c([nH0]c21)C(F)(F)F")));
     }
 
+
+    /**
+     * @see https://tech.knime.org/forum/cdk/buggy-behavior-of-molecule-to-cdk-node
+     */
+    @Test
+    public void assignDbStereo() throws Exception {
+        String in = "C(/N)=C\\C=C\\1/N=C1";
+        SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
+        IAtomContainer mol = smipar.parseSmiles(in);
+        Assert.assertEquals("C(/N)=C\\C=C\\1/N=C1", SmilesGenerator.isomeric().create(mol));
+    }
+
     static ITetrahedralChirality anticlockwise(IAtomContainer container, int central, int a1, int a2, int a3, int a4) {
         return new TetrahedralChirality(container.getAtom(central), new IAtom[]{container.getAtom(a1),
                                                                                 container.getAtom(a2), container.getAtom(a3), container.getAtom(a4)},