Round trip positional variation in Ctab V3000.

cdk · Nov 10, 2015 · e336783 · e336783
1 parent 378d50b
commit e336783
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Showing 5 changed files with 116 additions and 10 deletions.
diff --git a/storage/io/src/main/java/org/openscience/cdk/io/MDLV3000Reader.java b/storage/io/src/main/java/org/openscience/cdk/io/MDLV3000Reader.java
@@ -24,8 +24,11 @@
 import java.io.InputStreamReader;
 import java.io.Reader;
 import java.io.StringReader;
+import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Hashtable;
 import java.util.Iterator;
+import java.util.List;
 import java.util.Map;
 import java.util.StringTokenizer;
 import java.util.regex.Matcher;
@@ -46,6 +49,8 @@
 import org.openscience.cdk.interfaces.IPseudoAtom;
 import org.openscience.cdk.io.formats.IResourceFormat;
 import org.openscience.cdk.io.formats.MDLV3000Format;
+import org.openscience.cdk.sgroup.Sgroup;
+import org.openscience.cdk.sgroup.SgroupType;
 import org.openscience.cdk.tools.ILoggingTool;
 import org.openscience.cdk.tools.LoggingToolFactory;
 import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
@@ -142,7 +147,7 @@ public <T extends IChemObject> T read(T object) throws CDKException {
     }
 
     public IAtomContainer readMolecule(IChemObjectBuilder builder) throws CDKException {
-        return builder.newInstance(IAtomContainer.class, readConnectionTable(builder));
+        return readConnectionTable(builder);
     }
 
     public IAtomContainer readConnectionTable(IChemObjectBuilder builder) throws CDKException {
@@ -393,12 +398,14 @@ public void readBondBlock(IAtomContainer readData) throws CDKException {
                     logger.debug(exception);
                     throw new CDKException(error, exception);
                 }
+
+                List<IAtom> endpts = new ArrayList<>();
+                String attach = null;
+
                 // the rest are key=value fields
                 if (command.indexOf('=') != -1) {
                     Map<String, String> options = parseOptions(exhaustStringTokenizer(tokenizer));
-                    Iterator<String> keys = options.keySet().iterator();
-                    while (keys.hasNext()) {
-                        String key = keys.next();
+                    for (String key : options.keySet()) {
                         String value = options.get(key);
                         try {
                             if (key.equals("CFG")) {
@@ -412,12 +419,20 @@ public void readBondBlock(IAtomContainer readData) throws CDKException {
                                 } else if (configuration == 3) {
                                     bond.setStereo(IBond.Stereo.DOWN);
                                 }
+                            } else if (key.equals("ENDPTS")) {
+                                String[] endptStr = value.split(" ");
+                                // skip first value that is count
+                                for (int i = 1; i < endptStr.length; i++) {
+                                    endpts.add(readData.getAtom(Integer.parseInt(endptStr[i]) - 1));
+                                }
+                            } else if (key.equals("ATTACH")) {
+                                attach = value;
                             } else {
                                 logger.warn("Not parsing key: " + key);
                             }
                         } catch (Exception exception) {
                             String error = "Error while parsing key/value " + key + "=" + value + ": "
-                                    + exception.getMessage();
+                                           + exception.getMessage();
                             logger.error(error);
                             logger.debug(exception);
                             throw new CDKException(error, exception);
@@ -427,6 +442,22 @@ public void readBondBlock(IAtomContainer readData) throws CDKException {
 
                 // storing bond
                 readData.addBond(bond);
+
+                // storing positional variation
+                if ("ANY".equals(attach)) {
+                    Sgroup sgroup = new Sgroup();
+                    sgroup.setType(SgroupType.ExtMulticenter);
+                    sgroup.addAtom(bond.getAtom(0)); // could be other end?
+                    sgroup.addBond(bond);
+                    for (IAtom endpt : endpts)
+                        sgroup.addAtom(endpt);
+
+                    List<Sgroup> sgroups = readData.getProperty(CDKConstants.CTAB_SGROUPS);
+                    if (sgroups == null)
+                        readData.setProperty(CDKConstants.CTAB_SGROUPS, sgroups = new ArrayList<>(4));
+                    sgroups.add(sgroup);
+                }
+
                 logger.debug("Added bond: " + bond);
             }
         }

diff --git a/storage/io/src/main/java/org/openscience/cdk/io/MDLV3000Writer.java b/storage/io/src/main/java/org/openscience/cdk/io/MDLV3000Writer.java
@@ -316,6 +316,19 @@ private void writeBondBlock(IAtomContainer mol,
                                 Map<IChemObject, Integer> idxs) throws IOException, CDKException {
         if (mol.getBondCount() == 0)
             return;
+
+        // collect multicenter Sgroups before output
+        List<Sgroup> sgroups = mol.getProperty(CDKConstants.CTAB_SGROUPS);
+        Map<IBond,Sgroup> multicenterSgroups = new HashMap<>();
+        if (sgroups != null) {
+            for (Sgroup sgroup : sgroups) {
+                if (sgroup.getType() != SgroupType.ExtMulticenter)
+                    continue;
+                for (IBond bond : sgroup.getBonds())
+                    multicenterSgroups.put(bond, sgroup);
+            }
+        }
+
         writer.write("BEGIN BOND\n");
         int bondIdx = 0;
         for (IBond bond : mol.bonds()) {
@@ -373,6 +386,14 @@ private void writeBondBlock(IAtomContainer mol,
                     break;
             }
 
+            Sgroup sgroup = multicenterSgroups.get(bond);
+            if (sgroup != null) {
+                List<IAtom> atoms = new ArrayList<>(sgroup.getAtoms());
+                atoms.remove(bond.getAtom(0));
+                atoms.remove(bond.getAtom(1));
+                writer.write(" ATTACH=ANY ENDPTS=(").write(atoms, idxs).write(')');
+            }
+
             writer.write('\n');
         }
         writer.write("END BOND\n");
@@ -435,11 +456,6 @@ private List<Sgroup> getSgroups(IAtomContainer mol) {
      */
     private void writeSgroupBlock(List<Sgroup> sgroups, Map<IChemObject, Integer> idxs) throws IOException, CDKException {
 
-        if (sgroups.isEmpty())
-            return;
-
-        writer.write("BEGIN SGROUP\n");
-
         // going to reorder but keep the originals untouched
         sgroups = new ArrayList<>(sgroups);
 
@@ -450,6 +466,11 @@ private void writeSgroupBlock(List<Sgroup> sgroups, Map<IChemObject, Integer> id
                 iter.remove();
         }
 
+        if (sgroups.isEmpty())
+            return;
+
+        writer.write("BEGIN SGROUP\n");
+
         // Short of building a full dependency graph we write the parents
         // first, this sort is good for three levels of nesting. Not perfect
         // but really tools should be able to handle output of order parents

diff --git a/storage/io/src/test/java/org/openscience/cdk/io/MDLV3000ReaderTest.java b/storage/io/src/test/java/org/openscience/cdk/io/MDLV3000ReaderTest.java
@@ -25,18 +25,26 @@
 import org.junit.Assert;
 import org.junit.BeforeClass;
 import org.junit.Test;
+import org.openscience.cdk.CDKConstants;
 import org.openscience.cdk.DefaultChemObjectBuilder;
 import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.graph.GraphUtil;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.sgroup.Sgroup;
+import org.openscience.cdk.sgroup.SgroupType;
 import org.openscience.cdk.silent.AtomContainer;
 import org.openscience.cdk.interfaces.IPseudoAtom;
 import org.openscience.cdk.tools.ILoggingTool;
 import org.openscience.cdk.tools.LoggingToolFactory;
 
 import java.io.InputStream;
 import java.io.StringReader;
+import java.util.List;
+
+import static org.hamcrest.CoreMatchers.is;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertThat;
 
 /**
  * TestCase for the reading MDL V3000 mol files using one test file.
@@ -117,4 +125,13 @@ public void testPseudoAtomLabels() throws Exception {
         }
     }
 
+    @Test public void positionalVariation() throws Exception {
+        MDLV3000Reader reader = new MDLV3000Reader(getClass().getResourceAsStream("multicenterBond.mol"));
+        IAtomContainer container = reader.read(new org.openscience.cdk.AtomContainer(0,0,0,0));
+        assertThat(container.getBondCount(), is(8));
+        List<Sgroup> sgroups = container.getProperty(CDKConstants.CTAB_SGROUPS);
+        assertNotNull(sgroups);
+        assertThat(sgroups.size(), is(1));
+        assertThat(sgroups.get(0).getType(), is(SgroupType.ExtMulticenter));
+    }
 }
diff --git a/storage/io/src/test/java/org/openscience/cdk/io/MDLV3000WriterTest.java b/storage/io/src/test/java/org/openscience/cdk/io/MDLV3000WriterTest.java
@@ -392,6 +392,14 @@ public void roundTripOrderMixtures() throws IOException, CDKException {
         }
     }
 
+    @Test public void positionalVariationRoundTrip() throws Exception {
+        try (MDLV3000Reader mdlr = new MDLV3000Reader(getClass().getResourceAsStream("multicenterBond.mol"))) {
+            IAtomContainer mol = mdlr.read(new AtomContainer(0, 0, 0, 0));
+            String res = writeToStr(mol);
+            assertThat(res, CoreMatchers.containsString("M  V30 8 1 8 9 ATTACH=ANY ENDPTS=(5 2 3 4 5 6)\n"));
+        }
+    }
+
     private String writeToStr(IAtomContainer mol) throws IOException, CDKException {
         StringWriter sw = new StringWriter();
         try (MDLV3000Writer mdlw = new MDLV3000Writer(sw)) {

diff --git a/storage/io/src/test/resources/org/openscience/cdk/io/multicenterBond.mol b/storage/io/src/test/resources/org/openscience/cdk/io/multicenterBond.mol
@@ -0,0 +1,29 @@
+
+
+
+  0  0  0     0  0            999 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 9 8 0 0 0
+M  V30 BEGIN ATOM
+M  V30 1 C -2.7222 1.4289 0 0
+M  V30 2 C -4.0559 0.6589 0 0
+M  V30 3 C -4.0559 -0.8811 0 0
+M  V30 4 C -2.7222 -1.6511 0 0
+M  V30 5 C -1.3886 -0.8811 0 0
+M  V30 6 C -1.3886 0.6589 0 0
+M  V30 7 C -2.7222 2.9689 0 0
+M  V30 8 * -2.7222 -0.4191 0 0
+M  V30 9 O -2.7222 -2.7291 0 0
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 1 1 2
+M  V30 2 2 2 3
+M  V30 3 1 3 4
+M  V30 4 2 4 5
+M  V30 5 1 5 6
+M  V30 6 2 1 6
+M  V30 7 1 1 7
+M  V30 8 1 8 9 ENDPTS=(5 2 3 4 5 6) ATTACH=ANY
+M  V30 END BOND
+M  V30 END CTAB
+M  END