Merge pull request #302 from cdk/bug/sgroupreplace

Looks good to me.
cdk · Apr 23, 2017 · d42c6c7 · d42c6c7
2 parents 3b5a079 + bea78e7
commit d42c6c7
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Showing 8 changed files with 223 additions and 8 deletions.
diff --git a/...tandard/src/main/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java b/...tandard/src/main/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java
@@ -30,6 +30,7 @@
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
@@ -59,6 +60,8 @@
 import org.openscience.cdk.interfaces.IStereoElement;
 import org.openscience.cdk.interfaces.ITetrahedralChirality;
 import org.openscience.cdk.ringsearch.RingSearch;
+import org.openscience.cdk.sgroup.Sgroup;
+import org.openscience.cdk.sgroup.SgroupKey;
 import org.openscience.cdk.stereo.DoubleBondStereochemistry;
 import org.openscience.cdk.stereo.ExtendedTetrahedral;
 import org.openscience.cdk.stereo.TetrahedralChirality;
@@ -174,6 +177,37 @@ public static boolean replaceAtomByAtom(final IAtomContainer container, final IA
             stereoremapped.add(se.map(atomremap, bondremap));
         container.setStereoElements(stereoremapped);
 
+        List<Sgroup> sgrougs = container.getProperty(CDKConstants.CTAB_SGROUPS);
+        if (sgrougs != null) {
+            boolean updated = false;
+            List<Sgroup> replaced = new ArrayList<>();
+            for (Sgroup org : sgrougs) {
+                if (org.getAtoms().contains(oldAtom)) {
+                    updated = true;
+                    Sgroup cpy = new Sgroup();
+                    for (IAtom atom : org.getAtoms()) {
+                        if (atom != oldAtom)
+                            cpy.addAtom(atom);
+                        else
+                            cpy.addAtom(newAtom);
+                    }
+                    for (IBond bond : org.getBonds())
+                        cpy.addBond(bond);
+                    for (Sgroup parent : org.getParents())
+                        cpy.addParent(parent);
+                    for (SgroupKey key : org.getAttributeKeys())
+                        cpy.putValue(key, org.getValue(key));
+                    replaced.add(cpy);
+                } else {
+                    replaced.add(org);
+                }
+            }
+            if (updated) {
+                container.setProperty(CDKConstants.CTAB_SGROUPS,
+                                      Collections.unmodifiableList(replaced));
+            }
+        }
+
         return true;
     }
 

diff --git a/storage/io/src/main/java/org/openscience/cdk/io/MDLV2000Reader.java b/storage/io/src/main/java/org/openscience/cdk/io/MDLV2000Reader.java
@@ -492,10 +492,6 @@ private IAtomContainer readAtomContainer(IAtomContainer molecule) throws CDKExce
             // read potential SD file data between M  END and $$$$
             readNonStructuralData(input, outputContainer);
 
-            if (interpretHydrogenIsotopes.isSet()) {
-                fixHydrogenIsotopes(molecule, Isotopes.getInstance());
-            }
-
             // note: apply the valence model last so that all fixes (i.e. hydrogen
             // isotopes) are in place we need to use a offset as this atoms
             // could be added to a molecule which already had atoms present
@@ -1283,7 +1279,20 @@ static int length(final String str) {
      * @throws CDKException the symbol is not allowed
      */
     private IAtom createAtom(String symbol, IChemObjectBuilder builder, int lineNum) throws CDKException {
-        if (isPeriodicElement(symbol)) return builder.newInstance(IAtom.class, symbol);
+        if (isPeriodicElement(symbol))
+            return builder.newInstance(IAtom.class, symbol);
+        if (symbol.equals("D") && interpretHydrogenIsotopes.isSet()) {
+            if (mode == Mode.STRICT) throw new CDKException("invalid symbol: " + symbol);
+            IAtom atom = builder.newInstance(IAtom.class, "H");
+            atom.setMassNumber(2);
+            return atom;
+        }
+        if (symbol.equals("T") && interpretHydrogenIsotopes.isSet()) {
+            if (mode == Mode.STRICT) throw new CDKException("invalid symbol: " + symbol);
+            IAtom atom = builder.newInstance(IAtom.class, "H");
+            atom.setMassNumber(3);
+            return atom;
+        }
 
         if (!isPseudoElement(symbol)) {
             handleError("invalid symbol: " + symbol, lineNum, 31, 34);

diff --git a/storage/io/src/test/java/org/openscience/cdk/io/MDLV2000ReaderTest.java b/storage/io/src/test/java/org/openscience/cdk/io/MDLV2000ReaderTest.java
@@ -907,7 +907,7 @@ public void testDeuteriumProperties() throws Exception {
         reader.close();
         IAtom deuterium = molecule.getAtom(molecule.getAtomCount() - 1);
         assertTrue(1 == deuterium.getAtomicNumber());
-        assertTrue(2.014101778 == deuterium.getExactMass());
+        assertTrue(2 == deuterium.getMassNumber());
     }
 
     @Test
@@ -935,7 +935,7 @@ public void testTritiumProperties() throws Exception {
         reader.close();
         IAtom tritium = molecule.getAtom(molecule.getAtomCount() - 1);
         assertTrue(1 == tritium.getAtomicNumber());
-        assertTrue(3.016049278 == tritium.getExactMass());
+        assertTrue(3 == tritium.getMassNumber());
     }
 
     /**

diff --git a/storage/smiles/src/main/java/org/openscience/cdk/smiles/CxSmilesGenerator.java b/storage/smiles/src/main/java/org/openscience/cdk/smiles/CxSmilesGenerator.java
@@ -31,6 +31,7 @@
 import java.util.Comparator;
 import java.util.Iterator;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 import java.util.TreeMap;
 
@@ -265,7 +266,7 @@ public int compare(PolymerSgroup a, PolymerSgroup b) {
                 sb.append(':');
                 sb.append(sgroup.subscript);
                 sb.append(':');
-                sb.append(sgroup.supscript);
+                sb.append(sgroup.supscript.toLowerCase(Locale.ROOT));
             }
         }
 

diff --git a/storage/smiles/src/main/java/org/openscience/cdk/smiles/SmilesGenerator.java b/storage/smiles/src/main/java/org/openscience/cdk/smiles/SmilesGenerator.java
@@ -865,6 +865,9 @@ else if (val == CxSmilesState.Radical.Trivalent)
                     case CtabMultipleGroup:
                         // display shortcuts are not output
                         break;
+                    case CtabData:
+                        // can be generated but currently ignored
+                        break;
                     default:
                         throw new UnsupportedOperationException("Unsupported Sgroup Polymer");
 

diff --git a/storage/smiles/src/test/java/org/openscience/cdk/smiles/CxSmilesGeneratorTest.java b/storage/smiles/src/test/java/org/openscience/cdk/smiles/CxSmilesGeneratorTest.java
@@ -24,7 +24,13 @@
 package org.openscience.cdk.smiles;
 
 import org.junit.Test;
+import org.openscience.cdk.AtomContainer;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.io.MDLV2000Reader;
+import org.openscience.cdk.silent.SilentChemObjectBuilder;
 
+import java.io.IOException;
+import java.io.InputStream;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
@@ -82,4 +88,27 @@ public void radicals() {
                    is(" |^1:1,5,^2:3|"));
     }
 
+    /**
+     * Integration - test used to fail because the D (pseudo) was swapped out with a 2H after Sgroups were
+     * initialized.
+     */
+    @Test
+    public void chebi53695() throws Exception {
+        try (InputStream in = getClass().getResourceAsStream("CHEBI_53695.mol");
+             MDLV2000Reader mdlr = new MDLV2000Reader(in)) {
+            IAtomContainer mol = mdlr.read(SilentChemObjectBuilder.getInstance().newInstance(IAtomContainer.class));
+            SmilesGenerator smigen = new SmilesGenerator(SmiFlavor.CxSmiles | SmiFlavor.AtomicMassStrict);
+            assertThat(smigen.create(mol),
+                       is("C(C(=O)OC)(C*)*C(C(C1=C(C(=C(C(=C1[2H])[2H])[2H])[2H])[2H])(*)[2H])([2H])[2H] |Sg:n:0,1,2,3,4,5:n:ht,Sg:n:8,9,10,11,12,13,14,15,16,17,18,19,20,22,23,24:m:ht|"));
+        }
+    }
+
+
+    @Test public void chembl367774() throws Exception {
+        try (MDLV2000Reader mdlr = new MDLV2000Reader(getClass().getResourceAsStream("CHEMBL367774.mol"))) {
+            IAtomContainer container = mdlr.read(new AtomContainer());
+            SmilesGenerator smigen = new SmilesGenerator(SmiFlavor.CxSmiles);
+            assertThat(smigen.create(container), is("OC(=O)C1=CC(F)=CC=2NC(=NC12)C3=CC=C(C=C3F)C4=CC=CC=C4"));
+        }
+    }
 }
diff --git a/storage/smiles/src/test/resources/org/openscience/cdk/smiles/CHEBI_53695.mol b/storage/smiles/src/test/resources/org/openscience/cdk/smiles/CHEBI_53695.mol
@@ -0,0 +1,69 @@
+
+  Marvin  11260917092D
+
+ 25 25  0  0  0  0            999 V2000
+   -2.3138    0.5318    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.5321    1.0607    0.0000 *   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.8177    1.4732    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.1032    1.0607    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.1032    0.2357    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.8177   -0.1768    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.8177   -1.0018    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.1032   -1.4143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.6113   -1.0018    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.6113   -0.1768    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.3011    1.0694    0.0000 *   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.3138   -0.2932    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.5994   -0.7057    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.0283   -0.7057    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.7428   -0.2932    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.0283    0.9443    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.0624    0.9356    0.0000 *   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.2343    2.0566    0.0000 D   0  0  0  0  0  0  0  0  0  0  0  0
+    1.3258    0.2357    0.0000 D   0  0  0  0  0  0  0  0  0  0  0  0
+    1.3258   -1.4143    0.0000 D   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.1032   -2.2393    0.0000 D   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.5322   -1.4143    0.0000 D   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.5322    0.2357    0.0000 D   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.4011    2.0566    0.0000 D   0  0  0  0  0  0  0  0  0  0  0  0
+    0.3599    1.8595    0.0000 D   0  0  0  0  0  0  0  0  0  0  0  0
+  2  3  1  0  0  0  0
+  3  4  1  0  0  0  0
+  4  5  1  0  0  0  0
+  5  6  2  0  0  0  0
+  5 10  1  0  0  0  0
+  6  7  1  0  0  0  0
+  7  8  2  0  0  0  0
+  8  9  1  0  0  0  0
+  9 10  2  0  0  0  0
+  4 11  1  0  0  0  0
+  1 12  1  0  0  0  0
+ 12 13  2  0  0  0  0
+ 12 14  1  0  0  0  0
+ 14 15  1  0  0  0  0
+  1 16  1  0  0  0  0
+  1  2  1  0  0  0  0
+ 16 17  1  0  0  0  0
+  3 18  1  0  0  0  0
+ 10 19  1  0  0  0  0
+  9 20  1  0  0  0  0
+  8 21  1  0  0  0  0
+  7 22  1  0  0  0  0
+  6 23  1  0  0  0  0
+  3 24  1  0  0  0  0
+  4 25  1  0  0  0  0
+M  STY  2   1 SRU   2 SRU
+M  SCN  1   1 HT
+M  SAL   1  6   1  12  13  14  15  16
+M  SDI   1  4   -3.4506    0.5282   -3.4576    1.3532
+M  SDI   1  4   -2.2231    1.0912   -1.7608    0.4079
+M  SBL   1  2  16  17
+M  SMT   1 n
+M  SCN  1   2 HT
+M  SAL   2 15   3   4   5   6   7   8   9  10  18  19  20  21  22  23  24
+M  SAL   2  1  25
+M  SDI   2  4    0.4725    1.4768    0.4776    0.6518
+M  SDI   2  4   -0.9056    0.9461   -1.3181    1.6606
+M  SBL   2  2   1  10
+M  SMT   2 m
+M  END
diff --git a/storage/smiles/src/test/resources/org/openscience/cdk/smiles/CHEMBL367774.mol b/storage/smiles/src/test/resources/org/openscience/cdk/smiles/CHEMBL367774.mol
@@ -0,0 +1,70 @@
+
+  SciTegic05171617282D
+
+ 26 29  0  0  0  0            999 V2000
+    0.0446    3.6095    0.0000 O   0  0
+   -0.9971    3.0138    0.0000 C   0  0
+   -2.0337    3.6184    0.0000 O   0  0
+   -1.0028    1.5132    0.0000 C   0  0
+   -2.3155    0.7475    0.0000 C   0  0
+   -2.3155   -0.7475    0.0000 C   0  0
+   -3.3560   -1.3452    0.0000 F   0  0
+   -1.0028   -1.5132    0.0000 C   0  0
+    0.2917   -0.7475    0.0000 C   0  0
+    1.7138   -1.2033    0.0000 N   0  0
+    2.5889    0.0182    0.0000 C   0  0
+    1.7138    1.2033    0.0000 N   0  0
+    0.2917    0.7475    0.0000 C   0  0
+    4.0896    0.0290    0.0000 C   0  0
+    4.7453   -1.3220    0.0000 C   0  0
+    6.2418   -1.4248    0.0000 C   0  0
+    7.0791   -0.1803    0.0000 C   0  0
+    6.4199    1.1671    0.0000 C   0  0
+    4.9234    1.2700    0.0000 C   0  0
+    4.3957    2.3477    0.0000 F   0  0
+    8.5763   -0.2831    0.0000 C   0  0
+    9.2377   -1.6295    0.0000 C   0  0
+   10.7344   -1.7299    0.0000 C   0  0
+   11.5697   -0.4840    0.0000 C   0  0
+   10.9083    0.8623    0.0000 C   0  0
+    9.4117    0.9628    0.0000 C   0  0
+  1  2  1  0
+  2  3  2  0
+  2  4  1  0
+  4  5  2  0
+  5  6  1  0
+  6  7  1  0
+  6  8  2  0
+  8  9  1  0
+  9 10  1  0
+ 10 11  1  0
+ 11 12  2  0
+ 12 13  1  0
+  4 13  1  0
+  9 13  2  0
+ 11 14  1  0
+ 14 15  2  0
+ 15 16  1  0
+ 16 17  2  0
+ 17 18  1  0
+ 18 19  2  0
+ 14 19  1  0
+ 19 20  1  0
+ 17 21  1  0
+ 21 22  2  0
+ 22 23  1  0
+ 23 24  2  0
+ 24 25  1  0
+ 25 26  2  0
+ 21 26  1  0
+M  STY  2   1 DAT   2 DAT
+M  SLB  2   1   1   2   2
+M  SAL   1  1  10
+M  SDT   1 MRV_IMPLICIT_H
+M  SDD   1     0.5304   -0.4125    DR    ALL  0       0
+M  SED   1 IMPL_H1
+M  SAL   2  1  12
+M  SDT   2 MRV_IMPLICIT_H
+M  SDD   2     0.5304   -0.4125    DR    ALL  0       0
+M  SED   2 IMPL_H1
+M  END