Remove non-loops. RandomAccessSDFReader had a comment that MDLV2000Re…

…ader(IAtomContainer) didn't read properties which is why it used a IChemModel - this is no longer the case. The reset were cases where we want to select the first match.
cdk · Feb 19, 2022 · 5a0e966 · 5a0e966
1 parent 3a56550
commit 5a0e966
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Showing 5 changed files with 14 additions and 32 deletions.
diff --git a/legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/SmartsQueryVisitor.java b/legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/SmartsQueryVisitor.java
@@ -148,9 +148,8 @@ public Object visit(ASTRingIdentifier node, Object data) {
 
     public Object visit(ASTAtom node, Object data) {
         IQueryAtom atom = (IQueryAtom) node.jjtGetChild(0).jjtAccept(this, data);
-        for (int i = 1; i < node.jjtGetNumChildren(); i++) { // if there are ring identifiers
+        if (node.jjtGetNumChildren() > 1) // if there are ring identifiers
             throw new IllegalStateException();
-        }
         return atom;
     }
 

diff --git a/legacy/src/main/java/org/openscience/cdk/smsd/filters/ChemicalFilters.java b/legacy/src/main/java/org/openscience/cdk/smsd/filters/ChemicalFilters.java
@@ -329,11 +329,11 @@ public synchronized void sortResultsByEnergies() throws CDKException {
         boolean flag = false;
 
         double lowestEnergyScore = 99999999.99;
-        for (Integer key : energySelectionMap.keySet()) {
+        if (energySelectionMap.size() > 0) {
+            Integer key = energySelectionMap.keySet().iterator().next();
             lowestEnergyScore = energySelectionMap.get(key);
             flag = true;
             clear();
-            break;
         }
 
         int counter = 0;

diff --git a/storage/ctab/src/main/java/org/openscience/cdk/io/random/RandomAccessSDFReader.java b/storage/ctab/src/main/java/org/openscience/cdk/io/random/RandomAccessSDFReader.java
@@ -84,29 +84,7 @@ public IResourceFormat getFormat() {
 
     @Override
     protected IChemObject processContent() throws CDKException {
-        /*
-         * return chemObjectReader.read(builder.newInstance(IAtomContainer.class));
-         */
-        //read(IAtomContainer) doesn't read properties ...
-        IChemObject co = chemObjectReader.read(builder.newInstance(IChemFile.class));
-        if (co instanceof IChemFile) {
-            int c = ((IChemFile) co).getChemSequenceCount();
-            for (int i = 0; i < c; i++) {
-                for (IChemModel iChemModel : ((IChemFile) co).getChemSequence(i).chemModels()) {
-                    for (IAtomContainer container : iChemModel.getMoleculeSet().atomContainers()) {
-
-                        co = container;
-                        break;
-                    }
-                    break;
-                }
-                Iterator<IChemModel> cm = null;
-                break;
-            }
-            //cs = null;
-        }
-        return co;
-
+        return chemObjectReader.read(builder.newAtomContainer());
     }
 
     public void setReader(Reader reader) throws CDKException {

diff --git a/tool/sdg/src/main/java/org/openscience/cdk/layout/IdentityTemplateLibrary.java b/tool/sdg/src/main/java/org/openscience/cdk/layout/IdentityTemplateLibrary.java
@@ -350,7 +350,9 @@ boolean assignLayout(IAtomContainer container) {
             String smiles = cansmi(container, ordering);
 
             // find the points in the library
-            for (Point2d[] points : templateMap.getOrDefault(smiles, Collections.emptyList())) {
+            List<Point2d[]> templatePoints = templateMap.get(smiles);
+            if (templatePoints != null && templatePoints.size() > 0) {
+                Point2d[] points = templatePoints.get(0);
                 // set the points
                 for (int i = 0; i < n; i++) {
                     container.getAtom(i).setPoint2d(new Point2d(points[ordering[i]]));

diff --git a/tool/sdg/src/main/java/org/openscience/cdk/layout/TemplateHandler.java b/tool/sdg/src/main/java/org/openscience/cdk/layout/TemplateHandler.java
@@ -54,6 +54,7 @@
 import java.io.InputStreamReader;
 import java.util.ArrayList;
 import java.util.HashSet;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
@@ -330,8 +331,9 @@ public static TemplateHandler createSingleton(IAtomContainer template) {
      */
     public static TemplateHandler createFromSubstructure(Pattern ptrn, Iterable<IAtomContainer> mols) {
         for (IAtomContainer mol : mols) {
-            for (IAtomContainer template : ptrn.matchAll(mol).toSubstructures())
-                return createSingleton(template);
+            Iterator<IAtomContainer> matched = ptrn.matchAll(mol).toSubstructures().iterator();
+            if (matched.hasNext())
+                return createSingleton(matched.next());
         }
         throw new IllegalArgumentException("Pattern does not match any provided molecules");
     }
@@ -345,8 +347,9 @@ public static TemplateHandler createFromSubstructure(Pattern ptrn, Iterable<IAto
      * @return new template handler
      */
     public static TemplateHandler createFromSubstructure(Pattern ptrn, IAtomContainer mol) {
-        for (IAtomContainer template : ptrn.matchAll(mol).toSubstructures())
-            return createSingleton(template);
+        Iterator<IAtomContainer> matched = ptrn.matchAll(mol).toSubstructures().iterator();
+        if (matched.hasNext())
+            return createSingleton(matched.next());
         throw new IllegalArgumentException("Pattern does not match any provided molecules");
     }