This was a useful one, the "official" calculation is (int)1+(n/0.75) for the default load factor. However in all these cases we expected n to be small - say 100 or so. In which case 135 vs 200 (2*n) is fine.

johnmay · egonw · commit cbab6a6c5325 · 2022-01-01T11:32:07.000+01:00
diff --git a/base/core/src/main/java/org/openscience/cdk/graph/GraphUtil.java b/base/core/src/main/java/org/openscience/cdk/graph/GraphUtil.java
@@ -23,10 +23,10 @@
  */
 package org.openscience.cdk.graph;
 
-import com.google.common.collect.Maps;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IBond;
 
+import java.util.HashMap;
 import java.util.Map;
 import java.util.Set;
 
@@ -312,7 +312,7 @@ public static final class EdgeToBondMap {
          * @param n number of bonds expected
          */
         private EdgeToBondMap(int n) {
-            this.lookup = Maps.newHashMapWithExpectedSize(n);
+            this.lookup = new HashMap<>(2*n);
         }
 
         /**
diff --git a/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/QueryStereoFilter.java b/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/QueryStereoFilter.java
@@ -25,7 +25,6 @@
 
 package org.openscience.cdk.isomorphism;
 
-import com.google.common.collect.Maps;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IBond;
@@ -38,6 +37,7 @@
 import org.openscience.cdk.isomorphism.matchers.QueryBond;
 
 import java.util.Arrays;
+import java.util.HashMap;
 import java.util.Map;
 import java.util.function.Predicate;
 
@@ -372,7 +372,7 @@ private int otherIndex(int i) {
      * @return the index/lookup of atoms to the index they appear
      */
     private static Map<IAtom, Integer> indexAtoms(IAtomContainer container) {
-        Map<IAtom, Integer> map = Maps.newHashMapWithExpectedSize(container.getAtomCount());
+        Map<IAtom, Integer> map = new HashMap<>(2*container.getAtomCount());
         for (int i = 0; i < container.getAtomCount(); i++)
             map.put(container.getAtom(i), i);
         return map;
diff --git a/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/StereoMatch.java b/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/StereoMatch.java
@@ -24,7 +24,6 @@
 
 package org.openscience.cdk.isomorphism;
 
-import com.google.common.collect.Maps;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IBond;
@@ -33,6 +32,7 @@
 import org.openscience.cdk.interfaces.ITetrahedralChirality;
 
 import java.util.Arrays;
+import java.util.HashMap;
 import java.util.Map;
 import java.util.function.Predicate;
 
@@ -342,7 +342,7 @@ private int otherIndex(int i) {
      * @return the index/lookup of atoms to the index they appear
      */
     private static Map<IAtom, Integer> indexAtoms(IAtomContainer container) {
-        Map<IAtom, Integer> map = Maps.newHashMapWithExpectedSize(container.getAtomCount());
+        Map<IAtom, Integer> map = new HashMap<>(2*container.getAtomCount());
         for (int i = 0; i < container.getAtomCount(); i++)
             map.put(container.getAtom(i), i);
         return map;
diff --git a/base/standard/src/main/java/org/openscience/cdk/aromaticity/AtomTypeModel.java b/base/standard/src/main/java/org/openscience/cdk/aromaticity/AtomTypeModel.java
@@ -25,7 +25,6 @@
 package org.openscience.cdk.aromaticity;
 
 import com.google.common.collect.ImmutableMap;
-import com.google.common.collect.Maps;
 import org.openscience.cdk.CDKConstants;
 import org.openscience.cdk.config.AtomTypeFactory;
 import org.openscience.cdk.exception.NoSuchAtomTypeException;
@@ -36,6 +35,7 @@
 import org.openscience.cdk.ringsearch.RingSearch;
 
 import java.util.Arrays;
+import java.util.HashMap;
 import java.util.Map;
 import java.util.Objects;
 
@@ -86,7 +86,7 @@ int[] contribution(IAtomContainer container, RingSearch ringSearch) {
 
         Arrays.fill(electrons, -1);
 
-        final Map<IAtom, Integer> indexMap = Maps.newHashMapWithExpectedSize(nAtoms);
+        final Map<IAtom, Integer> indexMap = new HashMap<>(2*nAtoms);
 
         for (int i = 0; i < nAtoms; i++) {
 
diff --git a/base/standard/src/main/java/org/openscience/cdk/aromaticity/DaylightModel.java b/base/standard/src/main/java/org/openscience/cdk/aromaticity/DaylightModel.java
@@ -24,14 +24,14 @@
 
 package org.openscience.cdk.aromaticity;
 
-import com.google.common.collect.Maps;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IBond;
 import org.openscience.cdk.interfaces.IPseudoAtom;
 import org.openscience.cdk.ringsearch.RingSearch;
 
 import java.util.Arrays;
+import java.util.HashMap;
 import java.util.Map;
 import java.util.Objects;
 
@@ -93,7 +93,7 @@ int[] contribution(IAtomContainer container, RingSearch ringSearch) {
         Arrays.fill(exocyclicPiBond, -1);
 
         // index atoms and set the degree to the number of implicit hydrogens
-        Map<IAtom, Integer> atomIndex = Maps.newHashMapWithExpectedSize(n);
+        Map<IAtom, Integer> atomIndex = new HashMap<>(2*n);
         for (int i = 0; i < n; i++) {
             IAtom a = container.getAtom(i);
             atomIndex.put(a, i);
diff --git a/base/standard/src/main/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java b/base/standard/src/main/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java
@@ -24,7 +24,6 @@
  *  */
 package org.openscience.cdk.tools.manipulator;
 
-import com.google.common.collect.Maps;
 import org.openscience.cdk.CDKConstants;
 import org.openscience.cdk.atomtype.CDKAtomTypeMatcher;
 import org.openscience.cdk.config.Elements;
@@ -615,7 +614,7 @@ public static void convertImplicitToExplicitHydrogens(IAtomContainer atomContain
         List<IBond> newBonds = new ArrayList<IBond>();
 
         // store a single explicit hydrogen of each original neighbor
-        Map<IAtom, IAtom> hNeighbor = Maps.newHashMapWithExpectedSize(atomContainer.getAtomCount());
+        Map<IAtom, IAtom> hNeighbor = new HashMap<>(2*atomContainer.getAtomCount());
 
         for (IAtom atom : atomContainer.atoms()) {
             if (!"H".equals(atom.getSymbol())) {
diff --git a/legacy/src/main/java/org/openscience/cdk/isomorphism/SmartsStereoMatch.java b/legacy/src/main/java/org/openscience/cdk/isomorphism/SmartsStereoMatch.java
@@ -24,7 +24,6 @@
 
 package org.openscience.cdk.isomorphism;
 
-import com.google.common.collect.Maps;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IBond;
@@ -37,6 +36,7 @@
 import org.openscience.cdk.isomorphism.matchers.smarts.StereoBond;
 
 import java.util.Arrays;
+import java.util.HashMap;
 import java.util.Map;
 import java.util.function.Predicate;
 
@@ -320,7 +320,7 @@ private int otherIndex(int i) {
      * @return the index/lookup of atoms to the index they appear
      */
     private static Map<IAtom, Integer> indexAtoms(IAtomContainer container) {
-        Map<IAtom, Integer> map = Maps.newHashMapWithExpectedSize(container.getAtomCount());
+        Map<IAtom, Integer> map = new HashMap<>(2*container.getAtomCount());
         for (int i = 0; i < container.getAtomCount(); i++)
             map.put(container.getAtom(i), i);
         return map;
diff --git a/storage/ctab/src/main/java/org/openscience/cdk/io/MDLValence.java b/storage/ctab/src/main/java/org/openscience/cdk/io/MDLValence.java
@@ -32,11 +32,11 @@
 
 package org.openscience.cdk.io;
 
-import com.google.common.collect.Maps;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IBond;
 
+import java.util.HashMap;
 import java.util.Map;
 
 /**
@@ -63,7 +63,7 @@ static IAtomContainer apply(IAtomContainer container) {
 
         int[] valences = new int[n];
 
-        Map<IAtom, Integer> atomToIndex = Maps.newHashMapWithExpectedSize(n);
+        Map<IAtom, Integer> atomToIndex = new HashMap<>(2*n);
         for (IAtom atom : container.atoms())
             atomToIndex.put(atom, atomToIndex.size());
 
diff --git a/storage/smiles/src/main/java/org/openscience/cdk/smiles/CDKToBeam.java b/storage/smiles/src/main/java/org/openscience/cdk/smiles/CDKToBeam.java
@@ -24,7 +24,6 @@
 
 package org.openscience.cdk.smiles;
 
-import com.google.common.collect.Maps;
 
 import org.openscience.cdk.CDKConstants;
 import org.openscience.cdk.config.Isotopes;
@@ -50,6 +49,7 @@
 import uk.ac.ebi.beam.GraphBuilder;
 
 import java.io.IOException;
+import java.util.HashMap;
 import java.util.Map;
 import java.util.Objects;
 
@@ -132,7 +132,7 @@ static Graph toBeamGraph(IAtomContainer ac, int flavour) throws CDKException {
         int order = ac.getAtomCount();
 
         GraphBuilder gb = GraphBuilder.create(order);
-        Map<IAtom, Integer> indices = Maps.newHashMapWithExpectedSize(order);
+        Map<IAtom, Integer> indices = new HashMap<>(2*order);
 
         for (IAtom a : ac.atoms()) {
             indices.put(a, indices.size());
diff --git a/storage/smiles/src/main/java/org/openscience/cdk/smiles/SmilesParser.java b/storage/smiles/src/main/java/org/openscience/cdk/smiles/SmilesParser.java
@@ -24,7 +24,6 @@
 package org.openscience.cdk.smiles;
 
 import com.google.common.collect.HashMultimap;
-import com.google.common.collect.Maps;
 import com.google.common.collect.Multimap;
 import org.openscience.cdk.CDKConstants;
 import org.openscience.cdk.exception.InvalidSmilesException;
@@ -316,7 +315,7 @@ private void parseMolCXSMILES(String title, IAtomContainer mol) throws InvalidSm
                 // set the correct title
                 mol.setTitle(title.substring(pos));
 
-                final Map<IAtom, IAtomContainer> atomToMol = Maps.newHashMapWithExpectedSize(mol.getAtomCount());
+                final Map<IAtom, IAtomContainer> atomToMol = new HashMap<>(2*mol.getAtomCount());
                 final List<IAtom> atoms = new ArrayList<>(mol.getAtomCount());
 
                 for (IAtom atom : mol.atoms()) {
diff --git a/tool/sdg/src/main/java/org/openscience/cdk/layout/CorrectGeometricConfiguration.java b/tool/sdg/src/main/java/org/openscience/cdk/layout/CorrectGeometricConfiguration.java
@@ -25,7 +25,6 @@
 package org.openscience.cdk.layout;
 
 import com.google.common.collect.Iterables;
-import com.google.common.collect.Maps;
 import org.openscience.cdk.graph.GraphUtil;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
@@ -37,6 +36,7 @@
 
 import javax.vecmath.Point2d;
 import java.util.Arrays;
+import java.util.HashMap;
 import java.util.Map;
 
 /**
@@ -103,7 +103,7 @@ public static IAtomContainer correct(IAtomContainer container) {
         this.container = container;
         this.graph = graph;
         this.visited = new boolean[graph.length];
-        this.atomToIndex = Maps.newHashMapWithExpectedSize(container.getAtomCount());
+        this.atomToIndex = new HashMap<>(2*container.getAtomCount());
         this.ringSearch = new RingSearch(container, graph);
 
         for (int i = 0; i < container.getAtomCount(); i++) {
diff --git a/tool/sdg/src/main/java/org/openscience/cdk/layout/NonplanarBonds.java b/tool/sdg/src/main/java/org/openscience/cdk/layout/NonplanarBonds.java
@@ -24,7 +24,6 @@
 
 package org.openscience.cdk.layout;
 
-import com.google.common.collect.Maps;
 import com.google.common.primitives.Ints;
 import org.openscience.cdk.BondRef;
 import org.openscience.cdk.CDKConstants;
@@ -132,7 +131,7 @@ public static IAtomContainer assign(final IAtomContainer container) {
         this.tetrahedralElements = new ITetrahedralChirality[container.getAtomCount()];
         this.doubleBondElements = new IDoubleBondStereochemistry[container.getAtomCount()];
         this.graph = g;
-        this.atomToIndex = Maps.newHashMapWithExpectedSize(container.getAtomCount());
+        this.atomToIndex = new HashMap<>(2*container.getAtomCount());
         this.edgeToBond = edgeToBond;
         this.ringSearch = new RingSearch(container, graph);
 
