Merge pull request #269 from cdk/patch/newatom

Well, it makes PseudoAtom less important... so, yes, a functional change. As long as it is a conscious choice, I had my chance to express my mild concern. Downstream code/algorithms will now have to take into account that an IAtom implementation that is not an IPseudoAtom can still not have a valid atom number... I won't block :)
cdk · Feb 19, 2017 · f1e1e2c · f1e1e2c
2 parents c3f55ae + 8eb60ae
commit f1e1e2c
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Showing 3 changed files with 9 additions and 2 deletions.
diff --git a/base/data/src/main/java/org/openscience/cdk/Atom.java b/base/data/src/main/java/org/openscience/cdk/Atom.java
@@ -536,6 +536,10 @@ private static boolean parseAtomSymbol(IAtom atom, String str) {
             atom.setAtomicNumber(0);
             atom.setSymbol("R");
             return true;
+        } else if ("*".equals(str)) {
+            atom.setAtomicNumber(0);
+            atom.setSymbol("*");
+            return true;
         } else if ("D".equals(str)) {
             atom.setAtomicNumber(1);
             atom.setMassNumber(2);

diff --git a/base/silent/src/main/java/org/openscience/cdk/silent/Atom.java b/base/silent/src/main/java/org/openscience/cdk/silent/Atom.java
@@ -513,7 +513,6 @@ private static boolean isDigit(char c) {
     }
 
     private static boolean parseAtomSymbol(IAtom atom, String str) {
-
         Elements elem = Elements.ofString(str);
         if (elem != Elements.Unknown) {
             atom.setAtomicNumber(elem.number());
@@ -523,6 +522,10 @@ private static boolean parseAtomSymbol(IAtom atom, String str) {
             atom.setAtomicNumber(0);
             atom.setSymbol("R");
             return true;
+        } else if ("*".equals(str)) {
+            atom.setAtomicNumber(0);
+            atom.setSymbol("*");
+            return true;
         } else if ("D".equals(str)) {
             atom.setAtomicNumber(1);
             atom.setMassNumber(2);

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
@@ -1344,7 +1344,7 @@ public static IAtomContainer skeleton(IAtomContainer src) {
         IBond[] bonds = new IBond[src.getBondCount()];
 
         for (int i = 0; i < atoms.length; i++) {
-            atoms[i] = builder.newInstance(IAtom.class, src.getAtom(i).getSymbol());
+            atoms[i] = builder.newInstance(IAtom.class, src.getAtom(i).getAtomicNumber());
         }
         for (int i = 0; i < bonds.length; i++) {
             IBond bond = src.getBond(i);