sticks fix; code clean up

BobHanson · Oct 22, 2024 · ec8f691 · ec8f691
1 parent b87e003
commit ec8f691
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Showing 4 changed files with 3 additions and 6 deletions.
diff --git a/src/org/jmol/adapter/readers/cif/MSRdr.java b/src/org/jmol/adapter/readers/cif/MSRdr.java
@@ -1080,7 +1080,6 @@ private void trimAtomSet() {
     BS bs = asc.getBSAtoms(-1);
     int i0 = cr.asc.getLastAtomSetAtomIndex();
     double packing = cr.getPackingRangeValue(0.001d);
-    System.out.println("MSRDR " + i0 + " " + packing + " " + bs);
     for (int i = bs.nextSetBit(i0); i >= 0; i = bs.nextSetBit(i + 1)) {
       Atom a = atoms[i];
       boolean isOK = (!isCommensurate || modAverage || a.foccupancy >= 0.5d);
@@ -1101,8 +1100,6 @@ private void trimAtomSet() {
         //              minXYZ0.y, maxXYZ0.y, minXYZ0.z, maxXYZ0.z, 100))) {
         //              }
       }
-//      if (i/10 == i/10d)
-//      System.out.println("ms2 " + isOK + " " + i + " " + pt);
       if (isOK) {
 //        if (cr.fixJavaDouble)
 //          PT.fixPtDoubles(a, PT.FRACTIONAL_PRECISION);

diff --git a/src/org/jmol/adapter/smarter/XtalSymmetry.java b/src/org/jmol/adapter/smarter/XtalSymmetry.java
@@ -47,7 +47,6 @@
 import javajs.util.Lst;
 import javajs.util.M3d;
 import javajs.util.M4d;
-import javajs.util.Matrix;
 import javajs.util.P3d;
 import javajs.util.P3i;
 import javajs.util.PT;

diff --git a/src/org/jmol/shape/Sticks.java b/src/org/jmol/shape/Sticks.java
@@ -83,7 +83,9 @@ protected void setSize(int size, BS bsSelected) {
     short mad = (short) size;
     while (iter.hasNext()) {
       bsSizeSet.set(iter.nextIndex());
-      iter.next().setMad(mad);
+      Bond b = iter.next();
+      if (b != null)
+        b.setMad(mad);
     }
   }
 

diff --git a/src/org/jmol/symmetry/SpaceGroupFinder.java b/src/org/jmol/symmetry/SpaceGroupFinder.java
@@ -1243,7 +1243,6 @@ private static String[] getList(Viewer vwr, String[] list,
     if (list == null) {
       Lst<String> l = new Lst<String>();
       String line;
-      int i = 0;
       while ((line = rdr.readLine()) != null) {
 //        System.out.println(i++ + " "  + line);
         if (line.length() > 0) {