[Jmol-commits] SF.net SVN: jmol:[13054] trunk/Jmol/src/org/jmol/smiles

[<ha...@us...>]

Revision: 13054
          http://jmol.svn.sourceforge.net/jmol/?rev=13054&view=rev
Author:   hansonr
Date:     2010-05-10 20:06:00 +0000 (Mon, 10 May 2010)

Log Message:
-----------
3D SEARCH defaults for h, D, X, x, v, R, r

Modified Paths:
--------------
    trunk/Jmol/src/org/jmol/smiles/SmilesParser.java
    trunk/Jmol/src/org/jmol/smiles/SmilesSearch.java

Modified: trunk/Jmol/src/org/jmol/smiles/SmilesParser.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesParser.java	2010-05-10 19:37:11 UTC (rev 13053)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesParser.java	2010-05-10 20:06:00 UTC (rev 13054)
@@ -624,7 +624,7 @@
         }
       }
       if (hydrogenCount == Integer.MIN_VALUE && isBracketed)
-        hydrogenCount = Integer.MAX_VALUE;
+        hydrogenCount = Integer.MIN_VALUE + 1;
       newAtom.setExplicitHydrogenCount(hydrogenCount);
       // for stereochemistry only:
       molecule.atoms[newAtom.index].setExplicitHydrogenCount(hydrogenCount);
@@ -784,7 +784,7 @@
       SmilesAtom sAtom = molecule.getAtom(i);
       int stereoClass = sAtom.getChiralClass();
       int nBonds = sAtom.explicitHydrogenCount;
-      if (nBonds < 0 || nBonds == Integer.MAX_VALUE)
+      if (nBonds < 0)
         nBonds = 0;
       nBonds += sAtom.getBondsCount();
       switch (stereoClass) {

Modified: trunk/Jmol/src/org/jmol/smiles/SmilesSearch.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesSearch.java	2010-05-10 19:37:11 UTC (rev 13053)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesSearch.java	2010-05-10 20:06:00 UTC (rev 13054)
@@ -340,11 +340,8 @@
         bs.set(i);
         if (firstAtomOnly)
           break;
-        if (!isSearch) {
-          int npH = atoms[j].explicitHydrogenCount;
-          if (npH != Integer.MIN_VALUE && npH != Integer.MAX_VALUE)
-            getHydrogens(getJmolAtom(i), bs);
-        }
+        if (!isSearch && atoms[j].explicitHydrogenCount > 0)
+          getHydrogens(getJmolAtom(i), bs);
       }
       if (bsRequired != null && !bsRequired.intersects(bs))
         return true;
@@ -426,13 +423,12 @@
 
       // H explicit H count
       n = patternAtom.explicitHydrogenCount;
-      if (n != Integer.MIN_VALUE && n != Integer.MAX_VALUE
-          && n != atom.getCovalentHydrogenCount())
+      if (n >= 0 && n != atom.getCovalentHydrogenCount())
         break;
 
       // h implicit H count
       n = patternAtom.implicitHydrogenCount;
-      if (n != Integer.MIN_VALUE && n != Integer.MAX_VALUE) {
+      if (n != Integer.MIN_VALUE) {
         int nH = atom.getImplicitHydrogenCount();
         if (n == -1 && nH == 0 || n != -1 && n != nH)
           break;
@@ -500,7 +496,7 @@
       for (int k = 0; k < patternAtomCount; k++) {
         SmilesAtom sAtom = atoms[k];
         int nH = sAtom.explicitHydrogenCount;
-        if (nH == Integer.MAX_VALUE)
+        if (nH < 0)
           nH = 0;
         int chiralClass = sAtom.getChiralClass();
         int order = sAtom.getChiralOrder();


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