[Jmol-commits] CVS: Jmol/src/org/jmol/adapter/smarter Atom.java,1.6,1.7 PdbReader.java,1.7,1.8 SmarterModelAdapter.java,1.8,1.9

[Michael T H. <mic...@us...>]

Update of /cvsroot/jmol/Jmol/src/org/jmol/adapter/smarter
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv14805/src/org/jmol/adapter/smarter

Modified Files:
	Atom.java PdbReader.java SmarterModelAdapter.java 
Log Message:
moved isHetero and atomSerial out of PdbAtom and into Atom


Index: Atom.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/jmol/adapter/smarter/Atom.java,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- Atom.java	24 Mar 2004 21:52:34 -0000	1.6
+++ Atom.java	25 Mar 2004 09:16:34 -0000	1.7
@@ -35,6 +35,8 @@
   float vectorX = Float.NaN, vectorY = Float.NaN, vectorZ = Float.NaN;
   float bfactor = Float.NaN;
   int occupancy = 100;
+  boolean isHetero;
+  int atomSerial = Integer.MIN_VALUE;
   String pdbAtomRecord;
 
   Atom() {

Index: PdbReader.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/jmol/adapter/smarter/PdbReader.java,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- PdbReader.java	24 Mar 2004 21:52:34 -0000	1.7
+++ PdbReader.java	25 Mar 2004 09:16:34 -0000	1.8
@@ -112,6 +112,7 @@
   }
 
   void atom() {
+    boolean isHetero = line.startsWith("HETATM");
     try {
       // for now, we are only taking alternate location 'A'
       char charAlternateLocation = line.charAt(16);
@@ -199,6 +200,8 @@
       atom.occupancy = occupancy;
       atom.bfactor = bfactor;
       atom.x = x; atom.y = y; atom.z = z;
+      atom.isHetero = isHetero;
+      atom.atomSerial = serial;
       atom.pdbAtomRecord = line;
 
       // note that values are +1 in this serial map

Index: SmarterModelAdapter.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/jmol/adapter/smarter/SmarterModelAdapter.java,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- SmarterModelAdapter.java	24 Mar 2004 21:02:34 -0000	1.8
+++ SmarterModelAdapter.java	25 Mar 2004 09:16:34 -0000	1.9
@@ -164,6 +164,8 @@
     public float getVectorZ() { return atom.vectorZ; }
     public float getBfactor() { return atom.bfactor; }
     public int getOccupancy() { return atom.occupancy; }
+    public boolean getIsHetero() { return atom.isHetero; }
+    public int getAtomSerial() { return atom.atomSerial; }
     public String getPdbAtomRecord() { return atom.pdbAtomRecord; }
   }