[Jmol-commits] CVS: Jmol/src/org/openscience/jmol ProteinProp.java,1.5,1.6

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

Update of /cvsroot/jmol/Jmol/src/org/openscience/jmol
In directory sc8-pr-cvs1:/tmp/cvs-serv21842

Modified Files:
	ProteinProp.java 
Log Message:
most predefined sets now functioning


Index: ProteinProp.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/ProteinProp.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -r1.5 -r1.6
*** ProteinProp.java	22 Jan 2003 15:02:57 -0000	1.5
--- ProteinProp.java	25 Jan 2003 17:28:52 -0000	1.6
***************
*** 33,36 ****
--- 33,37 ----
    public String recordPdb;
    byte resid;
+   byte atomID;
  
    public ProteinProp(String recordPdb) {
***************
*** 39,42 ****
--- 40,45 ----
      Integer resInt = (Integer)htResidue.get(recordPdb.substring(17, 20));
      resid = (resInt != null) ? (byte)resInt.intValue() : -1;
+     Integer atomInt = (Integer)htAtom.get(getName());
+     atomID = (atomInt != null) ? (byte)atomInt.intValue() : -1;
    }
  
***************
*** 61,64 ****
--- 64,77 ----
    }
  
+   public byte getAtomID() {
+     return atomID;
+   }
+ 
+   public String getAtomName() {
+     if (atomID > -1)
+       return atomNames[atomID];
+     return getName();
+   }
+ 
    public boolean isResidueNameMatch(String strWildcard) {
      if (strWildcard.length() != 3) {
***************
*** 101,108 ****
    }
  
-   public boolean isAmino() {
-     return resid != -1 && resid < 23;
-   }
- 
    static String[] residues = {
      // tabel taken from rasmol source molecule.h
--- 114,117 ----
***************
*** 144,147 ****
--- 153,201 ----
      for (int i = 0; i < residues.length; ++i) {
        htResidue.put(residues[i], new Integer(i));
+     }
+   }
+ 
+   public final static int ATOM_BACKBONE_MIN =  0;
+   public final static int ATOM_BACKBONE_MAX =  3;
+   public final static int ATOM_SHAPELY_MAX  =  7;
+   public final static int ATOM_NUCLEIC_BACKBONE_MIN =  7;
+   public final static int ATOM_NICLEIC_BACKBONE_MAX = 18;
+ 
+   static String[] atomNames = {
+     "N",   // 0
+     "CA",
+     "C",
+     "O",   // 3
+     "C'",  // 4
+     "OT",
+     "S",
+     "P",   // 7
+     "O1P",
+     "O2P",
+     "O5*",
+     "C5*",
+     "C4*",
+     "O4*",
+     "C3*",
+     "O3*",
+     "C2*",
+     "O2*",
+     "C1*",
+     "CA2",
+     "SG",
+     "N1",
+     "N2",
+     "N3",
+     "N4",
+     "N6",
+     "O2",
+     "O4",
+     "O6"
+   };
+   
+   private static Hashtable htAtom = new Hashtable();
+   static {
+     for (int i = 0; i < atomNames.length; ++i) {
+       htAtom.put(atomNames[i], new Integer(i));
      }
    }