[Cdk-commits] CVS: cdk/src/org/openscience/cdk/tools MFAnalyser.java,1.5,1.6 SaturationChecker.java,1.5,1.6

[Egon W. <eg...@us...>]

Update of /cvsroot/cdk/cdk/src/org/openscience/cdk/tools
In directory usw-pr-cvs1:/tmp/cvs-serv24268/src/org/openscience/cdk/tools

Modified Files:
	MFAnalyser.java SaturationChecker.java 
Log Message:
Fixed typo in JCPController, 
added two methods, and work on Debian package.


Index: MFAnalyser.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/tools/MFAnalyser.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -r1.5 -r1.6
*** MFAnalyser.java	13 Sep 2002 16:40:12 -0000	1.5
--- MFAnalyser.java	21 Sep 2002 09:18:35 -0000	1.6
***************
*** 103,107 ****
  
  		
! 	/** Returns a set of nodes excluding all the hydrogens*/
  	public AtomContainer getHeavyAtoms()
  	{
--- 103,111 ----
  
  		
! 	/** 
!      * Returns a set of nodes excluding all the hydrogens
!      *
!      * @keyword hydrogen, removal
!      */
  	public AtomContainer getHeavyAtoms()
  	{
***************
*** 259,262 ****
--- 263,274 ----
          return results;
      }
+ 
+     /**
+      * Returns the number of distinct elements in the formula.
+      */
+     public int getElementCount() {
+         return getElements().size();
+     }
+ 
  }
  

Index: SaturationChecker.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/tools/SaturationChecker.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -r1.5 -r1.6
*** SaturationChecker.java	20 Sep 2002 09:40:45 -0000	1.5
--- SaturationChecker.java	21 Sep 2002 09:18:35 -0000	1.6
***************
*** 1,6 ****
! /*
!  *  SaturationChecker.java
   *
-  *  $RCSfile$    $Author$    $Date$  *
   *  Copyright (C) 1997-2002  The Chemistry Development Kit (CDK) project
   *
--- 1,7 ----
! /*  $RCSfile$    
!  *  $Author$    
!  *  $Date$
!  *  $Revision$
   *
   *  Copyright (C) 1997-2002  The Chemistry Development Kit (CDK) project
   *
***************
*** 231,233 ****
--- 232,264 ----
  	}
  
+     /**
+      * Method that saturates a molecule by adding hydrogens.
+      *
+      * @param molecule Molecule to saturate
+      * @keyword hydrogen, adding
+      */
+     public void saturateWithHydrogen(Molecule molecule) {
+         Atom partner = null;
+         Atom atom = null;
+         Atom[] partners = null;
+         AtomType[] atomTypes = null;
+         Bond bond = null;
+         for (int f = 0; f < molecule.getAtomCount(); f ++) {
+             atom = molecule.getAtomAt(f);
+             // set number of implicit hydrogens to zero
+             atom.setHydrogenCount(0);
+             // get default atom
+             atomTypes = atf.getAtomTypes(atom.getSymbol(), atf.ATOMTYPE_ID_STRUCTGEN);
+             AtomType defaultAtom = atomTypes[0];
+             // add explicit hydrogens
+             int missingHydrogen = (int)(defaultAtom.getMaxBondOrder() -
+                                         molecule.getBondOrderSum(atom));
+             for (int i = 1; i <= missingHydrogen; i++ ) {
+                 Atom hydrogen = new Atom("H");
+                 molecule.addAtom(hydrogen);
+                 Bond newBond = new Bond(atom, hydrogen, 1.0);
+                 molecule.addBond(newBond);
+             }
+         }
+     }
  }