Index: model.cpp
===================================================================
RCS file: /cvsroot/libghemical/src/model.cpp,v
retrieving revision 1.70
diff -c -5 -p -b -d -w -r1.70 model.cpp
*** model.cpp	23 Mar 2006 11:42:05 -0000	1.70
--- model.cpp	27 Mar 2006 18:23:26 -0000
*************** void model::AddHydrogens(void)
*** 1725,1736 ****
--- 1725,1753 ----
  	else
  	{
  		PrintToLog("Using default rules in AddHydrogens().\n");
  	}
  	
+ 	// first check to see if the user selected anything
+ 	// if so, only add hydrogens to the selected atoms
+ 	iter_al it1 = atom_list.begin();
+ 	bool atoms_selected = false; // is anything selected by the user?
+ 	while (it1 != atom_list.end())
+ 	  if ((* it1++).flags & ATOMFLAG_USER_SELECTED)
+ 	    {
+ 	      atoms_selected = true;
+ 	      break;
+ 	    }
+ 
+ 
  	for (iter_al it1 = atom_list.begin();it1 != atom_list.end();it1++)
  	{
+ 
+ 	  // if the user selected atoms, only do this if the atom is selected
+ 	  if (atoms_selected && (! (* it1).flags & ATOMFLAG_USER_SELECTED) )
+ 	    continue;
+ 
  		bool skip = true;
  		
  		fGL valence = NOT_DEFINED;
  		int an = (* it1).el.GetAtomicNumber();
  		switch (an)