@@ -1571,7 +1571,7 @@ def get_extensions(self, r=None, r_bonds=None, r_un=None, basename='', atm_ind=N
15711571 """
15721572 cython .declare (atoms = list , atm = GroupAtom , atm2 = GroupAtom , bd = GroupBond , i = int , j = int ,
15731573 extents = list , RnH = list , typ = list )
1574- print ( 'im in' )
1574+
15751575 extents = []
15761576 if r_bonds is None :
15771577 r_bonds = [1 , 1.5 , 2 , 3 , 4 ]
@@ -1684,7 +1684,6 @@ def get_extensions(self, r=None, r_bonds=None, r_un=None, basename='', atm_ind=N
16841684 elif typ [0 ].label == 'R!H' :
16851685 extents .extend (self .specify_atom_extensions (i , basename , list (set (atm .reg_dim_atm [0 ]) & set (r ))))
16861686 else :
1687- print (set (typ ), set (atm .reg_dim_atm [0 ]), list (set (typ ) & set (atm .reg_dim_atm [0 ])))
16881687 extents .extend (self .specify_atom_extensions (i , basename , list (set (typ ) & set (atm .reg_dim_atm [0 ]))))
16891688 if atm .reg_dim_u == []:
16901689 if len (atm .radical_electrons ) != 1 :
@@ -1756,6 +1755,7 @@ def specify_atom_extensions(self, i, basename, r):
17561755
17571756 #generate an extension without node splitting
17581757 if len (self .atoms [i ].atomtype )> len (Rset ):
1758+ print ('generating a non-splitting extension' )
17591759 if all (r in self .atoms [i ].atomtype for r in Rset ):
17601760 #that means even if we update the atomtype of the atom to the Rset, it will still be a specification
17611761 grp = deepcopy (self )
0 commit comments