@@ -1577,7 +1577,7 @@ def get_extensions(self, r=None, r_bonds=None, r_un=None, basename='', atm_ind=N
15771577 """
15781578 cython .declare (atoms = list , atm = GroupAtom , atm2 = GroupAtom , bd = GroupBond , i = int , j = int ,
15791579 extents = list , RnH = list , typ = list )
1580- print ( 'im in' )
1580+
15811581 extents = []
15821582 if r_bonds is None :
15831583 r_bonds = [1 , 1.5 , 2 , 3 , 4 ]
@@ -1690,7 +1690,6 @@ def get_extensions(self, r=None, r_bonds=None, r_un=None, basename='', atm_ind=N
16901690 elif typ [0 ].label == 'R!H' :
16911691 extents .extend (self .specify_atom_extensions (i , basename , list (set (atm .reg_dim_atm [0 ]) & set (r ))))
16921692 else :
1693- print (set (typ ), set (atm .reg_dim_atm [0 ]), list (set (typ ) & set (atm .reg_dim_atm [0 ])))
16941693 extents .extend (self .specify_atom_extensions (i , basename , list (set (typ ) & set (atm .reg_dim_atm [0 ]))))
16951694 if atm .reg_dim_u == []:
16961695 if len (atm .radical_electrons ) != 1 :
@@ -1762,6 +1761,7 @@ def specify_atom_extensions(self, i, basename, r):
17621761
17631762 #generate an extension without node splitting
17641763 if len (self .atoms [i ].atomtype )> len (Rset ):
1764+ print ('generating a non-splitting extension' )
17651765 if all (r in self .atoms [i ].atomtype for r in Rset ):
17661766 #that means even if we update the atomtype of the atom to the Rset, it will still be a specification
17671767 grp = deepcopy (self )
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