Add Na+ atomtype

ReactionMechanismGenerator · Sep 12, 2023 · 7e76a2a · 7e76a2a
1 parent 9300f51
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diff --git a/rmgpy/molecule/atomtype.py b/rmgpy/molecule/atomtype.py
@@ -637,6 +637,10 @@ def get_features(self):
                             single=[0,1], all_double=[0], r_double=[], o_double=[], s_double=[], triple=[0], quadruple=[0], benzene=[0], lone_pairs=[3], charge=[0])
 # examples for F1s: HF, [F], FO, CH3F, F2
 
+ATOMTYPES['Na'] = AtomType('Na', generic=['R', 'R!H', 'R!H!Val7'], specific=['Na+'])
+ATOMTYPES['Na+'] = AtomType('Na+', generic=['R', 'R!H', 'R!H!Val7'], specific=[],
+                            single=[0], all_double=[0], r_double=[0], o_double=[0], s_double=[0], triple=[0], quadruple=[0], benzene=[0], lone_pairs=[0], charge=[+1])
+
 ATOMTYPES['X'].set_actions(increment_bond=['X'], decrement_bond=['X'], form_bond=['X'], break_bond=['X'], increment_radical=[], decrement_radical=[], increment_lone_pair=[], decrement_lone_pair=[])
 ATOMTYPES['Xv'].set_actions(increment_bond=[], decrement_bond=[], form_bond=['Xo'], break_bond=[], increment_radical=[], decrement_radical=[], increment_lone_pair=[], decrement_lone_pair=[])
 ATOMTYPES['Xo'].set_actions(increment_bond=['Xo'], decrement_bond=['Xo'], form_bond=[], break_bond=['Xv'], increment_radical=[], decrement_radical=[], increment_lone_pair=[], decrement_lone_pair=[])

diff --git a/rmgpy/molecule/element.py b/rmgpy/molecule/element.py
@@ -125,7 +125,7 @@ class PeriodicSystem(object):
     valences = {'H': 1, 'He': 0, 'C': 4, 'N': 3, 'O': 2, 'F': 1, 'Ne': 0,
                 'Si': 4, 'P': 3, 'S': 2, 'Cl': 1, 'Br': 1, 'Ar': 0, 'I': 1, 'X': 4}
     valence_electrons = {'H': 1, 'He': 2, 'C': 4, 'N': 5, 'O': 6, 'F': 7, 'Ne': 8,
-                         'Si': 4, 'P': 5, 'S': 6, 'Cl': 7, 'Br': 7, 'Ar': 8, 'I': 7, 'X': 4}
+                         'Si': 4, 'P': 5, 'S': 6, 'Cl': 7, 'Br': 7, 'Ar': 8, 'I': 7, 'X': 4, 'Na': 1}
     lone_pairs = {'H': 0, 'He': 1, 'C': 0, 'N': 1, 'O': 2, 'F': 3, 'Ne': 4,
                   'Si': 0, 'P': 1, 'S': 2, 'Cl': 3, 'Br': 3, 'Ar': 4, 'I': 3, 'X': 0}
     electronegativity = {'H': 2.20, 'D': 2.20, 'T': 2.20, 'C': 2.55, 'C13': 2.55, 'N': 3.04, 'O': 3.44, 'O18': 3.44,