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Add new atom types to RMG to avoid atomtype error during dataset generation #2378

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Add new atom types to RMG to avoid atomtype error during dataset generation #2378

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9300f51
Add Cl- atomtype
hwpang Mar 2, 2023
7e76a2a
Add Na+ atomtype
hwpang Mar 2, 2023
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9 changes: 8 additions & 1 deletion rmgpy/molecule/atomtype.py
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Original file line number Diff line number Diff line change
Expand Up @@ -615,9 +615,12 @@ def get_features(self):
single=[0,1,2,3,4], all_double=[0, 1, 2], r_double=[], o_double=[], s_double=[], triple=[1, 2], quadruple=[], benzene=[0], lone_pairs=[0], charge=[-1, +1])
# *Composite atomtype; examples for S6tdc: [SH2+]#[C-], [N-]=[S+]#N

ATOMTYPES['Cl'] = AtomType('Cl', generic=['R', 'R!H', 'Val7'], specific=['Cl1s'])
ATOMTYPES['Cl'] = AtomType('Cl', generic=['R', 'R!H', 'Val7'], specific=['Cl1s','Cl-'])
ATOMTYPES['Cl1s'] = AtomType('Cl1s', generic=['R', 'R!H', 'Cl', 'Val7'], specific=[],
single=[0,1], all_double=[0], r_double=[], o_double=[], s_double=[], triple=[0], quadruple=[0], benzene=[0], lone_pairs=[3], charge=[0])
ATOMTYPES['Cl-'] = AtomType('Cl-', generic=['R', 'R!H', 'Cl', 'Val7'], specific=[],
single=[0], all_double=[0], r_double=[], o_double=[], s_double=[], triple=[0], quadruple=[0], benzene=[0], lone_pairs=[4], charge=[-1])

# examples for Cl1s: HCl, [Cl]
ATOMTYPES['Br'] = AtomType('Br', generic=['R', 'R!H', 'Val7'], specific=['Br1s'])
ATOMTYPES['Br1s'] = AtomType('Br1s', generic=['R', 'R!H', 'Br', 'Val7'], specific=[],
Expand All @@ -634,6 +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=[])
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2 changes: 1 addition & 1 deletion rmgpy/molecule/element.py
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Expand Up @@ -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,
Expand Down