From 6d4be35f24a36e26b9cd40b4ab1fa7ff806290ff Mon Sep 17 00:00:00 2001 From: Matt Johnson Date: Fri, 15 Mar 2024 17:36:48 -0700 Subject: [PATCH] format atomtype --- rmgpy/molecule/atomtype.py | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/rmgpy/molecule/atomtype.py b/rmgpy/molecule/atomtype.py index b34290c7f01..7ee6a1fe98c 100644 --- a/rmgpy/molecule/atomtype.py +++ b/rmgpy/molecule/atomtype.py @@ -240,7 +240,7 @@ def get_features(self): ATOMTYPES = {} -ATOMTYPES['Rx'] = AtomType(label='Rx', generic=[], specific=[ +ATOMTYPES['Rx'] = AtomType(label='Rx', generic=[], specific=[ 'H', 'R', 'R!H', @@ -259,7 +259,7 @@ def get_features(self): 'I','I1s', 'F','F1s','X','Xv','Xo']) -ATOMTYPES['Rx!H'] = AtomType(label='Rx!H', generic=['Rx'], specific=[ +ATOMTYPES['Rx!H'] = AtomType(label='Rx!H', generic=['Rx'], specific=[ 'R!H', 'R!H!Val7', 'Val4','Val5','Val6','Val7', @@ -276,20 +276,20 @@ def get_features(self): 'F','F1s','X','Xv','Xo']) # Surface sites: -ATOMTYPES['X'] = AtomType(label='X', generic=['Rx', 'Rx!H'], specific=['Xv', 'Xo']) +ATOMTYPES['X'] = AtomType(label='X', generic=['Rx', 'Rx!H'], specific=['Xv', 'Xo']) # Vacant surface site: -ATOMTYPES['Xv'] = AtomType('Xv', generic=['X','Rx', 'Rx!H'], specific=[], +ATOMTYPES['Xv'] = AtomType('Xv', generic=['X','Rx', 'Rx!H'], specific=[], single=[0], all_double=[0], r_double=[], o_double=[], s_double=[], triple=[0], quadruple=[0], benzene=[0], lone_pairs=[0]) # Occupied surface site: -ATOMTYPES['Xo'] = AtomType('Xo', generic=['X','Rx', 'Rx!H'], specific=[], +ATOMTYPES['Xo'] = AtomType('Xo', generic=['X','Rx', 'Rx!H'], specific=[], single=[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18], all_double=[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18], r_double=[], o_double=[], s_double=[], triple=[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18], quadruple=[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18], benzene=[0], lone_pairs=[0]) # Non-surface atomTypes, R being the most generic: -ATOMTYPES['R'] = AtomType(label='R', generic=['Rx'], specific=[ +ATOMTYPES['R'] = AtomType(label='R', generic=['Rx'], specific=[ 'H', 'R!H', 'R!H!Val7', @@ -306,7 +306,7 @@ def get_features(self): 'I','I1s', 'F','F1s']) -ATOMTYPES['R!H'] = AtomType(label='R!H', generic=['R', 'Rx', 'Rx!H'], specific=[ +ATOMTYPES['R!H'] = AtomType(label='R!H', generic=['R', 'Rx', 'Rx!H'], specific=[ 'Val4','Val5','Val6','Val7', 'He','Ne','Ar', 'C','Ca','Cs','Csc','Cd','CO','CS','Cdd','Cdc','Ctc','Ct','Cb','Cbf','Cq','C2s','C2sc','C2d','C2dc','C2tc', @@ -320,7 +320,7 @@ def get_features(self): 'I','I1s', 'F','F1s']) -ATOMTYPES['R!H!Val7'] = AtomType(label='R!H!Val7', generic=['R', 'Rx', 'Rx!H'], specific=[ +ATOMTYPES['R!H!Val7'] = AtomType(label='R!H!Val7', generic=['R', 'Rx', 'Rx!H'], specific=[ 'Val4','Val5','Val6', 'He','Ne','Ar', 'C','Ca','Cs','Csc','Cd','CO','CS','Cdd','Cdc','Ctc','Ct','Cb','Cbf','Cq','C2s','C2sc','C2d','C2dc','C2tc',