# The classification of the acids and bases is from the following publication:
# L Xing, RC Glen, RD Clark, JChInfCS, 2003, 43, 87-879
template = {}
### (I) ACIDS
# ===========
# ===========
# (1) Aromatic Acids; Sulfonic and Sulfinic Acids
# ===============================================
# distinction of ortho/meta/para is of paramount importance
# C.ar-C.ar O.co2
# / \ /
# C.ar C.ar-C.2
# \ / \
# C.ar-C.ar O.co2
template['SimpleBenzAcid']={'C.2':['O.co2','O.co2','C.ar']}
template['SortedSimpleBenzAcid']={'C.2':['C.ar','O.co2','O.co2']}
# (2) Phenols and Thiophenols
# ===============================================
# only 6 thiophenols in Glen's data set => too exotic
#
# again, detection of ortho/meta/para substitution needed!
# (3) Aliphatic and Alicyclic Carboxylic, Sulfonic, and Sulfinic Acids
# ===============================================
#
# O.co2
# /
# -C.ar-O.3-C.3-C.2
# \
# O.co2
template['SimpleAliphaticAcid']={'C.2': ['C.3','O.co2','O.co2'],
'C.3': ['C.2','H','H','O.3'],
'O.3': ['C.3','C.ar'],
'C.ar':['C.ar','C.ar','O.3'],
'root_atoms': ['C.2','C.3','O.3','C.ar']}
template['Acid_TypesNames']={'O1':{'sybylType':'O.co2','neighbours':['C3']},
'O2':{'sybylType':'O.co2','neighbours':['C3']},
'C3':{'sybylType':'C.2','neighbours':['O1','O2','C4']},
'C4':{'sybylType':'C.3','neighbours':['C3','C5','H4A','H4B']},
'O5':{'sybylType':'O.3','neighbours':['C4','C6']},
'C6':{'sybylType':'C.ar','neighbours':['O5','C6A','C6B']},
# 'O2':'O.co2',
# 'C3':'C.3',
# 'C4':'C.3',
# 'O5':'O.3',
# 'C6':'C.ar',
}
## template['AromaticMethoxyAceticAcid']={'atoms' : ['O.co2','C.2','O.co2','C.2','O.3','C.ar'],
## 'atomnames' : ['O1','C2','O3','C4','C5','O6'],
## 'atoms_lBondedAtoms' : ['C.3','O.co2','O.co2'], # for 1st C.2
## 'connectivity': [['atomnames'[0],'atomnames'[1]],['atomnames'[1],'atomnames'[2]]],
## 'c_sybylType' : [['O.co2','C.2'],['O.co2','C.2'],['C.3','C.2'],['C.3','O.3']],
## 'id' : [1,2,3,4,5,6],
## 'hyd_def_like': 'ASP',
## 'modelpK':2.90}
# (4) Aliphatic and Alicyclic Alcohols and Thiols
# ===============================================
# only alcohols with proximal strong electron withdrawing groups
# thiols are more considerably more acidic than alcohols
# (5) Acidic Nitrogens and Carbons
# ===============================================
# When strong electron withdrawing groups
# (e.g. nitro, nitrile, carbonyl, etc.) are
# attached to nitrogen or carbon the proton on the nitrogen or
# carbon atom may become appreciably acidic. Multiple
# tautomers usually coexist for these compounds, which can
# make it difficult to determine which class it belongs to.
#
#
# Well this might be to exotic in the moment...
### (I) BASES
# ===========
# (1a) Pyridines
# six-membered ring with one nitrogen
#
# C.ar-C.ar
# / \
# C.ar N.ar
# \ /
# C.ar-C.ar
#
# (1b) other six-membered rings
# pyridazine (2Ns, directly bonded)
# pyrimdine (2N, 1C in between)
# pyrazines (2N, 2C in between)
# (2) Anilines
# (3) Imidazoles
# (4) Alkylamines
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