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tautomers enumeration idea totally changed.
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@stsouko
stsouko committed Dec 10, 2020
1 parent 0d5f89b commit 10b81ac
Showing 1 changed file with 65 additions and 101 deletions.
166 changes: 65 additions & 101 deletions CGRtools/algorithms/tautomers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -279,37 +279,84 @@ def _enumerate_keto_enol_tautomers(self):
yield mol, ket and a

@class_cached_property
def __enol_rules(self):
rules = []
def __keto_enol_rules(self):
rules = [] # query, is ketone, bond fix

# C=C-[O,S,N]H
# first atom is acceptor of proton
# second is donor
# [C;X4,H]-[CH]=[O,S,N]
q = query.QueryContainer()
q.add_atom(ListElement(['O', 'S', 'N']), hydrogens=(1, 2))
q.add_atom(ListElement(['O', 'S', 'N']), neighbors=1) # acceptor
q.add_atom('C', hybridization=1, hydrogens=(1, 2, 3)) # donor
q.add_atom('C', neighbors=2)
q.add_atom('C', hybridization=2)
q.add_bond(1, 2, 1)
q.add_bond(2, 3, 2)
rules.append(q)
q.add_bond(1, 3, 2)
q.add_bond(2, 3, 1)
rules.append((q, True, (1, 3, 1), (2, 3, 2)))

# C=C(C)-[O,S,N]H
# [C;X4,H]-[CH]=N[C;a,X4]
q = query.QueryContainer()
q.add_atom(ListElement(['O', 'S', 'N']), hydrogens=(1, 2))
q.add_atom('N') # acceptor
q.add_atom('C', hybridization=1, hydrogens=(1, 2, 3)) # donor
q.add_atom('C', neighbors=2)
q.add_atom('C', hybridization=(1, 4))
q.add_bond(1, 3, 2)
q.add_bond(2, 3, 1)
q.add_bond(1, 4, 1)
rules.append((q, True, (1, 3, 1), (2, 3, 2)))

# [C;X4,H]-C(C)=[O,S,N;H]
q = query.QueryContainer()
q.add_atom(ListElement(['O', 'S', 'N']), neighbors=1) # acceptor
q.add_atom('C', hybridization=1, hydrogens=(1, 2, 3)) # donor
q.add_atom('C')
q.add_atom('C', hybridization=2)
q.add_atom('C')
q.add_bond(1, 2, 1)
q.add_bond(2, 3, 2)
q.add_bond(2, 4, 1)
rules.append(q)
q.add_bond(1, 3, 2)
q.add_bond(2, 3, 1)
q.add_bond(3, 4, 1)
rules.append((q, True, (1, 3, 1), (2, 3, 2)))

# [C;X4,H]-C(C)=N[C;a,X4]
q = query.QueryContainer()
q.add_atom('N') # acceptor
q.add_atom('C', hybridization=1, hydrogens=(1, 2, 3)) # donor
q.add_atom('C')
q.add_atom('C')
q.add_atom('C', hybridization=(1, 4))
q.add_bond(1, 3, 2)
q.add_bond(2, 3, 1)
q.add_bond(3, 4, 1)
q.add_bond(1, 5, 1)
rules.append((q, True, (1, 3, 1), (2, 3, 2)))

# C=[CH]-[O,S,N;H]
q = query.QueryContainer()
q.add_atom('C') # acceptor
q.add_atom(ListElement(['O', 'S', 'N']), hydrogens=(1, 2)) # donor
q.add_atom('C', neighbors=2)
q.add_bond(1, 3, 2)
q.add_bond(2, 3, 1)
rules.append((q, False, (1, 3, 1), (2, 3, 2)))

# C=C(C)-[O,S,N;H]
q = query.QueryContainer()
q.add_atom('C') # acceptor
q.add_atom(ListElement(['O', 'S', 'N']), hydrogens=(1, 2)) # donor
q.add_atom('C')
q.add_atom('C')
q.add_bond(1, 3, 2)
q.add_bond(2, 3, 1)
q.add_bond(4, 3, 1)
rules.append((q, False, (1, 3, 1), (2, 3, 2)))

# azo-Ar
# C=N-[NH]-R >> C-N=N-R
q = query.QueryContainer()
q.add_atom('N', hydrogens=(1, 2))
q.add_atom('N')
q.add_atom('C', hybridization=2)
q.add_bond(1, 2, 1)
q.add_bond(2, 3, 2)
rules.append(q)
# rules.append(q)

# C=C([O,S,N]H)-[O,S,N]
q = query.QueryContainer()
Expand All @@ -320,57 +367,7 @@ def __enol_rules(self):
q.add_bond(1, 2, 1)
q.add_bond(2, 3, 1)
q.add_bond(2, 4, 2)
rules.append(q)

return rules

@class_cached_property
def __ketone_rules(self):
rules = []

# C-C=[O,S,NH]
q = query.QueryContainer()
q.add_atom('C', neighbors=2)
q.add_atom(ListElement(['O', 'S', 'N']), neighbors=1)
q.add_atom('C')
q.add_bond(1, 2, 2)
q.add_bond(1, 3, 1)
rules.append(q)

# C-C=N-C
q = query.QueryContainer()
q.add_atom('C', neighbors=2)
q.add_atom('N')
q.add_atom('C')
q.add_atom('C')
q.add_bond(1, 2, 2)
q.add_bond(1, 3, 1)
q.add_bond(2, 4, 1)
rules.append(q)

# C-C(C)=[O,S,NH]
q = query.QueryContainer()
q.add_atom('C')
q.add_atom(ListElement(['O', 'S', 'N']), neighbors=1)
q.add_atom('C')
q.add_atom('C')
q.add_bond(1, 2, 2)
q.add_bond(1, 3, 1)
q.add_bond(1, 4, 1)
rules.append(q)

# C-C(C)=N-C
q = query.QueryContainer()
q.add_atom('C')
q.add_atom('N')
q.add_atom('C')
q.add_atom('C')
q.add_atom('C')
q.add_bond(1, 2, 2)
q.add_bond(1, 3, 1)
q.add_bond(1, 4, 1)
q.add_bond(2, 5, 1)
rules.append(q)
# rules.append(q)

# [NH:R6]-[C:R6](=[O,S,NH])[C:R6]. alpha-pyridone
q = query.QueryContainer()
Expand All @@ -381,40 +378,7 @@ def __ketone_rules(self):
q.add_bond(1, 2, 2)
q.add_bond(1, 3, 1)
q.add_bond(1, 4, 1)
rules.append(q)

# C-N=N-R
q = query.QueryContainer()
q.add_atom('N')
q.add_atom('N')
q.add_atom('C', hybridization=(1, 2))
q.add_bond(1, 2, 2)
q.add_bond(1, 3, 1)
rules.append(q)

return rules

@class_cached_property
def __keto_enol_rules(self):
rules = [] # query, is ketone, bond fix

# first atom is acceptor of proton
# second is donor
q = query.QueryContainer()
q.add_atom(ListElement(['O', 'S', 'N']), neighbors=1) # acceptor
q.add_atom('C', hybridization=1, hydrogens=(1, 2, 3)) # donor
q.add_atom('C', neighbors=2)
q.add_bond(1, 3, 2)
q.add_bond(2, 3, 1)
rules.append((q, True, (1, 3, 1), (2, 3, 2)))

q = query.QueryContainer()
q.add_atom('C') # acceptor
q.add_atom(ListElement(['O', 'S', 'N']), hydrogens=(1, 2)) # donor
q.add_atom('C', neighbors=2)
q.add_bond(1, 3, 2)
q.add_bond(2, 3, 1)
rules.append((q, False, (1, 3, 1), (2, 3, 2)))
# rules.append(q)

return rules

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