chython 2.19__cp313-cp313-win_amd64.whl

chython/algorithms/standardize/_groups.py

@@ -0,0 +1,958 @@
+# -*- coding: utf-8 -*-
+#
+#  Copyright 2021-2026 Ramil Nugmanov <nougmanoff@protonmail.com>
+#  This file is part of chython.
+#
+#  chython is free software; you can redistribute it and/or modify
+#  it under the terms of the GNU Lesser General Public License as published by
+#  the Free Software Foundation; either version 3 of the License, or
+#  (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+#  GNU Lesser General Public License for more details.
+#
+#  You should have received a copy of the GNU Lesser General Public License
+#  along with this program; if not, see <https://www.gnu.org/licenses/>.
+#
+from lazy_object_proxy import Proxy
+
+
+def _rules():
+    """
+    rules without overlapping. these rules can match once to same set of atoms.
+    """
+    from ... import smarts
+    from ...containers import QueryContainer
+
+    rules = []
+
+    #
+    #     A         A
+    #     |         |
+    #     P    >>  [P+]
+    #   / | \     / | \
+    #  A  A  A   A  A  A
+    #
+    q = smarts('[P;D4;x0;z1]')
+    atom_fix = {1: (1, None)}
+    bonds_fix = ()
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    # A   H   A     A     H   A
+    #  \ / \ /       \  .. \ /
+    #   B   B    >>   B     B
+    #  / \ / \       / \  .. \
+    # A   H   A     A   H     A
+    #
+    q = smarts('[B;z1:1]1[H;D2:3][B;z1:2][H;D2:4]1')
+    atom_fix = {}
+    bonds_fix = ((1, 3, 8), (2, 4, 8))
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    # OGB DS
+    #
+    # O*  A  [O-]  A
+    #  \ /     \  /
+    #   N  >>  [N+]
+    #   |       ||
+    #  C,N*     C,N
+    #
+    q = smarts('[O;D1;z1][N;D3;z1][C,N;z1] |^1:0,2|')
+    atom_fix = {1: (-1, False), 2: (1, None), 3: (0, False)}
+    bonds_fix = ((2, 3, 2),)
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    #       |            |
+    # O* -- S -- O* >> O=S=O
+    #       |            |
+    #
+    q = smarts('[O,S;D1;z1][S;D4;z1][O;D1;z1] |^1:0,2|')
+    atom_fix = {1: (0, False), 3: (0, False)}
+    bonds_fix = ((1, 2, 2), (2, 3, 2))
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    #      A         A
+    #     //        //
+    # B - N >> B .. N
+    #     \          \
+    #      A          A
+    #
+    q = smarts('[B]-[N;D3;z2]')
+    atom_fix = {}
+    bonds_fix = ((1, 2, 8),)
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    #     A             A
+    #     |             |
+    # B = N - A >> B .. N - A
+    #     |             |
+    #     A             A
+    #
+    q = smarts('[B;z1,z2]-,=[N;D4;z1,z2]')
+    atom_fix = {}
+    bonds_fix = ((1, 2, 8),)
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    # R2S - B >> R2S .. B
+    #
+    q = smarts('[B;z1]-[O,S;D3;z1]')
+    atom_fix = {}
+    bonds_fix = ((1, 2, 8),)
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    #  [B-] = [N+] >>  B - N
+    #
+    q = smarts('[B;z2;-]=[N;D1,D2,D3;z2;+]')
+    atom_fix = {1: (1, None), 2: (-1, None)}
+    bonds_fix = ((1, 2, 1),)
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    #        [A-]                 A
+    #         |                   |
+    # [A-] - [B+3] - [A-] >> A - [B-] - A
+    #         |                   |
+    #        [A-]                 A
+    #
+    q = smarts('[B;D4;z1;+3]([A;-])([A;-])([A;-])[A;-]')
+    atom_fix = {1: (-4, None), 2: (1, None), 3: (1, None), 4: (1, None), 5: (1, None)}
+    bonds_fix = ()
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    #        A             A
+    #        |             |
+    # [A-] - B - A >> A - [B-] - A
+    #        |             |
+    #        A             A
+    #
+    q = smarts('[B;D4;z1]-[A;-]')
+    atom_fix = {1: (-1, None), 2: (1, None)}
+    bonds_fix = ()
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    #      A             A
+    #      |             |
+    # A -  B - A >> A - [B-] - A
+    #      |             |
+    #      A             A
+    #
+    q = smarts('[B;D4;z1]')
+    atom_fix = {1: (-1, None)}
+    bonds_fix = ()
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    #     A         A
+    #     |         |
+    #     N    >>  [N+]
+    #   / | \     / | \
+    #  A  A  A   A  A  A
+    #
+    q = smarts('[N;D4;z1]')
+    atom_fix = {1: (1, None)}
+    bonds_fix = ()
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #  aci-nitro
+    #      O          O
+    #     //         //
+    # C = N  >> C - [N+]
+    #      \         \
+    #       OH       [O-]
+    #
+    q = smarts('[N;D3;z3;x2](=[O;D1])([O;D1])=C')
+    atom_fix = {1: (1, None), 3: (-1, None)}
+    bonds_fix = ((1, 4, 1),)
+    rules.append((q, atom_fix, bonds_fix, True))
+
+    #
+    #            O               [O-]
+    #           //               /
+    # [C,N,O] = N  >> [C,N,O] = [N+]
+    #           \                \
+    #            A                A
+    #
+    q = smarts('[N;D3;z3](=[O;D1])(=[C,N,O])-[A]')
+    atom_fix = {1: (1, None), 2: (-1, None)}
+    bonds_fix = ((1, 2, 1),)
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    # fix aci-nitro
+    #       [O-]          [O-]
+    #       /             /
+    # C = [N+ ] >>  C - [N+]
+    #      \             \\
+    #       OH            O
+    #
+    q = smarts('[N;D3;z2;x2;+]([O;D1;-])([O;D1])=C')
+    atom_fix = {}
+    bonds_fix = ((1, 3, 2), (1, 4, 1))
+    rules.append((q, atom_fix, bonds_fix, True))
+
+    # fix CN(=O)=N(=O)C
+    #
+    # [N+] = N = O >> [N+] = [N+] - O-
+    #        |                |
+    #        A                A
+    #
+    q = smarts('[N;D3;z3](=[N;D3;z2;+])(=[O;D1])[A]')
+    atom_fix = {1: (1, None), 3: (-1, None)}
+    bonds_fix = ((1, 3, 1),)
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    # Fix CN(=O)=N(=N)C
+    # [N+] = N = N - ? >> [N+] = [N+] - [N-] - ?
+    #        |                    |
+    #        A                    A
+    #
+    q = smarts('[N;D3;z3](=[N;D3;z2;+])(=[N;D1,D2;z2])[A]')
+    atom_fix = {1: (1, None), 3: (-1, None)}
+    bonds_fix = ((1, 3, 1),)
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    # For N-case is not unique!
+    #          N             [N-]
+    #         //             /
+    # [C,N] = N  >> [C,N] = [N+]
+    #         \              \
+    #          A              A
+    #
+    q = smarts('[N;D3;z3](=[N;D1,D2;z2])(=[C,N])[A]')
+    atom_fix = {1: (1, None), 2: (-1, None)}
+    bonds_fix = ((1, 2, 1),)
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    # [N-] - [N+] = O >> N = [N+] - [O-]
+    #         |               |
+    #         A               A
+    #
+    q = smarts('[N;D3;z2;+](=[O;D1])[N;D1,D2;z1;-]')
+    atom_fix = {2: (-1, None), 3: (1, None)}
+    bonds_fix = ((1, 2, 1), (1, 3, 2))
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    #         O              [O-]
+    #        //              /
+    # [A-] - N   >> [A-] - [N+]
+    #        \\             \\
+    #         O              O
+    #
+    q = smarts('[N;D3;z3](=[O;D1])(=[O;D1])[A;-]')
+    atom_fix = {1: (1, None), 2: (-1, None)}
+    bonds_fix = ((1, 2, 1),)
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    # O : N : O      O = [N+] - [O-]
+    #     |      >>       |
+    #     A               A
+    #
+    q = smarts('[N;D3;a](:[O;D1])(:[O;D1])[A]')
+    atom_fix = {1: (1, None), 2: (-1, None)}
+    bonds_fix = ((1, 2, 1), (1, 3, 2))
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    # Nitrite
+    #
+    #   O        [O-]
+    #  //        /
+    # [N-]  >>  N
+    #  \\       \\
+    #   O        O
+    #
+    q = smarts('[N;D2;z3;x2;-](=[O;D1])=[O;D1]')
+    atom_fix = {1: (1, None), 2: (-1, None)}
+    bonds_fix = ((1, 2, 1),)
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    # [O,C,N] = N # N >> [O,C,N] = [N+] = [N-]
+    #
+    q = smarts('[N;D2;z3](#[N;D1])=[C,N,O]')
+    atom_fix = {1: (1, None), 2: (-1, None)}
+    bonds_fix = ((1, 2, 2),)
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    # [C,N,O-] - [N+] # N  >> [C,N,O] = [N+] = [N-]
+    #
+    q = smarts('[N;D2;z3;+](#[N;D1])[C,N,O;z1;-]')
+    atom_fix = {2: (-1, None), 3: (1, None)}
+    bonds_fix = ((1, 2, 2), (1, 3, 2))
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    #  A - [N+] # N = [N-]  >> A - N = [N+] = [N-]
+    #
+    q = smarts('[N;D2;z3;x2](#[N;D2;+][A])=[N;D1;-]')
+    atom_fix = {1: (1, None), 2: (-1, None)}
+    bonds_fix = ((1, 2, 2),)
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    # A - N = N = N >> A - N = [N+] = [N-]
+    #
+    q = smarts('[N;D2;z3;x2](=[N;D2;z2])=[N;D1]')
+    atom_fix = {1: (1, None), 3: (-1, None)}
+    bonds_fix = ()
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    # A - NH - N # N >> A - N = [N+] = [N-]
+    #
+    q = smarts('[N;D2;z3;x2]([N;D2;z1])#[N;D1]')
+    atom_fix = {1: (1, None), 3: (-1, None)}
+    bonds_fix = ((1, 2, 2), (1, 3, 2))
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    # [N-] # N = N - A >> [N-] == [N+] == N - A
+    #
+    q = smarts('[N;D2;z3;x2](=[N;D2;z2])#[N;D1;-]')
+    atom_fix = {1: (1, None)}
+    bonds_fix = ((1, 3, 2),)
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    # [N-] == N # N >> [N-] == [N+] == [N-]
+    #
+    q = smarts('[N;D2;z3;x2](=[N;D1;-])#[N;D1]')
+    atom_fix = {1: (1, None), 3: (-1, None)}
+    bonds_fix = ((1, 3, 2),)
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    # A - C # N = NH >> A - [CH] = [N+] = [N-]
+    #
+    q = smarts('[N;D2;z3;x1](=[N;D1])#[C;D1,D2]')
+    atom_fix = {1: (1, None), 2: (-1, None)}
+    bonds_fix = ((1, 3, 2),)
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    # note: order dependent
+    # A - C # N = [O,N] >> A - C # [N+] - [O,N-]
+    #
+    q = smarts('[N;D2;z3;x1](=[N,O;z2])#[C;D1,D2]')
+    atom_fix = {1: (1, None), 2: (-1, None)}
+    bonds_fix = ((1, 2, 1),)
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    # [NH2,OH,SH] - N # C - A >> [NH,O,S-] - [N+] # C - A
+    #
+    q = smarts('[N;D2;z3;x1]([N,O,S;D1])#[C;D1,D2]')
+    atom_fix = {1: (1, None), 2: (-1, None)}
+    bonds_fix = ()
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    # A - [NH] - N # C >> A - [N-] - [N+] # C
+    #
+    q = smarts('[N;D2;z3;x1]([N;D2;z1])#[C;D1,D2]')
+    atom_fix = {1: (1, None), 2: (-1, None)}
+    bonds_fix = ()
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    # [NH2,OH,SH] - [N+] # [C-] >> [NH,O,S-] - [N+] # [CH]
+    #
+    q = smarts('[N;D2;z3;x1;+]([N,O,S;D1])#[C;D1;-]')
+    atom_fix = {2: (-1, None), 3: (1, None)}
+    bonds_fix = ()
+    rules.append((q, atom_fix, bonds_fix, True))
+
+    #
+    # A - [NH] - [N+] # [C-] >> A - [N-] - [N+] # [CH]
+    #
+    q = smarts('[N;D2;z3;x1;+]([N;D2;z1])#[C;D1;-]')
+    atom_fix = {2: (-1, None), 3: (1, None)}
+    bonds_fix = ()
+    rules.append((q, atom_fix, bonds_fix, True))
+
+    #
+    # A - N # C >> A - [N+] # [C-]
+    #
+    q = smarts('[N;D2;z3]([A])#[C;D1]')
+    atom_fix = {1: (1, None), 3: (-1, None)}
+    bonds_fix = ()
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    # fix old diazo rule
+    #
+    # A - [C-] = [N+] = [NH] >> A - [CH] = [N+] = [N-]
+    #
+    q = smarts('[N;D2;z3;x1;+](=[N;D1])=[C;D1,D2;z2;-]')
+    atom_fix = {2: (-1, None), 3: (1, None)}
+    bonds_fix = ()
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    #    |           |
+    #  - N -   >> - [N+] -
+    #    \\          |
+    #    [O,N]      [O,N-]
+    #
+    q = smarts('[N;D4;z2]=[O,N;z2]')
+    atom_fix = {1: (1, None), 2: (-1, None)}
+    bonds_fix = ((1, 2, 1),)
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    # N-oxide radical
+    #
+    #    |         |
+    #  - N*  >>  - N
+    #    \\        |
+    #     O        O*
+    #
+    q = smarts('[N;D3;z2]=[O;D1] |^1:0|')
+    atom_fix = {1: (0, False), 2: (0, True)}
+    bonds_fix = ((1, 2, 1),)
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    # false N-oxide radical
+    #
+    #    |        |
+    #  = N  >> = [N+]
+    #     \        \
+    #      O*       [O-]
+    #
+    q = smarts('[O;D1][N;D3;z2] |^1:0|')
+    atom_fix = {1: (-1, False), 2: (1, False)}
+    bonds_fix = ()
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    # C           C
+    #  \           \
+    #   N # N >>   [N+] = [N-]
+    #  /           /
+    # C           C
+    #
+    q = smarts('[N;D3;z3;x1](#[N;D1])(C)C')
+    atom_fix = {1: (1, None), 2: (-1, None)}
+    bonds_fix = ((1, 2, 2),)
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    #  C - N = [N+]  >>  C - [N+] # N
+    #
+    q = smarts('[N;D1;z2;x1;+]=[N;D2;x1;z2]')
+    atom_fix = {1: (-1, None), 2: (1, None)}
+    bonds_fix = ((1, 2, 3),)
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    #  [N+] - [C-] = O  >>  N = C = O
+    #
+    q = smarts('[C;D2;z2;x2;-]([N;D1,D2;z1;+])=[O;D1]')
+    atom_fix = {1: (1, None), 2: (-1, None)}
+    bonds_fix = ((1, 2, 2),)
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    #  N # C - OH  >>  HN = C = O
+    #
+    q = smarts('[N;D1;x0;z3]#[C;D2;z3;x2][O;D1]')
+    atom_fix = {}
+    bonds_fix = ((1, 2, 2), (2, 3, 2))
+    rules.append((q, atom_fix, bonds_fix, True))
+
+    #
+    #  N # C - [O-]  >>  [N-] = C = O
+    #
+    q = smarts('[N;D1;x0;z3]#[C;D2;z3;x2][O;D1;-]')
+    atom_fix = {1: (-1, None), 3: (1, None)}
+    bonds_fix = ((1, 2, 2), (2, 3, 2))
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    # - [N+] - [O-]  >>  - N = O
+    #
+    q = smarts('[O;D1;z1;x1;-][N;D2;z1;+]')
+    atom_fix = {1: (1, None), 2: (-1, None)}
+    bonds_fix = ((1, 2, 2),)
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    # CH-N=O >> C=N-OH
+    #
+    q = smarts('[O;D1;z2;x1]=[N;D2;x1;z2][C;D1,D2,D3;z1]')
+    atom_fix = {}
+    bonds_fix = ((1, 2, 1), (2, 3, 2))
+    rules.append((q, atom_fix, bonds_fix, True))
+
+    #
+    #       [O+]R           [O]R
+    #       //              /
+    # R2N - C  >> R2[N+] = C
+    #
+    q = smarts('[O;D2;z2;+]=[C;z2][N;D1,D2,D3;z1]')
+    atom_fix = {1: (-1, None), 3: (1, None)}
+    bonds_fix = ((1, 2, 1), (2, 3, 2))
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    # fix pyrylium dearomatization. restore O+ in aromatic ring from N+ form.
+    # e.g. O1C(=[NH+]...)... -> [O+]1=C(N...)...
+    #
+    q = smarts('[O;D2;r6]1[C;z2](=[N;+])[A;z2]-,=[A;z2]-,=[A;z2]-,=[A;z2]1')
+    atom_fix = {1: (1, None), 3: (-1, None)}
+    bonds_fix = ((1, 2, 2), (2, 3, 1))
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    # 6-membered ring amidation (kekule form: OH on C with C=N in ring)
+    # e.g. OC1=CC=NC=N1 >> O=C1NC=NC=C1 (pyrimidinone)
+    #      OC1=CC=CC=N1 >> O=C1NC=CC=C1 (pyridinone)
+    #
+    q = smarts('[O,S;D1;z1;x0]-[C;r6;z2]=2[N;z2]=[A;z2][A;z2]=[A;z2][A;z2]=2')
+    atom_fix = {}
+    bonds_fix = ((1, 2, 2), (2, 7, 1), (3, 4, 1), (4, 5, 2), (5, 6, 1), (6, 7, 2))
+    rules.append((q, atom_fix, bonds_fix, True))
+
+    #
+    # 6-membered ring 1,3-diketone amidation (one N already sp3)
+    # e.g. OC1=NC(=O)NC=C1 >> O=C1NC=CC(=O)N1 (uracil kekule)
+    #
+    q = smarts('[O,S;D1;z1;x0]-[C;r6;z2]=2[N;z1][C;z2][N;z2]=[A;z2][A;z2]=2')
+    atom_fix = {}
+    bonds_fix = ((1, 2, 2), (2, 7, 1), (7, 6, 2), (6, 5, 1))
+    rules.append((q, atom_fix, bonds_fix, True))
+
+    #
+    #      [O,S]H    [O,S]
+    #      /         //
+    # N = C  >> NH - C
+    #
+    q = smarts('[N;z2]=[C;D2,D3;z2]-[O,S;D1]')
+    atom_fix = {}
+    bonds_fix = ((1, 2, 1), (2, 3, 2))
+    rules.append((q, atom_fix, bonds_fix, True))
+
+    #
+    # 6-membered ring hydroxypyridine to pyridone
+    # e.g. OC1=CC=NC=C1 >> O=C1C=CNC=C1 (4-pyridone)
+    #
+    q = smarts('[O,S;D1;z1;x0]-[C;r6;z2]1=[A;z2][A;z2]=[N;D2][A;z2]-,=[A;z2]1')
+    atom_fix = {}
+    bonds_fix = ((1, 2, 2), (2, 3, 1), (3, 4, 2), (4, 5, 1))
+    rules.append((q, atom_fix, bonds_fix, True))
+
+    # acyclic keto-enol
+    #         OH                  O
+    #        /                   //
+    # C,H - C = C - C,H >> C,H - C - C - C,H
+    #
+    q = smarts('[O;D1;z1;x0][C;D2,D3;z2;x1;!R]=[C;z2;x0]')
+    atom_fix = {}
+    bonds_fix = ((1, 2, 2), (2, 3, 1))
+    rules.append((q, atom_fix, bonds_fix, True))
+
+    # 5-membered ring amidation (short flip, N adjacent to C=N)
+    # e.g. CN1C=CC(O)=N1 >> CN1NC(=O)C=C1
+    #
+    q = smarts('[O,S;D1;z1;x0]-[C;r5;z2]1=N[N;z1][A;z2]-,=[A;z2]1')
+    atom_fix = {}
+    bonds_fix = ((1, 2, 2), (2, 3, 1))
+    rules.append((q, atom_fix, bonds_fix, True))
+
+    # 5-membered ring amidation (long flip, N far from C=N)
+    # e.g. CN1N=CC=C1O >> CN1NC=CC1=O
+    #
+    q = smarts('[O,S;D1;z1;x0]-[C;r5;z2]1=[A;z2][A;z2]=N[N;z1]1')
+    atom_fix = {}
+    bonds_fix = ((1, 2, 2), (2, 3, 1), (3, 4, 2), (4, 5, 1))
+    rules.append((q, atom_fix, bonds_fix, True))
+
+    # 6-membered ring N=C-CH adjacent to C=O (short flip)
+    # e.g. O=C1C=CCC=N1 >> O=C1NC=CC=C1
+    #
+    q = smarts('[N;r6;z2]1=[A;z2][C;h1,h2][A;z2]-,=[A;z2]C1=O')
+    atom_fix = {}
+    bonds_fix = ((1, 2, 1), (2, 3, 2))
+    rules.append((q, atom_fix, bonds_fix, True))
+
+    # 6-membered ring N=C-C=C-CH adjacent to C=O (long flip)
+    # e.g. O=C1CC=CC=N1 >> O=C1NC=CC=C1
+    #
+    q = smarts('[N;r6;z2]1=[A;z2][A;z2]=[A;z2][C;h1,h2]C1=O')
+    atom_fix = {}
+    bonds_fix = ((1, 2, 1), (2, 3, 2), (3, 4, 1), (4, 5, 2))
+    rules.append((q, atom_fix, bonds_fix, True))
+
+    # 6-membered ring N=C-CH adjacent to C=O (C=O between CH and ring end)
+    # e.g. O=C1CC=NC=C1 >> O=C1C=CNC=C1
+    #
+    q = smarts('[N;r6;z2]1=[A;z2][C;h1,h2]C(=O)[A;z2]-,=[A;z2]1')
+    atom_fix = {}
+    bonds_fix = ((1, 2, 1), (2, 3, 2))
+    rules.append((q, atom_fix, bonds_fix, True))
+
+    # 5-membered ring N=C-CH >> NH-C=C
+    # e.g. C1C=NC=N1 >> N1C=CN=C1
+    #
+    q = smarts('[N;r5;z2]1=[A;z2][C;h1,h2][A;z2]-,=[A;z2]1')
+    atom_fix = {}
+    bonds_fix = ((1, 2, 1), (2, 3, 2))
+    rules.append((q, atom_fix, bonds_fix, True))
+
+    # 5-membered ring N=C-CH with sp3 N,O closure
+    # e.g. CN1N=CCC1=O >> CN1NC=CC1=O
+    #
+    q = smarts('[N;r5;z2]1=[A;z2][C;h1,h2][A;z2][N,O;z1]1')
+    atom_fix = {}
+    bonds_fix = ((1, 2, 1), (2, 3, 2))
+    rules.append((q, atom_fix, bonds_fix, True))
+
+    # N=C1NC=CC(=O)N1 >> NC1=NC=CC(=O)N1
+    q = smarts('[O,S;D1;z2]=[C;D3;r6]1[N;z1][C;D3:1](=[N:2])[N;h1:3][A]-,=[A]1')
+    atom_fix = {}
+    bonds_fix = ((1, 2, 1), (1, 3, 2))
+    rules.append((q, atom_fix, bonds_fix, True))
+
+    #
+    #       A                   A
+    #       |                   |
+    #  A - [P+] - [O-]  >>  A - P = O
+    #       |                   |
+    #       A                   A
+    #
+    q = smarts('[P;D4;z1;+][O;D1;-]')
+    atom_fix = {1: (-1, None), 2: (1, None)}
+    bonds_fix = ((1, 2, 2),)
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    #       A                   A
+    #       |                   |
+    #  A - [P-] - [C+]  >>  A - P = C
+    #       |                   |
+    #       A                   A
+    #
+    q = smarts('[P;D4;z1;-][C;D1,D2,D3;z1;+]')
+    atom_fix = {1: (1, None), 2: (-1, None)}
+    bonds_fix = ((1, 2, 2),)
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    #   F   F         F   F
+    #    \ /           \ /
+    # F - P - F >> F - [P-] - F
+    #    / \           / \
+    #   F   F         F   F
+    #
+    q = smarts('[P;D6;z1]([F;D1])([F;D1])([F;D1])([F;D1])([F;D1])[F;D1]')
+    atom_fix = {1: (-1, None)}
+    bonds_fix = ()
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    #     O               O
+    #     \\              \\
+    # A - [P-] - A  >> A - P - A
+    #     //              /
+    #     O              [O-]
+    #
+    q = smarts('[P;D4;z3;-](=[O;D1])(=[O;D1])([A])[A]')
+    atom_fix = {1: (1, None), 2: (-1, None)}
+    bonds_fix = ((1, 2, 1),)
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    #     O           [O-]
+    #     \\            \
+    # A -  P - A  >> A - P - A
+    #     /             //
+    #   [S-]            S
+    #
+    q = smarts('[S;D1;z1;x1;-][P;D4;z2]=[O;D1]')
+    atom_fix = {1: (1, None), 3: (-1, None)}
+    bonds_fix = ((1, 2, 2), (2, 3, 1))
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    #     O           [OH]
+    #     \\            \
+    # A -  P - A  >> A - P - A
+    #     /             //
+    #   [SH]            S
+    #
+    q = smarts('[S;D1;z1;x1][P;D4;z2]=[O;D1]')
+    atom_fix = {}
+    bonds_fix = ((1, 2, 2), (2, 3, 1))
+    rules.append((q, atom_fix, bonds_fix, True))
+
+    #
+    #     A                A
+    #     \\               \\
+    # A -  S - [S-]  >> A - S - [O-]
+    #     //               //
+    #     O                S
+    #
+    q = smarts('[S;D1;-][S;D4;z3](=[O;D1])(=[A])[A]')
+    atom_fix = {1: (1, None), 3: (-1, None)}
+    bonds_fix = ((1, 2, 2), (2, 3, 1))
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    #     A                A
+    #     \\               \
+    # A -  S - [SH]  >> A - S - [OH]
+    #     //               //
+    #     O                S
+    #
+    q = smarts('[S;D1][S;D4;z3](=[O;D1])(=[A])[A]')
+    atom_fix = {}
+    bonds_fix = ((1, 2, 2), (2, 3, 1))
+    rules.append((q, atom_fix, bonds_fix, True))
+
+    #
+    #           A                   A
+    #          /                   /
+    # [O-] - [S,Si,Se+]  >>  O = [S,Si,Se]
+    #          \                   \
+    #           A                   A
+    #
+    q = smarts('[S,Se,Si;D3;z1;+][O;D1;-]')
+    atom_fix = {1: (-1, None), 2: (1, None)}
+    bonds_fix = ((1, 2, 2),)
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    #       A?                  A?
+    #       |                   |
+    #  A = [S+] - [O-]  >>  A = S = O
+    #       |                   |
+    #       A?                  A?
+    #
+    q = smarts('[S;D2,D4;z2;+][O;D1;-]')
+    atom_fix = {1: (-1, None), 2: (1, None)}
+    bonds_fix = ((1, 2, 2),)
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    #       [O-]          O
+    #       /            //
+    # A = [S+2]  >>  A = S
+    #       \            \\
+    #       [O-]          O
+    #
+    q = smarts('[S;D3;z2;+2]([O;D1;-])[O;D1;-]')
+    atom_fix = {1: (-2, None), 2: (1, None), 3: (1, None)}
+    bonds_fix = ((1, 2, 2), (1, 3, 2))
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    #          A                  A
+    #          |                  |
+    # [O-] - [S+2] - [O-] >>  O = S = O
+    #          |                  |
+    #          A                  A
+    #
+    q = smarts('[S;D4;z1;+2]([O;D1;-])[O;D1;-]')
+    atom_fix = {1: (-2, None), 2: (1, None), 3: (1, None)}
+    bonds_fix = ((1, 2, 2), (1, 3, 2))
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    #  A - [S-] - [C+]  >>  A - S = C
+    #       |                   |
+    #       A                   A
+    #
+    q = smarts('[S;D3;z1;-]([C;D1,D2,D3;z1;+])')
+    atom_fix = {1: (1, None), 2: (-1, None)}
+    bonds_fix = ((1, 2, 2),)
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    #  O              O
+    #  \\             \\
+    #  [S-] - A  >>    S - A
+    #  //             /
+    #  O            [O-]
+    #
+    q = smarts('[S;D3;z3;-](=[O;D1])(=[O;D1])[A]')
+    atom_fix = {1: (1, None), 2: (-1, None)}
+    bonds_fix = ((1, 2, 1),)
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    #     O             [O-]
+    #     \\             \
+    # A - [S-] = O >> A - S = O
+    #     //             //
+    #     O              O
+    #
+    q = smarts('[S;D4;z3;-](=[O;D1])(=[O;D1])(=[O;D1])[A]')
+    atom_fix = {1: (1, None), 2: (-1, None)}
+    bonds_fix = ((1, 2, 1),)
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    #  O              [O-]
+    #  \\              \
+    #  [S-] - [S-] >>   S = S
+    #  //              /
+    #  O              [O-]
+    #
+    q = smarts('[S;D3;z3;x3;-]([S;D1;-])(=[O;D1])=[O;D1]')
+    atom_fix = {1: (1, None), 2: (1, None), 3: (-1, None), 4: (-1, None)}
+    bonds_fix = ((1, 2, 2), (1, 3, 1), (1, 4, 1))
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    #    A            A
+    #    \            \
+    # A - S = O >> A - S = O
+    #    /            //
+    #  [OH]           O
+    #
+    q = smarts('[S;D4;z2](=[O;D1])[O;D1]')
+    atom_fix = {}
+    bonds_fix = ((1, 3, 2),)
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    #    A            A
+    #    \            \
+    # A - S = O >> A - S = O
+    #    /            //
+    #  [NH]           N
+    #
+    q = smarts('[S;D4;z2](=[O;D1])[N;D1,D2;z1]')
+    atom_fix = {}
+    bonds_fix = ((1, 3, 2),)
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    #      A{1,3}               A{1,3}
+    #      |                    |
+    #  N = S - [OH]  >>  [NH] - S = O
+    #
+    q = smarts('[S;D3,D5;z2](=[N;D1,D2;z2])[O;D1]')
+    atom_fix = {}
+    bonds_fix = ((1, 2, 1), (1, 3, 2))
+    rules.append((q, atom_fix, bonds_fix, True))
+
+    #
+    #     [OH]                O
+    #      |                 //
+    #  N = S = A  >>  [NH] - S = A   (duplicated for overlapping groups)
+    #      |                 |
+    #      A                 A
+    #
+    q = smarts('[S;D4;z3:1]([O;D1:2])(=[N;D1,D2;z2:3])(=[A])[A]')
+    atom_fix = {}
+    bonds_fix = ((1, 2, 2), (1, 3, 1))
+    rules.append((q, atom_fix, bonds_fix, True))
+    rules.append((q, atom_fix, bonds_fix, True))  # second shot for overlapping groups
+
+    #
+    # C # C - [O,NH,S]H  >> C=C=[O,NH,S]
+    #
+    q = smarts('[C;D2;z3;x1]([N,O,S;D1])#[C;D1,D2]')
+    atom_fix = {}
+    bonds_fix = ((1, 2, 2), (1, 3, 2))
+    rules.append((q, atom_fix, bonds_fix, True))
+
+    #
+    # C # C - [NH]R  >> C=C=NR
+    #
+    q = smarts('[C;D2;z3;x1]([N;D2;z1])#[C;D1,D2]')
+    atom_fix = {}
+    bonds_fix = ((1, 2, 2), (1, 3, 2))
+    rules.append((q, atom_fix, bonds_fix, True))
+
+    # Carbon Monoxide
+    #
+    # [CX1] = O  >> [С-] # [O+]
+    #
+    q = smarts('[C;D1;x1;z2]=[O;D1] |^1:0|')
+    atom_fix = {1: (-1, False), 2: (1, None)}
+    bonds_fix = ((1, 2, 3),)
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    # Ozone
+    #
+    # [O*] -- O -- [O*]  >>  O == [O+] -- [O-]
+    #
+    q = smarts('[O;D1][O;D2][O;D1] |^1:0,2|')
+    atom_fix = {1: (0, False), 2: (1, None), 3: (-1, False)}
+    bonds_fix = ((1, 2, 2),)
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    # only after [A-] - [C+] rules!
+    #  [C+] - N(R2)  >> C = [N+](R2)
+    #
+    q = smarts('[C;D1,D2,D3;z1;+]-[N;D3;z1;x0]')
+    atom_fix = {1: (-1, None), 2: (1, None)}
+    bonds_fix = ((1, 2, 2),)
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    # low priority for hetero-N
+    #  [C+] - N(X2)  >> C = [N+](X2)
+    #
+    q = smarts('[C;D1,D2,D3;z1;+]-[N;D3;z1]')
+    atom_fix = {1: (-1, None), 2: (1, None)}
+    bonds_fix = ((1, 2, 2),)
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    #
+    #  [C+] = N(R)  >>  C # [N+](R)
+    #
+    q = smarts('[C;D1,D2;z2;x1;+]=[N;D1,D2;z2]')
+    atom_fix = {1: (-1, None), 2: (1, None)}
+    bonds_fix = ((1, 2, 3),)
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    # fix rdkit
+    # A-[Cl,Br,I+] - [O-] >> X = O
+    #
+    q = smarts('[Cl,Br,I;D2;z1;+][O;D1;-]')
+    atom_fix = {1: (-1, None), 2: (1, None)}
+    bonds_fix = ((1, 2, 2),)
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    # fix rdkit
+    # A-[Hal+2]([O-])2
+    #
+    q = smarts('[Cl,Br,I;D3;z1;+2]([O;D1;-])[O;D1;-]')
+    atom_fix = {1: (-2, None), 2: (1, None), 3: (1, None)}
+    bonds_fix = ((1, 2, 2), (1, 3, 2))
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    # fix rdkit
+    # A-[Hal+3]([O-])3
+    #
+    q = smarts('[Cl,Br,I;D4;z1;+3]([O;D1;-])([O;D1;-])[O;D1;-]')
+    atom_fix = {1: (-3, None), 2: (1, None), 3: (1, None), 4: (1, None)}
+    bonds_fix = ((1, 2, 2), (1, 3, 2), (1, 4, 2))
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    # fix reaxys [Cl-]=O > Cl-[O-]
+    q = smarts('[Cl,Br,I;D1;z2;-]=[O;D1]')
+    atom_fix = {1: (1, None), 2: (-1, None)}
+    bonds_fix = ((1, 2, 1),)
+    rules.append((q, atom_fix, bonds_fix, False))
+
+    return [(q, atom_fix, bonds_fix,
+             [n for n, a in q.atoms() if a.atomic_symbol == 'A' and n not in atom_fix], is_tautomer)
+            for q, atom_fix, bonds_fix, is_tautomer in rules]
+
+
+rules = Proxy(_rules)
+
+
+__all__ = ['rules']