chython 2.4__cp312-cp312-win_amd64.whl

chython/algorithms/standardize/salts.py

@@ -0,0 +1,128 @@
+# -*- coding: utf-8 -*-
+#
+#  Copyright 2021-2024 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 typing import TYPE_CHECKING, List, Tuple, Union
+from ._salts import acids, rules
+from ...periodictable import GroupI, GroupII
+
+
+if TYPE_CHECKING:
+    from chython import MoleculeContainer
+
+
+# atomic number constants
+H = 1
+N = 7
+
+
+class Salts:
+    __slots__ = ()
+
+    def remove_metals(self: 'MoleculeContainer', *, logging=False) -> Union[bool, List]:
+        """
+        Remove disconnected S-metals and ammonia.
+
+        :param logging: return deleted atoms list.
+        """
+        atoms = self._atoms
+        bonds = self._bonds
+
+        metals = []
+        for n, a in atoms.items():
+            if not bonds[n] and (a == N or isinstance(a, (GroupI, GroupII)) and a != H):
+                metals.append(n)
+
+        if 0 < len(metals) < len(self):
+            for n in metals:
+                del atoms[n]
+                del bonds[n]
+
+            self.flush_cache(keep_sssr=True)
+            if logging:
+                return metals
+            return True
+        elif logging:
+            return []
+        return False
+
+    def remove_acids(self: 'MoleculeContainer', *, logging=False) -> Union[bool, List[int]]:
+        """
+        Remove common acids from organic bases salts.
+        Works only for neutral pairs like HA+B. Use `neutralize` before.
+
+        :param logging: return deleted atoms list.
+        """
+        if self.connected_components_count > 1:
+            log = []
+            for c in self.connected_components:
+                if self.substructure(c, recalculate_hydrogens=False) in acids:
+                    log.extend(c)
+            if 0 < len(log) < len(self):  # prevent singularity
+                atoms = self._atoms
+                bonds = self._bonds
+
+                for n in log:
+                    del atoms[n]
+                    del bonds[n]
+
+                self.flush_cache()
+                if logging:
+                    return log
+                return True
+        if logging:
+            return []
+        return False
+
+    def split_metal_salts(self: 'MoleculeContainer', *, logging=False) -> Union[bool, List[Tuple[int, int]]]:
+        """
+        Split connected S-metal salts to cation/anion pairs.
+
+        :param logging: return deleted bonds list.
+        """
+        atoms = self._atoms
+        bonds = self._bonds
+
+        metals = [n for n, a in atoms.items() if isinstance(a, (GroupI, GroupII)) and a != H]
+        if metals:
+            acceptors = set()
+            log = []
+            for q in rules:
+                for mapping in q.get_mapping(self, automorphism_filter=False):
+                    acceptors.add(mapping[1])
+
+            for n in metals:
+                for m in acceptors & bonds[n].keys():
+                    if atoms[n].charge == 4:  # prevent overcharging
+                        break
+                    del bonds[n][m]
+                    del bonds[m][n]
+                    atoms[n]._charge += 1
+                    atoms[m]._charge -= 1
+                    log.append((n, m))
+            if log:
+                self.flush_cache()
+                self.fix_stereo()
+                if logging:
+                    return log
+                return True
+        if logging:
+            return []
+        return False
+
+
+__all__ = ['Salts']

chython/algorithms/standardize/saturation.py

@@ -0,0 +1,378 @@
+# -*- coding: utf-8 -*-
+#
+#  Copyright 2021-2024 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 collections import defaultdict
+from itertools import product
+from operator import itemgetter
+from random import shuffle
+from typing import TYPE_CHECKING, Dict, Optional, Union, List
+from ...containers.bonds import Bond
+from ...exceptions import ValenceError
+
+
+if TYPE_CHECKING:
+    from chython import MoleculeContainer
+
+# atom, charge, unsaturation
+tuned_priority = {(7, 0, 0): -3,  # amine
+                  (7, 0, 1): -3,  # X=N-X
+                  (7, 0, 2): -3,  # X#N
+                  (7, 1, 1): -2,  # X=[N+](-X)-X
+                  (7, 1, 2): -2,  # X=[N+]=X
+                  (7, -1, 0): -1,  # X-[N-]-X
+                  (7, -1, 1): -1,  # X=[N-]
+                  (8, 0, 0): -2,  # X-O-X
+                  (8, 0, 1): -2,  # X=O
+                  (8, -1, 0): -1,  # X-[O-]
+                  (8, 1, 1): -1,  # X=[O+]-X
+                  (16, 0, 0): -3,  # X-S-X
+                  (16, 0, 2): -2,  # X-S(-X)(=X)=X
+                  (16, 0, 1): -2,  # X-S(-X)(=X)
+                  (16, 0, 2): -2,  # X=S=X
+                  (16, 0, 0): -1,  # X-S(-X)(-X)-X
+                  (16, 0, 1): -1,  # X-[S+](-X)(-X)
+                  (16, 1, 1): -1,  # X=[S+]-X
+                  }
+charge_priority = {0: 0, -1: 1, 1: 2, 2: 3, 3: 4, -2: 5, 4: 6, -3: 7, -4: 8}
+
+
+class Saturation:
+    __slots__ = ()
+
+    def saturate(self: 'MoleculeContainer', neighbors_distances: Optional[Dict[int, Dict[int, float]]] = None,
+                 reset_electrons: bool = True, expected_charge: int = 0, expected_radicals_count: int = 0,
+                 allow_errors: bool = True, logging: bool = False) -> Union[bool, List[str]]:
+        """
+        Saturate molecules with double and triple bonds and charges and radical states to correct valences of atoms.
+        Note: works only with fully explicit hydrogens!
+
+        :param neighbors_distances: If given longest bonds can be removed if need.
+        :param reset_electrons: Can change charges and radicals if need.
+        :param expected_charge: Reset charge to given. Works only with reset_electrons=True.
+        :param expected_radicals_count: Reset radical atoms count to given. Works only with reset_electrons=True.
+        :param allow_errors: allow unbalanced result.
+        :param logging: return log.
+        """
+        if any(b != 1 for _, _, b in self.bonds()):
+            raise ValenceError('only single bonded skeleton can be saturated')
+        atoms = self._atoms
+        if not reset_electrons:
+            expected_radicals_count = sum(a.is_radical for a in atoms.values())
+            expected_charge = int(self)
+
+        if reset_electrons:
+            charges = {x: None for x in self}
+            radicals = {x: None for x in self}
+        else:
+            charges = {n: a.charge for n, a in self.atoms()}
+            radicals =  {n: a.is_radical for n, a in self.atoms()}
+        sat, adjacency = _find_possible_valences(atoms, neighbors_distances or self._bonds,
+                                                 charges, radicals, neighbors_distances is not None)
+        charges = {}  # new charge states
+        radicals = {}  # new radical states
+        bonds = {n: {} for n in atoms}  # new bonds
+
+        seen = set()
+        unsaturated = {}
+        for n, env in adjacency.items():  # set single bonds in molecule. collect unsaturated atoms
+            s = sat[n]
+            if len(s) == 1:
+                c, r, h = s.pop()
+                if not h:
+                    seen.add(n)
+                    charges[n] = c
+                    radicals[n] = r
+                    for m in env:
+                        if m not in seen:
+                            bonds[n][m] = bonds[m][n] = Bond(1)
+                else:
+                    unsaturated[n] = [(c, r, h)]
+            else:
+                # radicals have the lowest priority
+                # tuned priority
+                # multiple bonds have higher priority
+                # charges priority: 0>-1>1>2>3>-2>4>-3>-4
+                unsaturated[n] = sorted(s, key=lambda x: (x[1],
+                                                          tuned_priority.get((atoms[n].atomic_number, x[0], x[2]), 0),
+                                                          -x[2], charge_priority[x[0]]))
+
+        log = []
+        if (need_radicals := expected_radicals_count - sum(radicals.values())) < 0:
+            log.append('Radical state not balanced')
+            if not allow_errors:
+                if logging:
+                    return log
+                return False
+            need_radicals = 0  # reset to zero
+
+        if unsaturated:
+            # create graph of unsaturated atoms
+            bonds_graph = {n: {m for m in adjacency[n] if m in unsaturated} for n in unsaturated}
+            order = list(unsaturated)
+            # try to saturate with different random states
+            for _ in range(len(unsaturated)):
+                shuffle(order)
+                sb, sa, log_ = _saturate({n: bonds_graph[n].copy() for n in order}, unsaturated, need_radicals,
+                                         expected_charge - sum(charges.values()))
+                if not log_:  # success
+                    break
+            else:  # failed
+                if log_ == 1:
+                    log.append('Charge state not balanced')
+                elif log_ == 2:
+                    log.append('Radical state not balanced')
+                else:
+                    log.append('Charge state not balanced')
+                    log.append('Radical state not balanced')
+                if not allow_errors:  # all attempts failed
+                    if logging:
+                        return log
+                    return False
+
+            for n, m, b in sb:
+                bonds[n][m] = bonds[m][n] = Bond(b)
+            for n, c, r in sa:
+                charges[n] = c
+                radicals[n] = r
+        elif expected_charge != sum(charges.values()):  # check charge for saturated case
+            log.append('Charge state not balanced')
+            if not allow_errors:
+                if logging:
+                    return log
+                return False
+        # reset molecule
+        self._bonds = bonds
+        for n, r in radicals.items():
+            atoms[n]._is_radical = r
+        for n, c in charges.items():
+            atoms[n]._charge = c
+        for a in atoms.values():
+            a._implicit_hydrogens = 0  # reset invalid hydrogens counts.
+        self.flush_cache()
+        self.calc_labels()
+        if logging:
+            if not log:  # check for errors
+                log.append('Saturated successfully')
+            else:
+                log.append('Saturated with errors')
+            return log
+        return True
+
+
+def _find_possible_valences(atoms, neighbors_distances, charges, radicals, allow_deleting=True):
+    if allow_deleting:
+        possible_bonds = {n: md.copy() for n, md in neighbors_distances.items()}
+    else:
+        possible_bonds = {n: list(md) for n, md in neighbors_distances.items()}
+    while True:
+        saturation = defaultdict(set)
+        for n, env in possible_bonds.items():
+            env_atoms = None
+            el = len(env)
+            dc = charges[n]
+            dr = radicals[n]
+            for charge, is_radical, valence, implicit, explicit_dict in atoms[n]._compiled_saturation_rules:
+                if valence < el or dc is not None and dc != charge or dr is not None and dr != is_radical:
+                    continue  # skip impossible rules
+                if explicit_dict:
+                    if env_atoms is None:  # lazy caching
+                        env_atoms = defaultdict(int)
+                        for m in env:
+                            env_atoms[atoms[m].atomic_number] += 1
+                    env_atoms_copy = env_atoms.copy()
+                    for (b, a), c in explicit_dict.items():  # stage 1. find explicit valence
+                        if env_atoms_copy[a] < c:  # `c` always > 0
+                            break  # rule not matched
+                        env_atoms_copy[a] -= c
+                    else:  # stage 2. find possible valence
+                        if unmatched := sum(env_atoms_copy.values()):  # number of atoms outside rule
+                            if implicit >= unmatched:
+                                # number of implicit H should be greater or equal to number of neighbors
+                                saturation[n].add((charge, is_radical, valence - el))
+                        else:  # pattern fully matched. difference bw valence and connectivity is unsaturation.
+                            saturation[n].add((charge, is_radical, valence - el))
+                else:   # unspecific rule. found possible valence
+                    saturation[n].add((charge, is_radical, valence - el))
+            if n not in saturation:  # valence not found
+                break
+        else:  # all atoms passed
+            break
+        if allow_deleting:
+            out = max(env.items(), key=itemgetter(1))[0]
+            del possible_bonds[out][n]
+            del possible_bonds[n][out]
+        else:
+            raise ValenceError('Structure has invalid atoms neighbors count and electron states')
+    return saturation, possible_bonds
+
+
+def _saturate(bonds, atoms, expected_radicals_count, expected_charge):
+    atoms = {k: v.copy() for k, v in atoms.items()}
+    dots = []
+    saturation = []
+    electrons = []
+    while True:
+        # get isolated atoms. atoms should be charged or radical
+        to_del = []
+        for n, env in bonds.items():
+            if not env:
+                es = [(n, c, r) for c, r, h in atoms[n] if not h]
+                if not es:
+                    raise ValenceError('Saturation impossible. '
+                                       f"Isolated atom ({n}) doesn't have appropriate charge-radical state")
+                to_del.append(n)
+                dots.append(es)
+        for n in to_del:
+            del bonds[n]
+        if not bonds:
+            break
+
+        try:  # get terminal atom
+            n = next(n for n, ms in bonds.items() if len(ms) == 1)
+        except StopIteration:
+            # get ring or linker atom
+            n, _ = min(bonds.items(), key=lambda x: len(x[1]))
+            m = bonds[n].pop()
+            bonds[m].discard(n)
+
+            for (nc, nr, nh), (i, (mc, mr, mh)) in product(atoms[n], enumerate(atoms[m])):
+                if nh == mh:
+                    saturation.append((n, m, nh + 1))
+                    electrons.append((n, nc, nr))
+                    electrons.append((m, mc, mr))
+
+                    for x in bonds.pop(n):
+                        saturation.append((n, x, 1))
+                        bonds[x].discard(n)
+                    for x in bonds.pop(m):
+                        saturation.append((m, x, 1))
+                        bonds[x].discard(m)
+                    break
+                elif nh < mh:
+                    electrons.append((n, nc, nr))
+                    saturation.append((n, m, nh + 1))
+                    atoms[m].pop(i)
+                    atoms[m].insert(i, (mc, mr, mh - nh))
+
+                    for x in bonds.pop(n):
+                        saturation.append((n, x, 1))
+                        bonds[x].discard(n)
+                    break
+                elif nh > mh:
+                    electrons.append((m, mc, mr))
+                    saturation.append((n, m, mh + 1))
+                    atoms[n].pop(i)
+                    atoms[n].insert(i, (nc, nr, nh - mh))
+
+                    for x in bonds.pop(m):
+                        saturation.append((m, x, 1))
+                        bonds[x].discard(m)
+                    break
+        else:
+            m = bonds.pop(n).pop()
+            bonds[m].discard(n)
+
+            for (nc, nr, nh), (i, (mc, mr, mh)) in product(atoms[n], enumerate(atoms[m])):
+                if nh == mh:
+                    saturation.append((n, m, nh + 1))
+                    electrons.append((n, nc, nr))
+                    electrons.append((m, mc, mr))
+                    for x in bonds.pop(m):
+                        saturation.append((m, x, 1))
+                        bonds[x].discard(m)
+                    break
+                elif nh < mh and bonds[m]:
+                    electrons.append((n, nc, nr))
+                    saturation.append((n, m, nh + 1))
+                    atoms[m].pop(i)
+                    atoms[m].insert(i, (mc, mr, mh - nh))
+                    break
+            else:
+                saturation.append((n, m, 1))
+                if not bonds[m]:
+                    del bonds[m]
+
+    combo_ua = []  # possible single atoms electron states
+    for s in dots:
+        if len(s) == 1:
+            electrons.extend(s)
+        elif s:
+            combo_ua.append(s)
+
+    # if < 0 - we already in bad situation
+    # if > 0 - we need more radicals
+    need_radical = expected_radicals_count - sum(x for _, _, x in electrons)
+    need_charge = expected_charge - sum(x for _, x, _ in electrons)
+    if combo_ua:
+        # try randomly set charges and radicals.
+        # first pick required radical states.
+        # second try to minimize charge delta.
+        for attempt in range(1, len(combo_ua) + 1):
+            shuffle(combo_ua)
+            charges_radicals = []
+            rad = []
+            chg = []
+            for atom in combo_ua:
+                if len(rad) < need_radical:  # pick radicals
+                    r = next((x for x in atom if x[2]), None)
+                    if r:  # pick random radical states
+                        rad.append(r)
+                    else:  # not radical
+                        chg.append(atom)
+                else:  # pick not radical states
+                    c = [x for x in atom if not x[2]]
+                    if len(c) > 1:
+                        chg.append(c)
+                    elif c:
+                        charges_radicals.extend(c)
+                    elif attempt == len(combo_ua):  # all states has radical. balancing impossible
+                        chg.append(atom)  # fuck it horse. we in last attempt
+                    else:  # do next attempt
+                        break
+            else:
+                charges_radicals.extend(rad)
+                current_charge = need_charge - sum(x for _, x, _ in charges_radicals)
+                current_radical = need_radical - len(rad)
+                for x in chg:
+                    n, c, r = min(x, key=lambda x: abs(current_charge - x[1]))
+                    charges_radicals.append((n, c, r))
+                    current_charge -= c
+                    current_radical -= r
+
+                if current_radical:  # radical unbalanced
+                    if current_charge:
+                        log = 3
+                    else:
+                        log = 2
+                elif current_charge:
+                    log = 1
+                else:  # balanced!
+                    log = 0
+                    break
+
+        electrons.extend(charges_radicals)
+    elif need_radical:
+        log = 3 if need_charge else 2
+    elif need_charge:
+        log = 1
+    else:
+        log = 0
+    return saturation, electrons, log
+
+
+__all__ = ['Saturation']

chython/algorithms/standardize/test/__init__.py

@@ -0,0 +1,18 @@
+# -*- coding: utf-8 -*-
+#
+#  Copyright 2023 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/>.
+#

chython/algorithms/standardize/test/test_groups.py

@@ -0,0 +1,118 @@
+# -*- coding: utf-8 -*-
+#
+#  Copyright 2023 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 chython import smiles
+from pytest import mark
+
+
+data = [
+        ('CP(C)(C)C', 'C[P+](C)(C)C'),
+        ('CB1(C)[H]B(C)(C)[H]1', 'CB1(C)~[H]B(C)(C)~[H]1'),
+        ('[O]N(C)[NH]', '[O-][N+](C)=N'), ('[O]N(C)[CH2]', '[O-][N+](C)=C'),
+        ('[O]S(C)(C)[O]', 'O=S(C)(C)=O'), ('[O]S(C)(C)[S]', 'O=S(C)(C)=S'),
+        ('BN(C)=C', 'B~N(C)=C'),
+        ('B=N(C)(C)C', 'B~N(C)(C)C'),
+        ('BS(C)C', 'B~S(C)C'), ('BO(C)C', 'B~O(C)C'),
+        ('[B-]=[N+](C)C', 'BN(C)C'), ('C[B-]=[N+]C', 'CBNC'), ('[B-]=[N+]', 'BN'),
+        ('[O-][B+3]([O-])([O-])[O-]', 'O[B-](O)(O)O'),
+        ('[O-]B(O)(O)O', 'O[B-](O)(O)O'),
+        ('OB(O)(O)O', 'O[B-](O)(O)O'),
+        ('CN(C)(C)C', 'C[N+](C)(C)C'),
+        ('C=N(=O)O', 'C[N+](=O)[O-]'),
+        ('C=N(=O)C', 'C=[N+]([O-])C'), ('O=N(=O)C', 'O=[N+]([O-])C'), ('N=N(=O)C', 'N=[N+]([O-])C'),
+        ('C=[N+]([O-])O', 'C[N+](=O)[O-]'),
+        ('CN(=O)=N(=O)C', 'C[N+]([O-])=[N+]([O-])C'),
+        ('CN(=O)=N(=N)C', 'C[N+]([O-])=[N+]([NH-])C'), ('CN(=O)=N(=NC)C', 'C[N+]([O-])=[N+]([N-]C)C'),
+        ('C=N(=N)C', 'C=[N+]([N-])C'), ('C=N(=NC)C', 'C=[N+]([N-]C)C'), ('N=N(=N)C', 'N=[N+]([N-])C'),
+        ('[N-][N+](=O)C', 'N=[N+]([O-])C'), ('C[N-][N+](=O)C', 'CN=[N+]([O-])C'),
+        ('[O-]N(=O)=O', '[O-][N+](=O)[O-]'),
+        ('CN(:O):O', 'C[N+](=O)[O-]'),
+        ('O=[N-]=O', '[O-]N=O'),
+        ('O=N#N', 'O=[N+]=[N-]'), ('C=N#N', 'C=[N+]=[N-]'), ('N=N#N', 'N=[N+]=[N-]'),
+        ('[O-][N+]#N', 'O=[N+]=[N-]'), ('C[CH-][N+]#N', 'CC=[N+]=[N-]'), ('[NH-][N+]#N', 'N=[N+]=[N-]'),
+        ('C[N+]#N=[N-]', 'CN=[N+]=[N-]'),
+        ('CN=N=N', 'CN=[N+]=[N-]'),
+        ('CNN#N', 'CN=[N+]=[N-]'),
+        ('[N-]#N=NC', '[N-]=[N+]=NC'),
+        ('[N-]=N#N', '[N-]=[N+]=[N-]'),
+        ('CC#N=N', 'CC=[N+]=[N-]'),
+        ('CC#N=NC', 'CC#[N+][N-]C'), ('CC#N=O', 'CC#[N+][O-]'),
+        ('NN#C', '[NH-][N+]#C'), ('ON#CC', '[O-][N+]#CC'), ('SN#CC', '[S-][N+]#CC'),
+        ('CNN#C', 'C[N-][N+]#C'),
+        ('N[N+]#[C-]', '[NH-][N+]#C'), ('O[N+]#[C-]', '[O-][N+]#C'), ('S[N+]#[C-]', '[S-][N+]#C'),
+        ('CN[N+]#[C-]', 'C[N-][N+]#C'),
+        ('CN#C', 'C[N+]#[C-]'),
+        ('C[C-]=[N+]=N', 'CC=[N+]=[N-]'),
+        ('CN(C)(C)=O', 'C[N+](C)(C)[O-]'), ('CN(C)(C)=NC', 'C[N+](C)(C)[N-]C'),
+        ('C[N](C)=O |^1:1|', 'CN(C)[O] |^1:3|'),
+        ('C=N(C)[O] |^1:3|', 'C=[N+](C)[O-]'),
+        ('CN(C)#N', 'C[N+](C)=[N-]'),
+        ('CN=[N+]', 'C[N+]#N'),
+        ('[NH2+][C-]=O', 'N=C=O'), ('C[NH+][C-]=O', 'CN=C=O'),
+        ('N#CO', 'N=C=O'),
+        ('N#C[O-]', '[N-]=C=O'),
+        ('CC(C)(C)[N+][O-]', 'CC(C)(C)N=O'),
+        ('CN=O', 'C=NO'),
+        ('NC=[O+]C', '[NH2+]=COC'), ('CNC=[O+]C', 'C[NH+]=COC'), ('CN(C)C=[O+]C', 'C[N+](C)=COC'),
+        ('N=CO', 'NC=O'), ('N=CS', 'NC=S'),
+        ('O=C1NC=CC=C1', 'OC1=NC=CC=C1'), ('OC1=NC=CC=C1', 'OC1=NC=CC=C1'), ('N=C1NC=CC=C1', 'NC1=NC=CC=C1'),
+        ('CN=C1NC=CC=C1', 'CNC1=NC=CC=C1'),
+        ('O=C1C=CNC=C1', 'OC1=CC=NC=C1'), ('OC1=CC=NC=C1', 'OC1=CC=NC=C1'),
+        ('C=C(O)O', 'CC(=O)O'), ('C=C(O)N', 'CC(=O)N'),
+        ('OC=C', 'O=CC'), ('OC(C)=C', 'O=C(C)C'),
+        ('O=C1N=CC=CC1', 'OC=1N=CC=CC=1'), ('OC=1N=CC=CC=1', 'OC=1N=CC=CC=1'), ('N=C1N=CC=CC1', 'NC=1N=CC=CC=1'),
+        ('CN=C1N=CC=CC1', 'CNC=1N=CC=CC=1'),
+        ('[O-][P+](C)(C)C', 'O=P(C)(C)C'),
+        ('[CH2+][P-](C)(C)C', 'C=P(C)(C)C'),
+        ('FP(F)(F)(F)(F)F', 'F[P-](F)(F)(F)(F)F'),
+        ('C[P-](C)(=O)=O', 'CP(C)(=O)[O-]'),
+        ('CP(C)(=O)[S-]', 'CP(C)(=S)[O-]'),
+        ('CP(C)(=O)S', 'CP(C)(=S)O'),
+        ('CS(=O)(=O)[S-]', 'CS(=O)(=S)[O-]'),
+        ('CS(=O)(=O)S', 'CS(=O)(=S)O'),
+        ('C[S+](C)[O-]', 'CS(C)=O'),
+        ('O=[S+][O-]', 'O=S=O'), ('O=[S+](C)(C)[O-]', 'O=S(C)(C)=O'),
+        ('O=[S+2]([O-])[O-]', 'O=S(=O)=O'),
+        ('C[S+2](C)([O-])[O-]', 'CS(C)(=O)=O'),
+        ('C[S-](C)[CH2+]', 'CS(C)=C'),
+        ('O=[S-](C)=O', 'O=S(C)[O-]'),
+        ('O=[S-](C)(=O)=O', 'O=S(C)(=O)[O-]'),
+        ('O=[S-](=O)[S-]', 'S=S([O-])[O-]'),
+        ('CS(C)(=O)O', 'CS(C)(=O)=O'),
+        ('CS(C)(=O)N', 'CS(C)(=O)=N'),
+        ('N=S(C)O', 'NS(C)=O'), ('N=S(C)(C)(C)O', 'NS(C)(C)(C)=O'),
+        ('C#CO', 'C=C=O'),
+        ('C#CNC', 'C=C=NC'),
+        ('C=O |^1:0|', '[C-]#[O+]'),
+        ('[O]O[O] |^1:0,2|', 'O=[O+][O-]'),
+        ('[CH2+]N(C)C', 'C=[N+](C)C'),
+        ('[CH2+]N(C)O', 'C=[N+](C)O'),
+        ('[CH2+]=NC', 'C#[N+]C'),
+        ('O[Cl+][O-]', 'OCl=O'),
+        ('O[Cl+2]([O-])[O-]', 'OCl(=O)=O'),
+        ('O[Cl+3]([O-])([O-])[O-]', 'OCl(=O)(=O)=O'),
+        ('[Cl-]=O', 'Cl[O-]'),
+        ('OS(=N)(=N)O', 'O=S(N)(N)=O'), ('OS(=N)(=N)C', 'O=S(N)(=N)C')
+]
+
+
+@mark.parametrize('raw,result', data)
+def test_group(raw, result):
+    tmp = smiles(raw)
+    tmp.standardize()
+    assert tmp == smiles(result), f'{raw} > {tmp} != {result}'