chython 2.4__cp312-cp312-win_amd64.whl

chython/reactor/deprotection.py

@@ -0,0 +1,565 @@
+# -*- coding: utf-8 -*-
+#
+#  Copyright 2022-2024 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 .. import smarts, MoleculeContainer
+from .transformer import Transformer
+
+"""
+Predefined transformers for most common protection groups cleavage.
+"""
+
+_alcohol_thiocarbamate = (  # NaIO4 or H2O2/NaOH
+    ('[C;D2,D3,D4;z1;x1:1][O:2]C(=[S;D1])N([C;D1])[C;D1]', '[A:1][A:2]',  # rule
+     'CC(C)OC(=S)N(C)C', 'CC(C)O'),  # test
+)
+
+_alcohol_fmoc = (  # Et3N pKa ~ 10
+    ('[C;D2,D3,D4;z1;x1:1][O:2]C(=O)O[C;D2][C;D3]1C:2:[C;D2]:[C;D2]:[C;D2]:[C;D2]:C:2-C:3:[C;D2]:[C;D2]:[C;D2]:[C;D2]:C1:3',  # noqa
+     '[A:1][A:2]',
+     'CC(C)OC(=O)OCC1C2=CC=CC=C2C2=C1C=CC=C2', 'CC(C)O'),
+)
+
+_alcohol_troc = (  # [Zn]
+    ('[C;D2,D3,D4;z1;x1:1][O:2]C(=O)O[C;D2]C([Cl;D1])([Cl;D1])[Cl;D1]', '[A:1][A:2]',
+     'CC(C)OC(=O)OCC(Cl)(Cl)Cl', 'CC(C)O'),
+)
+
+_alcohol_teoc = (  # [F-]
+    ('[C;D2,D3,D4;z1;x1:1][O:2]C(=O)O[C;D2][C;D2][Si]([C;D1])([C;D1])[C;D1]', '[A:1][A:2]',
+     'CC(C)OC(=O)OCC[Si](C)(C)C', 'CC(C)O'),
+)
+
+_alcohol_alloc = (  # [Pd] + NuH
+    ('[C;D2,D3,D4;z1;x1:1][O:2]C(=O)O[C;D2][C;D2]=[C;D1]', '[A:1][A:2]',
+     'CC(C)OC(=O)OCC=C', 'CC(C)O'),
+)
+
+_alcohol_allyl = (  # basic or Metal isomerization + hydrolysis
+    ('[C;D2,D3,D4;z1;x1:1][O:2][C;D2][C;D2]=[C;D1]', '[A:1][A:2]',
+     'CC(C)OCC=C', 'CC(C)O'),
+)
+
+_alcohol_silyl = (  # TMS TES TBS TBDMS TIPS TBDPS: [F-] ion substitution
+    ('[C;D2,D3,D4;z1;x1:1][O:2][Si;D4;z1;x1]', '[A:1][A:2]',
+     'CC(C)O[Si](C)(C)CC', 'CC(C)O', 'CC(C)O[SiH](C)C', 'CC(C)O[Si](C)(C)OC'),
+)
+
+_alcohol_benzyl = (  # [H], ...
+    ('[C;D2,D3,D4;z1;x1:1][O:2][C;D2]C:1:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:1', '[A:1][A:2]',
+     'CC(C)OCc1ccccc1', 'CC(C)O', 'CC(C)OCc1cccc(C)c1', 'CC(C)OC(C)c1ccccc1'),  # test + decoys
+)
+
+_alcohol_o_nitrobenzyl = (  # UV-light
+    ('[C;D2,D3,D4;z1;x1:1][O:2][C;D2,D3;z1;x1]C:1:C([N+](=O)[O-]):[C;D2]:[C;D2]:[C;D2]:[C;D2]:1', '[A:1][A:2]',
+     'CC(C)OCc1c(N(=O)=O)cccc1', 'CC(C)O', 'CC(C)OC(OC)c1c(N(=O)=O)cccc1'),
+)
+
+_alcohol_methoxy_benzyl = (  # PMB or MPM
+    ('[C;D2,D3,D4;z1;x1:1][O:2][C;D2]C:1:[C;D2]:[C;D2]:C(O[C;D1]):[C;D2]:[C;D2]:1', '[A:1][A:2]',
+     'CC(C)OCc1ccc(OC)cc1', 'CC(C)O', 'CC(C)OCc1ccc(OCC)cc1', 'CC(C)OCc1cc(OC)ccc1'),
+)
+
+_alcohol_bom = (  # like Bn
+    ('[C;D2,D3,D4;z1;x1:1][O:2][C;D2]O[C;D2]C:1:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:1', '[A:1][A:2]',
+     'CC(C)OCOCc1ccccc1', 'CC(C)O'),
+)
+
+_alcohol_piv = (
+    ('[C;D2,D3,D4;z1;x1:1][O:2]C(=O)C([C;D1])([C;D1])[C;D1]', '[A:1][A:2]'),  # Piv
+)
+
+_alcohol_methoxy_benzoate = (
+    ('[C;D2,D3,D4;z1;x1:1][O:2]C(=O)C:1:[C;D2]:[C;D2]:C(O[C;D1]):[C;D2]:[C;D2]:1', '[A:1][A:2]'),  # pMeO-Bz
+)
+
+_alcohol_benzoate = (
+    ('[C;D2,D3,D4;z1;x1:1][O:2]C(=O)C:1:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:1', '[A:1][A:2]'),  # Bz
+)
+
+_alcohol_acyl = (
+    ('[C;D2,D3,D4;z1;x1:1][O:2]C(=O)[C;D1]', '[A:1][A:2]'),  # Ac
+)
+
+_alcohol_tfa = (
+    ('[C;D2,D3,D4;z1;x1:1][O:2]C(=O)C(F)(F)F', '[A:1][A:2]'),  # TFA
+)
+
+_alcohol_mom = (
+    ('[C;D2,D3,D4;z1;x1:1][O:2][C;D2]O[C;D1]', '[A:1][A:2]'),  # MOM
+)
+
+_alcohol_thp = (
+    ('[C;D2,D3,D4;z1;x1:1][O:2][C;D3]1[O][C;D2][C;D2][C;D2][C;D2]1', '[A:1][A:2]'),  # THP
+)
+
+_alcohol_tritil = (
+    ('[C;D2,D3,D4;z1;x1:1][O:2]C(C:1:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:1)(C:2:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:2)C:3:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:3',  # noqa
+     '[A:1][A:2]'),
+)
+
+_alcohol_tbu = (
+    ('[C;D2,D3,D4;z1;x1;M][O:1]-C([C;D1])([C;D1])[C;D1]', '[A:1]'),
+)
+
+_alcohol_amide_acetone = (  # N1CCOC1
+    ('[O:1]1[C;x1;z1;M][C;x1;z1;M][N:2]([C;M]=[O;M])-C1([C;D1])[C;D1]',
+     '[A:1].[A:2]'),
+)
+
+_diol12_acetone = (
+    ('[C;D3,D4;z1;x1:1]1[O:2]C([C;D1])([C;D1])[O:3][C;z1;x1:4]1', '[A:3][A:4][A:1][A:2]'),  # ketone
+)
+
+_diol12_formalin = (
+    ('[C;D3,D4;z1;x1:1]1[O:2][C;D2][O:3][C;z1;x1:4]1', '[A:3][A:4][A:1][A:2]'),  # formaldehyde
+)
+
+_diol12_cyclopentanone = (
+    ('[C;D3,D4;z1;x1:1]1[O:2]C2([C;D2][C;D2][C;D2][C;D2]2)[O:3][C;z1;x1:4]1', '[A:3][A:4][A:1][A:2]'),
+)
+
+_diol12_cyclohexanone = (
+    ('[C;D3,D4;z1;x1:1]1[O:2]C2([C;D2][C;D2][C;D2][C;D2][C;D2]2)[O:3][C;z1;x1:4]1', '[A:3][A:4][A:1][A:2]'),
+)
+
+_diol12_diacetal = (
+    ('[C;D3,D4;z1;x1:1]1[O:2]-C([C;D1])(O[C;D1])-C([C;D1])(O[C;D1])-[O:3][C;z1;x1:4]1',
+     '[A:3][A:4][A:1][A:2]'),
+)
+
+_diol13_formalin = (
+    ('[C:5]1[C;D3,D4;z1;x1:1][O:2][C;D2][O:3][C;z1;x1:4]1', '[A:3][A:4][A:5][A:1][A:2]'),  # formaldehyde
+)
+
+_diol13_acetone = (
+    ('[C:5]1[C;D3,D4;z1;x1:1][O:2]C([C;D1])([C;D1])[O:3][C;z1;x1:4]1', '[A:3][A:4][A:5][A:1][A:2]'),
+)
+
+_diol12_benzylidene = (
+    ('[C;D3,D4;z1;x1:1]1[O:2][C;D3](C:2:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:2)[O:3][C;z1;x1:4]1',
+     '[A:3][A:4][A:1][A:2]',
+     'CC1COC(O1)c1ccccc1', 'CC(O)CO'),
+)
+
+_diol13_cyclopentanone = (
+    ('[C:5]1[C;D3,D4;z1;x1:1][O:2]C2([C;D2][C;D2][C;D2][C;D2]2)[O:3][C;z1;x1:4]1',
+     '[A:3][A:4][A:5][A:1][A:2]'),
+)
+
+_diol13_cyclohexanone = (
+    ('[C:5]1[C;D3,D4;z1;x1:1][O:2]C2([C;D2][C;D2][C;D2][C;D2][C;D2]2)[O:3][C;z1;x1:4]1',
+     '[A:3][A:4][A:5][A:1][A:2]'),
+)
+
+_diol13_diacetal = (
+    ('[C:5]1[C;D3,D4;z1;x1:1][O:2]-C([C;D1])(O[C;D1])-C([C;D1])(O[C;D1])-[O:3][C;z1;x1:4]1',
+     '[A:3][A:4][A:5][A:1][A:2]'),
+)
+
+_diol13_benzylidene = (
+    ('[C:5]1[C;D3,D4;z1;x1:1][O:2][C;D3](C:2:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:2)[O:3][C;z1;x1:4]1',
+     '[A:3][A:4][A:5][A:1][A:2]',
+     'CC1CCOC(O1)c1ccccc1', 'CC(O)CCO'),
+)
+
+_carbonyl_dithiolane = (  # MeI - S methylation + hydrolysis
+    ('[C;D3,D4;z1;x2:1]1[S;D2:3][C;D2][C;D2][S;D2]1', '[A:1]=O'),
+)
+
+_carbonyl_dithiane = (  # MeI - S methylation + hydrolysis
+    ('[C;D3,D4;z1;x2:1]1[S;D2:3][C;D2][C;D2][C;D2][S;D2]1', '[A:1]=O'),
+)
+
+_carbonyl_dimethylsulfide = (  # MeI - S methylation + hydrolysis
+    ('[C;D3,D4;z1;x2:1]([S;D2:3][C;D1])[S;D2][C;D1]', '[A:1]=O'),
+)
+
+_carbonyl_dioxolane = (
+    ('[C;D3,D4;z1;x2:1]1[O;D2:3][C;D2][C;D2][O;D2]1', '[A:1]=O'),
+)
+
+_carbonyl_dioxane = (
+    ('[C;D3,D4;z1;x2:1]1[O;D2:3][C;D2][C;D2][C;D2][O;D2]1', '[A:1]=O'),
+)
+
+_carbonyl_dimethoxy = (
+    ('[C;D3,D4;z1;x2:1]([O;D2:3][C;D1])[O;D2][C;D1]', '[A:1]=O'),
+)
+
+_carboxyl_tbu = (
+    ('[C;D3;x2:1](=[O:2])[O:3]-C([C;D1])([C;D1])[C;D1]', '[A:1](=[A:2])[A:3]'),
+)
+
+_carboxyl_mpe = (
+    ('[C;D3;x2;M](=[O;M])[O:1]-C([C;D1])([C;D2][C;D1])[C;D2][C;D1]', '[A:1]'),
+)
+
+_carboxyl_methyl = (
+    ('[C;D3;x2:1](=[O:2])-[O:4]-[C;D1]', '[A:1](=[A:2])O'),  # Me
+)
+
+_carboxyl_trifluoroethyl = (
+    ('[C;D3;x2:1](=[O:2])-[O:4]-[C;D2]C(F)(F)F', '[A:1](=[A:2])O'),  # CF3-CH2-
+)
+
+_carboxyl_trioxabicyclooctane = (  # [H+]. Note! second step of basic hydrolysis required.
+    ('[C;D4;x3:1]12[O:4][C;D2]C([C;D1])([C;D2]O1)[C;D2]O2', '[A:1](=O)O',
+     'CC(C)C12OCC(C)(CO1)CO2', 'CC(C)C(O)=O', 'CC(C)C12OCC(CC)(CO1)CO2', 'CC(C)C12OC(C)C(C)(CO1)CO2'),
+)
+
+_carboxyl_allyl = (  # [Pd] + NuH
+    ('[C;D3;x2:1](=[O:2])[O:3]-[C;D2][C;D2]=[C;D1]', '[A:1](=[A:2])[A:3]'),
+)
+
+_carboxyl_benzyl = (  # [H] or Li/NH3
+    ('[C;D3;x2:1](=[O:2])[O:3]-[C;D2]C:1:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:1', '[A:1](=[A:2])[A:3]'),
+)
+
+_carboxyl_fm = (
+    ('[C;x2;M](=[O;M])[O:1][C;D2][C;D3]1C:2:[C;D2]:[C;D2]:[C;D2]:[C;D2]:C:2-C:3:[C;D2]:[C;D2]:[C;D2]:[C;D2]:C1:3',
+     '[A:1]'),
+)
+
+_carboxyl_dmab = (
+    ('[C;x2;M](=[O;M])[O:1]-[C;D2]-C:1:[C;D2]:[C;D2]:C(:[C;D2]:[C;D2]:1)-[N;D2]-C([C;D2][C;D3]([C;D1])[C;D1])=C1C(=O)[C;D2]C([C;D1])([C;D1])[C;D2]C1=O',
+     '[A:1]'),
+)
+
+_amine_methylcarbamate = (  # PrSLi or [OH-]
+    # Ar-NH2
+    ('[C;a:1][N;D2:2]-C(=O)O[C;D1]', '[A:1][A:2]',
+     'c1ccccc1NC(=O)OC', 'c1ccccc1N', 'c1ccccc1NC(=O)OCC', 'c1cccn1NC(=O)OC'),
+    # Alk-NH2
+    ('[C;D2,D3,D4;z1;x1:1][N;D2:2]-C(=O)O[C;D1]', '[A:1][A:2]',
+     'CC(C)NC(=O)OC', 'CC(C)N', 'CC(C)NC(=O)OCC', 'CONC(=O)OC', 'C=NC(=O)OC'),
+    # Alk-NH-Ar
+    ('[C;a:1][N:2]([C;z1;x1:3])-C(=O)O[C;D1]', '[A:1][A:2][A:3]',
+     'c1ccccc1N(C(C)C)C(=O)OC', 'c1ccccc1NC(C)C'),
+    # Alk2NH
+    ('[C;D2,D3,D4;z1;x1:1][N:2]([C;z1;x1:3])-C(=O)O[C;D1]', '[A:1][A:2][A:3]',
+     'CC(C)N(C(C)C)C(=O)OC', 'CC(C)NC(C)C'),
+)
+
+_amine_teoc = (  # [F-]
+    # Ar-NH2
+    ('[C;a:1][N;D2:2]-C(=O)O[C;D2][C;D2][Si]([C;D1])([C;D1])[C;D1]', '[A:1][A:2]',
+     'c1ccccc1NC(=O)OCC[Si](C)(C)C', 'c1ccccc1N'),
+    # Alk-NH2
+    ('[C;D2,D3,D4;z1;x1:1][N;D2:2]-C(=O)O[C;D2][C;D2][Si]([C;D1])([C;D1])[C;D1]', '[A:1][A:2]'),
+    ('[C;a:1][N:2]([C;z1;x1:3])-C(=O)O[C;D2][C;D2][Si]([C;D1])([C;D1])[C;D1]', '[A:1][A:2][A:3]'),  # Alk-NH-Ar
+    ('[C;D2,D3,D4;z1;x1:1][N:2]([C;z1;x1:3])-C(=O)O[C;D2][C;D2][Si]([C;D1])([C;D1])[C;D1]', '[A:1][A:2][A:3]'),  # Alk2NH
+)
+
+_amine_troc = (  # [Zn]
+    # Ar-NH2
+    ('[C;a:1][N;D2:2]-C(=O)O[C;D2]C(Cl)(Cl)Cl', '[A:1][A:2]',
+     'c1ccccc1NC(=O)OCC(Cl)(Cl)Cl', 'c1ccccc1N', 'c1ccccc1NC(=O)OC(C)C(Cl)(Cl)Cl'),
+    # Alk-NH2
+    ('[C;D2,D3,D4;z1;x1:1][N;D2:2]-C(=O)O[C;D2]C(Cl)(Cl)Cl', '[A:1][A:2]'),
+    # Alk-NH-Ar
+    ('[C;a:1][N:2]([C;z1;x1:3])-C(=O)O[C;D2]C(Cl)(Cl)Cl', '[A:1][A:2][A:3]'),
+    # Alk2NH
+    ('[C;D2,D3,D4;z1;x1:1][N:2]([C;z1;x1:3])-C(=O)O[C;D2]C(Cl)(Cl)Cl', '[A:1][A:2][A:3]'),
+)
+
+_amine_alloc = (  # [Pd]
+    # Ar-NH2
+    ('[C;a:1][N;D2:2]-C(=O)O[C;D2][C;D2]=[C;D1]', '[A:1][A:2]',
+     'c1ccccc1NC(=O)OCC=C', 'c1ccccc1N', 'c1ccccc1NC(=O)OCC=CC'),
+    # Alk-NH2
+    ('[C;D2,D3,D4;z1;x1:1][N;D2:2]-C(=O)O[C;D2][C;D2]=[C;D1]', '[A:1][A:2]'),
+    # Alk-NH-Ar
+    ('[C;a:1][N:2]([C;z1;x1:3])-C(=O)O[C;D2][C;D2]=[C;D1]', '[A:1][A:2][A:3]'),
+    # Alk2NH
+    ('[C;D2,D3,D4;z1;x1:1][N:2]([C;z1;x1:3])-C(=O)O[C;D2][C;D2]=[C;D1]', '[A:1][A:2][A:3]'),
+)
+
+_amine_cbz = (  # [Pd] or Na/NH3
+    # Ar-NH2
+    ('[C;a:1][N;D2:2]-C(=O)O[C;D2]C:1:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:1', '[A:1][A:2]',
+     'c1ccccc1NC(=O)OCc2ccccc2', 'c1ccccc1N', 'c1ccccc1NC(=O)OC(C)c2ccccc2'),
+    # Alk-NH2
+    ('[C;D2,D3,D4;z1;x1:1][N;D2:2]-C(=O)O[C;D2]C:1:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:1', '[A:1][A:2]'),
+    # Alk-NH-Ar
+    ('[C;a:1][N:2]([C;z1;x1:3])-C(=O)O[C;D2]C:1:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:1', '[A:1][A:2][A:3]'),
+    # Alk2NH
+    ('[C;D2,D3,D4;z1;x1:1][N:2]([C;z1;x1:3])-C(=O)O[C;D2]C:1:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:1', '[A:1][A:2][A:3]'),
+)
+
+_amine_chloro_cbz = (
+    # Ar-NH2
+    ('[C;a;M][N;D2:1]-C(=O)O[C;D2]C:1:C([Cl;D1]):[C;D2]:[C;D2]:[C;D2]:[C;D2]:1', '[A:1]',
+     'Clc1ccccc1COC(=O)Nc1ccccc1', 'c1ccccc1N', 'c1ccccc1NC(=O)OC(C)c2ccccc2'),
+    # Alk-NH2
+    ('[C;D2,D3,D4;z1;x1;M][N;D2:1]-C(=O)O[C;D2]C:1:C([Cl;D1]):[C;D2]:[C;D2]:[C;D2]:[C;D2]:1', '[A:1]'),
+    # Alk-NH-Ar
+    ('[C;a;M][N:1]([C;z1;x1;M])-C(=O)O[C;D2]C:1:C([Cl;D1]):[C;D2]:[C;D2]:[C;D2]:[C;D2]:1', '[A:1]'),
+    # Alk2NH
+    ('[C;D2,D3,D4;z1;x1;M][N:1]([C;z1;x1;M])-C(=O)O[C;D2]C:1:C([Cl;D1]):[C;D2]:[C;D2]:[C;D2]:[C;D2]:1', '[A:1]'),
+)
+
+_amine_nosyl = (  # NS. With SH-CH2-CH2-OH
+    # Ar-NH2
+    ('[C;a:1][N;D2:2]-S(=O)(=O)C:1:C([N+](=O)[O-]):[C;D2]:[C;D2]:[C;D2]:[C;D2]:1', '[A:1][A:2]',
+     '[O-][N+](=O)c1ccccc1S(=O)(=O)Nc1ccccc1', 'c1ccccc1N'),
+    # Alk-NH2
+    ('[C;D2,D3,D4;z1;x1:1][N;D2:2]-S(=O)(=O)C:1:C([N+](=O)[O-]):[C;D2]:[C;D2]:[C;D2]:[C;D2]:1', '[A:1][A:2]'),
+    # Alk-NH-Ar
+    ('[C;a:1][N:2]([C;z1;x1:3])-S(=O)(=O)C:1:C([N+](=O)[O-]):[C;D2]:[C;D2]:[C;D2]:[C;D2]:1', '[A:1][A:2][A:3]'),
+    # Alk2NH
+    ('[C;D2,D3,D4;z1;x1:1][N:2]([C;z1;x1:3])-S(=O)(=O)C:1:C([N+](=O)[O-]):[C;D2]:[C;D2]:[C;D2]:[C;D2]:1',
+     '[A:1][A:2][A:3]'),
+)
+
+_amine_boc = (
+    # Ar-NH2
+    ('[C;a;M][N;D2;x0;z1:1]-[C;x3;z2](=O)[O;x0;z1][C;D4;x1]([C;D1])([C;D1])[C;D1]', '[A:1]',
+     'c1ccccc1NC(=O)OC(C)(C)C', 'c1ccccc1N'),
+    # Alk-NH2
+    ('[C;D2,D3,D4;z1;x1;M][N;D2;x0;z1:1]-[C;x3;z2](=O)[O;x0;z1][C;D4;x1]([C;D1])([C;D1])[C;D1]', '[A:1]'),
+    # Alk-NH-Ar
+    ('[C;a;M][N;D3;x0;z1:1]([C;z1;x1;M])-[C;x3;z2](=O)[O;x0;z1][C;D4;x1]([C;D1])([C;D1])[C;D1]', '[A:1]'),
+    # Alk2NH
+    ('[C;D2,D3,D4;z1;x1;M][N;D3;x0;z1:1]([C;z1;x1;M])-[C;x3;z2](=O)[O;x0;z1][C;D4;x1]([C;D1])([C;D1])[C;D1]', '[A:1]'),
+    # Alk[NH]-O-Alk
+    ('[C;D2,D3,D4;z1;x1;M][N;D3;x1;z1:1]([O;D2;x1;z1;M][C;z1;x1;M])-[C;x3;z2](=O)[O;x0;z1][C;D4;x1]([C;D1])([C;D1])[C;D1]', '[A:1]'),
+    # Alk-[NH]-COC
+    ('[C;D2,D3,D4;z1;x1;r5;M]1-;@[N;D3;x0;z1:1](-;@[C;z1;x2;M]-;@[O,S;D2;x0;z1;M][C;z1;x1;M]1)-[C;x3;z2](=O)[O;x0;z1][C;D4;x1]([C;D1])([C;D1])[C;D1]', '[A:1]'),
+    ('[C;D2,D3,D4;z1;x1;r6,r7,r8,r9;M]-;@[N;D3;x0;z1:1](-;@[C;z1;x2;M]-;@[O,S;D2;x0;z1;M][C;z1;x1;M])-[C;x3;z2](=O)[O;x0;z1][C;D4;x1]([C;D1])([C;D1])[C;D1]', '[A:1]'),
+    # amino-pyrrolidine
+    ('[C;D3;z1;x2;r5;M](-;@[N;M])[N;D2;x0;z1:1]-[C;x3;z2](=O)[O;x0;z1][C;D4;x1]([C;D1])([C;D1])[C;D1]', '[A:1]',
+     'CC(C)(C)OC(=O)NC1CCCN1', 'NC1CCCN1'),
+)
+
+_amine_tfa = (
+    # Ar-NH2
+    ('[C;a:1][N;D2:2]-C(=O)C(F)(F)F', '[A:1][A:2]'),
+    # Alk-NH2
+    ('[C;D2,D3,D4;z1;x1:1][N;D2:2]-C(=O)C(F)(F)F', '[A:1][A:2]'),
+    # Alk-NH-Ar
+    ('[C;a:1][N:2]([C;z1;x1:3])-C(=O)C(F)(F)F', '[A:1][A:2][A:3]'),
+    # Alk2NH
+    ('[C;D2,D3,D4;z1;x1:1][N:2]([C;z1;x1:3])-C(=O)C(F)(F)F', '[A:1][A:2][A:3]'),
+)
+
+_amine_fmoc = (
+    # Ar-NH2
+    ('[C;a:1][N;D2:2]-C(=O)O[C;D2][C;D3]1C:2:[C;D2]:[C;D2]:[C;D2]:[C;D2]:C:2-C:3:[C;D2]:[C;D2]:[C;D2]:[C;D2]:C1:3',
+     '[A:1][A:2]',
+     'O=C(Nc1ccccc1)OCC1c2ccccc2-c2ccccc12', 'c1ccccc1N'),
+    # Alk-NH2
+    ('[C;D2,D3,D4;z1;x1:1][N;D2:2]-C(=O)O[C;D2][C;D3]1C:2:[C;D2]:[C;D2]:[C;D2]:[C;D2]:C:2-C:3:[C;D2]:[C;D2]:[C;D2]:[C;D2]:C1:3',  # noqa
+     '[A:1][A:2]'),
+    # Alk-NH-Ar
+    ('[C;a:1][N:2]([C;z1;x1:3])-C(=O)O[C;D2][C;D3]1C:2:[C;D2]:[C;D2]:[C;D2]:[C;D2]:C:2-C:3:[C;D2]:[C;D2]:[C;D2]:[C;D2]:C1:3',  # noqa
+     '[A:1][A:2][A:3]'),
+    # Alk2NH
+    ('[C;D2,D3,D4;z1;x1:1][N:2]([C;z1;x1:3])-C(=O)O[C;D2][C;D3]1C:2:[C;D2]:[C;D2]:[C;D2]:[C;D2]:C:2-C:3:[C;D2]:[C;D2]:[C;D2]:[C;D2]:C1:3',  # noqa
+     '[A:1][A:2][A:3]'),
+)
+
+_amine_pbf_pmc_mtr = (
+    # Ar-NH2
+    ('[C;a;M][N;D2:1]-S(=O)(=O)-C:1:C([C;D1]):C([C;D1]):C(O[C;x1;z1]):C:C([C;D1]):1',
+     '[A:1]'),
+    # Alk-NH2
+    ('[C;D2,D3,D4;z1;x1;M][N;D2:1]-S(=O)(=O)-C:1:C([C;D1]):C([C;D1]):C(O[C;x1;z1]):C:C([C;D1]):1',
+    '[A:1]'),
+    # Alk-NH-Ar
+    ('[C;a;M][N:1]([C;z1;x1;M])-S(=O)(=O)-C:1:C([C;D1]):C([C;D1]):C(O[C;x1;z1]):C:C([C;D1]):1',
+    '[A:1]'),
+    # Alk2NH
+    ('[C;D2,D3,D4;z1;x1;M][N:1]([C;z1;x1;M])-S(=O)(=O)-C:1:C([C;D1]):C([C;D1]):C(O[C;x1;z1]):C:C([C;D1]):1',
+    '[A:1]'),
+    # Guanidine
+    ('[N;M]=[C;M]([N;M])[N;D2:1]-S(=O)(=O)-C:1:C([C;D1]):C([C;D1]):C(O[C;x1;z1]):C:C([C;D1]):1',
+     '[A:1]'),
+    ('[N;M][C;M]([N;M])=[N:1]-S(=O)(=O)-C:1:C([C;D1]):C([C;D1]):C(O[C;x1;z1]):C:C([C;D1]):1',
+     '[A:1]'),
+)
+
+_amine_dde = (
+    # Ar-NH2
+    ('[C;a;M][N;D2:1]-C([C;D1])=C1C(=O)[C;D2]C([C;D1])([C;D1])[C;D2]C1=O', '[A:1]'),
+    # Alk-NH2
+    ('[C;D2,D3,D4;z1;x1;M][N;D2:1]-C([C;D1])=C1C(=O)[C;D2]C([C;D1])([C;D1])[C;D2]C1=O', '[A:1]'),
+    # Alk-NH-Ar
+    ('[C;a;M][N:1]([C;z1;x1;M])-C([C;D1])=C1C(=O)[C;D2]C([C;D1])([C;D1])[C;D2]C1=O', '[A:1]'),
+    # Alk2NH
+    ('[C;D2,D3,D4;z1;x1;M][N:1]([C;z1;x1;M])-C([C;D1])=C1C(=O)[C;D2]C([C;D1])([C;D1])[C;D2]C1=O', '[A:1]'),
+)
+
+_amine_ivdde = (
+    # Ar-NH2
+    ('[C;a;M][N;D2:1]-C([C;D2][C;D3]([C;D1])[C;D1])=C1C(=O)[C;D2]C([C;D1])([C;D1])[C;D2]C1=O', '[A:1]'),
+    # Alk-NH2
+    ('[C;D2,D3,D4;z1;x1;M][N;D2:1]-C([C;D2][C;D3]([C;D1])[C;D1])=C1C(=O)[C;D2]C([C;D1])([C;D1])[C;D2]C1=O', '[A:1]'),
+    # Alk-NH-Ar
+    ('[C;a;M][N:1]([C;z1;x1;M])-C([C;D2][C;D3]([C;D1])[C;D1])=C1C(=O)[C;D2]C([C;D1])([C;D1])[C;D2]C1=O', '[A:1]'),
+    # Alk2NH
+    ('[C;D2,D3,D4;z1;x1;M][N:1]([C;z1;x1;M])-C([C;D2][C;D3]([C;D1])[C;D1])=C1C(=O)[C;D2]C([C;D1])([C;D1])[C;D2]C1=O',
+     '[A:1]'),
+)
+
+_amine_mtt = (
+    # Ar-NH2
+    ('[C;a;M][N;D2:1]-C(C:1:[C;D2]:[C;D2]:C([C;D1]):[C;D2]:[C;D2]:1)(C:2:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:2)C:3:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:3',
+     '[A:1]'),
+    # Alk-NH2
+    ('[C;D2,D3,D4;z1;x1;M][N;D2:1]-C(C:1:[C;D2]:[C;D2]:C([C;D1]):[C;D2]:[C;D2]:1)(C:2:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:2)C:3:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:3',
+     '[A:1]'),
+    # Alk-NH-Ar
+    ('[C;a;M][N:1]([C;z1;x1;M])-C(C:1:[C;D2]:[C;D2]:C([C;D1]):[C;D2]:[C;D2]:1)(C:2:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:2)C:3:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:3',
+     '[A:1]'),
+    # Alk2NH
+    ('[C;D2,D3,D4;z1;x1;M][N:1]([C;z1;x1;M])-C(C:1:[C;D2]:[C;D2]:C([C;D1]):[C;D2]:[C;D2]:1)(C:2:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:2)C:3:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:3',
+     '[A:1]'),
+)
+
+_amine_bhoc = (
+    # Ar-NH2
+    ('[C;a;M][N;D2:1]-C(=O)O[C;D3](C:1:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:1)C:2:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:2',
+     '[A:1]'),
+    # Alk-NH2
+    ('[C;D2,D3,D4;z1;x1;M][N;D2:1]-C(=O)O[C;D3](C:1:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:1)C:2:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:2',
+     '[A:1]'),
+    # Alk-NH-Ar
+    ('[C;a;M][N:1]([C;z1;x1;M])-C(=O)O[C;D3](C:1:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:1)C:2:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:2',
+     '[A:1]'),
+    # Alk2NH
+    ('[C;D2,D3,D4;z1;x1;M][N:1]([C;z1;x1;M])-C(=O)O[C;D3](C:1:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:1)C:2:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:2',
+     '[A:1]'),
+    # Guanidine
+    ('[N;M]=[C;M]([N;M])[N;D2:1]-C(=O)O[C;D3](C:1:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:1)C:2:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:2',
+     '[A:1]'),
+    ('[N;M][C;M]([N;M])=[N:1]-C(=O)O[C;D3](C:1:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:1)C:2:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:2',
+     '[A:1]'),
+)
+
+_amide_tritil = (
+    ('[C;D3;x2;M](=[O;M])[N;D2:1]-C(C:1:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:1)(C:2:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:2)C:3:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:3',  # noqa
+     '[A:1]'),
+)
+
+_amide_boc = (
+    ('[N;D2,D3;x0;z1:1]([C;D3;x2;z2;M]=[O;M])-[C;x3;z2](=O)[O;x0;z1][C;D4;x1]([C;D1])([C;D1])[C;D1]', '[A:1]',
+     'CC(=O)NC(=O)OC(C)(C)C', 'CC(N)=O'),
+)
+
+_thiol_tritil = (
+    ('[C;D2,D3,D4;z1;x1;M][S;D2:1]-C(C:1:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:1)(C:2:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:2)C:3:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:3',  # noqa
+     '[A:1]'),
+)
+
+_thiol_mmt = (
+    ('[C;D2,D3,D4;z1;x1;M][S;D2:1]-C(C:1:[C;D2]:[C;D2]:C(-O[C;D1]):[C;D2]:[C;D2]:1)(C:2:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:2)C:3:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:3',  # noqa
+     '[A:1]'),
+)
+
+_thiol_benzyl = (
+    ('[C;D2,D3,D4;z1;x1;M][S;D2:1]-[C;D2]C:1:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:1', '[A:1]'),
+)
+
+_thiol_tbu = (
+    ('[C;D2,D3,D4;z1;x1;M][S;D2:1]-C([C;D1])([C;D1])[C;D1]', '[A:1]'),
+)
+
+_thiol_strimethoxyphenyl = (
+    ('[C;D2,D3,D4;z1;x1;M][S;D2:1]-[S;D2]-C:1:C(O[C;D1]):[C;D2]:C(O[C;D1]):[C;D2]:C:1-O[C;D1]', '[A:1]'),
+)
+
+_thiol_stbu = (
+    ('[C;D2,D3,D4;z1;x1;M][S;D2:1]-[S;D2]-C([C;D1])([C;D1])[C;D1]', '[A:1]'),
+)
+
+_thiol_amide_dimethoxybenzyl = (  # N1CCSC1
+    ('[S;D2:1]1[C;x1;z1;M][C;x1;z1;M][N:2]([C;M]=[O;M])-[C;D3]1-C:2:C(O[C;D1]):[C;D2]:C(O[C;D1]):[C;D2]:[C;D2]:2',
+     '[A:1].[A:2]'),
+)
+
+_pyrrole_boc = (
+    ('[N;a;r5:1]-C(=O)OC([C;D1])([C;D1])[C;D1]', '[A:1]'),
+)
+
+_pyrrole_chloro_tritil = (
+    ('[N;a;r5:1]-C(C:1:C([Cl;D1]):[C;D2]:[C;D2]:[C;D2]:[C;D2]:1)(C:2:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:2)C:3:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:3',
+     '[A:1]'),
+)
+
+_phenol_tbu = (
+    ('[C;a;M][O:1]-C([C;D1])([C;D1])[C;D1]', '[A:1]'),
+)
+
+_phenol_hydroxymethyl_acetone = (
+    ('[C;M]1:[C;M][O:1]C([C;D1])([C;D1])[O:2][C;z1;x1;M]1', '[A:1].[A:2]'),
+)
+
+_phosphate_benzyl = (
+    ('[O;M][P;M](=[O;M])([O;M])[O:1]-[C;D2]C:1:[C;D2]:[C;D2]:[C;D2]:[C;D2]:[C;D2]:1', '[A:1]'),
+)
+
+#################
+# Magic Factory #
+#################
+
+_groups = [k[1:] for k, v in globals().items() if k.startswith('_') and isinstance(v, tuple) and v]
+__all__ = ['apply_all'] + _groups
+_cache = {}
+
+
+def _prepare_reactor(rules, name):
+    rxn = [Transformer(smarts(r), smarts(p)) for r, p, *_ in rules]
+
+    def w(molecule: MoleculeContainer, /) -> MoleculeContainer:
+        """
+        Remove protective groups from the given molecule if applicable.
+        """
+        for r in rxn:
+            while True:
+                try:
+                    molecule = next(r(molecule))
+                except StopIteration:
+                    break
+        return molecule
+
+    w.__module__ = __name__
+    w.__qualname__ = w.__name__ = name
+    return w
+
+
+def apply_all(molecule: MoleculeContainer, /) -> MoleculeContainer:
+    """
+    Remove all found protective groups from the given molecule.
+    """
+    for name in _groups:
+        molecule = __getattr__(name)(molecule)
+    return molecule
+
+
+def __getattr__(name):
+    try:
+        return _cache[name]
+    except KeyError:
+        if name in _groups:
+            _cache[name] = t = _prepare_reactor(globals()[f'_{name}'], name)
+            return t
+        raise AttributeError
+
+
+def __dir__():
+    return __all__

chython/reactor/groups.py

@@ -0,0 +1,128 @@
+# -*- coding: utf-8 -*-
+#
+#  Copyright 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 ..files import smarts
+
+
+_groups = {
+    'Alkene': '[C;z2;x0]=[C;x0;z2]',
+    'Alkene hetero': '[C;z2;x1,x2]=[C;z2]',
+    'Alkene terminal': '[C;z2;x0;D1]=[C;x0;z2]',
+    'Alkene hetero terminal': '[C;z2;x0;D1]=[C;x1,x2;z2]',
+    'Alkyne': '[C;z3;x0]#[C;x0]',
+    'Alkyne hetero': '[C;z3;x1]#[C]',
+    'Alkyne terminal': '[C;z3;x0;D1]#[C;x0]',
+    'Alkyne hetero terminal': '[C;z3;x0;D1]#[C;x1]',
+
+    'Alkyl Halide': '[F,Cl,Br,I;D1][C;x1;z1]',
+    'Cyclopropyl Halide': '[F,Cl,Br,I;D1][C;x1;z1;r3]',
+
+    'Aryl Halide': '[F,Cl,Br,I;D1]-[C;a]',
+    'Aryl Fluoride': '[F;D1]-[C;a]',
+    'Aryl Chloride': '[Cl;D1]-[C;a]',
+    'Aryl Bromide': '[Br;D1]-[C;a]',
+    'Aryl Iodide': '[I;D1]-[C;a]',
+
+    'Aryl Halide SNAr alpha': '[F,Cl,Br,I;D1][C;a]:N',
+    'Aryl Halide SNAr gamma': '[F,Cl,Br,I;D1][C;a]:C:C:N',
+
+    'Aryl Fluoride SNAr alpha': '[F;D1][C;a]:N',
+    'Aryl Fluoride SNAr gamma': '[F;D1][C;a]:C:C:N',
+    'Aryl Chloride SNAr alpha': '[Cl;D1][C;a]:N',
+    'Aryl Chloride SNAr gamma': '[Cl;D1][C;a]:C:C:N',
+    'Aryl Bromide SNAr alpha': '[Br;D1][C;a]:N',
+    'Aryl Bromide SNAr gamma': '[Br;D1][C;a]:C:C:N',
+    'Aryl Iodide SNAr alpha': '[I;D1][C;a]:N',
+    'Aryl Iodide SNAr gamma': '[I;D1][C;a]:C:C:N',
+
+    'Alcohol aliphatic': '[O;D1;x0;z1][C;x1;z1]',
+    'Alcohol primary or secondary aliphatic': '[O;D1;x0;z1][C;D1,D2,D3;x1;z1]',
+    'Alcohol tertiary aliphatic': '[O;D1;x0;z1][C;D4;x1;z1]',
+
+    'Alcohol aromatic': '[O;D1;x0;z1][C;a]',
+
+    'Aldehyde': '[O;z2;x0]=[C;D1,D2;x1;z2]',
+    'Aldehyde aliphatic': '[O;z2;x0]=[C;D2;x1;z2][C;z1]',
+    'Aldehyde aromatic': '[O;z2;x0]=[C;D2;x1;z2][C;a]',
+    'Ketone': '[O;z2;x0]=[C;D3;x1;z2]',
+
+    'Carboxylic Acid': '[O;D1;z1;x0][C;D3;x2;z2]=O',
+    'Carboxylic Acid aliphatic': '[O;D1;z1;x0][C;D3;x2;z2](=O)[C;z1]',
+    'Carboxylic Acid aromatic': '[O;D1;z1;x0][C;D3;x2;z2](=O)[C;a]',
+
+    'Carboxylic Acid Ester': '[O;z2;x0]=[C;D3;x2;z2][O;D2;x0]',
+    'Carboxylic Acid Halide': '[F,Cl,Br,I;D1][C;D3;x2;z2]=O',
+
+    'Amine primary': '[N;D1;x0;z1][C;z1,z4;x1]',
+    'Amine primary aliphatic': '[N;D1;x0;z1][C;z1;x1]',
+    'Amine primary aromatic': '[N;D1;x0;z1][C;a]',
+    'Amine secondary': '[N;D2;x0;z1]([C;z1,z4;x1])[C;z1,z4;x1]',
+    'Amine secondary aliphatic': '[N;D2;x0;z1]([C;z1;x1])[C;z1;x1]',
+    'Amine secondary aromatic': '[N;D2;x0;z1]([C;a])[C;z1,z4;x1]',
+    'Amine tertiary': '[N;D3;x0;z1]([C;z1,z4;x1])([C;z1,z4;x1])[C;z1,z4;x1]',
+    'Amine cyclic': '[N;D2;x0;z1;r4,r5,r6,r7,r8]([C;z1;x1])[C;z1;x1]',
+
+    'Alpha-aminoacid': '[N;D1;x0;z1][C;z1;x1][C;D3;z2;x2](=O)[O;D1]',
+    'Beta-aminoacid': '[N;D1;x0;z1][C;z1;x1][C;z1][C;D3;z2;x2](=O)[O;D1]',
+    'Gamma-aminoacid': '[N;D1;x0;z1][C;z1;x1][C;z1][C;z1][C;D3;z2;x2](=O)[O;D1]',
+
+    'Alpha-aminoacid N-protected': '[N;D2;x0;z1]([C;z1;x1][C;D3;z2;x2](=O)[O;D1])[C;D3;z2;x3](=O)[O;D2;x0]C',
+    'Beta-aminoacid N-protected': '[N;D2;x0;z1]([C;z1;x1][C;z1][C;D3;z2;x2](=O)[O;D1])[C;D3;z2;x3](=O)[O;D2;x0]C',
+    'Gamma-aminoacid N-protected': '[N;D2;x0;z1]([C;z1;x1][C;z1][C;z1][C;D3;z2;x2](=O)[O;D1])[C;D3;z2;x3](=O)[O;D2;x0]C',
+
+    'Alpha-aminoacid O-protected': '[N;D1;x0;z1][C;z1;x1][C;D3;z2;x2](=O)[O;D2;x0][C;z1;x1]',
+    'Beta-aminoacid O-protected': '[N;D1;x0;z1][C;z1;x1][C;z1][C;D3;z2;x2](=O)[O;D2;x0][C;z1;x1]',
+    'Gamma-aminoacid O-protected': '[N;D1;x0;z1][C;z1;x1][C;z1][C;z1][C;D3;z2;x2](=O)[O;D2;x0][C;z1;x1]',
+
+    'Aryl Sulfone': '[S;D4;z3;x2](=O)(=O)(-[C;a])-[C;x1]',
+    'Azide': '[N-;D1;x1;z2]=[N+;D2;x2;z3]=[N;D2;x1;z2]',
+
+    'Boronic Acid': '[B;D3;x2;z1]([O;D1])[O;D1]',
+    'Boronic Acid Ester': '[B;D3;x2;z1]([O;D2;x1])([O;D2;x1])-;!@C',
+    'Boronic Acid Ester aliphatic': '[B;D3;x2;z1]([O;D2;x1])([O;D2;x1])-;!@[C;x1;z1]',
+    'Boronic Acid Ester aromatic': '[B;D3;x2;z1]([O;D2;x1])([O;D2;x1])-;!@[C;a]',
+    'Trifluoroborate': '[B;D4;x3;z1;-](F)(F)(F)',
+
+    'Thiol aliphatic': '[S;D1;x0;z1][C;x1;z1]',
+    'Thiol aromatic': '[S;D1;x0;z1][C;a]',
+
+    'Hydrazine aromatic': '[N;D1;x1;z1][N;D2;x1;z1][C;a]',
+    'Hydrazine aliphatic': '[N;D1;x1;z1][N;D2;x1;z1][C;x1;z1]',
+
+    'Isocyanate': '[O;D1;z2;x0]=[C;D2;x2;z3]=[N;D2;x0;z2]',
+    'Isothiocyanate': '[S;D1;z2;x0]=[C;D2;x2;z3]=[N;D2;x0;z2]',
+    'Nitrile': '[N;D1;z3;x0]#[C;D2;x1]',
+    'Isonitrile': '[C-;D1;x1;z3]#[N+;D2;x0]',
+    'Sulfonyl Halide': '[S;D4;z3;x3]([F,Cl,Br,I;D1])(=O)=O',
+    'Lactam': '[O;D1;x0;z2]=[C;D3;x2](-;@[N;x0;z1]-;@[C;x1;z1])[C;x0;z1]',
+    'Cyclic Anhydride': '[O;D1;x0;z2]=[C;D3;x2;z2;r4,r5,r6,r7,r8][O;D2;x0][C;D3;x2;z2]=O'
+}
+
+_smarts = {n.lower().replace(' ', '_'): smarts(s) for n, s in _groups.items()}
+__all__ = list(_smarts)
+
+
+def __getattr__(name):
+    try:
+        return _smarts[name]
+    except KeyError:
+        raise AttributeError
+
+
+def __dir__():
+    return __all__