Request to add the new reaction templates

chython/reactor/reactions/_DIBAL_reduction.py

@@ -0,0 +1,53 @@
+# -*- coding: utf-8 -*-
+#
+#  Copyright 2022-2024 Ramil Nugmanov <nougmanoff@protonmail.com>
+#  Copyright 2023 Timur Gimadiev <timur.gimadiev@gmail.com>
+#  Copyright 2025 Balasubramaniyan Sakthivel <sakthivelbala.s@gmail.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/>.
+#
+
+
+template = {
+    'name': 'DIBAL_Reduction',
+    'description': 'Reducing esters and nitriles to aldehydes using DIBAL-H',
+    'templates': [
+        # Template 1: Ester and DIBAL-H to CHO
+        {
+            'A': [
+                # Ester
+                '[O;x0;z2;M]=[C;D3;x2;z2:1][O;D2;x0;z1:2]'
+            ],
+            'product': '[A:1]',
+            'alerts': [],
+            'ufe': {
+                'A': 2
+            }
+        },
+        # Template 2: Nitriles and DIBAL-H to CHO
+       {
+            'A': [
+                # Nitrile
+                '[N;D1;z3;x0:2]#[C;D2;x1;z3:1]'
+            ],        
+            'product': '[A:1]=[O]',
+            'alerts': [],
+            'ufe': {
+                'A': 2
+            }
+        },  
+    ],
+    'alerts': []
+}

chython/reactor/reactions/__init__.py

@@ -29,6 +29,57 @@
 from ._sonogashira import template as songashira_template
 from ._sulfonamidation import template as sulfonamidation_template
 from ._suzuki_miyaura import template as suzuki_miyaura_template
+from ._aza_cope_mannich import template as aza_cope_mannich_template
+from ._DIBAL_reduction import template as DIBAL_reduction_template
+from ._diels_alder import template as diels_alder_template
+from ._evans_aldol import template as evans_aldol_template
+from ._biginelli import template as biginelli_template
+from ._swern_oxidation import template as swern_oxidation_template
+from ._ugi import template as ugi_template
+from ._bucherer_bergs import template as bucherer_bergs_template
+from ._hantzsch import template as hantzsch_template
+from ._gilman import template as gilman_template
+from ._heck import template as heck_template
+from ._horner_wadsworth_emmons import template as horner_wadsworth_emmons_template
+from ._nazarov_cyclization import template as nazarov_cyclization_template
+from ._kabachnik_fields import template as kabachnik_fields_template
+from ._mannich import template as mannich_template
+from ._passerini import template as passerini_template
+from ._pauson_khand import template as pauson_khand_template
+from ._robinson_annulation import template as robinson_annulation_template
+from ._gewald import template as gewald_template
+from ._petasis import template as petasis_template
+from ._pfitzinger import template as pfitzinger_template
+from ._arndt_eistert import template as arndt_eistert_template
+from ._baeyer_villiger import template as baeyer_villiger_template
+from ._baeyer_mills import template as baeyer_mills_template
+from ._balz_schiemann import template as balz_schiemann_template
+from ._baylis_hillman import template as baylis_hillman_template
+from ._beckmann import template as beckmann_template
+from ._chan_lam import template as chan_lam_template
+from ._click import template as click_template
+from ._doebner_miller import template as doebner_miller_template
+from ._eschenmoser import template as eschenmoser_template
+from ._ester_hydrolysis import template as ester_hydrolysis_template
+from ._fischer_indole import template as fischer_indole_template
+from ._gould_jacobs import template as gould_jacobs_template
+from ._hayashi_miyaura import template as hayashi_miyaura_template
+from ._knorr_quinoline import template as knorr_quinoline_template
+from ._olefin_metathesis import template as olefin_metathesis_template
+from ._paal_knorr_pyrrole import template as paal_knorr_pyrrole_template
+from ._perkin import template as perkin_template
+from ._pictet_spengler import template as pictet_spengler_template
+from ._prins_pinacol import template as prins_pinacol_template
+from ._reformatsky import template as reformatsky_template
+from ._riley_oxidations import template as riley_oxidations_template
+from ._sandmayer import template as sandmayer_template
+from ._schotten_baumann import template as schotten_baumann_template
+from ._stille_coupling import template as stille_coupling_template
+from ._ullmann import template as ullmann_template
+from ._wittig import template as wittig_template
+from ._wolff_rearrangement import template as wolff_rearrangement_template
+from ._wurtz import template as wurtz_template
+from ._wurtz_fittig import template as wurtz_fittig_template
 from ..reactor import Reactor, fix_mapping_overlap
 from ... import smarts, ReactionContainer, MoleculeContainer
 

chython/reactor/reactions/_arndt_eistert.py

@@ -0,0 +1,47 @@
+# -*- coding: utf-8 -*-
+#
+#  Copyright 2022-2024 Ramil Nugmanov <nougmanoff@protonmail.com>
+#  Copyright 2023 Timur Gimadiev <timur.gimadiev@gmail.com>
+#  Copyright 2025 Balasubramaniyan Sakthivel <sakthivelbala.s@gmail.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/>.
+#
+
+
+template = {
+    'name' : 'Arndt-Eistert Synthesis',
+    'description': 'Formation of homologated carboxylic acids by reaction of the activated carboxylic acids with diazomethane',
+    'templates': [
+        {
+            'A': [
+                # Ar-COOH
+                '[O;x0;z2;M]=[C;x2:1]([O;M])[C;a:2]',
+                # Alk-COOH
+                '[O;x0;z2;M]=[C;x2:1]([O;M])[C;z1:2]'
+            ],
+            'B': [
+                # CH2N2
+                '[C;x1;z2:3]=[N+;x1:4]=[N-;x1:5]'
+            ],
+            'product': '[A:2][A:3][A:1]',
+            'alerts': [],
+            'ufe': {
+                'A': 1,
+                'B': '[A:4][A:5]'
+            }
+        }
+    ],
+    'alerts':[]
+}

chython/reactor/reactions/_aza_cope_mannich.py

@@ -0,0 +1,64 @@
+# -*- coding: utf-8 -*-
+#
+#  Copyright 2022-2024 Ramil Nugmanov <nougmanoff@protonmail.com>
+#  Copyright 2023 Timur Gimadiev <timur.gimadiev@gmail.com>
+#  Copyright 2025 Balasubramaniyan Sakthivel <sakthivelbala.s@gmail.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/>.
+#
+
+
+template = {
+    'name': 'Aza-Cope Mannich Reaction',
+    'description': 'Sigmatropic rearrangement of an unsaturated iminium cation to complex cyclic molecules',
+    'templates' : [
+        #Three Aza-Cope Mannich Reaction
+        {
+            'A': [
+                # Alk#Alk-Alk-N
+                '[C;x0,x1;z2:1]=[C;x1;z2:2]([O;M])[C;x1;z1:3][N;z1:4][C;x1;z1;M][C;x0;z1;M][C;z3:5]#[C;z3:6]',
+                # Ar-N
+                '[C;x0,x1;z2:1]=[C;x1;z2:2]([O;M])[C;x1;z1:3][N;z1:4][C;x1;z1;M][C;a;M]:[C;a;M][C;z3:5]#[C;z3:6]',
+                # Alk#Alk-Alk-Alk-N
+                '[C;x0,x1;z2:1]=[C;x1;z2:2]([O;M])[C;x1;z1:3][N;z1:4][C;z1;M][C;z1;M][C;z1;M][C;z3:5]#[C;z3:6]'
+            ],
+            'product': '[A:1]1=[A:2][A:3][A:5]([A:4])[A:6]1',
+            'alerts': [],
+            'ufe': {
+                'A': '[A:1][A:6]'
+            }
+        },
+        #Two Aza-Cope Mannich Reaction
+        {
+            'A': [
+                # Iminium
+                '[N;D2;x0;z1:1][C;x1;z1:2][C;x1;z1:3]([O:4])[C;D2;x0;z2:5]=[C;x0;z2:6]'
+            ],
+            'B': [
+                # Formaldehyde
+                '[O;z2;x0:7]=[C;D1;x1;z2:8]',
+                # 2,2-dimethoxypropane
+                '[O;z1:7]-[C;x2;z1:8]-[O;z1:9]'
+            ],
+            'product': '[A:1]1[A:2][A:5]([A:3]=[A:4])[A:6][A:8]1',
+            'alerts': [],
+            'ufe': {
+                'A': '[A:1][A:6]',
+                'B': '[A:7][A:9]'
+            }
+        }
+    ],
+    'alerts': []
+}

chython/reactor/reactions/_baeyer_mills.py

@@ -0,0 +1,45 @@
+# -*- coding: utf-8 -*-
+#
+#  Copyright 2022-2024 Ramil Nugmanov <nougmanoff@protonmail.com>
+#  Copyright 2023 Timur Gimadiev <timur.gimadiev@gmail.com>
+#  Copyright 2025 Balasubramaniyan Sakthivel <sakthivelbala.s@gmail.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/>.
+#
+
+
+template = {
+    'name' : 'Baeyer-Mills Reaction',
+    'description': 'Aniline and a nitrosoarene to produce azobenzenes',
+    'templates': [
+        {
+            'A': [
+                # Ar-N=O
+                '[N;D2;x1;z2:1](=[O;x1;z2:2])[C;a;M]'
+            ],
+            'B': [
+                # Ar-NH2
+                '[N;D1;x0;z1:3][C;a;M]'
+            ],
+            'product': '[A:1]=[A:3]',
+            'alerts': [],
+            'ufe':{
+                'A':'[A:1][A:2]',
+                'B': '[A:3][At;M]'
+                }
+            }
+        ],
+        'alerts' : []
+}

chython/reactor/reactions/_baeyer_villiger.py

@@ -0,0 +1,56 @@
+# -*- coding: utf-8 -*-
+#
+#  Copyright 2022-2024 Ramil Nugmanov <nougmanoff@protonmail.com>
+#  Copyright 2023 Timur Gimadiev <timur.gimadiev@gmail.com>
+#  Copyright 2025 Balasubramaniyan Sakthivel <sakthivelbala.s@gmail.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/>.
+#
+
+
+template = {
+    'name': 'Baeyer-Villiger Oxidation',
+    'description': 'Ketones into esters using mCPBA or H2O2',
+    'templates': [
+        {
+            'A': [
+                # Ar-Ketone
+                '[O;z2;x0;M]=[C;D3;x1;z2:1]([C;z1;M])[C;a:2]',
+                '[O;z2;x0;M]=[C;D3;x1;z2:1]([C;a;M])[C;z1:2]',
+                # Alk-Ketone
+                '[O;z2;x0;M]=[C;D3;x1;z2:1]([C;z1;M])[C;D3,D2;z1,z2:2]',
+                # Alk-CHO
+                '[O;z2;x0;M]=[C;D2;x1;z2:1][C;D3,D2;x0,x1,x2;z1,z2:2]',
+                # Ar-CHO
+                '[O;z2;x0;M]=[C;D2;x1;z2:1][C;a:2]',
+                # Cyclic-Ketone
+                '[O;z2;x0;M]=[C;D3;x1;z2:1]([C;D2;x0,x1;z1;r4,r5,r6,r7,r8;M])[C;D2,D3;x0;z1;r4,r5,r6,r7,r8:2]'
+            ],
+            'B': [
+                # mCPBA
+                '[O;D1;x1;z1:3][O;D2;x1;z1:4][C;x2;z2:5](=[O;z2;x0:6])[C;a:7]',
+                # H2O2
+                '[O;D1:3][O;D1:4]'
+            ],
+            'product': '[A:2][A:3][A:1]',
+            'alerts': [],
+            'ufe': {
+                'A': 1,
+                'B': '[A:5][A:5][A:6]'
+            }
+        }
+    ],
+    'alerts':[]
+}

chython/reactor/reactions/_balz_schiemann.py

@@ -0,0 +1,45 @@
+# -*- coding: utf-8 -*-
+#
+#  Copyright 2022-2024 Ramil Nugmanov <nougmanoff@protonmail.com>
+#  Copyright 2023 Timur Gimadiev <timur.gimadiev@gmail.com>
+#  Copyright 2025 Balasubramaniyan Sakthivel <sakthivelbala.s@gmail.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/>.
+#
+
+
+template = {
+    'name': 'Balz-Schiemann Reaction',
+    'description': 'Fluoroarene formation from anilines using HBF4',
+    'templates': [
+        {
+            'A': [
+                # Ar-NH2
+                '[N;D1;x0;z1:1][C;a:2]'
+            ],
+            'B': [
+                # HBF4
+                '[H+:3].[B-;D4;x4;z1:4][F:5]'
+            ],
+            'product': '[A:2]-[A:5]',
+            'alerts': [],
+            'ufe': {
+                'A': 1,
+                'B': '[A:3][A:4]'
+            }
+        }
+    ],
+    'alerts': []
+}