chython 2.4__cp312-cp312-win_amd64.whl

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Files changed (171) hide show
  1. chython/__init__.py +31 -0
  2. chython/_functions.py +69 -0
  3. chython/algorithms/__init__.py +18 -0
  4. chython/algorithms/_isomorphism.cp312-win_amd64.pyd +0 -0
  5. chython/algorithms/_isomorphism.pyx +189 -0
  6. chython/algorithms/aromatics/__init__.py +27 -0
  7. chython/algorithms/aromatics/_rules.py +124 -0
  8. chython/algorithms/aromatics/kekule.py +530 -0
  9. chython/algorithms/aromatics/test/__init__.py +18 -0
  10. chython/algorithms/aromatics/test/test_kekule.py +160 -0
  11. chython/algorithms/aromatics/test/test_thiele.py +263 -0
  12. chython/algorithms/aromatics/thiele.py +226 -0
  13. chython/algorithms/calculate2d/__init__.py +23 -0
  14. chython/algorithms/calculate2d/clean2d.js +1 -0
  15. chython/algorithms/calculate2d/molecule.py +149 -0
  16. chython/algorithms/calculate2d/reaction.py +80 -0
  17. chython/algorithms/depict.py +523 -0
  18. chython/algorithms/fingerprints/__init__.py +48 -0
  19. chython/algorithms/fingerprints/linear.py +208 -0
  20. chython/algorithms/fingerprints/morgan.py +137 -0
  21. chython/algorithms/fingerprints/test/__init__.py +18 -0
  22. chython/algorithms/fingerprints/test/test_linear.py +127 -0
  23. chython/algorithms/fingerprints/test/test_morgan.py +79 -0
  24. chython/algorithms/isomorphism.py +667 -0
  25. chython/algorithms/mapping/__init__.py +28 -0
  26. chython/algorithms/mapping/_groups.py +94 -0
  27. chython/algorithms/mapping/_reactions.py +72 -0
  28. chython/algorithms/mapping/attention.py +216 -0
  29. chython/algorithms/mapping/fixmapper.py +84 -0
  30. chython/algorithms/mapping/groups.py +137 -0
  31. chython/algorithms/mcs.py +202 -0
  32. chython/algorithms/morgan.py +82 -0
  33. chython/algorithms/rings.py +551 -0
  34. chython/algorithms/smiles.py +556 -0
  35. chython/algorithms/standardize/__init__.py +30 -0
  36. chython/algorithms/standardize/_charged.py +115 -0
  37. chython/algorithms/standardize/_groups.py +926 -0
  38. chython/algorithms/standardize/_metal_organics.py +189 -0
  39. chython/algorithms/standardize/_reagents.py +44 -0
  40. chython/algorithms/standardize/_salts.py +68 -0
  41. chython/algorithms/standardize/molecule.py +479 -0
  42. chython/algorithms/standardize/reaction.py +429 -0
  43. chython/algorithms/standardize/resonance.py +196 -0
  44. chython/algorithms/standardize/salts.py +128 -0
  45. chython/algorithms/standardize/saturation.py +378 -0
  46. chython/algorithms/standardize/test/__init__.py +18 -0
  47. chython/algorithms/standardize/test/test_groups.py +118 -0
  48. chython/algorithms/stereo.py +1222 -0
  49. chython/algorithms/tautomers/__init__.py +171 -0
  50. chython/algorithms/tautomers/_acid.py +59 -0
  51. chython/algorithms/tautomers/_base.py +116 -0
  52. chython/algorithms/tautomers/_keto_enol.py +107 -0
  53. chython/algorithms/tautomers/acid_base.py +214 -0
  54. chython/algorithms/tautomers/heteroarenes.py +108 -0
  55. chython/algorithms/tautomers/keto_enol.py +148 -0
  56. chython/algorithms/tautomers/test/__init__.py +18 -0
  57. chython/algorithms/tautomers/test/test_tautomers.py +80 -0
  58. chython/algorithms/test/__init__.py +18 -0
  59. chython/algorithms/test/test_isomorphism.py +58 -0
  60. chython/algorithms/test/test_smiles.py +76 -0
  61. chython/algorithms/x3dom.py +355 -0
  62. chython/containers/__init__.py +43 -0
  63. chython/containers/_pack_v2.cp312-win_amd64.pyd +0 -0
  64. chython/containers/_pack_v2.pyx +271 -0
  65. chython/containers/_unpack_v0v2.cp312-win_amd64.pyd +0 -0
  66. chython/containers/_unpack_v0v2.pyx +300 -0
  67. chython/containers/bonds.py +255 -0
  68. chython/containers/cgr.py +115 -0
  69. chython/containers/graph.py +200 -0
  70. chython/containers/molecule.py +695 -0
  71. chython/containers/query.py +66 -0
  72. chython/containers/reaction.py +324 -0
  73. chython/exceptions.py +114 -0
  74. chython/files/MRVrw.py +523 -0
  75. chython/files/PDBrw.py +257 -0
  76. chython/files/RDFrw.py +298 -0
  77. chython/files/SDFrw.py +221 -0
  78. chython/files/__init__.py +29 -0
  79. chython/files/_convert.py +207 -0
  80. chython/files/_mapping.py +117 -0
  81. chython/files/_xyz.cp312-win_amd64.pyd +0 -0
  82. chython/files/_xyz.pyx +74 -0
  83. chython/files/daylight/__init__.py +24 -0
  84. chython/files/daylight/parser.py +157 -0
  85. chython/files/daylight/smarts.py +107 -0
  86. chython/files/daylight/smiles.py +245 -0
  87. chython/files/daylight/test/__init__.py +18 -0
  88. chython/files/daylight/test/test_daylight_smarts.py +289 -0
  89. chython/files/daylight/test/test_daylight_smiles.py +101 -0
  90. chython/files/daylight/test/test_parser.py +118 -0
  91. chython/files/daylight/test/test_tokenize.py +77 -0
  92. chython/files/daylight/tokenize.py +376 -0
  93. chython/files/libinchi/__init__.py +22 -0
  94. chython/files/libinchi/libinchi.dll +0 -0
  95. chython/files/libinchi/wrapper.py +555 -0
  96. chython/files/mdl/__init__.py +25 -0
  97. chython/files/mdl/emol.py +209 -0
  98. chython/files/mdl/erxn.py +67 -0
  99. chython/files/mdl/mol.py +144 -0
  100. chython/files/mdl/read.py +225 -0
  101. chython/files/mdl/rxn.py +67 -0
  102. chython/files/mdl/stereo.py +63 -0
  103. chython/files/mdl/write.py +165 -0
  104. chython/files/xyz.py +78 -0
  105. chython/periodictable/__init__.py +69 -0
  106. chython/periodictable/base/__init__.py +25 -0
  107. chython/periodictable/base/dynamic.py +149 -0
  108. chython/periodictable/base/element.py +452 -0
  109. chython/periodictable/base/groups.py +90 -0
  110. chython/periodictable/base/periods.py +46 -0
  111. chython/periodictable/base/query.py +473 -0
  112. chython/periodictable/base/vector.py +119 -0
  113. chython/periodictable/groupI.py +252 -0
  114. chython/periodictable/groupII.py +223 -0
  115. chython/periodictable/groupIII.py +1154 -0
  116. chython/periodictable/groupIV.py +210 -0
  117. chython/periodictable/groupIX.py +196 -0
  118. chython/periodictable/groupV.py +192 -0
  119. chython/periodictable/groupVI.py +183 -0
  120. chython/periodictable/groupVII.py +162 -0
  121. chython/periodictable/groupVIII.py +161 -0
  122. chython/periodictable/groupX.py +166 -0
  123. chython/periodictable/groupXI.py +164 -0
  124. chython/periodictable/groupXII.py +158 -0
  125. chython/periodictable/groupXIII.py +239 -0
  126. chython/periodictable/groupXIV.py +262 -0
  127. chython/periodictable/groupXV.py +276 -0
  128. chython/periodictable/groupXVI.py +457 -0
  129. chython/periodictable/groupXVII.py +324 -0
  130. chython/periodictable/groupXVIII.py +260 -0
  131. chython/reactor/__init__.py +24 -0
  132. chython/reactor/base.py +212 -0
  133. chython/reactor/deprotection.py +565 -0
  134. chython/reactor/groups.py +128 -0
  135. chython/reactor/reactions/__init__.py +157 -0
  136. chython/reactor/reactions/_amidation.py +58 -0
  137. chython/reactor/reactions/_amine_isocyanate.py +52 -0
  138. chython/reactor/reactions/_buchwald_hartwig.py +50 -0
  139. chython/reactor/reactions/_esterification.py +49 -0
  140. chython/reactor/reactions/_macmillan.py +43 -0
  141. chython/reactor/reactions/_reductive_amination.py +50 -0
  142. chython/reactor/reactions/_sonogashira.py +49 -0
  143. chython/reactor/reactions/_sulfonamidation.py +52 -0
  144. chython/reactor/reactions/_suzuki_miyaura.py +88 -0
  145. chython/reactor/reactions/ufe.py +99 -0
  146. chython/reactor/reactor.py +170 -0
  147. chython/reactor/retro/__init__.py +77 -0
  148. chython/reactor/retro/_amidation.py +39 -0
  149. chython/reactor/retro/_aryl_amination.py +32 -0
  150. chython/reactor/retro/_mitsunobu.py +49 -0
  151. chython/reactor/retro/_sonogashira.py +49 -0
  152. chython/reactor/retro/_suzuki_miyaura.py +54 -0
  153. chython/reactor/scaffold.py +122 -0
  154. chython/reactor/test/__init__.py +18 -0
  155. chython/reactor/test/test_deprotection.py +57 -0
  156. chython/reactor/test/test_reactor.py +40 -0
  157. chython/reactor/test/test_scaffold.py +57 -0
  158. chython/reactor/test/test_transformer.py +40 -0
  159. chython/reactor/transformer.py +62 -0
  160. chython/utils/__init__.py +57 -0
  161. chython/utils/free_wilson.py +114 -0
  162. chython/utils/grid.py +130 -0
  163. chython/utils/rdkit.py +165 -0
  164. chython/utils/retro.py +139 -0
  165. chython/utils/svg.py +57 -0
  166. chython/utils/test/__init__.py +18 -0
  167. chython/utils/test/test_rdkit.py +71 -0
  168. chython-2.4.dist-info/LICENSE +165 -0
  169. chython-2.4.dist-info/METADATA +101 -0
  170. chython-2.4.dist-info/RECORD +171 -0
  171. chython-2.4.dist-info/WHEEL +4 -0
chython/algorithms/standardize/_charged.py ADDED
@@ -0,0 +1,115 @@
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+ # -*- coding: utf-8 -*-
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+ #
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+ # Copyright 2021-2023 Ramil Nugmanov <nougmanoff@protonmail.com>
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+ # This file is part of chython.
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+ #
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+ # chython is free software; you can redistribute it and/or modify
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+ # it under the terms of the GNU Lesser General Public License as published by
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+ # the Free Software Foundation; either version 3 of the License, or
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+ # (at your option) any later version.
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+ #
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+ # This program is distributed in the hope that it will be useful,
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+ # but WITHOUT ANY WARRANTY; without even the implied warranty of
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+ # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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+ # GNU Lesser General Public License for more details.
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+ #
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+ # You should have received a copy of the GNU Lesser General Public License
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+ # along with this program; if not, see <https://www.gnu.org/licenses/>.
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+ #
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+ from lazy_object_proxy import Proxy
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+
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+
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+ def _fixed_rules():
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+ """
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+ Rules working without Morgan.
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+ These rules are used for charge canonization for heterocycles
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+ """
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+ from ... import smarts
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+
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+ rules = []
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+
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+ # N1C=CN2[NH+]=CC=C12>>N1C=CC2=[NH+]C=CN12
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+ # first and second atoms are ryrrole-like
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+ # second atom will be charged
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+ # if fix is True, third atom will be uncharged else first
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+ q = smarts('[N;a;r5;+:1]:1:[N;r5:3]:2:[C;r5](:[N;r5:2]:[C;r5]:[C;r5]:2):[C;r5]:[C;r5]:1')
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+ rules.append((q, False))
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+
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+ # N1C=C[N+]2=C1C=CN2>>N1C=CC2=[NH+]C=CN12
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+ q = smarts('[N;a;r5;+:3]:1:2:[N;r5:1]:[C;r5]:[C;r5]:[C;r5]:1:[N;r5:2]:[C;r5]:[C;r5]:2')
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+ rules.append((q, True))
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+
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+ # N1C=C2C=CN[N+]2=C1>>N1C=CC2=C[NH+]=CN12
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+ q = smarts('[N;a;r5;+:3]:1:2:[N;r5:1]:[C;r5]:[C;r5]:[C;r5]:1:[C;r5]:[N;r5:2]:[C;r5]:2')
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+ rules.append((q, True))
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+
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+ # N1C=C2NC=C[N+]2=C1>>N1C=CN2C=[NH+]C=C12
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+ q = smarts('[N;a;r5;+:3]:1:2:[C;r5](:[N;r5:1]:[C;r5]:[C;r5]:1):[C;r5]:[N;r5:2]:[C;r5]:2')
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+ rules.append((q, True))
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+
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+ # N1C2=[NH+]C=CC2=CC=C1>>N1C=CC2=CC=C[NH+]=C12
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+ q = smarts('[N;a;r5;+:1]:1:[C;r6]:2:[N;r6:2]:[C;r6]:[C;r6]:[C;r6]:[C;r5]:2:[C;r5]:[C;r5]:1')
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+ rules.append((q, False))
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+
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+ # N1C=C2C(=CC=[NH+]2)C=C1>>N1C=CC2=CC=[NH+]C=C12
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+ q = smarts('[N;a;r5;+:1]:1:[C;r6]:2:[C;r6]:[N;r6:2]:[C;r6]:[C;r6]:[C;r5]:2:[C;r5]:[C;r5]:1')
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+ rules.append((q, False))
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+
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+ # C1=CC=2C(=[NH+]1)C=CNC=2>>N1C=CC2=C[NH+]=CC=C12
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+ q = smarts('[N;a;r5;+:1]:1:[C;r6]:2:[C;r6]:[C;r6]:[N;r6:2]:[C;r6]:[C;r5]:2:[C;r5]:[C;r5]:1')
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+ rules.append((q, False))
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+
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+ # C=1C=[NH+]C=2C=1NC=CC=2>>N1C=CC2=[NH+]C=CC=C12
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+ q = smarts('[N;a;r5;+:1]:1:[C;r6]:2:[C;r6]:[C;r6]:[C;r6]:[N;r6:2]:[C;r5]:2:[C;r5]:[C;r5]:1')
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+ rules.append((q, False))
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+
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+ # C1=2C=[NH+]C=C1NC=CC=2>>N1C=C2C=CC=[NH+]C2=C1
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+ q = smarts('[N;a;r5;+:1]:1:[C;r5]:[C;r6]:2:[N;r6:2]:[C;r6]:[C;r6]:[C;r6]:[C;r5]:2:[C;r5]:1')
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+ rules.append((q, False))
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+
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+ # C1=2C=CNC=C1C=[NH+]C=2>>N1C=C2C=C[NH+]=CC2=C1
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+ q = smarts('[N;a;r5;+:1]:1:[C;r5]:[C;r6]:2:[C;r6]:[N;r6:2]:[C;r6]:[C;r6]:[C;r5]:2:[C;r5]:1')
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+ rules.append((q, False))
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+ return rules
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+
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+
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+ def _morgan_rules():
77
+ """
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+ Rules working with Morgan.
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+ These rules are for charge canonization
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+ """
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+ from ... import smarts
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+
83
+ rules = []
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+
85
+ # N1C=CC2=CC=[NH+]N12
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+ q = smarts('[N;a;r5;+:1]:1:[N;D3]:2:[N;r5:2]:[C;r5]:[C;r5]:[C;D3]:2:[C;r5]:[C;r5]:1')
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+ rules.append((q, False))
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+
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+ # N1C=CC2=[N+]1NC=C2
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+ q = smarts('[N;a;D3;r5;+:3]:1:2:[N;r5:1]:[C;r5]:[C;r5]:[C;D3]:1:[C;r5]:[C;r5]:[N;r5:2]:2')
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+ rules.append((q, True))
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+
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+ # N1C=CN2C=C[NH+]=C12
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+ q = smarts('[N;a;r5;+:1]:1:[C;D3]:2:[N;r5:2]:[C;r5]:[C;r5]:[N;D3]:2:[C;r5]:[C;r5]:1')
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+ rules.append((q, False))
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+
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+ # N1C=C[N+]2=C1NC=C2
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+ q = smarts('[N;a;D3;r5;+:3]:1:2:[C;D3](:[N;r5:1]:[C;r5]:[C;r5]:1):[N;r5:2]:[C;r5]:[C;r5]:2')
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+ rules.append((q, True))
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+
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+ # imidazole
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+ q = smarts('[N;a;r5;+:1]:1:[C;r5]:[N;r5:2]:[C;r5]:[C;r5]:1')
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+ rules.append((q, False))
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+
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+ # pyrazole+
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+ q = smarts('[N;a;r5;+:1]:1:[N;r5:2]:[C;r5]:[C;r5]:[C;r5]:1')
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+ rules.append((q, False))
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+ return rules
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+
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+
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+ fixed_rules = Proxy(_fixed_rules)
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+ morgan_rules = Proxy(_morgan_rules)
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+
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+
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+ __all__ = ['fixed_rules', 'morgan_rules']