diff --git a/.gitignore b/.gitignore index d829c166..9d3c42e7 100644 --- a/.gitignore +++ b/.gitignore @@ -44,9 +44,6 @@ rmgweb/media/rmg/tools/* .pydevproject .settings/* -# WSGI -apache/django.wsgi - # VS Code related files .history/* diff --git a/environment.yml b/environment.yml index 8678e419..529b598e 100644 --- a/environment.yml +++ b/environment.yml @@ -1,19 +1,19 @@ # First, install a conda environment with RMG-Py. # Then, update the environment using the constraints in this environment file. -name: rmg_env +name: rmg_website channels: - - rmg - conda-forge - - cantera + - simonabuzzi - fhvermei dependencies: - - docutils - - django =2.2 - - lxml + - django==4.2 - pip - pip: - - git+https://github.com/bp-kelley/descriptastorus@2.5.0 - - python >=3.7 - - solprop_ml >=1.2 + - git+https://github.com/bp-kelley/descriptastorus + - simonabuzzi::solprop_ml_mix + - wandb # Required for solprop_ml_mix + - python>=3.9 - xlsxwriter + - fhvermei::chemprop_solvation + - cantera==2.6.0* diff --git a/rmgweb/database/migrations/0014_alter_solubilitysearch_id_alter_solutesearch_id_and_more.py b/rmgweb/database/migrations/0014_alter_solubilitysearch_id_alter_solutesearch_id_and_more.py new file mode 100644 index 00000000..cc9b4d16 --- /dev/null +++ b/rmgweb/database/migrations/0014_alter_solubilitysearch_id_alter_solutesearch_id_and_more.py @@ -0,0 +1,588 @@ +# Generated by Django 4.2.23 on 2025-07-03 15:10 + +from django.db import migrations, models + + +class Migration(migrations.Migration): + + dependencies = [ + ("database", "0013_solubilitysearch"), + ] + + operations = [ + migrations.AlterField( + model_name="solubilitysearch", + name="id", + field=models.BigAutoField( + auto_created=True, primary_key=True, serialize=False, verbose_name="ID" + ), + ), + migrations.AlterField( + model_name="solutesearch", + name="id", + field=models.BigAutoField( + auto_created=True, primary_key=True, serialize=False, verbose_name="ID" + ), + ), + migrations.AlterField( + model_name="solutesearch", + name="solvent", + field=models.CharField( + blank=True, + choices=[ + ("water", "1. water"), + ("1-octanol", "2. 1-octanol"), + ("benzene", "3. benzene"), + ("cyclohexane", "4. cyclohexane"), + ("dibutylether", "5. dibutylether"), + ("octane", "6. octane"), + ("butanol", "7. butanol"), + ("carbontet", "8. carbontet"), + ("chloroform", "9. chloroform"), + ("decane", "10. decane"), + ("1,1-dichloroethane", "11. 1,1-dichloroethane"), + ("dimethylformamide", "12. dimethylformamide"), + ("dimethylsulfoxide", "13. dimethylsulfoxide"), + ("dodecane", "14. dodecane"), + ("ethanol", "15. ethanol"), + ("heptane", "16. heptane"), + ("hexadecane", "17. hexadecane"), + ("hexane", "18. hexane"), + ("isooctane", "19. isooctane"), + ("nonane", "20. nonane"), + ("pentane", "21. pentane"), + ("toluene", "22. toluene"), + ("undecane", "23. undecane"), + ("acetonitrile", "24. acetonitrile"), + ("ethylacetate", "25. ethylacetate"), + ("methanol", "26. methanol"), + ("methanol_50_water_50", "27. methanol_50_water_50"), + ("acetonitrile_40_water_60", "28. acetonitrile_40_water_60"), + ("acetonitrile_60_water_40", "29. acetonitrile_60_water_40"), + ("2-methylpyridine", "30. 2-methylpyridine"), + ("4-methylpentan-2-one", "31. 4-methylpentan-2-one"), + ("acetic acid", "32. acetic acid"), + ("1-phenylethanone", "33. 1-phenylethanone"), + ("aniline", "34. aniline"), + ("anisole", "35. anisole"), + ("benzonitrile", "36. benzonitrile"), + ("phenylmethanol", "37. phenylmethanol"), + ("bromobenzene", "38. bromobenzene"), + ("bromoethane", "39. bromoethane"), + ("bromoform", "40. bromoform"), + ("butan-2-one", "41. butan-2-one"), + ("butyl acetate", "42. butyl acetate"), + ("butylbenzene", "43. butylbenzene"), + ("carbon disulfide", "44. carbon disulfide"), + ("chlorobenzene", "45. chlorobenzene"), + ("1-chlorohexane", "46. 1-chlorohexane"), + ("cyclohexanone", "47. cyclohexanone"), + ("decalin", "48. decalin"), + ("decan-1-ol", "49. decan-1-ol"), + ("1,1-dibromoethane", "50. 1,1-dibromoethane"), + ("1,2-dichloroethane", "51. 1,2-dichloroethane"), + ("ethoxyethane", "52. ethoxyethane"), + ("2-propan-2-yloxypropane", "53. 2-propan-2-yloxypropane"), + ("N,N-dimethylacetamide", "54. N,N-dimethylacetamide"), + ("ethoxybenzene", "55. ethoxybenzene"), + ("ethylbenzene", "56. ethylbenzene"), + ("fluorobenzene", "57. fluorobenzene"), + ("heptan-1-ol", "58. heptan-1-ol"), + ("1-iodohexadecane", "59. 1-iodohexadecane"), + ("hexan-1-ol", "60. hexan-1-ol"), + ("iodobenzene", "61. iodobenzene"), + ("2-methylpropan-1-ol", "62. 2-methylpropan-1-ol"), + ("propan-2-ol", "63. propan-2-ol"), + ("cumene", "64. cumene"), + ("3-methylphenol", "65. 3-methylphenol"), + ("2-methoxyethanol", "66. 2-methoxyethanol"), + ("dichloromethane", "67. dichloromethane"), + ("N-methylformamide", "68. N-methylformamide"), + ("nitrobenzene", "69. nitrobenzene"), + ("1-nitroethane", "70. 1-nitroethane"), + ("nitromethane", "71. nitromethane"), + ("nonan-1-ol", "72. nonan-1-ol"), + ("1,2-dichlorobenzene", "73. 1,2-dichlorobenzene"), + ("pentadecane", "74. pentadecane"), + ("pentan-1-ol", "75. pentan-1-ol"), + ("hexafluorobenzene", "76. hexafluorobenzene"), + ("propan-1-ol", "77. propan-1-ol"), + ("pyridine", "78. pyridine"), + ("butan-2-ol", "79. butan-2-ol"), + ("tert-butylbenzene", "80. tert-butylbenzene"), + ("1,1,2,2-tetrachloroethene", "81. 1,1,2,2-tetrachloroethene"), + ("c", "82. c"), + ( + "1,2,3,4-tetrahydronaphthalene", + "83. 1,2,3,4-tetrahydronaphthalene", + ), + ("tributyl phosphate", "84. tributyl phosphate"), + ("N,N-diethylethanamine", "85. N,N-diethylethanamine"), + ("1,2,4-trimethylbenzene", "86. 1,2,4-trimethylbenzene"), + ("1,4-xylene", "87. 1,4-xylene"), + ("2-methylpropan-2-ol", "88. 2-methylpropan-2-ol"), + ("3-methylbutan-1-ol", "89. 3-methylbutan-1-ol"), + ("undecan-1-ol", "90. undecan-1-ol"), + ("propan-2-one", "91. propan-2-one"), + ("methyl acetate", "92. methyl acetate"), + ("propyl acetate", "93. propyl acetate"), + ("pentyl acetate", "94. pentyl acetate"), + ("2-methylbutan-2-ol", "95. 2-methylbutan-2-ol"), + ("4-methylpentan-2-ol", "96. 4-methylpentan-2-ol"), + ("2-methylpentan-1-ol", "97. 2-methylpentan-1-ol"), + ("2-ethylhexan-1-ol", "98. 2-ethylhexan-1-ol"), + ("2-methoxy-2-methylpropane", "99. 2-methoxy-2-methylpropane"), + ("dodecan-1-ol", "100. dodecan-1-ol"), + ("2-butoxyethanol", "101. 2-butoxyethanol"), + ("2-ethoxyethanol", "102. 2-ethoxyethanol"), + ("1-propoxypropane", "103. 1-propoxypropane"), + ("pentan-2-ol", "104. pentan-2-ol"), + ("2-methylbutan-1-ol", "105. 2-methylbutan-1-ol"), + ("pentan-3-ol", "106. pentan-3-ol"), + ("2-propoxyethanol", "107. 2-propoxyethanol"), + ("2-propan-2-yloxyethanol", "108. 2-propan-2-yloxyethanol"), + ("3-methoxybutan-1-ol", "109. 3-methoxybutan-1-ol"), + ("1-tert-butoxy-2-propanol", "110. 1-tert-butoxy-2-propanol"), + ("2-methoxy-2-methylbutane", "111. 2-methoxy-2-methylbutane"), + ("pentan-2-one", "112. pentan-2-one"), + ("ethyl butanoate", "113. ethyl butanoate"), + ("heptan-2-one", "114. heptan-2-one"), + ("hexyl acetate", "115. hexyl acetate"), + ("1-nitro-2-octoxybenzene", "116. 1-nitro-2-octoxybenzene"), + ("1-methylpyrrolidin-2-one", "117. 1-methylpyrrolidin-2-one"), + ("N-methylacetamide", "118. N-methylacetamide"), + ("morpholine-4-carbaldehyde", "119. morpholine-4-carbaldehyde"), + ("N,N-dibutylformamide", "120. N,N-dibutylformamide"), + ("formamide", "121. formamide"), + ("N,N-diethylacetamide", "122. N,N-diethylacetamide"), + ("1-methylpiperidin-2-one", "123. 1-methylpiperidin-2-one"), + ("N-ethylformamide", "124. N-ethylformamide"), + ("N-ethylacetamide", "125. N-ethylacetamide"), + ("triolein", "126. triolein"), + ("deca-1,9-diene", "127. deca-1,9-diene"), + ("hexadec-1-ene", "128. hexadec-1-ene"), + ("1,3-xylene", "129. 1,3-xylene"), + ("1,2-xylene", "130. 1,2-xylene"), + ("1,4-dioxane", "131. 1,4-dioxane"), + ("1-chlorobutane", "132. 1-chlorobutane"), + ("1,1,2,2-tetrabromoethane", "133. 1,1,2,2-tetrabromoethane"), + ("1,1,2,2-tetrachloroethane", "134. 1,1,2,2-tetrachloroethane"), + ("propane-1,2-diol", "135. propane-1,2-diol"), + ( + "1,3-dimethylimidazolidin-2-one", + "136. 1,3-dimethylimidazolidin-2-one", + ), + ("propane-1,3-diol", "137. propane-1,3-diol"), + ("butane-1,4-diol", "138. butane-1,4-diol"), + ("pentane-1,5-diol", "139. pentane-1,5-diol"), + ("1-bromonaphthalene", "140. 1-bromonaphthalene"), + ("1-chloronaphthalene", "141. 1-chloronaphthalene"), + ("dec-1-ene", "142. dec-1-ene"), + ("hex-1-ene", "143. hex-1-ene"), + ("1-nitropropane", "144. 1-nitropropane"), + ("oct-1-ene", "145. oct-1-ene"), + ("2-sulfanylethanol", "146. 2-sulfanylethanol"), + ( + "3-methylthiolane 1,1-dioxide", + "147. 3-methylthiolane 1,1-dioxide", + ), + ("hexanedinitrile", "148. hexanedinitrile"), + ("benzyl acetate", "149. benzyl acetate"), + ("cyclohexylcyclohexane", "150. cyclohexylcyclohexane"), + ("butanenitrile", "151. butanenitrile"), + ("cis-1,2-dichloroethene", "152. cis-1,2-dichloroethene"), + ("cis-decaline", "153. cis-decaline"), + ("cyclohexanol", "154. cyclohexanol"), + ("cyclohexylbenzene", "155. cyclohexylbenzene"), + ("cyclopentanone", "156. cyclopentanone"), + ("deuterated water", "157. deuterated water"), + ( + "bis(2-ethylhexyl) hexanedioate", + "158. bis(2-ethylhexyl) hexanedioate", + ), + ("2,2-dichloroacetic acid", "159. 2,2-dichloroacetic acid"), + ( + "diethyl benzene-1,2-dicarboxylate", + "160. diethyl benzene-1,2-dicarboxylate", + ), + ("2-(2-hydroxyethoxy)ethanol", "161. 2-(2-hydroxyethoxy)ethanol"), + ( + "1-ethoxy-2-(2-ethoxyethoxy)ethane", + "162. 1-ethoxy-2-(2-ethoxyethoxy)ethane", + ), + ( + "1-methoxy-2-(2-methoxyethoxy)ethane", + "163. 1-methoxy-2-(2-methoxyethoxy)ethane", + ), + ("diiodomethane", "164. diiodomethane"), + ( + "dibutyl benzene-1,2-dicarboxylate", + "165. dibutyl benzene-1,2-dicarboxylate", + ), + ( + "dinonyl benzene-1,2-dicarboxylate", + "166. dinonyl benzene-1,2-dicarboxylate", + ), + ("bis(2-ethylhexyl) phthalate", "167. bis(2-ethylhexyl) phthalate"), + ( + "3-(3-hydroxypropoxy)propan-1-ol", + "168. 3-(3-hydroxypropoxy)propan-1-ol", + ), + ("ethane-1,2-diol", "169. ethane-1,2-diol"), + ("furan-2-carbaldehyde", "170. furan-2-carbaldehyde"), + ("furan-2-ylmethanol", "171. furan-2-ylmethanol"), + ("oxolan-2-one", "172. oxolan-2-one"), + ("1H-indene", "173. 1H-indene"), + ("2-aminoethanol", "174. 2-aminoethanol"), + ("1-ethylpyrrolidin-2-one", "175. 1-ethylpyrrolidin-2-one"), + ("tetradecane", "176. tetradecane"), + ("tridecane", "177. tridecane"), + ( + "octamethylcyclotetrasiloxane", + "178. octamethylcyclotetrasiloxane", + ), + ("perflexane", "179. perflexane"), + ("perfluorooctane", "180. perfluorooctane"), + ("2-phenylacetonitrile", "181. 2-phenylacetonitrile"), + ("propanenitrile", "182. propanenitrile"), + ("4-methyl-1,3-dioxolan-2-one", "183. 4-methyl-1,3-dioxolan-2-one"), + ("quinoline", "184. quinoline"), + ("2-chlorobutane", "185. 2-chlorobutane"), + ("squalane", "186. squalane"), + ("tetraethylene glycol", "187. tetraethylene glycol"), + ("tetraglyme", "188. tetraglyme"), + ("thiodiglycol", "189. thiodiglycol"), + ("trans-1,2-dichloroethene", "190. trans-1,2-dichloroethene"), + ("trans-decalin", "191. trans-decalin"), + ("N,N-dipentylpentan-1-amine", "192. N,N-dipentylpentan-1-amine"), + ("tricaprylin", "193. tricaprylin"), + ("triethyl phosphate", "194. triethyl phosphate"), + ("triethylene glycol", "195. triethylene glycol"), + ("triglyme", "196. triglyme"), + ("N,N-dibutylbutan-1-amine", "197. N,N-dibutylbutan-1-amine"), + ("N,N-dioctyloctan-1-amine", "198. N,N-dioctyloctan-1-amine"), + ("hexamethylphosphoramide", "199. hexamethylphosphoramide"), + ("dimethyl carbonate", "200. dimethyl carbonate"), + ("diethyl carbonate", "201. diethyl carbonate"), + ( + "ethylene carbonate dimethyl carbonate 50:50", + "202. ethylene carbonate dimethyl carbonate 50:50", + ), + ("ethylene carbonate", "203. ethylene carbonate"), + ], + max_length=200, + verbose_name="Solvent (Optional)", + ), + ), + migrations.AlterField( + model_name="solvationsearchml", + name="id", + field=models.BigAutoField( + auto_created=True, primary_key=True, serialize=False, verbose_name="ID" + ), + ), + migrations.AlterField( + model_name="solvationsearchtempdep", + name="id", + field=models.BigAutoField( + auto_created=True, primary_key=True, serialize=False, verbose_name="ID" + ), + ), + migrations.AlterField( + model_name="solventselection", + name="id", + field=models.BigAutoField( + auto_created=True, primary_key=True, serialize=False, verbose_name="ID" + ), + ), + migrations.AlterField( + model_name="solventselection", + name="solvent", + field=models.CharField( + blank=True, + choices=[ + ("water", "1. water"), + ("1-octanol", "2. 1-octanol"), + ("benzene", "3. benzene"), + ("cyclohexane", "4. cyclohexane"), + ("dibutylether", "5. dibutylether"), + ("octane", "6. octane"), + ("butanol", "7. butanol"), + ("carbontet", "8. carbontet"), + ("chloroform", "9. chloroform"), + ("decane", "10. decane"), + ("1,1-dichloroethane", "11. 1,1-dichloroethane"), + ("dimethylformamide", "12. dimethylformamide"), + ("dimethylsulfoxide", "13. dimethylsulfoxide"), + ("dodecane", "14. dodecane"), + ("ethanol", "15. ethanol"), + ("heptane", "16. heptane"), + ("hexadecane", "17. hexadecane"), + ("hexane", "18. hexane"), + ("isooctane", "19. isooctane"), + ("nonane", "20. nonane"), + ("pentane", "21. pentane"), + ("toluene", "22. toluene"), + ("undecane", "23. undecane"), + ("acetonitrile", "24. acetonitrile"), + ("ethylacetate", "25. ethylacetate"), + ("methanol", "26. methanol"), + ("methanol_50_water_50", "27. methanol_50_water_50"), + ("acetonitrile_40_water_60", "28. acetonitrile_40_water_60"), + ("acetonitrile_60_water_40", "29. acetonitrile_60_water_40"), + ("2-methylpyridine", "30. 2-methylpyridine"), + ("4-methylpentan-2-one", "31. 4-methylpentan-2-one"), + ("acetic acid", "32. acetic acid"), + ("1-phenylethanone", "33. 1-phenylethanone"), + ("aniline", "34. aniline"), + ("anisole", "35. anisole"), + ("benzonitrile", "36. benzonitrile"), + ("phenylmethanol", "37. phenylmethanol"), + ("bromobenzene", "38. bromobenzene"), + ("bromoethane", "39. bromoethane"), + ("bromoform", "40. bromoform"), + ("butan-2-one", "41. butan-2-one"), + ("butyl acetate", "42. butyl acetate"), + ("butylbenzene", "43. butylbenzene"), + ("carbon disulfide", "44. carbon disulfide"), + ("chlorobenzene", "45. chlorobenzene"), + ("1-chlorohexane", "46. 1-chlorohexane"), + ("cyclohexanone", "47. cyclohexanone"), + ("decalin", "48. decalin"), + ("decan-1-ol", "49. decan-1-ol"), + ("1,1-dibromoethane", "50. 1,1-dibromoethane"), + ("1,2-dichloroethane", "51. 1,2-dichloroethane"), + ("ethoxyethane", "52. ethoxyethane"), + ("2-propan-2-yloxypropane", "53. 2-propan-2-yloxypropane"), + ("N,N-dimethylacetamide", "54. N,N-dimethylacetamide"), + ("ethoxybenzene", "55. ethoxybenzene"), + ("ethylbenzene", "56. ethylbenzene"), + ("fluorobenzene", "57. fluorobenzene"), + ("heptan-1-ol", "58. heptan-1-ol"), + ("1-iodohexadecane", "59. 1-iodohexadecane"), + ("hexan-1-ol", "60. hexan-1-ol"), + ("iodobenzene", "61. iodobenzene"), + ("2-methylpropan-1-ol", "62. 2-methylpropan-1-ol"), + ("propan-2-ol", "63. propan-2-ol"), + ("cumene", "64. cumene"), + ("3-methylphenol", "65. 3-methylphenol"), + ("2-methoxyethanol", "66. 2-methoxyethanol"), + ("dichloromethane", "67. dichloromethane"), + ("N-methylformamide", "68. N-methylformamide"), + ("nitrobenzene", "69. nitrobenzene"), + ("1-nitroethane", "70. 1-nitroethane"), + ("nitromethane", "71. nitromethane"), + ("nonan-1-ol", "72. nonan-1-ol"), + ("1,2-dichlorobenzene", "73. 1,2-dichlorobenzene"), + ("pentadecane", "74. pentadecane"), + ("pentan-1-ol", "75. pentan-1-ol"), + ("hexafluorobenzene", "76. hexafluorobenzene"), + ("propan-1-ol", "77. propan-1-ol"), + ("pyridine", "78. pyridine"), + ("butan-2-ol", "79. butan-2-ol"), + ("tert-butylbenzene", "80. tert-butylbenzene"), + ("1,1,2,2-tetrachloroethene", "81. 1,1,2,2-tetrachloroethene"), + ("c", "82. c"), + ( + "1,2,3,4-tetrahydronaphthalene", + "83. 1,2,3,4-tetrahydronaphthalene", + ), + ("tributyl phosphate", "84. tributyl phosphate"), + ("N,N-diethylethanamine", "85. N,N-diethylethanamine"), + ("1,2,4-trimethylbenzene", "86. 1,2,4-trimethylbenzene"), + ("1,4-xylene", "87. 1,4-xylene"), + ("2-methylpropan-2-ol", "88. 2-methylpropan-2-ol"), + ("3-methylbutan-1-ol", "89. 3-methylbutan-1-ol"), + ("undecan-1-ol", "90. undecan-1-ol"), + ("propan-2-one", "91. propan-2-one"), + ("methyl acetate", "92. methyl acetate"), + ("propyl acetate", "93. propyl acetate"), + ("pentyl acetate", "94. pentyl acetate"), + ("2-methylbutan-2-ol", "95. 2-methylbutan-2-ol"), + ("4-methylpentan-2-ol", "96. 4-methylpentan-2-ol"), + ("2-methylpentan-1-ol", "97. 2-methylpentan-1-ol"), + ("2-ethylhexan-1-ol", "98. 2-ethylhexan-1-ol"), + ("2-methoxy-2-methylpropane", "99. 2-methoxy-2-methylpropane"), + ("dodecan-1-ol", "100. dodecan-1-ol"), + ("2-butoxyethanol", "101. 2-butoxyethanol"), + ("2-ethoxyethanol", "102. 2-ethoxyethanol"), + ("1-propoxypropane", "103. 1-propoxypropane"), + ("pentan-2-ol", "104. pentan-2-ol"), + ("2-methylbutan-1-ol", "105. 2-methylbutan-1-ol"), + ("pentan-3-ol", "106. pentan-3-ol"), + ("2-propoxyethanol", "107. 2-propoxyethanol"), + ("2-propan-2-yloxyethanol", "108. 2-propan-2-yloxyethanol"), + ("3-methoxybutan-1-ol", "109. 3-methoxybutan-1-ol"), + ("1-tert-butoxy-2-propanol", "110. 1-tert-butoxy-2-propanol"), + ("2-methoxy-2-methylbutane", "111. 2-methoxy-2-methylbutane"), + ("pentan-2-one", "112. pentan-2-one"), + ("ethyl butanoate", "113. ethyl butanoate"), + ("heptan-2-one", "114. heptan-2-one"), + ("hexyl acetate", "115. hexyl acetate"), + ("1-nitro-2-octoxybenzene", "116. 1-nitro-2-octoxybenzene"), + ("1-methylpyrrolidin-2-one", "117. 1-methylpyrrolidin-2-one"), + ("N-methylacetamide", "118. N-methylacetamide"), + ("morpholine-4-carbaldehyde", "119. morpholine-4-carbaldehyde"), + ("N,N-dibutylformamide", "120. N,N-dibutylformamide"), + ("formamide", "121. formamide"), + ("N,N-diethylacetamide", "122. N,N-diethylacetamide"), + ("1-methylpiperidin-2-one", "123. 1-methylpiperidin-2-one"), + ("N-ethylformamide", "124. N-ethylformamide"), + ("N-ethylacetamide", "125. N-ethylacetamide"), + ("triolein", "126. triolein"), + ("deca-1,9-diene", "127. deca-1,9-diene"), + ("hexadec-1-ene", "128. hexadec-1-ene"), + ("1,3-xylene", "129. 1,3-xylene"), + ("1,2-xylene", "130. 1,2-xylene"), + ("1,4-dioxane", "131. 1,4-dioxane"), + ("1-chlorobutane", "132. 1-chlorobutane"), + ("1,1,2,2-tetrabromoethane", "133. 1,1,2,2-tetrabromoethane"), + ("1,1,2,2-tetrachloroethane", "134. 1,1,2,2-tetrachloroethane"), + ("propane-1,2-diol", "135. propane-1,2-diol"), + ( + "1,3-dimethylimidazolidin-2-one", + "136. 1,3-dimethylimidazolidin-2-one", + ), + ("propane-1,3-diol", "137. propane-1,3-diol"), + ("butane-1,4-diol", "138. butane-1,4-diol"), + ("pentane-1,5-diol", "139. pentane-1,5-diol"), + ("1-bromonaphthalene", "140. 1-bromonaphthalene"), + ("1-chloronaphthalene", "141. 1-chloronaphthalene"), + ("dec-1-ene", "142. dec-1-ene"), + ("hex-1-ene", "143. hex-1-ene"), + ("1-nitropropane", "144. 1-nitropropane"), + ("oct-1-ene", "145. oct-1-ene"), + ("2-sulfanylethanol", "146. 2-sulfanylethanol"), + ( + "3-methylthiolane 1,1-dioxide", + "147. 3-methylthiolane 1,1-dioxide", + ), + ("hexanedinitrile", "148. hexanedinitrile"), + ("benzyl acetate", "149. benzyl acetate"), + ("cyclohexylcyclohexane", "150. cyclohexylcyclohexane"), + ("butanenitrile", "151. butanenitrile"), + ("cis-1,2-dichloroethene", "152. cis-1,2-dichloroethene"), + ("cis-decaline", "153. cis-decaline"), + ("cyclohexanol", "154. cyclohexanol"), + ("cyclohexylbenzene", "155. cyclohexylbenzene"), + ("cyclopentanone", "156. cyclopentanone"), + ("deuterated water", "157. deuterated water"), + ( + "bis(2-ethylhexyl) hexanedioate", + "158. bis(2-ethylhexyl) hexanedioate", + ), + ("2,2-dichloroacetic acid", "159. 2,2-dichloroacetic acid"), + ( + "diethyl benzene-1,2-dicarboxylate", + "160. diethyl benzene-1,2-dicarboxylate", + ), + ("2-(2-hydroxyethoxy)ethanol", "161. 2-(2-hydroxyethoxy)ethanol"), + ( + "1-ethoxy-2-(2-ethoxyethoxy)ethane", + "162. 1-ethoxy-2-(2-ethoxyethoxy)ethane", + ), + ( + "1-methoxy-2-(2-methoxyethoxy)ethane", + "163. 1-methoxy-2-(2-methoxyethoxy)ethane", + ), + ("diiodomethane", "164. diiodomethane"), + ( + "dibutyl benzene-1,2-dicarboxylate", + "165. dibutyl benzene-1,2-dicarboxylate", + ), + ( + "dinonyl benzene-1,2-dicarboxylate", + "166. dinonyl benzene-1,2-dicarboxylate", + ), + ("bis(2-ethylhexyl) phthalate", "167. bis(2-ethylhexyl) phthalate"), + ( + "3-(3-hydroxypropoxy)propan-1-ol", + "168. 3-(3-hydroxypropoxy)propan-1-ol", + ), + ("ethane-1,2-diol", "169. ethane-1,2-diol"), + ("furan-2-carbaldehyde", "170. furan-2-carbaldehyde"), + ("furan-2-ylmethanol", "171. furan-2-ylmethanol"), + ("oxolan-2-one", "172. oxolan-2-one"), + ("1H-indene", "173. 1H-indene"), + ("2-aminoethanol", "174. 2-aminoethanol"), + ("1-ethylpyrrolidin-2-one", "175. 1-ethylpyrrolidin-2-one"), + ("tetradecane", "176. tetradecane"), + ("tridecane", "177. tridecane"), + ( + "octamethylcyclotetrasiloxane", + "178. octamethylcyclotetrasiloxane", + ), + ("perflexane", "179. perflexane"), + ("perfluorooctane", "180. perfluorooctane"), + ("2-phenylacetonitrile", "181. 2-phenylacetonitrile"), + ("propanenitrile", "182. propanenitrile"), + ("4-methyl-1,3-dioxolan-2-one", "183. 4-methyl-1,3-dioxolan-2-one"), + ("quinoline", "184. quinoline"), + ("2-chlorobutane", "185. 2-chlorobutane"), + ("squalane", "186. squalane"), + ("tetraethylene glycol", "187. tetraethylene glycol"), + ("tetraglyme", "188. tetraglyme"), + ("thiodiglycol", "189. thiodiglycol"), + ("trans-1,2-dichloroethene", "190. trans-1,2-dichloroethene"), + ("trans-decalin", "191. trans-decalin"), + ("N,N-dipentylpentan-1-amine", "192. N,N-dipentylpentan-1-amine"), + ("tricaprylin", "193. tricaprylin"), + ("triethyl phosphate", "194. triethyl phosphate"), + ("triethylene glycol", "195. triethylene glycol"), + ("triglyme", "196. triglyme"), + ("N,N-dibutylbutan-1-amine", "197. N,N-dibutylbutan-1-amine"), + ("N,N-dioctyloctan-1-amine", "198. N,N-dioctyloctan-1-amine"), + ("hexamethylphosphoramide", "199. hexamethylphosphoramide"), + ("dimethyl carbonate", "200. dimethyl carbonate"), + ("diethyl carbonate", "201. diethyl carbonate"), + ( + "ethylene carbonate dimethyl carbonate 50:50", + "202. ethylene carbonate dimethyl carbonate 50:50", + ), + ("ethylene carbonate", "203. ethylene carbonate"), + ], + max_length=200, + verbose_name="Solvent (Optional)", + ), + ), + migrations.AlterField( + model_name="solventselection", + name="solvent_temp", + field=models.CharField( + blank=True, + choices=[ + ("water", "1. water: ~298 K - 647.09 K"), + ("benzene", "3. benzene: ~298 K - 562.01 K"), + ("cyclohexane", "4. cyclohexane: ~298 K - 553.59 K"), + ("octane", "6. octane: ~298 K - 568.73 K"), + ("decane", "10. decane: ~298 K - 617.69 K"), + ("dodecane", "14. dodecane: ~298 K - 658.09 K"), + ("ethanol", "15. ethanol: ~298 K - 514.70 K"), + ("heptane", "16. heptane: ~298 K - 540.12 K"), + ("hexane", "18. hexane: ~298 K - 507.81 K"), + ("nonane", "20. nonane: ~298 K - 594.54 K"), + ("pentane", "21. pentane: ~298 K - 469.69 K"), + ("toluene", "22. toluene: ~298 K - 591.74 K"), + ("undecane", "23. undecane: ~298 K - 638.79 K"), + ("methanol", "26. methanol: ~298 K - 512.49 K"), + ("1,2-dichloroethane", "51. 1,2-dichloroethane: ~298 K - 561.59 K"), + ("ethoxyethane", "52. ethoxyethane: ~298 K - 466.69 K"), + ("ethylbenzene", "56. ethylbenzene: ~298 K - 617.11 K"), + ("1,4-xylene", "87. 1,4-xylene: ~298 K - 616.16 K"), + ("propan-2-one", "91. propan-2-one: ~298 K - 508.09 K"), + ("1,3-xylene", "129. 1,3-xylene: ~298 K - 616.88 K"), + ("1,2-xylene", "130. 1,2-xylene: ~298 K - 630.25 K"), + ( + "octamethylcyclotetrasiloxane", + "178. octamethylcyclotetrasiloxane: ~298 K - 586.49 K", + ), + ( + "dimethyl carbonate", + "200. dimethyl carbonate: ~298 K - 556.99 K", + ), + ], + max_length=200, + verbose_name="Solvent", + ), + ), + ] diff --git a/rmgweb/database/templates/kineticsTable.html b/rmgweb/database/templates/kineticsTable.html index c5a39ad1..8681560a 100644 --- a/rmgweb/database/templates/kineticsTable.html +++ b/rmgweb/database/templates/kineticsTable.html @@ -78,11 +78,11 @@ var treeChildren = new Array(); {% for entry in entries %} - {% ifequal entry.parent None %} + {% if entry.parent == None %} treeParent["{{ entry.index }}"] = ""; {% else %} treeParent["{{ entry.index }}"] = "{{ entry.parent.index }}"; - {% endifequal %} + {% endif %} treeChildren["{{ entry.index }}"] = [{% for child in entry.children %}"{{ child.index }}"{% if not forloop.last %}, {% endif %}{% endfor %}]; {% endfor %} diff --git a/rmgweb/database/templates/thermoEntry.html b/rmgweb/database/templates/thermoEntry.html index 83ba0aac..f0c71092 100644 --- a/rmgweb/database/templates/thermoEntry.html +++ b/rmgweb/database/templates/thermoEntry.html @@ -89,7 +89,7 @@

Structure

Thermodynamic Data

-{% ifequal thermo.0 'Link' %} +{% if thermo.0 == 'Link' %} @@ -98,7 +98,7 @@

Thermodynamic Data

Link:
{% else %} {{ thermo|render_thermo_math:user }} -{% endifequal %} +{% endif %} {% if nasa_string %}
diff --git a/rmgweb/database/tools.py b/rmgweb/database/tools.py index 648acf07..95a817f6 100644 --- a/rmgweb/database/tools.py +++ b/rmgweb/database/tools.py @@ -390,7 +390,6 @@ def generateReactions(database, reactants, products=None, only_families=None, re reactants, products, only_families=only_families, resonance=resonance) if len(reactants) == 1: # if only one reactant, react it with itself bimolecularly, with RMG-py - # the java version already does this (it includes A+A reactions when you react A) reactants2 = [reactants[0], reactants[0]] reaction_list.extend(database.kinetics.generate_reactions( reactants2, products, only_families=only_families, resonance=resonance)) diff --git a/rmgweb/database/views.py b/rmgweb/database/views.py index e84dfa36..4f1d635e 100644 --- a/rmgweb/database/views.py +++ b/rmgweb/database/views.py @@ -34,8 +34,8 @@ import math import os import re -import shutil import subprocess +import sys import urllib import pandas as pd import numpy as np @@ -43,12 +43,13 @@ from rdkit import Chem import rdkit.Chem.rdmolops as rdmolops from CoolProp.CoolProp import PropsSI +from contextlib import contextmanager from decimal import Decimal from chemprop_solvation.solvation_estimator import load_DirectML_Gsolv_estimator, load_DirectML_Hsolv_estimator, load_SoluteML_estimator -from solvation_predictor.solubility.solubility_calculator import SolubilityCalculations -from solvation_predictor.solubility.solubility_models import SolubilityModels -from solvation_predictor.solubility.solubility_predictions import SolubilityPredictions +from solvation_predictor.solubility.SolubilityCalculations import SolubilityCalculations +from solvation_predictor.solubility.SolubilityPredictions import SolubilityPredictions +from solvation_predictor.solubility.SolubilityData import SolubilityData import rmgpy import rmgpy.constants as constants @@ -57,7 +58,7 @@ TemplateReaction, LibraryReaction from rmgpy.data.kinetics.depository import DepositoryReaction from rmgpy.data.reference import Article, Book -from rmgpy.data.solvation import SoluteData, SolventData, SolvationCorrection +from rmgpy.data.solvation import SoluteData, SolventData from rmgpy.data.statmech import GroupFrequencies from rmgpy.data.thermo import find_cp0_and_cpinf from rmgpy.data.transport import CriticalPointGroupContribution, TransportData @@ -74,7 +75,7 @@ from rmgpy.thermo.thermoengine import process_thermo_data from django.contrib.auth.decorators import login_required -from django.contrib.staticfiles.templatetags.staticfiles import static +from django.templatetags.static import static from django.http import Http404, HttpResponseRedirect, HttpResponse, HttpResponseBadRequest from django.shortcuts import render from django.urls import reverse @@ -99,12 +100,33 @@ # Loading these ML estimators takes around 10 seconds. # Therefore, instead of loading these each time these estimators are used, let's # load them in the beginning only once and use them as needed. -global dGsolv_estimator, dHsolv_estimator, SoluteML_estimator, solub_models +global dGsolv_estimator, dHsolv_estimator, solub_models, SoluteML_estimator dGsolv_estimator = load_DirectML_Gsolv_estimator() dHsolv_estimator = load_DirectML_Hsolv_estimator() -solub_models = SolubilityModels(reduced_number=False, load_g=True, load_h=True, load_saq=True, - load_solute=True, logger=None, verbose=False) -SoluteML_estimator = solub_models.solute_models +solub_models, SoluteML_estimator = None, None + +@contextmanager +def fake_sys_argv(): + """ + Workaround to avoid problems with multiple argument parsers. + This was encountered with SolProp, but might occur with other packages. + """ + old_argv = sys.argv + try: + sys.argv = ['model_loader.py'] # empty or fake args + yield + finally: + sys.argv = old_argv + +from solvation_predictor.solubility.SolubilityModels import SolubilityModels +with fake_sys_argv(): + solub_models = SolubilityModels( + load_ghsolv=True, load_g=False, load_h=False, + reduced_number=False, load_saq=False, # TODO: need load_saq=True after it's added to SolProp + load_solute=True, logger=None, verbose=False + ) +# SoluteML_estimator = solub_models.solute_models + SoluteML_estimator = load_SoluteML_estimator() def load(request): """ @@ -113,13 +135,34 @@ def load(request): database.load() return HttpResponseRedirect(reverse('database:index')) - def index(request): """ The RMG database homepage. """ return render(request, 'database.html') +def return_common_entry_data(entries, section, subsection, index, data_type): + """ + A helper function that returns entry data for a species, after the relevant entries are determined. + """ + index = int(index) + if index != 0 and index != -1: + for entry in entries: + if entry.index == index: + break + else: + raise Http404 + else: + if index == 0: + index = min(entry.index for entry in entries if entry.index > 0) + else: + index = max(entry.index for entry in entries if entry.index > 0) + return HttpResponseRedirect(reverse(f'database:{data_type}-entry', + kwargs={'section': section, + 'subsection': subsection, + 'index': index, + })) + return entry ################################################################################################################################################# @@ -199,23 +242,7 @@ def transportEntry(request, section, subsection, index): except ValueError: raise Http404 - index = int(index) - if index != 0 and index != -1: - for entry in db.entries.values(): - if entry.index == index: - break - else: - raise Http404 - else: - if index == 0: - index = min(entry.index for entry in db.entries.values() if entry.index > 0) - else: - index = max(entry.index for entry in db.entries.values() if entry.index > 0) - return HttpResponseRedirect(reverse('database:transport-entry', - kwargs={'section': section, - 'subsection': subsection, - 'index': index, - })) + entry = return_common_entry_data(db.entries.values(), section, subsection, index, "transport") # Get the structure of the item we are viewing structure = getStructureInfo(entry.item) @@ -670,7 +697,7 @@ def get_temp_dep_logP(solvent_smiles, solute_smiles, temp_SI, solvation_298_resu solvation_298_results[pair_key_water] = (dGsolv298water, dHsolv298water, dSsolv298water) if dGsolv298water is not None and dHsolv298water is not None and dSsolv298water is not None: - dGsolv_water, Kfactor_water = db.get_T_dep_solvation_energy_from_input_298( + dGsolv_water, Kfactor_water, henry = db.get_T_dep_solvation_energy_from_input_298( dGsolv298water, dHsolv298water, dSsolv298water, 'water', temp_SI) logP = -(dGsolv - dGsolv_water) / (math.log(10) * constants.R * temp_SI) else: @@ -1403,23 +1430,7 @@ def statmechEntry(request, section, subsection, index): except ValueError: raise Http404 - index = int(index) - if index != 0 and index != -1: - for entry in db.entries.values(): - if entry.index == index: - break - else: - raise Http404 - else: - if index == 0: - index = min(entry.index for entry in db.entries.values() if entry.index > 0) - else: - index = max(entry.index for entry in db.entries.values() if entry.index > 0) - return HttpResponseRedirect(reverse('database:statmech-entry', - kwargs={'section': section, - 'subsection': subsection, - 'index': index, - })) + entry = return_common_entry_data(db.entries.values(), section, subsection, index, "statmech") # Get the structure of the item we are viewing structure = getStructureInfo(entry.item) @@ -1548,23 +1559,7 @@ def thermoEntry(request, section, subsection, index): db = database.get_thermo_database(section, subsection) except ValueError: raise Http404 - index = int(index) - if index != 0 and index != -1: - for entry in db.entries.values(): - if entry.index == index: - break - else: - raise Http404 - else: - if index == 0: - index = min(entry.index for entry in db.entries.values() if entry.index > 0) - else: - index = max(entry.index for entry in db.entries.values() if entry.index > 0) - return HttpResponseRedirect(reverse('database:thermo-entry', - kwargs={'section': section, - 'subsection': subsection, - 'index': index, - })) + entry = return_common_entry_data(db.entries.values(), section, subsection, index, "thermo") # Get the structure of the item we are viewing structure = getStructureInfo(entry.item) @@ -2488,49 +2483,29 @@ def kineticsEntryEdit(request, section, subsection, index): entry_string = entry_buffer.getvalue() entry_buffer.close() - if False: - # Just return the text. - return HttpResponse(entry_string, content_type="text/plain") - if False: - # Render it as if it were saved. - return render(request, 'kineticsEntry.html', - {'section': section, - 'subsection': subsection, - 'databaseName': db.name, - 'entry': new_entry, - 'reference': entry.reference, - 'kinetics': entry.data, - }) - if True: - # save it - db.entries[index] = new_entry - path = os.path.join(rmgweb.settings.DATABASE_PATH, 'kinetics', section, subsection + '.py') - db.save(path) - commit_author = "{0.first_name} {0.last_name} <{0.email}>".format(request.user) - commit_message = "{1}:{2} {3}\n\nChange to kinetics/{0}/{1} entry {2} submitted through RMG website:\n{3}\n{4}".format(section, subsection, index, form.cleaned_data['change'], commit_author) - commit_result = subprocess.check_output(['git', 'commit', '-m', commit_message, '--author', - commit_author, path], - cwd=rmgweb.settings.DATABASE_PATH, stderr=subprocess.STDOUT) - subprocess.check_output(['git', 'push'], cwd=rmgweb.settings.DATABASE_PATH, stderr=subprocess.STDOUT) - - # return HttpResponse(commit_result, content_type="text/plain") + db.entries[index] = new_entry + path = os.path.join(rmgweb.settings.DATABASE_PATH, 'kinetics', section, subsection + '.py') + db.save(path) + commit_author = "{0.first_name} {0.last_name} <{0.email}>".format(request.user) + commit_message = "{1}:{2} {3}\n\nChange to kinetics/{0}/{1} entry {2} submitted through RMG website:\n{3}\n{4}".format(section, subsection, index, form.cleaned_data['change'], commit_author) + commit_result = subprocess.check_output(['git', 'commit', '-m', commit_message, '--author', + commit_author, path], + cwd=rmgweb.settings.DATABASE_PATH, stderr=subprocess.STDOUT) + subprocess.check_output(['git', 'push'], cwd=rmgweb.settings.DATABASE_PATH, stderr=subprocess.STDOUT) - kwargs = {'section': section, - 'subsection': subsection, - 'index': index} - forward_url = reverse('database:kinetics-entry', kwargs=kwargs) - message = """ - Changes saved succesfully:
- 
{0}

- See result at {1}. - """.format(commit_result, forward_url) - return render(request, 'simple.html', - {'title': 'Change saved successfully.', - 'body': message, - }) - - # redirect - return HttpResponseRedirect(forward_url) + kwargs = {'section': section, + 'subsection': subsection, + 'index': index} + forward_url = reverse('database:kinetics-entry', kwargs=kwargs) + message = """ + Changes saved succesfully:
+ 
{0}

+ See result at {1}. + """.format(commit_result, forward_url) + return render(request, 'simple.html', + {'title': 'Change saved successfully.', + 'body': message, + }) else: # not POST # Get the entry as a entry_string @@ -2615,31 +2590,27 @@ def thermoEntryNew(request, section, subsection, adjlist): } forward_url = reverse('database:thermo-entry', kwargs=kwargs) - if False: - # Just return the text. - return HttpResponse(entry_string, content_type="text/plain") - if True: - # save it - db.entries[index] = new_entry - path = os.path.join(rmgweb.settings.DATABASE_PATH, 'thermo', section, subsection + '.py') - db.save(path) - commit_author = '{0.first_name} {0.last_name} <{0.email}>'.format(request.user) - commit_message = 'New Entry: {section}/{subsection}/{index}\n\n{msg}'.format(section=section, - subsection=subsection, - index=new_entry.index, - msg=msg) - commit_message += '\n\nSubmitted through the RMG website.' - commit_result = subprocess.check_output(['git', 'commit', '-m', commit_message, - '--author', commit_author, path], - cwd=rmgweb.settings.DATABASE_PATH, stderr=subprocess.STDOUT) - subprocess.check_output(['git', 'push'], cwd=rmgweb.settings.DATABASE_PATH, stderr=subprocess.STDOUT) - message = """ - New entry saved succesfully:
- 
{0}

- See result at {1}. - """.format(commit_result, forward_url) - return render(request, 'simple.html', - {'title': '', 'body': message}) + # save it + db.entries[index] = new_entry + path = os.path.join(rmgweb.settings.DATABASE_PATH, 'thermo', section, subsection + '.py') + db.save(path) + commit_author = '{0.first_name} {0.last_name} <{0.email}>'.format(request.user) + commit_message = 'New Entry: {section}/{subsection}/{index}\n\n{msg}'.format(section=section, + subsection=subsection, + index=new_entry.index, + msg=msg) + commit_message += '\n\nSubmitted through the RMG website.' + commit_result = subprocess.check_output(['git', 'commit', '-m', commit_message, + '--author', commit_author, path], + cwd=rmgweb.settings.DATABASE_PATH, stderr=subprocess.STDOUT) + subprocess.check_output(['git', 'push'], cwd=rmgweb.settings.DATABASE_PATH, stderr=subprocess.STDOUT) + message = """ + New entry saved succesfully:
+ 
{0}

+ See result at {1}. + """.format(commit_result, forward_url) + return render(request, 'simple.html', + {'title': '', 'body': message}) else: # not POST entry_string = """ label = "{label}", @@ -2713,49 +2684,32 @@ def thermoEntryEdit(request, section, subsection, index): entry_string = entry_buffer.getvalue() entry_buffer.close() - if False: - # Just return the text. - return HttpResponse(entry_string, content_type="text/plain") - if False: - # Render it as if it were saved. - return render(request, 'thermoEntry.html', - {'section': section, - 'subsection': subsection, - 'databaseName': db.name, - 'entry': new_entry, - 'reference': entry.reference, - 'kinetics': entry.data, - }) - if True: - # save it - db.entries[index] = new_entry - path = os.path.join(rmgweb.settings.DATABASE_PATH, 'thermo', section, subsection + '.py') - db.save(path) - commit_author = "{0.first_name} {0.last_name} <{0.email}>".format(request.user) - commit_message = "{1}:{2} {3}\n\nChange to thermo/{0}/{1} entry {2} submitted through RMG website:\n{3}\n{4}".format(section, subsection, index, form.cleaned_data['change'], commit_author) - commit_result = subprocess.check_output(['git', 'commit', '-m', commit_message, - '--author', commit_author, path], - cwd=rmgweb.settings.DATABASE_PATH, stderr=subprocess.STDOUT) - subprocess.check_output(['git', 'push'], cwd=rmgweb.settings.DATABASE_PATH, stderr=subprocess.STDOUT) - - # return HttpResponse(commit_result, content_type="text/plain") + # save it + db.entries[index] = new_entry + path = os.path.join(rmgweb.settings.DATABASE_PATH, 'thermo', section, subsection + '.py') + db.save(path) + commit_author = "{0.first_name} {0.last_name} <{0.email}>".format(request.user) + commit_message = "{1}:{2} {3}\n\nChange to thermo/{0}/{1} entry {2} submitted through RMG website:\n{3}\n{4}".format(section, subsection, index, form.cleaned_data['change'], commit_author) + commit_result = subprocess.check_output(['git', 'commit', '-m', commit_message, + '--author', commit_author, path], + cwd=rmgweb.settings.DATABASE_PATH, stderr=subprocess.STDOUT) + subprocess.check_output(['git', 'push'], cwd=rmgweb.settings.DATABASE_PATH, stderr=subprocess.STDOUT) - kwargs = {'section': section, - 'subsection': subsection, - 'index': index} - forward_url = reverse('database:thermo-entry', kwargs=kwargs) - message = """ - Changes saved succesfully:
- 
{0}

- See result at {1}. - """.format(commit_result, forward_url) - return render(request, 'simple.html', - {'title': 'Change saved successfully.', - 'body': message, - }) + # return HttpResponse(commit_result, content_type="text/plain") - # redirect - return HttpResponseRedirect(forward_url) + kwargs = {'section': section, + 'subsection': subsection, + 'index': index} + forward_url = reverse('database:thermo-entry', kwargs=kwargs) + message = """ + Changes saved succesfully:
+ 
{0}

+ See result at {1}. + """.format(commit_result, forward_url) + return render(request, 'simple.html', + {'title': 'Change saved successfully.', + 'body': message, + }) else: # not POST # Get the entry as a entry_string @@ -2784,8 +2738,7 @@ def thermoEntryEdit(request, section, subsection, index): 'entry': entry, 'form': form, }) - - + def kineticsEntry(request, section, subsection, index): """ A view for showing an entry in a kinetics database. @@ -2805,23 +2758,7 @@ def kineticsEntry(request, section, subsection, index): # if the entries are lists entries = reduce(lambda x, y: x + y, entries) - index = int(index) - if index != 0 and index != -1: - for entry in entries: - if entry.index == index: - break - else: - raise Http404 - else: - if index == 0: - index = min(entry.index for entry in entries if entry.index > 0) - else: - index = max(entry.index for entry in entries if entry.index > 0) - return HttpResponseRedirect(reverse('database:kinetics-entry', - kwargs={'section': section, - 'subsection': subsection, - 'index': index, - })) + entry = return_common_entry_data(entries, section, subsection, index, "kinetics") reference = entry.reference reference_type = '' @@ -3775,11 +3712,21 @@ def calc_solubility_no_ref(solvent_smiles=None, solute_smiles=None, temp=None, h Cp_solid = np.array([cp_solid_298]) if cp_solid_298 is not None else None Cp_gas = np.array([cp_gas_298]) if cp_gas_298 is not None else None - solub_data = SolubilityData(solvent_smiles=solvent_smiles, solute_smiles=solute_smiles, temp=temp) - predictions = SolubilityPredictions(solub_data, solub_models, predict_aqueous=True, - predict_reference_solvents=False, predict_t_dep=True, - predict_solute_parameters=True, verbose=False) - calculations = SolubilityCalculations(predictions, calculate_aqueous=True, + # Create dataframe with solvent and solute data + data = { + 'solvent_smiles': [solvent_smiles], + 'solute_smiles': [solute_smiles], + 'temperature': [temp], + 'reference_solubility': [None], + 'reference_solvent': [None], + } + df = pd.DataFrame(data) + + solub_data = SolubilityData(df=df) + predictions = SolubilityPredictions(predict_aqueous=True, predict_reference_solvents=False, + predict_t_dep=True, predict_solute_parameters=True, + data=solub_data, models=solub_models, verbose=False) + calculations = SolubilityCalculations(predictions=predictions, calculate_aqueous=True, calculate_reference_solvents=False, calculate_t_dep=True, calculate_t_dep_with_t_dep_hdiss=True, verbose=False, hsubl_298=hsubl_298, Cp_solid=Cp_solid, Cp_gas=Cp_gas) @@ -3795,12 +3742,20 @@ def calc_solubility_with_ref(solvent_smiles=None, solute_smiles=None, temp=None, Cp_solid = np.array([cp_solid_298]) if cp_solid_298 is not None else None Cp_gas = np.array([cp_gas_298]) if cp_gas_298 is not None else None - solub_data = SolubilityData(solvent_smiles=solvent_smiles, solute_smiles=solute_smiles, temp=temp, - ref_solub=ref_solubility298, ref_solv=ref_solvent_smiles) - predictions = SolubilityPredictions(solub_data, solub_models, predict_aqueous=False, - predict_reference_solvents=True, predict_t_dep=True, - predict_solute_parameters=True, verbose=False) - calculations = SolubilityCalculations(predictions, calculate_aqueous=False, + data = { + 'solvent_smiles': [solvent_smiles], + 'solute_smiles': [solute_smiles], + 'temperature': [temp], + 'reference_solubility': [ref_solubility298], + 'reference_solvent': [ref_solvent_smiles], + } + df = pd.DataFrame(data) + + solub_data = SolubilityData(df=df) + predictions = SolubilityPredictions(predict_aqueous=False, predict_reference_solvents=True, + predict_t_dep=True, predict_solute_parameters=True, + data=solub_data, models=solub_models, verbose=False) + calculations = SolubilityCalculations(predictions=predictions, calculate_aqueous=False, calculate_reference_solvents=True, calculate_t_dep=True, calculate_t_dep_with_t_dep_hdiss=True, verbose=False, hsubl_298=hsubl_298, Cp_solid=Cp_solid, Cp_gas=Cp_gas) @@ -3823,17 +3778,6 @@ def get_ref_solubility298(calculations_ref=None, ref_solubility=None): return ref_solubility298 -class SolubilityData: - """ - Class for storing the input data for solubility prediction - """ - def __init__(self, solvent_smiles=None, solute_smiles=None, temp=None, ref_solub=None, ref_solv=None): - self.smiles_pairs = [(solvent_smiles, solute_smiles)] - self.temperatures = np.array([temp]) if temp is not None else None - self.reference_solubility = np.array([ref_solub]) if ref_solub is not None else None - self.reference_solvents = np.array([ref_solv]) if ref_solv is not None else None - - def format_T_dep_hdiss_error_mesg(error_msg): """ Turn the error_msg for the T-dep Hdiss prediction into appropriate error and warning messages @@ -4058,7 +4002,8 @@ def json_to_adjlist(request): Interprets ChemDoodle JSON and returns an RMG adjacency list. """ adjlist = '' - if request.is_ajax() and request.method == 'POST': + is_ajax = request.META.get('HTTP_X_REQUESTED_WITH') == 'XMLHttpRequest' + if is_ajax and request.method == 'POST': cd_json_str = request.POST.get('data') cd_json = json.loads(cd_json_str) diff --git a/rmgweb/main/migrations/0002_alter_userprofile_id.py b/rmgweb/main/migrations/0002_alter_userprofile_id.py new file mode 100644 index 00000000..59e406c3 --- /dev/null +++ b/rmgweb/main/migrations/0002_alter_userprofile_id.py @@ -0,0 +1,20 @@ +# Generated by Django 4.2.23 on 2025-07-03 15:10 + +from django.db import migrations, models + + +class Migration(migrations.Migration): + + dependencies = [ + ("main", "0001_initial"), + ] + + operations = [ + migrations.AlterField( + model_name="userprofile", + name="id", + field=models.BigAutoField( + auto_created=True, primary_key=True, serialize=False, verbose_name="ID" + ), + ), + ] diff --git a/rmgweb/main/templatetags/render_solvation.py b/rmgweb/main/templatetags/render_solvation.py index 9e003955..e8a51b80 100644 --- a/rmgweb/main/templatetags/render_solvation.py +++ b/rmgweb/main/templatetags/render_solvation.py @@ -37,7 +37,7 @@ from rmgpy.data.base import Entry from rmgpy.species import Species from rmgpy.molecule.group import Group -from rmgpy.data.solvation import * +from rmgpy.data.solvation import SoluteData, SolventData, SolvationCorrection # Register this module as a Django template tag library register = template.Library() diff --git a/rmgweb/main/views.py b/rmgweb/main/views.py index 2db81f41..6f5e2398 100644 --- a/rmgweb/main/views.py +++ b/rmgweb/main/views.py @@ -44,6 +44,9 @@ from django.urls import reverse from django.views.decorators.csrf import csrf_exempt +from rmgpy.molecule.group import Group +from rmgpy.molecule.adjlist import InvalidAdjacencyListError + from rmgpy.molecule.atomtype import allElements as SUPPORTED_ELEMENTS from rmgweb.main.forms import * @@ -68,6 +71,10 @@ elif len(element) == 2: SUPPORTED_ELEMENTS_TWO_LETTERS.append(element) +# add conda environment bin to PATH. Added on 3 July 2025 to ensure graphviz is added to path, even if bashrc is not sourced. +bin = os.path.join(os.environ.get("CONDA_PREFIX", ""), "bin") +if bin and bin not in os.environ["PATH"]: + os.environ["PATH"] = bin + os.pathsep + os.environ["PATH"] def index(request): """ @@ -354,30 +361,28 @@ def drawGroup(request, adjlist, format='png'): Returns an image of the provided adjacency list `adjlist` for a molecular group. urllib is used to quote/unquote the adjacency list. """ - from rmgpy.molecule.group import Group - from rmgpy.molecule.adjlist import InvalidAdjacencyListError adjlist = urllib.parse.unquote(adjlist) - # try: - # group = Group().from_adjacency_list(adjlist) - # except (InvalidAdjacencyListError, ValueError): - # response = HttpResponseRedirect(static('img/invalid_icon.png')) - # else: - # if format == 'png': - # response = HttpResponse(content_type="image/png") - # response.write(group.draw('png')) - # elif format == 'svg': - # response = HttpResponse(content_type="image/svg+xml") - # svg_data = group.draw('svg') - # # Remove the scale and rotate transformations applied by pydot - # svg_data = re.sub(r'scale\(0\.722222 0\.722222\) rotate\(0\) ', '', svg_data) - # response.write(svg_data) - # else: - # response = HttpResponse('Image format not implemented.', status=501) - - # return response - return HttpResponse(content_type="image/png") # TODO: fix root cause. Added 3/31/25 as a stopgap to prevent 'neato not found' errors. + try: + group = Group().from_adjacency_list(adjlist) + except (InvalidAdjacencyListError, ValueError): + response = HttpResponseRedirect(static('img/invalid_icon.png')) + else: + if format == 'png': + response = HttpResponse(content_type="image/png") + response.write(group.draw('png')) + elif format == 'svg': + response = HttpResponse(content_type="image/svg+xml") + svg_data = group.draw('svg') + # Remove the scale and rotate transformations applied by pydot + svg_data = re.sub(r'scale\(0\.722222 0\.722222\) rotate\(0\) ', '', svg_data) + response.write(svg_data) + else: + response = HttpResponse('Image format not implemented.', status=501) + + return response +# return HttpResponse(content_type="image/svg+xml") @login_required diff --git a/rmgweb/pdep/models.py b/rmgweb/pdep/models.py index a95f138c..8b2fb738 100644 --- a/rmgweb/pdep/models.py +++ b/rmgweb/pdep/models.py @@ -72,7 +72,8 @@ def getDirname(self): Return the absolute path of the directory that the Network object uses to store files. """ - return os.path.join(settings.MEDIA_ROOT, 'pdep', 'networks', str(self.pk)) + pk_str = self.pk.decode() if isinstance(self.pk, bytes) else str(self.pk) + return os.path.join(settings.MEDIA_ROOT, 'pdep', 'networks', pk_str) def getInputFilename(self): """ diff --git a/rmgweb/rmg/migrations/0011_delete_adjlistconversion_remove_fluxdiagram_java_and_more.py b/rmgweb/rmg/migrations/0011_delete_adjlistconversion_remove_fluxdiagram_java_and_more.py new file mode 100644 index 00000000..ccae0c2e --- /dev/null +++ b/rmgweb/rmg/migrations/0011_delete_adjlistconversion_remove_fluxdiagram_java_and_more.py @@ -0,0 +1,603 @@ +# Generated by Django 4.2.23 on 2025-07-03 15:10 + +from django.db import migrations, models +import rmgweb.rmg.models + + +class Migration(migrations.Migration): + + dependencies = [ + ("rmg", "0010_auto_20220208_2307"), + ] + + operations = [ + migrations.DeleteModel( + name="AdjlistConversion", + ), + migrations.RemoveField( + model_name="fluxdiagram", + name="java", + ), + migrations.AlterField( + model_name="chemkin", + name="chem_file", + field=models.FileField( + blank=True, + null=True, + upload_to=rmgweb.rmg.models.uploadTo("chemkin/chem.inp"), + verbose_name="Chemkin File", + ), + ), + migrations.AlterField( + model_name="chemkin", + name="id", + field=models.BigAutoField( + auto_created=True, primary_key=True, serialize=False, verbose_name="ID" + ), + ), + migrations.AlterField( + model_name="diff", + name="chem_file1", + field=models.FileField( + blank=True, + null=True, + upload_to=rmgweb.rmg.models.uploadTo("chem1.inp"), + verbose_name="Model 1: Chemkin File", + ), + ), + migrations.AlterField( + model_name="diff", + name="chem_file2", + field=models.FileField( + blank=True, + null=True, + upload_to=rmgweb.rmg.models.uploadTo("chem2.inp"), + verbose_name="Model 2: Chemkin File", + ), + ), + migrations.AlterField( + model_name="diff", + name="dict_file1", + field=models.FileField( + blank=True, + null=True, + upload_to=rmgweb.rmg.models.uploadTo("RMG_Dictionary1.txt"), + verbose_name="Model 1: RMG Dictionary", + ), + ), + migrations.AlterField( + model_name="diff", + name="dict_file2", + field=models.FileField( + blank=True, + null=True, + upload_to=rmgweb.rmg.models.uploadTo("RMG_Dictionary2.txt"), + verbose_name="Model 2: RMG Dictionary", + ), + ), + migrations.AlterField( + model_name="diff", + name="id", + field=models.BigAutoField( + auto_created=True, primary_key=True, serialize=False, verbose_name="ID" + ), + ), + migrations.AlterField( + model_name="fluxdiagram", + name="id", + field=models.BigAutoField( + auto_created=True, primary_key=True, serialize=False, verbose_name="ID" + ), + ), + migrations.AlterField( + model_name="input", + name="id", + field=models.BigAutoField( + auto_created=True, primary_key=True, serialize=False, verbose_name="ID" + ), + ), + migrations.AlterField( + model_name="populatereactions", + name="id", + field=models.BigAutoField( + auto_created=True, primary_key=True, serialize=False, verbose_name="ID" + ), + ), + migrations.AlterField( + model_name="reactionlibrary", + name="id", + field=models.BigAutoField( + auto_created=True, primary_key=True, serialize=False, verbose_name="ID" + ), + ), + migrations.AlterField( + model_name="reactionlibrary", + name="reaction_lib", + field=models.CharField( + blank=True, + choices=[ + ("1989_Stewart_2CH3_to_C2H5_H", "1989_Stewart_2CH3_to_C2H5_H"), + ("2-BTP/full", "2-BTP/full"), + ("2-BTP/seed", "2-BTP/seed"), + ( + "2001_Tokmakov_H_Toluene_to_CH3_Benzene", + "2001_Tokmakov_H_Toluene_to_CH3_Benzene", + ), + ( + "2003_Miller_Propargyl_Recomb_High_P", + "2003_Miller_Propargyl_Recomb_High_P", + ), + ("2005_Senosiain_OH_C2H2", "2005_Senosiain_OH_C2H2"), + ("2006_Joshi_OH_CO", "2006_Joshi_OH_CO"), + ("2009_Sharma_C5H5_CH3_highP", "2009_Sharma_C5H5_CH3_highP"), + ("2015_Buras_C2H3_C4H6_highP", "2015_Buras_C2H3_C4H6_highP"), + ( + "Aromatics_high_pressure/C10H10_1", + "Aromatics_high_pressure/C10H10_1", + ), + ( + "Aromatics_high_pressure/C10H10_2", + "Aromatics_high_pressure/C10H10_2", + ), + ( + "Aromatics_high_pressure/C10H10_H_abstraction", + "Aromatics_high_pressure/C10H10_H_abstraction", + ), + ( + "Aromatics_high_pressure/C10H11_1", + "Aromatics_high_pressure/C10H11_1", + ), + ( + "Aromatics_high_pressure/C10H11_2", + "Aromatics_high_pressure/C10H11_2", + ), + ( + "Aromatics_high_pressure/C10H11_3", + "Aromatics_high_pressure/C10H11_3", + ), + ( + "Aromatics_high_pressure/C10H11_4", + "Aromatics_high_pressure/C10H11_4", + ), + ("Aromatics_high_pressure/C10H7", "Aromatics_high_pressure/C10H7"), + ( + "Aromatics_high_pressure/C10H8_H_abstraction_H_recomb", + "Aromatics_high_pressure/C10H8_H_abstraction_H_recomb", + ), + ( + "Aromatics_high_pressure/C10H9_1", + "Aromatics_high_pressure/C10H9_1", + ), + ( + "Aromatics_high_pressure/C10H9_2", + "Aromatics_high_pressure/C10H9_2", + ), + ( + "Aromatics_high_pressure/C10H9_3", + "Aromatics_high_pressure/C10H9_3", + ), + ( + "Aromatics_high_pressure/C10H9_4", + "Aromatics_high_pressure/C10H9_4", + ), + ( + "Aromatics_high_pressure/C12H10_1", + "Aromatics_high_pressure/C12H10_1", + ), + ( + "Aromatics_high_pressure/C12H10_2", + "Aromatics_high_pressure/C12H10_2", + ), + ( + "Aromatics_high_pressure/C12H10_H_abstraction", + "Aromatics_high_pressure/C12H10_H_abstraction", + ), + ( + "Aromatics_high_pressure/C12H11", + "Aromatics_high_pressure/C12H11", + ), + ( + "Aromatics_high_pressure/C12H8_H_abstraction", + "Aromatics_high_pressure/C12H8_H_abstraction", + ), + ("Aromatics_high_pressure/C12H9", "Aromatics_high_pressure/C12H9"), + ( + "Aromatics_high_pressure/C14H10_H_abstraction_H_recomb", + "Aromatics_high_pressure/C14H10_H_abstraction_H_recomb", + ), + ( + "Aromatics_high_pressure/C14H11_1", + "Aromatics_high_pressure/C14H11_1", + ), + ( + "Aromatics_high_pressure/C14H11_2", + "Aromatics_high_pressure/C14H11_2", + ), + ( + "Aromatics_high_pressure/C14H11_3", + "Aromatics_high_pressure/C14H11_3", + ), + ( + "Aromatics_high_pressure/C14H11_4", + "Aromatics_high_pressure/C14H11_4", + ), + ("Aromatics_high_pressure/C14H9", "Aromatics_high_pressure/C14H9"), + ( + "Aromatics_high_pressure/C16H11", + "Aromatics_high_pressure/C16H11", + ), + ("Aromatics_high_pressure/C7H8", "Aromatics_high_pressure/C7H8"), + ( + "Aromatics_high_pressure/C7H8_H_abstraction", + "Aromatics_high_pressure/C7H8_H_abstraction", + ), + ("Aromatics_high_pressure/C7H9", "Aromatics_high_pressure/C7H9"), + ( + "Aromatics_high_pressure/C8H6_H_abstraction", + "Aromatics_high_pressure/C8H6_H_abstraction", + ), + ("Aromatics_high_pressure/C8H7", "Aromatics_high_pressure/C8H7"), + ( + "Aromatics_high_pressure/C8H8_H_abstraction", + "Aromatics_high_pressure/C8H8_H_abstraction", + ), + ("Aromatics_high_pressure/C8H9", "Aromatics_high_pressure/C8H9"), + ( + "Aromatics_high_pressure/C9H10_H_abstraction", + "Aromatics_high_pressure/C9H10_H_abstraction", + ), + ("Aromatics_high_pressure/C9H11", "Aromatics_high_pressure/C9H11"), + ("Aromatics_high_pressure/C9H7", "Aromatics_high_pressure/C9H7"), + ( + "Aromatics_high_pressure/C9H8_1", + "Aromatics_high_pressure/C9H8_1", + ), + ( + "Aromatics_high_pressure/C9H8_2", + "Aromatics_high_pressure/C9H8_2", + ), + ( + "Aromatics_high_pressure/C9H8_H_abstraction", + "Aromatics_high_pressure/C9H8_H_abstraction", + ), + ( + "Aromatics_high_pressure/C9H9_1", + "Aromatics_high_pressure/C9H9_1", + ), + ( + "Aromatics_high_pressure/C9H9_2", + "Aromatics_high_pressure/C9H9_2", + ), + ("BurkeH2O2inArHe", "BurkeH2O2inArHe"), + ("BurkeH2O2inN2", "BurkeH2O2inN2"), + ("Butadiene_Dimerization", "Butadiene_Dimerization"), + ("C10H11", "C10H11"), + ("C12H11_pdep", "C12H11_pdep"), + ("C2H2_init", "C2H2_init"), + ("C2H4+O_Klipp2017", "C2H4+O_Klipp2017"), + ("C3", "C3"), + ("C6H5_C4H4_Mebel", "C6H5_C4H4_Mebel"), + ("CF2BrCl", "CF2BrCl"), + ("CH3Cl", "CH3Cl"), + ("Chernov", "Chernov"), + ("Chung_solvation_corrections", "Chung_solvation_corrections"), + ("CurranPentane", "CurranPentane"), + ("DMSOxy", "DMSOxy"), + ("DTU_mech_CH3Cl", "DTU_mech_CH3Cl"), + ("Dooley/C1", "Dooley/C1"), + ("Dooley/methylformate", "Dooley/methylformate"), + ("Dooley/methylformate_2", "Dooley/methylformate_2"), + ( + "Dooley/methylformate_all_ARHEbathgas", + "Dooley/methylformate_all_ARHEbathgas", + ), + ( + "Dooley/methylformate_all_N2bathgas", + "Dooley/methylformate_all_N2bathgas", + ), + ("ERC-FoundationFuelv0.9", "ERC-FoundationFuelv0.9"), + ("Ethylamine", "Ethylamine"), + ("FFCM1(-)", "FFCM1(-)"), + ( + "First_to_Second_Aromatic_Ring/2005_Ismail_C6H5_C4H6_highP", + "First_to_Second_Aromatic_Ring/2005_Ismail_C6H5_C4H6_highP", + ), + ( + "First_to_Second_Aromatic_Ring/2012_Matsugi_C3H3_C7H7_highP", + "First_to_Second_Aromatic_Ring/2012_Matsugi_C3H3_C7H7_highP", + ), + ( + "First_to_Second_Aromatic_Ring/2016_Mebel_C10H9_highP", + "First_to_Second_Aromatic_Ring/2016_Mebel_C10H9_highP", + ), + ( + "First_to_Second_Aromatic_Ring/2016_Mebel_C9H9_highP", + "First_to_Second_Aromatic_Ring/2016_Mebel_C9H9_highP", + ), + ( + "First_to_Second_Aromatic_Ring/2016_Mebel_Indene_CH3_highP", + "First_to_Second_Aromatic_Ring/2016_Mebel_Indene_CH3_highP", + ), + ( + "First_to_Second_Aromatic_Ring/2017_Buras_C6H5_C3H6_highP", + "First_to_Second_Aromatic_Ring/2017_Buras_C6H5_C3H6_highP", + ), + ( + "First_to_Second_Aromatic_Ring/2017_Mebel_C6H4C2H_C2H2_highP", + "First_to_Second_Aromatic_Ring/2017_Mebel_C6H4C2H_C2H2_highP", + ), + ( + "First_to_Second_Aromatic_Ring/2017_Mebel_C6H5C2H2_C2H2_highP", + "First_to_Second_Aromatic_Ring/2017_Mebel_C6H5C2H2_C2H2_highP", + ), + ( + "First_to_Second_Aromatic_Ring/2017_Mebel_C6H5_C2H2_highP", + "First_to_Second_Aromatic_Ring/2017_Mebel_C6H5_C2H2_highP", + ), + ( + "First_to_Second_Aromatic_Ring/2017_Mebel_C6H5_C4H4_highP", + "First_to_Second_Aromatic_Ring/2017_Mebel_C6H5_C4H4_highP", + ), + ( + "First_to_Second_Aromatic_Ring/phenyl_diacetylene_effective", + "First_to_Second_Aromatic_Ring/phenyl_diacetylene_effective", + ), + ("Fulvene_H", "Fulvene_H"), + ("GRI-HCO", "GRI-HCO"), + ("GRI-Mech3.0", "GRI-Mech3.0"), + ("GRI-Mech3.0-N", "GRI-Mech3.0-N"), + ("Glarborg/C0", "Glarborg/C0"), + ("Glarborg/C1", "Glarborg/C1"), + ("Glarborg/C2", "Glarborg/C2"), + ("Glarborg/C3", "Glarborg/C3"), + ("Glarborg/highP", "Glarborg/highP"), + ("HydrazinePDep", "HydrazinePDep"), + ("Iodine-R_recombination", "Iodine-R_recombination"), + ("JetSurF1.0", "JetSurF1.0"), + ("JetSurF2.0", "JetSurF2.0"), + ("Klippenstein_Glarborg2016", "Klippenstein_Glarborg2016"), + ("Lai_Hexylbenzene", "Lai_Hexylbenzene"), + ("LithiumAnalogyKinetics", "LithiumAnalogyKinetics"), + ("LithiumPrimaryChargedKinetics", "LithiumPrimaryChargedKinetics"), + ("LithiumPrimaryKinetics", "LithiumPrimaryKinetics"), + ("LithiumPrimaryKinetics2", "LithiumPrimaryKinetics2"), + ("LithiumSurface", "LithiumSurface"), + ("LithiumSurfaceAnalogy", "LithiumSurfaceAnalogy"), + ("Mebel_C6H5_C2H2", "Mebel_C6H5_C2H2"), + ("Mebel_Naphthyl", "Mebel_Naphthyl"), + ("Methylformate", "Methylformate"), + ("N-S_interactions", "N-S_interactions"), + ("NIST_Fluorine/CH2F2/full", "NIST_Fluorine/CH2F2/full"), + ("NIST_Fluorine/CH2F2/seed", "NIST_Fluorine/CH2F2/seed"), + ("NIST_Fluorine/full", "NIST_Fluorine/full"), + ("NIST_Fluorine/seed", "NIST_Fluorine/seed"), + ("NOx2018", "NOx2018"), + ("Narayanaswamy", "Narayanaswamy"), + ("Nitrogen_Dean_and_Bozzelli", "Nitrogen_Dean_and_Bozzelli"), + ( + "Nitrogen_Glarborg_Gimenez_et_al", + "Nitrogen_Glarborg_Gimenez_et_al", + ), + ( + "Nitrogen_Glarborg_Lucassen_et_al", + "Nitrogen_Glarborg_Lucassen_et_al", + ), + ("Nitrogen_Glarborg_Zhang_et_al", "Nitrogen_Glarborg_Zhang_et_al"), + ("Sulfur/DMDS", "Sulfur/DMDS"), + ("Sulfur/DMS", "Sulfur/DMS"), + ("Sulfur/DTBS", "Sulfur/DTBS"), + ("Sulfur/GlarborgBozzelli", "Sulfur/GlarborgBozzelli"), + ("Sulfur/GlarborgH2S", "Sulfur/GlarborgH2S"), + ("Sulfur/GlarborgH2S/alt", "Sulfur/GlarborgH2S/alt"), + ("Sulfur/GlarborgMarshall", "Sulfur/GlarborgMarshall"), + ("Sulfur/GlarborgNS", "Sulfur/GlarborgNS"), + ("Sulfur/HSSH_1bar", "Sulfur/HSSH_1bar"), + ("Sulfur/Hexanethial_nr", "Sulfur/Hexanethial_nr"), + ("Sulfur/Sendt", "Sulfur/Sendt"), + ("Sulfur/TP_Song", "Sulfur/TP_Song"), + ("Sulfur/Thial_Hydrolysis", "Sulfur/Thial_Hydrolysis"), + ("Surface/Ammonia/Duan_Ni111", "Surface/Ammonia/Duan_Ni111"), + ("Surface/Ammonia/Duan_Ni211", "Surface/Ammonia/Duan_Ni211"), + ( + "Surface/Ammonia/Kraehnert_Pt111", + "Surface/Ammonia/Kraehnert_Pt111", + ), + ("Surface/Ammonia/Novell_Pd111", "Surface/Ammonia/Novell_Pd111"), + ("Surface/Ammonia/Novell_Pt111", "Surface/Ammonia/Novell_Pt111"), + ("Surface/Ammonia/Novell_Rh111", "Surface/Ammonia/Novell_Rh111"), + ( + "Surface/Ammonia/Offermans_Pt111", + "Surface/Ammonia/Offermans_Pt111", + ), + ("Surface/Ammonia/Popa_Rh111", "Surface/Ammonia/Popa_Rh111"), + ("Surface/Ammonia/Rebrov_Pt111", "Surface/Ammonia/Rebrov_Pt111"), + ("Surface/Ammonia/Roldan_Ru0001", "Surface/Ammonia/Roldan_Ru0001"), + ("Surface/Ammonia/Scheuer_Pt", "Surface/Ammonia/Scheuer_Pt"), + ( + "Surface/Ammonia/Schneider_Pd111", + "Surface/Ammonia/Schneider_Pd111", + ), + ( + "Surface/Ammonia/Schneider_Pd211", + "Surface/Ammonia/Schneider_Pd211", + ), + ( + "Surface/Ammonia/Schneider_Pt111", + "Surface/Ammonia/Schneider_Pt111", + ), + ( + "Surface/Ammonia/Schneider_Pt211", + "Surface/Ammonia/Schneider_Pt211", + ), + ( + "Surface/Ammonia/Schneider_Rh111", + "Surface/Ammonia/Schneider_Rh111", + ), + ( + "Surface/Ammonia/Schneider_Rh211", + "Surface/Ammonia/Schneider_Rh211", + ), + ( + "Surface/Ammonia/Vlachos_Ru0001", + "Surface/Ammonia/Vlachos_Ru0001", + ), + ( + "Surface/CPOX_Pt/Deutschmann2006_adjusted", + "Surface/CPOX_Pt/Deutschmann2006_adjusted", + ), + ("Surface/DOC/Arevalo_Pt111", "Surface/DOC/Arevalo_Pt111"), + ("Surface/DOC/Ishikawa_Rh111", "Surface/DOC/Ishikawa_Rh111"), + ("Surface/DOC/Mhadeshwar_Pt111", "Surface/DOC/Mhadeshwar_Pt111"), + ("Surface/DOC/Nitrogen", "Surface/DOC/Nitrogen"), + ("Surface/Example", "Surface/Example"), + ( + "Surface/Hydrazine/Roldan_Cu111", + "Surface/Hydrazine/Roldan_Cu111", + ), + ( + "Surface/Hydrazine/Roldan_Ir111", + "Surface/Hydrazine/Roldan_Ir111", + ), + ( + "Surface/Methane/Deutschmann_Ni", + "Surface/Methane/Deutschmann_Ni", + ), + ( + "Surface/Methane/Deutschmann_Ni_full", + "Surface/Methane/Deutschmann_Ni_full", + ), + ( + "Surface/Methane/Deutschmann_Pt", + "Surface/Methane/Deutschmann_Pt", + ), + ("Surface/Methane/Vlachos_Pt111", "Surface/Methane/Vlachos_Pt111"), + ("Surface/Methane/Vlachos_Rh", "Surface/Methane/Vlachos_Rh"), + ("TEOS", "TEOS"), + ("Xu_cyclopentadiene", "Xu_cyclopentadiene"), + ("YF/full", "YF/full"), + ("YF/seed", "YF/seed"), + ("biCPD_H_shift", "biCPD_H_shift"), + ("c-C5H5_CH3_Sharma", "c-C5H5_CH3_Sharma"), + ("combustion_core/version2", "combustion_core/version2"), + ("combustion_core/version3", "combustion_core/version3"), + ("combustion_core/version4", "combustion_core/version4"), + ("combustion_core/version5", "combustion_core/version5"), + ("fascella", "fascella"), + ("kislovB", "kislovB"), + ("naphthalene_H", "naphthalene_H"), + ("primaryH2O2", "primaryH2O2"), + ("primaryNitrogenLibrary", "primaryNitrogenLibrary"), + ("primaryNitrogenLibrary/LowT", "primaryNitrogenLibrary/LowT"), + ("primarySulfurLibrary", "primarySulfurLibrary"), + ("vinylCPD_H", "vinylCPD_H"), + ], + max_length=200, + ), + ), + migrations.AlterField( + model_name="reactor", + name="id", + field=models.BigAutoField( + auto_created=True, primary_key=True, serialize=False, verbose_name="ID" + ), + ), + migrations.AlterField( + model_name="reactorspecies", + name="id", + field=models.BigAutoField( + auto_created=True, primary_key=True, serialize=False, verbose_name="ID" + ), + ), + migrations.AlterField( + model_name="thermolibrary", + name="id", + field=models.BigAutoField( + auto_created=True, primary_key=True, serialize=False, verbose_name="ID" + ), + ), + migrations.AlterField( + model_name="thermolibrary", + name="thermo_lib", + field=models.CharField( + blank=True, + choices=[ + ("2-BTP", "2-BTP"), + ("2-BTP_G4", "2-BTP_G4"), + ("BurcatNS", "BurcatNS"), + ("BurkeH2O2", "BurkeH2O2"), + ("Butadiene_Dimerization", "Butadiene_Dimerization"), + ("C10H11", "C10H11"), + ("C3", "C3"), + ("CBS_QB3_1dHR", "CBS_QB3_1dHR"), + ("CH", "CH"), + ("CHN", "CHN"), + ("CHO", "CHO"), + ("CHOBr_G4", "CHOBr_G4"), + ("CHOClBr_G4", "CHOClBr_G4"), + ("CHOCl_G4", "CHOCl_G4"), + ("CHOFBr_G4", "CHOFBr_G4"), + ("CHOFClBr_G4", "CHOFClBr_G4"), + ("CHOFCl_G4", "CHOFCl_G4"), + ("CHOF_G4", "CHOF_G4"), + ("CHON", "CHON"), + ("CHON_G4", "CHON_G4"), + ("CN", "CN"), + ("Chernov", "Chernov"), + ("Chlorinated_Hydrocarbons", "Chlorinated_Hydrocarbons"), + ("Chlorination", "Chlorination"), + ("CurranPentane", "CurranPentane"), + ("DFT_QCI_thermo", "DFT_QCI_thermo"), + ("Elliott_OOQOOH", "Elliott_OOQOOH"), + ("FFCM1(-)", "FFCM1(-)"), + ("Fluorine", "Fluorine"), + ("Fulvene_H", "Fulvene_H"), + ("GRI-Mech3.0", "GRI-Mech3.0"), + ("GRI-Mech3.0-N", "GRI-Mech3.0-N"), + ("JetSurF1.0", "JetSurF1.0"), + ("JetSurF2.0", "JetSurF2.0"), + ("Klippenstein_Glarborg2016", "Klippenstein_Glarborg2016"), + ("Lai_Hexylbenzene", "Lai_Hexylbenzene"), + ("LithiumAdditionalThermo", "LithiumAdditionalThermo"), + ("LithiumPrimaryThermo", "LithiumPrimaryThermo"), + ("LithiumPrimaryThermo2", "LithiumPrimaryThermo2"), + ("LithiumSurface", "LithiumSurface"), + ("NH3", "NH3"), + ("NISTThermoLibrary", "NISTThermoLibrary"), + ("NOx2018", "NOx2018"), + ("Narayanaswamy", "Narayanaswamy"), + ("NitrogenCurran", "NitrogenCurran"), + ("SABIC_aromatics", "SABIC_aromatics"), + ("SABIC_aromatics_1dHR", "SABIC_aromatics_1dHR"), + ("SABIC_aromatics_1dHR_extended", "SABIC_aromatics_1dHR_extended"), + ( + "Spiekermann_refining_elementary_reactions", + "Spiekermann_refining_elementary_reactions", + ), + ("SulfurGlarborgBozzelli", "SulfurGlarborgBozzelli"), + ("SulfurGlarborgH2S", "SulfurGlarborgH2S"), + ("SulfurGlarborgMarshall", "SulfurGlarborgMarshall"), + ("SulfurGlarborgNS", "SulfurGlarborgNS"), + ("SulfurHaynes", "SulfurHaynes"), + ("SulfurLibrary", "SulfurLibrary"), + ("USC-Mech-ii", "USC-Mech-ii"), + ("bio_oil", "bio_oil"), + ("computationalLithiumElectrode", "computationalLithiumElectrode"), + ("electrocatLiThermo", "electrocatLiThermo"), + ("electrocatThermo", "electrocatThermo"), + ("halogens", "halogens"), + ("heavy_oil_ccsdtf12_1dHR", "heavy_oil_ccsdtf12_1dHR"), + ("iodinated_Hydrocarbons", "iodinated_Hydrocarbons"), + ("naphthalene_H", "naphthalene_H"), + ("primaryNS", "primaryNS"), + ("primaryThermoLibrary", "primaryThermoLibrary"), + ("s3_5_7_ane", "s3_5_7_ane"), + ("surfaceThermoLi", "surfaceThermoLi"), + ("surfaceThermoNi111", "surfaceThermoNi111"), + ("surfaceThermoPt111", "surfaceThermoPt111"), + ("thermo_DFT_CCSDTF12_BAC", "thermo_DFT_CCSDTF12_BAC"), + ("vinylCPD_H", "vinylCPD_H"), + ], + max_length=200, + ), + ), + ] diff --git a/rmgweb/rmg/views.py b/rmgweb/rmg/views.py index 31b0339e..3253f2ce 100644 --- a/rmgweb/rmg/views.py +++ b/rmgweb/rmg/views.py @@ -129,8 +129,6 @@ def generateFlux(request): to generate a flux diagram video. """ - from rmgpy.tools.fluxdiagram import create_flux_diagram - flux = FluxDiagram() path = '' flux.deleteDir() @@ -144,7 +142,6 @@ def generateFlux(request): arguments["chem_output"] = '' if 'chem_output' in request.FILES: arguments["chem_output"] = os.path.join(flux.path, 'chemkin_output.out') - arguments['java'] = form.cleaned_data['java'] arguments['max_nodes'] = form.cleaned_data['max_nodes'] arguments['max_edges'] = form.cleaned_data['max_edges'] arguments['time_step'] = form.cleaned_data['time_step'] diff --git a/rmgweb/settings.py b/rmgweb/settings.py index 2cfdcdb8..0ee8e024 100644 --- a/rmgweb/settings.py +++ b/rmgweb/settings.py @@ -169,3 +169,7 @@ # Settings relating to user account management LOGIN_URL = '/login' LOGIN_REDIRECT_URL = '/' + +# Set auto field for auto-created primary key fields +DEFAULT_AUTO_FIELD = 'django.db.models.BigAutoField' +