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LeenFahoumLeenFahoum
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Added new test cases for hydrolysis reactions
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‎arc/job/adapters/ts/heuristics_test.py‎

Lines changed: 201 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -723,6 +723,181 @@ def setUpClass(cls):
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H 2.16545120 -0.18719811 0.32509986
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H 1.18773917 -1.27609387 -0.39480684""")
725725

726+
cls.ethylformate=ARCSpecies(label='ester', smiles='C(=O)OCC', xyz="""C 1.99586172 0.19036914 -0.36679471
727+
O 2.25425046 -0.87536273 -0.90186346
728+
O 0.78623654 0.59256044 0.09529054
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C -0.25788216 -0.37075951 -0.08947404
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C -1.54273468 0.20899764 0.46938847
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H 2.73205108 0.98834164 -0.18363561
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H -0.38138362 -0.58208128 -1.15762603
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H -0.00686243 -1.29503416 0.44303289
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H -1.79655123 1.14500808 -0.03910211
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H -1.42879816 0.44494449 1.53261426
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H -2.37206772 -0.49381423 0.35039549""")
737+
738+
cls.ethylacetate=ARCSpecies(label='ester', smiles='CC(=O)OCC', xyz="""C 2.44505336 0.33426556 -0.05839486
739+
C 1.22268719 -0.52813666 0.01896600
740+
O 1.23293886 -1.74943142 -0.03929182
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O 0.11391589 0.24824549 0.16222715
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C -1.11109125 -0.48993657 0.24566449
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C -2.25017001 0.49859954 0.40179846
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H 2.37692031 0.99705687 -0.92466676
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H 3.32902965 -0.29956749 -0.17330464
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H 2.54916374 0.91324784 0.86263828
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H -1.08105124 -1.15952384 1.11255293
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H -1.25277743 -1.07595826 -0.66934869
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H -2.28059310 1.18899674 -0.44763085
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H -3.21043340 -0.02017141 0.47000585
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H -2.11200849 1.10694712 1.30175876""")
752+
753+
cls.formamide=ARCSpecies(label='ester', smiles='C(=O)N', xyz="""C 0.66113164 0.06611808 0.00079506
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O 1.38598846 -0.91607505 -0.00735590
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N -0.69555709 -0.00881387 -0.00031363
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H 1.03653613 1.10209352 0.00978431
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H -1.12197750 -0.92617241 -0.00830616
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H -1.28689208 0.80964023 0.00647320""")
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cls.bnx_f1=ARCSpecies(label='ester', smiles='CCCOC1=CC=C(C=C1)C(=O)OC', xyz="""C 5.20467948 -0.15003714 0.72624211
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C 4.10767923 -0.62237574 -0.21087592
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C 4.34447914 -0.15561449 -1.64408558
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O 3.26890983 -0.64483699 -2.44578685
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C 3.29118735 -0.33412483 -3.77677733
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C 2.21433376 -0.83929261 -4.51055487
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C 2.10737798 -0.59936679 -5.88405259
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C 3.08616420 0.15493126 -6.54028399
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C 4.16565998 0.66124610 -5.80429918
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C 4.26795709 0.41803052 -4.42902757
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C 3.03042695 0.44566815 -7.99895653
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O 3.87543876 1.10179559 -8.58766345
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O 1.92861783 -0.11385308 -8.55840352
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C 1.80696249 0.12354204 -9.96147727
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H 5.25998359 0.94304563 0.74591684
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H 6.17994890 -0.53809376 0.41553910
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H 5.00941330 -0.49860062 1.74516771
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H 4.04319965 -1.71688718 -0.18678487
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H 3.13537739 -0.25529478 0.13923043
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H 4.36601425 0.94049954 -1.67205247
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H 5.29755064 -0.55929731 -2.00658691
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H 1.44982662 -1.42656261 -4.00648122
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H 1.25652022 -1.00756880 -6.42325179
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H 4.93613852 1.25022419 -6.29941869
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H 5.12177445 0.83074704 -3.90182581
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H 2.65750833 -0.30782687 -10.49860431
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H 0.89338267 -0.36617819 -10.30974208
787+
H 1.72346566 1.19609277 -10.16315965""")
788+
789+
cls.bnx_p1=ARCSpecies(label='ester', smiles='CCCOC1=CC=C(C=C1)C(=O)O', xyz="""O -1.05338860 -0.49459123 0.45433151
790+
O 5.13862140 -0.22094435 -0.68869777
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O 4.57807524 1.57965936 -1.88577315
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C -3.42085472 -0.25697186 0.64751969
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C -2.14761349 0.32332827 0.03912047
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C -4.64927948 0.54759838 0.26236254
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C 2.85198496 0.34993336 -0.74533293
796+
C 0.19173972 -0.14271806 0.01298509
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C 2.54764439 -0.73883412 0.07699459
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C 1.82173300 1.18938071 -1.18568364
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C 1.22241669 -0.97936348 0.45127419
800+
C 0.49608991 0.94385865 -0.80778309
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C 4.23881532 0.65281393 -1.17346771
802+
H -3.54124711 -1.29796685 0.32420967
803+
H -3.32455652 -0.28962027 1.73946984
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H -2.00693116 1.35011699 0.39775996
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H -2.22928736 0.31542364 -1.05448628
806+
H -4.78516465 0.56022893 -0.82375507
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H -4.56557677 1.58206173 0.61043580
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H -5.54595968 0.10957597 0.71173476
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H 0.99034676 -1.82776386 1.09127862
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H 3.32888325 -1.40574911 0.43254574
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H 2.04632409 2.04035660 -1.82637777
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H -0.27029742 1.61995156 -1.17214677
813+
H 5.99292660 0.09870349 -1.04724220""")
814+
815+
cls.bnx_f2=ARCSpecies(label='ester', smiles='NC1=CC=C(C=C1)C(=O)OC', xyz="""N -3.83649893 0.20343671 -0.01344052
816+
C -2.46917792 0.06645785 0.12630519
817+
C -1.59611579 0.72137484 -0.74500474
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C -0.20916256 0.60592246 -0.59423236
819+
C 0.32287720 -0.16660056 0.44440659
820+
C -0.54900848 -0.81517009 1.32649211
821+
C -1.93363867 -0.69364323 1.16769208
822+
C 1.78735796 -0.32670226 0.65590080
823+
O 2.27003903 -0.99451517 1.55712008
824+
O 2.48573817 0.36349500 -0.28051357
825+
C 3.90306571 0.25681748 -0.14109274
826+
H -4.46823135 -0.30566106 0.58926962
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H -4.22627728 0.71526682 -0.79270447
828+
H -1.98875564 1.33120830 -1.55469054
829+
H 0.43893324 1.12708495 -1.29394558
830+
H -0.15671628 -1.41682253 2.14413044
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H -2.59055688 -1.20169637 1.86896390
832+
H 4.22180193 -0.78471262 -0.24898609
833+
H 4.36682046 0.84482791 -0.93791520
834+
H 4.22549472 0.66412908 0.82231655""")
835+
836+
cls.bnx_p2=ARCSpecies(label='ester', smiles='NC1=CC=C(C=C1)C(=O)O', xyz="""N -3.03935021 0.17963190 -0.46954101
837+
C -1.68757548 0.08648801 -0.20050434
838+
C -0.89427381 -0.85322350 -0.86256026
839+
C 0.47926615 -0.93464609 -0.61086363
840+
C 1.07787117 -0.06475715 0.30599108
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C 0.29211829 0.88641610 0.96405605
842+
C -1.08121192 0.95998681 0.70551041
843+
C 2.53647223 -0.18454638 0.54276607
844+
O 3.28325243 -0.98321417 0.00797336
845+
O 2.99521383 0.70410483 1.44213129
846+
H -3.62254412 0.82732442 0.04190905
847+
H -3.48672273 -0.48088872 -1.08999192
848+
H -1.33901720 -1.53438323 -1.58339257
849+
H 1.07703448 -1.67719837 -1.13537512
850+
H 0.73476656 1.57709813 1.67712599
851+
H -1.67469669 1.70996460 1.22200843
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H 3.95423319 0.50884869 1.49388003""")
853+
854+
cls.bnx_f3=ARCSpecies(label='ester', smiles='COC1=CC=C(C=C1N)C(=O)OC', xyz="""C 3.96349539 -0.82819603 0.88278635
855+
O 3.16556014 -0.14971720 -0.07809650
856+
C 1.80079154 -0.23923549 0.06571082
857+
C 1.14606258 -0.99678896 1.04018439
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C -0.25081994 -1.01148655 1.09535720
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C -1.00593186 -0.26673524 0.18151953
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C -0.34985656 0.49149503 -0.79622199
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C 1.04702552 0.49730122 -0.87329841
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N 1.68300950 1.29493154 -1.81923559
863+
C -2.48881414 -0.31173585 0.29561235
864+
O -3.07825767 -0.95870154 1.14734564
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O -3.07038278 0.45086140 -0.66356065
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C -4.49772020 0.45538007 -0.61470557
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H 3.81022296 -1.91093833 0.82818088
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H 5.01307021 -0.62933882 0.64547019
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H 3.77404454 -0.45064023 1.89305626
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H 1.68917532 -1.58548813 1.77162056
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H -0.74796862 -1.60520090 1.86087085
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H -0.92024719 1.08519721 -1.50495557
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H 2.69357072 1.22047465 -1.87128966
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H 1.17697370 1.71765616 -2.58232968
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H -4.84764771 0.86636669 0.33747895
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H -4.88991912 -0.55466528 -0.76960053
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H -4.86209933 1.09574401 -1.42273018""")
878+
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cls.bnx_p3=ARCSpecies(label='ester', smiles='COC1=CC=C(C=C1N)C(=O)O', xyz="""C -3.38837853 -0.49895382 -0.13706963
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O -2.38459739 0.47549610 -0.38808324
881+
C -1.08586350 0.12525170 -0.10127915
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C -0.69181914 -1.08468098 0.47722510
883+
C 0.66111156 -1.33676259 0.72219228
884+
C 1.62896200 -0.38415069 0.38687723
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C 1.23730905 0.82850896 -0.19103200
886+
C -0.11517199 1.09919571 -0.42190169
887+
N -0.48556585 2.28805576 -1.04216410
888+
C 3.05092881 -0.70379748 0.65652633
889+
O 3.46693927 -1.73751752 1.14663053
890+
O 3.88884384 0.28633997 0.30248076
891+
H -3.45678090 -0.72774798 0.93147026
892+
H -4.34882856 -0.07668611 -0.44803400
893+
H -3.21735338 -1.40535412 -0.72721794
894+
H -1.40866191 -1.85218496 0.74840987
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H 0.95693243 -2.28298053 1.17190274
896+
H 1.98435681 1.56804597 -0.46560923
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H -1.48056061 2.46285041 -1.13469157
898+
H 0.16552277 3.04992341 -1.15562030
899+
H 4.77508221 -0.06185183 0.53448907""")
900+
726901
cls.zmat_1 = {'symbols': ('C', 'C', 'O', 'O', 'H', 'H', 'H', 'H', 'H', 'H'),
727902
'coords': ((None, None, None), ('R_1_0', None, None), ('R_2_1', 'A_2_1_0', None),
728903
('R_3_2', 'A_3_2_1', 'D_3_2_1_0'), ('R_4_0', 'A_4_0_1', 'D_4_0_1_3'),
@@ -2584,6 +2759,27 @@ def test_ester_hydrolysis(self):
25842759
aminobenzene=self.aminobenzene
25852760
carboxyl= self.carboxyl
25862761
rxn9=ARCReaction(r_species=[benzamide2, water], p_species=[aminobenzene, carboxyl])
2762+
#RXN10
2763+
ethylformate=self.ethylformate
2764+
rxn10=ARCReaction(r_species=[ethylformate, water], p_species=[formicacid, ethanol])
2765+
#RXN11
2766+
ethylacetate=self.ethylacetate
2767+
rxn11=ARCReaction(r_species=[ethylacetate, water], p_species=[acetic_acid, ethanol])
2768+
#RXN12
2769+
formamide=self.formamide
2770+
rxn12=ARCReaction(r_species=[formamide, water], p_species=[formicacid, ammonia])
2771+
#RXN13
2772+
bnx_f1=self.bnx_f1
2773+
bnx_p1=self.bnx_p1
2774+
rxn13=ARCReaction(r_species=[bnx_f1, water], p_species=[bnx_p1, methanol])
2775+
#RXN14
2776+
bnx_f2=self.bnx_f2
2777+
bnx_p2=self.bnx_p2
2778+
rxn14=ARCReaction(r_species=[bnx_f2, water], p_species=[bnx_p2, methanol])
2779+
#RXN15
2780+
bnx_f3=self.bnx_f3
2781+
bnx_p3=self.bnx_p3
2782+
rxn15=ARCReaction(r_species=[bnx_f3, water], p_species=[bnx_p3, methanol])
25872783

25882784
tested_rxn=rxn1
25892785
reactant = tested_rxn.r_species[0]
@@ -2603,6 +2799,7 @@ def test_ester_hydrolysis(self):
26032799
print(family)
26042800
a,b,f,O,H1,d= guess_block['indices'][0], guess_block['indices'][1], guess_block['indices'][2], guess_block['indices'][3], guess_block['indices'][4], guess_block['indices'][5]
26052801
print(a,b,f,d,O,H1)
2802+
print(guess_block['adjust_dihedral'])
26062803
for guess in guess_block['xyz_guesses']:
26072804
xyz_str = xyz_to_str(guess)
26082805
print(xyz_str)
@@ -2656,6 +2853,7 @@ def test_ether_hydrolysis(self):
26562853
print(guess_block['family'])
26572854
a, b, f, O, H1, d = guess_block['indices'][0], guess_block['indices'][1], guess_block['indices'][2], guess_block['indices'][3], guess_block['indices'][4], guess_block['indices'][5]
26582855
print(a, b, f, d, O, H1)
2856+
print(guess_block['adjust_dihedral'])
26592857
for guess in guess_block['xyz_guesses']:
26602858
xyz_str = xyz_to_str(guess)
26612859
print(xyz_str)
@@ -2708,6 +2906,7 @@ def test_imine_hydrolysis(self):
27082906
print(block['family'])
27092907
a, b, f, O, H1, d = block['indices'][0], block['indices'][1], block['indices'][2], block['indices'][3], block['indices'][4], block['indices'][5]
27102908
print(a, b, f, d, O, H1)
2909+
print(block['adjust_dihedral'])
27112910
for guess in block['xyz_guesses']:
27122911
xyz_str = xyz_to_str(guess)
27132912
print(xyz_str)
@@ -2757,8 +2956,9 @@ def test_nitrile_hydrolysis(self):
27572956
self.assertIn('nitrile_hydrolysis', families)
27582957
xyz_guesses_total, zmats_total = hydrolysis(tested_rxn)
27592958
for block in xyz_guesses_total:
2760-
a, b, f, O, H1 = block['indices'][0], block['indices'][1], block['indices'][2], block['indices'][4], block['indices'][5]
2959+
a, b, f, O, H1 = block['indices'][0], block['indices'][1], block['indices'][2], block['indices'][3], block['indices'][4],
27612960
print(block['family'])
2961+
print(block['adjust_dihedral'])
27622962
for guess in block['xyz_guesses']:
27632963
xyz_str = xyz_to_str(guess)
27642964
print(xyz_str)

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