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VRAI-selectivity_testTS1freq.log
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VRAI-selectivity_testTS1freq.log
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***********************************
VRAI-selectivity_
Python code to predict selectivity from two transition states
@author: Sanha Lee
University of Cambridge
Run date: 2020 Sep 13 13:56:53
***********************************
Reading TS1: testTS1freq.mol
Reading INT: testINTfreq.mol
Reading P1: testP1freq.mol
Reading P2: testP2freq.mol
Reading TS1 freq: testTS1freq.out
Reading INT freq: testINTfreq.out
Inputs detected for TS2A and TS2B
Reading TS2A freq: testTS2Afreq.out
Reading TS2B freq: testTS2Bfreq.out
No. of Atoms: 16
Alignment weight option is set equal for all atoms
RDKIT Mol object successfully created for: testTS1freq.mol
<rdkit.Chem.rdchem.Mol object at 0x120ff7210>
Mol object successfully created for: testINTfreq.mol
<rdkit.Chem.rdchem.Mol object at 0x120ff72f0>
Mol object successfully created for: testP1freq.mol
<rdkit.Chem.rdchem.Mol object at 0x120ff7360>
Mol object successfully created for: testP2freq.mol
<rdkit.Chem.rdchem.Mol object at 0x120ff73d0>
P1bonds:
1-2
1-5
1-7
1-11
2-3
2-12
3-4
3-13
4-5
4-6
4-14
5-15
5-16
6-7
7-8
8-9
8-10
P2bonds:
1-2
1-5
1-7
1-11
2-3
2-8
2-12
3-4
3-13
4-5
4-14
5-15
5-16
6-7
7-8
8-9
8-10
unidenticalP1P2: [[4, 6]]
unidenticalP2P1: [[2, 8]]
unidenticalTS1P1: []
unidenticalTS1P2: []
unidenticalP1TS1: [[1, 7], [4, 6]]
unidenticalP2TS1: [[1, 7], [2, 8]]
Intermediate option activated:
Combining unidentical P1/P2 bonds with unidentical P1/TS1 and P2/TS1 then ranking
bondpermutations: [[[4, 6], [2, 8]], [[4, 6], [1, 7]], [[4, 6], [2, 8]], [[1, 7], [2, 8]], [[1, 7], [2, 8]], [[4, 6], [2, 8]], [[4, 6], [1, 7]], [[4, 6], [2, 8]]]
rankedbond1 [[4, 6], [4, 6], [4, 6], [4, 6], [4, 6], [4, 6], [1, 7], [1, 7]]
rankedbond2 [[1, 7], [1, 7], [2, 8], [2, 8], [2, 8], [2, 8], [2, 8], [2, 8]]
BondrankP1: [[4, 6], [4, 6], [4, 6], [4, 6], [4, 6], [4, 6], [1, 7], [1, 7]]
BondrankP2: [[1, 7], [1, 7], [2, 8], [2, 8], [2, 8], [2, 8], [2, 8], [2, 8]]
The algorithm is current using the following bonds for the major product analysis:
orthbond1list: [4, 6]
orthbond1list: [1, 7]
-- Starting Vector Analysis --
coord1-1: [3.0799, -0.5654, -0.1496]
coord1-2: [0.4366, -1.7391, 0.0029]
coord2-1: [1.3032, 0.7235, 0.6823]
coord2-2: [-0.1062, -0.6685, 0.0766]
TS1_bond1: 2.89618073158
TS1_bond2: 2.0714595941
Bond Imaginary Eigenvector: [0.14818737736707632, 1.0750468413905097]
p1_:
-1.2854238501348352, -0.07551492140508032
p2_:
1.1532105693260841, -0.06347513316642472
imag_eigenvector:
0.42564, 0.39747, 0.1093
0.08942, 0.07612, 0.09078
0.04271, -0.04935, 0.02382
0.1238, 0.03639, 0.00995
0.17016, 0.11022, 0.02753
0.00174, -0.06137, -0.07659
-0.33078, -0.30014, -0.20329
-0.13822, -0.05069, 0.08826
0.02326, -0.03563, -0.02141
-0.16911, -0.01339, -0.00184
0.16959, 0.14477, 0.11491
0.04775, 0.02113, 0.06255
-0.07005, -0.1201, -0.00739
0.11334, 0.02667, 0.02203
0.28138, -0.15407, 0.14311
-0.06597, 0.13646, -0.05571
g_:
-0.12090170056774951, -0.46838070022376965
phi is 173.373748503 vector a_ will be inverted.
new phi is 6.62625149713
+mu_, -mu_, +lambda_, +lambda_ combination found. The algorithm wil continue.
angle(p1,p1): 173.488947497
|p1|: 1.28764008087
|p2|: 1.15495615057
|a|: 1.0000013632
|b|: 0.9999995753
|g|: 0.483733089154
theta1: 107.835790235
theta2: 78.6769867005
phi:
6.62625149713
Delta_G(INT-TS1) = -12.6 kJ/mol
Delta_G(INT-TS2A) = -5.2 kJ/mol
Delta_G(INT-TS2B) = -5.0 kJ/mol
DeltaDelta_G = -0.2 kJ/mol
The TS2 free energy is lower than -5 kJ/mol from TS1. The algorithm will not use TST to predict the selectivity
BondRealEigenVectors
[0.02100781777279881, -0.06020605352157338]
[-0.16966121034478343, 0.014505669486347017]
[0.41545627221007697, -0.10713951824945078]
[-0.3075626871829722, 0.07234018659047958]
[-0.2838445263648883, -0.018792098232967014]
[-0.1880235862915529, -0.2818862640879434]
[0.3072869952548811, 0.08462910711070926]
[0.22337295907405874, 0.3327782360006659]
[-0.08190807263666944, 0.05979906150438641]
[-0.2824662087260452, 0.17879485757607227]
[0.04879738969269454, 0.027030346878701206]
[-0.12582339833283562, 0.1297359657919972]
[0.12176562290912907, -0.18925683549774264]
[0.00044073125825994097, 0.019154504027349972]
[0.07788230777787453, -0.041441394455189684]
[-0.12495851701900706, 0.04864248466617971]
[0.080495757623114, 0.014313676125903285]
[-0.014369552811448472, 0.11163354218354815]
[-0.03414478972400081, -0.04319426148467187]
[0.0676312450937373, 0.008511731132367473]
[0.11502524410055504, 0.02811691733957744]
[0.0636231418168034, 0.004652914650166817]
[-0.03685946937884976, -0.033326262571094833]
[0.021610190637539883, -0.025326630339074008]
[-0.025670910071722286, 0.024070082566213902]
[0.01795380480899622, 0.003576566859349928]
[0.06907312562593448, -0.05111887202136778]
[0.0423973386565053, 0.15839946301282337]
[0.007668264851322437, 0.0057780390052988295]
[-0.042476135572272256, -0.01895388132133924]
[0.02432766027150368, 0.012356466805777622]
[-0.028536335394254486, 0.009651039237132952]
[0.010191169704344638, 0.11202917873313245]
[0.0245473490661694, -0.011469231673758795]
[0.011100051019983681, 0.11507001536983763]
[-0.0003677373803974149, -0.0008628846007936453]
[-0.000731468879085373, 6.329597119947294e-05]
[-0.020779302392165633, 0.0018338897292737855]
[0.014930517217465411, 0.009971646582449978]
[0.01876790316043131, -0.008967155086226697]
[-0.007483725008468056, -0.009686802086052548]
HalfWellWidths:
0.7176392323339713
0.597670557889869
0.4094257231736866
0.2907311795512921
0.2927512974240067
0.10371701554287598
0.09908421401098758
0.09599374603609838
0.21081767142612304
0.11098159887909473
0.10480743517533167
0.1308478103392867
0.09061923168890326
0.18805009063475006
0.10710333744873093
0.09459557246886986
0.1692236024994761
0.07060553097940094
0.14605443823284092
0.13428915773014902
0.14726609343051553
0.1574954346917416
0.14867837468890385
0.12415891531419285
0.1603760753945364
0.15214179576033152
0.15880122550447145
0.05179861357963101
0.13242333231098213
0.11617939818263526
0.12353811989643197
0.12270621713791925
0.08296094511705895
0.06777290187443834
0.037012427441839885
0.10187022457038412
0.09950446299483069
0.09791683082077647
0.09757186508439882
0.09712657297819502
0.09681813688614609
BondRealEigenvectorLengths:
0.0637659571262
0.17028018306
0.429048704099
0.315955549315
0.284465917296
0.338840279311
0.318727757221
0.400795250971
0.101414299386
0.334297412745
0.0557837332311
0.180728936222
0.225044477171
0.0191595738099
0.0882215565449
0.134092215621
0.0817584755212
0.11255457249
0.055060066205
0.0681647627429
0.118411856759
0.0637930543977
0.0496916518124
0.0332932206871
0.0351904035023
0.0183065818114
0.0859315760386
0.163975376834
0.00960145929413
0.0465131348148
0.0272858447956
0.0301241596744
0.112491763377
0.0270945681154
0.115604150314
0.000937976873504
0.000734202357011
0.0208600709357
0.0179542217862
0.020800097581
0.0122409262173
const_As:
11.254268965396703
3.5099243326495486
0.9542639781025521
0.9201648148965735
1.0291260907679571
0.3060941153567925
0.31087412930366193
0.23950819228382458
2.07877658972605
0.3319846180320079
1.8788171587773017
0.7240003348352503
0.4026725420154903
9.814941214292448
1.2140268392823903
0.7054516329001022
2.069798897553124
0.6273004234062677
2.652638260349467
1.9700671186461758
1.2436769210574676
2.4688492529293065
2.992019167527628
3.7292551682190815
4.557380974163787
8.310770264346047
1.8479961944744054
0.3158926332702881
13.792000596407219
2.4977761366823588
4.527553419071159
4.073349048209572
0.7374846177792448
2.501346453859672
0.32016521328390024
108.606328629219
135.52729985766163
4.6939835977740225
5.434480327053672
4.669524871212306
7.909379990341509
m1_lengths:
0.32673693222
0.596872319586
0.406702293892
0.289446953508
0.286734756994
0.0452316376
0.0910402327549
0.0421149377583
0.185648242819
0.101001357451
0.0838878098872
0.103069015205
0.058978783903
0.0213865027255
0.100535587458
0.0920122206727
0.161003854098
0.0184919914663
0.0740794633291
0.129700257366
0.136939264189
0.15403599608
0.0956352642695
0.0927322469502
0.130875479165
0.143753431319
0.139350880909
0.00643489431685
0.0938881592393
0.0986373758813
0.101473735444
0.120517766437
0.00383643049677
0.0647437372685
0.00151019090812
0.026767610099
0.0993767951801
0.0977995353486
0.0729797389618
0.0925340245754
0.0481750604789
ConstBs
0.170813578656
0.0935059355918
0.137228399028
0.192819803406
0.194643667398
1.23389529173
0.613037807383
1.32520924029
0.300628240937
0.552577768063
0.665306493837
0.541492557787
0.946291208098
2.6096414822
0.555137798296
0.606561870409
0.346644525898
3.01812299522
0.75339509985
0.430308357171
0.407561008907
0.36232508045
0.583582897982
0.60185217664
0.426444319654
0.388241895582
0.400507727742
8.6731967805
0.594442420896
0.565821060962
0.550005421872
0.46309441605
14.5476647417
0.862030939614
36.9563241121
2.08502382041
0.561611033748
0.570668403206
0.764747935052
0.603141438274
1.15850616724
majP: 0.382548036892
minP: 0.270925827548
majP: 0.652683424257
minP: 0.541061214914
majP: 0.462513398564
minP: 0.350891189221
majP: 0.345258058179
minP: 0.233635848836
majP: 0.342545861666
minP: 0.230923652323
majP: 0.0904632751999
minP: 0
majP: 0.146851337427
minP: 0.0352291280832
majP: 0.0842298755166
minP: 0
majP: 0.241459347491
minP: 0.129837138147
majP: 0.156812462123
minP: 0.0451902527794
majP: 0.139698914559
minP: 0.0280767052155
majP: 0.158880119876
minP: 0.0472579105329
majP: 0.114789888575
minP: 0.00316767923129
majP: 0.042773005451
minP: 0
majP: 0.15634669213
minP: 0.0447244827861
majP: 0.147823325344
minP: 0.036201116001
majP: 0.21681495877
minP: 0.105192749427
majP: 0.0369839829325
minP: 0
majP: 0.129890568001
minP: 0.0182683586574
majP: 0.185511362037
minP: 0.0738891526939
majP: 0.19275036886
minP: 0.0811281595168
majP: 0.209847100751
minP: 0.098224891408
majP: 0.151446368941
minP: 0.0398241595978
majP: 0.148543351622
minP: 0.0369211422785
majP: 0.186686583836
minP: 0.0750643744929
majP: 0.199564535991
minP: 0.0879423266474
majP: 0.195161985581
minP: 0.0835397762371
majP: 0.0128697886337
minP: 0
majP: 0.149699263911
minP: 0.0380770545676
majP: 0.154448480553
minP: 0.0428262712096
majP: 0.157284840115
minP: 0.0456626307721
majP: 0.176328871108
minP: 0.064706661765
majP: 0.00767286099353
minP: 0
majP: 0.12055484194
minP: 0.00893263259682
majP: 0.00302038181624
minP: 0
majP: 0.0535352201979
minP: 0
majP: 0.155187899852
minP: 0.0435656905084
majP: 0.15361064002
minP: 0.0419884306769
majP: 0.128790843634
minP: 0.0171686342901
majP: 0.148345129247
minP: 0.0367229199037
majP: 0.0963501209577
minP: 0
current major ratio:0.698534300061
current minor ratio:0.301465699939
the algorithm will change the major:minor product ratio for positive mu1_ (intermediate activation)
**** Analysis Completed ****
Major product is testP2freq.mol
Minor product is testP1freq.mol
mu1_ = -0.0441868111245
mu2_ = 0.0484860277906
lambda1_ = 0.432580161859
lambda2_ = 0.438546804793
|g_| = 0.483733089154
phi = 6.62625149713
The algorith will now proceed to estimate the major and minor product ratios
Product Ratio Calculation Completed:
Major Product : Minor Product ratio
82.9 : 30.1
****************************