Closed cpignedoli closed 11 months ago
I'll take a look, the error comes from the code that I introduced I think, thanks for the report!
The following SMILES code
C=CC1=C(C2=CC=C(C3=CC=CC=C3)C=C2)C=C(C=C)C(C4=CC=C(C(C=C5)=CC=C5C(C=C6C=C)=C(C=C)C=C6C7=CC=C(C(C=C8)=CC=C8C(C=C9C=C)=C(C=C)C=C9C%10=CC=CC=C%10)C=C7)C=C4)=C1
is correctly handled by Mathematica:
[image: smiles_mathematica] https://user-images.githubusercontent.com/22955065/263716526-9d585406-0c7b-4a47-bc13-89c65ee5f50f.png
while crashes the smiles widget: [image: image] https://user-images.githubusercontent.com/22955065/263716814-69e45759-65ea-4126-9980-698a530b9d85.png
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I noticed a strange thing. The input SMILES is not canonical (at least according to RDKit). The canonical version is
C=Cc1cc(-c2ccc(-c3ccc(-c4cc(C=C)c(-c5ccc(-c6ccc(-c7cc(C=C)c(-c8ccc(-c9ccccc9)cc8)cc7C=C)cc6)cc5)cc4C=C)cc3)cc2)c(C=C)cc1-c1ccccc1
When I input this smiles the generation succeeds. @cpignedoli could you please confirm that the following generated geometry is the molecule that you wanted?
CC @yakutovicha
126
C 10.789406146640598 11.093550987863887 10.775495335663638
C 10.300054323514150 10.660649966173487 9.612813917217883
C 11.044087458291084 9.754560238551454 8.694690148677905
C 12.450498975464544 9.771741109891606 8.658420277266600
C 13.171961786514769 8.899468916084674 7.828249211905409
C 14.653209329627982 8.943297720286033 7.879013462112862
C 15.388012861026390 7.798352029613464 8.223198046072158
C 16.783321971800845 7.845316400135173 8.282815349608248
C 17.470109441631713 9.041547639748901 8.008276391728797
C 18.953054753049308 9.091478726443864 8.071545358625475
C 19.725614259466418 8.029388783934873 7.568656068037813
C 21.120804560742720 8.075486213314020 7.629939944722656
C 21.770381820351080 9.179358278706633 8.203500102453024
C 23.250990599345592 9.231714826326275 8.264561432610403
C 23.903860660217664 10.317181478862233 7.659199481550609
C 25.307537098652755 10.382191256698256 7.589556714716446
C 25.973997006949350 11.575649813337492 7.005036031568991
C 25.459546275072285 12.283138130155274 5.999117896367571
C 26.071218969165187 9.328380939153275 8.145310409359372
C 27.551799643398276 9.304486191597727 8.067700837387832
C 28.200629370384807 9.358470201659426 6.824471161285891
C 29.595724240103443 9.322774291273271 6.752861709556376
C 30.368753975797965 9.225240082611922 7.923715482343153
C 31.851530863265936 9.189182848324915 7.848354553242594
C 32.498520133926782 8.444337812420816 6.846073418941604
C 33.893746958784689 8.412585059797328 6.774229885272454
C 34.668704626344180 9.131963426111268 7.696570000994615
C 36.148932965587925 9.092374267559924 7.621011285073506
C 36.784085051404418 7.841668003616832 7.668941392751486
C 38.181197066134025 7.732486698869110 7.686275138226859
C 38.759962686937143 6.368182790026544 7.677028261260971
C 39.778556186855347 6.021601610330768 6.891412668450279
C 38.967336916073641 8.911450468932689 7.720681660879677
C 40.439185456658208 8.879878098114695 7.896972531738566
C 41.010745158645960 8.212304238765498 8.991174281393935
C 42.397735379199887 8.188774928466096 9.159363589654875
C 43.239961819451224 8.839144066258630 8.239793939282444
C 44.714482325102651 8.812122182387412 8.416185778535240
C 45.285363329073931 8.952479315158913 9.695595094175022
C 46.673897610617388 8.926798320059179 9.858320666109636
C 47.506721361088310 8.760265310242879 8.749679440972686
C 46.952795498459238 8.619502021844056 7.475410832137726
C 45.565003229455471 8.645378209519945 7.306561612916231
C 42.662604235466041 9.517457504186828 7.151403427074022
C 41.275330967962212 9.541258091041994 6.984727986718346
C 38.333033396546355 10.161339273964789 7.646921101522342
C 36.938095770508767 10.268449383599863 7.564334633326729
C 36.364089825029517 11.628205771972041 7.430231241960009
C 35.400658467129780 11.922181039433509 6.558317030007844
C 34.027006019076033 9.866285048310409 8.705841117394819
C 32.631964088867754 9.897849333927708 8.779221220681968
C 29.714218482087361 9.160162695738345 9.166890732643022
C 28.318877538178867 9.195129477929447 9.237196179982393
C 25.418828699165509 8.255414266076892 8.770905851670630
C 24.021933361290465 8.202600853733518 8.859842757736988
C 23.427308688423405 7.057198372432805 9.588383186189890
C 22.455747608268631 7.200136211860595 10.488653947758950
C 21.003481997548349 10.246471114924656 8.695394946696492
C 19.608119385680904 10.201962924735863 8.633444238317603
C 16.729102135380188 10.189875669478356 7.675858344629621
C 15.333714719868826 10.141279710999150 7.615168369062982
C 12.477288869607099 7.990502072377453 6.995757061967427
C 13.213093255134526 7.109277147759734 6.051239790606723
C 12.773692378284579 5.906743639264395 5.679942999456125
C 11.071498194782144 7.994151376890070 7.009287419909342
C 10.353257752587758 8.867018227513944 7.837947106293956
C 8.877616222976119 8.814245396839564 7.790055342208218
C 8.151513284552880 9.840639960592810 7.165119474823999
C 6.755946034589012 9.776715715515992 7.104596794731544
C 6.080152942119149 8.685327336845436 7.658349037144509
C 6.799207251019130 7.654588807589116 8.270817026792406
C 8.194918656634179 7.715155678130834 8.333765972042571
H 10.187998832973708 11.737059662754781 11.404534282634245
H 11.764114959993565 10.795858302282882 11.136628800802134
H 9.290221802424384 10.956220827004273 9.362938407287576
H 13.000100177036481 10.469491980069327 9.277506467819432
H 14.879138008042695 6.870398399547538 8.453901947253922
H 17.324268738116558 6.950524501663429 8.564089722193611
H 19.251321174087089 7.171088303919048 7.109608770656157
H 21.695709247808900 7.252406395764151 7.223561170105164
H 23.304975543604328 11.118265163213557 7.244162688321445
H 26.945909550215539 11.868938711571502 7.382574710949359
H 24.521379841799316 12.015453820719166 5.532128624300915
H 26.002497335304323 13.133610001846623 5.607742899599813
H 27.625272617102461 9.426007378088457 5.909231364311240
H 30.070292283564193 9.386596515198457 5.781760355672381
H 31.925701011830238 7.872366526523075 6.127009930370598
H 34.370443100680191 7.833963395851809 5.992430958394171
H 36.181494549767855 6.940095581299777 7.696121104710627
H 38.271067545082929 5.593538580128561 8.255510903344966
H 40.135258752854334 5.000000000000002 6.889922264745703
H 40.247641216017684 6.734426057496647 6.225971309018672
H 40.381536456404611 7.709752009133784 9.715493596043469
H 42.812131037055963 7.647964473711428 10.000825072702174
H 44.659671225455170 9.099825884643387 10.566862830855973
H 47.104509635795864 9.039595224762294 10.844932218742178
H 48.581247668803620 8.740307461686040 8.878015009551341
H 47.599148205025443 8.486711379708337 6.617421846807042
H 45.156964538791854 8.517275073647095 6.311853839577731
H 43.283121160946237 10.044248838236575 6.437423010253032
H 40.852955639548725 10.068183478934014 6.137848332843241
H 38.934372606575458 11.064098885199279 7.656964436633652
H 36.815087887794554 12.438969257811296 7.989693494834360
H 35.046977416355709 12.940877525534470 6.468448378096624
H 34.975317897688242 11.167663516772809 5.909657658138290
H 34.607666893106163 10.414817138953397 9.437305830089247
H 32.163450585903206 10.489904539672279 9.555276847349536
H 30.280878870619237 9.064516032705486 10.084548914127485
H 27.835934549779580 9.143004197692148 10.205389013273969
H 26.008956681787602 7.453675198184930 9.201905509353221
H 23.869574619859996 6.076386161359432 9.461436510612879
H 22.086995002887136 6.336329937408444 11.026024089468677
H 22.038460563645636 8.171095925519843 10.721160239522604
H 21.486298836242295 11.107007270155737 9.142177215073238
H 19.040955735092723 11.028343747466316 9.042979283533709
H 17.229397877763770 11.121887701017874 7.444826371104768
H 14.783486923309535 11.035885711249289 7.350047226468363
H 14.173344855055177 7.434976141781370 5.670591862993399
H 11.851201038834116 5.491722005994449 6.063243322193171
H 13.363189850778491 5.305541540598276 5.000000000000000
H 10.520527090662846 7.341680007154315 6.342743039789817
H 8.666621598019660 10.687233839956454 6.727826414922109
H 6.198584338655685 10.571746109172304 6.626403954367804
H 5.000000000000000 8.636782669090945 7.610051385716330
H 6.275149763661059 6.808116303366591 8.695392002257584
H 8.743162017466393 6.910398516730581 8.808196661739872
Thanks a lot @danielhollas it is correct and with the canonical form you provided it works. So chemdraw is not producing canonical SMILES. How did you do the conversion? should we put it in the widget?
Yes, I will put up a PR with the canonicalization using rdkit. I am already using it in my app for some time and it works well.
great @danielhollas Thanks a lot :)
The following SMILES code
C=CC1=C(C2=CC=C(C3=CC=CC=C3)C=C2)C=C(C=C)C(C4=CC=C(C(C=C5)=CC=C5C(C=C6C=C)=C(C=C)C=C6C7=CC=C(C(C=C8)=CC=C8C(C=C9C=C)=C(C=C)C=C9C%10=CC=CC=C%10)C=C7)C=C4)=C1
is correctly handled by Mathematica:
while crashes the smiles widget:
https://github.com/aiidalab/aiidalab-widgets-base/blob/413c26c76ec438b9c70afe3437420923f738e50b/aiidalab_widgets_base/structures.py#L679