Fragmenter regression test

AIM

Regression test the new rewrite of fragmenter which is based on the openff-toolkit against the JACS ligands dataset which has been previously fragmented using fragmenter=0.0.7 and openeye-toolkits<=2019 .

Also, test the new interface with ambertools and rdkit to identify differences in performance.

Results for WBO Fragmentation

Overall fragment results.

Fragmentation failures occur when the stereochemistry of a fragment can not be fixed.

Fragmenter rewrite(OE) failure molecules (cmiles), note that molecule 1 also failed in fragmenter=0.0.7

"[H:41][c:13]1[c:12]([c:11]([c:10]([c:24]([c:23]1[N:22]([H:43])[c:1]2[n:21][c:20]3[c:17]([c:15]([n:14]2)[O:16][C:3]([H:26])([H:27])[C:4]4([C:5]([C:6]([C:7]([C:8]([C:9]4([H:37])[H:38])([H:35])[H:36])([H:33])[H:34])([H:31])[H:32])([H:29])[H:30])[H:28])[N:18]=[C:2]([N:19]3[H:42])[H:25])[H:44])[H:39])[S:45](=[O:46])[C:47]([H:48])([H:49])[H:50])[H:40]"
"[H:27][c:10]1[c:9]([c:8]([c:1]([c:3]([c:14]1[O:17][C:13]2=[C:7]([c:6]3[c:12]([n:18][c:4]([n:21][c:11]3[N:20]([C:2]2=[O:19])[C:15]([H:29])([H:30])[H:31])[N:22]([H:32])[C:5]([H:43])([C:34]([H:37])([H:38])[O:35][H:36])[C:24]([H:40])([H:41])[O:39][H:42])[H:28])[H:25])[F:16])[H:23])[F:33])[H:26]"
"[H:41][c:11]1[c:10]([c:2]([c:1]([c:8]([c:12]1[O:13][C:14]2=[C:15]([c:16]3[c:17]([n:18][c:24]([n:23][c:22]3[N:21]([C:19]2=[O:20])[C:6]([H:37])([H:38])[H:39])[N:25]([H:44])[C:26]([H:45])([C:3]([H:31])([H:32])[C:4]([H:33])([H:34])[O:29][H:49])[C:5]([H:35])([H:36])[C:27]([H:46])([H:47])[O:28][H:48])[H:43])[H:42])[F:7])[H:30])[F:9])[H:40]"

Fragmenter version	Total failed molecules	Total unique fragments	Number of fragments the same as parent	Total fragments

Fragmenter version	Total failed molecules	Total unique fragments	Number of fragments the same as parent	Total fragments
fragmenter=0.0.7	`1`	`373`	`45`	`1165`
fragmenter_rewrite(OE)	`3`	`347`	`58`	`1151`
fragmenter_rewrite (AT_RDKIT)	`3`	`363`	`55`	`1152`

Here we inspect the number of rotatable bonds in the fragments to get an idea of fragment size.

Fragmenter version	Maximum number of rotors	Minimum number of rotors	Mean number of rotors

Fragmenter version	Maximum number of rotors	Minimum number of rotors	Mean number of rotors
fragmenter=0.0.7	`10`	`1`	`4.78`
fragmenter_rewrite(OE)	`11`	`1`	`4.57`
fragmenter_rewrite(AT_RDKIT)	`10`	`1`	`4.75`

We can also look at the total molecular weight of the fragments.

Fragmenter version	Maximum weight	Minimum weight	Mean weight

Fragmenter version	Maximum weight	Minimum weight	Mean weight
fragmenter=0.0.7	`535.0002494199106`	`90.06807956`	`246.56539290510784`
fragmenter_rewrite(OE)	`478.09860146009026`	`90.06807956`	`241.69599142677208`
fragmenter_rewrite(AT_RDKIT)	`485.12103747991046`	`90.06807956`	`249.30037374553274``

Fragments the same as the parent (OE/AT_RDKIT)

Here we look at fragments that are the same as the parent using fragmenter_rewrite(OE) but produced a different fragment using fragmenter=0.0.7. The rest of the fragments that were the same as the parent in both the old and new version all had a -1e charge with a carboxylate group.

Note that most of the cases here have a +1e charge.

Parent molecule	Fragmenter=0.0.7 molecule

Parent molecule

Fragmenter=0.0.7 molecule

OE

[H:39][c:10]1[c:24]([c:23]([c:13]([c:12]([c:11]1[H:40])[O:45][C:46]([H:47])([H:48])[H:49])[H:41])[N:22]([H:43])[c:1]2[n:21][c:20]3[c:17]([c:15]([n:14]2)[O:16][C:3]([H:26])([H:27])[C:4]4([C:5]([C:6]([C:7]([C:8]([C:9]4([H:37])[H:38])([H:35])[H:36])([H:33])[H:34])([H:31])[H:32])([H:29])[H:30])[H:28])[N:18]=[C:2]([N:19]3[H:42])[H:25])[H:44]

[H:21][c:1]1[c:2]([c:7]([c:4]([c:8]([c:3]1[H:23])[O:19][C:12]([H:26])([H:27])[H:28])[H:24])[N:18]([H:33])[c:11]2[n:15][c:9]3[c:6]([c:10]([n:16]2)[O:20][C:13]([H:29])([H:30])[H:31])[N:14]=[C:5]([N:17]3[H:32])[H:25])[H:22]

OE

[H:1][c:2]1[c:7]([c:6]([c:5]([c:4]([c:3]1[H:45])[H:44])[N:10]([H:11])[c:12]2[n:13][c:14]3[c:15]([c:16]([n:17]2)[O:18][C:19]([H:20])([H:21])[C:22]4([C:27]([C:26]([C:25]([C:24]([C:23]4([H:36])[H:37])([H:34])[H:35])([H:32])[H:33])([H:30])[H:31])([H:28])[H:29])[H:38])[N:39]=[C:40]([N:41]3[H:42])[H:43])[H:9])[H:8]

[H:17][c:1]1[c:2]([c:4]([c:9]([c:5]([c:3]1[H:19])[H:21])[N:16]([H:25])[c:11]2[n:12][c:6]([c:8]3[c:10]([n:14]2)[N:15]([C:7](=[N:13]3)[H:23])[H:24])[H:22])[H:20])[H:18]

OE

[H:1][c:2]1[c:7]([c:6]([c:5]([c:4]([c:3]1[H:52])[H:51])[C:10]([H:11])([H:12])[C@:13]([H:14])([C:15](=[O:16])[N:17]2[C@:18]([C:19]([C:20]([C:21]2([H:22])[H:23])([H:24])[H:25])([H:26])[H:27])([H:28])[C:29](=[O:30])[N:31]([H:32])[C:33]([H:34])([H:35])[c:36]3[c:37]([c:38]([c:39]([c:40]([c:41]3[H:42])[Cl:43])[H:44])[H:45])[H:46])[N+:47]([H:48])([H:49])[H:50])[H:9])[H:8]

[H:22][c:1]1[c:2]([c:5]([c:4]([c:6]([c:3]1[H:24])[I:21])[H:25])[C:14]([H:36])([H:37])[N:17]([H:39])[C:7](=[O:19])[C@@:12]2([C:10]([C:9]([C:11]([N:16]2[C:8](=[O:20])[C@@:15]([H:38])([C:13]([H:33])([H:34])[H:35])[N+:18]([H:40])([H:41])[H:42])([H:30])[H:31])([H:26])[H:27])([H:28])[H:29])[H:32])[H:23]

OE+AT_RDKIT

[H:1][c:2]1[c:7]([c:6]([c:5]([c:4]([c:3]1[H:52])[H:51])[C:10]([H:11])([H:12])[C@:13]([H:14])([C:15](=[O:16])[N:17]2[C@:18]([C:19]([C:20]([C:21]2([H:22])[H:23])([H:24])[H:25])([H:26])[H:27])([H:28])[C:29](=[O:30])[N:31]([H:32])[C:33]([H:34])([H:35])[c:36]3[c:37]([c:38]([c:39]([c:40]([c:41]3[H:42])[I:43])[H:44])[H:45])[H:46])[N+:47]([H:48])([H:49])[H:50])[H:9])[H:8]

[H:22][c:1]1[c:2]([c:5]([c:4]([c:6]([c:3]1[H:24])[I:21])[H:25])[C:14]([H:36])([H:37])[N:17]([H:39])[C:7](=[O:19])[C@@:12]2([C:10]([C:9]([C:11]([N:16]2[C:8](=[O:20])[C@@:15]([H:38])([C:13]([H:33])([H:34])[H:35])[N+:18]([H:40])([H:41])[H:42])([H:30])[H:31])([H:26])[H:27])([H:28])[H:29])[H:32])[H:23]

OE

[H:1][c:2]1[c:7]([c:6]([c:5]([c:4]([c:3]1[H:58])[H:57])[C:10]([H:11])([H:12])[C@:13]([H:14])([C:15](=[O:16])[N:17]2[C@:18]([C:19]([C:20]([C:21]2([H:22])[H:23])([H:24])[H:25])([H:26])[H:27])([H:28])[C:29](=[O:30])[N:31]([H:32])[C:33]([H:34])([H:35])[c:36]3[c:37]([c:38]([c:39]([c:40]([c:41]3[H:42])[C:43]([H:44])([H:45])[C:46]([H:47])([H:48])[H:49])[H:50])[H:51])[H:52])[N+:53]([H:54])([H:55])[H:56])[H:9])[H:8]

[H:22][c:1]1[c:2]([c:5]([c:4]([c:6]([c:3]1[H:24])[C:15]([H:39])([H:40])[N:18]([H:42])[C:7](=[O:20])[C@@:12]2([C:10]([C:9]([C:11]([N:17]2[C:8](=[O:21])[C@@:16]([H:41])([C:14]([H:36])([H:37])[H:38])[N+:19]([H:43])([H:44])[H:45])([H:30])[H:31])([H:26])[H:27])([H:28])[H:29])[H:32])[H:25])[C:13]([H:33])([H:34])[H:35])[H:23]

OE+AT_RDKIT

[H:1][c:2]1[c:7]([c:6]([c:5]([c:4]([c:3]1[H:52])[H:51])[C:10]([H:11])([H:12])[C@:13]([H:14])([C:15](=[O:16])[N:17]2[C@:18]([C:19]([C:20]([C:21]2([H:22])[H:23])([H:24])[H:25])([H:26])[H:27])([H:28])[C:29](=[O:30])[N:31]([H:32])[C:33]([H:34])([H:35])[c:36]3[c:37]([c:38]([c:39]([c:40]([c:41]3[H:42])[F:43])[H:44])[H:45])[H:46])[N+:47]([H:48])([H:49])[H:50])[H:9])[H:8]

[H:22][c:1]1[c:2]([c:5]([c:4]([c:6]([c:3]1[H:24])[F:21])[H:25])[C:14]([H:36])([H:37])[N:17]([H:39])[C:7](=[O:19])[C@@:12]2([C:10]([C:9]([C:11]([N:16]2[C:8](=[O:20])[C@@:15]([H:38])([C:13]([H:33])([H:34])[H:35])[N+:18]([H:40])([H:41])[H:42])([H:30])[H:31])([H:26])[H:27])([H:28])[H:29])[H:32])[H:23]

OE

[H:1][c:2]1[c:7]([c:6]([c:5]([c:4]([c:3]1[H:52])[H:51])[C:10]([H:11])([H:12])[C@:13]([H:14])([C:15](=[O:16])[N:17]2[C@:18]([C:19]([C:20]([C:21]2([H:22])[H:23])([H:24])[H:25])([H:26])[H:27])([H:28])[C:29](=[O:30])[N:31]([H:32])[C:33]([H:34])([H:35])[c:36]3[c:37]([c:38]([c:39]([c:40]([c:41]3[Cl:42])[H:43])[H:44])[Cl:45])[H:46])[N+:47]([H:48])([H:49])[H:50])[H:9])[H:8]

[H:21][c:1]1[c:2]([c:6]([c:4]([c:3]([c:5]1[Cl:19])[H:23])[C:14]([H:34])([H:35])[N:16]([H:36])[C:7](=[O:17])[C@@:12]2([C:10]([C:9]([C:11]([N:15]2[C:8](=[O:18])[C:13]([H:31])([H:32])[H:33])([H:28])[H:29])([H:24])[H:25])([H:26])[H:27])[H:30])[Cl:20])[H:22]

OE

[H:1][c:2]1[c:7]([c:6]([c:5]([c:4]([c:3]1[H:58])[H:57])[C:10]([H:11])([H:12])[C@:13]([H:14])([C:15](=[O:16])[N:17]2[C@:18]([C:19]([C:20]([C:21]2([H:22])[H:23])([H:24])[H:25])([H:26])[H:27])([H:28])[C:29](=[O:30])[N:31]([H:32])[C:33]([H:34])([H:35])[c:36]3[c:37]([c:38]([c:39]([c:40]([c:41]3[C:42]([H:43])([H:44])[H:45])[H:46])[H:47])[C:48]([H:49])([H:50])[H:51])[H:52])[N+:53]([H:54])([H:55])[H:56])[H:9])[H:8]

[H:21][c:1]1[c:2]([c:4]([c:6]([c:5]([c:3]1[H:23])[H:25])[C:14]([H:36])([H:37])[C@:15]([H:38])([C:8](=[O:20])[N:16]2[C@:12]([C:10]([C:9]([C:11]2([H:30])[H:31])([H:26])[H:27])([H:28])[H:29])([H:32])[C:7](=[O:19])[N:17]([H:39])[C:13]([H:33])([H:34])[H:35])[N+:18]([H:40])([H:41])[H:42])[H:24])[H:22]

OE+AT_RDKIT

[H:1][c:2]1[c:7]([c:6]([c:5]([c:4]([c:3]1[H:55])[H:54])[C:10]([H:11])([H:12])[C@:13]([H:14])([C:15](=[O:16])[N:17]2[C@:18]([C:19]([C:20]([C:21]2([H:22])[H:23])([H:24])[H:25])([H:26])[H:27])([H:28])[C:29](=[O:30])[N:31]([H:32])[C:33]([H:34])([H:35])[c:36]3[c:37]([c:38]([c:39]([c:40]([c:41]3[H:42])[C:43]([H:44])([H:45])[H:46])[H:47])[H:48])[H:49])[N+:50]([H:51])([H:52])[H:53])[H:9])[H:8]

[H:21][c:1]1[c:2]([c:4]([c:6]([c:5]([c:3]1[H:23])[H:25])[C:14]([H:36])([H:37])[C@:15]([H:38])([C:8](=[O:20])[N:16]2[C@:12]([C:10]([C:9]([C:11]2([H:30])[H:31])([H:26])[H:27])([H:28])[H:29])([H:32])[C:7](=[O:19])[N:17]([H:39])[C:13]([H:33])([H:34])[H:35])[N+:18]([H:40])([H:41])[H:42])[H:24])[H:22]

OE

[H:1][c:2]1[c:7]([c:6]([c:5]([c:4]([c:3]1[H:52])[H:51])[C:10]([H:11])([H:12])[C@:13]([H:14])([C:15](=[O:16])[N:17]2[C@:18]([C:19]([C:20]([C:21]2([H:22])[H:23])([H:24])[H:25])([H:26])[H:27])([H:28])[C:29](=[O:30])[N:31]([H:32])[C:33]([H:34])([H:35])[c:36]3[c:41]([c:40]([c:39]([c:38]([c:37]3[H:46])[H:45])[H:44])[H:43])[H:42])[N+:47]([H:48])([H:49])[H:50])[H:9])[H:8]

[H:21][c:1]1[c:2]([c:4]([c:6]([c:5]([c:3]1[H:23])[H:25])[C:14]([H:36])([H:37])[N:17]([H:39])[C:7](=[O:19])[C@@:12]2([C:10]([C:9]([C:11]([N:16]2[C:8](=[O:20])[C@@:15]([H:38])([C:13]([H:33])([H:34])[H:35])[N+:18]([H:40])([H:41])[H:42])([H:30])[H:31])([H:26])[H:27])([H:28])[H:29])[H:32])[H:24])[H:22]

OE+AT_RDKIT

[H:1][c:2]1[c:7]([c:6]([c:5]([c:4]([c:3]1[H:55])[H:54])[C:10]([H:11])([H:12])[C@:13]([H:14])([C:15](=[O:16])[N:17]2[C@:18]([C:19]([C:20]([C:21]2([H:22])[H:23])([H:24])[H:25])([H:26])[H:27])([H:28])[C:29](=[O:30])[N:31]([H:32])[C:33]([H:34])([H:35])[c:36]3[c:37]([c:38]([c:39]([c:40]([c:41]3[C:42]([H:43])([H:44])[H:45])[H:46])[H:47])[Cl:48])[H:49])[N+:50]([H:51])([H:52])[H:53])[H:9])[H:8]

[H:21][c:1]1[c:2]([c:4]([c:6]([c:5]([c:3]1[H:23])[H:25])[C:14]([H:36])([H:37])[C@:15]([H:38])([C:8](=[O:20])[N:16]2[C@:12]([C:10]([C:9]([C:11]2([H:30])[H:31])([H:26])[H:27])([H:28])[H:29])([H:32])[C:7](=[O:19])[N:17]([H:39])[C:13]([H:33])([H:34])[H:35])[N+:18]([H:40])([H:41])[H:42])[H:24])[H:22]

OE+AT_RDKIT

[H:1][c:2]1[c:7]([c:6]([c:5]([c:4]([c:3]1[H:52])[H:51])[C:10]([H:11])([H:12])[C@:13]([H:14])([C:15](=[O:16])[N:17]2[C@:18]([C:19]([C:20]([C:21]2([H:22])[H:23])([H:24])[H:25])([H:26])[H:27])([H:28])[C:29](=[O:30])[N:31]([H:32])[C:33]([H:34])([H:35])[c:36]3[c:37]([c:38]([c:39]([c:40]([c:41]3[F:42])[H:43])[H:44])[Cl:45])[H:46])[N+:47]([H:48])([H:49])[H:50])[H:9])[H:8]

[H:23][c:1]1[c:2]([c:6]([c:3]([c:4]([c:5]1[F:21])[C:14]([H:36])([H:37])[N:17]([H:39])[C:7](=[O:19])[C@@:12]2([C:10]([C:9]([C:11]([N:16]2[C:8](=[O:20])[C@@:15]([H:38])([C:13]([H:33])([H:34])[H:35])[N+:18]([H:40])([H:41])[H:42])([H:30])[H:31])([H:26])[H:27])([H:28])[H:29])[H:32])[H:25])[Cl:22])[H:24]

OE+AT_RDKIT

[H:1][c:2]1[c:7]([c:6]([c:5]([c:4]([c:3]1[H:52])[H:51])[C:10]([H:11])([H:12])[C@:13]([H:14])([C:15](=[O:16])[N:17]2[C@:18]([C:19]([C:20]([C:21]2([H:22])[H:23])([H:24])[H:25])([H:26])[H:27])([H:28])[C:29](=[O:30])[N:31]([H:32])[C:33]([H:34])([H:35])[c:36]3[c:37]([c:38]([c:39]([c:40]([c:41]3[H:42])[Br:43])[H:44])[H:45])[H:46])[N+:47]([H:48])([H:49])[H:50])[H:9])[H:8]

[H:22][c:1]1[c:2]([c:5]([c:4]([c:6]([c:3]1[H:24])[Br:21])[H:25])[C:14]([H:36])([H:37])[N:17]([H:39])[C:7](=[O:19])[C@@:12]2([C:10]([C:9]([C:11]([N:16]2[C:8](=[O:20])[C@@:15]([H:38])([C:13]([H:33])([H:34])[H:35])[N+:18]([H:40])([H:41])[H:42])([H:30])[H:31])([H:26])[H:27])([H:28])[H:29])[H:32])[H:23]

OE

[H:1][c:2]1[c:3]([c:4]([c:5]([c:6]([c:7]1[O:8][C:9]2=[C:10]([c:11]3[c:12]([n:13][c:14]([n:15][c:16]3[N:17]([C:18]2=[O:19])[C:20]([H:21])([H:22])[H:23])[N:24]([H:25])[C:26]([C:27]([H:28])([H:29])[H:30])([C:31]([H:32])([H:33])[H:34])[C:35]([H:36])([H:37])[O:38][H:39])[H:40])[H:41])[F:42])[H:43])[F:44])[H:45]

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AT_RDKIT

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AT_RDKIT

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AT_RDKIT (2021.03.1)

Using rdkit=2020.09.3 resolves this issue, so there must be a difference in the conformer generation which is causing the difference in fragments for this tyk2 series.

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AT_RDKIT

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AT_RDKIT

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AT_RDKIT

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AT_RDKIT

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AT_RDKIT

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Other cases

After filtering out all charged parent molecules we can now look at comparing the exact fragments produced for each bond in the parent and where the old and new(OE) fragmenter are different to find systematic differences.

Case 1) The fragmentation in both cases was done with the option keep_non_rotor_ring_substituents=True however in a lot of cases we see nitrile groups being replaced with methyls in the new implementation.

Examples

Parent	old	new

Parent	old	new

case2) Improvements, in some cases, we have slightly different molecules where the stereochemistry has been correctly fixed.

Parent	old	new

Parent	old	new