Skip to content

Commit

Permalink
feat!: update OpenChemLib to v2022.8.1
Browse files Browse the repository at this point in the history
  • Loading branch information
@targos
targos committed Aug 15, 2022
1 parent 1092b98 commit 1ac3899
Show file tree
Hide file tree
Showing 416 changed files with 19,344 additions and 67,129 deletions.
12 changes: 6 additions & 6 deletions .github/workflows/lactame.yml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8,16 +8,16 @@ jobs:
deploy:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/setup-java@v2
- uses: actions/checkout@v3
- uses: actions/setup-java@v3
with:
distribution: 'zulu'
java-version: '15.x'
- name: Install GWT 2.9
java-version: '17.x'
- name: Install GWT
run: ./scripts/get-gwt.sh
- uses: actions/setup-node@v2
- uses: actions/setup-node@v3
with:
node-version: 16.x
node-version: 18.x
- name: Install dependencies
run: npm ci
- name: Build project
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/nodejs.yml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
node-version: [12.x, 14.x, 16.x, 18.x]
node-version: [14.x, 16.x, 18.x]
steps:
- uses: actions/checkout@v3
- uses: actions/setup-java@v3
Expand Down
60 changes: 30 additions & 30 deletions __tests__/__snapshots__/conformers.js.snap
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,21 +5,21 @@ exports[`ConformerGenerator should generate conformers 1`] = `
Actelion Java MolfileCreator 1.0
15 14 0 0 0 0 0 0 0 0999 V2000
-1.4023 -1.7420 5.2037 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3608 -1.1727 4.4711 O 0 0 0 0 0 0 0 0 0 0 0 0
0.1032 0.0932 4.9457 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2275 0.6140 4.0808 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7501 0.9730 2.7964 O 0 0 0 0 0 0 0 0 0 0 0 0
1.7087 1.4629 1.9283 N 0 0 0 0 0 0 0 0 0 0 0 0
-2.1098 -1.1008 5.4198 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.0909 -2.1606 6.0367 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.7854 -2.4604 4.6283 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.6316 0.7507 4.9839 H 0 0 0 0 0 0 0 0 0 0 0 0
0.4208 -0.0415 5.8810 H 0 0 0 0 0 0 0 0 0 0 0 0
1.6997 1.3387 4.5418 H 0 0 0 0 0 0 0 0 0 0 0 0
1.9202 -0.1290 3.9610 H 0 0 0 0 0 0 0 0 0 0 0 0
2.4667 0.9938 1.9511 H 0 0 0 0 0 0 0 0 0 0 0 0
1.3961 1.4277 1.1065 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0209 -2.5358 6.9912 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4019 -1.6934 5.6364 O 0 0 0 0 0 0 0 0 0 0 0 0
0.2666 -0.0439 5.7657 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7123 0.7908 4.2081 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.4234 0.4480 3.0453 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.1832 1.1036 1.6138 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.9350 -2.1387 7.5082 H 0 0 0 0 0 0 0 0 0 0 0 0
0.8873 -2.5457 7.7647 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.1686 -3.6460 6.6492 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.8241 0.2442 6.0545 H 0 0 0 0 0 0 0 0 0 0 0 0
0.9037 0.3671 6.6327 H 0 0 0 0 0 0 0 0 0 0 0 0
0.7892 1.9248 4.3812 H 0 0 0 0 0 0 0 0 0 0 0 0
1.7629 0.4125 3.8524 H 0 0 0 0 0 0 0 0 0 0 0 0
0.7009 0.8284 1.1579 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.9561 0.8636 0.9815 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
Expand All @@ -43,21 +43,21 @@ exports[`ConformerGenerator should generate conformers 2`] = `
Actelion Java MolfileCreator 1.0
15 14 0 0 0 0 0 0 0 0999 V2000
0.3665 -2.2797 4.9083 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3608 -1.1727 4.4711 O 0 0 0 0 0 0 0 0 0 0 0 0
0.1032 0.0932 4.9457 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2275 0.6140 4.0808 C 0 0 0 0 0 0 0 0 0 0 0 0
1.6863 1.8685 4.5523 O 0 0 0 0 0 0 0 0 0 0 0 0
2.4449 1.8209 5.7076 N 0 0 0 0 0 0 0 0 0 0 0 0
0.5661 -2.2491 5.8663 H 0 0 0 0 0 0 0 0 0 0 0 0
1.2084 -2.3952 4.4144 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.2042 -3.0762 4.7249 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.6316 0.7507 4.9839 H 0 0 0 0 0 0 0 0 0 0 0 0
0.4208 -0.0415 5.8810 H 0 0 0 0 0 0 0 0 0 0 0 0
1.9347 -0.0604 4.0047 H 0 0 0 0 0 0 0 0 0 0 0 0
0.8750 0.7468 3.1297 H 0 0 0 0 0 0 0 0 0 0 0 0
3.0423 1.1589 5.7010 H 0 0 0 0 0 0 0 0 0 0 0 0
2.8848 2.5783 5.7931 H 0 0 0 0 0 0 0 0 0 0 0 0
1.9089 -2.2937 5.8792 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4019 -1.6934 5.6364 O 0 0 0 0 0 0 0 0 0 0 0 0
0.2666 -0.0439 5.7657 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7123 0.7908 4.2081 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5603 2.4347 4.3914 O 0 0 0 0 0 0 0 0 0 0 0 0
1.7021 3.1562 5.2356 N 0 0 0 0 0 0 0 0 0 0 0 0
2.4428 -1.8047 6.7817 H 0 0 0 0 0 0 0 0 0 0 0 0
2.5852 -2.1850 4.9413 H 0 0 0 0 0 0 0 0 0 0 0 0
1.7771 -3.4431 6.0962 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.8241 0.2442 6.0545 H 0 0 0 0 0 0 0 0 0 0 0 0
0.9037 0.3671 6.6327 H 0 0 0 0 0 0 0 0 0 0 0 0
1.7868 0.5114 3.9093 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.0017 0.4248 3.3540 H 0 0 0 0 0 0 0 0 0 0 0 0
2.6525 3.0566 4.8460 H 0 0 0 0 0 0 0 0 0 0 0 0
1.4966 4.1586 5.3228 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
Expand Down
30 changes: 15 additions & 15 deletions __tests__/__snapshots__/force-field-mmff94.js.snap
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,21 +5,21 @@ exports[`ForceFieldMMFF94 should generate force field 1`] = `
Actelion Java MolfileCreator 1.0
15 14 0 0 0 0 0 0 0 0999 V2000
-1.1823 -1.8787 5.4230 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1689 -1.3450 4.5817 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.0219 0.0677 4.7622 C 0 0 0 0 0 0 0 0 0 0 0 0
1.1020 0.5876 3.8706 C 0 0 0 0 0 0 0 0 0 0 0 0
2.3619 0.1733 4.4177 O 0 0 0 0 0 0 0 0 0 0 0 0
3.4290 0.7663 3.6172 N 0 0 0 0 0 0 0 0 0 0 0 0
-2.1495 -1.4197 5.1964 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.9279 -1.7222 6.4757 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.2535 -2.9537 5.2372 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.9629 0.5558 4.4856 H 0 0 0 0 0 0 0 0 0 0 0 0
0.2040 0.2740 5.8146 H 0 0 0 0 0 0 0 0 0 0 0 0
1.0050 0.1852 2.8558 H 0 0 0 0 0 0 0 0 0 0 0 0
1.0676 1.6828 3.8432 H 0 0 0 0 0 0 0 0 0 0 0 0
4.0224 1.1628 4.3475 H 0 0 0 0 0 0 0 0 0 0 0 0
3.9127 -0.0733 3.2930 H 0 0 0 0 0 0 0 0 0 0 0 0
0.3531 -2.1287 6.8340 C 0 0 0 0 0 0 0 0 0 0 0 0
0.6562 -1.5101 5.5910 O 0 0 0 0 0 0 0 0 0 0 0 0
0.2639 -0.1332 5.5764 C 0 0 0 0 0 0 0 0 0 0 0 0
0.6454 0.4978 4.2405 C 0 0 0 0 0 0 0 0 0 0 0 0
2.0674 0.6836 4.2007 O 0 0 0 0 0 0 0 0 0 0 0 0
2.4060 1.3845 2.9656 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.7236 -2.0955 7.0261 H 0 0 0 0 0 0 0 0 0 0 0 0
0.8967 -1.6395 7.6479 H 0 0 0 0 0 0 0 0 0 0 0 0
0.6670 -3.1747 6.7838 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.8220 -0.0770 5.7099 H 0 0 0 0 0 0 0 0 0 0 0 0
0.7633 0.3915 6.3988 H 0 0 0 0 0 0 0 0 0 0 0 0
0.3480 -0.1520 3.4095 H 0 0 0 0 0 0 0 0 0 0 0 0
0.1551 1.4736 4.1458 H 0 0 0 0 0 0 0 0 0 0 0 0
3.0103 2.1262 3.3223 H 0 0 0 0 0 0 0 0 0 0 0 0
3.0309 0.7055 2.5268 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
Expand Down
32 changes: 16 additions & 16 deletions __tests__/__snapshots__/reaction.js.snap
View file
Original file line number Diff line number Diff line change
Expand Up @@ -72,12 +72,12 @@ OCL_RXN_V1.0:gJX@@eKU@@ gGQHDHaInfh@!gJX@@eKU@@ fHdP@@##!ROvp@[C}c@FNZz@@ !R_\`C
M V30 BEGIN CTAB
M V30 COUNTS 6 5 0 0 0
M V30 BEGIN ATOM
M V30 1 Cl 3.4243 0 0 0
M V30 2 C 3.4089 1.9655 0 0
M V30 3 O 5.0829 2.9483 0 0
M V30 4 C 1.7044 2.9483 0 0
M V30 5 C 1.6892 4.9139 0 0
M V30 6 C 0 1.9809 0 0
M V30 1 Cl 1.7471 0 0 0
M V30 2 C 1.7392 1.0028 0 0
M V30 3 O 2.5933 1.5042 0 0
M V30 4 C 0.8696 1.5042 0 0
M V30 5 C 0.8618 2.5071 0 0
M V30 6 C 0 1.0107 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
Expand All @@ -90,11 +90,11 @@ M V30 END CTAB
M V30 BEGIN CTAB
M V30 COUNTS 5 4 0 0 0
M V30 BEGIN ATOM
M V30 1 N 3.4253 0 0 0
M V30 2 C 5.111 0.99 0 0
M V30 3 C 1.7126 0.99 0 0
M V30 4 C 6.7969 0.0267 0 0
M V30 5 C 0 0.0267 0 0
M V30 1 N 1.7476 0 0 0
M V30 2 C 2.6077 0.5051 0 0
M V30 3 C 0.8737 0.5051 0 0
M V30 4 C 3.4678 0.0136 0 0
M V30 5 C 0 0.0136 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
Expand All @@ -108,11 +108,11 @@ M V30 BEGIN PRODUCT
M V30 BEGIN CTAB
M V30 COUNTS 5 4 0 0 0
M V30 BEGIN ATOM
M V30 1 N 3.4253 0 0 0
M V30 2 C 5.111 0.99 0 0
M V30 3 C 1.7126 0.99 0 0
M V30 4 C 6.7969 0.0267 0 0
M V30 5 C 0 0.0267 0 0
M V30 1 N 1.7476 0 0 0
M V30 2 C 2.6077 0.5051 0 0
M V30 3 C 0.8737 0.5051 0 0
M V30 4 C 3.4678 0.0136 0 0
M V30 5 C 0 0.0136 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
Expand Down
6 changes: 3 additions & 3 deletions __tests__/conformers.js
View file
Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@ describe('ConformerGenerator', () => {

const conf1 = gen.getNextConformerAsMolecule();
expect(gen.getConformerCount()).toBe(1);
expect(gen.getPreviousConformerContribution()).toBeCloseTo(0.155, 2);
expect(gen.getPreviousConformerContribution()).toBeCloseTo(0.17, 2);
const conf1Molfile = conf1.toMolfile();
expect(conf1Molfile).toMatchSnapshot();

Expand Down Expand Up @@ -63,10 +63,10 @@ describe('ConformerGenerator', () => {
gen.initializeConformers(mol);

const allConformers = [...gen.molecules()];
expect(allConformers).toHaveLength(42);
expect(allConformers).toHaveLength(26);

// All molecules should be different
expect(new Set(allConformers).size).toBe(42);
expect(new Set(allConformers).size).toBe(26);

expect(allConformers[0].getAtomZ(0)).not.toBe(allConformers[1].getAtomZ(1));

Expand Down
2 changes: 1 addition & 1 deletion openchemlib
Submodule openchemlib updated 692 files
Loading

0 comments on commit 1ac3899

Please sign in to comment.