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Merged
dwhswenson merged 26 commits into from
Oct 10, 2023
Merged

Add notebooks for cookbook #84

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315b441
Add smallligandcomponent->ligandnetwork notebook
Yoshanuikabundi Sep 4, 2023
2a48344
More cookbooks
Yoshanuikabundi Sep 5, 2023
f5a32d5
Merge branch 'main' into cookbook
Yoshanuikabundi Sep 6, 2023
c4a22f9
Add LigandNetwork visualization notebook
Yoshanuikabundi Sep 12, 2023
a9f3154
Hide cells with uncooperative widgets in sphinx
Yoshanuikabundi Sep 13, 2023
ea08271
Add protocol creation cookbook
Yoshanuikabundi Sep 13, 2023
3bf91a5
Line length discipline
Yoshanuikabundi Sep 13, 2023
bcea7c6
Nbsphinx-compatible cookbook notebooks
Yoshanuikabundi Sep 18, 2023
1cc4f3d
Update cookbook/generate_ligand_network.ipynb
Yoshanuikabundi Sep 19, 2023
d8ba75e
Update cookbook/generate_ligand_network.ipynb
Yoshanuikabundi Sep 19, 2023
98c0a7f
Update cookbook/hand_write_ligand_network.ipynb
Yoshanuikabundi Sep 20, 2023
be9126b
Update cookbook/hand_write_ligand_network.ipynb
Yoshanuikabundi Sep 20, 2023
88ca303
Apply suggestions from code review
Yoshanuikabundi Sep 20, 2023
68d2aaf
Update cookbook/load_ligand_network.ipynb
Yoshanuikabundi Sep 20, 2023
2d2a943
Update cookbook/load_ligand_network.ipynb
Yoshanuikabundi Sep 20, 2023
c40336c
Update cookbook/load_ligand_network.ipynb
Yoshanuikabundi Sep 20, 2023
6fed061
Tweak phrasing
Yoshanuikabundi Sep 20, 2023
fe9421e
Apply suggestions from code review
Yoshanuikabundi Sep 20, 2023
a8ef38e
Include 2d mapping visualization
Yoshanuikabundi Sep 20, 2023
96f8c9f
visualizing nodes -> visualizing ligand overlap
Yoshanuikabundi Sep 20, 2023
1dd8ad9
Describe protocol immutability in choose_protocol.ipynb
Yoshanuikabundi Sep 20, 2023
f59f8ef
Add comment describing name choice
Yoshanuikabundi Sep 20, 2023
0b778d5
Rename load_ligand_network
Yoshanuikabundi Sep 20, 2023
4331e66
Update binder environment
Yoshanuikabundi Sep 20, 2023
88f5102
Remove broken widget
Yoshanuikabundi Sep 20, 2023
7c35aa9
switch GHA Python to 3.11 as well
dwhswenson Sep 22, 2023
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8 changes: 4 additions & 4 deletions .binder/environment.yml
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Expand Up @@ -6,7 +6,7 @@ dependencies:
- MDAnalysis
- click
- coverage
- ipywidgets==7.*
- ipywidgets
- lomap2
- lxml
- mdtraj
Expand All @@ -24,9 +24,9 @@ dependencies:
- pytest-cov
- pytest-xdist
- pydantic
- python==3.10.*
- python==3.11.*
- rdkit
- typing_extensions
- gufe>=0.7.1
- openfe>=0.10.1
- gufe>=0.9.4
- openfe>=0.13.0
- py3dmol
2 changes: 1 addition & 1 deletion .github/workflows/CI.yml
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Expand Up @@ -32,7 +32,7 @@ jobs:
fail-fast: false
matrix:
os: [ubuntu-latest, macos-latest]
python-version: ["3.10",]
python-version: ["3.11",]

steps:
- uses: actions/checkout@v2.4.0
Expand Down
1 change: 1 addition & 0 deletions cookbook/.gitignore
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transformations/
33 changes: 33 additions & 0 deletions cookbook/assets/benzene.mol2
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@<TRIPOS>MOLECULE
benzene
12 12 1 0 0
SMALL
NO_CHARGES
@<TRIPOS>ATOM
1 C1 1.207 2.091 0.000 C.ar 1 BENZENE 0.000
2 C2 2.414 1.394 0.000 C.ar 1 BENZENE 0.000
3 C3 2.414 0.000 0.000 C.ar 1 BENZENE 0.000
4 C4 1.207 -0.697 0.000 C.ar 1 BENZENE 0.000
5 C5 0.000 0.000 0.000 C.ar 1 BENZENE 0.000
6 C6 0.000 1.394 0.000 C.ar 1 BENZENE 0.000
7 H1 1.207 3.175 0.000 H 1 BENZENE 0.000
8 H2 3.353 1.936 0.000 H 1 BENZENE 0.000
9 H3 3.353 -0.542 0.000 H 1 BENZENE 0.000
10 H4 1.207 -1.781 0.000 H 1 BENZENE 0.000
11 H5 -0.939 -0.542 0.000 H 1 BENZENE 0.000
12 H6 -0.939 1.936 0.000 H 1 BENZENE 0.000
@<TRIPOS>BOND
1 1 2 ar
2 1 6 ar
3 2 3 ar
4 3 4 ar
5 4 5 ar
6 5 6 ar
7 1 7 1
8 2 8 1
9 3 9 1
10 4 10 1
11 5 11 1
12 6 12 1
@<TRIPOS>SUBSTRUCTURE
1 BENZENE 1 PERM 0 **** **** 0 ROOT
30 changes: 30 additions & 0 deletions cookbook/assets/benzene.sdf
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benzene
PyMOL2.5 3D 0

12 12 0 0 0 0 0 0 0 0999 V2000
25.9780 5.3270 4.7790 C 0 0 0 0 0 0 0 0 0 0 0 0
26.3950 5.0740 3.4990 C 0 0 0 0 0 0 0 0 0 0 0 0
27.3400 5.8600 2.9020 C 0 0 0 0 0 0 0 0 0 0 0 0
27.8370 6.9210 3.5690 C 0 0 0 0 0 0 0 0 0 0 0 0
27.4200 7.1960 4.8560 C 0 0 0 0 0 0 0 0 0 0 0 0
26.4980 6.3790 5.4690 C 0 0 0 0 0 0 0 0 0 0 0 0
25.2298 4.6859 5.2451 H 0 0 0 0 0 0 0 0 0 0 0 0
25.9676 4.2351 2.9497 H 0 0 0 0 0 0 0 0 0 0 0 0
27.6890 5.6311 1.8951 H 0 0 0 0 0 0 0 0 0 0 0 0
28.5730 7.5660 3.0889 H 0 0 0 0 0 0 0 0 0 0 0 0
27.8209 8.0598 5.3863 H 0 0 0 0 0 0 0 0 0 0 0 0
26.1874 6.5720 6.4958 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 4 0 0 0 0
1 6 4 0 0 0 0
1 7 1 0 0 0 0
2 3 4 0 0 0 0
2 8 1 0 0 0 0
3 4 4 0 0 0 0
3 9 1 0 0 0 0
4 5 4 0 0 0 0
4 10 1 0 0 0 0
5 6 4 0 0 0 0
5 11 1 0 0 0 0
6 12 1 0 0 0 0
M END
$$$$
240 changes: 240 additions & 0 deletions cookbook/assets/somebenzenes.sdf
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benzene
PyMOL2.5 3D 0

12 12 0 0 0 0 0 0 0 0999 V2000
25.9780 5.3270 4.7790 C 0 0 0 0 0 0 0 0 0 0 0 0
26.3950 5.0740 3.4990 C 0 0 0 0 0 0 0 0 0 0 0 0
27.3400 5.8600 2.9020 C 0 0 0 0 0 0 0 0 0 0 0 0
27.8370 6.9210 3.5690 C 0 0 0 0 0 0 0 0 0 0 0 0
27.4200 7.1960 4.8560 C 0 0 0 0 0 0 0 0 0 0 0 0
26.4980 6.3790 5.4690 C 0 0 0 0 0 0 0 0 0 0 0 0
25.2298 4.6859 5.2451 H 0 0 0 0 0 0 0 0 0 0 0 0
25.9676 4.2351 2.9497 H 0 0 0 0 0 0 0 0 0 0 0 0
27.6890 5.6311 1.8951 H 0 0 0 0 0 0 0 0 0 0 0 0
28.5730 7.5660 3.0889 H 0 0 0 0 0 0 0 0 0 0 0 0
27.8209 8.0598 5.3863 H 0 0 0 0 0 0 0 0 0 0 0 0
26.1874 6.5720 6.4958 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 4 0 0 0 0
1 6 4 0 0 0 0
1 7 1 0 0 0 0
2 3 4 0 0 0 0
2 8 1 0 0 0 0
3 4 4 0 0 0 0
3 9 1 0 0 0 0
4 5 4 0 0 0 0
4 10 1 0 0 0 0
5 6 4 0 0 0 0
5 11 1 0 0 0 0
6 12 1 0 0 0 0
M END
$$$$
toluene
PyMOL2.5 3D 0

15 15 0 0 0 0 0 0 0 0999 V2000
28.9072 8.7434 5.1220 H 0 0 0 0 0 0 0 0 0 0 0 0
28.1966 8.1433 6.6393 H 0 0 0 0 0 0 0 0 0 0 0 0
27.9864 8.4164 5.6052 C 0 0 0 0 0 0 0 0 0 0 0 0
27.2579 9.2269 5.5838 H 0 0 0 0 0 0 0 0 0 0 0 0
25.9780 5.3270 4.7790 C 0 0 0 0 0 0 0 0 0 0 0 0
26.3950 5.0740 3.4990 C 0 0 0 0 0 0 0 0 0 0 0 0
27.3400 5.8600 2.9020 C 0 0 0 0 0 0 0 0 0 0 0 0
27.8370 6.9210 3.5690 C 0 0 0 0 0 0 0 0 0 0 0 0
27.4200 7.1960 4.8560 C 0 0 0 0 0 0 0 0 0 0 0 0
26.4980 6.3790 5.4690 C 0 0 0 0 0 0 0 0 0 0 0 0
25.2298 4.6859 5.2451 H 0 0 0 0 0 0 0 0 0 0 0 0
25.9676 4.2351 2.9497 H 0 0 0 0 0 0 0 0 0 0 0 0
27.6890 5.6311 1.8951 H 0 0 0 0 0 0 0 0 0 0 0 0
28.5730 7.5660 3.0889 H 0 0 0 0 0 0 0 0 0 0 0 0
26.1874 6.5720 6.4958 H 0 0 0 0 0 0 0 0 0 0 0 0
1 3 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
5 6 4 0 0 0 0
5 10 4 0 0 0 0
5 11 1 0 0 0 0
6 7 4 0 0 0 0
6 12 1 0 0 0 0
7 8 4 0 0 0 0
7 13 1 0 0 0 0
8 9 4 0 0 0 0
8 14 1 0 0 0 0
3 9 1 0 0 0 0
9 10 4 0 0 0 0
10 15 1 0 0 0 0
M END
$$$$
phenol
PyMOL2.5 3D 0

13 13 0 0 0 0 0 0 0 0999 V2000
25.9780 5.3270 4.7790 C 0 0 0 0 0 0 0 0 0 0 0 0
26.3950 5.0740 3.4990 C 0 0 0 0 0 0 0 0 0 0 0 0
27.3400 5.8600 2.9020 C 0 0 0 0 0 0 0 0 0 0 0 0
27.8370 6.9210 3.5690 C 0 0 0 0 0 0 0 0 0 0 0 0
27.4200 7.1960 4.8560 C 0 0 0 0 0 0 0 0 0 0 0 0
26.4980 6.3790 5.4690 C 0 0 0 0 0 0 0 0 0 0 0 0
25.2298 4.6859 5.2451 H 0 0 0 0 0 0 0 0 0 0 0 0
25.9676 4.2351 2.9497 H 0 0 0 0 0 0 0 0 0 0 0 0
27.6890 5.6311 1.8951 H 0 0 0 0 0 0 0 0 0 0 0 0
28.5730 7.5660 3.0889 H 0 0 0 0 0 0 0 0 0 0 0 0
28.1311 8.0887 6.4624 H 0 0 0 0 0 0 0 0 0 0 0 0
26.1874 6.5720 6.4958 H 0 0 0 0 0 0 0 0 0 0 0 0
27.9460 8.3293 5.5517 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 4 0 0 0 0
1 6 4 0 0 0 0
1 7 1 0 0 0 0
2 3 4 0 0 0 0
2 8 1 0 0 0 0
3 4 4 0 0 0 0
3 9 1 0 0 0 0
4 5 4 0 0 0 0
4 10 1 0 0 0 0
5 6 4 0 0 0 0
5 13 1 0 0 0 0
6 12 1 0 0 0 0
11 13 1 0 0 0 0
M END
$$$$
benzonitrile
PyMOL2.5 3D 0

13 13 0 0 0 0 0 0 0 0999 V2000
28.5559 9.5700 6.2831 N 0 0 0 0 0 0 0 0 0 0 0 0
27.9981 8.4043 5.5824 C 0 0 0 0 0 0 0 0 0 0 0 0
25.9780 5.3270 4.7790 C 0 0 0 0 0 0 0 0 0 0 0 0
26.3950 5.0740 3.4990 C 0 0 0 0 0 0 0 0 0 0 0 0
27.3400 5.8600 2.9020 C 0 0 0 0 0 0 0 0 0 0 0 0
27.8370 6.9210 3.5690 C 0 0 0 0 0 0 0 0 0 0 0 0
27.4200 7.1960 4.8560 C 0 0 0 0 0 0 0 0 0 0 0 0
26.4980 6.3790 5.4690 C 0 0 0 0 0 0 0 0 0 0 0 0
25.2298 4.6859 5.2451 H 0 0 0 0 0 0 0 0 0 0 0 0
25.9676 4.2351 2.9497 H 0 0 0 0 0 0 0 0 0 0 0 0
27.6890 5.6311 1.8951 H 0 0 0 0 0 0 0 0 0 0 0 0
28.5730 7.5660 3.0889 H 0 0 0 0 0 0 0 0 0 0 0 0
26.1874 6.5720 6.4958 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 3 0 0 0 0
3 4 4 0 0 0 0
3 8 4 0 0 0 0
3 9 1 0 0 0 0
4 5 4 0 0 0 0
4 10 1 0 0 0 0
5 6 4 0 0 0 0
5 11 1 0 0 0 0
6 7 4 0 0 0 0
6 12 1 0 0 0 0
2 7 1 0 0 0 0
7 8 4 0 0 0 0
8 13 1 0 0 0 0
M END
$$$$
anisole
PyMOL2.5 3D 0

16 16 0 0 0 0 0 0 0 0999 V2000
29.2873 8.8784 4.9226 C 0 0 0 0 0 0 0 0 0 0 0 0
29.5502 9.7990 5.4437 H 0 0 0 0 0 0 0 0 0 0 0 0
28.0548 8.3459 5.4720 O 0 0 0 0 0 0 0 0 0 0 0 0
30.0866 8.1484 5.0502 H 0 0 0 0 0 0 0 0 0 0 0 0
29.1525 9.0868 3.8612 H 0 0 0 0 0 0 0 0 0 0 0 0
25.9780 5.3270 4.7790 C 0 0 0 0 0 0 0 0 0 0 0 0
26.3950 5.0740 3.4990 C 0 0 0 0 0 0 0 0 0 0 0 0
27.3400 5.8600 2.9020 C 0 0 0 0 0 0 0 0 0 0 0 0
27.8370 6.9210 3.5690 C 0 0 0 0 0 0 0 0 0 0 0 0
27.4200 7.1960 4.8560 C 0 0 0 0 0 0 0 0 0 0 0 0
26.4980 6.3790 5.4690 C 0 0 0 0 0 0 0 0 0 0 0 0
25.2298 4.6859 5.2451 H 0 0 0 0 0 0 0 0 0 0 0 0
25.9676 4.2351 2.9497 H 0 0 0 0 0 0 0 0 0 0 0 0
27.6890 5.6311 1.8951 H 0 0 0 0 0 0 0 0 0 0 0 0
28.5730 7.5660 3.0889 H 0 0 0 0 0 0 0 0 0 0 0 0
26.1874 6.5720 6.4958 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 4 1 0 0 0 0
1 5 1 0 0 0 0
1 3 1 0 0 0 0
6 7 4 0 0 0 0
6 11 4 0 0 0 0
6 12 1 0 0 0 0
7 8 4 0 0 0 0
7 13 1 0 0 0 0
8 9 4 0 0 0 0
8 14 1 0 0 0 0
9 10 4 0 0 0 0
9 15 1 0 0 0 0
3 10 1 0 0 0 0
10 11 4 0 0 0 0
11 16 1 0 0 0 0
M END
$$$$
benzaldehyde
PyMOL2.5 3D 0

14 14 0 0 0 0 0 0 0 0999 V2000
29.2079 8.8492 4.9632 O 0 0 0 0 0 0 0 0 0 0 0 0
27.5482 8.8691 6.4597 H 0 0 0 0 0 0 0 0 0 0 0 0
27.9981 8.4043 5.5824 C 0 0 0 0 0 0 0 0 0 0 0 0
25.9780 5.3270 4.7790 C 0 0 0 0 0 0 0 0 0 0 0 0
26.3950 5.0740 3.4990 C 0 0 0 0 0 0 0 0 0 0 0 0
27.3400 5.8600 2.9020 C 0 0 0 0 0 0 0 0 0 0 0 0
27.8370 6.9210 3.5690 C 0 0 0 0 0 0 0 0 0 0 0 0
27.4200 7.1960 4.8560 C 0 0 0 0 0 0 0 0 0 0 0 0
26.4980 6.3790 5.4690 C 0 0 0 0 0 0 0 0 0 0 0 0
25.2298 4.6859 5.2451 H 0 0 0 0 0 0 0 0 0 0 0 0
25.9676 4.2351 2.9497 H 0 0 0 0 0 0 0 0 0 0 0 0
27.6890 5.6311 1.8951 H 0 0 0 0 0 0 0 0 0 0 0 0
28.5730 7.5660 3.0889 H 0 0 0 0 0 0 0 0 0 0 0 0
26.1874 6.5720 6.4958 H 0 0 0 0 0 0 0 0 0 0 0 0
1 3 2 0 0 0 0
2 3 1 0 0 0 0
4 5 4 0 0 0 0
4 9 4 0 0 0 0
4 10 1 0 0 0 0
5 6 4 0 0 0 0
5 11 1 0 0 0 0
6 7 4 0 0 0 0
6 12 1 0 0 0 0
7 8 4 0 0 0 0
7 13 1 0 0 0 0
3 8 1 0 0 0 0
8 9 4 0 0 0 0
9 14 1 0 0 0 0
M END
$$$$
styrene
PyMOL2.5 3D 0

16 16 0 0 0 0 0 0 0 0999 V2000
29.2873 8.8784 4.9226 C 0 0 0 0 0 0 0 0 0 0 0 0
29.6609 8.3486 4.0463 H 0 0 0 0 0 0 0 0 0 0 0 0
29.8344 9.7353 5.3157 H 0 0 0 0 0 0 0 0 0 0 0 0
27.5365 8.8812 6.4825 H 0 0 0 0 0 0 0 0 0 0 0 0
27.9864 8.4164 5.6052 C 0 0 0 0 0 0 0 0 0 0 0 0
25.9780 5.3270 4.7790 C 0 0 0 0 0 0 0 0 0 0 0 0
26.3950 5.0740 3.4990 C 0 0 0 0 0 0 0 0 0 0 0 0
27.3400 5.8600 2.9020 C 0 0 0 0 0 0 0 0 0 0 0 0
27.8370 6.9210 3.5690 C 0 0 0 0 0 0 0 0 0 0 0 0
27.4200 7.1960 4.8560 C 0 0 0 0 0 0 0 0 0 0 0 0
26.4980 6.3790 5.4690 C 0 0 0 0 0 0 0 0 0 0 0 0
25.2298 4.6859 5.2451 H 0 0 0 0 0 0 0 0 0 0 0 0
25.9676 4.2351 2.9497 H 0 0 0 0 0 0 0 0 0 0 0 0
27.6890 5.6311 1.8951 H 0 0 0 0 0 0 0 0 0 0 0 0
28.5730 7.5660 3.0889 H 0 0 0 0 0 0 0 0 0 0 0 0
26.1874 6.5720 6.4958 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
1 5 2 0 0 0 0
4 5 1 0 0 0 0
6 7 4 0 0 0 0
6 11 4 0 0 0 0
6 12 1 0 0 0 0
7 8 4 0 0 0 0
7 13 1 0 0 0 0
8 9 4 0 0 0 0
8 14 1 0 0 0 0
9 10 4 0 0 0 0
9 15 1 0 0 0 0
5 10 1 0 0 0 0
10 11 4 0 0 0 0
11 16 1 0 0 0 0
M END
$$$$
6 changes: 6 additions & 0 deletions cookbook/assets/somebenzenes_fepp.edge
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1c91235:9c91235 # benzene -> toluene
1c91235:7876633 # benzene -> phenol
1c91235:2a51f95 # benzene -> benzonitrile
1c91235:efja0bc # benzene -> anisole
1c91235:7877722 # benzene -> styrene
1c91235:99930cd # benzene -> benzaldehyde
8 changes: 8 additions & 0 deletions cookbook/assets/somebenzenes_nes.dat
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# Total number of edges: 6
# ------------------------
benzene >> toluene
benzene >> phenol
benzene >> benzonitrile
benzene >> anisole
benzene >> styrene
benzene >> benzaldehyde
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