Skip to content

Add notebook for creating AlchemicalNetworks from external files #79

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
IAlibay merged 1 commit into from
Aug 18, 2023
Merged

Add notebook for creating AlchemicalNetworks from external files #79

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
349 changes: 349 additions & 0 deletions networks/creating_networks_from_external_files.ipynb
View file
Open in desktop

Large diffs are not rendered by default.

240 changes: 240 additions & 0 deletions networks/data/benzene_modifications.sdf
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,240 @@
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
$$$$
8 changes: 8 additions & 0 deletions networks/data/benzenes.dat
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,8 @@
# Total number of edges: 6
# ------------------------
benzene >> toluene
benzene >> phenol
benzene >> benzonitrile
benzene >> anisole
benzene >> styrene
benzene >> benzaldehyde
6 changes: 6 additions & 0 deletions networks/data/benzenes.edge
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
1c91235:9c91235 # benzene -> toluene
1c91235:7876633 # benzene -> phenol
1c91235:2a51f95 # benzene -> benzonitrile
1c91235:efja0bc # benzene -> anisole
1c91235:7877722 # benzene -> styrene
1c91235:99930cd # benzene -> benzaldehyde