[DNM] Add spectrum workflow - #140

Open

apayne97 wants to merge 66 commits into

mainfrom

add-spectrum-workflow

Commits on Jul 25, 2025

change toml files
Maria Castellanos
committed
c77f9c2
delete asap- mentions in docstrings
Maria Castellanos
committed
8418cf1

Commits on Jul 30, 2025

Merge branch 'main' of github.com:choderalab/drugforge
Maria Castellanos
committed
be98b46
Update guides
Maria Castellanos
committed
88aa7f9
Merge branch 'main' of github.com:choderalab/drugforge into update-documentation
Maria Castellanos
committed
7bbd638
update main readme
apayne97
committed
674cd19
Merge branch 'update-readme' into update-documentation
apayne97
committed
2932183
update docs readme
apayne97
committed
3755ba1
update a few of the tutorials
apayne97
committed
338e050
formatting
apayne97
committed
573e89a

Commits on Jul 31, 2025

update documentation on spectrum pt.1
Maria Castellanos
committed
f43cf73
add all docs building requirements to yaml file
apayne97
committed
71e3958
fix requirements name and docs
apayne97
committed
e80b7c4
add sphinx reqs back to requirements.yaml
apayne97
committed
8651706
update docs landing page
apayne97
committed
b6d1749
Merge remote-tracking branch 'origin/update-documentation' into update-documentation
apayne97
committed
a70d65a
add logo image
apayne97
committed
698e94d
Add files for tutorial to aws
Maria Castellanos
committed
78991d3

Commits on Aug 1, 2025

Merge branch 'update-documentation' of github.com:choderalab/drugforge into update-documentation
Maria Castellanos
committed
7b9044f
update spectrum tutorial 2
Maria Castellanos
committed
d54d47c
add alignment image for tutorial
Maria Castellanos
committed
ed60cd4

Commits on Aug 5, 2025

changes for tutorial
Maria Castellanos
committed
7b26d87

Commits on Aug 6, 2025

corrected mentions of bespoke fit
Maria Castellanos
committed
9d1ef96

Commits on Aug 25, 2025

show blast score in html
Maria Castellanos
committed
392807a

Commits on Aug 26, 2025

Add option to calculate bsite similarity
Maria Castellanos
committed
9a5bd25
Merge branch 'main' of github.com:choderalab/drugforge into add-spectrum-improvements
Maria Castellanos
committed
adba7b0

Commits on Sep 2, 2025

Merge branch 'main' into add-spectrum-improvements
mariacm12
authored
3b4e9b4

Commits on Sep 23, 2025

Merge branch 'main' into add-spectrum-improvements
ijpulidos
authored
562dc1d

Commits on Oct 14, 2025

Merge branch 'main' into add-spectrum-improvements
ijpulidos
authored
b61e2e3

Commits on Dec 10, 2025

Merge branch 'main' into add-spectrum-improvements
mariacm12
authored
384f077
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot]
committed
860c1d7
Fix pre-commit error
Maria Castellanos
committed
0feca65

Commits on Dec 11, 2025

get rid of mgltool dependency
Maria Castellanos
committed
396655f
Finish removing mgl dependency
Maria Castellanos
committed
4387ca3

Commits on Dec 12, 2025

Merge branch 'add-spectrum-improvements' of github.com:choderalab/drugforge into add-spectrum-improvements
Maria Castellanos
committed
fb15f77
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot]
committed
fa96c8d

Commits on Feb 24, 2026

Merge branch 'main' into add-spectrum-improvements
apayne97
authored
a3f85bd

Commits on Feb 27, 2026

Merge branch 'main' into add-spectrum-improvements
apayne97
authored
461f7cc

Commits on Mar 3, 2026

Commits on Mar 4, 2026

Merge branch 'main' into add-spectrum-improvements
apayne97
authored
ea44131
add initial pdbqt conversion test
apayne97
committed
b9663db
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot]
committed
5145160
test whether file generated by convert_to_pdbqt can be used by vina
apayne97
committed
e67fedc
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot]
committed
eb37101
add probably redundant and unnecessary spectrum schema
apayne97
committed
f0938f2

Commits on Mar 5, 2026

add some more basic tests
apayne97
committed
ae48d45
add some more CLI commands
apayne97
committed
71d8d50
add independent spectrum cli with alphafold support
apayne97
committed
58829c2
fix logging file handling :(
apayne97
committed
2abbb2f
change default alphafold json version to version 2
apayne97
committed
e9ecb34
change default alphafold json version to version 2
apayne97
committed
530aa79
add structure alignment command for alphafold generated data
apayne97
committed
5e604f9
update file handling for alphafold
apayne97
committed
667de72
add option to run boltz
apayne97
committed
e1d37d0
make directory before running logging
apayne97
committed
633df61
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot]
committed
7691688
Merge branch 'main' into add-spectrum-workflow
apayne97
authored
02692bc
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot]
committed
25d1091
add more minimal ligand transfer docking implementation
apayne97
committed
41b1eaf
Merge remote-tracking branch 'origin/add-spectrum-workflow' into add-spectrum-workflow
apayne97
committed
66c062e
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot]
committed
a18f00b