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[DRAFT] Schrodinger solvation shell extraction #23

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[DRAFT] Schrodinger solvation shell extraction #23

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c431bea
automated solvation shell extraction workflow
Apr 22, 2024
9c75284
begin addressing Daniel comments
May 15, 2024
ef3e241
operate on pairwise distances, account for PBCs
May 15, 2024
f092257
switch to kabsch rmsd
May 15, 2024
14749ae
add pdb file example
May 15, 2024
4280670
add dependencies to setup
May 15, 2024
09031e2
rename from rmse to rmsd
May 15, 2024
70de4e1
random seed for rmsd set instead of always starting at 0, remove reor…
May 15, 2024
3868637
start adding support for multiatom solutes, not working yet
May 17, 2024
6b8e9a7
fix star import, add al_cl04 test file
May 17, 2024
88832da
update extraction script to be the non-working Al_Cl04 one
May 17, 2024
0af4830
correct charge assignment
May 20, 2024
006c1ee
initial biolip_extraction
levineds May 31, 2024
53f52f9
metal-organics bug
levineds May 31, 2024
869b81a
minor changes
levineds May 31, 2024
bdcb588
refactor make_gaps_gly
levineds Jun 4, 2024
3334e95
Merge remote-tracking branch 'origin/main'
levineds Jun 4, 2024
4a3fcc8
Add memory estimate function
levineds Jun 4, 2024
3e5ce54
docstrings
levineds Jun 4, 2024
5e5fff3
merge conflicts
levineds Jun 4, 2024
6d327fc
Refactor
levineds Jun 5, 2024
e3182e6
docstrings
levineds Jun 5, 2024
2401268
black
levineds Jun 5, 2024
5dcc01c
isort
levineds Jun 5, 2024
adc3ebe
missing docstring
levineds Jun 5, 2024
9abc9cf
Schrodinger is Python 3.8
levineds Jun 5, 2024
8536dd7
filter to minimal pockets
levineds Jun 6, 2024
a280702
make more efficient/pythonic
levineds Jun 6, 2024
7edbc07
black
levineds Jun 6, 2024
ea015e7
store biolip_df as pickle
levineds Jun 6, 2024
7b800d6
cleanup
levineds Jun 6, 2024
68fa23c
black
levineds Jun 6, 2024
d46a506
use FAIR cluster Schrodinger
levineds Jun 12, 2024
4c5603e
disable ligand size limit
levineds Jun 12, 2024
d852562
move error message
levineds Jun 14, 2024
ce26492
alternate multiprocessing
levineds Jun 14, 2024
923168c
correct cif outname error
levineds Jun 14, 2024
c460cb7
try multiple times to download if needed
levineds Jun 14, 2024
a26d9bb
formatting
levineds Jun 14, 2024
42536c3
change for smaller sampling
levineds Jun 14, 2024
bad07e7
add error checking around mutation
levineds Jun 14, 2024
2e72c49
protection for SMARTS evaluation
levineds Jun 15, 2024
901567b
BioLiP errors
levineds Jun 15, 2024
db18286
remove duplicate "BS"
levineds Jun 17, 2024
8c2e2e6
add timeout to architector structure generation
levineds Jun 18, 2024
cdfbb02
formatting
levineds Jun 18, 2024
f36e450
improve xyz generation
levineds Jun 18, 2024
46df040
add slightly more error checking
levineds Jun 20, 2024
301c199
more fixes
levineds Jun 25, 2024
b56de8d
function already exists of course
levineds Jun 26, 2024
30ed02c
trying to handle multi-atom solutes, committing before migrating to s…
Jun 27, 2024
1c7fd1a
start schrodinger workflow
Jul 1, 2024
d65860f
can extract shells, now need to loop over solutes, apply pbcs and add…
Jul 1, 2024
ed22d93
loop over solutes
Jul 1, 2024
82fff88
fix loop nesting
Jul 1, 2024
1ef6e1b
add partial charge assignment
Jul 1, 2024
4a55633
fix pbc wrapping index error
Jul 1, 2024
66b4afd
append central atom to shell if not already present, have fully runni…
Jul 2, 2024
ac25b01
cleanup files
Jul 2, 2024
46aab0d
ignore readme
Jul 2, 2024
af2245b
begin solvent-solvent stuff, not working
Jul 2, 2024
e0479be
revert to working solvent-solvent interactions, need to implement PBCs
Jul 2, 2024
9bc0a70
uncomment solvent part
Jul 2, 2024
e31bf22
switch to superimpose version of rmsd
Jul 2, 2024
3ee9aa0
make size checking caps hard
Jul 2, 2024
8e2a1e0
address some more pr comments - more accurate comments, restructuring…
Jul 2, 2024
b2b836d
option to skip solvent centered shells
Jul 2, 2024
cb1139c
remove equals from dir name
Jul 2, 2024
f7bd798
assign partial charges once outside loop
Jul 2, 2024
68dabb2
partial charge assignment once up front
Jul 2, 2024
ca95322
remove size filtering function
Jul 2, 2024
eb12dd8
more explicit version of expand shells function
Jul 2, 2024
f432765
fix central solute molecule bug
Jul 2, 2024
53b6101
simplify filter solute function
Jul 2, 2024
1af70a4
filter after batches are made
levineds Jul 3, 2024
4d9f53b
label ligands after coordinating groups
levineds Jul 3, 2024
aa7d024
turn off shell expansion if there are no solvents
Jul 4, 2024
34d2f21
lognormal sampling of max size
Jul 4, 2024
a51ea9b
option to subsample solutes/solvents per frame
Jul 4, 2024
23e320a
fix chain-labeling/angle adjustment bug
levineds Jul 5, 2024
c0f36e8
add cleanup script for pdb pockets
levineds Jul 5, 2024
b487187
cleanup cleanup.py
levineds Jul 5, 2024
b24eac1
add combine_pockets.py to merge certain pockets
levineds Jul 5, 2024
d413430
flake8
levineds Jul 5, 2024
39abfb0
remove correct directory
levineds Jul 5, 2024
66fcc21
updates
levineds Jul 8, 2024
c48f21e
Take PDBs first over CIFs
levineds Jul 8, 2024
3e65d58
speedups for are_conformers
levineds Jul 9, 2024
0e54a94
cleanup
levineds Jul 9, 2024
6720a55
Merge remote-tracking branch 'refs/remotes/origin/main'
levineds Jul 9, 2024
3966421
some logging, restrict to 100 frames for now
levineds Jul 10, 2024
c877a8b
basic docstrings
levineds Jul 10, 2024
2963480
refactor into separate functions, re-use code
levineds Jul 10, 2024
f225f37
refactor bug
levineds Jul 10, 2024
aff9ec2
make solute-free assertion a warning instead
Jul 10, 2024
9657238
add max frames argument
Jul 10, 2024
e0f2321
arg bug
Jul 10, 2024
dd8e52d
update cleanup printing
levineds Jul 15, 2024
7a05a75
delete old files after combining pockets
levineds Jul 15, 2024
23763fb
some more cleanup tools
levineds Jul 16, 2024
02ce480
there are nitriles...
levineds Jul 17, 2024
bd6aa7d
threshold was a little too tight
levineds Jul 18, 2024
44a56ea
also remove totally overlapping atoms (this may be addressed by chang…
levineds Jul 18, 2024
9bcc118
oops
levineds Jul 18, 2024
53e4901
deprotonate carboxylic acids always
levineds Jul 19, 2024
bef0a7e
add more cleanup steps that probably aren't needed
levineds Jul 19, 2024
d19e4a7
partition off nuclear option in cleanup.py
levineds Jul 19, 2024
60f627e
don't try and redownload if we already have it
levineds Jul 19, 2024
47d9295
oops
levineds Jul 19, 2024
514ea62
make sure COOH is deprotonated
levineds Jul 19, 2024
7b1d14a
add files for running MD with Desmond
levineds Jul 19, 2024
07b391d
use absolute path
levineds Jul 20, 2024
abf0607
ensure ligand chain is present
levineds Jul 22, 2024
6128728
Use chain to identify solvent vs. solute
levineds Jul 26, 2024
b3eaf6c
Merge remote-tracking branch 'refs/remotes/origin/main'
levineds Jul 31, 2024
65b9c0b
Sample OOD solvation shells for 10% of inputs
levineds Jul 31, 2024
2cc5793
merge main
levineds Aug 13, 2024
a477ada
Revert "merge main"
levineds Aug 13, 2024
abe6e40
Reapply "merge main"
levineds Aug 13, 2024
23bcacf
Revert "merge main"
levineds Aug 13, 2024
654a8a6
Reapply "merge main"
levineds Aug 13, 2024
a9b5124
refactor and add some comments
Aug 23, 2024
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2 changes: 2 additions & 0 deletions .gitattributes
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Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
.pdb filter=lfs diff=lfs merge=lfs -text
*.pdb filter=lfs diff=lfs merge=lfs -text
19 changes: 19 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@ checkpoints
results
logs
*.traj
*.pdb
experimental

# Byte-compiled / optimized / DLL files
Expand Down Expand Up @@ -111,3 +112,21 @@ Local

# VS Code
.vscode/

# testfiles
testfiles/
testfiles_old/
*mae

# Schrodinger stuff
maestro_package/

# Jupyter Notebook
.ipynb_checkpoints/
*ipynb

# Misc
notes.txt
*prof


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