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[WIP] SepTop Protocol #1057

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3a64347
Initial commit SepTop settings
hannahbaumann Oct 23, 2024
066c47b
Initial SepTop protocol work
hannahbaumann Oct 24, 2024
08ef427
Some fixes
hannahbaumann Oct 24, 2024
26b4b92
Implement a Setup unit and empty Run unit
hannahbaumann Oct 24, 2024
3261ba2
Updating positions in the solvent and complex
hannahbaumann Oct 25, 2024
b9c4e70
Add some femto utils, setup alchemical system
hannahbaumann Nov 11, 2024
43fc5af
Work on implementing restraints
hannahbaumann Nov 15, 2024
d8ff3b1
Some more changes
hannahbaumann Nov 19, 2024
5753689
Add some femto utils
hannahbaumann Nov 19, 2024
3a71963
Some fixes for the restraints
hannahbaumann Nov 19, 2024
0b6d7ba
Create separate solvation settings for solvent and complex
hannahbaumann Nov 19, 2024
6894cd9
Testing some things
hannahbaumann Nov 19, 2024
107d603
Testing some things
hannahbaumann Nov 19, 2024
2a017d5
Fix comp_resids_B
hannahbaumann Nov 19, 2024
74a9818
Fix restraints complex mdtraj
hannahbaumann Nov 19, 2024
427aee4
Update restraint selection
hannahbaumann Nov 19, 2024
8b88214
More edits Boresch restraints
hannahbaumann Nov 20, 2024
52992d8
Change type check restraints
hannahbaumann Nov 20, 2024
5a90c55
Changes unitcell lengths
hannahbaumann Nov 20, 2024
b4ffd2b
Small test unit cell
hannahbaumann Nov 20, 2024
0e32007
Update unit cell length
hannahbaumann Nov 21, 2024
90b1679
Update unit cell length2
hannahbaumann Nov 21, 2024
3ca733d
small fix
hannahbaumann Nov 21, 2024
82da7c8
More changes restraints
hannahbaumann Nov 21, 2024
df637bc
Print statements to help troubleshoot restraints
hannahbaumann Nov 21, 2024
c4671e4
Update indices
hannahbaumann Nov 21, 2024
ae1a2b4
Fix units
hannahbaumann Nov 21, 2024
5ca9923
Update units
hannahbaumann Nov 21, 2024
ca72561
Small fixes
hannahbaumann Nov 21, 2024
fe1bad6
Change lambda settings
hannahbaumann Nov 22, 2024
e4713a4
Serialize system
hannahbaumann Nov 26, 2024
9eb40d2
small fix
hannahbaumann Nov 26, 2024
6f53741
Only store system, topology
hannahbaumann Nov 26, 2024
0a5206c
Start of run unit
hannahbaumann Nov 26, 2024
5d0c10f
Add run unit to create method
hannahbaumann Nov 26, 2024
8cafbe8
Add missing import
hannahbaumann Nov 26, 2024
2829604
Write run unit
hannahbaumann Nov 27, 2024
52eef2e
Remove unnecessary import
hannahbaumann Nov 27, 2024
eda32c2
Remove verbose
hannahbaumann Nov 27, 2024
7663e2d
Add states to run unit
hannahbaumann Nov 27, 2024
1551bc2
Add simtype
hannahbaumann Nov 27, 2024
eebff50
Remove nocutoff
hannahbaumann Nov 27, 2024
4a5922d
Small fixes
hannahbaumann Nov 27, 2024
bcaefd8
Change monotonic check
hannahbaumann Nov 27, 2024
23aecb5
Put troubleshooting pdb files in the sharedbase path for now
hannahbaumann Nov 27, 2024
27e1ea7
Fix scaling restraints
hannahbaumann Nov 28, 2024
026a0ef
Update boresch scaling
hannahbaumann Nov 28, 2024
a78481f
testing something
hannahbaumann Nov 28, 2024
b262a9e
Test out not doing a preequ
hannahbaumann Dec 2, 2024
063c59a
Change min length solvent
hannahbaumann Dec 2, 2024
702b639
Change phase detection
hannahbaumann Dec 3, 2024
13c7724
Adding print statements for debugging
hannahbaumann Dec 3, 2024
6b393d5
Add print statements to help debug
hannahbaumann Dec 4, 2024
f86601e
Save prequ file
hannahbaumann Dec 4, 2024
7372985
Run short equ
hannahbaumann Dec 4, 2024
a401c98
Update gather to separate setup and run results
hannahbaumann Dec 4, 2024
c2e2d8a
Fix gather
hannahbaumann Dec 5, 2024
588a1d2
Testing out using the openmmtools alchemical factory instead of femto
hannahbaumann Dec 6, 2024
b7f7a50
Add imports
hannahbaumann Dec 6, 2024
4159e69
Adapt Lambda states
hannahbaumann Dec 9, 2024
1ce8dba
Add individual lambda restraints
hannahbaumann Dec 9, 2024
97f0285
Small FIx
hannahbaumann Dec 9, 2024
51ebfac
Fix restraints sign
hannahbaumann Dec 9, 2024
bd69a8b
More tests and fixes
hannahbaumann Dec 10, 2024
b4c06ba
More updates
hannahbaumann Dec 10, 2024
274c204
Merge branch 'main' into start_septop
hannahbaumann Dec 11, 2024
e6dae2f
Update compute location
hannahbaumann Dec 11, 2024
782de90
Small fix
hannahbaumann Dec 11, 2024
14ae69f
Adding some more docstrings
hannahbaumann Dec 11, 2024
e4c25e1
AlchemicalFactory changes
hannahbaumann Dec 12, 2024
e780a94
Add slow energy test
hannahbaumann Dec 13, 2024
b5cdaf4
Move energy test to slow
hannahbaumann Dec 13, 2024
ee984b4
Fix energy test
hannahbaumann Dec 13, 2024
8796be2
Fix off molecule
hannahbaumann Dec 13, 2024
43ad90b
Merge branch 'main' into start_septop
hannahbaumann Dec 16, 2024
6c628dd
Subclass Parameterstate
hannahbaumann Dec 16, 2024
92690d8
Change AlchemicalRegion name
hannahbaumann Dec 16, 2024
2d1eba4
Update restraint lambda parameter
hannahbaumann Dec 16, 2024
3849778
Update settings
hannahbaumann Dec 16, 2024
d989feb
Change alchemical state def
hannahbaumann Dec 16, 2024
6311a92
Remove copy of AlchemicalFactory
hannahbaumann Dec 17, 2024
bc489e3
Remove femto alchemy
hannahbaumann Dec 17, 2024
228c1c9
Remove unnecessary file
hannahbaumann Dec 17, 2024
a727ec2
Small fixes
hannahbaumann Dec 17, 2024
32e541f
Some fixes
hannahbaumann Dec 17, 2024
a7d7b2e
Update tests
hannahbaumann Dec 17, 2024
2d42497
Merge branch 'main' into start_septop
hannahbaumann Dec 18, 2024
ac9f1a8
Add tests protocol results
hannahbaumann Dec 19, 2024
22f9b79
Merge branch 'main' into start_septop
hannahbaumann Dec 19, 2024
d1d1b04
debug failing test
hannahbaumann Dec 20, 2024
153ffec
Test restraints closer
hannahbaumann Dec 20, 2024
9efab61
Test restraints closer 2
hannahbaumann Dec 20, 2024
e9d0a19
Merge branch 'main' into start_septop
hannahbaumann Jan 8, 2025
a61268b
Fix tests
hannahbaumann Jan 8, 2025
91599f0
Some mypy fixes
hannahbaumann Jan 8, 2025
a046e86
small fixes
hannahbaumann Jan 8, 2025
8d8e56d
More mypy fixes
hannahbaumann Jan 8, 2025
6dafe6b
Add gather test
hannahbaumann Jan 8, 2025
2c297c2
Merge branch 'main' into start_septop
hannahbaumann Jan 10, 2025
b24ea6b
Some restaints updates
hannahbaumann Jan 10, 2025
ee11781
Dry run and make run function in the RunUnit
hannahbaumann Jan 13, 2025
06b04a2
Delete commented out parts
hannahbaumann Jan 13, 2025
fd81c70
Add test for user charges
hannahbaumann Jan 13, 2025
f26f886
Small test
hannahbaumann Jan 14, 2025
69e6d8c
Small fix
hannahbaumann Jan 14, 2025
4f59bc5
Add more tests
hannahbaumann Jan 14, 2025
101f49a
More tests
hannahbaumann Jan 14, 2025
98059a0
Add tests for cutoff and pressure
hannahbaumann Jan 14, 2025
080526f
Merge branch 'main' into start_septop
hannahbaumann Jan 15, 2025
0bd8b7d
Add tests for reference xml
hannahbaumann Jan 16, 2025
40c3772
Merge branch 'start_septop' of github.com:hannahbaumann/openfe_septop…
hannahbaumann Jan 16, 2025
7faae6e
Test distance solvent restraint in dry run
hannahbaumann Jan 16, 2025
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24 changes: 24 additions & 0 deletions openfe/protocols/openmm_septop/__init__.py
Original file line number Diff line number Diff line change
@@ -0,0 +1,24 @@
# This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""
Run SepTop free energy calculations using OpenMM and OpenMMTools.

"""

from .equil_septop_method import (
SepTopProtocol,
SepTopSettings,
SepTopProtocolResult,
SepTopComplexSetupUnit,
SepTopSolventSetupUnit,
SepTopSolventRunUnit,
SepTopComplexRunUnit,
)

__all__ = [
"SepTopProtocol",
"SepTopSettings",
"SepTopProtocolResult",
"SepTopComplexSetupUnit",
"SepTopSolventSetupUnit",
]
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