Skip to content

chore: update rbfe-end-to-end to work with new versions of tool #204

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

Closed
sg-s wants to merge 3 commits into from
Closed

chore: update rbfe-end-to-end to work with new versions of tool #204

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
7cd13de
chore: update rbfe-end-to-end to work with new versions of tool
sg-s Apr 24, 2025
ab7ad79
Merge branch 'main' into rbfe-fixes
sg-s Apr 28, 2025
d325854
chore: bumped rbfe-end-to-end to 0.2.5
sg-s Apr 28, 2025
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
2 changes: 1 addition & 1 deletion src/drug_discovery/utils.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -84,7 +84,7 @@ def _start_tool_run(
# tool key mapper
tool_key_mapper = dict(
ABFE="deeporigin.abfe-end-to-end/0.2.5",
RBFE="deeporigin.rbfe-end-to-end",
RBFE="deeporigin.rbfe-end-to-end/0.2.5",
Docking="deeporigin.bulk-docking/0.3.0",
)

Expand Down
110 changes: 57 additions & 53 deletions src/json/rbfe_end_to_end.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,17 +1,17 @@
{
"binding": {
"add_fep_repeats": 0,
"amend": "__NO_AMEND",
"annihilate": true,
"atom_mapping_paths": null,
"atom_mapping_threshold": 0.01,
"em_all": true,
"em_solvent": true,
"emeq_md_options": {
"T": 298.15,
"cutoff": 0.9,
"dt": 0.004,
"fourier_spacing": 0.12,
"hydrogen_mass": 2.0,
"Δt": 0.004
"hydrogen_mass": 2.0
},
"fep_windows": [
{
Expand Down Expand Up @@ -93,24 +93,19 @@
"barostat": "MonteCarloBarostat",
"barostat_exchange_interval": 500,
"cutoff": 0.9,
"dt": 0.004,
"fourier_spacing": 0.12,
"hydrogen_mass": 2.0,
"integrator": "BAOABIntegrator",
"Δt": 0.004
"integrator": "BAOABIntegrator"
},
"repeats": 1,
"skip_emeq": "__NO",
"softcore_alpha": 0.5,
"steps": 1250000,
"test_run": 0,
"thread_pinning": 0,
"thread_pinning_offset": 0,
"threads": 0,
"workers": 0
"thread_pinning": 0
},
"complex_prep": {
"include_ligands": 1,
"include_protein": 1,
"sysprep_params": {
"charge_method": "bcc",
"do_loop_modelling": false,
Expand All @@ -120,12 +115,11 @@
"keep_waters": true,
"lig_force_field": "gaff2",
"padding": 1.0,
"pdb_id": null,
"save_gmx_files": false
}
},
"ligand1_prep": {
"include_ligands": 1,
"include_protein": 0,
"sysprep_params": {
"charge_method": "bcc",
"do_loop_modelling": false,
Expand All @@ -135,12 +129,11 @@
"keep_waters": true,
"lig_force_field": "gaff2",
"padding": 1.0,
"pdb_id": null,
"save_gmx_files": false
}
},
"ligand2_prep": {
"include_ligands": 1,
"include_protein": 0,
"sysprep_params": {
"charge_method": "bcc",
"do_loop_modelling": false,
Expand All @@ -150,46 +143,55 @@
"keep_waters": true,
"lig_force_field": "gaff2",
"padding": 1.0,
"pdb_id": null,
"save_gmx_files": false
}
},
"solvation1": {
"add_fep_repeats": 0,
"amend": "__NO_AMEND",
"annihilate": true,
"atom_mapping_paths": null,
"atom_mapping_threshold": 0.01,
"em_all": true,
"em_solvent": true,
"emeq_md_options": {
"T": 298.15,
"cutoff": 0.9,
"dt": 0.004,
"fourier_spacing": 0.12,
"hydrogen_mass": 2.0,
"Δt": 0.004
"hydrogen_mass": 2.0
},
"fep_windows": [
{
"coul_A": [
1.0,
0.9,
0.8,
0.7,
0.6,
0.5,
0.4,
0.3,
0.2,
0.1,
0.0
]
},
{
"vdw_A": [
1.0,
0.9,
0.8,
0.7,
0.6,
0.5,
0.4,
0.3,
0.2,
0.1,
0.923,
0.846,
0.769,
0.692,
0.615,
0.538,
0.462,
0.385,
0.308,
0.231,
0.154,
0.077,
0.0
]
}
Expand All @@ -202,58 +204,63 @@
"barostat": "MonteCarloBarostat",
"barostat_exchange_interval": 500,
"cutoff": 0.9,
"dt": 0.004,
"fourier_spacing": 0.12,
"hydrogen_mass": 2.0,
"integrator": "BAOABIntegrator",
"Δt": 0.004
"integrator": "BAOABIntegrator"
},
"repeats": 1,
"skip_emeq": "__NO",
"softcore_alpha": 0.5,
"steps": 300000,
"steps": 500000,
"test_run": 0,
"thread_pinning": 0,
"thread_pinning_offset": 0,
"threads": 0,
"workers": 0
"thread_pinning": 0
},
"solvation2": {
"add_fep_repeats": 0,
"amend": "__NO_AMEND",
"annihilate": true,
"atom_mapping_paths": null,
"atom_mapping_threshold": 0.01,
"em_all": true,
"em_solvent": true,
"emeq_md_options": {
"T": 298.15,
"cutoff": 0.9,
"dt": 0.004,
"fourier_spacing": 0.12,
"hydrogen_mass": 2.0,
"Δt": 0.004
"hydrogen_mass": 2.0
},
"fep_windows": [
{
"coul_A": [
1.0,
0.9,
0.8,
0.7,
0.6,
0.5,
0.4,
0.3,
0.2,
0.1,
0.0
]
},
{
"vdw_A": [
1.0,
0.9,
0.8,
0.7,
0.6,
0.5,
0.4,
0.3,
0.2,
0.1,
0.923,
0.846,
0.769,
0.692,
0.615,
0.538,
0.462,
0.385,
0.308,
0.231,
0.154,
0.077,
0.0
]
}
Expand All @@ -266,19 +273,16 @@
"barostat": "MonteCarloBarostat",
"barostat_exchange_interval": 500,
"cutoff": 0.9,
"dt": 0.004,
"fourier_spacing": 0.12,
"hydrogen_mass": 2.0,
"integrator": "BAOABIntegrator",
"Δt": 0.004
"integrator": "BAOABIntegrator"
},
"repeats": 1,
"skip_emeq": "__NO",
"softcore_alpha": 0.5,
"steps": 300000,
"steps": 500000,
"test_run": 0,
"thread_pinning": 0,
"thread_pinning_offset": 0,
"threads": 0,
"workers": 0
"thread_pinning": 0
}
}
4 changes: 4 additions & 0 deletions src/tools/run.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -317,6 +317,10 @@ def _process_job(
metadata=metadata,
)

import json

print(json.dumps(payload, indent=2))

response = run_tool(
data=payload,
tool_key=tool_key,
Expand Down