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

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

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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
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2 changes: 1 addition & 1 deletion src/drug_discovery/utils.py
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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
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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
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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