deeporigin.drug_discovery.fep_common¶
Shared FEP parameter types and serialization helpers used by ABFE and RBFE.
ABFEParams— absolute FEP defaults (binding_n_windows=48,solvation_n_windows=32)RBFEParams— relative FEP defaults (binding_n_windows=24,solvation_n_windows=24), matching MDSuite whenn_windowsis unset for a two-ligand (relative) run
Shared FEP parameter serialization for ABFE and RBFE workflow tools.
Classes¶
dataclass
¶
FEP calculation parameters for absolute binding free energy (ABFE).
Attributes:
| Name | Type | Description |
|---|---|---|
annihilate |
bool
|
Whether to annihilate the ligand. |
dt |
float
|
Time step in ps. Used for both emeq_md_options and prod_md_options. |
temperature |
float
|
Temperature in K. Used for both emeq_md_options and prod_md_options. |
cutoff |
float
|
Cutoff distance in nm. Used for both emeq_md_options and prod_md_options. |
repeats |
int
|
Number of repeats. |
replex_period_ps |
float
|
Replica exchange period in ps. |
test_run |
int
|
Test run flag. |
binding_n_windows |
int
|
Number of windows for binding calculation. |
binding_npt_reduce_restraints_ns |
float
|
NPT reduce restraints time in ns for binding. |
binding_nvt_heating_ns |
float
|
NVT heating time in ns for binding. |
binding_steps |
int
|
Number of steps for binding calculation. |
solvation_n_windows |
int
|
Number of windows for solvation calculation. |
solvation_npt_reduce_restraints_ns |
float
|
NPT reduce restraints time in ns for solvation. |
solvation_nvt_heating_ns |
float
|
NVT heating time in ns for solvation. |
solvation_steps |
int
|
Number of steps for solvation calculation. |
dataclass
¶
Bases: ABFEParams
FEP calculation parameters for relative binding free energy (RBFE).
Window defaults match MDSuite relative-FEP (is_relative) when n_windows
is unset: 24 for both binding and solvation (vs ABFE's 48 / 32).