deeporigin.drug_discovery.fep_common¶
Shared FEP parameter types and serialization helpers used by ABFE and RBFE.
Shared FEP parameter serialization for ABFE and RBFE workflow tools.
Classes¶
dataclass
¶
FEP calculation parameters shared by ABFE and RBFE.
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. |