ABFE

This reference page provides information on function signature for every function in the ABFE module.

src.tools.abfe

this module contains various functions to run steps of an ABFE workflow

Attributes

integrators module-attribute

integrators = Literal[
    "BAOABIntegrator",
    "LangevinIntegrator",
    "SteepestDescentMinimizer",
    "LeapFrogIntegrator",
    "SoluteSolventSplittingIntegrator",
]

Integrator available for simulation

force_fields module-attribute

force_fields = Literal['ff14SB', 'ff99SB-ildn']

Available force fields

charge_methods module-attribute

charge_methods = Literal['gas', 'bcc']

Available charge methods

Functions

init

init(*, ligand_file: str, protein_file: str) -> str

Initialize an ABFE run. Upload ligand and protein files to Data Hub.

complex_prep

complex_prep(
    row_id: str,
    *,
    keep_waters: bool = True,
    save_gmx_files: bool = False,
    is_lig_protonated: bool = True,
    is_protein_protonated: bool = True,
    do_loop_modelling: bool = False,
    charge_method: charge_methods = "bcc",
    lig_force_field: ligand_force_fields = "gaff2",
    padding: float = 1.0,
    system_name: str = "complex",
    force_field: force_fields = "ff14SB"
) -> None

Function to prepare uploaded Ligand and protein files using Deep Origin MDSuite. Use this function to run system prep on a ligand and protein pair, that exist as files on a row in the ABFE database.

Parameters:

Name	Type	Description	Default
row_id	str	row id that contains the ligand and protein files.	required
keep_waters	bool	whether to keep water molecules in the system. Defaults to True.	True
save_gmx_files	bool	whether to save gmx files. Defaults to False.	False
is_lig_protonated	bool	whether the ligand is protonated. Defaults to True.	True
is_protein_protonated	bool	whether the protein is protonated. Defaults to True.	True
do_loop_modelling	bool	whether to do loop modelling. Defaults to False.	False
charge_method	str	method to use for charge assignment. Defaults to "bcc".	'bcc'
lig_force_field	str	ligand force field. Defaults to "gaff2".	'gaff2'
padding	float	padding to use. Defaults to 1.0.	1.0
force_field	str	force field. Defaults to "ff14SB".	'ff14SB'
system_name	str	name of the system. Defaults to "complex". This name can be anything.	'complex'

emeq

emeq(
    row_id: str,
    *,
    system_name: str = "complex",
    fourier_spacing: float = 0.12,
    hydrogen_mass: int = 2,
    cutoff: float = 0.9,
    T: float = 298.15,
    Δt: float = 0.004,
    npt_reduce_restraints_ns: float = 0.2,
    nvt_heating_ns: float = 0.1
) -> None

Run emeq on a ligand and protein pair, that exist as files on a row in the ABFE database. For this to work, the complex prep step must have been run first.

Parameters:

Name	Type	Description	Default
row_id	str	row id that contains the ligand and protein files.	required
system_name	str	name of the system. Defaults to "complex". This name can be anything.	'complex'
fourier_spacing	float	spacing of the fourier grid. Defaults to 0.12.	0.12
hydrogen_mass	int	hydrogen mass. Defaults to 2.	2
cutoff	float	cutoff. Defaults to 0.9.	0.9
T	float	temperature. Defaults to 298.15.	298.15
Δt	float	time step. Defaults to 0.004.	0.004
npt_reduce_restraints_ns	float	time step. Defaults to 0.2.	0.2
nvt_heating_ns	float	time step. Defaults to 0.1.	0.1

solvation_prep

solvation_prep(
    row_id: str,
    *,
    is_lig_protonated: bool = True,
    charge_method: charge_methods = "bcc",
    lig_force_field: ligand_force_fields = "gaff2",
    system_name: str = "ligand_prep",
    force_field: force_fields = "ff14SB"
) -> None

Function to prepare uploaded Ligand and protein files using Deep Origin MDSuite. Use this function to run system prep on a ligand and protein pair, that exist as files on a row in the ABFE database.

Parameters:

Name	Type	Description	Default
row_id	str	row id that contains the ligand and protein files.	required
is_lig_protonated	bool	whether the ligand is protonated. Defaults to True.	True
charge_method	str	method to use for charge assignment. Defaults to "bcc".	'bcc'
lig_force_field	str	ligand force field. Defaults to "gaff2".	'gaff2'
system_name	str	name of the system. Defaults to "ligand_prep". This name can be anything.	'ligand_prep'
force_field	str	force field. Defaults to "ff14SB".	'ff14SB'

solvation_fep

solvation_fep(
    row_id: str,
    *,
    integrator: integrators = "BAOABIntegrator",
    softcore_alpha: float = 0.5,
    steps: int = 300000,
    repeats: int = 1,
    threads: int = 0,
    annihilate: bool = True,
    hydrogen_mass: int = 2,
    T: float = 298.15
) -> None

Run a solvation simulation

Parameters:

Name	Type	Description	Default
row_id	str	row id of the ligand and protein files.	required
integrator	integrators	integrator. Defaults to "BAOABIntegrator".	'BAOABIntegrator'
softcore_alpha	float	softcore alpha. Defaults to 0.5.	0.5
steps	int	The number of steps to run the simulation for the prod step.	300000
repeats	int	The number of repeats for prod step.	1
threads	int	The number of threads per worker. By default the number of threads will be determined by the number of windows and available cores on the CPU. Defaults to 0.	0
annihilate	bool	Whether to annihilate the ligand or decouple it. Defaults to True.	True

simple_md

simple_md(
    row_id: str,
    *,
    integrator: integrators = "BAOABIntegrator",
    run_name: str = "complex_1ns_md",
    steps: int = 250000,
    threads: int = 0,
    Δt: float = 0.004,
    temperature: float = 298.15,
    cutoff: float = 0.9,
    fourier_spacing: float = 0.12
)

Run a simple MD simulation

Parameters:

Name	Type	Description	Default
row_id	str	row id of the ligand and protein files.	required
integrator	integrators	integrator. Defaults to "BAOABIntegrator".	'BAOABIntegrator'
run_name	str	run name. Defaults to "complex_1ns_md".	'complex_1ns_md'
steps	int	The number of steps to run the simulation for the prod step.	250000
threads	int	The number of threads per worker. By default the number of threads will be determined by the number of windows and available cores on the CPU. Defaults to 0.	0
Δt	float	The time step in femtoseconds. Defaults to 0.004.	0.004
temperature	float	The temperature in kelvin. Defaults to 298.15.	298.15
cutoff	float	The cutoff distance in angstroms. Defaults to 0.9.	0.9
fourier_spacing	float	The Fourier spacing in femtoseconds. Defaults to 0.12.	0.12

binding_fep

binding_fep(
    row_id,
    *,
    run_name: str = "annihilation_fep",
    softcore_alpha: float = 0.5,
    annihilate: bool = True,
    em_solvent: bool = True,
    em_all: bool = True,
    nvt_heating_ns: int = 1,
    npt_reduce_restraints_ns: int = 2,
    steps: int = 1250000,
    repeats: int = 1,
    threads: int = 0,
    integrator: integrators = "BAOABIntegrator",
    Δt: float = 0.004,
    T: float = 298.15
)

Run an ABFE simulation

Parameters:

Name	Type	Description	Default
row_id	str	row id of the ligand and protein files.	required
run_name	str	run name. Defaults to "annihilation_fep".	'annihilation_fep'
softcore_alpha	float	softcore alpha. Defaults to 0.5.	0.5
annihilate	bool	Whether to annihilate the ligand or decouple it. Defaults to True.	True
em_solvent	bool	Whether to use em solvent. Defaults to True.	True
em_all	bool	Whether to use em all. Defaults to True.	True
nvt_heating_ns	int	The number of nvt heating steps. Defaults to 1.	1
npt_reduce_restraints_ns	int	The number of npt reduce restraints steps. Defaults to 2.	2
steps	int	The number of steps to run the simulation for the prod step.	1250000
threads	int	The number of threads per worker. By default the number of threads will be determined by the number of windows and available cores on the CPU. Defaults to 0.	0
integrator	integrators	integrator. Defaults to "BAOABIntegrator".	'BAOABIntegrator'
Δt	float	The time step in femtoseconds. Defaults to 0.004.	0.004
T	float	The temperature in kelvin. Defaults to 298.15.	298.15