BioSimSpace.FreeEnergy.ATM¶

class BioSimSpace.FreeEnergy.ATM(system, protocol, platform='CPU', work_dir=None, setup_only=False, property_map={})[source]¶

A class for setting up, running, and analysis RBFE calculations using the Alchemical Transfer Method.

__init__(system, protocol, platform='CPU', work_dir=None, setup_only=False, property_map={})[source]¶

Constructor.

Parameters:

system (BioSimSpace._SireWrappers.System) – A prepared ATM system containing a protein and two ligands, one bound and one free. Assumed to already be equilibrated.
protocol (BioSimSpace.Protocol.ATM) – The ATM protocol to use for the simulation.
platform (str) – The platform for the simulation: “CPU”, “CUDA”, or “OPENCL”. For CUDA use the CUDA_VISIBLE_DEVICES environment variable to set the GPUs on which to run, e.g. to run on two GPUs indexed 0 and 1 use: CUDA_VISIBLE_DEVICES=0,1. For OPENCL, instead use OPENCL_VISIBLE_DEVICES.
work_dir (str) – The working directory for the simulation.
setup_only (bool) – Whether to only support simulation setup. If True, then no simulation processes objects will be created, only the directory hierarchy and input files to run a simulation externally. This can be useful when you don’t intend to use BioSimSpace to run the simulation. Note that a ‘work_dir’ must also be specified.
property_map (dict) – A dictionary that maps system “properties” to their user defined values. This allows the user to refer to properties with their own naming scheme, e.g. { “charge” : “my-charge” }

Methods

`__init__`(system, protocol[, platform, ...])	Constructor.
`analyse`(work_dir[, method, ignore_lower, ...])	Analyse the ATM simulation.
`getData`([name, file_link, work_dir])	Return a link to a zip file containing the data files required for post-simulation analysis.
`kill`(index)	Kill a process for a specific lambda window.
`killAll`()	Kill any running processes for all lambda windows.
`run`([serial])	Run the simulations.
`wait`()	Wait for the simulation to finish.
`workDir`()	Return the working directory.

static analyse(work_dir, method='UWHAM', ignore_lower=0, ignore_upper=None, inflex_indices=None)[source]¶

Analyse the ATM simulation.

Parameters:

work_dir (str) – The working directory where the ATM simulation is located.
method (str) – The method to use for the analysis. Currently only UWHAM is supported.
ignore_lower (int) – Ignore the first N samples when analysing.
inflex_indices ([int]) – The indices at which the direction changes. For example, if direction=[1,1,-1,-1], then inflex_indices=[1,2]. If None, the inflexion point will be found automatically.

Returns:

ddg (BioSimSpace.Types.Energy) – The free energy difference between the two ligands.
ddg_err BioSimSpace.Types.Energy – The error in the free energy difference.

getData(name='data', file_link=False, work_dir=None)[source]¶

Return a link to a zip file containing the data files required for post-simulation analysis.

Parameters:

name (str) – The name of the zip file.
file_link (bool) – Whether to return a FileLink when working in Jupyter.
work_dir (str) – The working directory for the free-energy perturbation simulation.

Returns:

output – A path, or file link, to an archive of the process input.

Return type:

str, IPython.display.FileLink

kill(index)[source]¶

Kill a process for a specific lambda window.

run(serial=True)[source]¶

Run the simulations.

Return the working directory.