BioSimSpace.FreeEnergy.ATMSetup

class BioSimSpace.FreeEnergy.ATMSetup(system=None, receptor=None, ligand_bound=None, ligand_free=None, protein_index=0, ligand_bound_index=1, ligand_free_index=2)[source]

A class for setting up a system for ATM simulations.

__init__(system=None, receptor=None, ligand_bound=None, ligand_free=None, protein_index=0, ligand_bound_index=1, ligand_free_index=2)[source]

Constructor for the ATM class.

Parameters:

  • system (System) – A pre-prepared ATM system containing protein and ligands placed in their correct positions. If provided takes precedence over protein, ligand_bound and ligand_free.

  • receptor (Molecule) – A receptor molecule. Will be used along with ligand_bound and ligand_free to create a system.

  • ligand_bound (Molecule) – The bound ligand. Will be used along with protein and ligand_free to create a system.

  • ligand_free (Molecule) – The free ligand. Will be used along with protein and ligand_bound to create a system.

  • protein_index (int, [int]) – If passing a pre-prepared system, the index (or indices) of the protein molecule in the system (Default 0).

  • ligand_bound_index (int) – If passing a pre-prepared system, the index of the bound ligand molecule in the system (Default 1).

  • ligand_free_index (int) – If passing a pre-prepared system, the index of the free ligand molecule in the system (Default 2).

Methods

__init__([system, receptor, ligand_bound, ...])

Constructor for the ATM class.

prepare(ligand_bound_rigid_core, ...[, ...])

Prepare the system for an ATM simulation.

viewRigidCores([system, ligand_bound, ...])

View the rigid cores of the ligands.
prepare(ligand_bound_rigid_core, ligand_free_rigid_core, displacement='20A', protein_com_atoms=None, ligand_bound_com_atoms=None, ligand_free_com_atoms=None)[source]

Prepare the system for an ATM simulation.

Parameters:

  • ligand_bound_rigid_core ([int]) – A list of three atom indices that define the rigid core of the bound ligand. Indices are set relative to the ligand, not the system and are 0-indexed.

  • ligand_free_rigid_core ([int]) – A list of three atom indices that define the rigid core of the free ligand. Indices are set relative to the ligand, not the system and are 0-indexed.

  • displacement (float, string, [float, float, float]) – The diplacement between the bound and free ligands. If a float or string is given, BioSimSpace will attempt to find the ideal vector along which to displace the ligand by the given magnitude. If a list is given, the vector will be used directly.

  • protein_com_atoms ([int]) – A list of atom indices that define the center of mass of the protein. If None, the center of mass of the protein will be found automatically.

  • ligand_bound_com_atoms ([int]) – A list of atom indices that define the center of mass of the bound ligand. If None, the center of mass of the bound ligand will be found automatically.

  • ligand_free_com_atoms ([int]) – A list of atom indices that define the center of mass of the free ligand. If None, the center of mass of the free ligand will be found automatically.

Returns:

  • system (System) – The prepared system, including protein and ligands in their correct positions.

  • data (dict) – A dictionary containing the data needed for the ATM simulation. This is also encoded in the system for consistency, but is returned so that the user can easily query and validate the data.

static viewRigidCores(system=None, ligand_bound=None, ligand_free=None, ligand_bound_rigid_core=None, ligand_free_rigid_core=None)[source]

View the rigid cores of the ligands. Rigid core atoms within the bound ligand are shown in green, those within the free ligand are shown in red.

Parameters:

  • system (System) – The system for the ATM simulation that has been prepared ATM.prepare(). All other arguments are ignored if this is provided.

  • ligand_bound (Molecule) – The bound ligand.

  • ligand_free (Molecule) – The free ligand.

  • ligand_bound_rigid_core (list) – The indices for the rigid core atoms of the bound ligand.

  • ligand_free_rigid_core (list) – The indices for the rigid core atoms of the free ligand.