molecular_simulations.analysis.interaction_energy module

class molecular_simulations.analysis.interaction_energy.DynamicInteractionEnergy(top, traj, stride=1, chain='A', platform='CUDA', first_residue=None, last_residue=None, progress_bar=False)

Bases: object

Class for obtaining interaction energies of a trajectory. Utilizes the InteractionEnergyFrame child class to run per-frame energy calculations and orchestrates the trajectory operations.

Parameters:

top (PathLike) – Path to prmtop topology file.
traj (PathLike) – Path to DCD trajectory file.
stride (int) – Defaults to 1. The stride with which to move through the trajectory.
chain (str) – Defaults to A. The chain for which to compute the energy between. Computes energy between this chain and all other components in PDB file. Set to a whitespace if there are no chains in your PDB.
platform (str) – Defaults to CUDA. Supports running on GPU for speed.
first_residue (int | None) – Defaults to None. If set, will restrict the calculation to residues beginning with resid first_residue.
last_residue (int | None) – Defaults to None. If set, will restrict the calculation to residues ending with resid last_residue.
progress_bar (bool) – Defaults to False. If True a tqdm progress bar will display progress.

build_system(top)

Builds OpenMM system for both pdb and prmtop topology files.

Parameters:: top (PathLike) – Path to topology file.
Returns:: OpenMM system object.
Return type:: (System)

compute_energies()

Computes the energy for each frame in trajectory, storing internally.

Return type:: None
Returns:: None

load_traj(top, traj)

Loads trajectory into mdtraj and extracts full coordinate array.

Parameters:

top (PathLike) – Path to topology file.
traj (PathLike) – Path to trajectory file.

Returns:

Coordinate array of shape (n_frames, n_atoms, 3)

Return type:

(np.ndarray)

setup_pbar()

Builds tqdm progress bar.

Return type:: None
Returns:: None

class molecular_simulations.analysis.interaction_energy.InteractionEnergy

Bases: ABC

abstractmethod compute()

abstractmethod energy()

abstractmethod get_selection()

class molecular_simulations.analysis.interaction_energy.InteractionEnergyFrame(system, top, chain='A', platform='CUDA', first_residue=None, last_residue=None)

Bases: StaticInteractionEnergy

Inherits from StaticInteractionEnergy and overloads get_system to allow for more easily running this analysis on a trajectory of frames. Requires the OpenMM system and topology to be built externally and passed in rather than beginning from a PDB file.

Parameters:

system (System) – OpenMM system object.
top (Topology) – OpenMM topology object.
chain (str) – Defaults to A. The chain for which to compute the energy between. Computes energy between this chain and all other components in PDB file. Set to a whitespace if there are no chains in your PDB.
platform (str) – Defaults to CUDA. Supports running on GPU for speed.
first_residue (int | None) – Defaults to None. If set, will restrict the calculation to residues beginning with resid first_residue.
last_residue (int | None) – Defaults to None. If set, will restrict the calculation to residues ending with resid last_residue.

get_system()

Sets self.selection via self.get_selection and returns existing OpenMM system object.

Returns:: OpenMM system object.
Return type:: (System)

class molecular_simulations.analysis.interaction_energy.StaticInteractionEnergy(pdb, chain='A', platform='CUDA', first_residue=None, last_residue=None)

Bases: InteractionEnergy

Computes the linear interaction energy between specified chain and other simulation components. Can specify a range of residues in chain to limit calculation to. Works on a static model but can be adapted to run on dynamics data.

Inputs:

pdb (str): Path to input PDB file chain (str): Defaults to A. The chain for which to compute the energy between.

Computes energy between this chain and all other components in PDB file. Set to a whitespace if there are no chains in your PDB.

platform (str): Defaults to CUDA. Supports running on GPU for speed. first_residue (int | None): Defaults to None. If set, will restrict the

calculation to residues beginning with resid first_residue.

last_residue (int | None): Defaults to None. If set, will restrict the: calculation to residues ending with resid last_residue.

Parameters:

pdb (str)
chain (str)
platform (str)
first_residue (int | None)
last_residue (int | None)

compute(positions=None)

Compute interaction energy of system. Can optionally provide atomic positions such that this operation can be scaled onto a trajectory of frames rather than a static model.

Parameters:: positions (np.ndarray | None) – Defaults to None. If provided, inject the positions into the OpenMM context.
Return type:: None
Returns:: None

static energy(context, solute_coulomb_scale=0, solute_lj_scale=0, solvent_coulomb_scale=0, solvent_lj_scale=0)

Computes the potential energy for provided context object.

Parameters:

context (Context) – OpenMM context object.
solute_coulomb_scale (int) – Defaults to 0. If 1 we will consider solute contributions to coulombic non-bonded energy.
solute_lj_scale (int) – Defaults to 0. If 1 we will consider solute contributions to LJ non-bonded energy.
solvent_coulomb_scale (int) – Defaults to 0. If 1 we will consider solvent contributions to coulombic non-bonded energy.
solvent_lj_scale (int) – Defaults to 0. If 1 we will consider solvent contributions to LJ non-bonded energy.

Returns:

Computed energy term.

Return type:

(float)

fix_pdb()

Using the OpenMM adjacent tool, PDBFixer, repair input PDB by adding hydrogens, and missing atoms such that we can actually construct an OpenMM system.

Return type:: None
Returns:: None

get_selection(topology)

Using the poorly documented OpenMM selection language, get indices of atoms that we want to isolate for pairwise interaction energy calculation.

Parameters:: topology (Topology) – OpenMM topology object.
Return type:: None
Returns:: None

get_system()

Builds implicit solvent OpenMM system.

Returns:: OpenMM system object.
Return type:: (System)

property interactions: ndarray

Places the LJ and coulombic energies into an array of shape (1, 2).

Returns:: Energy array.
Return type:: (np.ndarray)