molecular_simulations.analysis.fingerprinter module

class molecular_simulations.analysis.fingerprinter.Fingerprinter(topology, trajectory=None, target_selection='segid A', binder_selection=None, out_path=None, out_name=None)

Bases: object

Calculates interaction energy fingerprint between target and binder chains.

Parameters:

  • topology (PathLike) – Path to topology file.

  • trajectory (OptPath) – Defaults to None. If not None, should be a path to a trajectory file or coordinates file.

  • target_selection (str) – Defaults to ‘segid A’. Any MDAnalysis selection string that encompasses target.

  • binder_selection (str | None) – Defaults to None. If None, binder is defined as anything that is not the target. Otherwise should be an MDAnalysis selection string that encompasses the binder.

  • out_path (OptPath) – Defaults to None. If provided will be where outputs are saved to, otherwise the topology parent path is used.

  • out_name (str | None) – Defaults to None. If None, output file will be called ‘fingerprint.npz’.

Usage:

m = Fingerprinter(*args) m.run() m.save()

assign_nonbonded_params()
Return type:

None

assign_residue_mapping()

Map each residue index (1-based) to corresponding atom indices.

Return type:

None

Returns:

None

calculate_fingerprints(frame_index)

Calculates fingerprints for a given frame of the trajectory.

Parameters:

frame_index (int) – Frame index, since frame number and index might be discontinuous.

Return type:

None

Returns:

None

iterate_frames()

Runs calculations over each frame.

Return type:

None

Returns:

None

load_pdb()

Loads topology into MDAnalysis universe object. Can take either a PDB or an AMBER prmtop. If trajectory was not specified, will look for either inpcrd or rst7 with the same path and stem as the topology file.

Return type:

None

Returns:

None

run()

Main logic. Obtains parameters, loads PDB and then iterates through trajectory to obtain fingerprints.

Return type:

None

Returns:

None

save()

Saves data to an npz stack.

Return type:

None

Returns:

None

molecular_simulations.analysis.fingerprinter.dist_mat(xyz1, xyz2)
Return type:

ndarray

Parameters:
molecular_simulations.analysis.fingerprinter.electrostatic(distance, charge_i, charge_j)

Calculate electrostatic energy between two particles. Cutoff at 12 Angstrom without switching.

Parameters:

  • distance (float) – distance between particles i and j (nm)

  • charge_i (float) – charge of particle i (e-)

  • charge_j (float) – charge of particle j (e-)

Returns:

Electrostatic energy between particles (kJ/mol)

Return type:

energy (float)

molecular_simulations.analysis.fingerprinter.electrostatic_sum(distances, charge_is, charge_js)

Calculate sum of all electrostatic interactions between two sets of particles.

Parameters:

  • distances (np.ndarray) – distances between particles, shape: (len(charge_is),len(charge_js))

  • charge_is (np.ndarray) – group i charges

  • charge_js (np.ndarray) – group j charges

molecular_simulations.analysis.fingerprinter.fingerprints(xyzs, charges, sigmas, epsilons, target_resmap, binder_inds)

Calculates electrostatic fingerprint. ES energy between each target residue and all binder residues.

Returns:

(np.ndarray, np.ndarray),

shape=(n_target_residues, n_target_residues)

Return type:

fingerprints

molecular_simulations.analysis.fingerprinter.lennard_jones(distance, sigma_i, sigma_j, epsilon_i, epsilon_j)

Calculate LJ energy between two particles. Cutoff at 12 Angstrom without switching.

Parameters:

  • (float) (epsilon_j)

  • (float)

  • (float)

  • (float)

  • (float)

  • Returns (energy (float): LJ interaction energy (kJ/mol))

molecular_simulations.analysis.fingerprinter.lennard_jones_sum(distances, sigma_is, sigma_js, epsilon_is, epsilon_js)

Calculate sum of all LJ interactions between two sets of particles.

Parameters:

  • distances (np.ndarray) – distances between particles, shape: (len(sigma_is),len(sigma_js))

  • sigma_is (np.ndarray) – group i sigma parameters

  • sigma_js (np.ndarray) – group j sigma parameters

  • epsilon_is (np.ndarray) – group i epsilon parameters

  • epsilon_js (np.ndarray) – group j epsilon parameters

molecular_simulations.analysis.fingerprinter.unravel_index(n1, n2)
Return type:

tuple[ndarray, ndarray]

Parameters: