pysoftk.pysoftwhere package

Submodules

pysoftk.pysoftwhere.icsi module

class pysoftk.pysoftwhere.icsi.icsi(u, cluster_resids, cluster_atoms_positions, core_sel_atoms_positions, shell_sel_atoms_positions, frame=-1, no_bins=31, no_random_points=10000, normalisation_run=False)[source]

Bases: object

Calculates the intrinsic surface density (ISD) of a cluster in a molecular simulation.

This class implements the Intrinsic Surface Density (ISD) calculation as described in [Reference]. It takes a universe (u), cluster definition information, and options for frame and binning as input and returns the intrinsic radius, spherical radius, and interface values.

Parameters:

  • u – An MDAnalysis universe object.

  • cluster_resids – A list of residue indices that define the cluster.

  • cluster_atoms_positions – A 3D NumPy array of atomic positions in the cluster across all frames.

  • core_sel_atoms_positions – A 3D NumPy array of atomic positions for the core region of the cluster.

  • shell_sel_atoms_positions – A 3D NumPy array of atomic positions for the shell region of the cluster.

  • frame – The frame index to use for the calculation (default: -1 for the last frame).

  • no_bins – The number of bins for the 2D histogram (default: 31).

  • no_random_points – The number of random points to use for normalization (default: 10000).

  • normalisation_run – Whether to use random points for normalization (default: False).

Returns:

A list of intrinsic radii. spherical_r: A list of spherical radii. interface_vals: A 2D NumPy array of interface values.

Return type:

intrinsic_r

Raises:

ValueError – If an invalid frame index is provided.

Module contents