molsysmt.structure.show_contacts#

molsysmt.structure.show_contacts(molecular_system, selection=None, center_of_atoms=False, weights=None, structure_indices='all', selection_2=None, center_of_atoms_2=False, weights_2=None, structure_indices_2=None, threshold='12 angstroms', pbc=False, syntax='MolSysMT', style='plotly', show=True, skip_digestion=False)[source]#

Visualize the contact map between two sets of atoms as a 2-D heatmap.

Computes the contact map via get_contacts and renders the first frame as a heatmap using either Plotly or Matplotlib.

Parameters:

  • molecular_system (molecular system) – Input system in any form supported by MolSysMT.

  • selection (str, list, tuple or numpy.ndarray, optional) – First set of atoms (rows of the contact matrix). Nested iterables are treated as groups of atoms when center_of_atoms=True.

  • center_of_atoms (bool, default False) – If True, use the (weighted) centroid of each group in selection.

  • weights (array-like, optional) – Per-atom weights for centroid computation of the first selection.

  • structure_indices ('all' or array-like, default 'all') – Frame indices over which contacts are evaluated. Only the first frame of the resulting contact map is visualised.

  • selection_2 (str, list, tuple or numpy.ndarray or None, default None) – Second set of atoms (columns of the contact matrix). When None, contacts are computed within selection itself.

  • center_of_atoms_2 (bool, default False) – If True, use the (weighted) centroid of each group in selection_2.

  • weights_2 (array-like, optional) – Per-atom weights for centroid computation of the second selection.

  • structure_indices_2 ('all', array-like or None, default None) – Frame indices for the second selection. When None, the same frames as structure_indices are used.

  • threshold (str or quantity, default '12 angstroms') – Distance cutoff for defining a contact. Accepts any PyUnitWizard-parseable length quantity.

  • pbc (bool, default False) – Apply minimum-image convention for periodic boundary conditions.

  • syntax (str, default 'MolSysMT') – Selection syntax used when selections are strings.

  • style ({'plotly', 'matplotlib'}, default 'plotly') – Plotting backend used to render the heatmap.

  • show (bool, default True) – If True, the figure is displayed immediately (figure.show() for Plotly or plt.show() for Matplotlib).

  • skip_digestion (bool, default False) – Whether to skip argument digestion (for internal use on trusted hot paths).

Returns:

  • plotly.graph_objects.Figure or matplotlib.figure.Figure – The figure object produced by the selected plotting backend, containing the contact-map heatmap of the first frame.

  • .. versionadded:: 1.0.0

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