molsysmt.third_party.nglview.add_contacts#

molsysmt.third_party.nglview.add_contacts(view, 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=None, pbc=False, atom_pairs=None, color='#808080', color_2=None, radius='0.1 angstroms', color_values=None, min_color_value=None, mid_color_value=None, max_color_value=None, color_values_scale='linear', colormap='bwr', color_values_2=None, min_color_value_2=None, mid_color_value_2=None, max_color_value_2=None, color_values_scale_2=None, colormap_2=None, syntax='MolSysMT', skip_digestion=False)[source]#

Adding visual contact lines or cylinders between atom pairs in NGLWidget.

Parameters:

  • view (nglview.NGLWidget) – Target molecular viewer instance.

  • selection (str, list, tuple, or numpy.ndarray, default=None) – Selection string or boolean/integer array specifying elements.

  • center_of_atoms (bool, default=False) – Whether to compute distances relative to geometric centers.

  • weights (numpy.ndarray, list, or tuple, default=None) – Atomic mass weights array for center calculation.

  • structure_indices (int, list, tuple, or numpy.ndarray, default='all') – Structure indices (0-based) to include or process.

  • selection_2 (str, list, tuple, or numpy.ndarray, default=None) – Second selection string or boolean/integer array.

  • center_of_atoms_2 (bool, default=False) – Whether to compute distances relative to geometric centers for selection_2.

  • weights_2 (numpy.ndarray, list, or tuple, default=None) – Atomic mass weights array for selection_2.

  • structure_indices_2 (int, list, tuple, or numpy.ndarray, default=None) – Structure indices (0-based) for the second selection.

  • threshold (float or quantity, default=None) – Distance cutoff threshold quantity.

  • pbc (bool, default=False) – Whether to take periodic boundary conditions into account.

  • atom_pairs (numpy.ndarray, list, or tuple, default=None) – Explicit pairs of atom indices to visualize.

  • color (object, default='#808080') – Argument color.

  • color_2 (object, default=None) – Secondary color string or RGB tuple.

  • radius (object, default='0.1 angstroms') – Argument radius.

  • color_values (numpy.ndarray, list, or tuple, default=None) – Scalar numerical values used to color contacts.

  • min_color_value (float or quantity, default=None) – Minimum value for contact colormap normalization.

  • mid_color_value (float or quantity, default=None) – Midpoint value for contact colormap normalization.

  • max_color_value (float or quantity, default=None) – Maximum value for contact colormap normalization.

  • color_values_scale (str, default='linear') – Scaling mode for contact colormap (‘linear’, ‘log’).

  • colormap (str, default='bwr') – Colormap name for contact coloring.

  • color_values_2 (numpy.ndarray, list, or tuple, default=None) – Secondary scalar values array for coloring.

  • min_color_value_2 (float or quantity, default=None) – Minimum value for secondary colormap.

  • mid_color_value_2 (float or quantity, default=None) – Midpoint value for secondary colormap.

  • max_color_value_2 (float or quantity, default=None) – Maximum value for secondary colormap.

  • color_values_scale_2 (str, default=None) – Scaling mode for secondary colormap.

  • colormap_2 (str, default=None) – Secondary colormap name.

  • syntax (str, default='MolSysMT') – Selection syntax used to evaluate selection (e.g., ‘MolSysMT’, ‘MDTraj’).

  • skip_digestion (bool, default=False) – Whether to skip MolSysMT’s internal argument digestion mechanism.

  • versionadded: (..) – 1.0.0:

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