molsysmt.third_party.nglview.add_cylinders#

molsysmt.third_party.nglview.add_cylinders(view, bottom=None, top=None, vectors=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, skip_digestion=False)[source]#

Adding 3D cylinders connecting coordinates or atom pairs in NGLWidget.

Parameters:

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

  • bottom (object, default=None) – Argument bottom.

  • top (object, default=None) – Argument top.

  • vectors (numpy.ndarray, list, or tuple, default=None) – Direction and magnitude vectors array.

  • 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.

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

  • versionadded: (..) – 1.0.0:

On this page