PoreMS 0.2
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        • Pore.attach

    Pore.attach¶

    Pore.attach(self, mol, mount, axis, sites, amount, normal, scale=1, trials=1000, pos_list=[], site_type='in', is_proxi=True, is_random=True, is_rotate=False)¶

    Attach molecules on the surface.

    Parameters:
    mol : Molecule

    Molecule object to attach

    mount : integer

    Atom id of the molecule that is placed on the surface silicon atom

    axis : list

    List of two atom ids of the molecule that define the molecule axis

    sites : list

    List of silicon ids of which binding sites should be picked

    amount : int

    Number of molecules to attach

    normal : function

    Function that returns the normal vector of the surface for a given position

    scale : float, optional

    Circumference scaling around the molecule position

    trials : integer, optional

    Number of trials picking a random site

    pos_list : list, optional

    List of positions to find nearest available binding site for

    site_type : string, optional

    Site type - interior in, exterior ex

    is_proxi : bool, optional

    True to fill binding sites in proximity of filled binding site

    is_random : bool, optional

    True to randomly pick a binding site from given list

    is_rotate : bool, optional

    True to randomly rotate molecule around own axis

    Returns:
    mol_list : list

    List of molecule objects that are attached on the surface

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