Pore.attach¶

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

Attach molecules on the surface.

Parameters:

molMolecule: Molecule object to attach
mountinteger: Atom id of the molecule that is placed on the surface silicon atom
axislist: List of two atom ids of the molecule that define the molecule axis
siteslist: List of silicon ids of which binding sites should be picked
amountint: Number of molecules to attach
scalefloat, optional: Circumference scaling around the molecule position
trialsinteger, optional: Number of trials picking a random site
pos_listlist, optional: List of positions (cartesian) to find nearest available binding site for
site_typestring, optional: Site type - interior in, exterior ex
is_proxibool, optional: True to fill binding sites in proximity of filled binding site
is_randombool, optional: True to randomly pick a binding site from given list
is_rotatebool, optional: True to randomly rotate molecule around own axis

Returns:

mol_listlist: List of molecule objects that are attached on the surface