PoreCylinder.attach¶

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

Attach molecule 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
amountint: Number of molecules to attach
site_typestring, optional: Use in for the interior surface and ex for the exterior
inpstring, optional: Input type: num - Number of molecules, molar - \(\frac{\mu\text{mol}}{\text{m}^2}\), percent - \(\%\) of OH groups
pos_listlist, optional: List of positions (Cartesian) to find nearest available binding site for
scalefloat, optional: Circumference scaling around the molecule position
trialsinteger, optional: Number of trials picking a random site
is_proxibool, optional: True to fill binding sites in proximity of filled binding site
is_rotatebool, optional: True to randomly rotate molecule around own axis