porems.pore.
Pore
(block, matrix)¶This class prepares and converts a given molecule block into a pore system.
Methods are provided for preparing the surface according to procedures described in literature and for functionalizing the surface with any desired molecule objects.
Parameters: |
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Surface preperation
amorph (self[, dist, accept, trials]) |
Make Structure amorphous. |
exterior (self, gap) |
Create an exterior surface for reservoir attachement. |
prepare (self) |
For the purpose of ensuring chemical propriety, the carved out surface needs to be processed based on a set of rules as proposed by Coasne et al. |
sites (self) |
Create binding site dictionary of the format |
Attachement
attach (self, mol, mount, axis, sites, …[, …]) |
Attach molecules on the surface. |
siloxane (self, sites, amount, normal[, …]) |
Attach siloxane bridges on the surface similar to Krishna et al. |
fill_sites (self, sites, normal, site_type) |
Fill list of given sites that are empty with silanol and geminal silanol molecules, respectively. |
Finalization
objectify (self, atoms) |
Create molecule objects of specified list of atoms. |
reservoir (self, size) |
Create a reservoir with given length on each side of pore system. |
Setter Methods
set_box (self, box) |
Set the box size. |
set_name (self, name) |
Set the pore name. |
Getter Methods
get_block (self) |
Return the block molecule. |
get_box (self) |
Return the box size of the pore. |
get_name (self) |
Return the pore name. |
get_num_in_ex (self) |
Return the number of geminal si-binding sites that have one OH on the interior surface and on on the exterior surface. |
get_sites (self) |
Return the binding sites dictionary. |
get_mol_dict (self) |
Return the dictionary of all molecules. |
get_site_dict (self) |
Return the molecule dictionary with site type differentiation. |