PoreMS 0.2
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        • Pore

    Pore¶

    class 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:
    block : Molecule

    Block molecule to be prepared as a pore

    matrix : Matrix

    Matrix object containing all bond information of given block molecule

    Surface preperation

    amorph(self[, dist, accept, trials]) Make Structure amorphous.
    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[, exterior]) 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.

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    © Copyright 2021, Hamzeh Kraus.
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