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.
Block molecule to be prepared as a pore
Matrix object containing all bond information of given block molecule
Methods
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Make Structure amorphous. |
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Attach molecules on the surface. |
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Create an exterior surface for reservoir attachement. |
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Fill list of given sites that are empty with silanol and geminal silanol molecules, respectively. |
Return the block molecule. |
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Return the box size of the pore. |
Return the dictionary of all molecules. |
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Return the pore name. |
Return the number of geminal si-binding sites that have one OH on the interior surface and on on the exterior surface. |
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Return the molecule dictionary with site type differentiation. |
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Return the binding sites dictionary. |
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Create molecule objects of specified list of atoms. |
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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. (2008). |
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Create a reservoir with given length on each side of pore system. |
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Set the box size. |
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Set the pore name. |
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Attach siloxane bridges on the surface similar to Krishna et al. (2009). |
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Create binding site dictionary of the format |