PoreMS 0.2
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    Store¶

    class porems.store.Store(inp, link='./', sort_list=[])¶

    This class converts a molecule object to a structure file of different possible formats. Currently only PDB and GRO are fully supported.

    For pore objects two additional methods are available for generating the main topology file and a topology file containing grid molecule parameters and charges. Currently only the GROMACS format is supported.

    Furthermore, there is an automized routine for generating topologies with Antechamber where job-file for this tool are created.

    Parameters:
    inp : Molecule, Pore

    Molecule or Pore object

    link : string, optional

    Folder link for output

    sort_list : list, optional

    Optionally provide a sorting list in case a dictionary of molecules is given

    Examples

    Assuming a pore or molecule object have already been created, the structure files can be generated like following examples

    Store(mol).pdb()
    Store(pore, "output").gro("pore.gro")
    

    Structure Methods

    gro(self[, name, use_atom_names]) Generate the structure file for the defined molecule in the GRO format.
    pdb(self[, name, use_atom_names]) Generate the structure file for the defined molecule in the PDB format.
    xyz(self[, name, use_atom_names]) Generate the structure file for the defined molecule in the XYZ format for running qm-simulations.
    obj(self[, name]) Save the molecule object or the dictionary of those using pickle.
    job(self[, name, master]) Create job file to run with Antechamber.

    Topology Methods

    grid(self[, name, charges]) Store the grid.itp file containing the necessary parameters and charges of the grid molecules.
    top(self[, name]) Store the topology file for a pore.

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    © Copyright 2021, Hamzeh Kraus.
    Created using Sphinx 1.6.6.