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:

inpMolecule, Pore: Molecule or Pore object
linkstring, optional: Folder link for output
sort_listlist, 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")

Methods

`grid`([name, charges])	Store the grid.itp file containing the necessary parameters and charges of the grid molecules.
`gro`([name, use_atom_names])	Generate the structure file for the defined molecule in the GRO format.
`job`([name, master])	Create job file to run with Antechamber.
`lmp`([name])	Generate the structure file for the defined molecule in the LAMMPS format.
`obj`([name])	Save the molecule object or the dictionary of those using pickle.
`pdb`([name, use_atom_names])	Generate the structure file for the defined molecule in the PDB format.
`top`([name])	Store the topology file for a pore.
`xyz`([name, use_atom_names])	Generate the structure file for the defined molecule in the XYZ format for running qm-simulations.