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: |
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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. |
lmp (self[, name]) |
Generate the structure file for the defined molecule in the LAMMPS 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. |