siter module

class pyIsoP.siter.siter(grid_obj, path_to_component_pdb, ntoms_gas, spacing=1.0, model_number=0, optim_method='l-bfgs-b')

Bases: object

• Contains the subroutine to assign molecule beads to minima inside a MOF

grid = None

Initializes the siter object

Parameters

• grid_obj (instance of the grid 3D class) – contains all the information regarding the grid

• path_to_component_pdb (str) – path to the RASPA output component file including extension

• ntoms_gas (int) – number of atoms in one molecule of the guest

• spacing (float) – grid spacing DEFAULT: 1 A

• model_number (int) – configuration from the pdb file that you want to read

• optim_method (str) – method for minimization from scipy.optimize.minimize

Raises

Return type

an instance of the siter class

molecule2minima()

Assigns molecule to the nearest minima for siting analyzes

:param siter_obj:contains all the information regarding the siting analysis

Raises

Return type

assignment array, warning array (0- safe, 1-warning), shortest_dist array