Index

A

acylidricity() (in module pywindow.utilities) align_principal_ax() (in module pywindow.utilities) analysis() (pywindow.trajectory.DLPOLY method) (pywindow.trajectory.PDB method) (pywindow.trajectory.XYZ method)

analysis_output (pywindow.trajectory.DLPOLY attribute) (pywindow.trajectory.XYZ attribute) angle_between_vectors() (in module pywindow.utilities) asphericity() (in module pywindow.utilities) atom_ids (pywindow.molecular.Molecule attribute)

C

calc_acylidricity() (in module pywindow.utilities) calc_asphericity() (in module pywindow.utilities) calc_relative_shape_anisotropy() (in module pywindow.utilities) calculate_average_diameter() (pywindow.molecular.Molecule method) calculate_centre_of_mass() (pywindow.molecular.Molecule method) calculate_maximum_diameter() (pywindow.molecular.Molecule method) calculate_pore_diameter() (pywindow.molecular.Molecule method) calculate_pore_diameter_opt() (pywindow.molecular.Molecule method) calculate_pore_shape() (in module pywindow.utilities) calculate_pore_volume() (pywindow.molecular.Molecule method) calculate_pore_volume_opt() (pywindow.molecular.Molecule method)

calculate_window_diameter() (in module pywindow.utilities) calculate_windows() (pywindow.molecular.Molecule method) cart2frac_all() (in module pywindow.utilities) cartisian_from_fractional() (in module pywindow.utilities) center_of_coor() (in module pywindow.utilities) center_of_mass() (in module pywindow.utilities) circumcircle() (in module pywindow.utilities) circumcircle_window() (in module pywindow.utilities) compose_atom_list() (in module pywindow.utilities) coordinates (pywindow.molecular.Molecule attribute) correct_pore_diameter() (in module pywindow.utilities) create_supercell() (in module pywindow.utilities)

D

decipher_atom_key() (in module pywindow.utilities) decipher_atom_keys() (pywindow.molecular.MolecularSystem method) decompose_atom_list() (in module pywindow.utilities) discrete_molecules() (in module pywindow.utilities) distance() (in module pywindow.utilities) dlf_notation() (in module pywindow.utilities)

DLPOLY (class in pywindow.trajectory) dump2file() (pywindow.io_tools.Output method) dump2json() (pywindow.io_tools.Output method) dump_molecule() (pywindow.molecular.Molecule method) dump_properties_json() (pywindow.molecular.Molecule method) dump_system() (pywindow.molecular.MolecularSystem method) dump_system_json() (pywindow.molecular.MolecularSystem method)

E

elements (pywindow.molecular.Molecule attribute)

F

filename (pywindow.trajectory.XYZ attribute) filepath (pywindow.trajectory.DLPOLY attribute) (pywindow.trajectory.XYZ attribute) find_average_diameter() (in module pywindow.utilities) find_windows() (in module pywindow.utilities)

find_windows_new() (in module pywindow.utilities) frac2cart_all() (in module pywindow.utilities) fractional_from_cartesian() (in module pywindow.utilities) frames (pywindow.trajectory.DLPOLY attribute) (pywindow.trajectory.XYZ attribute) full_analysis() (pywindow.molecular.Molecule method)

G

get_frames() (pywindow.trajectory.DLPOLY method) (pywindow.trajectory.PDB method) (pywindow.trajectory.XYZ method)

get_gyration_tensor() (in module pywindow.utilities) get_inertia_tensor() (in module pywindow.utilities) get_tensor_eigenvalues() (in module pywindow.utilities) get_window_com() (in module pywindow.utilities)

I

Input (class in pywindow.io_tools)

is_inside_polyhedron() (in module pywindow.utilities) is_number() (in module pywindow.utilities)

L

lattice_array_to_unit_cell() (in module pywindow.utilities) load_file() (pywindow.io_tools.Input method) (pywindow.molecular.MolecularSystem class method)

load_rdkit_mol() (pywindow.io_tools.Input method) (pywindow.molecular.MolecularSystem class method) load_system() (pywindow.molecular.MolecularSystem class method)

M

make_modular() (pywindow.molecular.MolecularSystem method) make_supercell() (in module pywindow.trajectory) max_dim() (in module pywindow.utilities) mol (pywindow.molecular.Molecule attribute) molecular_weight() (in module pywindow.utilities) (pywindow.molecular.Molecule method)

MolecularSystem (class in pywindow.molecular) Molecule (class in pywindow.molecular) molecule_id (pywindow.molecular.Molecule attribute) molecules (pywindow.molecular.MolecularSystem attribute)

N

no_of_atoms (pywindow.molecular.Molecule attribute)

normal_vector() (in module pywindow.utilities) normalize_vector() (in module pywindow.utilities)

O

opls_notation() (in module pywindow.utilities) opt_pore_diameter() (in module pywindow.utilities)

optimise_xy() (in module pywindow.utilities) optimise_z() (in module pywindow.utilities) Output (class in pywindow.io_tools)

P

parent_system (pywindow.molecular.Molecule attribute) PDB (class in pywindow.trajectory) pore_diameter() (in module pywindow.utilities) principal_axes() (in module pywindow.utilities) properties (pywindow.molecular.Molecule attribute)

pywindow (module) pywindow.io_tools (module) pywindow.molecular (module) pywindow.tables (module) pywindow.trajectory (module) pywindow.utilities (module)

R

rebuild_system() (pywindow.molecular.MolecularSystem method)

relative_shape_anisotropy() (in module pywindow.utilities) rotation_matrix_arbitrary_axis() (in module pywindow.utilities)

S

save_analysis() (pywindow.trajectory.DLPOLY method) (pywindow.trajectory.PDB method) (pywindow.trajectory.XYZ method) save_frames() (pywindow.trajectory.DLPOLY method) (pywindow.trajectory.PDB method) (pywindow.trajectory.XYZ method) shift_com() (in module pywindow.utilities)

shift_to_origin() (pywindow.molecular.Molecule method) sphere_volume() (in module pywindow.utilities) swap_atom_keys() (pywindow.molecular.MolecularSystem method) system (pywindow.molecular.MolecularSystem attribute) system_id (pywindow.molecular.MolecularSystem attribute) (pywindow.trajectory.DLPOLY attribute) (pywindow.trajectory.XYZ attribute) system_to_molecule() (pywindow.molecular.MolecularSystem method)

T

to_list() (in module pywindow.utilities)

U

unique() (in module pywindow.utilities)

unit_cell_to_lattice_array() (in module pywindow.utilities)

V

vector_analysis() (in module pywindow.utilities) vector_analysis_pore_shape() (in module pywindow.utilities) vector_analysis_reversed() (in module pywindow.utilities)

vector_preanalysis() (in module pywindow.utilities) volume_from_cell_parameters() (in module pywindow.utilities) volume_from_lattice_array() (in module pywindow.utilities)

W

window_analysis() (in module pywindow.utilities)

window_shape() (in module pywindow.utilities)

X

XYZ (class in pywindow.trajectory)