pywindow
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Index
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C
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D
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E
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F
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G
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I
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
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X
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)