cctk
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Index
_
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A
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B
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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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H
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I
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J
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K
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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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Q
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R
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S
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T
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V
|
W
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X
_
__init__() (cctk.ConformationalEnsemble method)
(cctk.Ensemble method)
(cctk.File method)
(cctk.GaussianFile method)
(cctk.Group method)
(cctk.LazyLineObject method)
(cctk.MAEFile method)
(cctk.MOL2File method)
(cctk.Molecule method)
(cctk.OneIndexedArray method)
(cctk.OrcaFile method)
(cctk.PDBFile method)
(cctk.SIFile method)
(cctk.VibrationalMode method)
(cctk.XYZFile method)
_items (cctk.Ensemble attribute)
_map_from_truncated (cctk.Group attribute)
A
add_atom() (cctk.Group method)
(cctk.Molecule method)
add_atom_at_centroid() (cctk.Group method)
(cctk.Molecule method)
add_attachment_point() (cctk.Group method)
add_bond() (cctk.Group method)
(cctk.Molecule method)
add_custom_basis_set() (cctk.GaussianFile method)
add_group_to_molecule() (cctk.Group static method)
add_molecule() (cctk.ConformationalEnsemble method)
(cctk.Ensemble method)
adjacent (cctk.Group attribute)
align() (cctk.ConformationalEnsemble method)
align_matrices() (in module cctk.helper_functions)
ALIGNED (cctk.OneIndexedArray attribute)
all() (cctk.OneIndexedArray method)
any() (cctk.OneIndexedArray method)
append_to_file() (cctk.File static method)
(cctk.GaussianFile static method)
(cctk.MAEFile static method)
(cctk.MOL2File static method)
(cctk.OrcaFile static method)
(cctk.PDBFile static method)
(cctk.SIFile static method)
(cctk.XYZFile static method)
are_connected() (cctk.Group method)
(cctk.Molecule method)
argmax() (cctk.OneIndexedArray method)
argmin() (cctk.OneIndexedArray method)
argpartition() (cctk.OneIndexedArray method)
argsort() (cctk.OneIndexedArray method)
assign_connectivity() (cctk.ConformationalEnsemble method)
(cctk.Group method)
(cctk.Molecule method)
astype() (cctk.OneIndexedArray method)
atom_string() (cctk.Group method)
(cctk.Molecule method)
atomic_numbers (cctk.Molecule attribute)
atomic_symbols() (cctk.Group method)
(cctk.Molecule method)
atoms_moving_in_imaginary() (cctk.Group method)
(cctk.Molecule method)
attach_to (cctk.Group attribute)
B
base (cctk.OneIndexedArray attribute)
BEHAVED (cctk.OneIndexedArray attribute)
blocks (cctk.OrcaFile attribute)
boltzmann_average() (cctk.ConformationalEnsemble method)
bonds (cctk.Molecule attribute)
bytes_to_numpy() (in module cctk.helper_functions)
byteswap() (cctk.OneIndexedArray method)
C
C_CONTIGUOUS (cctk.OneIndexedArray attribute)
calculate_mass_spectrum() (cctk.Group method)
(cctk.Molecule method)
CARRAY (cctk.OneIndexedArray attribute)
cctk.helper_functions
module
center() (cctk.Group method)
(cctk.Molecule method)
center_of_mass() (cctk.Group method)
(cctk.Molecule method)
center_periodic() (cctk.Group method)
(cctk.Molecule method)
charge (cctk.Molecule attribute)
check_for_conflicts() (cctk.Group method)
(cctk.Molecule method)
check_has_properties() (cctk.GaussianFile method)
(cctk.OrcaFile method)
choose() (cctk.OneIndexedArray method)
choose_level() (cctk.VibrationalMode method)
classical_distribution_value() (cctk.VibrationalMode method)
classical_turning_point() (cctk.VibrationalMode method)
clip() (cctk.OneIndexedArray method)
combine_molecules() (cctk.Group class method)
(cctk.Molecule class method)
combined_properties() (cctk.ConformationalEnsemble method)
(cctk.Ensemble method)
compress() (cctk.OneIndexedArray method)
compute_angle_between() (in module cctk.helper_functions)
compute_chirality() (in module cctk.helper_functions)
compute_dihedral_between() (in module cctk.helper_functions)
compute_distance_between() (in module cctk.helper_functions)
compute_energy() (cctk.Group method)
(cctk.Molecule method)
compute_mass_spectrum() (in module cctk.helper_functions)
compute_RMSD() (in module cctk.helper_functions)
compute_rotation_matrix() (in module cctk.helper_functions)
compute_unit_vector() (in module cctk.helper_functions)
ConformationalEnsemble (class in cctk)
conj() (cctk.OneIndexedArray method)
conjugate() (cctk.OneIndexedArray method)
copy() (cctk.OneIndexedArray method)
coulomb_analysis() (cctk.Group method)
(cctk.Molecule method)
csearch() (cctk.Group method)
(cctk.Molecule method)
ctypes (cctk.OneIndexedArray attribute)
cumprod() (cctk.OneIndexedArray method)
cumsum() (cctk.OneIndexedArray method)
D
data (cctk.OneIndexedArray attribute)
diagonal() (cctk.OneIndexedArray method)
displacements (cctk.VibrationalMode attribute)
dot() (cctk.OneIndexedArray method)
draw_isotopologue() (in module cctk.helper_functions)
dtype (cctk.OneIndexedArray attribute)
dump() (cctk.OneIndexedArray method)
dumps() (cctk.OneIndexedArray method)
E
elapsed_time (cctk.GaussianFile attribute)
(cctk.OrcaFile attribute)
eliminate_redundant() (cctk.ConformationalEnsemble method)
energy() (cctk.VibrationalMode method)
ensemble (cctk.GaussianFile attribute)
(cctk.MAEFile attribute)
(cctk.MOL2File attribute)
(cctk.OrcaFile attribute)
(cctk.SIFile attribute)
(cctk.XYZFile attribute)
Ensemble (class in cctk)
epimerize() (cctk.Group method)
(cctk.Molecule method)
equal() (cctk.Group class method)
(cctk.Molecule class method)
F
F_CONTIGUOUS (cctk.OneIndexedArray attribute)
FARRAY (cctk.OneIndexedArray attribute)
File (class in cctk)
fill() (cctk.OneIndexedArray method)
find_parameter() (cctk.LazyLineObject method)
flags (cctk.OneIndexedArray attribute)
flat (cctk.OneIndexedArray attribute)
flatten() (cctk.OneIndexedArray method)
FNC (cctk.OneIndexedArray attribute)
footer (cctk.GaussianFile attribute)
FORC (cctk.OneIndexedArray attribute)
force_constant (cctk.VibrationalMode attribute)
formula() (cctk.Group method)
(cctk.Molecule method)
formula_dict_from_string() (in module cctk.helper_functions)
fragment() (cctk.Group method)
(cctk.Molecule method)
frequency (cctk.VibrationalMode attribute)
from_string() (cctk.Group class method)
(cctk.Molecule class method)
(cctk.VibrationalMode method)
full_text() (cctk.LazyLineObject method)
G
GaussianFile (class in cctk)
geometry (cctk.Molecule attribute)
get_adjacent_atoms() (cctk.Group method)
(cctk.Molecule method)
get_angle() (cctk.Group method)
(cctk.Molecule method)
get_atomic_number() (cctk.Group method)
(cctk.Molecule method)
get_atomic_symbol() (cctk.Group method)
(cctk.Molecule method)
get_atomic_symbols() (cctk.Group method)
(cctk.Molecule method)
get_atoms_by_symbol() (cctk.Group method)
(cctk.Molecule method)
get_avg_mass() (in module cctk.helper_functions)
get_bond_order() (cctk.Group method)
(cctk.Molecule method)
get_components() (cctk.Group method)
(cctk.Molecule method)
get_corrected_free_energy() (in module cctk.helper_functions)
get_covalent_radius() (in module cctk.helper_functions)
get_dihedral() (cctk.Group method)
(cctk.Molecule method)
get_distance() (cctk.Group method)
(cctk.Molecule method)
get_entropy() (in module cctk.helper_functions)
get_geometric_parameters() (cctk.ConformationalEnsemble method)
get_heavy_atoms() (cctk.Group method)
(cctk.Molecule method)
get_isotopic_distribution() (in module cctk.helper_functions)
get_molecule() (cctk.GaussianFile method)
(cctk.MAEFile method)
(cctk.MOL2File method)
(cctk.OrcaFile method)
(cctk.XYZFile method)
get_n_atoms() (cctk.Group method)
(cctk.Molecule method)
get_number() (in module cctk.helper_functions)
get_properties_dict() (cctk.ConformationalEnsemble method)
(cctk.Ensemble method)
get_property() (cctk.ConformationalEnsemble method)
(cctk.Ensemble method)
get_sq_distance() (cctk.Group method)
(cctk.Molecule method)
get_symbol() (in module cctk.helper_functions)
get_symmetric_atoms() (cctk.Group method)
(cctk.Molecule method)
get_vdw_radius() (in module cctk.helper_functions)
get_vector() (cctk.Group method)
(cctk.Molecule method)
get_z_from_mass() (in module cctk.helper_functions)
getfield() (cctk.OneIndexedArray method)
Group (class in cctk)
H
has_property() (cctk.ConformationalEnsemble method)
(cctk.Ensemble method)
header (cctk.OrcaFile attribute)
I
imag (cctk.OneIndexedArray attribute)
imaginaries() (cctk.GaussianFile method)
(cctk.OrcaFile method)
intensity (cctk.VibrationalMode attribute)
is_atom_in_ring() (cctk.Group method)
(cctk.Molecule method)
isomorphic (cctk.Group attribute)
item() (cctk.OneIndexedArray method)
items() (cctk.ConformationalEnsemble method)
(cctk.Ensemble method)
itemset() (cctk.OneIndexedArray method)
itemsize (cctk.OneIndexedArray attribute)
J
job_types (cctk.GaussianFile attribute)
(cctk.OrcaFile attribute)
join_ensembles() (cctk.ConformationalEnsemble class method)
(cctk.Ensemble class method)
K
keys() (cctk.ConformationalEnsemble method)
(cctk.Ensemble method)
L
LazyLineObject (class in cctk)
limit_solvent_shell() (cctk.Group method)
(cctk.Molecule method)
link0 (cctk.GaussianFile attribute)
lowest_molecules() (cctk.ConformationalEnsemble method)
(cctk.Ensemble method)
M
MAEFile (class in cctk)
map_from_truncated() (cctk.Group method)
max() (cctk.OneIndexedArray method)
mean() (cctk.OneIndexedArray method)
min() (cctk.OneIndexedArray method)
module
cctk.helper_functions
MOL2File (class in cctk)
mol_from_lines() (cctk.XYZFile class method)
molecule (cctk.XYZFile attribute)
Molecule (class in cctk)
molecule_list() (cctk.ConformationalEnsemble method)
(cctk.Ensemble method)
molecules (cctk.Ensemble attribute)
multiplicity (cctk.Molecule attribute)
N
name (cctk.Ensemble attribute)
(cctk.MAEFile attribute)
(cctk.MOL2File attribute)
(cctk.Molecule attribute)
nbytes (cctk.OneIndexedArray attribute)
ndim (cctk.OneIndexedArray attribute)
new_from_molecule() (cctk.Group class method)
new_from_name() (cctk.Group class method)
(cctk.Molecule class method)
new_from_smiles() (cctk.Group class method)
(cctk.Molecule class method)
newbyteorder() (cctk.OneIndexedArray method)
nonzero() (cctk.OneIndexedArray method)
num_atoms() (cctk.Group method)
(cctk.Molecule method)
num_imaginaries() (cctk.GaussianFile method)
(cctk.OrcaFile method)
num_neighbors_by_atom() (cctk.Group method)
(cctk.Molecule method)
numpy_to_bytes() (in module cctk.helper_functions)
O
OneIndexedArray (class in cctk)
optimize() (cctk.Group method)
(cctk.Molecule method)
optimize_dihedral() (cctk.Group method)
(cctk.Molecule method)
OrcaFile (class in cctk)
OWNDATA (cctk.OneIndexedArray attribute)
P
partition() (cctk.OneIndexedArray method)
PDBFile (class in cctk)
perturb() (cctk.Group method)
(cctk.Molecule method)
principal_axes_of_rotation() (cctk.Group method)
(cctk.Molecule method)
prod() (cctk.OneIndexedArray method)
properties() (cctk.ConformationalEnsemble method)
(cctk.Ensemble method)
properties_list() (cctk.ConformationalEnsemble method)
(cctk.Ensemble method)
ptp() (cctk.OneIndexedArray method)
put() (cctk.OneIndexedArray method)
Q
quantum_distribution_max() (cctk.VibrationalMode method)
quantum_distribution_value() (cctk.VibrationalMode method)
R
random_displacement() (cctk.VibrationalMode method)
ravel() (cctk.OneIndexedArray method)
read_ensemble() (cctk.XYZFile class method)
read_file() (cctk.File static method)
(cctk.GaussianFile class method)
(cctk.MAEFile class method)
(cctk.MOL2File class method)
(cctk.OrcaFile class method)
(cctk.PDBFile class method)
(cctk.SIFile static method)
(cctk.XYZFile class method)
read_trajectory() (cctk.XYZFile class method)
real (cctk.OneIndexedArray attribute)
reduced_mass (cctk.VibrationalMode attribute)
remove_atom() (cctk.Group method)
(cctk.Molecule method)
remove_bond() (cctk.Group method)
(cctk.Molecule method)
remove_group_from_molecule() (cctk.Group static method)
renumber_to_match() (cctk.Group method)
(cctk.Molecule method)
repeat() (cctk.OneIndexedArray method)
reshape() (cctk.OneIndexedArray method)
resize() (cctk.OneIndexedArray method)
rms_distance_between_atoms() (cctk.Group method)
(cctk.Molecule method)
rotate_molecule() (cctk.Group method)
(cctk.Molecule method)
round() (cctk.OneIndexedArray method)
route_card (cctk.GaussianFile attribute)
S
scale_nmr_shifts() (in module cctk.helper_functions)
search_for_block() (cctk.LazyLineObject method)
searchsorted() (cctk.OneIndexedArray method)
set_angle() (cctk.Group method)
(cctk.Molecule method)
set_dihedral() (cctk.Group method)
(cctk.Molecule method)
set_distance() (cctk.Group method)
(cctk.Molecule method)
setfield() (cctk.OneIndexedArray method)
setflags() (cctk.OneIndexedArray method)
shape (cctk.OneIndexedArray attribute)
SIFile (class in cctk)
size (cctk.OneIndexedArray attribute)
sort() (cctk.OneIndexedArray method)
sort_by() (cctk.ConformationalEnsemble method)
(cctk.Ensemble method)
squeeze() (cctk.OneIndexedArray method)
std() (cctk.OneIndexedArray method)
strides (cctk.OneIndexedArray attribute)
successful_terminations (cctk.GaussianFile attribute)
(cctk.OrcaFile attribute)
sum() (cctk.OneIndexedArray method)
swap_atom_numbers() (cctk.Group method)
(cctk.Molecule method)
swapaxes() (cctk.OneIndexedArray method)
T
T (cctk.OneIndexedArray attribute)
take() (cctk.OneIndexedArray method)
title (cctk.GaussianFile attribute)
titles (cctk.SIFile attribute)
(cctk.XYZFile attribute)
to_string() (cctk.Group method)
(cctk.Molecule method)
(cctk.VibrationalMode method)
tobytes() (cctk.OneIndexedArray method)
tofile() (cctk.OneIndexedArray method)
tolist() (cctk.OneIndexedArray method)
tostring() (cctk.OneIndexedArray method)
trace() (cctk.OneIndexedArray method)
translate_molecule() (cctk.Group method)
(cctk.Molecule method)
transpose() (cctk.OneIndexedArray method)
V
values() (cctk.ConformationalEnsemble method)
(cctk.Ensemble method)
var() (cctk.OneIndexedArray method)
variables (cctk.OrcaFile attribute)
velocities (cctk.VibrationalMode attribute)
vibrational_modes (cctk.Molecule attribute)
VibrationalMode (class in cctk)
view() (cctk.OneIndexedArray method)
volume() (cctk.Group method)
(cctk.Molecule method)
W
write_ensemble_to_file() (cctk.GaussianFile class method)
(cctk.MOL2File class method)
(cctk.XYZFile class method)
write_ensemble_to_trajectory() (cctk.PDBFile class method)
write_file() (cctk.File static method)
(cctk.GaussianFile method)
(cctk.MAEFile static method)
(cctk.MOL2File method)
(cctk.OrcaFile method)
(cctk.PDBFile static method)
(cctk.SIFile method)
(cctk.XYZFile method)
write_molecule_to_file() (cctk.GaussianFile class method)
(cctk.MOL2File class method)
(cctk.OrcaFile class method)
(cctk.PDBFile class method)
(cctk.XYZFile class method)
WRITEABLE (cctk.OneIndexedArray attribute)
WRITEBACKIFCOPY (cctk.OneIndexedArray attribute)
X
XYZFile (class in cctk)