sitator
py3
sitator
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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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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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U
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V
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W
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Z
A
add_edge_attribute() (sitator.SiteNetwork method)
add_site_attribute() (sitator.SiteNetwork method)
all_in_unit_cell() (sitator.util.PBCCalculator method)
ase2cuc() (sitator.util.zeo.Zeopy static method)
assign_to_last_known_site() (sitator.SiteTrajectory method)
ATTR_NAME_REGEX (sitator.SiteNetwork attribute)
average() (sitator.util.PBCCalculator method)
AverageVibrationalFrequency (class in sitator.dynamics)
B
backend_dscribe() (sitator.site_descriptors.SOAP.SOAP method)
backend_quip() (sitator.site_descriptors.SOAP.SOAP method)
C
cell_centroid (sitator.util.PBCCalculator attribute)
centers (sitator.SiteNetwork attribute)
,
[1]
check_multiple_occupancy() (sitator.SiteTrajectory method)
clear_attributes() (sitator.SiteNetwork method)
clear_computed_attributes() (sitator.SiteNetwork method)
cluster_centers (sitator.util.DotProdClassifier attribute)
cluster_counts (sitator.util.DotProdClassifier attribute)
CLUSTERING_CLUSTER_SIZE (sitator.landmark.LandmarkAnalysis attribute)
CLUSTERING_CONFIDENCES (sitator.landmark.LandmarkAnalysis attribute)
CLUSTERING_LABELS (sitator.landmark.LandmarkAnalysis attribute)
CLUSTERING_LANDMARK_GROUPINGS (sitator.landmark.LandmarkAnalysis attribute)
CLUSTERING_REPRESENTATIVE_LANDMARKS (sitator.landmark.LandmarkAnalysis attribute)
color_for_species() (in module sitator.visualization.common)
compute() (sitator.descriptors.ConfigurationalEntropy method)
compute_accessable_volumes() (sitator.site_descriptors.SiteVolumes method)
compute_avg_vibrational_freq() (sitator.dynamics.AverageVibrationalFrequency method)
compute_site_occupancies() (sitator.SiteTrajectory method)
compute_volumes() (sitator.site_descriptors.SiteVolumes method)
confidences (sitator.SiteTrajectory attribute)
ConfigurationalEntropy (class in sitator.descriptors)
connectivity_jump_lag_biased() (sitator.dynamics.MergeSitesByDynamics static method)
connectivity_n_ij() (sitator.dynamics.MergeSitesByDynamics static method)
copy() (sitator.SiteNetwork method)
(sitator.SiteTrajectory method)
cov2corr() (in module sitator.landmark.cluster.mcl)
cutoff (sitator.landmark.LandmarkAnalysis attribute)
D
DEFAULT_LINESTYLES (sitator.visualization.SiteNetworkPlotter attribute)
DEFAULT_MARKERS (sitator.visualization.SiteNetworkPlotter attribute)
DEFAULT_SITE_MAPPINGS (sitator.visualization.SiteNetworkPlotter attribute)
DiffusionPathwayAnalysis (class in sitator.network)
distances() (sitator.util.PBCCalculator method)
do_landmark_clustering() (in module sitator.landmark.cluster.dotprod)
(in module sitator.landmark.cluster.mcl)
DotProdClassifier (class in sitator.util)
dscribe_soap_backend() (in module sitator.site_descriptors.backend.dscribe)
E
edge_attributes (sitator.SiteNetwork attribute)
EDGE_GROUP_COLORS (sitator.visualization.SiteNetworkPlotter attribute)
F
fit_centers (sitator.util.DotProdClassifier attribute)
fit_predict (sitator.util.DotProdClassifier attribute)
frame (sitator.landmark.errors.StaticLatticeError attribute)
(sitator.landmark.errors.ZeroLandmarkError attribute)
from_file() (in module sitator.misc.oldio)
G
GenerateAroundSites (class in sitator.misc)
GenerateClampedTrajectory (class in sitator.misc)
get_descriptors() (sitator.site_descriptors.SOAP.SOAP method)
(sitator.site_descriptors.SOAP.SOAPSampledCenters method)
get_edge() (sitator.SiteNetwork method)
get_site() (sitator.SiteNetwork method)
get_structure_with_sites() (sitator.SiteNetwork method)
grid() (in module sitator.visualization.common)
H
has_attribute() (sitator.SiteNetwork method)
I
index_of_elbow() (in module sitator.util.elbow)
is_in_image_of_cell() (sitator.util.PBCCalculator method)
is_in_unit_cell() (sitator.util.PBCCalculator method)
J
jump_lag_by_type() (sitator.dynamics.JumpAnalysis method)
JumpAnalysis (class in sitator.dynamics)
jumps() (sitator.SiteTrajectory method)
jumps_by_frame() (sitator.SiteTrajectory method)
L
landmark_dimension (sitator.landmark.LandmarkAnalysis attribute)
landmark_vectors (sitator.landmark.LandmarkAnalysis attribute)
LandmarkAnalysis (class in sitator.landmark)
LandmarkAnalysisError
lattice_atoms (sitator.landmark.errors.StaticLatticeError attribute)
layers() (in module sitator.visualization.common)
M
markov_clustering() (in module sitator.util.mcl)
MergeSitesByBarrier (class in sitator.network)
MergeSitesByDynamics (class in sitator.dynamics)
MergeSitesByThreshold (class in sitator.dynamics)
merging (in module sitator.network)
min_image() (sitator.util.PBCCalculator method)
mobile_index (sitator.landmark.errors.ZeroLandmarkError attribute)
N
n_assigned (sitator.SiteTrajectory attribute)
n_clusters (sitator.util.DotProdClassifier attribute)
n_frames (sitator.SiteTrajectory attribute)
n_sites (sitator.SiteNetwork attribute)
n_total (sitator.SiteNetwork attribute)
n_types (sitator.SiteNetwork attribute)
n_unassigned (sitator.SiteTrajectory attribute)
NAvgsPerSite (class in sitator.misc)
NO_PATHWAY (sitator.network.DiffusionPathwayAnalysis attribute)
number_of_vertices (sitator.SiteNetwork attribute)
O
of_type() (sitator.SiteNetwork method)
P
pairwise_distances() (sitator.util.PBCCalculator method)
parse_nt2() (sitator.util.zeo.Zeopy static method)
parse_v1_cell() (sitator.util.zeo.Zeopy static method)
PBCCalculator (class in sitator.util)
percent_unassigned (sitator.SiteTrajectory attribute)
plot() (sitator.SiteNetwork method)
plot_atoms() (in module sitator.visualization.atoms)
plot_clustering() (sitator.site_descriptors.SiteTypeAnalysis method)
plot_dpc_decision_plot() (sitator.site_descriptors.SiteTypeAnalysis method)
plot_dpc_delta_density() (sitator.site_descriptors.SiteTypeAnalysis method)
plot_dvecs() (sitator.site_descriptors.SiteTypeAnalysis method)
plot_frame() (sitator.SiteTrajectory method)
(sitator.visualization.SiteTrajectoryPlotter method)
plot_jump_lag() (sitator.dynamics.JumpAnalysis method)
plot_particle_trajectory() (sitator.SiteTrajectory method)
(sitator.visualization.SiteTrajectoryPlotter method)
plot_points() (in module sitator.visualization.atoms)
plot_site() (sitator.SiteTrajectory method)
(sitator.visualization.SiteTrajectoryPlotter method)
plot_voting() (sitator.site_descriptors.SiteTypeAnalysis method)
plotter() (in module sitator.visualization.common)
predict (sitator.util.DotProdClassifier attribute)
Q
quip_soap_backend() (in module sitator.site_descriptors.backend.quip)
R
real_positions_for_site() (sitator.SiteTrajectory method)
real_trajectory (sitator.SiteTrajectory attribute)
RecenterTrajectory (class in sitator.util)
remove_attribute() (sitator.SiteNetwork method)
remove_real_traj() (sitator.SiteTrajectory method)
RemoveUnoccupiedSites (class in sitator.dynamics)
run (sitator.misc.GenerateClampedTrajectory attribute)
(sitator.util.RecenterTrajectory attribute)
run() (sitator.dynamics.JumpAnalysis method)
(sitator.dynamics.RemoveUnoccupiedSites method)
(sitator.landmark.LandmarkAnalysis method)
(sitator.misc.GenerateAroundSites method)
(sitator.misc.NAvgsPerSite method)
(sitator.network.DiffusionPathwayAnalysis method)
(sitator.site_descriptors.SiteCoordinationEnvironment method)
(sitator.site_descriptors.SiteTypeAnalysis method)
(sitator.site_descriptors.SiteVolumes method)
(sitator.voronoi.VoronoiSiteGenerator method)
S
s_tilde() (sitator.descriptors.ConfigurationalEntropy method)
save() (in module sitator.misc.oldio)
set_axes_equal() (in module sitator.visualization.common)
set_cluster_centers (sitator.util.DotProdClassifier attribute)
set_real_traj() (sitator.SiteTrajectory method)
sitator (module)
sitator.descriptors (module)
sitator.dynamics (module)
sitator.landmark (module)
sitator.landmark.cluster (module)
sitator.landmark.cluster.dotprod (module)
sitator.landmark.cluster.mcl (module)
sitator.landmark.errors (module)
sitator.landmark.helpers (module)
sitator.misc (module)
sitator.misc.oldio (module)
sitator.network (module)
sitator.site_descriptors (module)
sitator.site_descriptors.backend (module)
sitator.site_descriptors.backend.dscribe (module)
sitator.site_descriptors.backend.quip (module)
sitator.site_descriptors.SOAP (module)
sitator.util (module)
sitator.util.elbow (module)
sitator.util.mcl (module)
sitator.util.progress (module)
sitator.util.zeo (module)
sitator.visualization (module)
sitator.visualization.atoms (module)
sitator.visualization.common (module)
sitator.voronoi (module)
site_attributes (sitator.SiteNetwork attribute)
SITE_CENTERS_REAL_UNWEIGHTED (sitator.landmark.LandmarkAnalysis attribute)
SITE_CENTERS_REAL_WEIGHTED (sitator.landmark.LandmarkAnalysis attribute)
SITE_CENTERS_REPRESENTATIVE_LANDMARK (sitator.landmark.LandmarkAnalysis attribute)
site_ids (sitator.SiteNetwork attribute)
site_network (sitator.SiteTrajectory attribute)
site_types (sitator.SiteNetwork attribute)
,
[1]
SITE_UNKNOWN (sitator.SiteTrajectory attribute)
SiteCoordinationEnvironment (class in sitator.site_descriptors)
SiteNetwork (class in sitator)
SiteNetworkPlotter (class in sitator.visualization)
SiteTrajectory (class in sitator)
SiteTrajectoryPlotter (class in sitator.visualization)
SiteTypeAnalysis (class in sitator.site_descriptors)
SiteVolumes (class in sitator.site_descriptors)
SOAP (class in sitator.site_descriptors.SOAP)
SOAPCenters (class in sitator.site_descriptors.SOAP)
SOAPDescriptorAverages (class in sitator.site_descriptors.SOAP)
SOAPSampledCenters (class in sitator.site_descriptors.SOAP)
StaticLatticeError
T
time_average() (sitator.util.PBCCalculator method)
to_cell_coords() (sitator.util.PBCCalculator method)
to_real_coords() (sitator.util.PBCCalculator method)
traj (sitator.SiteTrajectory attribute)
trajectory_for_particle() (sitator.SiteTrajectory method)
TRY_RECENTERING_MSG (sitator.landmark.errors.StaticLatticeError attribute)
types (sitator.SiteNetwork attribute)
U
update_centers() (sitator.SiteNetwork method)
V
vertices (sitator.SiteNetwork attribute)
,
[1]
voronoi() (sitator.util.zeo.Zeopy method)
VoronoiSiteGenerator (class in sitator.voronoi)
W
wrap_point() (sitator.util.PBCCalculator method)
wrap_points() (sitator.util.PBCCalculator method)
Z
Zeopy (class in sitator.util.zeo)
ZeroLandmarkError
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