Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
K
|
L
|
M
|
N
|
O
|
P
|
R
|
S
|
T
|
U
|
V
|
W
A
add_xray2psf() (hop.density.PDBDensity method)
analyze_density() (in module hop.interactive)
append() (hop.utilities.Ringbuffer method)
args() (hop.analysis.LegendContainer method)
asiterable() (in module hop.utilities)
ATOM() (hop.qhull.VertexPDBWriter method)
autocorrelation() (hop.MCMC.MCMCsampler method)
autocorrelation_fft() (in module hop.utilities)
averaged_autocorrelation() (hop.MCMC.MCMCsampler method)
(in module hop.utilities)
B
BfactorDensityCreator (class in hop.density)
build_hoppinggraph() (in module hop.interactive)
build_hoppinggraph_fromfiles() (in module hop.interactive)
C
centers() (hop.sitemap.Grid method)
close_log() (in module hop.utilities)
CombinedGraph (class in hop.graph)
compute_site_occupancy() (hop.graph.HoppingGraph method)
(hop.graph.TransportNetwork method)
compute_site_times() (hop.graph.HoppingGraph method)
(hop.graph.TransportNetwork method)
connectedness() (hop.graph.HoppingGraph method)
convert_density() (hop.sitemap.Grid method)
convert_length() (hop.sitemap.Grid method)
ConvexHull (class in hop.qhull)
CustomProgressMeter (class in hop.utilities)
D
DefaultDict (class in hop.utilities)
Density (class in hop.sitemap)
Density() (hop.qhull.ConvexHull method)
density_from_trajectory() (in module hop.density)
density_from_Universe() (in module hop.density)
DensityCollector (class in hop.density)
DensityScanner (class in hop.analysis)
E
easy_load() (in module hop.utilities)
echo() (hop.utilities.CustomProgressMeter method)
equivalence_sites() (hop.density.PDBDensity method)
equivalent_sites_stats() (hop.graph.CombinedGraph method)
(hop.graph.HoppingGraph method)
export() (hop.graph.CombinedGraph method)
(hop.graph.HoppingGraph method)
(hop.graph.TransportNetwork method)
(hop.sitemap.Grid method)
export3D() (hop.graph.CombinedGraph method)
(hop.graph.HoppingGraph method)
(hop.sitemap.Density method)
export_map() (hop.sitemap.Density method)
F
f_factory() (hop.graph.fit_func method)
(hop.graph.fitExp method)
(hop.graph.fitExp2 method)
(hop.graph.fitlin method)
Fifo (class in hop.utilities)
fileextension() (in module hop.utilities)
filename() (hop.analysis.HeatmapAnalysis method)
(hop.graph.HoppingGraph method)
(hop.trajectory.HoppingTrajectory method)
(hop.trajectory.TAPtrajectory method)
(hop.utilities.Saveable method)
filename_function() (in module hop.utilities)
filter() (hop.graph.HoppingGraph method)
find_common_sites() (in module hop.sitemap)
find_equivalence_sites_with() (hop.sitemap.Density method)
find_overlap_coeff() (in module hop.sitemap)
firstsiteindex (hop.MCMC.MCMCsampler attribute)
fit() (hop.graph.fit_func method)
fit_func (class in hop.graph)
fitExp (class in hop.graph)
fitExp2 (class in hop.graph)
fitlin (class in hop.graph)
fixedwidth_bins() (in module hop.utilities)
flatiter() (in module hop.utilities)
flatten() (in module hop.utilities)
from_site() (hop.graph.HoppingGraph method)
G
generate_densities() (in module hop.interactive)
graph_alltransitions() (hop.graph.TransportNetwork method)
Grid (class in hop.sitemap)
H
has_bulk() (hop.sitemap.Density method)
HeatmapAnalysis (class in hop.analysis)
hop.analysis (module)
hop.constants (module)
hop.density (module)
hop.graph (module)
hop.interactive (module)
hop.MCMC (module)
hop.qhull (module)
hop.sitemap (module)
hop.trajectory (module)
hop.utilities (module)
hopgraph_basic_analysis() (in module hop.interactive)
HopgraphAnalysis (class in hop.analysis)
HoppingGraph (class in hop.graph)
HoppingGraph() (hop.graph.TransportNetwork method)
HoppingTrajectory (class in hop.trajectory)
I
importdx() (hop.sitemap.Grid method)
index2node (hop.MCMC.MCMCsampler attribute)
init_state() (hop.MCMC.MCMCsampler method)
initial_values() (hop.graph.fit_func method)
(hop.graph.fitExp method)
(hop.graph.fitExp2 method)
(hop.graph.fitlin method)
internal_sites() (hop.graph.HoppingGraph method)
IntrospectiveDict (class in hop.utilities)
is_connected() (hop.graph.CombinedGraph method)
(hop.graph.HoppingGraph method)
is_from_bulk() (hop.graph.HoppingGraph method)
is_internal() (hop.graph.HoppingGraph method)
is_isolated() (hop.graph.HoppingGraph method)
isolated_sites() (hop.graph.HoppingGraph method)
iterable() (in module hop.utilities)
K
kill_R() (in module hop.analysis)
L
labels() (hop.analysis.HeatmapAnalysis method)
LegendContainer (class in hop.analysis)
linfit() (in module hop.utilities)
load() (hop.analysis.DensityScanner method)
(hop.graph.CombinedGraph method)
(hop.graph.HoppingGraph method)
(hop.utilities.Saveable method)
M
make_density() (hop.sitemap.Grid method)
(in module hop.interactive)
make_hoppingtraj() (in module hop.interactive)
make_xstal_density() (in module hop.interactive)
map_dcd() (hop.trajectory.HoppingTrajectory method)
(hop.trajectory.TAPtrajectory method)
map_hilo() (hop.sitemap.Density method)
map_sites() (hop.sitemap.Density method)
masked_density() (hop.sitemap.Density method)
MCMCsampler (class in hop.MCMC)
mean() (hop.MCMC.MCMCsampler method)
mean_std() (hop.MCMC.MCMCsampler method)
mkdir_p() (in module hop.utilities)
msg() (in module hop.utilities)
multi_plot() (in module hop.MCMC)
MultiPscan (class in hop.MCMC)
N
next() (hop.trajectory.HoppingTrajectory method)
(hop.trajectory.TAPtrajectory method)
node2index (hop.MCMC.MCMCsampler attribute)
normalize() (hop.analysis.HeatmapAnalysis method)
number_of_hops() (hop.graph.HoppingGraph method)
O
occupancy() (hop.MCMC.MCMCsampler method)
occupancy_mean_correl() (hop.MCMC.MCMCsampler method)
(hop.MCMC.Pscan method)
occupancy_std_correl() (hop.MCMC.MCMCsampler method)
P
PDBDensity (class in hop.density)
PDBDensity() (hop.density.BfactorDensityCreator method)
Pearson_r() (in module hop.utilities)
plot() (hop.analysis.DensityScanner method)
(hop.MCMC.MCMCsampler method)
(hop.analysis.HeatmapAnalysis method)
(hop.graph.CombinedGraph method)
plot_correl() (hop.MCMC.MCMCsampler method)
plot_fits() (hop.graph.CombinedGraph method)
(hop.graph.HoppingGraph method)
plot_occupancy() (hop.MCMC.MCMCsampler method)
(hop.MCMC.Pscan method)
plot_occupancy_mean_correl() (hop.MCMC.Pscan method)
plot_residency_times() (hop.graph.TransportNetwork method)
plot_site_occupancy() (hop.graph.TransportNetwork method)
plot_states() (hop.MCMC.Pscan method)
point_inside() (hop.qhull.ConvexHull method)
points_from_selection() (in module hop.qhull)
points_inside() (hop.qhull.ConvexHull method)
pop() (hop.utilities.Fifo method)
print_combined_equivalence_sites() (in module hop.density)
Pscan (class in hop.MCMC)
R
rate() (hop.graph.HoppingGraph method)
rates() (hop.graph.HoppingGraph method)
read_planes() (hop.qhull.ConvexHull method)
read_vertices() (hop.qhull.ConvexHull method)
remap_density() (in module hop.sitemap)
REMARK() (hop.qhull.VertexPDBWriter method)
remove_equivalence_sites() (hop.sitemap.Density method)
Ringbuffer (class in hop.utilities)
run() (hop.MCMC.MCMCsampler method)
(in module hop.MCMC)
S
sample() (hop.MCMC.MCMCsampler method)
save() (hop.graph.HoppingGraph method)
(hop.MCMC.Pscan method)
(hop.utilities.Saveable method)
Saveable (class in hop.utilities)
select_graph() (hop.graph.HoppingGraph method)
set_verbosity() (in module hop.utilities)
show_rates() (hop.graph.HoppingGraph method)
show_site() (hop.graph.HoppingGraph method)
show_total_rates() (hop.graph.HoppingGraph method)
site2resid() (hop.density.PDBDensity method)
site_insert_bulk() (hop.sitemap.Density method)
site_insert_nobulk() (hop.density.PDBDensity method)
(hop.sitemap.Density method)
site_labels() (hop.sitemap.Density method)
site_occupancy() (hop.sitemap.Density method)
site_properties (hop.graph.CombinedGraph attribute)
(hop.graph.HoppingGraph attribute)
site_remove_bulk() (hop.sitemap.Density method)
site_volume() (hop.sitemap.Density method)
sites (hop.MCMC.MCMCsampler attribute)
statevector (hop.MCMC.MCMCsampler attribute)
stats() (hop.graph.CombinedGraph method)
(hop.graph.HoppingGraph method)
(hop.sitemap.Density method)
std() (hop.MCMC.MCMCsampler method)
subsites_of() (hop.sitemap.Density method)
survivalfunction() (in module hop.graph)
T
tabulate_k() (hop.graph.CombinedGraph method)
(hop.graph.HoppingGraph method)
TAPtrajectory (class in hop.trajectory)
ThinDCDReader (class in hop.trajectory)
TITLE() (hop.qhull.VertexPDBWriter method)
to_site() (hop.graph.HoppingGraph method)
TransportNetwork (class in hop.graph)
ts (hop.trajectory.HoppingTrajectory attribute)
U
unique_tuplelist() (in module hop.sitemap)
Unitstep() (in module hop.graph)
unlink_f() (in module hop.utilities)
V
VertexPDBWriter (class in hop.qhull)
visualize_density() (in module hop.interactive)
W
W() (hop.density.PDBDensity method)
waitingtime_fit() (hop.graph.HoppingGraph method)
wd() (hop.qhull.ConvexHull method)
Wequiv() (hop.density.PDBDensity method)
write() (hop.qhull.VertexPDBWriter method)
(hop.trajectory.HoppingTrajectory method)
(hop.trajectory.TAPtrajectory method)
write_coordinates() (in module hop.qhull)
write_psf() (hop.graph.HoppingGraph method)
(hop.trajectory.HoppingTrajectory method)
Hop
Solvent analysis of MD simulations
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hop.interactive
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