PyBILT
stable
Contents:
Py
thon based lipid
BIL
ayer molecular simulation analysis
T
oolkit
Install
Documentation and Usage
Contact
Contributing
License
Acknowledgments
Citing
Analyses available to the BilayerAnalyzer
pybilt
PyBILT
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Index
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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I
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K
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L
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M
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N
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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
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Y
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Z
A
area_compressibility_modulus() (in module pybilt.mda_tools.mda_area_compressibility_modulus)
area_per_lipid() (pybilt.lipid_grid.lipid_grid.LipidGrids method)
(pybilt.lipid_grid.lipid_grid_mda.LipidGrids method)
average_thickness() (pybilt.lipid_grid.lipid_grid.LipidGrids method)
(pybilt.lipid_grid.lipid_grid_mda.LipidGrids method)
averages_of_blocks() (pybilt.common.running_stats.BlockAverager method)
B
binned_average() (in module pybilt.common.running_stats)
block_average_bse_v_size() (in module pybilt.common.running_stats)
block_avg_hist() (in module pybilt.common.running_stats)
BlockAverager (class in pybilt.common.running_stats)
C
conditional_mutual_information() (in module pybilt.common.knn_entropy)
curvature() (pybilt.lipid_grid.lipid_grid.LipidGrids method)
(pybilt.lipid_grid.lipid_grid_mda.LipidGrids method)
D
deviation() (pybilt.common.running_stats.RunningStats method)
diffusion_coefficient_anomalous_fit() (in module pybilt.diffusion.diffusion_coefficients)
diffusion_coefficient_Einstein() (in module pybilt.diffusion.diffusion_coefficients)
diffusion_coefficient_linear_fit() (in module pybilt.diffusion.diffusion_coefficients)
distance_cutoff_clustering() (in module pybilt.common.distance_cutoff_clustering)
distance_euclidean() (in module pybilt.common.distance_cutoff_clustering)
distance_euclidean_pbc() (in module pybilt.common.distance_cutoff_clustering)
E
eval() (pybilt.common.gaussian.Gaussian method)
(pybilt.common.gaussian.GaussianRange method)
F
frame (pybilt.lipid_grid.lipid_grid.LipidGrid2d attribute)
G
Gaussian (class in pybilt.common.gaussian)
GaussianRange (class in pybilt.common.gaussian)
gen_running_average() (in module pybilt.common.running_stats)
gen_step_vector_ghost_tails() (in module pybilt.plot_generation.plot_generation_functions)
gen_step_vector_net_ghost_tails() (in module pybilt.plot_generation.plot_generation_functions)
gen_step_vector_smooth_ghost_tails() (in module pybilt.plot_generation.plot_generation_functions)
gen_step_vector_smooth_ghost_tails_forwards() (in module pybilt.plot_generation.plot_generation_functions)
get() (pybilt.common.running_stats.BlockAverager method)
get_index_at() (pybilt.lipid_grid.lipid_grid.LipidGrid2d method)
(pybilt.lipid_grid.lipid_grid_curv.LipidGrid_2d method)
(pybilt.lipid_grid.lipid_grid_mda.LipidGrid_2d method)
get_integer_type_arrays() (pybilt.lipid_grid.lipid_grid.LipidGrids method)
(pybilt.lipid_grid.lipid_grid_mda.LipidGrids method)
get_one_array_per_leaflet() (pybilt.lipid_grid.lipid_grid.LipidGrids method)
(pybilt.lipid_grid.lipid_grid_mda.LipidGrids method)
get_values() (pybilt.common.gaussian.GaussianRange method)
get_xyzc() (pybilt.lipid_grid.lipid_grid.LipidGrids method)
(pybilt.lipid_grid.lipid_grid_mda.LipidGrids method)
get_z_at() (pybilt.lipid_grid.lipid_grid.LipidGrid2d method)
(pybilt.lipid_grid.lipid_grid_curv.LipidGrid_2d method)
(pybilt.lipid_grid.lipid_grid_mda.LipidGrid_2d method)
grid_curvature() (in module pybilt.lipid_grid.lipid_grid)
grid_surface_area() (in module pybilt.lipid_grid.lipid_grid)
grid_to_dict() (pybilt.lipid_grid.lipid_grid.LipidGrids method)
(pybilt.lipid_grid.lipid_grid_mda.LipidGrids method)
I
integrate_range() (pybilt.common.gaussian.GaussianRange method)
K
k_nearest_neighbors() (in module pybilt.common.knn_entropy)
kth_nearest_neighbor_distances() (in module pybilt.common.knn_entropy)
L
lipid_grid (pybilt.lipid_grid.lipid_grid.LipidGrid2d attribute)
lipid_grid_z (pybilt.lipid_grid.lipid_grid.LipidGrid2d attribute)
LipidGrid2d (class in pybilt.lipid_grid.lipid_grid)
LipidGrid_2d (class in pybilt.lipid_grid.lipid_grid_curv)
(class in pybilt.lipid_grid.lipid_grid_mda)
LipidGrids (class in pybilt.lipid_grid.lipid_grid)
(class in pybilt.lipid_grid.lipid_grid_curv)
(class in pybilt.lipid_grid.lipid_grid_mda)
lower (pybilt.common.gaussian.GaussianRange attribute)
M
map_to_grid() (pybilt.lipid_grid.lipid_grid.LipidGrids method)
(pybilt.lipid_grid.lipid_grid_mda.LipidGrids method)
mean (pybilt.common.gaussian.Gaussian attribute)
(pybilt.common.gaussian.GaussianRange attribute)
mean() (pybilt.common.running_stats.RunningStats method)
mutual_information() (in module pybilt.common.knn_entropy)
N
n (pybilt.common.running_stats.RunningStats attribute)
n_block() (pybilt.common.running_stats.BlockAverager method)
n_blocks (pybilt.common.running_stats.BlockAverager attribute)
norm_displacement_cross_correlation() (pybilt.lipid_grid.lipid_grid_curv.LipidGrids method)
normalize() (pybilt.common.gaussian.GaussianRange method)
npoints (pybilt.common.gaussian.GaussianRange attribute)
number_of_blocks() (pybilt.common.running_stats.BlockAverager method)
P
pair_ttest() (in module pybilt.common.running_stats)
plot() (in module pybilt.plot_generation.plot_generation_functions)
plot_area_per_lipid() (in module pybilt.plot_generation.plot_generation_functions)
plot_average_deuterium_op() (in module pybilt.plot_generation.plot_generation_functions)
plot_bilayer_thickness() (in module pybilt.plot_generation.plot_generation_functions)
plot_corr_mat() (in module pybilt.plot_generation.plot_generation_functions)
plot_corr_mat_as_scatter() (in module pybilt.plot_generation.plot_generation_functions)
plot_dc_cluster_dat_number() (in module pybilt.plot_generation.plot_generation_functions)
plot_dc_cluster_dat_number_comtraj() (in module pybilt.plot_generation.plot_generation_functions)
plot_dc_cluster_dat_size() (in module pybilt.plot_generation.plot_generation_functions)
plot_dc_cluster_dat_size_comtraj() (in module pybilt.plot_generation.plot_generation_functions)
plot_dc_cluster_maps_comtraj() (in module pybilt.plot_generation.plot_generation_functions)
plot_density_profile() (in module pybilt.plot_generation.plot_generation_functions)
plot_displacement_lipid_type_cross_correlation() (in module pybilt.plot_generation.plot_generation_functions)
plot_ebar_hists() (in module pybilt.plot_generation.plot_generation_functions)
plot_grid_as_scatter() (in module pybilt.plot_generation.plot_generation_functions)
plot_lipid_grid_thickness_map_2d() (in module pybilt.plot_generation.plot_generation_functions)
plot_msd() (in module pybilt.plot_generation.plot_generation_functions)
plot_position_density_map_2d() (in module pybilt.plot_generation.plot_generation_functions)
plot_position_density_map_2d_scatter() (in module pybilt.plot_generation.plot_generation_functions)
plot_spark() (in module pybilt.plot_generation.plot_generation_functions)
plot_spark_error() (in module pybilt.plot_generation.plot_generation_functions)
plot_spark_error_marker() (in module pybilt.plot_generation.plot_generation_functions)
plot_spark_marker() (in module pybilt.plot_generation.plot_generation_functions)
plot_spark_multi() (in module pybilt.plot_generation.plot_generation_functions)
plot_step_vectors() (in module pybilt.plot_generation.plot_generation_functions)
plot_step_vectors_comtraj() (in module pybilt.plot_generation.plot_generation_functions)
plot_step_vectors_stroboscopic() (in module pybilt.plot_generation.plot_generation_functions)
plot_xygrid_as_imshow() (in module pybilt.plot_generation.plot_generation_functions)
points_per_block() (pybilt.common.running_stats.BlockAverager method)
push() (pybilt.common.running_stats.RunningStats method)
push_container() (pybilt.common.running_stats.BlockAverager method)
push_single() (pybilt.common.running_stats.BlockAverager method)
pybilt (module)
pybilt.com_trajectory (module)
pybilt.common (module)
pybilt.common.distance_cutoff_clustering (module)
pybilt.common.gaussian (module)
pybilt.common.knn_entropy (module)
pybilt.common.running_stats (module)
pybilt.diffusion (module)
pybilt.diffusion.diffusion_coefficients (module)
pybilt.lipid_grid (module)
pybilt.lipid_grid.lipid_grid (module)
pybilt.lipid_grid.lipid_grid_mda (module)
pybilt.mda_tools.mda_area_compressibility_modulus (module)
pybilt.plot_generation (module)
pybilt.plot_generation.plot_generation_functions (module)
R
reset() (pybilt.common.running_stats.RunningStats method)
reset_mean() (pybilt.common.gaussian.Gaussian method)
(pybilt.common.gaussian.GaussianRange method)
RunningStats (class in pybilt.common.running_stats)
S
shannon_entropy() (in module pybilt.common.knn_entropy)
shannon_entropy_pc() (in module pybilt.common.knn_entropy)
standards_of_blocks() (pybilt.common.running_stats.BlockAverager method)
std (pybilt.common.gaussian.Gaussian attribute)
(pybilt.common.gaussian.GaussianRange attribute)
sum_range() (pybilt.common.gaussian.GaussianRange method)
surface_area() (pybilt.lipid_grid.lipid_grid.LipidGrids method)
T
thickness_grid() (pybilt.lipid_grid.lipid_grid.LipidGrids method)
(pybilt.lipid_grid.lipid_grid_mda.LipidGrids method)
U
update_rcparams() (in module pybilt.plot_generation.plot_generation_functions)
upper (pybilt.common.gaussian.GaussianRange attribute)
V
variance() (pybilt.common.running_stats.RunningStats method)
vector_difference_pbc() (in module pybilt.common.distance_cutoff_clustering)
W
write_pdb() (pybilt.lipid_grid.lipid_grid.LipidGrids method)
write_xyz() (pybilt.lipid_grid.lipid_grid.LipidGrid2d method)
(pybilt.lipid_grid.lipid_grid.LipidGrids method)
(pybilt.lipid_grid.lipid_grid_mda.LipidGrid_2d method)
(pybilt.lipid_grid.lipid_grid_mda.LipidGrids method)
X
x_centers (pybilt.lipid_grid.lipid_grid.LipidGrid2d attribute)
,
[1]
x_edges (pybilt.lipid_grid.lipid_grid.LipidGrid2d attribute)
x_incr (pybilt.lipid_grid.lipid_grid.LipidGrid2d attribute)
x_max (pybilt.lipid_grid.lipid_grid.LipidGrid2d attribute)
x_min (pybilt.lipid_grid.lipid_grid.LipidGrid2d attribute)
x_nbins (pybilt.lipid_grid.lipid_grid.LipidGrid2d attribute)
Y
y_centers (pybilt.lipid_grid.lipid_grid.LipidGrid2d attribute)
,
[1]
y_edges (pybilt.lipid_grid.lipid_grid.LipidGrid2d attribute)
y_incr (pybilt.lipid_grid.lipid_grid.LipidGrid2d attribute)
y_max (pybilt.lipid_grid.lipid_grid.LipidGrid2d attribute)
y_min (pybilt.lipid_grid.lipid_grid.LipidGrid2d attribute)
y_nbins (pybilt.lipid_grid.lipid_grid.LipidGrid2d attribute)
Z
z_perturb_grid() (pybilt.lipid_grid.lipid_grid.LipidGrid2d method)
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