mdigest
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mdigest
mdigest
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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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V
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W
A
adjust_topology() (mdigest.utils.simulation.MDTUniverse method)
align_md_traj() (mdigest.utils.simulation.MDTUniverse method)
align_traj() (mdigest.core.analysis.MDS_analysis method)
(mdigest.core.parsetrajectory.MDS method)
(mdigest.utils.simulation.MDAUniverse method)
assign_filters() (mdigest.core.networkcommunities.CMTY method)
B
best_iteration_louvain() (mdigest.core.networkcommunities.CMTY method)
C
calc_chi1() (mdigest.core.analysis.MDS_analysis method)
calc_NH_order_params() (mdigest.core.analysis.MDS_analysis method)
calc_rms_quant() (mdigest.core.analysis.MDS_analysis method)
calc_rmsd_2frames() (mdigest.utils.simulation.MDTUniverse method)
calculate_betweenness() (mdigest.core.networkcommunities.CMTY method)
center_pdb() (in module mdigest.utils.pdbhandler)
centroid() (mdigest.utils.simulation.MDTUniverse method)
CMTY (class in mdigest.core.networkcommunities)
community_data() (mdigest.core.networkcommunities.CMTY method)
compute_angles() (mdigest.utils.simulation.MDTUniverse method)
compute_DCC() (in module mdigest.core.auxiliary)
compute_DCC_matrix() (in module mdigest.core.auxiliary)
compute_dihed() (mdigest.utils.simulation.MDTUniverse method)
compute_distance_matrix() (in module mdigest.core.auxiliary)
compute_distances() (mdigest.utils.simulation.MDTUniverse method)
compute_distances_parallel() (mdigest.core.kscorrelation.KS_Energy method)
compute_EEC() (mdigest.core.kscorrelation.KS_Energy method)
compute_eigenvector_centrality() (in module mdigest.core.auxiliary)
compute_generalized_correlation_coefficients() (in module mdigest.core.auxiliary)
compute_KS_energy() (mdigest.core.kscorrelation.KS_Energy method)
compute_optimal_paths() (mdigest.core.networkcommunities.CMTY method)
compute_radius_of_gyration() (mdigest.core.analysis.MDS_analysis method)
compute_rmsd() (mdigest.utils.simulation.MDAUniverse method)
coordinate_reshape() (in module mdigest.core.auxiliary)
corr() (in module mdigest.core.auxiliary)
corrNetworkPymol() (mdigest.core.networkcanvas.ProcCorr method)
create_graph() (in module mdigest.core.auxiliary)
create_matrix_dict() (mdigest.core.networkcommunities.CMTY method)
D
df_to_pdb() (in module mdigest.utils.pdbhandler)
dict2list() (in module mdigest.core.toolkit)
DihDynCorr (class in mdigest.core.dcorrelation)
display_community() (in module mdigest.core.networkcanvas)
display_shortes_path() (in module mdigest.core.networkcommunities)
do_dihedral_calcs() (mdigest.core.analysis.MDS_analysis method)
do_ss_calculation() (mdigest.core.analysis.MDS_analysis method)
draw_electrostatic_network() (in module mdigest.core.networkcanvas)
dump() (in module mdigest.core.toolkit)
DynCorr (class in mdigest.core.correlation)
E
edge_exclusion() (mdigest.core.correlation.DynCorr method)
evaluate_covariance_matrix() (in module mdigest.core.auxiliary)
F
file_exists() (in module mdigest.core.toolkit)
fill_topology_df() (in module mdigest.utils.pdbhandler)
filter_adjacency() (in module mdigest.core.auxiliary)
filter_adjacency_inv() (in module mdigest.core.auxiliary)
filter_by_distance() (mdigest.core.networkcanvas.ProcCorr method)
find_shift() (mdigest.utils.simulation.MDAUniverse method)
(mdigest.utils.simulation.MDTUniverse method)
folder_exists() (in module mdigest.core.toolkit)
G
get_centrality_df() (in module mdigest.core.auxiliary)
get_degree() (mdigest.core.networkcommunities.CMTY method)
get_NGLselection_from_node() (in module mdigest.core.toolkit)
get_or_minus1() (in module mdigest.core.toolkit)
get_path() (in module mdigest.core.toolkit)
get_selection_from_node() (in module mdigest.core.toolkit)
get_selection_fromMDS() (mdigest.core.networkcanvas.ProcCorr method)
get_universe() (mdigest.core.analysis.MDS_analysis method)
(mdigest.core.parsetrajectory.MDS method)
girvannewman() (mdigest.core.networkcommunities.CMTY method)
I
intersection() (in module mdigest.core.toolkit)
K
keywithmaxval() (in module mdigest.core.toolkit)
KS_Box (class in mdigest.core.kscorrelation)
KS_Energy (class in mdigest.core.kscorrelation)
KS_pipeline() (mdigest.core.kscorrelation.KS_Energy method)
L
linfit() (in module mdigest.core.auxiliary)
list2dict() (in module mdigest.core.toolkit)
load_class_from_file() (mdigest.core.analysis.MDS_analysis method)
load_from_file() (mdigest.core.savedata.MDSdata method)
load_graph() (mdigest.core.networkcommunities.CMTY method)
load_matrix_dictionary() (mdigest.core.networkcanvas.ProcCorr method)
load_parameters() (mdigest.core.plots.plot_correlation.Plots method)
load_system() (mdigest.core.analysis.MDS_analysis method)
(mdigest.core.parsetrajectory.MDS method)
load_universe() (mdigest.utils.simulation.MDAUniverse method)
(mdigest.utils.simulation.MDTUniverse method)
log_progress() (in module mdigest.core.toolkit)
M
mdatopology_to_dataframe() (in module mdigest.utils.pdbhandler)
MDAUniverse (class in mdigest.utils.simulation)
mdigest
module
mdigest.core
module
mdigest.core.analysis
module
mdigest.core.auxiliary
module
mdigest.core.correlation
module
mdigest.core.dcorrelation
module
mdigest.core.imports
module
mdigest.core.kscorrelation
module
mdigest.core.networkcanvas
module
mdigest.core.networkcommunities
module
mdigest.core.parsetrajectory
module
mdigest.core.plots
module
mdigest.core.plots.dim_reduction_plots
module
mdigest.core.plots.general_plots
module
mdigest.core.plots.plot_correlation
module
mdigest.core.savedata
module
mdigest.core.toolkit
module
mdigest.utils
module
mdigest.utils.imports
module
mdigest.utils.pdbhandler
module
mdigest.utils.simulation
module
mdigest.utils.toolkit
module
MDS (class in mdigest.core.parsetrajectory)
MDS_analysis (class in mdigest.core.analysis)
MDSdata (class in mdigest.core.savedata)
MDTUniverse (class in mdigest.utils.simulation)
module
mdigest
mdigest.core
mdigest.core.analysis
mdigest.core.auxiliary
mdigest.core.correlation
mdigest.core.dcorrelation
mdigest.core.imports
mdigest.core.kscorrelation
mdigest.core.networkcanvas
mdigest.core.networkcommunities
mdigest.core.parsetrajectory
mdigest.core.plots
mdigest.core.plots.dim_reduction_plots
mdigest.core.plots.general_plots
mdigest.core.plots.plot_correlation
mdigest.core.savedata
mdigest.core.toolkit
mdigest.utils
mdigest.utils.imports
mdigest.utils.pdbhandler
mdigest.utils.simulation
mdigest.utils.toolkit
most_valuable_edge() (mdigest.core.networkcommunities.CMTY method)
most_valuable_edge_fw() (mdigest.core.networkcommunities.CMTY method)
N
normalize() (in module mdigest.core.toolkit)
normalize_array() (in module mdigest.core.toolkit)
P
parse_dih_dynamics() (mdigest.core.dcorrelation.DihDynCorr method)
parse_dynamics() (mdigest.core.correlation.DynCorr method)
partition2dict() (in module mdigest.core.toolkit)
pkl_dump() (in module mdigest.utils.simulation)
plot_eigcent_per_replica() (mdigest.core.plots.plot_correlation.Plots method)
plot_eigenvalues_distribution() (in module mdigest.core.plots.general_plots)
plot_gcc_per_replica() (mdigest.core.plots.plot_correlation.Plots method)
plot_pca_space() (in module mdigest.core.plots.dim_reduction_plots)
Plots (class in mdigest.core.plots.plot_correlation)
populate_attributes() (mdigest.core.networkcanvas.ProcCorr method)
populate_filters() (mdigest.core.networkcommunities.CMTY method)
prepare_kabsch_sander_arrays() (mdigest.core.kscorrelation.KS_Energy method)
print_screen_logfile() (in module mdigest.utils.toolkit)
ProcCorr (class in mdigest.core.networkcanvas)
prune_adjacency() (in module mdigest.core.auxiliary)
R
read_pdb_file() (in module mdigest.utils.pdbhandler)
reduce_mdt_trajectory() (in module mdigest.utils.toolkit)
reduce_trajectory() (in module mdigest.core.auxiliary)
(in module mdigest.utils.toolkit)
retrieve() (in module mdigest.core.toolkit)
retrieve_path() (mdigest.core.networkcommunities.CMTY method)
run_cmty_louvain() (mdigest.core.networkcommunities.CMTY method)
run_cmtys_louvain() (mdigest.core.networkcommunities.CMTY method)
S
save_class() (mdigest.core.analysis.MDS_analysis method)
(mdigest.core.correlation.DynCorr method)
(mdigest.core.dcorrelation.DihDynCorr method)
(mdigest.core.kscorrelation.KS_Energy method)
(mdigest.core.networkcommunities.CMTY method)
save_to_file() (mdigest.core.savedata.MDSdata method)
select_frame() (in module mdigest.utils.pdbhandler)
select_frame_coordinates() (mdigest.core.networkcanvas.ProcCorr method)
set_backbone_dictionary() (mdigest.core.kscorrelation.KS_Energy method)
set_charges_array() (mdigest.core.kscorrelation.KS_Energy method)
set_distances_cache() (mdigest.utils.simulation.MDTUniverse method)
set_logfile() (mdigest.utils.simulation.MDTUniverse method)
set_mapping_chainid() (mdigest.utils.simulation.MDTUniverse method)
set_mapping_segid() (mdigest.utils.simulation.MDTUniverse method)
set_name() (mdigest.utils.simulation.MDAUniverse method)
(mdigest.utils.simulation.MDTUniverse method)
set_NH_selections() (mdigest.core.analysis.MDS_analysis method)
set_node_type_sele() (mdigest.core.analysis.MDS_analysis method)
set_num_replicas() (mdigest.core.analysis.MDS_analysis method)
(mdigest.core.parsetrajectory.MDS method)
set_offset() (mdigest.core.kscorrelation.KS_Energy method)
set_outputparams() (mdigest.core.networkcanvas.ProcCorr method)
set_parameters() (mdigest.core.networkcommunities.CMTY method)
set_selection() (mdigest.core.analysis.MDS_analysis method)
(mdigest.core.kscorrelation.KS_Energy method)
(mdigest.core.networkcanvas.ProcCorr method)
(mdigest.core.parsetrajectory.MDS method)
(mdigest.utils.simulation.MDAUniverse method)
(mdigest.utils.simulation.MDTUniverse method)
set_selection_alignment() (mdigest.utils.simulation.MDTUniverse method)
set_selection_alignment_ref() (mdigest.utils.simulation.MDTUniverse method)
set_selection_ref() (mdigest.utils.simulation.MDAUniverse method)
set_selection_rmsd() (mdigest.utils.simulation.MDAUniverse method)
set_thresholds() (mdigest.core.networkcanvas.ProcCorr method)
set_use_frame() (mdigest.utils.simulation.MDTUniverse method)
sort_cmty() (mdigest.core.networkcommunities.CMTY method)
sorted_eig() (in module mdigest.core.auxiliary)
source_system() (mdigest.core.parsetrajectory.MDS method)
source_universe() (mdigest.core.networkcanvas.ProcCorr method)
(mdigest.utils.simulation.MDAUniverse method)
(mdigest.utils.simulation.MDTUniverse method)
ss_network() (in module mdigest.core.networkcanvas)
stride_trajectory() (mdigest.core.analysis.MDS_analysis method)
(mdigest.core.parsetrajectory.MDS method)
T
to_df() (mdigest.core.networkcanvas.ProcCorr method)
to_pickle() (in module mdigest.core.auxiliary)
V
vec_query() (in module mdigest.core.auxiliary)
W
write_universe() (in module mdigest.utils.toolkit)
writePDBforframe() (mdigest.core.networkcanvas.ProcCorr method)
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