Index

A

AnalysisResult (class in packing_defect.core.analyzers.base)

apply_pbc() (in module packing_defect.utils) average_std_per_frame() (in module packing_defect.core.stats)

B

BaseDefectAnalyzer (class in packing_defect.core.analyzers.base)

build_packing_analyzer() (in module packing_defect.run_defect) build_radius_analyzer() (in module packing_defect.run_radius)

C

ClassificationStrategy (class in packing_defect.core.classification) classify() (packing_defect.core.classification.ClassificationStrategy method) (packing_defect.core.classification.DefaultClassification method) (packing_defect.core.classification.UserDictClassification method) cluster_positions() (in module packing_defect.core.stats)

cluster_sizes() (in module packing_defect.core.stats) (packing_defect.core.grid.DefectGrid method) cluster_sizes_from_mask() (packing_defect.core.cluster.DefectClustering static method) compute_pairwise_distances() (in module packing_defect.utils) count_defect_types() (in module packing_defect.core.stats)

D

data (packing_defect.core.analyzers.base.AnalysisResult attribute) DefaultClassification (class in packing_defect.core.classification) defect_distribution() (in module packing_defect.core.stats)

defect_distro_stats() (in module packing_defect.core.stats) defect_size() (packing_defect.core.cluster.DefectClustering static method) DefectClustering (class in packing_defect.core.cluster) DefectGrid (class in packing_defect.core.grid)

F

from_json() (packing_defect.core.classification.UserDictClassification class method)

G

get_binary_mask() (packing_defect.core.grid.DefectGrid method)

get_coordinates() (packing_defect.core.grid.DefectGrid method) global_avg_std_defect_size() (in module packing_defect.core.stats)

I

initialize_empty_defect_universe() (in module packing_defect.utils)

L

LeafletVisualizer (class in packing_defect.core.visualization)

M

main() (in module packing_defect.core.stats) (in module packing_defect.core.vis) meta (packing_defect.core.analyzers.base.AnalysisResult attribute) module packing_defect packing_defect.core packing_defect.core.analyzers packing_defect.core.analyzers.base packing_defect.core.analyzers.packing packing_defect.core.analyzers.radius packing_defect.core.classification packing_defect.core.cluster packing_defect.core.grid packing_defect.core.interactions packing_defect.core.stats packing_defect.core.topology packing_defect.core.vis packing_defect.core.visualization packing_defect.core.writer packing_defect.data packing_defect.data.files packing_defect.io packing_defect.io.writer packing_defect.run_defect packing_defect.run_radius packing_defect.run_utils packing_defect.tests packing_defect.utils

O

open_gro() (in module packing_defect.core.stats)

P

packing_defect module packing_defect.core module packing_defect.core.analyzers module packing_defect.core.analyzers.base module packing_defect.core.analyzers.packing module packing_defect.core.analyzers.radius module packing_defect.core.classification module packing_defect.core.cluster module packing_defect.core.grid module packing_defect.core.interactions module packing_defect.core.stats module packing_defect.core.topology module packing_defect.core.vis module packing_defect.core.visualization module

packing_defect.core.writer module packing_defect.data module packing_defect.data.files module packing_defect.io module packing_defect.io.writer module packing_defect.run_defect module packing_defect.run_radius module packing_defect.run_utils module packing_defect.tests module packing_defect.utils module PackingDefectAnalyzer (class in packing_defect.core.analyzers.packing) plot() (packing_defect.core.analyzers.base.BaseDefectAnalyzer method) (packing_defect.core.analyzers.packing.PackingDefectAnalyzer method) (packing_defect.core.analyzers.radius.RadiusDefectAnalyzer method) plot_defect_data() (in module packing_defect.core.visualization) plot_frame() (packing_defect.core.visualization.LeafletVisualizer method) process_multiple() (in module packing_defect.core.interactions) ProteinDefectInteractions (class in packing_defect.core.interactions)

R

RadiusDefectAnalyzer (class in packing_defect.core.analyzers.radius) read() (packing_defect.core.topology.TopologyReader method) render_frame() (packing_defect.core.visualization.LeafletVisualizer method) render_frames() (packing_defect.core.visualization.LeafletVisualizer method) return_stats() (in module packing_defect.core.stats)

run() (in module packing_defect.core.interactions) (packing_defect.core.analyzers.base.BaseDefectAnalyzer method) (packing_defect.core.analyzers.packing.PackingDefectAnalyzer method) (packing_defect.core.analyzers.radius.RadiusDefectAnalyzer method) run_analysis() (in module packing_defect.run_utils)

S

save_results() (packing_defect.core.analyzers.base.BaseDefectAnalyzer method) (packing_defect.core.analyzers.packing.PackingDefectAnalyzer method) (packing_defect.core.analyzers.radius.RadiusDefectAnalyzer method)

T

TopologyReader (class in packing_defect.core.topology)

track_frame() (packing_defect.core.interactions.ProteinDefectInteractions method)

U

update() (packing_defect.core.grid.DefectGrid method)

UserDictClassification (class in packing_defect.core.classification)

V

validate_defect_thresholds() (in module packing_defect.utils)

W

write_combined_gro() (in module packing_defect.core.writer) (in module packing_defect.utils)

write_defect_coordinates() (in module packing_defect.core.writer) (in module packing_defect.io.writer)