PyeMap
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Contents:
Installation
Tutorial: Single Protein
Tutorial: Protein Graph Mining
Developer Reference
Bibliography
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Credits
PyeMap
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Index
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Index
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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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I
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L
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M
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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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Y
_
__init__() (pyemap.emap method)
(pyemap.graph_mining.PDBGroup method)
(pyemap.graph_mining.SubgraphPattern method)
__str__() (pyemap.Branch method)
_do_clustering() (pyemap.graph_mining.SubgraphPattern method)
_subgraph_rmsd() (pyemap.graph_mining.SubgraphPattern method)
_subgraph_seq_dist() (pyemap.graph_mining.SubgraphPattern method)
A
add_emap() (pyemap.graph_mining.PDBGroup method)
add_path() (pyemap.Branch method)
aligned_fasta (pyemap.graph_mining.PDBGroup attribute)
B
Branch (class in pyemap)
branch_id (pyemap.Branch attribute)
branches (pyemap.emap attribute)
C
calculate_residue_depth() (in module pyemap.process_data)
calculate_rsa() (in module pyemap.process_data)
chain_list (pyemap.emap attribute)
cleanup_bonding() (in module pyemap.structures)
color_list (pyemap.ShortestPath attribute)
create_graph() (in module pyemap.process_data)
D
dijkstras_shortest_paths() (in module pyemap.shortest_paths)
E
edges (pyemap.ShortestPath attribute)
emap (class in pyemap)
emaps (pyemap.graph_mining.PDBGroup attribute)
eta_moieties (pyemap.emap attribute)
F
fasta (pyemap.graph_mining.PDBGroup attribute)
fetch_and_parse() (in module pyemap)
file_path (pyemap.emap attribute)
filter_by_degree() (in module pyemap.process_data)
filter_by_percent() (in module pyemap.process_data)
find_conjugated_systems() (in module pyemap.custom_residues)
find_paths() (in module pyemap.pathway_analysis)
find_protein_subgraphs() (pyemap.graph_mining.SubgraphPattern method)
find_subgraph() (pyemap.graph_mining.PDBGroup method)
full_report() (pyemap.graph_mining.SubgraphPattern method)
G
G (pyemap.graph_mining.SubgraphPattern attribute)
general_report() (pyemap.graph_mining.SubgraphPattern method)
generate_graph_database() (pyemap.graph_mining.PDBGroup method)
get_surface_exposed_residues() (pyemap.emap method)
groups (pyemap.graph_mining.SubgraphPattern attribute)
I
id (pyemap.graph_mining.SubgraphPattern attribute)
init_graph (pyemap.emap attribute)
init_graph_to_file() (pyemap.emap method)
init_graph_to_Image() (pyemap.emap method)
L
label_texts (pyemap.ShortestPath attribute)
labeled_atoms (pyemap.ShortestPath attribute)
length (pyemap.ShortestPath attribute)
M
mining_report() (pyemap.graph_mining.PDBGroup method)
module
pyemap.pathway_analysis
P
parse() (in module pyemap)
path (pyemap.ShortestPath attribute)
path_id (pyemap.ShortestPath attribute)
paths (pyemap.Branch attribute)
(pyemap.emap attribute)
paths_graph (pyemap.emap attribute)
paths_graph_to_file() (pyemap.emap method)
paths_graph_to_Image() (pyemap.emap method)
pathways_model() (in module pyemap.process_data)
PDBGroup (class in pyemap.graph_mining)
process() (in module pyemap)
process_custom_residues() (in module pyemap.custom_residues)
process_emaps() (pyemap.graph_mining.PDBGroup method)
protein_subgraphs (pyemap.graph_mining.SubgraphPattern attribute)
pyemap.pathway_analysis
module
R
remove_side_chains() (in module pyemap.structures)
report() (pyemap.emap method)
residue_to_file() (pyemap.emap method)
residue_to_Image() (pyemap.emap method)
residues (pyemap.emap attribute)
run_gspan() (pyemap.graph_mining.PDBGroup method)
S
save_fasta() (pyemap.graph_mining.PDBGroup method)
selection_strs (pyemap.ShortestPath attribute)
sequences (pyemap.emap attribute)
set_clustering() (pyemap.graph_mining.SubgraphPattern method)
set_id() (pyemap.ShortestPath method)
set_visualization() (pyemap.ShortestPath method)
ShortestPath (class in pyemap)
subgraph_patterns (pyemap.graph_mining.PDBGroup attribute)
subgraph_to_file() (pyemap.graph_mining.SubgraphPattern method)
subgraph_to_Image() (pyemap.graph_mining.SubgraphPattern method)
SubgraphPattern (class in pyemap.graph_mining)
support (pyemap.graph_mining.SubgraphPattern attribute)
support_number (pyemap.graph_mining.SubgraphPattern attribute)
T
target (pyemap.Branch attribute)
title (pyemap.graph_mining.PDBGroup attribute)
U
user_residues (pyemap.emap attribute)
V
visualize_pathway_in_nglview() (pyemap.emap method)
visualize_subgraph_in_nglview() (pyemap.graph_mining.SubgraphPattern method)
W
write_graph_smiles() (in module pyemap.graph_mining)
Y
yens_shortest_paths() (in module pyemap.shortest_paths)
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