Index

A

add_clusters() (in module structural.clusters) add_networks() (in module structural.hh_networks)

area() (structural.clusters.Cluster property) Atom (class in structural.clusters) avg_len() (database.data.Result property)

B

BackboneClashError build_chimeras() (builder.builder.Builder method) Builder (class in builder.builder)

builder.builder module builder.chimera module

C

ca_pair() (database.data.Hit property) ca_tm() (database.data.Hit property) ca_tm_pair() (database.data.Hit property) calc_contact_order() (in module structural.analysis) calc_dist_matrix() (in module structural.analysis) calc_dssp() (in module structural.analysis) calc_resid_dist() (builder.chimera.Chimera method) calc_sasa() (in module structural.analysis)

Chimera (class in builder.chimera) Cluster (class in structural.clusters) cols() (database.data.Hit property) compute_hydrogen_networks() (builder.chimera.Chimera method) compute_hydrophobic_clusters() (builder.chimera.Chimera method) contacts() (structural.clusters.Cluster property) create_graph() (in module structural.clusters) create_network() (network.networks.Network method)

D

database.data module

E

eval() (database.data.Hit property)

F

fetch_by_domain() (in module database.data) fetch_by_domains() (in module database.data) fetch_byPDB() (in module database.data) fetch_byPDBs() (in module database.data) fetch_group() (in module database.data) fetch_id() (in module database.data)

fetch_subspace() (in module database.data) fill_matrices() (in module structural.clusters) filter_hits_domain() (in module database.data) filter_mol() (in module structural.clusters) find_nonstandards() (builder.builder.Builder static method) fragments() (network.networks.Network property)

G

generate_sphere_points() (in module structural.clusters) get_alignment() (builder.builder.Builder method) get_FUZZLE_hhs() (in module builder.chimera)

get_neighbors() (structural.clusters.Atom method) get_representative_domain() (network.networks.Network method) get_SCOP_domain() (in module builder.chimera)

H

hhbond_plot() (in module structural.analysis)

Hit (class in database.data) hmm() (database.data.Hit property)

I

id() (database.data.Hit property)

ident() (database.data.Hit property) ids() (database.data.Result property)

L

list_fams() (database.data.Result property)

list_folds() (database.data.Result property) list_sufams() (database.data.Result property)

M

make_graph_hh() (in module structural.hh_networks) minimize_potential_energy() (in module scorer.mm_energies) module builder.builder builder.chimera database.data network.networks scorer.mm_energies structural.analysis structural.clusters structural.hh_networks structural.salt_bridges

mutate_nonstandards() (builder.builder.Builder static method)

N

Network (class in network.networks) network.networks module

no() (database.data.Hit property) NotCorrectPDBError NotDiverseChimeraError

P

parse_hit() (in module database.data) plot_curves() (builder.builder.Builder method) plot_graph() (network.networks.Network method) postprocess_session() (in module structural.clusters)

prepare_protein() (in module scorer.mm_energies) prob() (database.data.Hit property) protonate_mol() (in module structural.hh_networks) pval() (database.data.Hit property)

Q

q_cluster() (database.data.Hit property) q_end() (database.data.Hit property) q_fold_id() (database.data.Hit property) q_scop_id() (database.data.Hit property)

q_start() (database.data.Hit property) q_sufam_id() (database.data.Hit property) q_tm_end() (database.data.Hit property) q_tm_start() (database.data.Hit property) query() (database.data.Hit property)

R

ratio_area_residue() (structural.clusters.Cluster property) ratio_contacts_residue() (structural.clusters.Cluster property) remove_residue() (builder.builder.Builder static method) residues() (structural.clusters.Cluster property) Result (class in database.data)

retrieve_indices() (in module structural.clusters) retrieve_neighbor_positions() (in module structural.clusters) rmsd_pair() (database.data.Hit property) rmsd_tm() (database.data.Hit property) rmsd_tm_pair() (database.data.Hit property)

S

s_cluster() (database.data.Hit property) s_desc() (database.data.Hit property) s_end() (database.data.Hit property) s_fold_id() (database.data.Hit property) s_scop_id() (database.data.Hit property) s_start() (database.data.Hit property) s_sufam_id() (database.data.Hit property) s_tm_end() (database.data.Hit property) s_tm_start() (database.data.Hit property) sbjct() (database.data.Hit property) score() (database.data.Hit property) score_tm() (database.data.Hit property) score_tm_pair() (database.data.Hit property) scorer.mm_energies module

seq2pdbaln() (builder.builder.Builder method) show_component() (network.networks.Network method) show_edge() (network.networks.Network method) show_vertex() (network.networks.Network method) sizes() (network.networks.Network property) ss() (database.data.Hit property) std_len() (database.data.Result property) structural.analysis module structural.clusters module structural.hh_networks module structural.salt_bridges module superimpose_structures() (builder.builder.Builder method)

U

unique_clusters() (database.data.Result property)

unique_domains() (database.data.Result property)

V

validate_scopid() (in module database.data)

W

write_clusters() (in module structural.clusters) write_largest_cluster() (in module structural.clusters)

write_networks() (in module structural.hh_networks) write_salt_bridges() (in module structural.salt_bridges)