Index

A

aa_length() (Disctransformation.align_axis.pdbclass.PDB method) (Disctransformation.transform.pdbclass.PDB method) add_atom_in_model() (Disctransformation.align_axis.pdbclass.PDB method) (Disctransformation.transform.pdbclass.PDB method) align() (in module Disctransformation.align_axis.main) alignx() (in module Disctransformation.align_axis.main) aligny() (in module Disctransformation.align_axis.main)

alignz() (in module Disctransformation.align_axis.main) altLoc() (Disctransformation.align_axis.pdbclass.PDB method) (Disctransformation.transform.pdbclass.PDB method) aphase() (Disctransformation.core.discstructure.discstructure method) Arguments_Parse() (in module Disctransformation.core.addoptions) Arguments_Parse_v2() (in module Disctransformation.core.addoptions) avg_zstep_distance() (in module Disctransformation.align_axis.fourier_transform) (in module Disctransformation.align_axis.fourier_transform2D)

B

build_disc() (Disctransformation.core.Build_Disc_Model.Build_Disc_Model method)

Build_Disc_Model (class in Disctransformation.core.Build_Disc_Model) Build_Graph_Model (class in Disctransformation.core.create_graph)

C

calculate_accessibility() (Disctransformation.core.Score_Model.Score_Model method) calculate_angle() (Disctransformation.core.disc_state.disc_state method) calculate_state() (Disctransformation.core.disc_state.disc_state method) chainID() (Disctransformation.align_axis.pdbclass.PDB method) (Disctransformation.transform.pdbclass.PDB method) clash_and_compactness_finding_function_for_last_disc() (Disctransformation.core.Score_Model.Score_Model method) clash_finding_function_all_vs_all() (Disctransformation.core.Score_Model.Score_Model method)

clash_finding_function_last_vs_all() (Disctransformation.core.Score_Model.Score_Model method) clash_score() (Disctransformation.core.Disctransformation.DiscTransformation method) (Disctransformation.core.Score_Model.Score_Model method) cluster_models() (in module Disctransformation.core.cluster) compactness_finding_function_first_last_disc() (Disctransformation.core.Score_Model.Score_Model method) create_orientation_matrix() (in module Disctransformation.align_axis.align) createmode() (Disctransformation.core.transformation.transformation method) crossProductdirection() (Disctransformation.core.disc_state.disc_state method)

D

D3distance() (Disctransformation.core.Score_Model.Score_Model method) disc_clash_counter() (Disctransformation.core.Score_Model.Score_Model method) Disc_clash_counter_function() (Disctransformation.core.Score_Model.Score_Model method) disc_state (class in Disctransformation.core.disc_state) discstructure (class in Disctransformation.core.discstructure) Disctransformation module DiscTransformation (class in Disctransformation.core.Disctransformation) Disctransformation.align_axis module Disctransformation.align_axis.align module Disctransformation.align_axis.fourier_transform module Disctransformation.align_axis.fourier_transform2D module Disctransformation.align_axis.getorientation module Disctransformation.align_axis.main module Disctransformation.align_axis.makemove module Disctransformation.align_axis.parsepdb module Disctransformation.align_axis.pdbclass module Disctransformation.align_axis.rewritepdb2 module Disctransformation.align_axis.roration_matrix2 module Disctransformation.core module Disctransformation.core.addoptions module Disctransformation.core.Build_Disc_Model module

Disctransformation.core.cluster module Disctransformation.core.create_graph module Disctransformation.core.disc_state module Disctransformation.core.discstructure module Disctransformation.core.Disctransformation module Disctransformation.core.Initiate_Search module Disctransformation.core.Print_Disc_Model module Disctransformation.core.Score_Model module Disctransformation.core.transformation module Disctransformation.example module Disctransformation.example.disctrans_example module Disctransformation.transform module Disctransformation.transform.DTransform module Disctransformation.transform.pdbclass module distance() (Disctransformation.core.Score_Model.Score_Model method) distance_matrix() (Disctransformation.core.Score_Model.Score_Model method) Distbd() (Disctransformation.core.disc_state.disc_state method) Drawfinal_structure() (Disctransformation.core.Print_Disc_Model.Print_Disc_Model method) DrawInteractingSites() (Disctransformation.core.Print_Disc_Model.Print_Disc_Model method) drawmode() (Disctransformation.core.transformation.transformation method) DTransform() (in module Disctransformation.transform.DTransform) dvec() (Disctransformation.core.discstructure.discstructure method)

E

example_sampling_run() (in module Disctransformation.example.disctrans_example)

example_single_run() (in module Disctransformation.example.disctrans_example) example_single_run_withpdb() (in module Disctransformation.example.disctrans_example)

F

fixed() (Disctransformation.core.discstructure.discstructure method)

fourier_transform() (in module Disctransformation.align_axis.fourier_transform) (in module Disctransformation.align_axis.fourier_transform2D)

G

gaussian_distance() (Disctransformation.core.Score_Model.Score_Model method) gaussian_phase() (Disctransformation.core.Score_Model.Score_Model method) generate_ensemble() (in module Disctransformation.core.Initiate_Search) generate_ensemble_configurations() (in module Disctransformation.core.Initiate_Search) generate_ensemble_inputparams() (in module Disctransformation.core.Initiate_Search) generate_model_file() (in module Disctransformation.core.Initiate_Search) generate_pdb_CAmodel() (in module Disctransformation.core.Initiate_Search) generate_pdb_model() (in module Disctransformation.core.Initiate_Search) generate_single_configuration() (in module Disctransformation.core.Initiate_Search) generate_single_configuration_withpdb() (in module Disctransformation.core.Initiate_Search) get_accessibility() (Disctransformation.core.Score_Model.Score_Model method) get_all_atoms() (in module Disctransformation.core.Initiate_Search) get_all_CA_atoms() (in module Disctransformation.core.Initiate_Search) get_all_interacting_atoms() (in module Disctransformation.core.Initiate_Search) get_arbitrary_perpendicular_vector() (in module Disctransformation.align_axis.align) (in module Disctransformation.align_axis.main) get_ARG5() (Disctransformation.core.Build_Disc_Model.Build_Disc_Model method) get_ARG_ALL() (Disctransformation.core.Build_Disc_Model.Build_Disc_Model method) get_arguments() (Disctransformation.core.Build_Disc_Model.Build_Disc_Model method) get_atomclash() (Disctransformation.core.Score_Model.Score_Model method) get_cc_pairing() (Disctransformation.core.Score_Model.Score_Model method) get_cc_score() (Disctransformation.core.Score_Model.Score_Model method) get_connection() (Disctransformation.core.create_graph.node method) get_dbwd() (Disctransformation.core.Build_Disc_Model.Build_Disc_Model method) get_discs() (Disctransformation.core.Build_Disc_Model.Build_Disc_Model method) get_drad() (Disctransformation.core.Build_Disc_Model.Build_Disc_Model method)

get_electronic_density() (Disctransformation.core.Score_Model.Score_Model method) get_full_sample_space() (in module Disctransformation.core.Initiate_Search) get_head_positions() (Disctransformation.core.Score_Model.Score_Model method) get_id() (Disctransformation.core.discstructure.discstructure method) get_index() (Disctransformation.core.create_graph.node method) get_input_fstr() (in module Disctransformation.core.Initiate_Search) get_interacting_atoms() (in module Disctransformation.core.Initiate_Search) Get_InteractingSites() (Disctransformation.core.discstructure.discstructure method) get_maxdist() (Disctransformation.core.Build_Disc_Model.Build_Disc_Model method) get_mindist() (Disctransformation.core.Build_Disc_Model.Build_Disc_Model method) get_mode_positions() (Disctransformation.core.Build_Disc_Model.Build_Disc_Model method) (Disctransformation.core.Score_Model.Score_Model method) get_model() (Disctransformation.core.Build_Disc_Model.Build_Disc_Model method) get_model_id() (Disctransformation.core.Build_Disc_Model.Build_Disc_Model method) get_nod() (Disctransformation.core.Build_Disc_Model.Build_Disc_Model method) get_nodelist() (Disctransformation.core.create_graph.Build_Graph_Model method) get_outfile() (Disctransformation.core.Build_Disc_Model.Build_Disc_Model method) get_probe() (Disctransformation.core.Score_Model.Score_Model method) get_sum_dist() (in module Disctransformation.core.cluster) get_traverse_order() (Disctransformation.core.create_graph.Build_Graph_Model method) get_visit() (Disctransformation.core.create_graph.node method) get_xlink_score() (Disctransformation.core.Score_Model.Score_Model method) get_xlinkscore() (Disctransformation.core.Score_Model.Score_Model method) getdc() (Disctransformation.core.discstructure.discstructure method) GetDiscRepresentation() (in module Disctransformation.transform.DTransform) GetDiscRepresentation_nthCA() (in module Disctransformation.transform.DTransform) getorientation() (in module Disctransformation.align_axis.getorientation)

H

harmonic_distance() (Disctransformation.core.Score_Model.Score_Model method)

harmonic_phase() (Disctransformation.core.Score_Model.Score_Model method)

I

init_new_starting_disc() (Disctransformation.core.discstructure.discstructure method) initdisc() (Disctransformation.core.discstructure.discstructure method)

initnxtdisc() (Disctransformation.core.discstructure.discstructure method) iter_length() (Disctransformation.align_axis.pdbclass.PDB method) (Disctransformation.transform.pdbclass.PDB method)

L

l() (Disctransformation.core.discstructure.discstructure method)

M

m() (Disctransformation.core.discstructure.discstructure method) main() (Disctransformation.core.Disctransformation.DiscTransformation method) (in module Disctransformation.align_axis.align) max_dist() (Disctransformation.core.Disctransformation.DiscTransformation method) (Disctransformation.core.Score_Model.Score_Model method) model_mean() (Disctransformation.core.Disctransformation.DiscTransformation method) (Disctransformation.core.Score_Model.Score_Model method) model_score() (Disctransformation.core.Disctransformation.DiscTransformation method) (Disctransformation.core.Score_Model.Score_Model method) module Disctransformation Disctransformation.align_axis Disctransformation.align_axis.align Disctransformation.align_axis.fourier_transform Disctransformation.align_axis.fourier_transform2D Disctransformation.align_axis.getorientation Disctransformation.align_axis.main Disctransformation.align_axis.makemove Disctransformation.align_axis.parsepdb Disctransformation.align_axis.pdbclass Disctransformation.align_axis.rewritepdb2 Disctransformation.align_axis.roration_matrix2 Disctransformation.core Disctransformation.core.addoptions Disctransformation.core.Build_Disc_Model Disctransformation.core.cluster Disctransformation.core.create_graph Disctransformation.core.disc_state Disctransformation.core.discstructure Disctransformation.core.Disctransformation Disctransformation.core.Initiate_Search Disctransformation.core.Print_Disc_Model Disctransformation.core.Score_Model Disctransformation.core.transformation Disctransformation.example Disctransformation.example.disctrans_example Disctransformation.transform Disctransformation.transform.DTransform Disctransformation.transform.pdbclass

move() (in module Disctransformation.align_axis.makemove)

N

name() (Disctransformation.align_axis.pdbclass.PDB method) (Disctransformation.transform.pdbclass.PDB method)

node (class in Disctransformation.core.create_graph)

P

p() (Disctransformation.core.discstructure.discstructure method) parsepdb() (in module Disctransformation.align_axis.parsepdb) PDB (class in Disctransformation.align_axis.pdbclass) (class in Disctransformation.transform.pdbclass) pdb_line() (in module Disctransformation.align_axis.pdbclass) (in module Disctransformation.transform.pdbclass)

Print_Disc_Model (class in Disctransformation.core.Print_Disc_Model) print_model() (Disctransformation.core.Disctransformation.DiscTransformation method) printdata() (Disctransformation.core.Print_Disc_Model.Print_Disc_Model method) probe (Disctransformation.core.Score_Model.Score_Model attribute)

Q

q() (Disctransformation.core.discstructure.discstructure method)

R

r() (Disctransformation.core.discstructure.discstructure method) radial_density() (Disctransformation.core.Disctransformation.DiscTransformation method) (Disctransformation.core.Score_Model.Score_Model method) radial_dist_function() (Disctransformation.core.Score_Model.Score_Model method) random() (in module Disctransformation.core.Score_Model) read_allowed_states() (Disctransformation.core.Score_Model.Score_Model method) read_arguments_1() (Disctransformation.core.Build_Disc_Model.Build_Disc_Model method)

read_arguments_2() (Disctransformation.core.Build_Disc_Model.Build_Disc_Model method) resName() (Disctransformation.align_axis.pdbclass.PDB method) (Disctransformation.transform.pdbclass.PDB method) resSeq() (Disctransformation.align_axis.pdbclass.PDB method) (Disctransformation.transform.pdbclass.PDB method) rotate() (Disctransformation.core.transformation.transformation method) rotation_matrix() (in module Disctransformation.align_axis.roration_matrix2) roundupto_x() (Disctransformation.core.Score_Model.Score_Model method)

S

s() (Disctransformation.core.discstructure.discstructure method) save_as_pdf() (Disctransformation.core.Print_Disc_Model.Print_Disc_Model method) save_as_png() (Disctransformation.core.Print_Disc_Model.Print_Disc_Model method) Score_Model (class in Disctransformation.core.Score_Model) scoring_function() (Disctransformation.core.Score_Model.Score_Model method) sdistance() (Disctransformation.core.Score_Model.Score_Model method) search_allowed_state() (Disctransformation.core.Score_Model.Score_Model method) sequence() (Disctransformation.align_axis.pdbclass.PDB method) (Disctransformation.transform.pdbclass.PDB method) sequence_map() (Disctransformation.align_axis.pdbclass.PDB method) (Disctransformation.transform.pdbclass.PDB method) serial() (Disctransformation.align_axis.pdbclass.PDB method) (Disctransformation.transform.pdbclass.PDB method) set_aphase() (Disctransformation.core.discstructure.discstructure method) set_connection() (Disctransformation.core.create_graph.node method) set_dcolor() (Disctransformation.core.discstructure.discstructure method) set_dvec() (Disctransformation.core.discstructure.discstructure method) set_fixed() (Disctransformation.core.discstructure.discstructure method) set_id() (Disctransformation.core.discstructure.discstructure method) set_index() (Disctransformation.core.create_graph.node method) Set_InteractingSites() (Disctransformation.core.discstructure.discstructure method) Set_InteractionSitesCENTER() (Disctransformation.core.discstructure.discstructure method)

set_iter_length() (Disctransformation.align_axis.pdbclass.PDB method) (Disctransformation.transform.pdbclass.PDB method) set_l() (Disctransformation.core.discstructure.discstructure method) set_m() (Disctransformation.core.discstructure.discstructure method) set_mode_positions() (Disctransformation.core.Build_Disc_Model.Build_Disc_Model method) set_p() (Disctransformation.core.discstructure.discstructure method) set_q() (Disctransformation.core.discstructure.discstructure method) set_r() (Disctransformation.core.discstructure.discstructure method) set_s() (Disctransformation.core.discstructure.discstructure method) set_shear() (Disctransformation.core.discstructure.discstructure method) set_T() (Disctransformation.align_axis.pdbclass.PDB method) (Disctransformation.transform.pdbclass.PDB method) set_theta1() (Disctransformation.core.discstructure.discstructure method) set_theta2() (Disctransformation.core.discstructure.discstructure method) set_visit() (Disctransformation.core.create_graph.node method) set_x() (Disctransformation.align_axis.pdbclass.PDB method) (Disctransformation.transform.pdbclass.PDB method) set_y() (Disctransformation.align_axis.pdbclass.PDB method) (Disctransformation.transform.pdbclass.PDB method) set_z() (Disctransformation.align_axis.pdbclass.PDB method) (Disctransformation.transform.pdbclass.PDB method) shear() (Disctransformation.core.discstructure.discstructure method) sqrdistance() (in module Disctransformation.transform.DTransform)

T

T() (Disctransformation.align_axis.pdbclass.PDB method) (Disctransformation.transform.pdbclass.PDB method) Tetramer_min_dist_function() (Disctransformation.core.Score_Model.Score_Model method) tetramer_score() (Disctransformation.core.Score_Model.Score_Model method) theta1() (Disctransformation.core.discstructure.discstructure method) theta2() (Disctransformation.core.discstructure.discstructure method)

transform_Interacting_Sites() (Disctransformation.core.transformation.transformation method) transformation (class in Disctransformation.core.transformation) translate() (Disctransformation.core.transformation.transformation method) Translate_Interacting_Sites() (Disctransformation.core.Build_Disc_Model.Build_Disc_Model method) translatepoint() (Disctransformation.core.Score_Model.Score_Model method) traverse() (Disctransformation.core.create_graph.Build_Graph_Model method)

V

validate_args() (in module Disctransformation.core.addoptions)

validate_paths() (in module Disctransformation.core.Initiate_Search)

W

write() (Disctransformation.align_axis.pdbclass.PDB method) (Disctransformation.transform.pdbclass.PDB method) write_all_chains() (Disctransformation.align_axis.pdbclass.PDB method) (Disctransformation.transform.pdbclass.PDB method) write_dtsampling_input_file() (in module Disctransformation.core.Initiate_Search) write_label() (Disctransformation.core.Print_Disc_Model.Print_Disc_Model method)

write_output_file() (Disctransformation.core.Build_Disc_Model.Build_Disc_Model method) write_samplespace() (in module Disctransformation.core.Initiate_Search) write_selection() (Disctransformation.align_axis.pdbclass.PDB method) (Disctransformation.transform.pdbclass.PDB method) write_selection_multimdl() (Disctransformation.align_axis.pdbclass.PDB method) (Disctransformation.transform.pdbclass.PDB method) writeCA() (Disctransformation.align_axis.pdbclass.PDB method)

X

x() (Disctransformation.align_axis.pdbclass.PDB method) (Disctransformation.transform.pdbclass.PDB method)

Y

y() (Disctransformation.align_axis.pdbclass.PDB method) (Disctransformation.transform.pdbclass.PDB method)

Z

z() (Disctransformation.align_axis.pdbclass.PDB method) (Disctransformation.transform.pdbclass.PDB method)