Disctransformation.core package

Submodules

Disctransformation.core.Build_Disc_Model module

class Disctransformation.core.Build_Disc_Model.Build_Disc_Model(args)

Bases: object

Summary

Translate_Interacting_Sites(InteractingSites)

Summary

Parameters:

InteractingSites (TYPE) – Description

Returns:

Description

Return type:

TYPE

build_disc()

Summary

Returns:

Description

Return type:

TYPE

get_ARG5(sl)

Summary

Parameters:

sl (TYPE) – Description

Returns:

Description

Return type:

TYPE

get_ARG_ALL(sl)

Summary

Parameters:

sl (TYPE) – Description

Returns:

Description

Return type:

TYPE

get_arguments()

Summary

Returns:

Description

Return type:

TYPE

get_dbwd()

Summary

Returns:

Description

Return type:

TYPE

get_discs()

Summary

Returns:

Description

Return type:

TYPE

get_drad()

Summary

Returns:

Description

Return type:

TYPE

get_maxdist()

Summary

Returns:

Description

Return type:

TYPE

get_mindist()

Summary

Returns:

Description

Return type:

TYPE

get_mode_positions()

Summary

Returns:

Description

Return type:

TYPE

get_model()

Summary

Returns:

Description

Return type:

TYPE

get_model_id()

Summary

Returns:

Description

Return type:

TYPE

get_nod()

Summary

Returns:

Description

Return type:

TYPE

get_outfile()

Summary

Returns:

Description

Return type:

TYPE

read_arguments_1(fname)

Summary

Parameters:

fname (TYPE) – Description

Returns:

Description

Return type:

TYPE

read_arguments_2(file_str)

Summary

Parameters:

file_str (TYPE) – Description

Returns:

Description

Return type:

TYPE

set_mode_positions(probe)

Summary

Parameters:

probe (TYPE) – Description

Returns:

Description

Return type:

TYPE

write_output_file(d, score_obj)

Summary

Parameters:

• d (TYPE) – Description

• score_obj (TYPE) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.core.Disctransformation module

class Disctransformation.core.Disctransformation.DiscTransformation

Bases: object

Summary

clash_score()

Summary

Returns:

Description

Return type:

TYPE

main(args, InteractingSites=[[], [], [], [None, None]])

Summary

Parameters:

• args (TYPE) – Description

• InteractingSites (list, optional) – Description

Returns:

Description

Return type:

TYPE

max_dist()

Summary

Returns:

Description

Return type:

TYPE

model_mean()

Summary

Returns:

Description

Return type:

TYPE

model_score()

Summary

Returns:

Description

Return type:

TYPE

print_model(discs, bdm, score_obj)

Summary

Parameters:

• discs (TYPE) – Description

• bdm (TYPE) – Description

• score_obj (TYPE) – Description

Returns:

Description

Return type:

TYPE

radial_density()

Summary

Returns:

Description

Return type:

TYPE

Disctransformation.core.Initiate_Search module

Disctransformation.core.Initiate_Search.generate_ensemble(mdl, output_dir, dtmdl_params)

Summary

Parameters:

• mdl (TYPE) – Description

• output_dir (TYPE) – Description

• dtmdl_params (TYPE) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.core.Initiate_Search.generate_ensemble_configurations(dt_ifile, input_pdb, output_dir, align_flag=True)

Summary

Parameters:

• dt_ifile (TYPE) – Description

• input_pdb (TYPE) – Description

• output_dir (TYPE) – Description

• align_flag (bool, optional) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.core.Initiate_Search.generate_ensemble_inputparams(mdl, dtmdl_params, DiscRad)

Summary

Parameters:

• mdl (TYPE) – Description

• dtmdl_params (TYPE) – Description

• DiscRad (TYPE) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.core.Initiate_Search.generate_model_file(mdl, dtfile, output_dir)

Summary

Parameters:

• mdl (TYPE) – Description

• dtfile (TYPE) – Description

• output_dir (TYPE) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.core.Initiate_Search.generate_pdb_CAmodel(mdl, dtmdl_params, discs, output_dir, counter)

Summary

Parameters:

• mdl (TYPE) – Description

• dtmdl_params (TYPE) – Description

• discs (TYPE) – Description

• output_dir (TYPE) – Description

• counter (TYPE) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.core.Initiate_Search.generate_pdb_model(mdl, dtmdl_params, discs, output_dir, counter)

Summary

Parameters:

• mdl (TYPE) – Description

• dtmdl_params (TYPE) – Description

• discs (TYPE) – Description

• output_dir (TYPE) – Description

• counter (TYPE) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.core.Initiate_Search.generate_single_configuration(dt_ifile)

Summary

Parameters:

dt_ifile (TYPE) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.core.Initiate_Search.generate_single_configuration_withpdb(dt_ifile, input_pdb, output_dir, align_flag=True)

Summary

Parameters:

• dt_ifile (TYPE) – Description

• input_pdb (TYPE) – Description

• output_dir (TYPE) – Description

• align_flag (bool, optional) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.core.Initiate_Search.get_all_CA_atoms(mdl)

Summary

Parameters:

mdl (TYPE) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.core.Initiate_Search.get_all_atoms(mdl)

Summary

Parameters:

mdl (TYPE) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.core.Initiate_Search.get_all_interacting_atoms(mdl)

Summary

Parameters:

mdl (TYPE) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.core.Initiate_Search.get_full_sample_space(Number_of_Modes, theta1_step, overlapRad, dwd_step)

Summary

Parameters:

• Number_of_Modes (TYPE) – Description

• theta1_step (TYPE) – Description

• overlapRad (TYPE) – Description

• dwd_step (TYPE) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.core.Initiate_Search.get_input_fstr(arg1, arg2, arg3, arg4, arg5, arg6, arg7, arg8, arg9, arg10)

Summary

Parameters:

• arg1 (TYPE) – Description

• arg2 (TYPE) – Description

• arg3 (TYPE) – Description

• arg4 (TYPE) – Description

• arg5 (TYPE) – Description

• arg6 (TYPE) – Description

• arg7 (TYPE) – Description

• arg8 (TYPE) – Description

• arg9 (TYPE) – Description

• arg10 (TYPE) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.core.Initiate_Search.get_interacting_atoms(mdl)

Summary

Parameters:

mdl (TYPE) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.core.Initiate_Search.validate_paths(dtpath)

Summary

Parameters:

dtpath (TYPE) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.core.Initiate_Search.write_dtsampling_input_file(file_str, dtmdl_params, output_dir, counter)

Summary

Parameters:

• file_str (TYPE) – Description

• dtmdl_params (TYPE) – Description

• output_dir (TYPE) – Description

• counter (TYPE) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.core.Initiate_Search.write_samplespace(Sample_PARAMs, output_dir, swlines)

Summary

Parameters:

• Sample_PARAMs (TYPE) – Description

• output_dir (TYPE) – Description

• swlines (TYPE) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.core.Print_Disc_Model module

class Disctransformation.core.Print_Disc_Model.Print_Disc_Model(d, bdm)

Bases: object

Summary

DrawInteractingSites(canvas, discx)

Summary

Parameters:

• canvas (TYPE) – Description

• discx (TYPE) – Description

Returns:

Description

Return type:

TYPE

Drawfinal_structure(d, str1, end, fname, score_obj)

Summary

Parameters:

• d (TYPE) – Description

• str1 (TYPE) – Description

• end (TYPE) – Description

• fname (TYPE) – Description

• score_obj (TYPE) – Description

Returns:

Description

Return type:

TYPE

printdata(d, fname, score_obj)

Summary

Parameters:

• d (TYPE) – Description

• fname (TYPE) – Description

• score_obj (TYPE) – Description

Returns:

Description

Return type:

TYPE

save_as_pdf(canvas, fname)

Summary

Parameters:

• canvas (TYPE) – Description

• fname (TYPE) – Description

Returns:

Description

Return type:

TYPE

save_as_png(canvas, fname)

Summary

Parameters:

• canvas (TYPE) – Description

• fname (TYPE) – Description

Returns:

Description

Return type:

TYPE

write_label(canvas, x, y, string)

Summary

Parameters:

• canvas (TYPE) – Description

• x (TYPE) – Description

• y (TYPE) – Description

• string (TYPE) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.core.Score_Model module

class Disctransformation.core.Score_Model.Score_Model(bdm, ds, d)

Bases: object

Summary

probe

Description

Type:

int

D3distance(coord1, coord2)

Summary

Parameters:

• coord1 (TYPE) – Description

• coord2 (TYPE) – Description

Returns:

Description

Return type:

TYPE

Disc_clash_counter_function()

Summary

Returns:

Description

Return type:

TYPE

Tetramer_min_dist_function()

Summary

Returns:

Description

Return type:

TYPE

calculate_accessibility(bdm)

Summary

Parameters:

bdm (TYPE) – Description

Returns:

Description

Return type:

TYPE

clash_and_compactness_finding_function_for_last_disc()

Summary

Returns:

Description

Return type:

TYPE

clash_finding_function_all_vs_all(bdm)

Summary

Parameters:

bdm (TYPE) – Description

Returns:

Description

Return type:

TYPE

clash_finding_function_last_vs_all()

Summary

Returns:

Description

Return type:

TYPE

clash_score()

Summary

Returns:

Description

Return type:

TYPE

compactness_finding_function_first_last_disc()

Summary

Returns:

Description

Return type:

TYPE

disc_clash_counter()

Summary

Returns:

Description

Return type:

TYPE

distance(d1, d2)

Summary

Parameters:

• d1 (TYPE) – Description

• d2 (TYPE) – Description

Returns:

Description

Return type:

TYPE

distance_matrix()

Summary

Returns:

Description

Return type:

TYPE

gaussian_distance(d1, d2, mu, sigma)

Summary

Parameters:

• d1 (TYPE) – Description

• d2 (TYPE) – Description

• mu (TYPE) – Description

• sigma (TYPE) – Description

Returns:

Description

Return type:

TYPE

gaussian_phase(d1, d2, mu, sigma)

Summary

Parameters:

• d1 (TYPE) – Description

• d2 (TYPE) – Description

• mu (TYPE) – Description

• sigma (TYPE) – Description

Returns:

Description

Return type:

TYPE

get_accessibility()

Summary

Returns:

Description

Return type:

TYPE

get_atomclash()

Summary

Returns:

Description

Return type:

TYPE

get_cc_pairing(mdl, IterIdxs, discs)

Summary

Parameters:

• mdl (TYPE) – Description

• IterIdxs (TYPE) – Description

• discs (TYPE) – Description

Returns:

Description

Return type:

TYPE

get_cc_score()

Summary

Returns:

Description

Return type:

TYPE

get_electronic_density(bdm, discs, args)

Summary

Parameters:

• bdm (TYPE) – Description

• discs (TYPE) – Description

• args (TYPE) – Description

Returns:

Description

Return type:

TYPE

get_head_positions(bdm)

Summary

Parameters:

bdm (TYPE) – Description

Returns:

Description

Return type:

TYPE

get_mode_positions()

Summary

Returns:

Description

Return type:

TYPE

get_probe()

Summary

Returns:

Description

Return type:

TYPE

get_xlink_score(mdl, IterIdxs, discs, XlinkIdxs)

Summary

Parameters:

• mdl (TYPE) – Description

• IterIdxs (TYPE) – Description

• discs (TYPE) – Description

• XlinkIdxs (TYPE) – Description

Returns:

Description

Return type:

TYPE

get_xlinkscore()

Summary

Returns:

Description

Return type:

TYPE

harmonic_distance(d2, k, mean)

Summary

Parameters:

• d1 (TYPE) – Description

• d2 (TYPE) – Description

• k (TYPE) – Description

• mean (TYPE) – Description

Returns:

Description

Return type:

TYPE

harmonic_phase(d2, k, mean)

Summary

Parameters:

• d1 (TYPE) – Description

• d2 (TYPE) – Description

• k (TYPE) – Description

• mean (TYPE) – Description

Returns:

Description

Return type:

TYPE

max_dist()

Summary

Returns:

Description

Return type:

TYPE

model_mean()

Summary

Returns:

Description

Return type:

TYPE

model_score()

Summary

Returns:

Description

Return type:

TYPE

radial_density()

Summary

Returns:

Description

Return type:

TYPE

radial_dist_function()

Summary

Returns:

Description

Return type:

TYPE

read_allowed_states(filename)

Summary

Parameters:

filename (TYPE) – Description

Returns:

Description

Return type:

TYPE

roundupto_x(x)

Summary

Parameters:

• num (TYPE) – Description

• x (TYPE) – Description

Returns:

Description

Return type:

TYPE

scoring_function(bdm, ds)

Summary

Parameters:

• bdm (TYPE) – Description

• ds (TYPE) – Description

Returns:

Description

Return type:

TYPE

sdistance(coord1, coord2)

Summary

Parameters:

• coord1 (TYPE) – Description

• coord2 (TYPE) – Description

Returns:

Description

Return type:

TYPE

search_allowed_state()

Summary

Parameters:

disc_state (TYPE) – Description

Returns:

Description

Return type:

TYPE

tetramer_score()

Summary

Returns:

Description

Return type:

TYPE

translatepoint(P, shear, pvX)

Summary

Parameters:

• P (TYPE) – Description

• shear (TYPE) – Description

• pvX (TYPE) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.core.Score_Model.random() → x in the interval [0, 1).

Disctransformation.core.addoptions module

Disctransformation.core.addoptions.Arguments_Parse()

Summary

Returns:

Description

Return type:

TYPE

Disctransformation.core.addoptions.Arguments_Parse_v2()

Summary

Returns:

Description

Return type:

TYPE

Disctransformation.core.addoptions.validate_args(DTparams)

Summary

Parameters:

DTparams (TYPE) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.core.cluster module

Disctransformation.core.cluster.cluster_models(MODELS)

Summary

Parameters:

MODELS (TYPE) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.core.cluster.get_sum_dist(distX)

Summary

Parameters:

distX (TYPE) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.core.create_graph module

class Disctransformation.core.create_graph.Build_Graph_Model(adj_matrix)

Bases: object

Summary

get_nodelist()

Summary

Returns:

Description

Return type:

TYPE

get_traverse_order()

Summary

Returns:

Description

Return type:

TYPE

traverse(node)

Summary

Parameters:

node (TYPE) – Description

Returns:

Description

Return type:

TYPE

class Disctransformation.core.create_graph.node

Bases: object

Summary

get_connection()

Summary

Returns:

Description

Return type:

TYPE

get_index()

Summary

Returns:

Description

Return type:

TYPE

get_visit()

Summary

Returns:

Description

Return type:

TYPE

set_connection(value)

Summary

Parameters:

value (TYPE) – Description

Returns:

Description

Return type:

TYPE

set_index(value)

Summary

Parameters:

value (TYPE) – Description

Returns:

Description

Return type:

TYPE

set_visit(value)

Summary

Parameters:

value (TYPE) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.core.disc_state module

class Disctransformation.core.disc_state.disc_state(bdm, discs)

Bases: object

Summary

Distbd(c1, c2)

Summary

Parameters:

• c1 (TYPE) – Description

• c2 (TYPE) – Description

Returns:

Description

Return type:

TYPE

calculate_angle(c1, c2, c3)

Summary

Parameters:

• c1 (TYPE) – Description

• c2 (TYPE) – Description

• c3 (TYPE) – Description

Returns:

Description

Return type:

TYPE

calculate_state(d1, d2)

Summary

Parameters:

• d1 (TYPE) – Description

• d2 (TYPE) – Description

Returns:

Description

Return type:

TYPE

crossProductdirection(c1, c2, c3)

Summary

Parameters:

• c1 (TYPE) – Description

• c2 (TYPE) – Description

• c3 (TYPE) – Description

Returns:

Description

Return type:

TYPE

Disctransformation.core.discstructure module

class Disctransformation.core.discstructure.discstructure

Bases: object

Summary

Get_InteractingSites()

Summary

Returns:

Description

Return type:

TYPE

Set_InteractingSites(InteractingSites)

Summary

Parameters:

InteractingSites (TYPE) – Description

Returns:

Description

Return type:

TYPE

Set_InteractionSitesCENTER(center)

Summary

Parameters:

center (TYPE) – Description

Returns:

Description

Return type:

TYPE

aphase()

Summary

Returns:

Description

Return type:

TYPE

dvec()

Summary

Returns:

Description

Return type:

TYPE

fixed()

Summary

Returns:

Description

Return type:

TYPE

get_id()

Summary

Returns:

Description

Return type:

TYPE

getdc()

Summary

Returns:

Description

Return type:

TYPE

init_new_starting_disc(d, x, y, drad)

Summary

Parameters:

• d (TYPE) – Description

• x (TYPE) – Description

• y (TYPE) – Description

• drad (TYPE) – Description

Returns:

Description

Return type:

TYPE

initdisc(x, y, drad, vec)

Summary

Parameters:

• x (TYPE) – Description

• y (TYPE) – Description

• drad (TYPE) – Description

• vec (TYPE) – Description

Returns:

Description

Return type:

TYPE

initnxtdisc(d, drad, dbwd, x, y, vec)

Summary

Parameters:

• d (TYPE) – Description

• drad (TYPE) – Description

• dbwd (TYPE) – Description

• x (TYPE) – Description

• y (TYPE) – Description

• vec (TYPE) – Description

Returns:

Description

Return type:

TYPE

l()

Summary

Returns:

Description

Return type:

TYPE

m()

Summary

Returns:

Description

Return type:

TYPE

p()

Summary

Returns:

Description

Return type:

TYPE

q()

Summary

Returns:

Description

Return type:

TYPE

r()

Summary

Returns:

Description

Return type:

TYPE

s()

Summary

Returns:

Description

Return type:

TYPE

set_aphase(val)

Summary

Parameters:

val (TYPE) – Description

set_dcolor(val)

Summary

Parameters:

val (TYPE) – Description

set_dvec(val)

Summary

Parameters:

val (TYPE) – Description

set_fixed(flag)

Summary

Parameters:

flag (TYPE) – Description

set_id(value)

Summary

Parameters:

value (TYPE) – Description

Returns:

Description

Return type:

TYPE

set_l(val)

Summary

Parameters:

val (TYPE) – Description

set_m(val)

Summary

Parameters:

val (TYPE) – Description

set_p(val)

Summary

Parameters:

val (TYPE) – Description

set_q(val)

Summary

Parameters:

val (TYPE) – Description

set_r(val)

Summary

Parameters:

val (TYPE) – Description

set_s(val)

Summary

Parameters:

val (TYPE) – Description

set_shear(val)

Summary

Parameters:

val (TYPE) – Description

set_theta1(val)

Summary

Parameters:

val (TYPE) – Description

set_theta2(val)

Summary

Parameters:

val (TYPE) – Description

shear()

Summary

Returns:

Description

Return type:

TYPE

theta1()

Summary

Returns:

Description

Return type:

TYPE

theta2()

Summary

Returns:

Description

Return type:

TYPE

Disctransformation.core.transformation module

class Disctransformation.core.transformation.transformation

Bases: object

• This method rotates the point C with angle theta with respect to pivot PV

• @param C Point to rotate

• @param PV Pivot point

• @param theta angle to rotate

• @return C return the new transformed coordinates

createmode(d, j, i, mode)

Summary

Parameters:

• d (TYPE) – Description

• j (TYPE) – Description

• i (TYPE) – Description

• mode (TYPE) – Description

Returns:

Description

Return type:

TYPE

drawmode(d, j, i, x, y, mode, drad, dbwd)

Summary

Parameters:

• d (TYPE) – Description

• j (TYPE) – Description

• i (TYPE) – Description

• x (TYPE) – Description

• y (TYPE) – Description

• mode (TYPE) – Description

• drad (TYPE) – Description

• dbwd (TYPE) – Description

rotate(C, PV, theta)

Summary

Parameters:

• C (TYPE) – Description

• PV (TYPE) – Description

• theta (TYPE) – Description

Returns:

Description

Return type:

TYPE

transform_Interacting_Sites(discx, PV1x, modex)

Summary

Parameters:

• discx (TYPE) – Description

• PV1x (TYPE) – Description

• modex (TYPE) – Description

Returns:

Description

Return type:

TYPE

translate(DC, dist2)

Summary

Parameters:

• C (TYPE) – Description

• DC (TYPE) – Description

• dist2 (TYPE) – Description

Returns:

Description

Return type:

TYPE

Module contents