coconut.src.Core package

Submodules

coconut.src.Core.BaseScores module

class coconut.src.Core.BaseScores.BaseScoresAlign(fname)

Bases: object

Summary

scoremat

Description

Type

dict

get_scoremat()

Summary

Returns

Description

Return type

TYPE

read_matrix_file(fname)

Summary

Parameters

fname (TYPE) – Description

Returns

Description

Return type

TYPE

coconut.src.Core.CoiledCoilAlignClass module

Summary

class coconut.src.Core.CoiledCoilAlignClass.CoiledCoilAlign(ppath, prot1_prot2, pc_prot1_file, pc_prot2_file, PROB_CUTOFF, BaseAlignmentFile=None)

Bases: object

Summary

BaseAlignmentFile

Description

Type

TYPE

constant_score

Description

Type

float

fsseq1

Description

Type

TYPE

fsseq2

Description

Type

TYPE

pc_prot1_file

Description

Type

TYPE

pc_prot2_file

Description

Type

TYPE

ppath

Description

Type

TYPE

PROB_CUTOFF

Description

Type

TYPE

prot1

Description

Type

TYPE

prot2

Description

Type

TYPE

topk

Description

Type

int

Filter_OffDiagonal_Segments(Segment_Dict_full, n, m, bandwidth1, bandwidth2, score_cutoff)

Summary

Parameters

• Segment_Dict_full (TYPE) – Description

• n (TYPE) – Description

• m (TYPE) – Description

• bandwidth1 (TYPE) – Description

• bandwidth2 (TYPE) – Description

• score_cutoff (TYPE) – Description

Returns

Description

Return type

TYPE

Write_Topn_Alignments(oaname, topn, prot1, prot2, seq1, seq2, TRACE, TRACE_SEGMENT, ALI1, ALI2, ALISCORE)

Summary

Parameters

• oaname (TYPE) – Description

• topn (TYPE) – Description

• prot1 (TYPE) – Description

• prot2 (TYPE) – Description

• seq1 (TYPE) – Description

• seq2 (TYPE) – Description

• TRACE (TYPE) – Description

• TRACE_SEGMENT (TYPE) – Description

• ALI1 (TYPE) – Description

• ALI2 (TYPE) – Description

• ALISCORE (TYPE) – Description

Returns

Description

Return type

TYPE

add_alignment_scores_segmentdict(Segment_Dict_full, seq1, seq2, alignment_file, constant_score)

Summary

Parameters

• Segment_Dict_full (TYPE) – Description

• seq1 (TYPE) – Description

• seq2 (TYPE) – Description

• alignment_file (TYPE) – Description

• constant_score (TYPE) – Description

Returns

Description

Return type

TYPE

add_sequence_at_cterm(ali1, ali2, seq1, seq2, ali1e, ali2e, segment)

Summary

Parameters

• ali1 (TYPE) – Description

• ali2 (TYPE) – Description

• seq1 (TYPE) – Description

• seq2 (TYPE) – Description

• ali1e (TYPE) – Description

• ali2e (TYPE) – Description

• segment (TYPE) – Description

Returns

Description

Return type

TYPE

add_sequence_with_gaps(ali1, ali2, seq1, seq2, ali1e, ali2e, segment)

Summary

Parameters

• ali1 (TYPE) – Description

• ali2 (TYPE) – Description

• seq1 (TYPE) – Description

• seq2 (TYPE) – Description

• ali1e (TYPE) – Description

• ali2e (TYPE) – Description

• segment (TYPE) – Description

Returns

Description

Return type

TYPE

coconut_align(seq1, seq2, ppath, prot1_prot2, plotchart=False)

Summary

Parameters

• seq1 (TYPE) – Description

• seq2 (TYPE) – Description

• ppath (TYPE) – Description

• prot1_prot2 (TYPE) – Description

• plotchart (bool, optional) – Description

Returns

Description

Return type

TYPE

create_base_alignment()

Summary

Returns

Description

Return type

TYPE

get_hamming_distances()

Summary

Returns

Description

Return type

TYPE

get_next_segment_lists(tracekey, Segment_Dict_full, KDtree, Segment_Data)

Summary

Parameters

• tracekey (TYPE) – Description

• Segment_Dict_full (TYPE) – Description

• KDtree (TYPE) – Description

• Segment_Data (TYPE) – Description

Returns

Description

Return type

TYPE

get_tracepath_alignments(alignments, sourceid, targetid, seq1, seq2, topk)

Summary

Parameters

• alignments (TYPE) – Description

• sourceid (TYPE) – Description

• targetid (TYPE) – Description

• seq1 (TYPE) – Description

• seq2 (TYPE) – Description

• topk (TYPE) – Description

Returns

Description

Return type

TYPE

get_tracepath_alignments_fullseq(alignments, sourceid, targetid, seq1, seq2, topk)

Summary

Parameters

• alignments (TYPE) – Description

• sourceid (TYPE) – Description

• targetid (TYPE) – Description

• seq1 (TYPE) – Description

• seq2 (TYPE) – Description

• topk (TYPE) – Description

Returns

Description

Return type

TYPE

k_shortest_paths(G, source, target, k, weight=None)

Summary

Parameters

• G (TYPE) – Description

• source (TYPE) – Description

• target (TYPE) – Description

• k (TYPE) – Description

• weight (None, optional) – Description

Returns

Description

Return type

TYPE

load_Coiled_Coil_Segments_full(fname)

Summary

Parameters

fname (TYPE) – Description

Returns

Description

Return type

TYPE

load_paircoil_alignment(pc_file)

Summary

Parameters

pc_file (TYPE) – Description

Returns

Description

Return type

TYPE

plot_alignment_segments(TRACE_SEGMENTi, ax, lwd, seg_color)

Summary

Parameters

• TRACE_SEGMENTi (TYPE) – Description

• ax (TYPE) – Description

• lwd (TYPE) – Description

• seg_color (TYPE) – Description

Returns

Description

Return type

TYPE

plot_segments(Segment_Dict_full, ax, lwd, ssize, seg_color, score_cutoff)

Summary

Parameters

• Segment_Dict_full (TYPE) – Description

• ax (TYPE) – Description

• lwd (TYPE) – Description

• ssize (TYPE) – Description

• seg_color (TYPE) – Description

• score_cutoff (TYPE) – Description

Returns

Description

Return type

TYPE

plot_tree(alignments, fname)

Summary

Parameters

• alignments (TYPE) – Description

• fname (TYPE) – Description

Returns

Description

Return type

TYPE

plot_tree_simple(alignments, fname)

Summary

Parameters

• alignments (TYPE) – Description

• fname (TYPE) – Description

Returns

Description

Return type

TYPE

read_aligned_fasta(fname)

Summary

Parameters

fname (TYPE) – Description

Returns

Description

Return type

TYPE

read_coco_alignment_graph(seq1, seq2, ppath, prot1_prot2)

Summary

Parameters

• seq1 (TYPE) – Description

• seq2 (TYPE) – Description

• ppath (TYPE) – Description

• prot1_prot2 (TYPE) – Description

read_coco_alignment_graph_new(seq1, seq2, ppath, prot1_prot2, topk)

Summary

Parameters

• seq1 (TYPE) – Description

• seq2 (TYPE) – Description

• ppath (TYPE) – Description

• prot1_prot2 (TYPE) – Description

• topk (TYPE) – Description

Returns

Description

Return type

TYPE

read_fasta(fname)

Summary

Parameters

fname (TYPE) – Description

Returns

Description

Return type

TYPE

segment_traceback(tracekey, alignments, Segment_Dict_full, KDtree, Segment_Data, max_depth, sourceid, currentid)

Summary

Parameters

• tracekey (TYPE) – Description

• alignments (TYPE) – Description

• Segment_Dict_full (TYPE) – Description

• KDtree (TYPE) – Description

• Segment_Data (TYPE) – Description

• max_depth (TYPE) – Description

• sourceid (TYPE) – Description

• currentid (TYPE) – Description

Returns

Description

Return type

TYPE

write_alignment(alignment, prot1, prot2, outfilename)

Summary

Parameters

• alignment (TYPE) – Description

• prot1 (TYPE) – Description

• prot2 (TYPE) – Description

• outfilename (TYPE) – Description

Returns

Description

Return type

TYPE

write_alignment_with_heptad(alignment, prot1, prot2, p1_PC, p2_PC, outfilename)

Summary

Parameters

• alignment (TYPE) – Description

• prot1 (TYPE) – Description

• prot2 (TYPE) – Description

• p1_PC (TYPE) – Description

• p2_PC (TYPE) – Description

• outfilename (TYPE) – Description

Returns

Description

Return type

TYPE

class coconut.src.Core.CoiledCoilAlignClass.DefaultDictNoAdd

Bases: defaultdict

Summary

coconut.src.Core.CoiledCoilClass module

class coconut.src.Core.CoiledCoilClass.CoiledCoil(CCid, num_monomers=2)

Bases: object

Summary

CC

Description

Type

list

display_CC()

Summary

Returns

Description

Return type

TYPE

get_CC()

Summary

Returns

Description

Return type

TYPE

get_num_monomers()

Summary

Returns

Description

Return type

TYPE

set_CC_orientation(orientation)

Summary

Parameters

orientation (TYPE) – Description

Returns

Description

Return type

TYPE

set_CC_values(monomer_idx, monomer_seq, monomer_hep)

Summary

Parameters

• monomer_idx (TYPE) – Description

• monomer_seq (TYPE) – Description

• monomer_hep (TYPE) – Description

Returns

Description

Return type

TYPE

coconut.src.Core.ExtendCCClass module

class coconut.src.Core.ExtendCCClass.DefaultDictNoAdd

Bases: defaultdict

Summary

class coconut.src.Core.ExtendCCClass.ExtendCoiledCoil(ppath, prot1_prot2, pc_prot1_file, pc_prot2_file, PROB_CUTOFF)

Bases: object

Summary

DistDict

Description

Type

TYPE

DistMat

Description

Type

TYPE

p1_PC

Description

Type

TYPE

p2_PC

Description

Type

TYPE

pc_prot1_file

Description

Type

TYPE

pc_prot2_file

Description

Type

TYPE

phep1

Description

Type

str

phep2

Description

Type

str

ppath

Description

Type

TYPE

PROB_CUTOFF

Description

Type

TYPE

prot1

Description

Type

TYPE

prot1_max

Description

Type

TYPE

prot1_min

Description

Type

TYPE

prot1res

Description

Type

TYPE

prot2

Description

Type

TYPE

prot2_max

Description

Type

TYPE

prot2_min

Description

Type

TYPE

Generate_Alignments_Scores(Segments, APFlag, plot_True)

Summary

Parameters

• Segments (TYPE) – Description

• APFlag (TYPE) – Description

• plot_True (TYPE) – Description

Returns

Description

Return type

TYPE

Sample_Plot_Combine(APFlag)

Summary

Parameters

APFlag (TYPE) – Description

Returns

Description

Return type

TYPE

def_value()

Summary

Returns

Description

Return type

TYPE

extend_segment(Segments, APFlag)

Summary

Parameters

• Segments (TYPE) – Description

• APFlag (TYPE) – Description

Returns

Description

Return type

TYPE

get_parallel_diagonal_alignment(Segments_New, fileAPname)

Summary

Parameters

• Segments_New (TYPE) – Description

• fileAPname (TYPE) – Description

Returns

Description

Return type

TYPE

load_paircoil_alignment(pc_file)

Summary

Parameters

pc_file (TYPE) – Description

Returns

Description

Return type

TYPE

plot_alignment(APFlag, figsize1=(6, 3), fscale=1)

Summary

Parameters

• APFlag (TYPE) – Description

• figsize1 (tuple, optional) – Description

• fscale (int, optional) – Description

Returns

Description

Return type

TYPE

plot_individual_cc_scores(Segments_Temp)

Summary

Parameters

Segments_Temp (TYPE) – Description

Returns

Description

Return type

TYPE

coconut.src.Core.InputClass module

class coconut.src.Core.InputClass.InputCC(input_filename)

Bases: object

Summary

input_filename

Description

Type

TYPE

interface_dict

Description

Type

TYPE

num_monomers

Description

Type

int

valid_aas

Description

Type

TYPE

valid_hep

Description

Type

list

check_aa_hep(aa_hep)

Summary

Parameters

aa_hep (TYPE) – Description

Returns

Description

Return type

TYPE

check_aa_seq(aa_seq)

Summary

Parameters

aa_seq (TYPE) – Description

Returns

Description

Return type

TYPE

check_inp_len(aa_seq, aa_hep)

Summary

Parameters

• aa_seq (TYPE) – Description

• aa_hep (TYPE) – Description

Returns

Description

Return type

TYPE

correct_P_AP_compatibility(dseq, dhep)

Summary

Parameters

• dseq (TYPE) – Description

• dhep (TYPE) – Description

Returns

Description

Return type

TYPE

get_cc_orientation(value)

Summary

Parameters

value (TYPE) – Description

Returns

Description

Return type

TYPE

load_CCData()

Summary

Returns

Description

Return type

TYPE

print_input_info()

Summary

Returns

Description

Return type

TYPE

raise_error(flag)

Summary

Parameters

flag (TYPE) – Description

Returns

Description

Return type

TYPE

coconut.src.Core.PairCoilClass module

class coconut.src.Core.PairCoilClass.DefaultDictNoAdd

Bases: defaultdict

Summary

class coconut.src.Core.PairCoilClass.PairCoilParse(pc_prot1_file, PROB_CUTOFF, probability_type='pcoil')

Bases: object

Summary

header

Description

Type

str

p1_PC

Description

Type

TYPE

pc_prot1_file

Description

Type

TYPE

phep1

Description

Type

str

phep2

Description

Type

str

PROB_CUTOFF

Description

Type

TYPE

correct_incorrectly_Indentified_heptad()

Summary

Returns

Description

Return type

TYPE

get_heptad_repeats_pairs()

Summary

Returns

Description

Return type

TYPE

get_pc_seq()

Summary

Returns

Description

Return type

TYPE

hamming_distance(s1, s2, resrange)

Summary

Parameters

• s1 (TYPE) – Description

• s2 (TYPE) – Description

• resrange (TYPE) – Description

Returns

Description

Return type

TYPE

load_Pcoil_alignment(pc_file)

Summary

Parameters

pc_file (TYPE) – Description

Returns

Description

Return type

TYPE

load_Pcoil_alignment_backup(pc_file, prob_col=3)

Summary

Parameters

• pc_file (TYPE) – Description

• prob_col (int, optional) – Description

Returns

Description

Return type

TYPE

load_paircoil_alignment(pc_file)

Summary

Parameters

pc_file (TYPE) – Description

Returns

Description

Return type

TYPE

write_Updated_Paircoil_Probs(fname)

Summary

Parameters

fname (TYPE) – Description

Returns

Description

Return type

TYPE

coconut.src.Core.ScoringClass module

class coconut.src.Core.ScoringClass.ScoreCC

Bases: object

Summary

ALLPROBS

Description

Type

TYPE

ALLSCORES

Description

Type

list

AP_Prior_Prob

Description

Type

float

AP_Prior_Prob_dimer

Description

Type

TYPE

branching_dict

Description

Type

TYPE

D_PREDS

Description

Type

list

D_PROBS

Description

Type

list

D_PROBS_mean

Description

Type

TYPE

Distributions

Description

Type

TYPE

P_Prior_Prob

Description

Type

float

P_Prior_Prob_dimer

Description

Type

TYPE

Generate_CC_Bayesian_Scores(DIMERS, model_obj, CCDSDIR)

Summary

Parameters

• DIMERS (TYPE) – Description

• model_obj (TYPE) – Description

• CCDSDIR (TYPE) – Description

Returns

Description

Return type

TYPE

Generate_CC_RF_Scores(DIMERS, model_obj, CCDSDIR)

Summary

Parameters

• DIMERS (TYPE) – Description

• model_obj (TYPE) – Description

• CCDSDIR (TYPE) – Description

Returns

Description

Return type

TYPE

Generate_CC_Scores_Bayes(input_obj, model_obj)

Summary

Parameters

• input_obj (TYPE) – Description

• model_obj (TYPE) – Description

Returns

Description

Return type

TYPE

Generate_CC_Scores_RF(input_obj, model_obj)

Summary

Parameters

• input_obj (TYPE) – Description

• model_obj (TYPE) – Description

Returns

Description

Return type

TYPE

Get_Prediction_Probs()

Summary

Returns

Description

Return type

TYPE

Get_Predictions()

Summary

Predict_CC_Stability(model_obj)

Summary

Parameters

model_obj (TYPE) – Description

Returns

Description

Return type

TYPE

Score_Coiled_coil(input_obj, model_obj)

Summary

Parameters

• input_obj (TYPE) – Description

• model_obj (TYPE) – Description

Returns

Description

Return type

TYPE

Write_Bayesian_Probabilities(input_obj, fname)

Summary

Parameters

• input_obj (TYPE) – Description

• fname (TYPE) – Description

Returns

Description

Return type

TYPE

Write_Raw_Scores(input_obj, fname)

Summary

Parameters

• input_obj (TYPE) – Description

• fname (TYPE) – Description

Returns

Description

Return type

TYPE

calculate_prior_probabilities(DIMERS, outputdir)

Summary

Parameters

• DIMERS (TYPE) – Description

• outputdir (TYPE) – Description

Returns

Description

Return type

TYPE

find_score_ada_ada(AA1, AA2, AA3, AA4, AAscores)

Summary

Parameters

• AA1 (TYPE) – Description

• AA2 (TYPE) – Description

• AA3 (TYPE) – Description

• AA4 (TYPE) – Description

• AAscores (TYPE) – Description

Returns

Description

Return type

TYPE

find_score_ada_dad(AA1, AA2, AA3, AA4, AAscores)

Summary

Parameters

• AA1 (TYPE) – Description

• AA2 (TYPE) – Description

• AA3 (TYPE) – Description

• AA4 (TYPE) – Description

• AAscores (TYPE) – Description

Returns

Description

Return type

TYPE

find_score_dad_ada(AA1, AA2, AA3, AA4, AAscores)

Summary

Parameters

• AA1 (TYPE) – Description

• AA2 (TYPE) – Description

• AA3 (TYPE) – Description

• AA4 (TYPE) – Description

• AAscores (TYPE) – Description

Returns

Description

Return type

TYPE

find_score_dad_dad(AA1, AA2, AA3, AA4, AAscores)

Summary

Parameters

• AA1 (TYPE) – Description

• AA2 (TYPE) – Description

• AA3 (TYPE) – Description

• AA4 (TYPE) – Description

• AAscores (TYPE) – Description

Returns

Description

Return type

TYPE

get_BS(value)

Summary

Parameters

value (TYPE) – Description

Returns

Description

Return type

TYPE

get_Distributions()

Summary

Returns

Description

Return type

TYPE

load_prior_probabilities()

Summary

Returns

Description

Return type

TYPE

score_dimer_RF(scoring_dicts, Hexpairs, dimer, max_hexpairs_length)

Summary

Parameters

• scoring_dicts (TYPE) – Description

• Hexpairs (TYPE) – Description

• dimer (TYPE) – Description

• max_hexpairs_length (TYPE) – Description

Returns

Description

Return type

TYPE

score_dimer_bayesian(scoring_dicts, Hexpairs, dimer)

Summary

Parameters

• scoring_dicts (TYPE) – Description

• Hexpairs (TYPE) – Description

• dimer (TYPE) – Description

Returns

Description

Return type

TYPE

coconut.src.Core.SlidingWindowsClass module

class coconut.src.Core.SlidingWindowsClass.DefaultDictNoAdd

Bases: defaultdict

Summary

class coconut.src.Core.SlidingWindowsClass.SlidingWindows(pc_prot1_file, pc_prot2_file, sw_file_a, sw_file_d, PROB_CUTOFF=0.2, swlen=18)

Bases: object

Summary

pc_prot1_file

Description

Type

TYPE

pc_prot2_file

Description

Type

TYPE

PROB_CUTOFF

Description

Type

TYPE

prot1_seq

Description

Type

TYPE

prot2_seq

Description

Type

TYPE

sw_file_a

Description

Type

TYPE

sw_file_d

Description

Type

TYPE

swlen

Description

Type

TYPE

swlen_d

Description

Type

TYPE

Get_Sliding_Windows(prot_seq)

Summary

Parameters

prot_seq (TYPE) – Description

Returns

Description

Return type

TYPE

Write_CC_InputFile(SeqHep1, SeqHep2, fname)

Summary

Parameters

• SeqHep1 (TYPE) – Description

• SeqHep2 (TYPE) – Description

• fname (TYPE) – Description

Returns

Description

Return type

TYPE

check_heptad_repeat(hep)

Summary

Parameters

hep (TYPE) – Description

Returns

Description

Return type

TYPE

load_paircoil_alignment(pc_file)

Summary

Parameters

pc_file (TYPE) – Description

Returns

Description

Return type

TYPE

coconut.src.Core.ml_prediction module

Summary

coconut.src.Core.ml_prediction.load_dataset(fname)

Summary

Parameters

fname (TYPE) – Description

Returns

Description

Return type

TYPE

coconut.src.Core.ml_prediction.pred_round(X)

Summary

Parameters

X (TYPE) – Description

Returns

Description

Return type

TYPE

coconut.src.Core.ml_prediction.train_RF_models(CCDDIR, CCNETDIR, CCPLOTDIR, DIMERS, KFold_CV=10)

Summary

Parameters

• CCDDIR (TYPE) – Description

• CCNETDIR (TYPE) – Description

• CCPLOTDIR (TYPE) – Description

• DIMERS (TYPE) – Description

• KFold_CV (TYPE) – Description

Returns

Description

Return type

TYPE

coconut.src.Core.ml_prediction.train_RF_models_plot(CCDDIR, CCNETDIR, CCPLOTDIR, DIMERS, model_obj)

Summary

Parameters

• CCDDIR (TYPE) – Description

• CCNETDIR (TYPE) – Description

• CCPLOTDIR (TYPE) – Description

• DIMERS (TYPE) – Description

• model_obj (TYPE) – Description

Returns

Description

Return type

TYPE

coconut.src.Core.ml_prediction.train_bayesian_models(CCDDIR, CCNETDIR, CCPLOTDIR, DIMERS)

Summary

Parameters

• CCDDIR (TYPE) – Description

• CCNETDIR (TYPE) – Description

• CCPLOTDIR (TYPE) – Description

• DIMERS (TYPE) – Description

Returns

Description

Return type

TYPE

coconut.src.Core.predict_cc module

coconut.src.Core.predict_cc.predict_coiled_coil(argv='')

coconut.src.Core.read_CC_properties module

coconut.src.Core.read_CC_properties.check_heptad_repeat(hep)

Summary

Parameters

hep (TYPE) – Description

Returns

Description

Return type

TYPE

coconut.src.Core.read_CC_properties.generate_AA_pairs_antiparallel_dimers(key, v, Res_stats)

Summary

Parameters

• key (TYPE) – Description

• v (TYPE) – Description

• Res_stats (TYPE) – Description

Returns

Description

Return type

TYPE

coconut.src.Core.read_CC_properties.generate_AA_pairs_frequency(dimers)

Summary

Parameters

dimers (TYPE) – Description

Returns

Description

Return type

TYPE

coconut.src.Core.read_CC_properties.generate_AA_pairs_parallel_dimers(key, v, Res_stats)

Summary

Parameters

• key (TYPE) – Description

• v (TYPE) – Description

• Res_stats (TYPE) – Description

Returns

Description

Return type

TYPE

coconut.src.Core.read_CC_properties.generate_Hex_pairs_antiparallel_dimers(key, v)

Summary

Parameters

• key (TYPE) – Description

• v (TYPE) – Description

Returns

Description

Return type

TYPE

coconut.src.Core.read_CC_properties.generate_Hex_pairs_dimers(dimers)

Summary

Parameters

dimers (TYPE) – Description

Returns

Description

Return type

TYPE

coconut.src.Core.read_CC_properties.generate_Hex_pairs_parallel_dimers(key, v)

Summary

Parameters

• key (TYPE) – Description

• v (TYPE) – Description

Returns

Description

Return type

TYPE

coconut.src.Core.read_CC_properties.max_normalize_dicts(Res_stats)

Summary

Parameters

Res_stats (TYPE) – Description

Returns

Description

Return type

TYPE

coconut.src.Core.read_CC_properties.shifting_align_dimer(value)

Summary

Parameters

value (TYPE) – Description

Returns

Description

Return type

TYPE

coconut.src.Core.read_CC_properties.total_normalize_dicts(Res_stats)

Summary

Parameters

Res_stats (TYPE) – Description

Returns

Description

Return type

TYPE

coconut.src.Core.read_CC_properties.write_unique_hexpairs(Realdimers)

Summary

Parameters

Realdimers (TYPE) – Description

Returns

Description

Return type

TYPE

coconut.src.Core.read_frequency_scores module

coconut.src.Core.read_frequency_scores.load_AA_Frequency_scores(fname)

Summary

Parameters

fname (TYPE) – Description

Returns

Description

Return type

TYPE

coconut.src.Core.read_frequency_scores.load_AA_Frequency_scores_logs(fname)

Summary

Parameters

fname (TYPE) – Description

Returns

Description

Return type

TYPE

coconut.src.Core.test_model_database module

coconut.src.Core.test_model_database.test_model()

Summary

Returns

Description

Return type

TYPE

coconut.src.Core.train_models module

coconut.src.Core.train_models.bin_values(values, num_bins)

Summary

Parameters

• values (TYPE) – Description

• num_bins (TYPE) – Description

Returns

Description

Return type

TYPE

coconut.src.Core.train_models.calculate_feature_values(dodecp)

Summary

Parameters

dodecp (TYPE) – Description

Returns

Description

Return type

TYPE

coconut.src.Core.train_models.check_distribution_pval(pval, CI)

Summary

Parameters

• pval (TYPE) – Description

• CI (TYPE) – Description

Returns

Description

Return type

TYPE

coconut.src.Core.train_models.check_heptad_repeat(hep)

Summary

Parameters

hep (TYPE) – Description

Returns

Description

Return type

TYPE

coconut.src.Core.train_models.dump_frequency_models(DISTDIR, Res_stats)

Summary

Parameters

• DISTDIR (TYPE) – Description

• Res_stats (TYPE) – Description

Returns

Description

Return type

TYPE

coconut.src.Core.train_models.filter_dimer(dimers, min_length_cutoff, max_length_cutoff)

Summary

Parameters

• dimers (TYPE) – Description

• min_length_cutoff (TYPE) – Description

• max_length_cutoff (TYPE) – Description

Returns

Description

Return type

TYPE

coconut.src.Core.train_models.generate_dodec_pairs(MODDIR, dimers)

Summary

Parameters

• MODDIR (TYPE) – Description

• dimers (TYPE) – Description

Returns

Description

Return type

TYPE

coconut.src.Core.train_models.get_BS(value)

Summary

Parameters

value (TYPE) – Description

Returns

Description

Return type

TYPE

coconut.src.Core.train_models.get_kerneldensity(atomdensity, fcolor=None, PlotData=True)

Summary

Parameters

• atomdensity (TYPE) – Description

• fcolor (None, optional) – Description

• PlotData (bool, optional) – Description

Returns

Description

Return type

TYPE

coconut.src.Core.train_models.load_training_data(CCDDIR)

Summary

Parameters

CCDDIR (TYPE) – Description

Returns

Description

Return type

TYPE

coconut.src.Core.train_models.load_training_data_singlefile(CCDDIR, skip_filtering=False)

Summary

Parameters

CCDDIR (TYPE) – Description

Returns

Description

Return type

TYPE

coconut.src.Core.train_models.read_cc_file(fname, redundancy_cutoff, alignment, skip_redundancy_check=False)

Summary

Parameters

• fname (TYPE) – Description

• redundancy_cutoff (TYPE) – Description

• alignment (TYPE) – Description

Returns

Description

Return type

TYPE

coconut.src.Core.train_models.read_dodec_pairs(fname)

Summary

Parameters

fname (TYPE) – Description

Returns

Description

Return type

TYPE

coconut.src.Core.train_models.train_kde_models(DODEC_DIR, ESTM_DIR, PLOT_DIR, PlotData=True)

Summary

Parameters

• DODEC_DIR (TYPE) – Description

• ESTM_DIR (TYPE) – Description

• PLOT_DIR (TYPE) – Description

• PlotData (bool, optional) – Description

Returns

Description

Return type

TYPE

coconut.src.Core.train_models.write_dict(Res_pairs, fname)

Summary

Parameters

• Res_pairs (TYPE) – Description

• fname (TYPE) – Description

Returns

Description

Return type

TYPE

Module contents