Index

A

add_alignment_scores_segmentdict() (coconut.src.Core.CoiledCoilAlignClass.CoiledCoilAlign method) add_sequence_at_cterm() (coconut.src.Core.CoiledCoilAlignClass.CoiledCoilAlign method) add_sequence_with_gaps() (coconut.src.Core.CoiledCoilAlignClass.CoiledCoilAlign method)

ALLPROBS (coconut.src.Core.ScoringClass.ScoreCC attribute) ALLSCORES (coconut.src.Core.ScoringClass.ScoreCC attribute) AP_Prior_Prob (coconut.src.Core.ScoringClass.ScoreCC attribute) AP_Prior_Prob_dimer (coconut.src.Core.ScoringClass.ScoreCC attribute)

B

BaseAlignmentFile (coconut.src.Core.CoiledCoilAlignClass.CoiledCoilAlign attribute) BaseScoresAlign (class in coconut.src.Core.BaseScores)

bin_values() (in module coconut.src.Core.train_models) branching_dict (coconut.src.Core.ScoringClass.ScoreCC attribute)

C

calculate_feature_values() (in module coconut.src.Core.train_models) calculate_prior_probabilities() (coconut.src.Core.ScoringClass.ScoreCC method) CC (coconut.src.Core.CoiledCoilClass.CoiledCoil attribute) check_aa_hep() (coconut.src.Core.InputClass.InputCC method) check_aa_seq() (coconut.src.Core.InputClass.InputCC method) check_distribution_pval() (in module coconut.src.Core.train_models) check_heptad_repeat() (coconut.src.Core.SlidingWindowsClass.SlidingWindows method) (in module coconut.src.Core.read_CC_properties) (in module coconut.src.Core.train_models) check_inp_len() (coconut.src.Core.InputClass.InputCC method) coconut module COCONUT (class in coconut.src.CoconutClass) coconut.example module coconut.Externals module coconut.src module coconut.src.CoconutClass module coconut.src.Core module coconut.src.Core.BaseScores module coconut.src.Core.CoiledCoilAlignClass module coconut.src.Core.CoiledCoilClass module coconut.src.Core.ExtendCCClass module coconut.src.Core.InputClass module

coconut.src.Core.ml_prediction module coconut.src.Core.PairCoilClass module coconut.src.Core.predict_cc module coconut.src.Core.read_CC_properties module coconut.src.Core.read_frequency_scores module coconut.src.Core.ScoringClass module coconut.src.Core.SlidingWindowsClass module coconut.src.Core.test_model_database module coconut.src.Core.train_models module coconut.src.Models module coconut.src.Models.ModelClass module coconut.version module coconut_align() (coconut.src.Core.CoiledCoilAlignClass.CoiledCoilAlign method) CoiledCoil (class in coconut.src.Core.CoiledCoilClass) CoiledCoilAlign (class in coconut.src.Core.CoiledCoilAlignClass) constant_score (coconut.src.Core.CoiledCoilAlignClass.CoiledCoilAlign attribute) correct_incorrectly_Indentified_heptad() (coconut.src.Core.PairCoilClass.PairCoilParse method) correct_P_AP_compatibility() (coconut.src.Core.InputClass.InputCC method) create_base_alignment() (coconut.src.Core.CoiledCoilAlignClass.CoiledCoilAlign method)

D

D_PREDS (coconut.src.Core.ScoringClass.ScoreCC attribute) D_PROBS (coconut.src.Core.ScoringClass.ScoreCC attribute) D_PROBS_mean (coconut.src.Core.ScoringClass.ScoreCC attribute) def_value() (coconut.src.Core.ExtendCCClass.ExtendCoiledCoil method) DefaultDictNoAdd (class in coconut.src.Core.CoiledCoilAlignClass) (class in coconut.src.Core.ExtendCCClass) (class in coconut.src.Core.PairCoilClass) (class in coconut.src.Core.SlidingWindowsClass)

display_CC() (coconut.src.Core.CoiledCoilClass.CoiledCoil method) DistDict (coconut.src.Core.ExtendCCClass.ExtendCoiledCoil attribute) DistMat (coconut.src.Core.ExtendCCClass.ExtendCoiledCoil attribute) Distributions (coconut.src.Core.ScoringClass.ScoreCC attribute) dump_frequency_models() (in module coconut.src.Core.train_models)

E

extend_segment() (coconut.src.Core.ExtendCCClass.ExtendCoiledCoil method)

ExtendCoiledCoil (class in coconut.src.Core.ExtendCCClass)

F

filter_dimer() (in module coconut.src.Core.train_models) Filter_OffDiagonal_Segments() (coconut.src.Core.CoiledCoilAlignClass.CoiledCoilAlign method) find_score_ada_ada() (coconut.src.Core.ScoringClass.ScoreCC method) find_score_ada_dad() (coconut.src.Core.ScoringClass.ScoreCC method)

find_score_dad_ada() (coconut.src.Core.ScoringClass.ScoreCC method) find_score_dad_dad() (coconut.src.Core.ScoringClass.ScoreCC method) fsseq1 (coconut.src.Core.CoiledCoilAlignClass.CoiledCoilAlign attribute) fsseq2 (coconut.src.Core.CoiledCoilAlignClass.CoiledCoilAlign attribute)

G

generate_AA_pairs_antiparallel_dimers() (in module coconut.src.Core.read_CC_properties) generate_AA_pairs_frequency() (in module coconut.src.Core.read_CC_properties) generate_AA_pairs_parallel_dimers() (in module coconut.src.Core.read_CC_properties) Generate_Alignments_Scores() (coconut.src.Core.ExtendCCClass.ExtendCoiledCoil method) Generate_CC_Bayesian_Scores() (coconut.src.Core.ScoringClass.ScoreCC method) Generate_CC_RF_Scores() (coconut.src.Core.ScoringClass.ScoreCC method) Generate_CC_Scores_Bayes() (coconut.src.Core.ScoringClass.ScoreCC method) Generate_CC_Scores_RF() (coconut.src.Core.ScoringClass.ScoreCC method) generate_dodec_pairs() (in module coconut.src.Core.train_models) generate_Hex_pairs_antiparallel_dimers() (in module coconut.src.Core.read_CC_properties) generate_Hex_pairs_dimers() (in module coconut.src.Core.read_CC_properties) generate_Hex_pairs_parallel_dimers() (in module coconut.src.Core.read_CC_properties) get_BS() (coconut.src.Core.ScoringClass.ScoreCC method) (in module coconut.src.Core.train_models) get_CC() (coconut.src.Core.CoiledCoilClass.CoiledCoil method) get_cc_orientation() (coconut.src.Core.InputClass.InputCC method) get_Distributions() (coconut.src.Core.ScoringClass.ScoreCC method)

get_hamming_distances() (coconut.src.Core.CoiledCoilAlignClass.CoiledCoilAlign method) get_heptad_repeats_pairs() (coconut.src.Core.PairCoilClass.PairCoilParse method) get_KDE_Models() (coconut.src.Models.ModelClass.Models method) get_kerneldensity() (in module coconut.src.Core.train_models) get_next_segment_lists() (coconut.src.Core.CoiledCoilAlignClass.CoiledCoilAlign method) get_num_monomers() (coconut.src.Core.CoiledCoilClass.CoiledCoil method) get_padding_size() (coconut.src.Models.ModelClass.Models method) get_parallel_diagonal_alignment() (coconut.src.Core.ExtendCCClass.ExtendCoiledCoil method) get_pc_seq() (coconut.src.Core.PairCoilClass.PairCoilParse method) Get_Prediction_Probs() (coconut.src.Core.ScoringClass.ScoreCC method) Get_Predictions() (coconut.src.Core.ScoringClass.ScoreCC method) get_RF_Models() (coconut.src.Models.ModelClass.Models method) get_scoremat() (coconut.src.Core.BaseScores.BaseScoresAlign method) get_scoring_dicts() (coconut.src.Models.ModelClass.Models method) Get_Sliding_Windows() (coconut.src.Core.SlidingWindowsClass.SlidingWindows method) get_tracepath_alignments() (coconut.src.Core.CoiledCoilAlignClass.CoiledCoilAlign method) get_tracepath_alignments_fullseq() (coconut.src.Core.CoiledCoilAlignClass.CoiledCoilAlign method)

H

hamming_distance() (coconut.src.Core.PairCoilClass.PairCoilParse method)

header (coconut.src.Core.PairCoilClass.PairCoilParse attribute) Hexscores (coconut.src.Models.ModelClass.Models attribute)

I

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

interface_dict (coconut.src.Core.InputClass.InputCC attribute) inverse() (coconut.src.CoconutClass.MidpointNormalize method)

K

k_shortest_paths() (coconut.src.Core.CoiledCoilAlignClass.CoiledCoilAlign method)

L

load_AA_distributions() (coconut.src.Models.ModelClass.Models method) load_AA_Frequency_scores() (in module coconut.src.Core.read_frequency_scores) load_AA_Frequency_scores_logs() (in module coconut.src.Core.read_frequency_scores) load_CCData() (coconut.src.Core.InputClass.InputCC method) load_Coiled_Coil_Segments_full() (coconut.src.Core.CoiledCoilAlignClass.CoiledCoilAlign method) load_dataset() (in module coconut.src.Core.ml_prediction) load_kde_models() (coconut.src.Models.ModelClass.Models method) load_paircoil_alignment() (coconut.src.Core.CoiledCoilAlignClass.CoiledCoilAlign method) (coconut.src.Core.ExtendCCClass.ExtendCoiledCoil method) (coconut.src.Core.PairCoilClass.PairCoilParse method) (coconut.src.Core.SlidingWindowsClass.SlidingWindows method)

load_Pcoil_alignment() (coconut.src.Core.PairCoilClass.PairCoilParse method) load_Pcoil_alignment_backup() (coconut.src.Core.PairCoilClass.PairCoilParse method) load_prior_probabilities() (coconut.src.Core.ScoringClass.ScoreCC method) load_RF_models() (coconut.src.Models.ModelClass.Models method) load_training_data() (in module coconut.src.Core.train_models) load_training_data_singlefile() (in module coconut.src.Core.train_models)

M

max_normalize_dicts() (in module coconut.src.Core.read_CC_properties) MidpointNormalize (class in coconut.src.CoconutClass) Models (class in coconut.src.Models.ModelClass) module coconut coconut.example coconut.Externals coconut.src coconut.src.CoconutClass coconut.src.Core coconut.src.Core.BaseScores coconut.src.Core.CoiledCoilAlignClass coconut.src.Core.CoiledCoilClass coconut.src.Core.ExtendCCClass coconut.src.Core.InputClass coconut.src.Core.ml_prediction coconut.src.Core.PairCoilClass coconut.src.Core.predict_cc coconut.src.Core.read_CC_properties coconut.src.Core.read_frequency_scores coconut.src.Core.ScoringClass coconut.src.Core.SlidingWindowsClass coconut.src.Core.test_model_database coconut.src.Core.train_models coconut.src.Models coconut.src.Models.ModelClass coconut.version

N

num_monomers (coconut.src.Core.InputClass.InputCC attribute)

P

p1_PC (coconut.src.Core.ExtendCCClass.ExtendCoiledCoil attribute) (coconut.src.Core.PairCoilClass.PairCoilParse attribute) p2_PC (coconut.src.Core.ExtendCCClass.ExtendCoiledCoil attribute) P_Prior_Prob (coconut.src.Core.ScoringClass.ScoreCC attribute) P_Prior_Prob_dimer (coconut.src.Core.ScoringClass.ScoreCC attribute) PairCoilParse (class in coconut.src.Core.PairCoilClass) pc_prot1_file (coconut.src.Core.CoiledCoilAlignClass.CoiledCoilAlign attribute) (coconut.src.Core.ExtendCCClass.ExtendCoiledCoil attribute) (coconut.src.Core.PairCoilClass.PairCoilParse attribute) (coconut.src.Core.SlidingWindowsClass.SlidingWindows attribute) pc_prot2_file (coconut.src.Core.CoiledCoilAlignClass.CoiledCoilAlign attribute) (coconut.src.Core.ExtendCCClass.ExtendCoiledCoil attribute) (coconut.src.Core.SlidingWindowsClass.SlidingWindows attribute) phep1 (coconut.src.Core.ExtendCCClass.ExtendCoiledCoil attribute) (coconut.src.Core.PairCoilClass.PairCoilParse attribute) phep2 (coconut.src.Core.ExtendCCClass.ExtendCoiledCoil attribute) (coconut.src.Core.PairCoilClass.PairCoilParse attribute) plot_alignment() (coconut.src.Core.ExtendCCClass.ExtendCoiledCoil method) plot_alignment_segments() (coconut.src.Core.CoiledCoilAlignClass.CoiledCoilAlign method) plot_dimer_length_distribution() (coconut.src.CoconutClass.COCONUT method) plot_individual_cc_scores() (coconut.src.Core.ExtendCCClass.ExtendCoiledCoil method) plot_KDE_Models() (coconut.src.Models.ModelClass.Models method) plot_pairwise_distributions() (coconut.src.CoconutClass.COCONUT method) plot_segments() (coconut.src.Core.CoiledCoilAlignClass.CoiledCoilAlign method)

plot_tree() (coconut.src.Core.CoiledCoilAlignClass.CoiledCoilAlign method) plot_tree_simple() (coconut.src.Core.CoiledCoilAlignClass.CoiledCoilAlign method) ppath (coconut.src.Core.CoiledCoilAlignClass.CoiledCoilAlign attribute) (coconut.src.Core.ExtendCCClass.ExtendCoiledCoil attribute) pred_round() (in module coconut.src.Core.ml_prediction) Predict_CC_Stability() (coconut.src.Core.ScoringClass.ScoreCC method) predict_coiled_coil() (coconut.src.CoconutClass.COCONUT method) (in module coconut.src.Core.predict_cc) prediction_example() (coconut.src.CoconutClass.COCONUT method) print_input_info() (coconut.src.Core.InputClass.InputCC method) PROB_CUTOFF (coconut.src.Core.CoiledCoilAlignClass.CoiledCoilAlign attribute) (coconut.src.Core.ExtendCCClass.ExtendCoiledCoil attribute) (coconut.src.Core.PairCoilClass.PairCoilParse attribute) (coconut.src.Core.SlidingWindowsClass.SlidingWindows attribute) prot1 (coconut.src.Core.CoiledCoilAlignClass.CoiledCoilAlign attribute) (coconut.src.Core.ExtendCCClass.ExtendCoiledCoil attribute) prot1_max (coconut.src.Core.ExtendCCClass.ExtendCoiledCoil attribute) prot1_min (coconut.src.Core.ExtendCCClass.ExtendCoiledCoil attribute) prot1_seq (coconut.src.Core.SlidingWindowsClass.SlidingWindows attribute) prot1res (coconut.src.Core.ExtendCCClass.ExtendCoiledCoil attribute) prot2 (coconut.src.Core.CoiledCoilAlignClass.CoiledCoilAlign attribute) (coconut.src.Core.ExtendCCClass.ExtendCoiledCoil attribute) prot2_max (coconut.src.Core.ExtendCCClass.ExtendCoiledCoil attribute) prot2_min (coconut.src.Core.ExtendCCClass.ExtendCoiledCoil attribute) prot2_seq (coconut.src.Core.SlidingWindowsClass.SlidingWindows attribute)

R

raise_error() (coconut.src.Core.InputClass.InputCC method) read_aligned_fasta() (coconut.src.Core.CoiledCoilAlignClass.CoiledCoilAlign method) read_cc_file() (in module coconut.src.Core.train_models) read_coco_alignment_graph() (coconut.src.Core.CoiledCoilAlignClass.CoiledCoilAlign method) read_coco_alignment_graph_new() (coconut.src.Core.CoiledCoilAlignClass.CoiledCoilAlign method)

read_dodec_pairs() (in module coconut.src.Core.train_models) read_fasta() (coconut.src.Core.CoiledCoilAlignClass.CoiledCoilAlign method) read_matrix_file() (coconut.src.Core.BaseScores.BaseScoresAlign method) RF_Models (coconut.src.Models.ModelClass.Models attribute) RF_PaddingSize (coconut.src.Models.ModelClass.Models attribute)

S

Sample_Plot_Combine() (coconut.src.Core.ExtendCCClass.ExtendCoiledCoil method) Score_Coiled_coil() (coconut.src.Core.ScoringClass.ScoreCC method) score_dimer_bayesian() (coconut.src.Core.ScoringClass.ScoreCC method) score_dimer_RF() (coconut.src.Core.ScoringClass.ScoreCC method) ScoreCC (class in coconut.src.Core.ScoringClass) scoremat (coconut.src.Core.BaseScores.BaseScoresAlign attribute) scoring_dicts (coconut.src.Models.ModelClass.Models attribute) segment_traceback() (coconut.src.Core.CoiledCoilAlignClass.CoiledCoilAlign method)

set_CC_orientation() (coconut.src.Core.CoiledCoilClass.CoiledCoil method) set_CC_values() (coconut.src.Core.CoiledCoilClass.CoiledCoil method) shifting_align_dimer() (in module coconut.src.Core.read_CC_properties) SlidingWindows (class in coconut.src.Core.SlidingWindowsClass) sw_file_a (coconut.src.Core.SlidingWindowsClass.SlidingWindows attribute) sw_file_d (coconut.src.Core.SlidingWindowsClass.SlidingWindows attribute) swlen (coconut.src.Core.SlidingWindowsClass.SlidingWindows attribute) swlen_d (coconut.src.Core.SlidingWindowsClass.SlidingWindows attribute)

T

test_coconut_models() (coconut.src.CoconutClass.COCONUT method) test_model() (in module coconut.src.Core.test_model_database) topk (coconut.src.Core.CoiledCoilAlignClass.CoiledCoilAlign attribute) total_normalize_dicts() (in module coconut.src.Core.read_CC_properties)

train_bayesian_models() (in module coconut.src.Core.ml_prediction) train_coconut_models() (coconut.src.CoconutClass.COCONUT method) train_kde_models() (in module coconut.src.Core.train_models) train_RF_models() (in module coconut.src.Core.ml_prediction) train_RF_models_plot() (in module coconut.src.Core.ml_prediction)

V

valid_aas (coconut.src.Core.InputClass.InputCC attribute)

valid_hep (coconut.src.Core.InputClass.InputCC attribute) vcenter (coconut.src.CoconutClass.MidpointNormalize attribute)

W

write_alignment() (coconut.src.Core.CoiledCoilAlignClass.CoiledCoilAlign method) write_alignment_with_heptad() (coconut.src.Core.CoiledCoilAlignClass.CoiledCoilAlign method) Write_Bayesian_Probabilities() (coconut.src.Core.ScoringClass.ScoreCC method) Write_CC_InputFile() (coconut.src.Core.SlidingWindowsClass.SlidingWindows method)

write_dict() (in module coconut.src.Core.train_models) Write_Raw_Scores() (coconut.src.Core.ScoringClass.ScoreCC method) Write_Topn_Alignments() (coconut.src.Core.CoiledCoilAlignClass.CoiledCoilAlign method) write_unique_hexpairs() (in module coconut.src.Core.read_CC_properties) write_Updated_Paircoil_Probs() (coconut.src.Core.PairCoilClass.PairCoilParse method)