Index

_

__init__() (mdciao.contacts.ContactGroup method) (mdciao.contacts.ContactPair method) (mdciao.contacts.GroupOfInterfaces method) (mdciao.contacts.Residues method) (mdciao.nomenclature.AlignerConsensus method) (mdciao.nomenclature.LabelerCGN method) (mdciao.nomenclature.LabelerConsensus method) (mdciao.nomenclature.LabelerGPCR method) (mdciao.nomenclature.LabelerKLIFS method) (mdciao.nomenclature.Literature method)

A

AA2conlab (mdciao.nomenclature.LabelerCGN property) (mdciao.nomenclature.LabelerConsensus property) (mdciao.nomenclature.LabelerGPCR property) (mdciao.nomenclature.LabelerKLIFS property) AAresSeq (mdciao.nomenclature.AlignerConsensus property) AAresSeq_match() (mdciao.nomenclature.AlignerConsensus method) AAtype() (in module mdciao.utils.residue_and_atom), [1] abs() (mdciao.utils.sequence.AlignmentDataFrame method), [1] add() (mdciao.utils.sequence.AlignmentDataFrame method), [1] add_bezier_curves() (in module mdciao.flare) add_fragment_labels() (in module mdciao.flare) add_prefix() (mdciao.utils.sequence.AlignmentDataFrame method), [1] add_suffix() (mdciao.utils.sequence.AlignmentDataFrame method), [1] agg() (mdciao.utils.sequence.AlignmentDataFrame method), [1] aggregate() (mdciao.utils.sequence.AlignmentDataFrame method), [1] align() (mdciao.utils.sequence.AlignmentDataFrame method), [1] align_tops_or_seqs() (in module mdciao.utils.sequence), [1] AlignerConsensus (class in mdciao.nomenclature) alignment_result_to_list_of_dicts() (in module mdciao.utils.sequence), [1] AlignmentDataFrame (class in mdciao.utils.sequence), [1] aligntop() (mdciao.nomenclature.LabelerCGN method) (mdciao.nomenclature.LabelerConsensus method) (mdciao.nomenclature.LabelerGPCR method) (mdciao.nomenclature.LabelerKLIFS method)

all() (mdciao.utils.sequence.AlignmentDataFrame method), [1] anchor_fragment_color (mdciao.contacts.ContactGroup property) anchor_index (mdciao.contacts.Residues property) anchor_res_and_fragment_str (mdciao.contacts.ContactGroup property) anchor_res_and_fragment_str_short (mdciao.contacts.ContactGroup property) anchor_residue (mdciao.contacts.Residues property) anchor_residue_index (mdciao.contacts.Residues property) any() (mdciao.utils.sequence.AlignmentDataFrame method), [1] apply() (mdciao.utils.sequence.AlignmentDataFrame method), [1] applymap() (mdciao.utils.sequence.AlignmentDataFrame method), [1] archive() (mdciao.contacts.ContactGroup method) asfreq() (mdciao.utils.sequence.AlignmentDataFrame method), [1] asof() (mdciao.utils.sequence.AlignmentDataFrame method), [1] assert_min_len() (in module mdciao.utils.lists), [1] assert_no_intersection() (in module mdciao.utils.lists), [1] assign() (mdciao.utils.sequence.AlignmentDataFrame method), [1] assign_fragments() (in module mdciao.fragments) astype() (mdciao.utils.sequence.AlignmentDataFrame method), [1] at (mdciao.utils.sequence.AlignmentDataFrame property), [1] at_time() (mdciao.utils.sequence.AlignmentDataFrame method), [1] atom_type() (in module mdciao.utils.residue_and_atom), [1] attrs (mdciao.utils.sequence.AlignmentDataFrame property), [1] average_freq_dict() (in module mdciao.utils.str_and_dict), [1] axes (mdciao.utils.sequence.AlignmentDataFrame property), [1]

B

backfill() (mdciao.utils.sequence.AlignmentDataFrame method), [1] between_time() (mdciao.utils.sequence.AlignmentDataFrame method), [1] bfill() (mdciao.utils.sequence.AlignmentDataFrame method), [1] binarize_trajs() (mdciao.contacts.ContactGroup method) (mdciao.contacts.ContactPair method)

bonded_neighborlist_from_top() (in module mdciao.utils.bonds), [1] bool() (mdciao.utils.sequence.AlignmentDataFrame method), [1] boxplot() (mdciao.utils.sequence.AlignmentDataFrame method), [1]

C

CAidxs (mdciao.nomenclature.AlignerConsensus property) CAidxs_match() (mdciao.nomenclature.AlignerConsensus method) CGNLabeler_gnas2_human() (in module mdciao.examples) choose_options_descencing() (in module mdciao.utils.str_and_dict), [1] circle_plot_residues() (in module mdciao.flare) clip() (mdciao.utils.sequence.AlignmentDataFrame method), [1] color_dict_guesser() (in module mdciao.plots) columns (mdciao.utils.sequence.AlignmentDataFrame attribute), [1] combine() (mdciao.utils.sequence.AlignmentDataFrame method), [1] combine_first() (mdciao.utils.sequence.AlignmentDataFrame method), [1] compare() (in module mdciao.cli) (mdciao.contacts.GroupOfInterfaces method) (mdciao.utils.sequence.AlignmentDataFrame method), [1] compare_groups_of_contacts() (in module mdciao.plots) compare_violins() (in module mdciao.plots) conlab2AA (mdciao.nomenclature.LabelerCGN property) (mdciao.nomenclature.LabelerConsensus property) (mdciao.nomenclature.LabelerGPCR property) (mdciao.nomenclature.LabelerKLIFS property) conlab2idx (mdciao.nomenclature.LabelerCGN property) (mdciao.nomenclature.LabelerConsensus property) (mdciao.nomenclature.LabelerGPCR property) (mdciao.nomenclature.LabelerKLIFS property) conlab2matidx (mdciao.contacts.GroupOfInterfaces property) conlab2residx() (mdciao.nomenclature.LabelerCGN method) (mdciao.nomenclature.LabelerConsensus method) (mdciao.nomenclature.LabelerGPCR method) (mdciao.nomenclature.LabelerKLIFS method)

conlabs2confrags() (in module mdciao.nomenclature) connected_sets() (in module mdciao.utils.bonds), [1] consensus_labels (mdciao.contacts.ContactGroup property) (mdciao.contacts.Residues property) consensuslabel2resname (mdciao.contacts.ContactGroup property) contact_matrix() (in module mdciao.utils.contact_matrix), [1] contact_matrix_slim() (in module mdciao.utils.contact_matrix), [1] contact_pairs (mdciao.contacts.ContactGroup property) ContactGroup (class in mdciao.contacts) ContactGroupL394() (in module mdciao.examples) ContactPair (class in mdciao.contacts) contiguous_ranges() (in module mdciao.utils.lists), [1] convert_dtypes() (mdciao.utils.sequence.AlignmentDataFrame method), [1] copy() (mdciao.contacts.ContactGroup method) (mdciao.contacts.ContactPair method) (mdciao.utils.sequence.AlignmentDataFrame method), [1] corr() (mdciao.utils.sequence.AlignmentDataFrame method), [1] corrwith() (mdciao.utils.sequence.AlignmentDataFrame method), [1] count() (mdciao.utils.sequence.AlignmentDataFrame method), [1] count_formed_atom_pairs() (mdciao.contacts.ContactPair method) cov() (mdciao.utils.sequence.AlignmentDataFrame method), [1] ctc_labels (mdciao.contacts.ContactGroup property) ctc_labels_short (mdciao.contacts.ContactGroup property) ctc_labels_w_fragments_short_AA (mdciao.contacts.ContactGroup property) cummax() (mdciao.utils.sequence.AlignmentDataFrame method), [1] cummin() (mdciao.utils.sequence.AlignmentDataFrame method), [1] cumprod() (mdciao.utils.sequence.AlignmentDataFrame method), [1] cumsum() (mdciao.utils.sequence.AlignmentDataFrame method), [1]

D

dataframe (mdciao.nomenclature.LabelerCGN property) (mdciao.nomenclature.LabelerConsensus property) (mdciao.nomenclature.LabelerGPCR property) (mdciao.nomenclature.LabelerKLIFS property) defrag_key() (in module mdciao.utils.str_and_dict), [1] delete_exp_in_keys() (in module mdciao.utils.str_and_dict), [1] describe() (mdciao.utils.sequence.AlignmentDataFrame method), [1] df2maps() (in module mdciao.utils.sequence), [1] df_str_formatters() (in module mdciao.utils.str_and_dict), [1] diff() (mdciao.utils.sequence.AlignmentDataFrame method), [1] distribution_dicts() (mdciao.contacts.ContactGroup method)

distro_overall_trajs() (mdciao.contacts.ContactPair method) div() (mdciao.utils.sequence.AlignmentDataFrame method), [1] divide() (mdciao.utils.sequence.AlignmentDataFrame method), [1] does_not_contain_strings() (in module mdciao.utils.lists), [1] dot() (mdciao.utils.sequence.AlignmentDataFrame method), [1] drop() (mdciao.utils.sequence.AlignmentDataFrame method), [1] drop_duplicates() (mdciao.utils.sequence.AlignmentDataFrame method), [1] droplevel() (mdciao.utils.sequence.AlignmentDataFrame method), [1] dropna() (mdciao.utils.sequence.AlignmentDataFrame method), [1] dtypes (mdciao.utils.sequence.AlignmentDataFrame property), [1] duplicated() (mdciao.utils.sequence.AlignmentDataFrame method), [1]

E

empty (mdciao.utils.sequence.AlignmentDataFrame property), [1] eq() (mdciao.utils.sequence.AlignmentDataFrame method), [1] equals() (mdciao.utils.sequence.AlignmentDataFrame method), [1] eval() (mdciao.utils.sequence.AlignmentDataFrame method), [1]

ewm() (mdciao.utils.sequence.AlignmentDataFrame method), [1] exclude_same_fragments_from_residx_pairlist() (in module mdciao.utils.lists), [1] expanding() (mdciao.utils.sequence.AlignmentDataFrame method), [1] explode() (mdciao.utils.sequence.AlignmentDataFrame method), [1]

F

fetch_example_data() (in module mdciao.examples) ffill() (mdciao.utils.sequence.AlignmentDataFrame method), [1] FilenameGenerator (class in mdciao.utils.str_and_dict), [1] filenames (in module mdciao.examples) fillna() (mdciao.utils.sequence.AlignmentDataFrame method), [1] filter() (mdciao.utils.sequence.AlignmentDataFrame method), [1] find_AA() (in module mdciao.utils.residue_and_atom), [1] find_CA() (in module mdciao.utils.residue_and_atom), [1] find_parent_list() (in module mdciao.utils.lists), [1] first() (mdciao.utils.sequence.AlignmentDataFrame method), [1] first_valid_index() (mdciao.utils.sequence.AlignmentDataFrame method), [1] flags (mdciao.utils.sequence.AlignmentDataFrame property), [1] floordiv() (mdciao.utils.sequence.AlignmentDataFrame method), [1] fnmatch_ex() (in module mdciao.utils.str_and_dict), [1] force_iterable() (in module mdciao.utils.lists), [1] fragment_names (mdciao.nomenclature.LabelerCGN property) (mdciao.nomenclature.LabelerConsensus property) (mdciao.nomenclature.LabelerGPCR property) (mdciao.nomenclature.LabelerKLIFS property) fragment_names_best (mdciao.contacts.ContactGroup property) fragment_overview() (in module mdciao.cli) fragment_slice() (in module mdciao.fragments) fragments (mdciao.nomenclature.LabelerCGN property) (mdciao.nomenclature.LabelerConsensus property) (mdciao.nomenclature.LabelerGPCR property) (mdciao.nomenclature.LabelerKLIFS property) fragments_as_conlabs (mdciao.nomenclature.LabelerCGN property) (mdciao.nomenclature.LabelerConsensus property) (mdciao.nomenclature.LabelerGPCR property) (mdciao.nomenclature.LabelerKLIFS property)

fragments_as_idxs (mdciao.nomenclature.LabelerCGN property) (mdciao.nomenclature.LabelerGPCR property) (mdciao.nomenclature.LabelerKLIFS property) fragments_as_resSeqs (mdciao.nomenclature.LabelerCGN property) (mdciao.nomenclature.LabelerConsensus property) (mdciao.nomenclature.LabelerGPCR property) (mdciao.nomenclature.LabelerKLIFS property) freq_ascii2dict() (in module mdciao.utils.str_and_dict), [1] freq_file2dict() (in module mdciao.utils.str_and_dict), [1] freqs2chord() (in module mdciao.flare) freqs2flare() (in module mdciao.flare) frequency_as_contact_matrix() (mdciao.contacts.ContactGroup method) frequency_as_contact_matrix_CG() (mdciao.contacts.ContactGroup method) frequency_dataframe() (mdciao.contacts.ContactGroup method) frequency_delta() (mdciao.contacts.ContactGroup method) frequency_dict() (mdciao.contacts.ContactPair method) frequency_dict_by_consensus_labels() (mdciao.contacts.ContactGroup method) frequency_dicts() (mdciao.contacts.ContactGroup method) frequency_overall_trajs() (mdciao.contacts.ContactPair method) frequency_per_contact() (mdciao.contacts.ContactGroup method) frequency_per_traj() (mdciao.contacts.ContactGroup method) (mdciao.contacts.ContactPair method) frequency_spreadsheet() (mdciao.contacts.ContactGroup method) frequency_str_ASCII_file() (mdciao.contacts.ContactGroup method) frequency_sum_per_residue_idx_dict() (mdciao.contacts.ContactGroup method) frequency_sum_per_residue_names() (mdciao.contacts.ContactGroup method) frequency_table() (mdciao.contacts.ContactGroup method) frequency_to_bfactor() (mdciao.contacts.ContactGroup method) from_dict() (mdciao.utils.sequence.AlignmentDataFrame class method), [1] from_records() (mdciao.utils.sequence.AlignmentDataFrame class method), [1]

G

ge() (mdciao.utils.sequence.AlignmentDataFrame method), [1] gen_ctc_labels() (mdciao.contacts.ContactGroup method) gen_label() (mdciao.contacts.ContactPair method) geom2COMdist() (in module mdciao.utils.COM), [1] geom2COMxyz() (in module mdciao.utils.COM), [1] geom2max_residue_radius() (in module mdciao.utils.COM), [1] get() (mdciao.utils.sequence.AlignmentDataFrame method), [1]

get_fragments() (in module mdciao.fragments) get_SS() (in module mdciao.utils.residue_and_atom), [1] get_trajectories_from_input() (in module mdciao.utils.str_and_dict), [1] GPCRLabeler_ardb2_human() (in module mdciao.examples) groupby() (mdciao.utils.sequence.AlignmentDataFrame method), [1] GroupOfInterfaces (class in mdciao.contacts) gt() (mdciao.utils.sequence.AlignmentDataFrame method), [1] guess_by_nomenclature() (in module mdciao.nomenclature)

H

hash_list() (in module mdciao.utils.lists), [1]

head() (mdciao.utils.sequence.AlignmentDataFrame method), [1] hist() (mdciao.utils.sequence.AlignmentDataFrame method), [1]

I

iat (mdciao.utils.sequence.AlignmentDataFrame property), [1] idx2conlab (mdciao.nomenclature.LabelerCGN property) (mdciao.nomenclature.LabelerConsensus property) (mdciao.nomenclature.LabelerGPCR property) (mdciao.nomenclature.LabelerKLIFS property) idx_at_fraction() (in module mdciao.utils.lists), [1] idxmax() (mdciao.utils.sequence.AlignmentDataFrame method), [1] idxmin() (mdciao.utils.sequence.AlignmentDataFrame method), [1] idxs_pair (mdciao.contacts.Residues property) iloc (mdciao.utils.sequence.AlignmentDataFrame property), [1] in_what_fragment() (in module mdciao.utils.lists), [1] in_what_N_fragments() (in module mdciao.utils.lists), [1] index (mdciao.utils.sequence.AlignmentDataFrame attribute), [1] infer_objects() (mdciao.utils.sequence.AlignmentDataFrame method), [1] info() (mdciao.utils.sequence.AlignmentDataFrame method), [1] inform_about_trajectories() (in module mdciao.utils.str_and_dict), [1] insert() (mdciao.utils.sequence.AlignmentDataFrame method), [1] int_from_AA_code() (in module mdciao.utils.residue_and_atom), [1] intblocks_in_str() (in module mdciao.utils.str_and_dict), [1] interface() (in module mdciao.cli) Interface_B2AR_Gas() (in module mdciao.examples)

interface_fragments (mdciao.contacts.ContactGroup property) interface_frequency_dict_by_consensus_labels() (mdciao.contacts.GroupOfInterfaces method) interface_frequency_matrix() (mdciao.contacts.ContactGroup method) interface_labels_consensus (mdciao.contacts.ContactGroup property) (mdciao.contacts.GroupOfInterfaces property) interface_matrix() (mdciao.contacts.GroupOfInterfaces method) interface_names (mdciao.contacts.GroupOfInterfaces property) interface_residue_names_w_best_fragments_short (mdciao.contacts.ContactGroup property) interface_residxs (mdciao.contacts.ContactGroup property) interface_reslabels_short (mdciao.contacts.ContactGroup property) interpolate() (mdciao.utils.sequence.AlignmentDataFrame method), [1] is_interface (mdciao.contacts.ContactGroup property) is_iterable() (in module mdciao.utils.lists), [1] is_neighborhood (mdciao.contacts.ContactGroup property) isetitem() (mdciao.utils.sequence.AlignmentDataFrame method), [1] isin() (mdciao.utils.sequence.AlignmentDataFrame method), [1] isna() (mdciao.utils.sequence.AlignmentDataFrame method), [1] isnull() (mdciao.utils.sequence.AlignmentDataFrame method), [1] items() (mdciao.utils.sequence.AlignmentDataFrame method), [1] iterate_and_inform_lambdas() (in module mdciao.utils.str_and_dict), [1] iterrows() (mdciao.utils.sequence.AlignmentDataFrame method), [1] itertuples() (mdciao.utils.sequence.AlignmentDataFrame method), [1]

J

join() (mdciao.utils.sequence.AlignmentDataFrame method), [1]

join_lists() (in module mdciao.utils.lists), [1]

K

keys (mdciao.nomenclature.AlignerConsensus property) keys() (mdciao.utils.sequence.AlignmentDataFrame method), [1]

KLIFSLabeler_P31751() (in module mdciao.examples) kurt() (mdciao.utils.sequence.AlignmentDataFrame method), [1] kurtosis() (mdciao.utils.sequence.AlignmentDataFrame method), [1]

L

label_flex() (mdciao.contacts.ContactPair method) LabelerCGN (class in mdciao.nomenclature) LabelerConsensus (class in mdciao.nomenclature) LabelerGPCR (class in mdciao.nomenclature) LabelerKLIFS (class in mdciao.nomenclature) last() (mdciao.utils.sequence.AlignmentDataFrame method), [1] last_valid_index() (mdciao.utils.sequence.AlignmentDataFrame method), [1]

latex_mathmode() (in module mdciao.utils.str_and_dict), [1] latex_superscript_fragments() (in module mdciao.utils.str_and_dict), [1] le() (mdciao.utils.sequence.AlignmentDataFrame method), [1] lexsort_ctc_labels() (in module mdciao.utils.str_and_dict), [1] Literature (class in mdciao.nomenclature) loc (mdciao.utils.sequence.AlignmentDataFrame property), [1] lt() (mdciao.utils.sequence.AlignmentDataFrame method), [1]

M

maps (mdciao.nomenclature.AlignerConsensus property) maptops() (in module mdciao.utils.sequence), [1] mask() (mdciao.utils.sequence.AlignmentDataFrame method), [1] match_dict_by_patterns() (in module mdciao.utils.str_and_dict), [1] match_fragments() (in module mdciao.fragments) matching_fragments() (in module mdciao.nomenclature) max() (mdciao.utils.sequence.AlignmentDataFrame method), [1] max_cutoff_Ang (mdciao.contacts.ContactGroup property) maxima (mdciao.contacts.ContactGroup property) mdciao module mdciao.cli module mdciao.contacts module mdciao.examples module mdciao.flare module mdciao.fragments module mdciao.nomenclature module mdciao.pdb module mdciao.plots module mdciao.sites module mdciao.utils module, [1] mdciao.utils.bonds module, [1] mdciao.utils.COM module, [1] mdciao.utils.contact_matrix module, [1] mdciao.utils.lists module, [1] mdciao.utils.residue_and_atom module, [1] mdciao.utils.sequence module, [1]

mdciao.utils.str_and_dict module, [1] mean() (mdciao.utils.sequence.AlignmentDataFrame method), [1] means (mdciao.contacts.ContactGroup property) median() (mdciao.utils.sequence.AlignmentDataFrame method), [1] melt() (mdciao.utils.sequence.AlignmentDataFrame method), [1] memory_usage() (mdciao.utils.sequence.AlignmentDataFrame method), [1] merge() (mdciao.utils.sequence.AlignmentDataFrame method), [1] min() (mdciao.utils.sequence.AlignmentDataFrame method), [1] minima (mdciao.contacts.ContactGroup property) mod() (mdciao.utils.sequence.AlignmentDataFrame method), [1] mode() (mdciao.utils.sequence.AlignmentDataFrame method), [1] modes (mdciao.contacts.ContactGroup property) module mdciao mdciao.cli mdciao.contacts mdciao.examples mdciao.flare mdciao.fragments mdciao.nomenclature mdciao.pdb mdciao.plots mdciao.sites mdciao.utils, [1] mdciao.utils.bonds, [1] mdciao.utils.COM, [1] mdciao.utils.contact_matrix, [1] mdciao.utils.lists, [1] mdciao.utils.residue_and_atom, [1] mdciao.utils.sequence, [1] mdciao.utils.str_and_dict, [1] most_recent_alignment (mdciao.nomenclature.LabelerCGN property) (mdciao.nomenclature.LabelerConsensus property) (mdciao.nomenclature.LabelerGPCR property) (mdciao.nomenclature.LabelerKLIFS property) most_recent_top2labels (mdciao.nomenclature.LabelerCGN property) (mdciao.nomenclature.LabelerConsensus property) (mdciao.nomenclature.LabelerGPCR property) (mdciao.nomenclature.LabelerKLIFS property) mul() (mdciao.utils.sequence.AlignmentDataFrame method), [1] multiply() (mdciao.utils.sequence.AlignmentDataFrame method), [1] my_bioalign() (in module mdciao.utils.sequence), [1]

N

n_ctcs (mdciao.contacts.ContactGroup property) n_ctcs_timetraces() (mdciao.contacts.ContactGroup method) n_frames (mdciao.contacts.ContactGroup property) n_frames_total (mdciao.contacts.ContactGroup property) n_trajs (mdciao.contacts.ContactGroup property) name (mdciao.contacts.ContactGroup property) name_from_AA() (in module mdciao.utils.residue_and_atom), [1] names (mdciao.contacts.Residues property) names_short (mdciao.contacts.Residues property)

ndim (mdciao.utils.sequence.AlignmentDataFrame property), [1] ne() (mdciao.utils.sequence.AlignmentDataFrame method), [1] neighborlists_from_adjacency_matrix() (in module mdciao.utils.bonds), [1] neighbors_excluded (mdciao.contacts.ContactGroup property) nlargest() (mdciao.utils.sequence.AlignmentDataFrame method), [1] notebooks() (in module mdciao.examples) notna() (mdciao.utils.sequence.AlignmentDataFrame method), [1] notnull() (mdciao.utils.sequence.AlignmentDataFrame method), [1] nsmallest() (mdciao.utils.sequence.AlignmentDataFrame method), [1] nunique() (mdciao.utils.sequence.AlignmentDataFrame method), [1]

O

overview() (in module mdciao.fragments)

P

pad() (mdciao.utils.sequence.AlignmentDataFrame method), [1] parse_and_list_AAs_input() (in module mdciao.utils.residue_and_atom), [1] partial_counts_formed_atom_pairs() (mdciao.contacts.ContactPair method) partner_fragment_colors (mdciao.contacts.ContactGroup property) partner_index (mdciao.contacts.Residues property) partner_res_and_fragment_labels (mdciao.contacts.ContactGroup property) partner_res_and_fragment_labels_short (mdciao.contacts.ContactGroup property) partner_residue (mdciao.contacts.Residues property) partner_residue_index (mdciao.contacts.Residues property) pct_change() (mdciao.utils.sequence.AlignmentDataFrame method), [1] pdb() (in module mdciao.cli) pdb2ref() (in module mdciao.pdb) pdb2traj() (in module mdciao.pdb) per_traj_ctc() (in module mdciao.contacts) per_traj_mindist_lower_bound() (in module mdciao.contacts) pipe() (mdciao.utils.sequence.AlignmentDataFrame method), [1] pivot() (mdciao.utils.sequence.AlignmentDataFrame method), [1] pivot_table() (mdciao.utils.sequence.AlignmentDataFrame method), [1] plot (mdciao.utils.sequence.AlignmentDataFrame attribute), [1] plot_distance_distribution() (mdciao.contacts.ContactPair method) plot_distance_distributions() (mdciao.contacts.ContactGroup method) plot_freqs_as_bars() (mdciao.contacts.ContactGroup method)

plot_freqs_as_flareplot() (mdciao.contacts.ContactGroup method) plot_frequency_sums_as_bars() (mdciao.contacts.ContactGroup method) plot_histogram_w_smoothing_auto() (in module mdciao.plots) plot_interface_frequency_matrix() (mdciao.contacts.ContactGroup method) plot_matrix() (in module mdciao.plots) plot_neighborhood_freqs() (mdciao.contacts.ContactGroup method) plot_timedep_ctcs() (mdciao.contacts.ContactGroup method) plot_timedep_ctcs_matrix() (mdciao.contacts.ContactGroup method) plot_timetrace() (mdciao.contacts.ContactPair method) plot_unified_distro_dicts() (in module mdciao.plots) plot_unified_freq_dicts() (in module mdciao.plots) plot_violins() (mdciao.contacts.ContactGroup method) plot_w_smoothing_auto() (in module mdciao.plots) pop() (mdciao.utils.sequence.AlignmentDataFrame method), [1] pow() (mdciao.utils.sequence.AlignmentDataFrame method), [1] print_frag() (in module mdciao.fragments) print_fragments() (in module mdciao.fragments) print_verbose_dataframe() (in module mdciao.utils.sequence), [1] print_wrap() (in module mdciao.utils.str_and_dict), [1] prod() (mdciao.utils.sequence.AlignmentDataFrame method), [1] product() (mdciao.utils.sequence.AlignmentDataFrame method), [1] put_this_idx_first_in_pair() (in module mdciao.utils.lists), [1]

Q

quantile() (mdciao.utils.sequence.AlignmentDataFrame method), [1]

query() (mdciao.utils.sequence.AlignmentDataFrame method), [1]

R

radd() (mdciao.utils.sequence.AlignmentDataFrame method), [1] rangeexpand() (in module mdciao.utils.lists), [1] rangeexpand_residues2residxs() (in module mdciao.utils.residue_and_atom), [1] rank() (mdciao.utils.sequence.AlignmentDataFrame method), [1] rdiv() (mdciao.utils.sequence.AlignmentDataFrame method), [1] re_match_df() (in module mdciao.utils.sequence), [1] re_warp() (in module mdciao.utils.lists), [1] references() (in module mdciao.nomenclature) reindex() (mdciao.utils.sequence.AlignmentDataFrame method), [1] reindex_like() (mdciao.utils.sequence.AlignmentDataFrame method), [1] relabel_consensus() (mdciao.contacts.ContactGroup method) (mdciao.contacts.GroupOfInterfaces method) relative_frequency_formed_atom_pairs_overall_trajs() (mdciao.contacts.ContactGroup method) relative_frequency_of_formed_atom_pairs_overall_trajs() (mdciao.contacts.ContactPair method) remove_from_lists() (in module mdciao.utils.lists), [1] rename() (mdciao.utils.sequence.AlignmentDataFrame method), [1] rename_axis() (mdciao.utils.sequence.AlignmentDataFrame method), [1] reorder_levels() (mdciao.utils.sequence.AlignmentDataFrame method), [1] repframes() (mdciao.contacts.ContactGroup method) replace() (mdciao.utils.sequence.AlignmentDataFrame method), [1] replace4latex() (in module mdciao.utils.str_and_dict), [1] replace_w_dict() (in module mdciao.utils.str_and_dict), [1] res_idxs_pairs (mdciao.contacts.ContactGroup property) resample() (mdciao.utils.sequence.AlignmentDataFrame method), [1] reset_index() (mdciao.utils.sequence.AlignmentDataFrame method), [1]

residue_line() (in module mdciao.utils.residue_and_atom), [1] residue_names_long (mdciao.contacts.ContactGroup property) residue_names_short (mdciao.contacts.ContactGroup property) residue_neighborhoods() (in module mdciao.cli) residue_selection() (in module mdciao.cli) Residues (class in mdciao.contacts) residues_from_descriptors() (in module mdciao.utils.residue_and_atom), [1] residx2consensuslabel (mdciao.contacts.ContactGroup property) residx2ctcidx() (mdciao.contacts.ContactGroup method) residx2fragnamebest (mdciao.contacts.ContactGroup property) residx2resnamefragnamebest() (mdciao.contacts.ContactGroup method) residx2resnamelong (mdciao.contacts.ContactGroup property) residx2resnameshort (mdciao.contacts.ContactGroup property) residxs (mdciao.nomenclature.AlignerConsensus property) residxs_match() (mdciao.nomenclature.AlignerConsensus method) retop() (mdciao.contacts.ContactGroup method) (mdciao.contacts.ContactPair method) rfloordiv() (mdciao.utils.sequence.AlignmentDataFrame method), [1] rmod() (mdciao.utils.sequence.AlignmentDataFrame method), [1] rmul() (mdciao.utils.sequence.AlignmentDataFrame method), [1] rolling() (mdciao.utils.sequence.AlignmentDataFrame method), [1] round() (mdciao.utils.sequence.AlignmentDataFrame method), [1] rpow() (mdciao.utils.sequence.AlignmentDataFrame method), [1] rsub() (mdciao.utils.sequence.AlignmentDataFrame method), [1] rtruediv() (mdciao.utils.sequence.AlignmentDataFrame method), [1]

S

sample() (mdciao.utils.sequence.AlignmentDataFrame method), [1] save() (mdciao.contacts.ContactGroup method) (mdciao.contacts.ContactPair method) save_trajs() (mdciao.contacts.ContactGroup method) select_and_report_residue_neighborhood_idxs() (in module mdciao.contacts) select_by_frames() (mdciao.contacts.ContactGroup method) select_by_residues() (mdciao.contacts.ContactGroup method) select_dtypes() (mdciao.utils.sequence.AlignmentDataFrame method), [1] sem() (mdciao.utils.sequence.AlignmentDataFrame method), [1] seq (mdciao.nomenclature.LabelerCGN property) (mdciao.nomenclature.LabelerConsensus property) (mdciao.nomenclature.LabelerGPCR property) (mdciao.nomenclature.LabelerKLIFS property) sequence_match() (mdciao.nomenclature.AlignerConsensus method) set_axis() (mdciao.utils.sequence.AlignmentDataFrame method), [1] set_flags() (mdciao.utils.sequence.AlignmentDataFrame method), [1] set_index() (mdciao.utils.sequence.AlignmentDataFrame method), [1] shape (mdciao.utils.sequence.AlignmentDataFrame property), [1] shared_anchor_residue_index (mdciao.contacts.ContactGroup property) shift() (mdciao.utils.sequence.AlignmentDataFrame method), [1] shorten_AA() (in module mdciao.utils.residue_and_atom), [1]

sites() (in module mdciao.cli) sites_to_res_pairs() (in module mdciao.sites) size (mdciao.utils.sequence.AlignmentDataFrame property), [1] skew() (mdciao.utils.sequence.AlignmentDataFrame method), [1] sort_dict_by_asc_values() (in module mdciao.utils.str_and_dict), [1] sort_index() (mdciao.utils.sequence.AlignmentDataFrame method), [1] sort_values() (mdciao.utils.sequence.AlignmentDataFrame method), [1] sparse (mdciao.utils.sequence.AlignmentDataFrame attribute), [1] splitlabel() (in module mdciao.utils.str_and_dict), [1] squeeze() (mdciao.utils.sequence.AlignmentDataFrame method), [1] stack() (mdciao.utils.sequence.AlignmentDataFrame method), [1] stacked_time_traces (mdciao.contacts.ContactGroup property) (mdciao.contacts.ContactPair property) std() (mdciao.utils.sequence.AlignmentDataFrame method), [1] style (mdciao.utils.sequence.AlignmentDataFrame property), [1] sub() (mdciao.utils.sequence.AlignmentDataFrame method), [1] subtract() (mdciao.utils.sequence.AlignmentDataFrame method), [1] sum() (mdciao.utils.sequence.AlignmentDataFrame method), [1] sum_dict_per_residue() (in module mdciao.utils.str_and_dict), [1] superpose_w_CA_align() (in module mdciao.utils.sequence), [1] swapaxes() (mdciao.utils.sequence.AlignmentDataFrame method), [1] swaplevel() (mdciao.utils.sequence.AlignmentDataFrame method), [1]

T

T (mdciao.utils.sequence.AlignmentDataFrame property), [1] tablefile (mdciao.nomenclature.LabelerCGN property) (mdciao.nomenclature.LabelerConsensus property) (mdciao.nomenclature.LabelerGPCR property) (mdciao.nomenclature.LabelerKLIFS property) tail() (mdciao.utils.sequence.AlignmentDataFrame method), [1] take() (mdciao.utils.sequence.AlignmentDataFrame method), [1] time_arrays (mdciao.contacts.ContactGroup property) time_max (mdciao.contacts.ContactGroup property) (mdciao.contacts.ContactPair property) time_min (mdciao.contacts.ContactGroup property) (mdciao.contacts.ContactPair property) time_traces (mdciao.contacts.ContactPair property) to_clipboard() (mdciao.utils.sequence.AlignmentDataFrame method), [1] to_ContactGroups_per_traj() (mdciao.contacts.ContactGroup method) to_csv() (mdciao.utils.sequence.AlignmentDataFrame method), [1] to_dict() (mdciao.utils.sequence.AlignmentDataFrame method), [1] to_excel() (mdciao.utils.sequence.AlignmentDataFrame method), [1] to_feather() (mdciao.utils.sequence.AlignmentDataFrame method), [1] to_gbq() (mdciao.utils.sequence.AlignmentDataFrame method), [1] to_hdf() (mdciao.utils.sequence.AlignmentDataFrame method), [1] to_html() (mdciao.utils.sequence.AlignmentDataFrame method), [1] to_json() (mdciao.utils.sequence.AlignmentDataFrame method), [1] to_latex() (mdciao.utils.sequence.AlignmentDataFrame method), [1] to_markdown() (mdciao.utils.sequence.AlignmentDataFrame method), [1] to_numpy() (mdciao.utils.sequence.AlignmentDataFrame method), [1] to_orc() (mdciao.utils.sequence.AlignmentDataFrame method), [1] to_parquet() (mdciao.utils.sequence.AlignmentDataFrame method), [1] to_period() (mdciao.utils.sequence.AlignmentDataFrame method), [1] to_pickle() (mdciao.utils.sequence.AlignmentDataFrame method), [1] to_records() (mdciao.utils.sequence.AlignmentDataFrame method), [1] to_sql() (mdciao.utils.sequence.AlignmentDataFrame method), [1]

to_stata() (mdciao.utils.sequence.AlignmentDataFrame method), [1] to_string() (mdciao.utils.sequence.AlignmentDataFrame method), [1] to_timestamp() (mdciao.utils.sequence.AlignmentDataFrame method), [1] to_xarray() (mdciao.utils.sequence.AlignmentDataFrame method), [1] to_xml() (mdciao.utils.sequence.AlignmentDataFrame method), [1] top (mdciao.contacts.ContactGroup property) (mdciao.contacts.ContactPair property) top2domains() (mdciao.nomenclature.LabelerGPCR method) top2frags() (mdciao.nomenclature.LabelerCGN method) (mdciao.nomenclature.LabelerConsensus method) (mdciao.nomenclature.LabelerGPCR method) (mdciao.nomenclature.LabelerKLIFS method) top2labels() (mdciao.nomenclature.LabelerCGN method) (mdciao.nomenclature.LabelerConsensus method) (mdciao.nomenclature.LabelerGPCR method) (mdciao.nomenclature.LabelerKLIFS method) top2lsd() (in module mdciao.utils.residue_and_atom), [1] top2residue_bond_matrix() (in module mdciao.utils.bonds), [1] top2residue_bond_matrix_naive() (in module mdciao.utils.bonds), [1] top2seq() (in module mdciao.utils.sequence), [1] topology (mdciao.contacts.ContactGroup property) (mdciao.contacts.ContactPair property) tops (mdciao.nomenclature.AlignerConsensus property) trajlabels (mdciao.contacts.ContactGroup property) trajs2ctcs() (in module mdciao.contacts) trajs2lower_bounds() (in module mdciao.contacts) transform() (mdciao.utils.sequence.AlignmentDataFrame method), [1] transpose() (mdciao.utils.sequence.AlignmentDataFrame method), [1] truediv() (mdciao.utils.sequence.AlignmentDataFrame method), [1] truncate() (mdciao.utils.sequence.AlignmentDataFrame method), [1] tz_convert() (mdciao.utils.sequence.AlignmentDataFrame method), [1] tz_localize() (mdciao.utils.sequence.AlignmentDataFrame method), [1]

U

unify_freq_dicts() (in module mdciao.utils.str_and_dict), [1] unique_list_of_iterables_by_tuple_hashing() (in module mdciao.utils.lists), [1]

unique_product_w_intersection() (in module mdciao.utils.lists), [1] unstack() (mdciao.utils.sequence.AlignmentDataFrame method), [1] update() (mdciao.utils.sequence.AlignmentDataFrame method), [1]

V

value_counts() (mdciao.utils.sequence.AlignmentDataFrame method), [1]

values (mdciao.utils.sequence.AlignmentDataFrame property), [1] var() (mdciao.utils.sequence.AlignmentDataFrame method), [1]

W

where() (mdciao.utils.sequence.AlignmentDataFrame method), [1]

window_average_fast() (in module mdciao.utils.lists), [1]

X

x2site() (in module mdciao.sites)

xs() (mdciao.utils.sequence.AlignmentDataFrame method), [1] xtcs2ctc_mat_dict() (in module mdciao.utils.contact_matrix), [1]