mdciao
0.0.6
Installation
CLI Tutorial
API Jupyter Notebook Tutorial
Covid-19 Spike Protein Example 1: Residue Neighborhoods
Covid-19 Spike Protein Example 2: RBD-ACE Interface
CLI Reference
API Reference
Jupyter Notebook Gallery
mdciao
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Index
Index
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A
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B
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C
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D
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E
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F
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G
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H
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I
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J
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K
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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X
_
__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.LabelerGPCR method)
(mdciao.nomenclature.LabelerKLIFS method)
(mdciao.nomenclature.Literature method)
A
AA2conlab() (mdciao.nomenclature.LabelerCGN 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.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]
append() (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_3SN6() (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.LabelerGPCR property)
(mdciao.nomenclature.LabelerKLIFS property)
conlab2idx() (mdciao.nomenclature.LabelerCGN property)
(mdciao.nomenclature.LabelerGPCR property)
(mdciao.nomenclature.LabelerKLIFS property)
conlab2matidx() (mdciao.contacts.GroupOfInterfaces property)
conlab2residx() (mdciao.nomenclature.LabelerCGN method)
(mdciao.nomenclature.LabelerGPCR method)
(mdciao.nomenclature.LabelerKLIFS method)
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]
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.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)
distributions_of_distances() (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]
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.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.LabelerGPCR property)
(mdciao.nomenclature.LabelerKLIFS property)
fragments_as_conlabs() (mdciao.nomenclature.LabelerCGN property)
(mdciao.nomenclature.LabelerGPCR property)
(mdciao.nomenclature.LabelerKLIFS property)
fragments_as_idxs() (mdciao.nomenclature.LabelerCGN 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.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)
geom() (mdciao.nomenclature.LabelerCGN property)
(mdciao.nomenclature.LabelerGPCR property)
(mdciao.nomenclature.LabelerKLIFS property)
geom2COMdist() (in module mdciao.utils.COM)
,
[1]
geom2COMxyz() (in module mdciao.utils.COM)
,
[1]
get() (mdciao.utils.sequence.AlignmentDataFrame method)
,
[1]
get_fragments() (in module mdciao.fragments)
get_sorted_trajectories() (in module mdciao.utils.str_and_dict)
,
[1]
get_SS() (in module mdciao.utils.residue_and_atom)
,
[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)
guess_nomenclature_fragments() (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.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)
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]
iteritems() (mdciao.utils.sequence.AlignmentDataFrame method)
,
[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)
(mdciao.utils.sequence.AlignmentDataFrame method)
,
[1]
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)
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]
lookup() (mdciao.utils.sequence.AlignmentDataFrame method)
,
[1]
lt() (mdciao.utils.sequence.AlignmentDataFrame method)
,
[1]
M
mad() (mdciao.utils.sequence.AlignmentDataFrame method)
,
[1]
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)
max() (mdciao.utils.sequence.AlignmentDataFrame method)
,
[1]
max_cutoff_Ang() (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]
mod() (mdciao.utils.sequence.AlignmentDataFrame method)
,
[1]
mode() (mdciao.utils.sequence.AlignmentDataFrame method)
,
[1]
modes() (mdciao.contacts.ContactGroup property)
most_recent_alignment() (mdciao.nomenclature.LabelerCGN property)
(mdciao.nomenclature.LabelerGPCR property)
(mdciao.nomenclature.LabelerKLIFS property)
most_recent_top2labels() (mdciao.nomenclature.LabelerCGN 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)
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_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_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_unified_distro_dicts() (in module mdciao.plots)
plot_unified_freq_dicts() (in module mdciao.plots)
plot_violins() (mdciao.contacts.ContactGroup method)
pop() (mdciao.utils.sequence.AlignmentDataFrame method)
,
[1]
pow() (mdciao.utils.sequence.AlignmentDataFrame method)
,
[1]
print_frag() (in module mdciao.fragments)
print_verbose_dataframe() (in module mdciao.utils.sequence)
,
[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]
ref_PDB() (mdciao.nomenclature.LabelerCGN property)
(mdciao.nomenclature.LabelerGPCR property)
(mdciao.nomenclature.LabelerKLIFS property)
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_dtypes() (mdciao.utils.sequence.AlignmentDataFrame method)
,
[1]
sem() (mdciao.utils.sequence.AlignmentDataFrame method)
,
[1]
seq() (mdciao.nomenclature.LabelerCGN property)
(mdciao.nomenclature.LabelerGPCR property)
(mdciao.nomenclature.LabelerKLIFS property)
set_axis() (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]
slice_shift() (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)
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
tablefile() (mdciao.nomenclature.LabelerCGN 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_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_new_ContactGroup() (mdciao.contacts.ContactGroup method)
to_numpy() (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]
top() (mdciao.contacts.ContactGroup property)
(mdciao.contacts.ContactPair property)
(mdciao.nomenclature.LabelerCGN property)
(mdciao.nomenclature.LabelerGPCR property)
(mdciao.nomenclature.LabelerKLIFS property)
top2frags() (mdciao.nomenclature.LabelerCGN method)
(mdciao.nomenclature.LabelerGPCR method)
(mdciao.nomenclature.LabelerKLIFS method)
top2labels() (mdciao.nomenclature.LabelerCGN 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)
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]
tshift() (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]