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[nomenclature._sort_all_consensus_labels] API CHANGE return also sort… #52

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Sep 4, 2024
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5d76a56
[nomenclature._sort_all_consensus_labels] API CHANGE return also sort…
gph82 Aug 12, 2024
d70a5ed
[nomenclature._sort_all_consensus_labels] API CHANGE return also sort…
gph82 Aug 12, 2024
26fbd8e
[nomeclature._sort_consensus_labels] API CHANGE don't de-duplicate, i…
gph82 Aug 12, 2024
6318535
[nomeclature._sort_consensus_labels] return right indices for duplicates
gph82 Aug 12, 2024
3a6e18a
[nomeclature._lexsort_consensus_ctc_labels] new method for lexsorting…
gph82 Aug 12, 2024
e5b2d9e
Merge branch 'interface_selection' of https://github.com/gph82/mdciao…
gph82 Aug 12, 2024
f6fd896
[ContactPair.label_flex] refactor split_label -> pad_label
gph82 Aug 13, 2024
45d4f0e
[ContactPair.label_flex] better docs, better ValueError message
gph82 Aug 13, 2024
2d46d71
[ContactPair.gen_label] AA_short can handle consensus options, tests
gph82 Aug 13, 2024
d9e9cb0
[contacts.ContactGroup.frequency_sum_per_residue_names] API BREAK ref…
gph82 Aug 13, 2024
00ebbd1
[contacts.ContactGroup.select_by_residues] Allow selection via consen…
gph82 Aug 13, 2024
d4cc447
[test_contacts] refactor ._contacts -> contact_pairs (don't test usin…
gph82 Aug 13, 2024
aa1e969
[nomeclature._lexsort_consensus_ctc_labels] fix
gph82 Aug 13, 2024
c3c451b
[siteIO.sites_to_res_pairs] don't fail if conlab is missing (return n…
gph82 Aug 13, 2024
400f58a
[residue_and_atom] typos
gph82 Aug 13, 2024
5d6fb6b
[plots._sorter_by_key_or_val] new option 'consensus' for 'sort_by' ar…
gph82 Aug 13, 2024
00113c7
[plots.compare_groups_of_contacts] adapt to refactor shorten_AAs -> A…
gph82 Aug 13, 2024
da1c6a3
[nomenclature] make tuples instead of lists for the consensus fragmen…
gph82 Aug 13, 2024
a7f1cae
[fragments.get_fragments] minor docs
gph82 Aug 13, 2024
ff27991
[fragments.check_if_fragment_clashes] correct typo in input prompt
gph82 Aug 13, 2024
ffd31a3
[fragments._fragments_strings_to_fragments] pass "method" directly to…
gph82 Aug 13, 2024
8a27a7f
[fragments.frag_list_2_frag_groups] can expand ranges, prompting expr…
gph82 Aug 13, 2024
c9d107f
[cli._parse_consensus_option] minor
gph82 Aug 13, 2024
1a5bf25
[cli.residue_neighborhoods] don't store `user_wants_consensus`
gph82 Aug 13, 2024
092a5bf
[cli.residue_selection] minor
gph82 Aug 13, 2024
63abc34
[fragments.frag_dict_2_frag_groups] new optarg fail_on_empty, tests
gph82 Aug 13, 2024
07a668c
[ContactGroup.plot_frequency_sums_as_bars] use AA_format when calling…
gph82 Aug 13, 2024
40e9c6a
[nomenclature.conlabs2confrags] refactor from _map2defs, simplify usi…
gph82 Aug 14, 2024
a0bdd91
[nomenclature.conlabs2confrags] new optarg replace_GPCR_frags
gph82 Aug 14, 2024
55f9e3f
[nomenclature.LabelerConsensus.top2labels] top arg can be a path to a…
gph82 Aug 15, 2024
bb0b795
[contacts.ContactGroup.plot_freqs_as_flareplot] minor docs
gph82 Aug 15, 2024
7b7cf25
[cli._parse_consensus_option] minor
gph82 Aug 15, 2024
ddc15f9
[cli._parse_consensus_options_and_return_fragment_defs] Return consen…
gph82 Aug 15, 2024
8352caf
[cli.interface] When calling plot_freqs_as_flareplot include consensu…
gph82 Aug 15, 2024
0701310
[cli.interface] new optarg AA_selection, tests
gph82 Aug 15, 2024
f57dd6b
[fragments._fragments_strings_to_fragments] sort the output of unsort…
gph82 Aug 15, 2024
0f6a848
[cli.interface] better fragment handling
gph82 Aug 15, 2024
91a6f09
[cli.interface] API BREAK frag_idxs_group_1, frag_idxs_group_2 become…
gph82 Aug 15, 2024
338fbe2
[examples and parsers] refactor frag_idxs_group_1 -> interface_select…
gph82 Aug 15, 2024
767d56b
[examples.notebook] update to the refactor frag_idxs_group_1 -> inter…
gph82 Aug 15, 2024
7336ba2
[examples.notebook.Missing_Contacts] add a cell showcasing AA_selection
gph82 Aug 15, 2024
dcb3bc0
[cli._parse_fragdefs_fragnames_consensus] don't use consensus_labeler…
gph82 Aug 15, 2024
602238c
[examples.fetch_example_data] new dataset ghrelin@ghsr
gph82 Aug 15, 2024
2aabdd5
[contacts.ContactGroup.plot_freqs_as_bars] refactor truncate_at -> lo…
gph82 Aug 16, 2024
9c7facd
[contacts.ContactGroup.plot_frequency_sums_as_bars] refactor truncate…
gph82 Aug 16, 2024
55635cc
[nomenclature.LabelerConsensus.top2frags] docs: also mention that the…
gph82 Aug 17, 2024
a1d36c6
[nomenclature] minor docs
gph82 Aug 25, 2024
05522e7
[plots.compare_violins] return the representative frames, tests
gph82 Aug 25, 2024
7556f8d
[contacts.ContactGroup.repframes] use fstring
gph82 Aug 25, 2024
f6c188f
[contacts.ConatactGroup.frequency_as_contact_matrix_CG] use 'fragment…
gph82 Aug 25, 2024
6dc0897
[utils.residue_and_atom._top2AAmap] new method, tests
gph82 Aug 25, 2024
9c223af
[utils.residue_and_atom.rangeexpand_residues2residxs] accept expressi…
gph82 Aug 25, 2024
7f5163c
[cli.sites] return None instead of "NA" for missing consensus labels …
gph82 Aug 25, 2024
0934a1f
[contacts.ContactGroup._args2df] new colum "self interface residx" to…
gph82 Aug 26, 2024
347e62d
[contacts.ContactGroup] docs
gph82 Aug 26, 2024
3e46c64
[contacts.ContactGroup._full_color_list] Handle color in specific sit…
gph82 Aug 26, 2024
6f2f1b4
[plots.compare_groups_of_contacts] Remove unused optarg exclude
gph82 Aug 27, 2024
3669e46
[contacts.ContactGroup._args2df] "self interface residx" only if inte…
gph82 Aug 27, 2024
d61fef5
[contacts.ContactGroup.repframes] docs
gph82 Aug 28, 2024
3701747
[cli.interface] use the repframe instead of refgeom for SS display in…
gph82 Aug 28, 2024
2ea269a
[flare.freqs2flare] docs
gph82 Aug 28, 2024
c8e7824
[contacts.ContactGroup.plot_freqs_as_flareplot] API CHANGE: optarg fr…
gph82 Aug 28, 2024
45a84cb
[cli.interface] adapt to new return behavior of plot_freqs_as_flareplot
gph82 Aug 28, 2024
15a7419
[contacts.ContactGroup.repframes] API CHANGE: returned value 'trajs' …
gph82 Aug 30, 2024
8101d69
[examples/notebooks] Adapt to new API behavior (repframes and flarepl…
gph82 Aug 30, 2024
3cf8278
[examples/notebooks] add numbering to notebooks
gph82 Aug 30, 2024
8954697
[examples._recursive_prompt] new optarg skip_on_existing, tests
gph82 Aug 31, 2024
ec82046
[examples._down_url_safely] new optarg skip_on_existing, tests
gph82 Aug 31, 2024
e5c53c7
[examples.fetch_example_data] new optarg skip_on_existing, new unzip …
gph82 Aug 31, 2024
319e06e
[nomenclature._GPCRdb_web_lookup] avoid usage of pandas _read_json
gph82 Sep 1, 2024
86b65f6
[examples.fetch_example_data] unify names
gph82 Sep 1, 2024
773c605
[examples/notebooks] new notebook 09.Consensus_Labels.ipynb
gph82 Sep 1, 2024
4d5f7dc
[examples.fetch_example_data] complete data usages
gph82 Sep 1, 2024
dbcc09f
[general] rename prot.pdb -> top.pdb
gph82 Sep 1, 2024
c79d565
[doc/FAQ & doc/gallery] include new notebook, renaming of links to nu…
gph82 Sep 2, 2024
5855683
[examples/notebooks] update hrefs to new numbered notebooks (plus som…
gph82 Sep 2, 2024
e4d16bd
minor
gph82 Sep 2, 2024
60ed142
minor
gph82 Sep 2, 2024
6a0acd7
[cli.interface] interface members 'intf_frags_as_residxs' get unique'…
gph82 Sep 2, 2024
e5111bf
[cli.interface] API CHANGE wrt to self_interface, dont raise Assertio…
gph82 Sep 2, 2024
cb6af80
[cli.interface] Refactor how contact-list reduction is reported and b…
gph82 Sep 2, 2024
98d0c48
[nomenclature] minor
gph82 Sep 3, 2024
2456f44
[everywhere] refactor typo GPCRmd -> GPRCdb
gph82 Sep 3, 2024
44c5a2d
[test_examples.Test_fetch_example_data.test_alias_unzip_to_otherfile]…
gph82 Sep 3, 2024
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[cli._parse_consensus_option] minor
gph82 committed Aug 15, 2024
commit 7b7cf25358699dca7fd9b67bfd9e57d3c00b659a
15 changes: 6 additions & 9 deletions mdciao/cli/cli.py
Original file line number Diff line number Diff line change
@@ -102,16 +102,13 @@ def _parse_consensus_option(option, consensus_type,
full of Nones is returned
* str
The needed identifier to instantiate an
`LabelerGPCR`, :obj:`LabelerCGN` or :obj:`LabelerKLIFS` object.
Examples would be a `UniProt_name`, a `ref_PDB`, or
an `UniProt_AC`
respectively
* :obj:`LabelerConsensus`
An already instantiated :obj:`LabelerGPCR`,
:obj:`LabelerCGN` or :obj:`LabelerKLIFS` object.
`LabelerGPCR`, `LabelerCGN` or `LabelerKLIFS` object.
* a `LabelerConsensus` object
An already instantiated `LabelerGPCR`,
`LabelerCGN` or `LabelerKLIFS` object.
The method then does nothing. Usecase are repeated
calls to any of the methods in :obj:`command_line_tools`
without each call instantiating its own :obj:`LabelerConsensus`
calls to any of the methods in `mdciao.cli`
without each call instantiating its own `LabelerConsensus`
* iterable
An iterable (list, dict, array) mapping
residue indices of 'top` to consensus labels.