| biobb_common/biobb_common/__init__.py |
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CmdWrapper.__init__ |
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CmdWrapper.log_output |
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CmdWrapper.launch |
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trans_galaxy_charmap |
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| biobb_common/biobb_common/configuration/settings.py |
ConfReader.__init__ |
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| biobb_common/biobb_common/configuration/settings.py |
ConfReader.get_working_dir_path |
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ConfReader._read_config |
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ConfReader._get_global_properties |
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ConfReader._get_step_properties |
14 |
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ConfReader.get_prop_dic |
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ConfReader.get_paths_dic |
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ConfReader._get_step_paths |
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ConfReader._solve_dependency |
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BiobbObject.__init__ |
45 |
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BiobbObject.check_arguments |
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BiobbObject.check_properties |
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BiobbObject.check_restart |
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BiobbObject.stage_files |
25 |
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BiobbObject.create_cmd_line |
76 |
69 |
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BiobbObject.execute_command |
6 |
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| biobb_common/biobb_common/generic/biobb_object.py |
BiobbObject.copy_to_host |
8 |
2 |
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| biobb_common/biobb_common/generic/biobb_object.py |
BiobbObject.run_biobb |
2 |
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| biobb_common/biobb_common/generic/biobb_object.py |
BiobbObject.remove_tmp_files |
2 |
0 |
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| biobb_common/biobb_common/generic/biobb_object.py |
(no function) |
23 |
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| biobb_common/biobb_common/tools/__init__.py |
(no function) |
0 |
0 |
0 |
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| biobb_common/biobb_common/tools/file_utils.py |
create_unique_file_path |
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| biobb_common/biobb_common/tools/file_utils.py |
create_dir |
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create_stdin_file |
4 |
4 |
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create_unique_dir |
21 |
10 |
0 |
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| biobb_common/biobb_common/tools/file_utils.py |
get_working_dir_path |
10 |
2 |
0 |
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| biobb_common/biobb_common/tools/file_utils.py |
zip_list |
15 |
15 |
0 |
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unzip_list |
8 |
8 |
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search_topology_files |
14 |
14 |
0 |
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| biobb_common/biobb_common/tools/file_utils.py |
zip_top |
5 |
5 |
0 |
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| biobb_common/biobb_common/tools/file_utils.py |
unzip_top |
10 |
10 |
0 |
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| biobb_common/biobb_common/tools/file_utils.py |
get_logs_prefix |
1 |
1 |
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| biobb_common/biobb_common/tools/file_utils.py |
create_incremental_name |
7 |
5 |
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get_logs |
30 |
1 |
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launchlogger |
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launchlogger.wrapper_log |
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log |
4 |
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human_readable_time |
7 |
7 |
0 |
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| biobb_common/biobb_common/tools/file_utils.py |
check_properties |
8 |
8 |
0 |
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create_name |
15 |
5 |
0 |
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write_failed_output |
2 |
2 |
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rm |
12 |
6 |
0 |
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| biobb_common/biobb_common/tools/file_utils.py |
rm_file_list |
4 |
0 |
0 |
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| biobb_common/biobb_common/tools/file_utils.py |
check_complete_files |
5 |
5 |
0 |
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| biobb_common/biobb_common/tools/file_utils.py |
copy_to_container |
15 |
15 |
0 |
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| biobb_common/biobb_common/tools/file_utils.py |
copy_to_host |
7 |
7 |
0 |
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| biobb_common/biobb_common/tools/file_utils.py |
create_cmd_line |
55 |
55 |
0 |
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| biobb_common/biobb_common/tools/file_utils.py |
get_doc_dicts |
26 |
2 |
0 |
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| biobb_common/biobb_common/tools/file_utils.py |
check_argument |
27 |
14 |
0 |
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| biobb_common/biobb_common/tools/file_utils.py |
(no function) |
44 |
0 |
0 |
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| biobb_common/biobb_common/tools/test_fixtures.py |
test_setup |
16 |
3 |
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test_teardown |
3 |
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exe_success |
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not_empty |
2 |
0 |
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compare_hash |
8 |
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0 |
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equal |
26 |
21 |
0 |
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compare_line_by_line |
10 |
1 |
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equal_txt |
1 |
1 |
0 |
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| biobb_common/biobb_common/tools/test_fixtures.py |
compare_zip |
15 |
15 |
0 |
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| biobb_common/biobb_common/tools/test_fixtures.py |
compare_pdb |
34 |
4 |
0 |
88% |
| biobb_common/biobb_common/tools/test_fixtures.py |
compare_top_itp |
8 |
8 |
0 |
0% |
| biobb_common/biobb_common/tools/test_fixtures.py |
compare_ignore_first |
8 |
8 |
0 |
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| biobb_common/biobb_common/tools/test_fixtures.py |
compare_size |
13 |
13 |
0 |
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| biobb_common/biobb_common/tools/test_fixtures.py |
compare_xvg |
9 |
9 |
0 |
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| biobb_common/biobb_common/tools/test_fixtures.py |
compare_images |
21 |
21 |
0 |
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| biobb_common/biobb_common/tools/test_fixtures.py |
compare_object_pickle |
21 |
21 |
0 |
0% |
| biobb_common/biobb_common/tools/test_fixtures.py |
compare_dictionaries |
22 |
22 |
0 |
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| biobb_common/biobb_common/tools/test_fixtures.py |
validate_json |
16 |
16 |
0 |
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| biobb_common/biobb_common/tools/test_fixtures.py |
(no function) |
32 |
0 |
0 |
100% |
| biobb_model/__init__.py |
(no function) |
4 |
0 |
0 |
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| biobb_model/model/__init__.py |
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15 |
0 |
0 |
100% |
| biobb_model/model/checking_log.py |
CheckingLog.__init__ |
8 |
0 |
0 |
100% |
| biobb_model/model/checking_log.py |
CheckingLog.launch |
12 |
3 |
0 |
75% |
| biobb_model/model/checking_log.py |
checking_log |
2 |
1 |
0 |
50% |
| biobb_model/model/checking_log.py |
main |
9 |
9 |
0 |
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| biobb_model/model/checking_log.py |
(no function) |
13 |
1 |
0 |
92% |
| biobb_model/model/common.py |
modeller_installed |
9 |
9 |
0 |
0% |
| biobb_model/model/common.py |
_from_string_to_list |
8 |
5 |
0 |
38% |
| biobb_model/model/common.py |
(no function) |
5 |
0 |
0 |
100% |
| biobb_model/model/fix_altlocs.py |
FixAltLocs.__init__ |
9 |
0 |
0 |
100% |
| biobb_model/model/fix_altlocs.py |
FixAltLocs.launch |
15 |
4 |
0 |
73% |
| biobb_model/model/fix_altlocs.py |
fix_altlocs |
2 |
1 |
0 |
50% |
| biobb_model/model/fix_altlocs.py |
main |
9 |
9 |
0 |
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(no function) |
14 |
1 |
0 |
93% |
| biobb_model/model/fix_amides.py |
FixAmides.__init__ |
8 |
0 |
0 |
100% |
| biobb_model/model/fix_amides.py |
FixAmides.launch |
12 |
3 |
0 |
75% |
| biobb_model/model/fix_amides.py |
fix_amides |
2 |
1 |
0 |
50% |
| biobb_model/model/fix_amides.py |
main |
9 |
9 |
0 |
0% |
| biobb_model/model/fix_amides.py |
(no function) |
13 |
1 |
0 |
92% |
| biobb_model/model/fix_backbone.py |
FixBackbone.__init__ |
9 |
9 |
0 |
0% |
| biobb_model/model/fix_backbone.py |
FixBackbone.launch |
19 |
19 |
0 |
0% |
| biobb_model/model/fix_backbone.py |
fix_backbone |
2 |
2 |
0 |
0% |
| biobb_model/model/fix_backbone.py |
main |
10 |
10 |
0 |
0% |
| biobb_model/model/fix_backbone.py |
(no function) |
14 |
1 |
0 |
93% |
| biobb_model/model/fix_chirality.py |
FixChirality.__init__ |
8 |
0 |
0 |
100% |
| biobb_model/model/fix_chirality.py |
FixChirality.launch |
12 |
3 |
0 |
75% |
| biobb_model/model/fix_chirality.py |
fix_chirality |
2 |
1 |
0 |
50% |
| biobb_model/model/fix_chirality.py |
main |
9 |
9 |
0 |
0% |
| biobb_model/model/fix_chirality.py |
(no function) |
13 |
1 |
0 |
92% |
| biobb_model/model/fix_pdb.py |
FixPdb.__init__ |
9 |
1 |
0 |
89% |
| biobb_model/model/fix_pdb.py |
FixPdb.launch |
25 |
4 |
0 |
84% |
| biobb_model/model/fix_pdb.py |
fix_pdb |
2 |
1 |
0 |
50% |
| biobb_model/model/fix_pdb.py |
main |
9 |
9 |
0 |
0% |
| biobb_model/model/fix_pdb.py |
(no function) |
14 |
1 |
0 |
93% |
| biobb_model/model/fix_pdb_utils.py |
Atom.__init__ |
6 |
0 |
0 |
100% |
| biobb_model/model/fix_pdb_utils.py |
Atom.__repr__ |
1 |
1 |
0 |
0% |
| biobb_model/model/fix_pdb_utils.py |
Atom.__eq__ |
1 |
1 |
0 |
0% |
| biobb_model/model/fix_pdb_utils.py |
Atom.get_structure |
1 |
0 |
0 |
100% |
| biobb_model/model/fix_pdb_utils.py |
Atom.get_index |
1 |
1 |
0 |
0% |
| biobb_model/model/fix_pdb_utils.py |
Atom.get_residue_index |
1 |
0 |
0 |
100% |
| biobb_model/model/fix_pdb_utils.py |
Atom.set_residue_index |
7 |
7 |
0 |
0% |
| biobb_model/model/fix_pdb_utils.py |
Atom.get_residue |
3 |
1 |
0 |
67% |
| biobb_model/model/fix_pdb_utils.py |
Atom.set_residue |
4 |
4 |
0 |
0% |
| biobb_model/model/fix_pdb_utils.py |
Atom.get_chain_index |
1 |
0 |
0 |
100% |
| biobb_model/model/fix_pdb_utils.py |
Atom.get_chain |
1 |
0 |
0 |
100% |
| biobb_model/model/fix_pdb_utils.py |
Residue.__init__ |
7 |
0 |
0 |
100% |
| biobb_model/model/fix_pdb_utils.py |
Residue.__repr__ |
1 |
1 |
0 |
0% |
| biobb_model/model/fix_pdb_utils.py |
Residue.__eq__ |
3 |
3 |
0 |
0% |
| biobb_model/model/fix_pdb_utils.py |
Residue.__hash__ |
1 |
1 |
0 |
0% |
| biobb_model/model/fix_pdb_utils.py |
Residue.same_inputs_as |
1 |
0 |
0 |
100% |
| biobb_model/model/fix_pdb_utils.py |
Residue.get_structure |
1 |
1 |
0 |
0% |
| biobb_model/model/fix_pdb_utils.py |
Residue.get_index |
1 |
0 |
0 |
100% |
| biobb_model/model/fix_pdb_utils.py |
Residue.get_atom_indices |
1 |
0 |
0 |
100% |
| biobb_model/model/fix_pdb_utils.py |
Residue.set_atom_indices |
9 |
9 |
0 |
0% |
| biobb_model/model/fix_pdb_utils.py |
Residue.get_atoms |
4 |
4 |
0 |
0% |
| biobb_model/model/fix_pdb_utils.py |
Residue.set_atoms |
7 |
7 |
0 |
0% |
| biobb_model/model/fix_pdb_utils.py |
Residue.add_atom |
4 |
4 |
0 |
0% |
| biobb_model/model/fix_pdb_utils.py |
Residue.remove_atom |
2 |
2 |
0 |
0% |
| biobb_model/model/fix_pdb_utils.py |
Residue.get_chain_index |
1 |
0 |
0 |
100% |
| biobb_model/model/fix_pdb_utils.py |
Residue.set_chain_index |
7 |
7 |
0 |
0% |
| biobb_model/model/fix_pdb_utils.py |
Residue.get_chain |
3 |
3 |
0 |
0% |
| biobb_model/model/fix_pdb_utils.py |
Residue.set_chain |
14 |
14 |
0 |
0% |
| biobb_model/model/fix_pdb_utils.py |
Chain.__init__ |
4 |
0 |
0 |
100% |
| biobb_model/model/fix_pdb_utils.py |
Chain.__repr__ |
1 |
1 |
0 |
0% |
| biobb_model/model/fix_pdb_utils.py |
Chain.__eq__ |
1 |
0 |
0 |
100% |
| biobb_model/model/fix_pdb_utils.py |
Chain.get_structure |
1 |
0 |
0 |
100% |
| biobb_model/model/fix_pdb_utils.py |
Chain.get_index |
1 |
1 |
0 |
0% |
| biobb_model/model/fix_pdb_utils.py |
Chain.set_index |
3 |
3 |
0 |
0% |
| biobb_model/model/fix_pdb_utils.py |
Chain.get_residue_indices |
1 |
0 |
0 |
100% |
| biobb_model/model/fix_pdb_utils.py |
Chain.set_residue_indices |
11 |
8 |
0 |
27% |
| biobb_model/model/fix_pdb_utils.py |
Chain.get_residues |
4 |
1 |
0 |
75% |
| biobb_model/model/fix_pdb_utils.py |
Chain.set_residues |
7 |
7 |
0 |
0% |
| biobb_model/model/fix_pdb_utils.py |
Chain.add_residue |
3 |
3 |
0 |
0% |
| biobb_model/model/fix_pdb_utils.py |
Chain.remove_residue |
4 |
4 |
0 |
0% |
| biobb_model/model/fix_pdb_utils.py |
Chain.get_atom_indices |
1 |
1 |
0 |
0% |
| biobb_model/model/fix_pdb_utils.py |
Chain.get_atoms |
1 |
1 |
0 |
0% |
| biobb_model/model/fix_pdb_utils.py |
Chain.get_sequence |
1 |
1 |
0 |
0% |
| biobb_model/model/fix_pdb_utils.py |
Structure.__init__ |
9 |
0 |
0 |
100% |
| biobb_model/model/fix_pdb_utils.py |
Structure.__repr__ |
1 |
1 |
0 |
0% |
| biobb_model/model/fix_pdb_utils.py |
Structure.set_new_atom |
4 |
0 |
0 |
100% |
| biobb_model/model/fix_pdb_utils.py |
Structure.set_new_residue |
7 |
0 |
0 |
100% |
| biobb_model/model/fix_pdb_utils.py |
Structure.set_new_chain |
7 |
0 |
0 |
100% |
| biobb_model/model/fix_pdb_utils.py |
Structure.purge_chain |
8 |
8 |
0 |
0% |
| biobb_model/model/fix_pdb_utils.py |
Structure.from_pdb_file |
45 |
1 |
0 |
98% |
| biobb_model/model/fix_pdb_utils.py |
Structure.generate_pdb_file |
19 |
1 |
0 |
95% |
| biobb_model/model/fix_pdb_utils.py |
Structure.get_chain_by_name |
1 |
1 |
0 |
0% |
| biobb_model/model/fix_pdb_utils.py |
Structure.display_summary |
6 |
6 |
0 |
0% |
| biobb_model/model/fix_pdb_utils.py |
Structure.raw_protein_chainer |
13 |
13 |
0 |
0% |
| biobb_model/model/fix_pdb_utils.py |
Structure.get_next_available_chain_name |
2 |
2 |
0 |
0% |
| biobb_model/model/fix_pdb_utils.py |
calculate_distance |
5 |
5 |
0 |
0% |
| biobb_model/model/fix_pdb_utils.py |
residue_name_2_letter |
9 |
4 |
0 |
56% |
| biobb_model/model/fix_pdb_utils.py |
generate_map_online |
31 |
13 |
0 |
58% |
| biobb_model/model/fix_pdb_utils.py |
generate_map_online.match_sequences |
25 |
5 |
0 |
80% |
| biobb_model/model/fix_pdb_utils.py |
format_topology_data |
24 |
3 |
0 |
88% |
| biobb_model/model/fix_pdb_utils.py |
map_sequence |
8 |
8 |
0 |
0% |
| biobb_model/model/fix_pdb_utils.py |
get_chain_sequences |
13 |
0 |
0 |
100% |
| biobb_model/model/fix_pdb_utils.py |
align |
29 |
3 |
0 |
90% |
| biobb_model/model/fix_pdb_utils.py |
blast |
9 |
9 |
0 |
0% |
| biobb_model/model/fix_pdb_utils.py |
get_uniprot_reference |
9 |
3 |
0 |
67% |
| biobb_model/model/fix_pdb_utils.py |
(no function) |
108 |
1 |
0 |
99% |
| biobb_model/model/fix_side_chain.py |
FixSideChain.__init__ |
9 |
0 |
0 |
100% |
| biobb_model/model/fix_side_chain.py |
FixSideChain.launch |
16 |
6 |
0 |
62% |
| biobb_model/model/fix_side_chain.py |
fix_side_chain |
2 |
1 |
0 |
50% |
| biobb_model/model/fix_side_chain.py |
main |
9 |
9 |
0 |
0% |
| biobb_model/model/fix_side_chain.py |
(no function) |
15 |
1 |
0 |
93% |
| biobb_model/model/fix_ssbonds.py |
FixSSBonds.__init__ |
8 |
0 |
0 |
100% |
| biobb_model/model/fix_ssbonds.py |
FixSSBonds.launch |
12 |
3 |
0 |
75% |
| biobb_model/model/fix_ssbonds.py |
fix_ssbonds |
2 |
1 |
0 |
50% |
| biobb_model/model/fix_ssbonds.py |
main |
9 |
9 |
0 |
0% |
| biobb_model/model/fix_ssbonds.py |
(no function) |
13 |
1 |
0 |
92% |
| biobb_model/model/mutate.py |
Mutate.__init__ |
10 |
0 |
0 |
100% |
| biobb_model/model/mutate.py |
Mutate.launch |
19 |
6 |
0 |
68% |
| biobb_model/model/mutate.py |
mutate |
2 |
1 |
0 |
50% |
| biobb_model/model/mutate.py |
main |
9 |
9 |
0 |
0% |
| biobb_model/model/mutate.py |
(no function) |
15 |
1 |
0 |
93% |
| biobb_model/test/__init__.py |
(no function) |
0 |
0 |
0 |
100% |
| biobb_model/test/unitests/test_model/test_checking_log.py |
TestCheckingLog.setup_class |
1 |
0 |
0 |
100% |
| biobb_model/test/unitests/test_model/test_checking_log.py |
TestCheckingLog.teardown_class |
1 |
0 |
0 |
100% |
| biobb_model/test/unitests/test_model/test_checking_log.py |
TestCheckingLog.test_launch |
3 |
0 |
0 |
100% |
| biobb_model/test/unitests/test_model/test_checking_log.py |
(no function) |
6 |
0 |
0 |
100% |
| biobb_model/test/unitests/test_model/test_fix_altlocs.py |
TestFixAltlocs.setup_class |
1 |
0 |
0 |
100% |
| biobb_model/test/unitests/test_model/test_fix_altlocs.py |
TestFixAltlocs.teardown_class |
1 |
0 |
0 |
100% |
| biobb_model/test/unitests/test_model/test_fix_altlocs.py |
TestFixAltlocs.test_launch |
3 |
0 |
0 |
100% |
| biobb_model/test/unitests/test_model/test_fix_altlocs.py |
(no function) |
6 |
0 |
0 |
100% |
| biobb_model/test/unitests/test_model/test_fix_amides.py |
TestFixAmides.setup_class |
1 |
0 |
0 |
100% |
| biobb_model/test/unitests/test_model/test_fix_amides.py |
TestFixAmides.teardown_class |
1 |
0 |
0 |
100% |
| biobb_model/test/unitests/test_model/test_fix_amides.py |
TestFixAmides.test_launch |
3 |
0 |
0 |
100% |
| biobb_model/test/unitests/test_model/test_fix_amides.py |
(no function) |
6 |
0 |
0 |
100% |
| biobb_model/test/unitests/test_model/test_fix_chirality.py |
TestFixChirality.setup_class |
1 |
0 |
0 |
100% |
| biobb_model/test/unitests/test_model/test_fix_chirality.py |
TestFixChirality.teardown_class |
1 |
0 |
0 |
100% |
| biobb_model/test/unitests/test_model/test_fix_chirality.py |
TestFixChirality.test_launch |
3 |
0 |
0 |
100% |
| biobb_model/test/unitests/test_model/test_fix_chirality.py |
(no function) |
6 |
0 |
0 |
100% |
| biobb_model/test/unitests/test_model/test_fix_pdb.py |
TestFixPdb.setup_class |
1 |
0 |
0 |
100% |
| biobb_model/test/unitests/test_model/test_fix_pdb.py |
TestFixPdb.teardown_class |
1 |
0 |
0 |
100% |
| biobb_model/test/unitests/test_model/test_fix_pdb.py |
TestFixPdb.test_launch |
3 |
0 |
0 |
100% |
| biobb_model/test/unitests/test_model/test_fix_pdb.py |
(no function) |
6 |
0 |
0 |
100% |
| biobb_model/test/unitests/test_model/test_fix_side_chain.py |
TestFixSideChain.setup_class |
1 |
0 |
0 |
100% |
| biobb_model/test/unitests/test_model/test_fix_side_chain.py |
TestFixSideChain.teardown_class |
1 |
0 |
0 |
100% |
| biobb_model/test/unitests/test_model/test_fix_side_chain.py |
TestFixSideChain.test_launch |
3 |
0 |
0 |
100% |
| biobb_model/test/unitests/test_model/test_fix_side_chain.py |
(no function) |
6 |
0 |
0 |
100% |
| biobb_model/test/unitests/test_model/test_fix_ssbonds.py |
TestFixSSBonds.setup_class |
1 |
0 |
0 |
100% |
| biobb_model/test/unitests/test_model/test_fix_ssbonds.py |
TestFixSSBonds.teardown_class |
1 |
0 |
0 |
100% |
| biobb_model/test/unitests/test_model/test_fix_ssbonds.py |
TestFixSSBonds.test_launch |
3 |
0 |
0 |
100% |
| biobb_model/test/unitests/test_model/test_fix_ssbonds.py |
(no function) |
6 |
0 |
0 |
100% |
| biobb_model/test/unitests/test_model/test_mutate.py |
TestFixSideChain.setup_class |
1 |
0 |
0 |
100% |
| biobb_model/test/unitests/test_model/test_mutate.py |
TestFixSideChain.teardown_class |
1 |
0 |
0 |
100% |
| biobb_model/test/unitests/test_model/test_mutate.py |
TestFixSideChain.test_launch |
3 |
0 |
0 |
100% |
| biobb_model/test/unitests/test_model/test_mutate.py |
(no function) |
6 |
0 |
0 |
100% |
| setup.py |
(no function) |
4 |
4 |
0 |
0% |