| model_workflow/__init__.py |
(no function) |
11 |
6 |
0 |
45% |
| model_workflow/__main__.py |
(no function) |
3 |
3 |
0 |
0% |
| model_workflow/analyses/__init__.py |
(no function) |
0 |
0 |
0 |
100% |
| model_workflow/analyses/area_per_lipid.py |
area_per_lipid |
19 |
0 |
0 |
100% |
| model_workflow/analyses/area_per_lipid.py |
process_apl |
15 |
0 |
0 |
100% |
| model_workflow/analyses/area_per_lipid.py |
(no function) |
11 |
0 |
0 |
100% |
| model_workflow/analyses/clusters.py |
clusters_analysis |
106 |
5 |
0 |
95% |
| model_workflow/analyses/clusters.py |
clustering |
8 |
0 |
0 |
100% |
| model_workflow/analyses/clusters.py |
(no function) |
12 |
0 |
0 |
100% |
| model_workflow/analyses/density.py |
density |
26 |
0 |
0 |
100% |
| model_workflow/analyses/density.py |
(no function) |
6 |
0 |
0 |
100% |
| model_workflow/analyses/dihedral_energies.py |
compute_dihedral_energies |
42 |
42 |
0 |
0% |
| model_workflow/analyses/dihedral_energies.py |
(no function) |
7 |
0 |
0 |
100% |
| model_workflow/analyses/distance_per_residue.py |
distance_per_residue |
47 |
5 |
0 |
89% |
| model_workflow/analyses/distance_per_residue.py |
distance_per_residue.residue_2_pytraj_residue_index |
10 |
4 |
0 |
60% |
| model_workflow/analyses/distance_per_residue.py |
(no function) |
9 |
0 |
0 |
100% |
| model_workflow/analyses/energies.py |
energies |
71 |
10 |
0 |
86% |
| model_workflow/analyses/energies.py |
energies.pdb2cmip |
41 |
2 |
0 |
95% |
| model_workflow/analyses/energies.py |
energies.adapt_cmip_grid |
30 |
7 |
0 |
77% |
| model_workflow/analyses/energies.py |
energies.get_cmip_energies |
21 |
6 |
0 |
71% |
| model_workflow/analyses/energies.py |
energies.get_frame_energy |
50 |
20 |
0 |
60% |
| model_workflow/analyses/energies.py |
set_cmip_elements |
17 |
3 |
0 |
82% |
| model_workflow/analyses/energies.py |
name_terminal_residues |
11 |
2 |
0 |
82% |
| model_workflow/analyses/energies.py |
mine_cmip_output |
20 |
4 |
0 |
80% |
| model_workflow/analyses/energies.py |
compute_new_grid |
14 |
0 |
0 |
100% |
| model_workflow/analyses/energies.py |
format_data |
39 |
0 |
0 |
100% |
| model_workflow/analyses/energies.py |
(no function) |
31 |
0 |
0 |
100% |
| model_workflow/analyses/helical_parameters.py |
helical_parameters |
28 |
3 |
0 |
89% |
| model_workflow/analyses/helical_parameters.py |
hydrogen_bonds |
17 |
2 |
0 |
88% |
| model_workflow/analyses/helical_parameters.py |
hydrogen_bonds.renumber_dat_file |
16 |
0 |
0 |
100% |
| model_workflow/analyses/helical_parameters.py |
hydrogen_bonds.compress_dat_to_bin |
39 |
3 |
0 |
92% |
| model_workflow/analyses/helical_parameters.py |
terminal_execution |
28 |
3 |
0 |
89% |
| model_workflow/analyses/helical_parameters.py |
send_files |
19 |
0 |
0 |
100% |
| model_workflow/analyses/helical_parameters.py |
get_stiffness |
16 |
0 |
0 |
100% |
| model_workflow/analyses/helical_parameters.py |
transform |
26 |
2 |
0 |
92% |
| model_workflow/analyses/helical_parameters.py |
get_stiffness_seq |
17 |
0 |
0 |
100% |
| model_workflow/analyses/helical_parameters.py |
get_subunit_stiffness |
23 |
0 |
0 |
100% |
| model_workflow/analyses/helical_parameters.py |
get_subunit_stiffness.circ_avg |
5 |
0 |
0 |
100% |
| model_workflow/analyses/helical_parameters.py |
checking |
5 |
0 |
0 |
100% |
| model_workflow/analyses/helical_parameters.py |
checking2 |
7 |
7 |
0 |
0% |
| model_workflow/analyses/helical_parameters.py |
read_series |
7 |
3 |
0 |
57% |
| model_workflow/analyses/helical_parameters.py |
flow_files_average |
23 |
0 |
0 |
100% |
| model_workflow/analyses/helical_parameters.py |
average_std |
6 |
0 |
0 |
100% |
| model_workflow/analyses/helical_parameters.py |
average_std_intra |
6 |
0 |
0 |
100% |
| model_workflow/analyses/helical_parameters.py |
flow_files_backbone |
24 |
0 |
0 |
100% |
| model_workflow/analyses/helical_parameters.py |
sugar_puckering |
9 |
0 |
0 |
100% |
| model_workflow/analyses/helical_parameters.py |
fix_angles |
3 |
0 |
0 |
100% |
| model_workflow/analyses/helical_parameters.py |
cpuck |
7 |
0 |
0 |
100% |
| model_workflow/analyses/helical_parameters.py |
canonical_alphagamma |
18 |
0 |
0 |
100% |
| model_workflow/analyses/helical_parameters.py |
fix_angles2 |
4 |
0 |
0 |
100% |
| model_workflow/analyses/helical_parameters.py |
check_alpgamm |
7 |
0 |
0 |
100% |
| model_workflow/analyses/helical_parameters.py |
bi_populations |
20 |
0 |
0 |
100% |
| model_workflow/analyses/helical_parameters.py |
angles_diff_ze |
5 |
0 |
0 |
100% |
| model_workflow/analyses/helical_parameters.py |
bi_pop |
3 |
0 |
0 |
100% |
| model_workflow/analyses/helical_parameters.py |
flow_files_timeseries |
22 |
22 |
0 |
0% |
| model_workflow/analyses/helical_parameters.py |
time_series |
9 |
9 |
0 |
0% |
| model_workflow/analyses/helical_parameters.py |
(no function) |
53 |
0 |
0 |
100% |
| model_workflow/analyses/hydrogen_bonds.py |
hydrogen_bonds |
84 |
10 |
0 |
88% |
| model_workflow/analyses/hydrogen_bonds.py |
hydrogen_bonds.pytraj_residue_number_2_residue |
12 |
4 |
0 |
67% |
| model_workflow/analyses/hydrogen_bonds.py |
hydrogen_bonds.get_populated_value |
3 |
3 |
0 |
0% |
| model_workflow/analyses/hydrogen_bonds.py |
(no function) |
9 |
0 |
0 |
100% |
| model_workflow/analyses/lipid_interactions.py |
lipid_interactions |
26 |
0 |
0 |
100% |
| model_workflow/analyses/lipid_interactions.py |
(no function) |
9 |
0 |
0 |
100% |
| model_workflow/analyses/lipid_order.py |
lipid_order |
31 |
0 |
0 |
100% |
| model_workflow/analyses/lipid_order.py |
get_all_acyl_chains |
13 |
0 |
0 |
100% |
| model_workflow/analyses/lipid_order.py |
get_all_acyl_chains.explore_carbon_group |
14 |
1 |
0 |
93% |
| model_workflow/analyses/lipid_order.py |
find_CH_bonds |
19 |
2 |
0 |
89% |
| model_workflow/analyses/lipid_order.py |
natural_sort_key |
2 |
0 |
0 |
100% |
| model_workflow/analyses/lipid_order.py |
(no function) |
11 |
0 |
0 |
100% |
| model_workflow/analyses/markov.py |
markov |
52 |
49 |
0 |
6% |
| model_workflow/analyses/markov.py |
(no function) |
6 |
0 |
0 |
100% |
| model_workflow/analyses/markov_2.py |
markov |
45 |
45 |
0 |
0% |
| model_workflow/analyses/markov_2.py |
(no function) |
5 |
5 |
0 |
0% |
| model_workflow/analyses/nassa.py |
BasePairCorrelation.__init__ |
1 |
0 |
0 |
100% |
| model_workflow/analyses/nassa.py |
BasePairCorrelation.extract |
20 |
0 |
0 |
100% |
| model_workflow/analyses/nassa.py |
BasePairCorrelation.extraer_tetramero_central |
1 |
1 |
0 |
0% |
| model_workflow/analyses/nassa.py |
BasePairCorrelation.transform |
12 |
0 |
0 |
100% |
| model_workflow/analyses/nassa.py |
BasePairCorrelation.iterate_trajectory |
15 |
2 |
0 |
87% |
| model_workflow/analyses/nassa.py |
BasePairCorrelation.get_correlation |
12 |
0 |
0 |
100% |
| model_workflow/analyses/nassa.py |
BasePairCorrelation.get_corr_by_method |
8 |
0 |
0 |
100% |
| model_workflow/analyses/nassa.py |
BasePairCorrelation.circular |
7 |
0 |
0 |
100% |
| model_workflow/analyses/nassa.py |
BasePairCorrelation.circlineal |
12 |
0 |
0 |
100% |
| model_workflow/analyses/nassa.py |
BasePairCorrelation.make_tables |
1 |
0 |
0 |
100% |
| model_workflow/analyses/nassa.py |
BasePairCorrelation.make_plots |
1 |
0 |
0 |
100% |
| model_workflow/analyses/nassa.py |
BConformations.__init__ |
7 |
7 |
0 |
0% |
| model_workflow/analyses/nassa.py |
BConformations.extract |
20 |
20 |
0 |
0% |
| model_workflow/analyses/nassa.py |
BConformations.transform |
17 |
17 |
0 |
0% |
| model_workflow/analyses/nassa.py |
BConformations.get_angles_difference |
17 |
17 |
0 |
0% |
| model_workflow/analyses/nassa.py |
BConformations.get_angles_difference.fix_angle_range |
5 |
5 |
0 |
0% |
| model_workflow/analyses/nassa.py |
BConformations.make_tables |
4 |
4 |
0 |
0% |
| model_workflow/analyses/nassa.py |
BConformations.make_plots |
4 |
4 |
0 |
0% |
| model_workflow/analyses/nassa.py |
CoordinateCorrelation.__init__ |
1 |
1 |
0 |
0% |
| model_workflow/analyses/nassa.py |
CoordinateCorrelation.extract |
20 |
20 |
0 |
0% |
| model_workflow/analyses/nassa.py |
CoordinateCorrelation.transform |
7 |
7 |
0 |
0% |
| model_workflow/analyses/nassa.py |
CoordinateCorrelation.iterate_trajectory |
24 |
24 |
0 |
0% |
| model_workflow/analyses/nassa.py |
CoordinateCorrelation.get_corr_method |
8 |
8 |
0 |
0% |
| model_workflow/analyses/nassa.py |
CoordinateCorrelation.circular |
7 |
7 |
0 |
0% |
| model_workflow/analyses/nassa.py |
CoordinateCorrelation.circlineal |
10 |
10 |
0 |
0% |
| model_workflow/analyses/nassa.py |
CoordinateCorrelation.make_tables |
8 |
8 |
0 |
0% |
| model_workflow/analyses/nassa.py |
CoordinateCorrelation.make_plots |
4 |
4 |
0 |
0% |
| model_workflow/analyses/nassa.py |
CoordinateDistributions.__init__ |
5 |
0 |
0 |
100% |
| model_workflow/analyses/nassa.py |
CoordinateDistributions.extract |
20 |
0 |
0 |
100% |
| model_workflow/analyses/nassa.py |
CoordinateDistributions.transform |
8 |
0 |
0 |
100% |
| model_workflow/analyses/nassa.py |
CoordinateDistributions.coordinate_iteration |
9 |
2 |
0 |
78% |
| model_workflow/analyses/nassa.py |
CoordinateDistributions.duplicate_trajectory_iteration |
23 |
23 |
0 |
0% |
| model_workflow/analyses/nassa.py |
CoordinateDistributions.trajectory_iteration |
23 |
4 |
0 |
83% |
| model_workflow/analyses/nassa.py |
CoordinateDistributions.subunit_iteration |
5 |
0 |
0 |
100% |
| model_workflow/analyses/nassa.py |
CoordinateDistributions.add_modality_labels |
15 |
0 |
0 |
100% |
| model_workflow/analyses/nassa.py |
CoordinateDistributions.make_tables |
2 |
0 |
0 |
100% |
| model_workflow/analyses/nassa.py |
CoordinateDistributions.make_plots |
5 |
0 |
0 |
100% |
| model_workflow/analyses/nassa.py |
StiffnessDistributions.__init__ |
1 |
0 |
0 |
100% |
| model_workflow/analyses/nassa.py |
StiffnessDistributions.extract |
23 |
2 |
0 |
91% |
| model_workflow/analyses/nassa.py |
StiffnessDistributions.transform |
13 |
0 |
0 |
100% |
| model_workflow/analyses/nassa.py |
StiffnessDistributions.get_stiffness |
18 |
0 |
0 |
100% |
| model_workflow/analyses/nassa.py |
StiffnessDistributions.get_subunit_stiffness |
35 |
13 |
0 |
63% |
| model_workflow/analyses/nassa.py |
StiffnessDistributions.circ_avg |
5 |
0 |
0 |
100% |
| model_workflow/analyses/nassa.py |
StiffnessDistributions.unimod_labels |
8 |
0 |
0 |
100% |
| model_workflow/analyses/nassa.py |
StiffnessDistributions.make_tables |
10 |
0 |
0 |
100% |
| model_workflow/analyses/nassa.py |
StiffnessDistributions.make_plots |
11 |
0 |
0 |
100% |
| model_workflow/analyses/nassa.py |
run_nassa |
23 |
7 |
0 |
70% |
| model_workflow/analyses/nassa.py |
workflow_nassa |
92 |
64 |
0 |
30% |
| model_workflow/analyses/nassa.py |
(no function) |
77 |
0 |
0 |
100% |
| model_workflow/analyses/pca.py |
pca |
53 |
8 |
0 |
85% |
| model_workflow/analyses/pca.py |
get_closer_value_index |
2 |
0 |
0 |
100% |
| model_workflow/analyses/pca.py |
(no function) |
9 |
0 |
0 |
100% |
| model_workflow/analyses/pca_contacts.py |
pytraj_residue_pairs |
2 |
2 |
0 |
0% |
| model_workflow/analyses/pca_contacts.py |
mdtraj_residue_pairs |
2 |
2 |
0 |
0% |
| model_workflow/analyses/pca_contacts.py |
pytraj_distances |
3 |
3 |
0 |
0% |
| model_workflow/analyses/pca_contacts.py |
mdtraj_distances |
2 |
2 |
0 |
0% |
| model_workflow/analyses/pca_contacts.py |
get_most_frequent_pairs |
6 |
6 |
0 |
0% |
| model_workflow/analyses/pca_contacts.py |
sigmoid |
1 |
1 |
0 |
0% |
| model_workflow/analyses/pca_contacts.py |
pca_contacts |
33 |
33 |
0 |
0% |
| model_workflow/analyses/pca_contacts.py |
(no function) |
13 |
13 |
0 |
0% |
| model_workflow/analyses/pockets.py |
pockets |
189 |
18 |
0 |
90% |
| model_workflow/analyses/pockets.py |
pockets.get_index |
2 |
0 |
0 |
100% |
| model_workflow/analyses/pockets.py |
pockets.get_colliding_points |
15 |
6 |
0 |
60% |
| model_workflow/analyses/pockets.py |
pockets.set_pocket |
14 |
0 |
0 |
100% |
| model_workflow/analyses/pockets.py |
pockets.is_pocket_base |
7 |
0 |
0 |
100% |
| model_workflow/analyses/pockets.py |
pockets.get_coordinates |
3 |
0 |
0 |
100% |
| model_workflow/analyses/pockets.py |
(no function) |
17 |
0 |
0 |
100% |
| model_workflow/analyses/rgyr.py |
rgyr |
25 |
6 |
0 |
76% |
| model_workflow/analyses/rgyr.py |
(no function) |
11 |
0 |
0 |
100% |
| model_workflow/analyses/rmsd_check.py |
check_trajectory_integrity |
76 |
37 |
0 |
51% |
| model_workflow/analyses/rmsd_check.py |
check_trajectory_integrity_per_fragment |
71 |
71 |
0 |
0% |
| model_workflow/analyses/rmsd_check.py |
check_trajectory_integrity_per_fragment_2 |
66 |
66 |
0 |
0% |
| model_workflow/analyses/rmsd_check.py |
check_trajectory_integrity_per_residue |
98 |
98 |
0 |
0% |
| model_workflow/analyses/rmsd_check.py |
(no function) |
17 |
0 |
0 |
100% |
| model_workflow/analyses/rmsd_pairwise.py |
rmsd_pairwise |
41 |
10 |
0 |
76% |
| model_workflow/analyses/rmsd_pairwise.py |
(no function) |
7 |
0 |
0 |
100% |
| model_workflow/analyses/rmsd_per_residue.py |
rmsd_per_residue |
25 |
5 |
0 |
80% |
| model_workflow/analyses/rmsd_per_residue.py |
(no function) |
7 |
0 |
0 |
100% |
| model_workflow/analyses/rmsds.py |
rmsds |
37 |
2 |
0 |
95% |
| model_workflow/analyses/rmsds.py |
rmsd |
15 |
4 |
0 |
73% |
| model_workflow/analyses/rmsds.py |
(no function) |
9 |
0 |
0 |
100% |
| model_workflow/analyses/rmsf.py |
rmsf |
15 |
3 |
0 |
80% |
| model_workflow/analyses/rmsf.py |
(no function) |
7 |
0 |
0 |
100% |
| model_workflow/analyses/sasa.py |
sasa |
60 |
9 |
0 |
85% |
| model_workflow/analyses/sasa.py |
(no function) |
10 |
0 |
0 |
100% |
| model_workflow/analyses/thickness.py |
thickness |
24 |
0 |
0 |
100% |
| model_workflow/analyses/thickness.py |
(no function) |
8 |
0 |
0 |
100% |
| model_workflow/analyses/tmscores.py |
tmscores |
46 |
8 |
0 |
83% |
| model_workflow/analyses/tmscores.py |
(no function) |
8 |
0 |
0 |
100% |
| model_workflow/console.py |
CustomHelpFormatter.__init__ |
1 |
0 |
0 |
100% |
| model_workflow/console.py |
CustomHelpFormatter._split_lines |
7 |
0 |
0 |
100% |
| model_workflow/console.py |
CustomHelpFormatter._format_usage |
13 |
0 |
0 |
100% |
| model_workflow/console.py |
CustomHelpFormatter._format_action_invocation |
14 |
1 |
0 |
93% |
| model_workflow/console.py |
CustomArgumentParser.error |
16 |
0 |
0 |
100% |
| model_workflow/console.py |
main |
102 |
39 |
0 |
62% |
| model_workflow/console.py |
custom.__call__ |
3 |
0 |
0 |
100% |
| model_workflow/console.py |
pretty_list |
8 |
1 |
0 |
88% |
| model_workflow/console.py |
(no function) |
126 |
0 |
0 |
100% |
| model_workflow/mwf.py |
Task.__init__ |
11 |
0 |
0 |
100% |
| model_workflow/mwf.py |
Task._get_parent_output |
1 |
0 |
0 |
100% |
| model_workflow/mwf.py |
Task._set_parent_output |
1 |
0 |
0 |
100% |
| model_workflow/mwf.py |
Task._get_parent_output_filepath |
1 |
0 |
0 |
100% |
| model_workflow/mwf.py |
Task._set_parent_output_filepath |
1 |
0 |
0 |
100% |
| model_workflow/mwf.py |
Task.get_output |
3 |
3 |
0 |
0% |
| model_workflow/mwf.py |
Task.get_output_filepath |
6 |
1 |
0 |
83% |
| model_workflow/mwf.py |
Task.get_output_file |
2 |
0 |
0 |
100% |
| model_workflow/mwf.py |
Task.__repr__ |
1 |
0 |
0 |
100% |
| model_workflow/mwf.py |
Task.__call__ |
69 |
6 |
0 |
91% |
| model_workflow/mwf.py |
Task.find_arg_value |
11 |
1 |
0 |
91% |
| model_workflow/mwf.py |
Task.get_changed_inputs |
12 |
0 |
0 |
100% |
| model_workflow/mwf.py |
MD.__init__ |
36 |
4 |
0 |
89% |
| model_workflow/mwf.py |
MD.__repr__ |
1 |
1 |
0 |
0% |
| model_workflow/mwf.py |
MD.pathify |
1 |
0 |
0 |
100% |
| model_workflow/mwf.py |
MD.get_input_structure_filepath |
14 |
3 |
0 |
79% |
| model_workflow/mwf.py |
MD.get_input_structure_filepath.relativize_and_parse_paths |
31 |
15 |
0 |
52% |
| model_workflow/mwf.py |
MD.get_input_structure_file |
12 |
2 |
0 |
83% |
| model_workflow/mwf.py |
MD.get_input_trajectory_filepaths |
12 |
2 |
0 |
83% |
| model_workflow/mwf.py |
MD.get_input_trajectory_filepaths.relativize_and_parse_paths |
35 |
14 |
0 |
60% |
| model_workflow/mwf.py |
MD.get_input_trajectory_filepaths.relativize_and_parse_paths.parse_all_glob |
4 |
0 |
0 |
100% |
| model_workflow/mwf.py |
MD.get_input_trajectory_files |
19 |
3 |
0 |
84% |
| model_workflow/mwf.py |
MD.get_md_inputs |
16 |
2 |
0 |
88% |
| model_workflow/mwf.py |
MD.get_file |
8 |
4 |
0 |
50% |
| model_workflow/mwf.py |
MD.print_tests_summary |
15 |
5 |
0 |
67% |
| model_workflow/mwf.py |
MD._issue_required_test_warnings |
11 |
11 |
0 |
0% |
| model_workflow/mwf.py |
MD.get_structure_file |
12 |
5 |
0 |
58% |
| model_workflow/mwf.py |
MD.get_trajectory_file |
15 |
13 |
0 |
13% |
| model_workflow/mwf.py |
MD.get_topology_file |
1 |
0 |
0 |
100% |
| model_workflow/mwf.py |
MD.get_reference_bonds |
1 |
0 |
0 |
100% |
| model_workflow/mwf.py |
MD.get_structure |
10 |
2 |
0 |
80% |
| model_workflow/mwf.py |
MD.input_getter |
2 |
0 |
0 |
100% |
| model_workflow/mwf.py |
MD.input_getter.getter |
4 |
1 |
0 |
75% |
| model_workflow/mwf.py |
MD._set_pbc_selection |
29 |
9 |
0 |
69% |
| model_workflow/mwf.py |
MD.get_pbc_selection |
4 |
0 |
0 |
100% |
| model_workflow/mwf.py |
MD.get_pbc_residues |
8 |
4 |
0 |
50% |
| model_workflow/mwf.py |
MD._set_cg_selection |
23 |
8 |
0 |
65% |
| model_workflow/mwf.py |
MD.get_cg_selection |
4 |
1 |
0 |
75% |
| model_workflow/mwf.py |
MD.get_cg_residues |
8 |
4 |
0 |
50% |
| model_workflow/mwf.py |
MD.get_populations |
1 |
0 |
0 |
100% |
| model_workflow/mwf.py |
MD.get_transitions |
1 |
1 |
0 |
0% |
| model_workflow/mwf.py |
MD.get_protein_map |
1 |
1 |
0 |
0% |
| model_workflow/mwf.py |
MD.is_trajectory_integral |
4 |
1 |
0 |
75% |
| model_workflow/mwf.py |
Project.__init__ |
85 |
10 |
0 |
88% |
| model_workflow/mwf.py |
Project.__repr__ |
1 |
1 |
0 |
0% |
| model_workflow/mwf.py |
Project.pathify |
1 |
0 |
0 |
100% |
| model_workflow/mwf.py |
Project.check_md_directories |
4 |
2 |
0 |
50% |
| model_workflow/mwf.py |
Project.get_md_directories |
21 |
7 |
0 |
67% |
| model_workflow/mwf.py |
Project.get_reference_md_index |
8 |
1 |
0 |
88% |
| model_workflow/mwf.py |
Project.get_reference_md |
4 |
0 |
0 |
100% |
| model_workflow/mwf.py |
Project.get_mds |
20 |
0 |
0 |
100% |
| model_workflow/mwf.py |
Project.is_inputs_file_available |
7 |
1 |
0 |
86% |
| model_workflow/mwf.py |
Project.get_inputs_file |
8 |
1 |
0 |
88% |
| model_workflow/mwf.py |
Project.guess_input_topology_filepath |
20 |
11 |
0 |
45% |
| model_workflow/mwf.py |
Project.guess_input_topology_filepath.find_first_accepted_topology_filename |
9 |
0 |
0 |
100% |
| model_workflow/mwf.py |
Project.get_input_topology_filepath |
13 |
2 |
0 |
85% |
| model_workflow/mwf.py |
Project.get_input_topology_filepath.parse |
10 |
4 |
0 |
60% |
| model_workflow/mwf.py |
Project.get_input_topology_file |
19 |
6 |
0 |
68% |
| model_workflow/mwf.py |
Project.get_input_structure_file |
1 |
1 |
0 |
0% |
| model_workflow/mwf.py |
Project.get_input_trajectory_files |
1 |
1 |
0 |
0% |
| model_workflow/mwf.py |
Project.get_populations_file |
3 |
1 |
0 |
67% |
| model_workflow/mwf.py |
Project.get_transitions_file |
3 |
1 |
0 |
67% |
| model_workflow/mwf.py |
Project.get_file |
1 |
0 |
0 |
100% |
| model_workflow/mwf.py |
Project.get_inputs |
15 |
3 |
0 |
80% |
| model_workflow/mwf.py |
Project.get_input |
6 |
0 |
0 |
100% |
| model_workflow/mwf.py |
Project.input_getter |
2 |
0 |
0 |
100% |
| model_workflow/mwf.py |
Project.input_getter.getter |
1 |
0 |
0 |
100% |
| model_workflow/mwf.py |
Project.get_input_pbc_selection |
6 |
1 |
0 |
83% |
| model_workflow/mwf.py |
Project.get_input_cg_selection |
6 |
1 |
0 |
83% |
| model_workflow/mwf.py |
Project.check_is_time_dependent |
5 |
3 |
0 |
40% |
| model_workflow/mwf.py |
Project.inherit_topology_filename |
9 |
2 |
0 |
78% |
| model_workflow/mwf.py |
Project.get_topology_filepath |
5 |
0 |
0 |
100% |
| model_workflow/mwf.py |
Project.get_topology_file |
11 |
5 |
0 |
55% |
| model_workflow/mwf.py |
Project.get_structure_file |
1 |
0 |
0 |
100% |
| model_workflow/mwf.py |
Project.get_trajectory_file |
1 |
0 |
0 |
100% |
| model_workflow/mwf.py |
Project.get_structure |
1 |
0 |
0 |
100% |
| model_workflow/mwf.py |
Project.get_pbc_residues |
1 |
0 |
0 |
100% |
| model_workflow/mwf.py |
Project.get_cg_residues |
1 |
0 |
0 |
100% |
| model_workflow/mwf.py |
Project.get_snaphsots |
1 |
1 |
0 |
0% |
| model_workflow/mwf.py |
Project.get_check_stable_bonds |
4 |
4 |
0 |
0% |
| model_workflow/mwf.py |
Project.get_topology_reader |
3 |
0 |
0 |
100% |
| model_workflow/mwf.py |
Project.get_dihedrals |
3 |
0 |
0 |
100% |
| model_workflow/mwf.py |
Project.get_populations |
6 |
3 |
0 |
50% |
| model_workflow/mwf.py |
Project.get_transitions |
6 |
6 |
0 |
0% |
| model_workflow/mwf.py |
Project.get_pdb_ids |
14 |
2 |
0 |
86% |
| model_workflow/mwf.py |
read_file |
5 |
5 |
0 |
0% |
| model_workflow/mwf.py |
name_2_directory |
4 |
0 |
0 |
100% |
| model_workflow/mwf.py |
check_directory |
3 |
1 |
0 |
67% |
| model_workflow/mwf.py |
directory_2_name |
2 |
0 |
0 |
100% |
| model_workflow/mwf.py |
remove_final_slash |
3 |
1 |
0 |
67% |
| model_workflow/mwf.py |
workflow |
59 |
21 |
0 |
64% |
| model_workflow/mwf.py |
(no function) |
330 |
2 |
0 |
99% |
| model_workflow/resources/covid_variants.py |
(no function) |
1 |
0 |
0 |
100% |
| model_workflow/tools/__init__.py |
(no function) |
2 |
0 |
0 |
100% |
| model_workflow/tools/chains.py |
request_interpsocan |
13 |
13 |
0 |
0% |
| model_workflow/tools/chains.py |
check_interproscan_status |
12 |
12 |
0 |
0% |
| model_workflow/tools/chains.py |
check_interproscan_result |
14 |
14 |
0 |
0% |
| model_workflow/tools/chains.py |
check_sequence_in_mddb |
14 |
8 |
0 |
43% |
| model_workflow/tools/chains.py |
get_protein_parsed_chains |
13 |
0 |
0 |
100% |
| model_workflow/tools/chains.py |
import_chains |
6 |
6 |
0 |
0% |
| model_workflow/tools/chains.py |
prepare_chain_references |
25 |
5 |
0 |
80% |
| model_workflow/tools/chains.py |
get_interproscan_results |
28 |
24 |
0 |
14% |
| model_workflow/tools/chains.py |
(no function) |
18 |
0 |
0 |
100% |
| model_workflow/tools/check_inputs.py |
check_inputs |
52 |
30 |
0 |
42% |
| model_workflow/tools/check_inputs.py |
check_inputs.get_structure_atoms |
2 |
0 |
0 |
100% |
| model_workflow/tools/check_inputs.py |
check_inputs.get_structure_and_trajectory_atoms |
6 |
0 |
0 |
100% |
| model_workflow/tools/check_inputs.py |
check_inputs.get_topology_and_trajectory_atoms |
58 |
31 |
0 |
47% |
| model_workflow/tools/check_inputs.py |
(no function) |
25 |
0 |
0 |
100% |
| model_workflow/tools/conversions.py |
convert |
36 |
7 |
0 |
81% |
| model_workflow/tools/conversions.py |
convert.convert_structure |
20 |
8 |
0 |
60% |
| model_workflow/tools/conversions.py |
convert.convert_trajectory |
24 |
8 |
0 |
67% |
| model_workflow/tools/conversions.py |
(no function) |
16 |
0 |
0 |
100% |
| model_workflow/tools/filter_atoms.py |
filter_atoms |
65 |
30 |
0 |
54% |
| model_workflow/tools/filter_atoms.py |
standard_topology_filter |
50 |
50 |
0 |
0% |
| model_workflow/tools/filter_atoms.py |
standard_topology_filter.filter_by_indices |
3 |
3 |
0 |
0% |
| model_workflow/tools/filter_atoms.py |
(no function) |
15 |
0 |
0 |
100% |
| model_workflow/tools/find_interaction_types.py |
find_interaction_types |
35 |
7 |
0 |
80% |
| model_workflow/tools/find_interaction_types.py |
(no function) |
3 |
0 |
0 |
100% |
| model_workflow/tools/fix_gromacs_masses.py |
fix_gromacs_masses |
2 |
0 |
0 |
100% |
| model_workflow/tools/fix_gromacs_masses.py |
(no function) |
7 |
0 |
0 |
100% |
| model_workflow/tools/generate_ligands_desc.py |
get_drugbank_smiles |
13 |
13 |
0 |
0% |
| model_workflow/tools/generate_ligands_desc.py |
get_chembl_smiles |
17 |
17 |
0 |
0% |
| model_workflow/tools/generate_ligands_desc.py |
get_pubchem_data |
96 |
34 |
0 |
65% |
| model_workflow/tools/generate_ligands_desc.py |
find_drugbank_pubchem |
18 |
18 |
0 |
0% |
| model_workflow/tools/generate_ligands_desc.py |
find_chembl_pubchem |
24 |
24 |
0 |
0% |
| model_workflow/tools/generate_ligands_desc.py |
obtain_mordred_morgan_descriptors |
19 |
2 |
0 |
89% |
| model_workflow/tools/generate_ligands_desc.py |
check_matched_ligand |
12 |
4 |
0 |
67% |
| model_workflow/tools/generate_ligands_desc.py |
generate_ligand_mapping |
91 |
25 |
0 |
73% |
| model_workflow/tools/generate_ligands_desc.py |
import_ligands |
6 |
6 |
0 |
0% |
| model_workflow/tools/generate_ligands_desc.py |
obtain_ligand_data_from_file |
4 |
2 |
0 |
50% |
| model_workflow/tools/generate_ligands_desc.py |
obtain_ligand_data_from_pubchem |
15 |
8 |
0 |
47% |
| model_workflow/tools/generate_ligands_desc.py |
count_atom_elements_per_residue |
12 |
0 |
0 |
100% |
| model_workflow/tools/generate_ligands_desc.py |
nest_brackets |
10 |
3 |
0 |
70% |
| model_workflow/tools/generate_ligands_desc.py |
parse_compound |
5 |
0 |
0 |
100% |
| model_workflow/tools/generate_ligands_desc.py |
split_when |
9 |
0 |
0 |
100% |
| model_workflow/tools/generate_ligands_desc.py |
count_atom_elements |
4 |
0 |
0 |
100% |
| model_workflow/tools/generate_ligands_desc.py |
parse_splits |
14 |
1 |
0 |
93% |
| model_workflow/tools/generate_ligands_desc.py |
match_ligandsID_to_res |
16 |
0 |
0 |
100% |
| model_workflow/tools/generate_ligands_desc.py |
map_ligand_residues |
12 |
1 |
0 |
92% |
| model_workflow/tools/generate_ligands_desc.py |
smiles_to_pubchem_id |
26 |
26 |
0 |
0% |
| model_workflow/tools/generate_ligands_desc.py |
pdb_ligand_to_pubchem |
7 |
0 |
0 |
100% |
| model_workflow/tools/generate_ligands_desc.py |
pdb_ligand_to_pubchem_RAW |
17 |
8 |
0 |
53% |
| model_workflow/tools/generate_ligands_desc.py |
pdb_ligand_to_pubchem_RAW_RAW |
18 |
6 |
0 |
67% |
| model_workflow/tools/generate_ligands_desc.py |
get_pdb_ligand_codes |
15 |
1 |
0 |
93% |
| model_workflow/tools/generate_ligands_desc.py |
get_prd_ligand_code |
11 |
5 |
0 |
55% |
| model_workflow/tools/generate_ligands_desc.py |
pdb_to_pubchem |
15 |
2 |
0 |
87% |
| model_workflow/tools/generate_ligands_desc.py |
(no function) |
41 |
0 |
0 |
100% |
| model_workflow/tools/generate_lipid_references.py |
generate_lipid_references |
24 |
8 |
0 |
67% |
| model_workflow/tools/generate_lipid_references.py |
(no function) |
5 |
0 |
0 |
100% |
| model_workflow/tools/generate_map.py |
add_leading_and_trailing_gaps |
10 |
0 |
0 |
100% |
| model_workflow/tools/generate_map.py |
generate_protein_mapping |
92 |
43 |
0 |
53% |
| model_workflow/tools/generate_map.py |
generate_protein_mapping.get_reference |
8 |
2 |
0 |
75% |
| model_workflow/tools/generate_map.py |
generate_protein_mapping.match_sequences |
73 |
15 |
0 |
79% |
| model_workflow/tools/generate_map.py |
export_references |
15 |
2 |
0 |
87% |
| model_workflow/tools/generate_map.py |
import_references |
7 |
0 |
0 |
100% |
| model_workflow/tools/generate_map.py |
get_parsed_chains |
13 |
0 |
0 |
100% |
| model_workflow/tools/generate_map.py |
align |
31 |
6 |
0 |
81% |
| model_workflow/tools/generate_map.py |
blast |
10 |
10 |
0 |
0% |
| model_workflow/tools/generate_map.py |
get_mdposit_reference |
18 |
12 |
0 |
33% |
| model_workflow/tools/generate_map.py |
get_uniprot_reference |
69 |
18 |
0 |
74% |
| model_workflow/tools/generate_map.py |
pdb_to_uniprot |
36 |
19 |
0 |
47% |
| model_workflow/tools/generate_map.py |
get_sequence_metadata |
66 |
24 |
0 |
64% |
| model_workflow/tools/generate_map.py |
get_sequence_metadata.in_range |
4 |
0 |
0 |
100% |
| model_workflow/tools/generate_map.py |
(no function) |
30 |
0 |
0 |
100% |
| model_workflow/tools/generate_membrane_mapping.py |
generate_membrane_mapping |
58 |
10 |
0 |
83% |
| model_workflow/tools/generate_membrane_mapping.py |
(no function) |
7 |
0 |
0 |
100% |
| model_workflow/tools/generate_metadata.py |
prepare_project_metadata |
67 |
23 |
0 |
66% |
| model_workflow/tools/generate_metadata.py |
generate_md_metadata |
17 |
3 |
0 |
82% |
| model_workflow/tools/generate_metadata.py |
(no function) |
9 |
0 |
0 |
100% |
| model_workflow/tools/generate_pdb_references.py |
prepare_pdb_references |
16 |
6 |
0 |
62% |
| model_workflow/tools/generate_pdb_references.py |
get_pdb_reference |
32 |
5 |
0 |
84% |
| model_workflow/tools/generate_pdb_references.py |
DEPRECATED_download_pdb_data |
30 |
30 |
0 |
0% |
| model_workflow/tools/generate_pdb_references.py |
(no function) |
9 |
0 |
0 |
100% |
| model_workflow/tools/generate_topology.py |
generate_topology |
40 |
4 |
0 |
90% |
| model_workflow/tools/generate_topology.py |
(no function) |
4 |
0 |
0 |
100% |
| model_workflow/tools/get_atoms_count.py |
get_atoms_count |
37 |
0 |
0 |
100% |
| model_workflow/tools/get_atoms_count.py |
(no function) |
1 |
0 |
0 |
100% |
| model_workflow/tools/get_bonds.py |
get_excluded_atoms_selection |
3 |
0 |
0 |
100% |
| model_workflow/tools/get_bonds.py |
do_bonds_match |
26 |
6 |
0 |
77% |
| model_workflow/tools/get_bonds.py |
get_most_stable_bonds |
22 |
0 |
0 |
100% |
| model_workflow/tools/get_bonds.py |
get_bonds_canonical_frame |
29 |
13 |
0 |
55% |
| model_workflow/tools/get_bonds.py |
get_bonds_canonical_frame.format_row |
1 |
1 |
0 |
0% |
| model_workflow/tools/get_bonds.py |
mine_topology_bonds |
30 |
13 |
0 |
57% |
| model_workflow/tools/get_bonds.py |
get_tpr_bonds |
6 |
3 |
0 |
50% |
| model_workflow/tools/get_bonds.py |
get_tpr_bonds_mdanalysis |
4 |
4 |
0 |
0% |
| model_workflow/tools/get_bonds.py |
sort_bonds |
6 |
0 |
0 |
100% |
| model_workflow/tools/get_bonds.py |
find_safe_bonds |
20 |
8 |
0 |
60% |
| model_workflow/tools/get_bonds.py |
discard_coarse_grain_bonds |
2 |
1 |
0 |
50% |
| model_workflow/tools/get_bonds.py |
(no function) |
21 |
0 |
0 |
100% |
| model_workflow/tools/get_box_size.py |
get_box_size |
16 |
2 |
0 |
88% |
| model_workflow/tools/get_box_size.py |
(no function) |
5 |
0 |
0 |
100% |
| model_workflow/tools/get_charges.py |
get_charges |
20 |
7 |
0 |
65% |
| model_workflow/tools/get_charges.py |
get_topology_charges |
7 |
4 |
0 |
43% |
| model_workflow/tools/get_charges.py |
get_topology_charges_pytraj |
3 |
0 |
0 |
100% |
| model_workflow/tools/get_charges.py |
get_topology_charges_mdanalysis |
4 |
4 |
0 |
0% |
| model_workflow/tools/get_charges.py |
generate_raw_energies_file |
3 |
3 |
0 |
0% |
| model_workflow/tools/get_charges.py |
get_raw_charges |
6 |
6 |
0 |
0% |
| model_workflow/tools/get_charges.py |
get_tpr_charges |
6 |
0 |
0 |
100% |
| model_workflow/tools/get_charges.py |
get_tpr_charges_mdanalysis |
4 |
0 |
0 |
100% |
| model_workflow/tools/get_charges.py |
(no function) |
16 |
0 |
0 |
100% |
| model_workflow/tools/get_first_frame.py |
get_first_frame |
9 |
4 |
0 |
56% |
| model_workflow/tools/get_first_frame.py |
(no function) |
5 |
0 |
0 |
100% |
| model_workflow/tools/get_inchi_keys.py |
get_connected_residues |
13 |
1 |
0 |
92% |
| model_workflow/tools/get_inchi_keys.py |
residue_to_inchi |
4 |
0 |
0 |
100% |
| model_workflow/tools/get_inchi_keys.py |
get_inchi_keys |
40 |
3 |
0 |
92% |
| model_workflow/tools/get_inchi_keys.py |
is_in_LIPID_MAPS |
10 |
1 |
0 |
90% |
| model_workflow/tools/get_inchi_keys.py |
is_in_swiss_lipids |
7 |
0 |
0 |
100% |
| model_workflow/tools/get_inchi_keys.py |
get_atoms_info |
2 |
2 |
0 |
0% |
| model_workflow/tools/get_inchi_keys.py |
inchi_2_mol |
15 |
15 |
0 |
0% |
| model_workflow/tools/get_inchi_keys.py |
Residue_2_Mol |
20 |
20 |
0 |
0% |
| model_workflow/tools/get_inchi_keys.py |
(no function) |
16 |
0 |
0 |
100% |
| model_workflow/tools/get_pdb_frames.py |
get_pdb_frames |
5 |
0 |
0 |
100% |
| model_workflow/tools/get_pdb_frames.py |
get_pdb_frames.frames_generator |
13 |
0 |
0 |
100% |
| model_workflow/tools/get_pdb_frames.py |
get_pdb_frame |
5 |
0 |
0 |
100% |
| model_workflow/tools/get_pdb_frames.py |
(no function) |
8 |
0 |
0 |
100% |
| model_workflow/tools/get_reduced_trajectory.py |
calculate_frame_step |
3 |
0 |
0 |
100% |
| model_workflow/tools/get_reduced_trajectory.py |
get_reduced_trajectory |
21 |
16 |
0 |
24% |
| model_workflow/tools/get_reduced_trajectory.py |
(no function) |
6 |
0 |
0 |
100% |
| model_workflow/tools/get_screenshot.py |
get_screenshot |
162 |
18 |
0 |
89% |
| model_workflow/tools/get_screenshot.py |
get_screenshot.display_vector |
6 |
6 |
0 |
0% |
| model_workflow/tools/get_screenshot.py |
tuple_to_vmd |
1 |
0 |
0 |
100% |
| model_workflow/tools/get_screenshot.py |
rotate_vector |
9 |
0 |
0 |
100% |
| model_workflow/tools/get_screenshot.py |
calculate_distance |
6 |
0 |
0 |
100% |
| model_workflow/tools/get_screenshot.py |
point_adds_vector |
1 |
1 |
0 |
0% |
| model_workflow/tools/get_screenshot.py |
multiply_vector |
1 |
1 |
0 |
0% |
| model_workflow/tools/get_screenshot.py |
(no function) |
19 |
0 |
0 |
100% |
| model_workflow/tools/get_summarized_trajectory.py |
get_summarized_trajectory |
4 |
4 |
0 |
0% |
| model_workflow/tools/get_summarized_trajectory.py |
(no function) |
3 |
3 |
0 |
0% |
| model_workflow/tools/guess_and_filter.py |
guess_and_filter_topology |
28 |
28 |
0 |
0% |
| model_workflow/tools/guess_and_filter.py |
(no function) |
11 |
0 |
0 |
100% |
| model_workflow/tools/image_and_fit.py |
get_chains |
3 |
3 |
0 |
0% |
| model_workflow/tools/image_and_fit.py |
set_chains |
3 |
3 |
0 |
0% |
| model_workflow/tools/image_and_fit.py |
image_and_fit |
70 |
70 |
0 |
0% |
| model_workflow/tools/image_and_fit.py |
reset_structure |
5 |
5 |
0 |
0% |
| model_workflow/tools/image_and_fit.py |
(no function) |
11 |
0 |
0 |
100% |
| model_workflow/tools/nassa_base.py |
Base.__init__ |
21 |
1 |
0 |
95% |
| model_workflow/tools/nassa_base.py |
Base.extract |
1 |
1 |
0 |
0% |
| model_workflow/tools/nassa_base.py |
Base.transform |
1 |
1 |
0 |
0% |
| model_workflow/tools/nassa_base.py |
Base.make_tables |
1 |
1 |
0 |
0% |
| model_workflow/tools/nassa_base.py |
Base.make_plots |
1 |
1 |
0 |
0% |
| model_workflow/tools/nassa_base.py |
Base.load |
2 |
2 |
0 |
0% |
| model_workflow/tools/nassa_base.py |
Base.run |
10 |
0 |
0 |
100% |
| model_workflow/tools/nassa_base.py |
Base.save_path |
11 |
7 |
0 |
36% |
| model_workflow/tools/nassa_base.py |
Base.create_logger |
7 |
1 |
0 |
86% |
| model_workflow/tools/nassa_base.py |
(no function) |
20 |
0 |
0 |
100% |
| model_workflow/tools/nassa_loaders.py |
load_sequence |
10 |
5 |
0 |
50% |
| model_workflow/tools/nassa_loaders.py |
load_sequence2 |
11 |
5 |
0 |
55% |
| model_workflow/tools/nassa_loaders.py |
reverse_sequence |
8 |
1 |
0 |
88% |
| model_workflow/tools/nassa_loaders.py |
write_sequence |
3 |
3 |
0 |
0% |
| model_workflow/tools/nassa_loaders.py |
load_serfile |
10 |
1 |
0 |
90% |
| model_workflow/tools/nassa_loaders.py |
write_serfile |
10 |
10 |
0 |
0% |
| model_workflow/tools/nassa_loaders.py |
(no function) |
10 |
0 |
0 |
100% |
| model_workflow/tools/process_input_files.py |
process_input_files |
137 |
28 |
0 |
80% |
| model_workflow/tools/process_input_files.py |
(no function) |
20 |
0 |
0 |
100% |
| model_workflow/tools/process_interactions.py |
process_interactions |
117 |
66 |
0 |
44% |
| model_workflow/tools/process_interactions.py |
load_interactions |
7 |
7 |
0 |
0% |
| model_workflow/tools/process_interactions.py |
add_residues_indices |
7 |
0 |
0 |
100% |
| model_workflow/tools/process_interactions.py |
(no function) |
13 |
0 |
0 |
100% |
| model_workflow/tools/remove_trash.py |
remove_trash |
6 |
0 |
0 |
100% |
| model_workflow/tools/remove_trash.py |
(no function) |
4 |
0 |
0 |
100% |
| model_workflow/tools/residue_mapping.py |
generate_residue_mapping |
57 |
21 |
0 |
63% |
| model_workflow/tools/residue_mapping.py |
(no function) |
3 |
0 |
0 |
100% |
| model_workflow/tools/structure_corrector.py |
structure_corrector |
100 |
61 |
0 |
39% |
| model_workflow/tools/structure_corrector.py |
structure_corrector.check_stable_bonds |
29 |
7 |
0 |
76% |
| model_workflow/tools/structure_corrector.py |
(no function) |
10 |
0 |
0 |
100% |
| model_workflow/tools/xvg_parse.py |
xvg_parse |
14 |
0 |
0 |
100% |
| model_workflow/tools/xvg_parse.py |
(no function) |
1 |
0 |
0 |
100% |
| model_workflow/utils/__init__.py |
(no function) |
0 |
0 |
0 |
100% |
| model_workflow/utils/arg_cksum.py |
get_cksum_id |
24 |
3 |
0 |
88% |
| model_workflow/utils/arg_cksum.py |
(no function) |
11 |
0 |
0 |
100% |
| model_workflow/utils/auxiliar.py |
is_imported |
1 |
0 |
0 |
100% |
| model_workflow/utils/auxiliar.py |
NoReferableException.__str__ |
1 |
0 |
0 |
100% |
| model_workflow/utils/auxiliar.py |
NoReferableException.__repr__ |
1 |
0 |
0 |
100% |
| model_workflow/utils/auxiliar.py |
NoReferableException.get_sequence |
1 |
1 |
0 |
0% |
| model_workflow/utils/auxiliar.py |
custom_excepthook |
4 |
4 |
0 |
0% |
| model_workflow/utils/auxiliar.py |
get_new_letter |
1 |
1 |
0 |
0% |
| model_workflow/utils/auxiliar.py |
all_cases |
7 |
0 |
0 |
100% |
| model_workflow/utils/auxiliar.py |
residue_name_to_letter |
1 |
0 |
0 |
100% |
| model_workflow/utils/auxiliar.py |
protein_residue_name_to_letter |
1 |
0 |
0 |
100% |
| model_workflow/utils/auxiliar.py |
load_json |
6 |
2 |
0 |
67% |
| model_workflow/utils/auxiliar.py |
save_json |
6 |
3 |
0 |
50% |
| model_workflow/utils/auxiliar.py |
load_yaml |
7 |
3 |
0 |
57% |
| model_workflow/utils/auxiliar.py |
save_yaml |
2 |
2 |
0 |
0% |
| model_workflow/utils/auxiliar.py |
delete_previous_log |
1 |
0 |
0 |
100% |
| model_workflow/utils/auxiliar.py |
reprint |
2 |
0 |
0 |
100% |
| model_workflow/utils/auxiliar.py |
warn |
1 |
0 |
0 |
100% |
| model_workflow/utils/auxiliar.py |
mean |
1 |
1 |
0 |
0% |
| model_workflow/utils/auxiliar.py |
round_to_hundredths |
1 |
1 |
0 |
0% |
| model_workflow/utils/auxiliar.py |
round_to_thousandths |
1 |
0 |
0 |
100% |
| model_workflow/utils/auxiliar.py |
ranger |
25 |
1 |
0 |
96% |
| model_workflow/utils/auxiliar.py |
otherwise |
3 |
0 |
0 |
100% |
| model_workflow/utils/auxiliar.py |
list_files |
1 |
0 |
0 |
100% |
| model_workflow/utils/auxiliar.py |
is_directory_empty |
1 |
0 |
0 |
100% |
| model_workflow/utils/auxiliar.py |
is_glob |
9 |
0 |
0 |
100% |
| model_workflow/utils/auxiliar.py |
parse_glob |
4 |
0 |
0 |
100% |
| model_workflow/utils/auxiliar.py |
store_binary_data |
8 |
8 |
0 |
0% |
| model_workflow/utils/auxiliar.py |
CaptureOutput.__init__ |
6 |
6 |
0 |
0% |
| model_workflow/utils/auxiliar.py |
CaptureOutput.__enter__ |
4 |
4 |
0 |
0% |
| model_workflow/utils/auxiliar.py |
CaptureOutput.__exit__ |
7 |
7 |
0 |
0% |
| model_workflow/utils/auxiliar.py |
CaptureOutput.readOutput |
4 |
4 |
0 |
0% |
| model_workflow/utils/auxiliar.py |
request_pdb_data |
16 |
7 |
0 |
56% |
| model_workflow/utils/auxiliar.py |
request_replaced_pdb |
9 |
9 |
0 |
0% |
| model_workflow/utils/auxiliar.py |
numerate_filename |
3 |
0 |
0 |
100% |
| model_workflow/utils/auxiliar.py |
glob_filename |
3 |
3 |
0 |
0% |
| model_workflow/utils/auxiliar.py |
purge_glob |
4 |
4 |
0 |
0% |
| model_workflow/utils/auxiliar.py |
get_analysis_name |
4 |
1 |
0 |
75% |
| model_workflow/utils/auxiliar.py |
safe_hasattr |
1 |
0 |
0 |
100% |
| model_workflow/utils/auxiliar.py |
safe_getattr |
2 |
0 |
0 |
100% |
| model_workflow/utils/auxiliar.py |
(no function) |
74 |
0 |
0 |
100% |
| model_workflow/utils/bibitransformer_nassa.py |
BiBiTransformer.__init__ |
4 |
1 |
0 |
75% |
| model_workflow/utils/bibitransformer_nassa.py |
BiBiTransformer.GMM_models |
3 |
0 |
0 |
100% |
| model_workflow/utils/bibitransformer_nassa.py |
BiBiTransformer.fit |
3 |
0 |
0 |
100% |
| model_workflow/utils/bibitransformer_nassa.py |
BiBiTransformer.transform |
31 |
0 |
0 |
100% |
| model_workflow/utils/bibitransformer_nassa.py |
BiBiTransformer.bayes_factor_criteria |
11 |
4 |
0 |
64% |
| model_workflow/utils/bibitransformer_nassa.py |
BiBiTransformer.is_unimodal |
4 |
0 |
0 |
100% |
| model_workflow/utils/bibitransformer_nassa.py |
(no function) |
10 |
0 |
0 |
100% |
| model_workflow/utils/cache.py |
Cache.__init__ |
8 |
0 |
0 |
100% |
| model_workflow/utils/cache.py |
Cache.retrieve |
1 |
0 |
0 |
100% |
| model_workflow/utils/cache.py |
Cache.update |
2 |
0 |
0 |
100% |
| model_workflow/utils/cache.py |
Cache.delete |
3 |
0 |
0 |
100% |
| model_workflow/utils/cache.py |
Cache.reset |
2 |
2 |
0 |
0% |
| model_workflow/utils/cache.py |
Cache.save |
2 |
0 |
0 |
100% |
| model_workflow/utils/cache.py |
(no function) |
9 |
0 |
0 |
100% |
| model_workflow/utils/constants.py |
(no function) |
139 |
1 |
0 |
99% |
| model_workflow/utils/file.py |
File.__init__ |
26 |
1 |
0 |
96% |
| model_workflow/utils/file.py |
File.__repr__ |
3 |
1 |
0 |
67% |
| model_workflow/utils/file.py |
File.__str__ |
1 |
1 |
0 |
0% |
| model_workflow/utils/file.py |
File.__hash__ |
1 |
0 |
0 |
100% |
| model_workflow/utils/file.py |
File.__bool__ |
1 |
0 |
0 |
100% |
| model_workflow/utils/file.py |
File.__eq__ |
3 |
0 |
0 |
100% |
| model_workflow/utils/file.py |
File.check_existence |
1 |
0 |
0 |
100% |
| model_workflow/utils/file.py |
File.get_format |
6 |
2 |
0 |
67% |
| model_workflow/utils/file.py |
File.get_mtime |
2 |
0 |
0 |
100% |
| model_workflow/utils/file.py |
File.get_size |
1 |
0 |
0 |
100% |
| model_workflow/utils/file.py |
File.get_cksum |
4 |
0 |
0 |
100% |
| model_workflow/utils/file.py |
File.is_pytraj_supported |
1 |
0 |
0 |
100% |
| model_workflow/utils/file.py |
File.get_pytraj_parm_format |
1 |
1 |
0 |
0% |
| model_workflow/utils/file.py |
File.remove |
1 |
0 |
0 |
100% |
| model_workflow/utils/file.py |
File.get_standard_file |
3 |
1 |
0 |
67% |
| model_workflow/utils/file.py |
File.reformat |
5 |
0 |
0 |
100% |
| model_workflow/utils/file.py |
File.get_prefixed_file |
1 |
0 |
0 |
100% |
| model_workflow/utils/file.py |
File.get_neighbour_file |
1 |
1 |
0 |
0% |
| model_workflow/utils/file.py |
File.get_symlink |
4 |
4 |
0 |
0% |
| model_workflow/utils/file.py |
File.set_symlink_to |
8 |
3 |
0 |
62% |
| model_workflow/utils/file.py |
File.is_symlink |
1 |
0 |
0 |
100% |
| model_workflow/utils/file.py |
File.copy_to |
1 |
1 |
0 |
0% |
| model_workflow/utils/file.py |
File.rename_to |
1 |
0 |
0 |
100% |
| model_workflow/utils/file.py |
(no function) |
38 |
0 |
0 |
100% |
| model_workflow/utils/filters.py |
filter_atoms |
72 |
34 |
0 |
53% |
| model_workflow/utils/filters.py |
(no function) |
13 |
0 |
0 |
100% |
| model_workflow/utils/formats.py |
get_format |
3 |
1 |
0 |
67% |
| model_workflow/utils/formats.py |
get_format_set_suitable_function |
17 |
1 |
0 |
94% |
| model_workflow/utils/formats.py |
get_common_argument_formats |
17 |
3 |
0 |
82% |
| model_workflow/utils/formats.py |
check_format_sets_compability |
25 |
8 |
0 |
68% |
| model_workflow/utils/formats.py |
get_format_set_suitable_combination |
9 |
0 |
0 |
100% |
| model_workflow/utils/formats.py |
get_format_set_suitable_combination.get_combinations |
26 |
2 |
0 |
92% |
| model_workflow/utils/formats.py |
get_format_set_suitable_combination.combined_function |
57 |
12 |
0 |
79% |
| model_workflow/utils/formats.py |
is_pdb |
1 |
1 |
0 |
0% |
| model_workflow/utils/formats.py |
is_psf |
1 |
1 |
0 |
0% |
| model_workflow/utils/formats.py |
is_tpr |
1 |
1 |
0 |
0% |
| model_workflow/utils/formats.py |
is_gro |
1 |
1 |
0 |
0% |
| model_workflow/utils/formats.py |
is_prmtop |
1 |
1 |
0 |
0% |
| model_workflow/utils/formats.py |
is_top |
1 |
1 |
0 |
0% |
| model_workflow/utils/formats.py |
is_xtc |
1 |
1 |
0 |
0% |
| model_workflow/utils/formats.py |
is_dcd |
1 |
1 |
0 |
0% |
| model_workflow/utils/formats.py |
is_netcdf |
1 |
1 |
0 |
0% |
| model_workflow/utils/formats.py |
are_xtc |
1 |
1 |
0 |
0% |
| model_workflow/utils/formats.py |
are_dcd |
1 |
1 |
0 |
0% |
| model_workflow/utils/formats.py |
are_netcdf |
1 |
1 |
0 |
0% |
| model_workflow/utils/formats.py |
is_pytraj_supported |
1 |
1 |
0 |
0% |
| model_workflow/utils/formats.py |
get_pytraj_parm_format |
9 |
9 |
0 |
0% |
| model_workflow/utils/formats.py |
(no function) |
22 |
0 |
0 |
100% |
| model_workflow/utils/gmx_spells.py |
get_first_frame |
10 |
5 |
0 |
50% |
| model_workflow/utils/gmx_spells.py |
get_structure |
1 |
1 |
0 |
0% |
| model_workflow/utils/gmx_spells.py |
get_structure_alone |
1 |
0 |
0 |
100% |
| model_workflow/utils/gmx_spells.py |
merge_and_convert_trajectories |
21 |
21 |
0 |
0% |
| model_workflow/utils/gmx_spells.py |
get_trajectory_subset |
10 |
2 |
0 |
80% |
| model_workflow/utils/gmx_spells.py |
filter_structure |
14 |
2 |
0 |
86% |
| model_workflow/utils/gmx_spells.py |
filter_trajectory |
14 |
2 |
0 |
86% |
| model_workflow/utils/gmx_spells.py |
mine_system_atoms_count |
5 |
2 |
0 |
60% |
| model_workflow/utils/gmx_spells.py |
get_tpr_atom_count |
8 |
1 |
0 |
88% |
| model_workflow/utils/gmx_spells.py |
get_tpr_content |
2 |
0 |
0 |
100% |
| model_workflow/utils/gmx_spells.py |
get_tpr_charges |
9 |
2 |
0 |
78% |
| model_workflow/utils/gmx_spells.py |
get_tpr_bonds |
26 |
7 |
0 |
73% |
| model_workflow/utils/gmx_spells.py |
filter_tpr |
12 |
12 |
0 |
0% |
| model_workflow/utils/gmx_spells.py |
merge_xtc_files |
4 |
4 |
0 |
0% |
| model_workflow/utils/gmx_spells.py |
generate_frames_ndx |
11 |
2 |
0 |
82% |
| model_workflow/utils/gmx_spells.py |
parse_xpm |
34 |
34 |
0 |
0% |
| model_workflow/utils/gmx_spells.py |
pdb_filter |
9 |
4 |
0 |
56% |
| model_workflow/utils/gmx_spells.py |
xtc_filter |
11 |
4 |
0 |
64% |
| model_workflow/utils/gmx_spells.py |
tpr_filter |
9 |
4 |
0 |
56% |
| model_workflow/utils/gmx_spells.py |
make_index |
11 |
11 |
0 |
0% |
| model_workflow/utils/gmx_spells.py |
(no function) |
42 |
0 |
0 |
100% |
| model_workflow/utils/heatmaps_nassa.py |
get_axes |
26 |
12 |
0 |
54% |
| model_workflow/utils/heatmaps_nassa.py |
reorder_labels_rotated_plot |
50 |
23 |
0 |
54% |
| model_workflow/utils/heatmaps_nassa.py |
reorder_labels_straight_plot |
50 |
23 |
0 |
54% |
| model_workflow/utils/heatmaps_nassa.py |
arlequin_plot |
78 |
4 |
0 |
95% |
| model_workflow/utils/heatmaps_nassa.py |
bconf_heatmap |
46 |
46 |
0 |
0% |
| model_workflow/utils/heatmaps_nassa.py |
correlation_plot |
36 |
36 |
0 |
0% |
| model_workflow/utils/heatmaps_nassa.py |
basepair_plot |
35 |
0 |
0 |
100% |
| model_workflow/utils/heatmaps_nassa.py |
(no function) |
16 |
0 |
0 |
100% |
| model_workflow/utils/httpsf.py |
FileHandler.__init__ |
8 |
8 |
0 |
0% |
| model_workflow/utils/httpsf.py |
FileHandler.__init__.create_whistleblower |
2 |
2 |
0 |
0% |
| model_workflow/utils/httpsf.py |
FileHandler.__init__.create_whistleblower.whistleblower |
1 |
1 |
0 |
0% |
| model_workflow/utils/httpsf.py |
FileHandler.__call__ |
2 |
2 |
0 |
0% |
| model_workflow/utils/httpsf.py |
FileHandler._get_file_size |
4 |
4 |
0 |
0% |
| model_workflow/utils/httpsf.py |
FileHandler._fetch_file_content |
2 |
2 |
0 |
0% |
| model_workflow/utils/httpsf.py |
FileHandler.getattr |
5 |
5 |
0 |
0% |
| model_workflow/utils/httpsf.py |
FileHandler.open |
3 |
3 |
0 |
0% |
| model_workflow/utils/httpsf.py |
FileHandler.read |
3 |
3 |
0 |
0% |
| model_workflow/utils/httpsf.py |
FileHandler.destroy |
2 |
2 |
0 |
0% |
| model_workflow/utils/httpsf.py |
mount |
4 |
4 |
0 |
0% |
| model_workflow/utils/httpsf.py |
(no function) |
25 |
25 |
0 |
0% |
| model_workflow/utils/mda_spells.py |
to_MDAnalysis_topology |
12 |
0 |
0 |
100% |
| model_workflow/utils/mda_spells.py |
get_mda_universe |
2 |
0 |
0 |
100% |
| model_workflow/utils/mda_spells.py |
get_mda_universe_cksum |
2 |
0 |
0 |
100% |
| model_workflow/utils/mda_spells.py |
(no function) |
10 |
0 |
0 |
100% |
| model_workflow/utils/mdt_spells.py |
merge_and_convert_trajectories |
7 |
2 |
0 |
71% |
| model_workflow/utils/mdt_spells.py |
merge_and_convert_trajectories_alternative |
25 |
25 |
0 |
0% |
| model_workflow/utils/mdt_spells.py |
merge_and_convert_trajectories_unefficient |
11 |
11 |
0 |
0% |
| model_workflow/utils/mdt_spells.py |
get_trajectory_subset |
38 |
38 |
0 |
0% |
| model_workflow/utils/mdt_spells.py |
get_first_frame |
1 |
1 |
0 |
0% |
| model_workflow/utils/mdt_spells.py |
split_merged_trajectories |
24 |
24 |
0 |
0% |
| model_workflow/utils/mdt_spells.py |
sort_trajectory_atoms |
24 |
24 |
0 |
0% |
| model_workflow/utils/mdt_spells.py |
(no function) |
28 |
0 |
0 |
100% |
| model_workflow/utils/nassa_file.py |
generate_nassa_config |
69 |
30 |
0 |
57% |
| model_workflow/utils/nassa_file.py |
(no function) |
8 |
0 |
0 |
100% |
| model_workflow/utils/nucleicacid.py |
NucleicAcid.__init__ |
13 |
3 |
0 |
77% |
| model_workflow/utils/nucleicacid.py |
NucleicAcid.__len__ |
1 |
1 |
0 |
0% |
| model_workflow/utils/nucleicacid.py |
NucleicAcid.__repr__ |
5 |
5 |
0 |
0% |
| model_workflow/utils/nucleicacid.py |
NucleicAcid.size |
1 |
0 |
0 |
100% |
| model_workflow/utils/nucleicacid.py |
NucleicAcid.bases |
1 |
1 |
0 |
0% |
| model_workflow/utils/nucleicacid.py |
NucleicAcid.baselen |
4 |
1 |
0 |
75% |
| model_workflow/utils/nucleicacid.py |
NucleicAcid.flanksize |
1 |
0 |
0 |
100% |
| model_workflow/utils/nucleicacid.py |
NucleicAcid.ic_sequence |
3 |
3 |
0 |
0% |
| model_workflow/utils/nucleicacid.py |
NucleicAcid._adenine_complement |
9 |
4 |
0 |
56% |
| model_workflow/utils/nucleicacid.py |
NucleicAcid.inverse_complement |
2 |
0 |
0 |
100% |
| model_workflow/utils/nucleicacid.py |
NucleicAcid.get_subunit |
2 |
0 |
0 |
100% |
| model_workflow/utils/nucleicacid.py |
NucleicAcid.get_all_subunits |
2 |
0 |
0 |
100% |
| model_workflow/utils/nucleicacid.py |
NucleicAcid.get_all_ic_subunits |
1 |
0 |
0 |
100% |
| model_workflow/utils/nucleicacid.py |
NucleicAcid.search_subunit |
8 |
8 |
0 |
0% |
| model_workflow/utils/nucleicacid.py |
(no function) |
20 |
0 |
0 |
100% |
| model_workflow/utils/pyt_spells.py |
get_pytraj_trajectory |
14 |
9 |
0 |
36% |
| model_workflow/utils/pyt_spells.py |
get_reduced_pytraj_trajectory |
8 |
0 |
0 |
100% |
| model_workflow/utils/pyt_spells.py |
get_frames_count |
11 |
3 |
0 |
73% |
| model_workflow/utils/pyt_spells.py |
filter_topology |
6 |
6 |
0 |
0% |
| model_workflow/utils/pyt_spells.py |
find_first_corrupted_frame |
9 |
9 |
0 |
0% |
| model_workflow/utils/pyt_spells.py |
get_average_structure |
5 |
0 |
0 |
100% |
| model_workflow/utils/pyt_spells.py |
(no function) |
17 |
0 |
0 |
100% |
| model_workflow/utils/register.py |
Register.__init__ |
17 |
3 |
0 |
82% |
| model_workflow/utils/register.py |
Register.__repr__ |
1 |
1 |
0 |
0% |
| model_workflow/utils/register.py |
Register.to_dict |
2 |
0 |
0 |
100% |
| model_workflow/utils/register.py |
Register.update_test |
2 |
0 |
0 |
100% |
| model_workflow/utils/register.py |
Register.get_warnings |
1 |
1 |
0 |
0% |
| model_workflow/utils/register.py |
Register.add_warning |
6 |
6 |
0 |
0% |
| model_workflow/utils/register.py |
Register.remove_warnings |
2 |
0 |
0 |
100% |
| model_workflow/utils/register.py |
Register.save |
4 |
1 |
0 |
75% |
| model_workflow/utils/register.py |
(no function) |
15 |
0 |
0 |
100% |
| model_workflow/utils/remote.py |
Remote.__init__ |
6 |
0 |
0 |
100% |
| model_workflow/utils/remote.py |
Remote.get_project_data |
11 |
7 |
0 |
36% |
| model_workflow/utils/remote.py |
Remote.get_available_files |
9 |
2 |
0 |
78% |
| model_workflow/utils/remote.py |
Remote.download_file |
8 |
4 |
0 |
50% |
| model_workflow/utils/remote.py |
Remote.download_standard_topology |
6 |
6 |
0 |
0% |
| model_workflow/utils/remote.py |
Remote.download_standard_structure |
6 |
2 |
0 |
67% |
| model_workflow/utils/remote.py |
Remote.download_trajectory |
18 |
4 |
0 |
78% |
| model_workflow/utils/remote.py |
Remote.download_inputs_file |
12 |
5 |
0 |
58% |
| model_workflow/utils/remote.py |
Remote.download_analysis_data |
8 |
8 |
0 |
0% |
| model_workflow/utils/remote.py |
my_hook |
3 |
0 |
0 |
100% |
| model_workflow/utils/remote.py |
my_hook.update_to |
4 |
0 |
0 |
100% |
| model_workflow/utils/remote.py |
(no function) |
17 |
0 |
0 |
100% |
| model_workflow/utils/selections.py |
Selection.__init__ |
1 |
0 |
0 |
100% |
| model_workflow/utils/selections.py |
Selection.__repr__ |
1 |
1 |
0 |
0% |
| model_workflow/utils/selections.py |
Selection.__hash__ |
1 |
1 |
0 |
0% |
| model_workflow/utils/selections.py |
Selection.__len__ |
1 |
0 |
0 |
100% |
| model_workflow/utils/selections.py |
Selection.__bool__ |
1 |
0 |
0 |
100% |
| model_workflow/utils/selections.py |
Selection.__eq__ |
3 |
0 |
0 |
100% |
| model_workflow/utils/selections.py |
Selection.__add__ |
1 |
0 |
0 |
100% |
| model_workflow/utils/selections.py |
Selection.__sub__ |
1 |
0 |
0 |
100% |
| model_workflow/utils/selections.py |
Selection.__and__ |
1 |
0 |
0 |
100% |
| model_workflow/utils/selections.py |
Selection.__or__ |
1 |
1 |
0 |
0% |
| model_workflow/utils/selections.py |
Selection.merge |
4 |
0 |
0 |
100% |
| model_workflow/utils/selections.py |
Selection.substract |
4 |
0 |
0 |
100% |
| model_workflow/utils/selections.py |
Selection.intersection |
6 |
0 |
0 |
100% |
| model_workflow/utils/selections.py |
Selection.to_mdanalysis |
2 |
2 |
0 |
0% |
| model_workflow/utils/selections.py |
Selection.to_pytraj |
3 |
0 |
0 |
100% |
| model_workflow/utils/selections.py |
Selection.to_ngl |
1 |
0 |
0 |
100% |
| model_workflow/utils/selections.py |
Selection.to_bash |
4 |
4 |
0 |
0% |
| model_workflow/utils/selections.py |
Selection.to_vmd |
2 |
0 |
0 |
100% |
| model_workflow/utils/selections.py |
Selection.to_ndx |
13 |
1 |
0 |
92% |
| model_workflow/utils/selections.py |
Selection.to_ndx_file |
3 |
0 |
0 |
100% |
| model_workflow/utils/selections.py |
(no function) |
23 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Atom.__init__ |
6 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Atom.__repr__ |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Atom.__eq__ |
3 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Atom.__hash__ |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Atom.get_structure |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Atom.get_index |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Atom.get_residue_index |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Atom.set_residue_index |
9 |
1 |
0 |
89% |
| model_workflow/utils/structures.py |
Atom.get_residue |
3 |
1 |
0 |
67% |
| model_workflow/utils/structures.py |
Atom.set_residue |
4 |
1 |
0 |
75% |
| model_workflow/utils/structures.py |
Atom.get_chain_index |
3 |
1 |
0 |
67% |
| model_workflow/utils/structures.py |
Atom.set_chain_index |
13 |
3 |
0 |
77% |
| model_workflow/utils/structures.py |
Atom.get_chain |
3 |
1 |
0 |
67% |
| model_workflow/utils/structures.py |
Atom.get_bonds |
10 |
2 |
0 |
80% |
| model_workflow/utils/structures.py |
Atom.get_bonded_atoms |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Atom.get_selection |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Atom.copy |
5 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Atom.is_fatty_candidate |
9 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Atom.is_carbohydrate_candidate |
12 |
7 |
0 |
42% |
| model_workflow/utils/structures.py |
Atom.is_ion |
1 |
1 |
0 |
0% |
| model_workflow/utils/structures.py |
Atom.guess_element |
12 |
3 |
0 |
75% |
| model_workflow/utils/structures.py |
Atom.get_name_suggested_element |
21 |
2 |
0 |
90% |
| model_workflow/utils/structures.py |
Atom.get_label |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Atom.is_cg |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Residue.__init__ |
8 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Residue.__repr__ |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Residue.__eq__ |
3 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Residue.__hash__ |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Residue.get_structure |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Residue.get_index |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Residue.set_index |
5 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Residue.get_atom_indices |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Residue.set_atom_indices |
9 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Residue.get_atoms |
4 |
1 |
0 |
75% |
| model_workflow/utils/structures.py |
Residue.set_atoms |
7 |
1 |
0 |
86% |
| model_workflow/utils/structures.py |
Residue.get_atom_count |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Residue.add_atom |
4 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Residue.remove_atom |
4 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Residue.get_chain_index |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Residue.set_chain_index |
9 |
1 |
0 |
89% |
| model_workflow/utils/structures.py |
Residue.get_chain |
3 |
1 |
0 |
67% |
| model_workflow/utils/structures.py |
Residue.set_chain |
13 |
2 |
0 |
85% |
| model_workflow/utils/structures.py |
Residue.get_bonded_atom_indices |
5 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Residue.get_bonded_atoms |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Residue.get_bonded_residue_indices |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Residue.get_bonded_residues |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Residue.is_bonded_with_residue |
3 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Residue.get_classification |
71 |
10 |
0 |
86% |
| model_workflow/utils/structures.py |
Residue.get_classification.get_bonded_fatty_atoms_recursive |
11 |
2 |
0 |
82% |
| model_workflow/utils/structures.py |
Residue.get_classification_by_name |
17 |
10 |
0 |
41% |
| model_workflow/utils/structures.py |
Residue.get_selection |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Residue.copy |
6 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Residue.get_letter |
1 |
1 |
0 |
0% |
| model_workflow/utils/structures.py |
Residue.get_formula |
8 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Residue.find_rings |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Residue.split |
25 |
7 |
0 |
72% |
| model_workflow/utils/structures.py |
Residue.split_by_atom_names |
11 |
5 |
0 |
55% |
| model_workflow/utils/structures.py |
Residue.get_atom_by_name |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Residue.get_label |
2 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Residue.is_cg |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Chain.__init__ |
5 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Chain.__repr__ |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Chain.__eq__ |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Chain.__hash__ |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Chain.get_structure |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Chain.get_index |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Chain.set_index |
3 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Chain.get_residue_indices |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Chain.set_residue_indices |
11 |
1 |
0 |
91% |
| model_workflow/utils/structures.py |
Chain.get_residues |
4 |
1 |
0 |
75% |
| model_workflow/utils/structures.py |
Chain.set_residues |
7 |
1 |
0 |
86% |
| model_workflow/utils/structures.py |
Chain.add_residue |
3 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Chain.remove_residue |
4 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Chain.get_atom_indices |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Chain.get_atoms |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Chain.get_atom_count |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Chain.get_residue_count |
1 |
1 |
0 |
0% |
| model_workflow/utils/structures.py |
Chain.get_classification |
4 |
1 |
0 |
75% |
| model_workflow/utils/structures.py |
Chain.set_classification |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Chain.get_sequence |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Chain.get_selection |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Chain.copy |
5 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Chain.has_cg |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Chain.find_residue |
4 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.__init__ |
17 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.__repr__ |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.get_bonds |
4 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.set_bonds |
2 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.get_fragments |
4 |
1 |
0 |
75% |
| model_workflow/utils/structures.py |
Structure.find_fragments |
18 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.find_whole_fragments |
3 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.name_selection |
14 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.set_new_atom |
4 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.set_new_residue |
7 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.purge_residue |
9 |
2 |
0 |
78% |
| model_workflow/utils/structures.py |
Structure.set_new_chain |
7 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.purge_chain |
8 |
2 |
0 |
75% |
| model_workflow/utils/structures.py |
Structure.from_pdb |
71 |
10 |
0 |
86% |
| model_workflow/utils/structures.py |
Structure.from_pdb_file |
9 |
2 |
0 |
78% |
| model_workflow/utils/structures.py |
Structure.from_mmcif |
47 |
6 |
0 |
87% |
| model_workflow/utils/structures.py |
Structure.from_mmcif_file |
9 |
2 |
0 |
78% |
| model_workflow/utils/structures.py |
Structure.from_mdanalysis |
32 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.from_prmtop_file |
11 |
3 |
0 |
73% |
| model_workflow/utils/structures.py |
Structure.from_tpr_file |
11 |
3 |
0 |
73% |
| model_workflow/utils/structures.py |
Structure.from_file |
10 |
1 |
0 |
90% |
| model_workflow/utils/structures.py |
Structure.get_atom_count |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.get_residue_count |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.get_chain_count |
1 |
1 |
0 |
0% |
| model_workflow/utils/structures.py |
Structure.fix_atom_elements |
26 |
4 |
0 |
85% |
| model_workflow/utils/structures.py |
Structure.set_new_coordinates |
4 |
1 |
0 |
75% |
| model_workflow/utils/structures.py |
Structure.get_ion_atom_indices |
8 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.get_dummy_atom_indices |
8 |
1 |
0 |
88% |
| model_workflow/utils/structures.py |
Structure.generate_pdb |
21 |
2 |
0 |
90% |
| model_workflow/utils/structures.py |
Structure.generate_pdb_file |
3 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.get_pytraj_topology |
7 |
1 |
0 |
86% |
| model_workflow/utils/structures.py |
Structure.select |
19 |
5 |
0 |
74% |
| model_workflow/utils/structures.py |
Structure.select_atom_indices |
5 |
1 |
0 |
80% |
| model_workflow/utils/structures.py |
Structure.select_residue_indices |
4 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.select_all |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.select_by_classification |
5 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.select_water |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.select_ions |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.select_counter_ions |
14 |
2 |
0 |
86% |
| model_workflow/utils/structures.py |
Structure.select_water_and_counter_ions |
1 |
1 |
0 |
0% |
| model_workflow/utils/structures.py |
Structure.select_heavy_atoms |
5 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.select_protein |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.select_nucleic |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.select_lipids |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.select_carbohydrates |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.select_pbc_guess |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.select_cg |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.select_cartoon |
13 |
1 |
0 |
92% |
| model_workflow/utils/structures.py |
Structure.invert_selection |
4 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.get_selection_residue_indices |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.get_selection_residues |
2 |
2 |
0 |
0% |
| model_workflow/utils/structures.py |
Structure.get_selection_chain_indices |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.get_selection_chains |
2 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.get_selection_classification |
30 |
16 |
0 |
47% |
| model_workflow/utils/structures.py |
Structure.filter |
53 |
1 |
0 |
98% |
| model_workflow/utils/structures.py |
Structure.chainer |
10 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.auto_chainer |
14 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.raw_protein_chainer |
12 |
2 |
0 |
83% |
| model_workflow/utils/structures.py |
Structure.set_selection_chain_name |
7 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.get_available_chain_name |
5 |
1 |
0 |
80% |
| model_workflow/utils/structures.py |
Structure.get_next_available_chain_name |
14 |
6 |
0 |
57% |
| model_workflow/utils/structures.py |
Structure.get_chain_by_name |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.find_residue |
3 |
3 |
0 |
0% |
| model_workflow/utils/structures.py |
Structure.display_summary |
6 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.check_repeated_chains |
48 |
16 |
0 |
67% |
| model_workflow/utils/structures.py |
Structure.check_repeated_residues |
104 |
25 |
0 |
76% |
| model_workflow/utils/structures.py |
Structure.check_repeated_residues.by_index |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.check_repeated_residues.trajectory_atom_sorter |
1 |
1 |
0 |
0% |
| model_workflow/utils/structures.py |
Structure.check_repeated_atoms |
29 |
2 |
0 |
93% |
| model_workflow/utils/structures.py |
Structure.check_incoherent_bonds |
27 |
3 |
0 |
89% |
| model_workflow/utils/structures.py |
Structure.get_covalent_bonds |
8 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.copy_bonds |
7 |
2 |
0 |
71% |
| model_workflow/utils/structures.py |
Structure.copy |
6 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.merge |
23 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.find_rings |
17 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.find_rings.find_rings_recursive |
22 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.get_selection_outer_bonds |
6 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
Structure.find_ptms |
27 |
6 |
0 |
78% |
| model_workflow/utils/structures.py |
Structure.has_cg |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
calculate_distance |
4 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
calculate_angle |
8 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
calculate_torsion |
13 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
get_next_letter |
6 |
1 |
0 |
83% |
| model_workflow/utils/structures.py |
first_cap_only |
5 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
get_lower_numbers |
1 |
0 |
0 |
100% |
| model_workflow/utils/structures.py |
filter_model |
17 |
17 |
0 |
0% |
| model_workflow/utils/structures.py |
(no function) |
245 |
0 |
0 |
100% |
| model_workflow/utils/subsets.py |
get_trajectory_subset |
25 |
9 |
0 |
64% |
| model_workflow/utils/subsets.py |
(no function) |
8 |
0 |
0 |
100% |
| model_workflow/utils/topologies.py |
Topology.__init__ |
4 |
0 |
0 |
100% |
| model_workflow/utils/topologies.py |
Topology.read_raw_content |
8 |
3 |
0 |
62% |
| model_workflow/utils/topologies.py |
Topology.get_flag_summary |
20 |
0 |
0 |
100% |
| model_workflow/utils/topologies.py |
Topology.mine_amber_flag |
11 |
0 |
0 |
100% |
| model_workflow/utils/topologies.py |
Topology.get_dihedrals_data |
2 |
1 |
0 |
50% |
| model_workflow/utils/topologies.py |
Topology._get_dihedrals_data_amber |
52 |
1 |
0 |
98% |
| model_workflow/utils/topologies.py |
(no function) |
15 |
0 |
0 |
100% |
| model_workflow/utils/type_hints.py |
(no function) |
10 |
7 |
0 |
30% |
| model_workflow/utils/vmd_spells.py |
escape_tcl_selection |
4 |
0 |
0 |
100% |
| model_workflow/utils/vmd_spells.py |
vmd_to_pdb |
17 |
17 |
0 |
0% |
| model_workflow/utils/vmd_spells.py |
chainer |
29 |
29 |
0 |
0% |
| model_workflow/utils/vmd_spells.py |
merge_and_convert_trajectories |
16 |
3 |
0 |
81% |
| model_workflow/utils/vmd_spells.py |
get_vmd_selection_atom_indices |
19 |
2 |
0 |
89% |
| model_workflow/utils/vmd_spells.py |
get_covalent_bonds |
47 |
3 |
0 |
94% |
| model_workflow/utils/vmd_spells.py |
get_covalent_bonds_between |
70 |
6 |
0 |
91% |
| model_workflow/utils/vmd_spells.py |
get_interface_atom_indices |
66 |
2 |
0 |
97% |
| model_workflow/utils/vmd_spells.py |
get_interface_atom_indices.process_vmd_output |
3 |
0 |
0 |
100% |
| model_workflow/utils/vmd_spells.py |
(no function) |
21 |
0 |
0 |
100% |
| model_workflow/utils/warnings.py |
warning_on_one_line |
1 |
0 |
0 |
100% |
| model_workflow/utils/warnings.py |
warn |
1 |
0 |
0 |
100% |
| model_workflow/utils/warnings.py |
(no function) |
4 |
0 |
0 |
100% |