| mddb_workflow / __init__.py |
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19 |
8 |
0 |
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58% |
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3 |
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| mddb_workflow / analyses / __init__.py |
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0 |
0 |
0 |
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100% |
| mddb_workflow / analyses / area_per_lipid.py |
area_per_lipid |
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19 |
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0 |
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| mddb_workflow / analyses / area_per_lipid.py |
process_apl |
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15 |
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0 |
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plot_apl |
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20 |
20 |
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12 |
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channels |
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40 |
2 |
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8 |
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clusters_analysis |
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108 |
6 |
0 |
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clustering |
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8 |
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13 |
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26 |
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plot_density |
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24 |
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compute_dihedral_energies |
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42 |
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7 |
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distance_per_residue |
|
47 |
44 |
0 |
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6% |
| mddb_workflow / analyses / distance_per_residue.py |
distance_per_residue.residue_2_pytraj_residue_index |
|
10 |
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0 |
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| mddb_workflow / analyses / distance_per_residue.py |
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9 |
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energies |
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71 |
68 |
0 |
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4% |
| mddb_workflow / analyses / energies.py |
energies.pdb2cmip |
|
41 |
41 |
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| mddb_workflow / analyses / energies.py |
energies.adapt_cmip_grid |
|
30 |
30 |
0 |
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| mddb_workflow / analyses / energies.py |
energies.get_cmip_energies |
|
27 |
27 |
0 |
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| mddb_workflow / analyses / energies.py |
energies.get_frame_energy |
|
68 |
68 |
0 |
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| mddb_workflow / analyses / energies.py |
set_cmip_elements |
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17 |
17 |
0 |
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name_terminal_residues |
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11 |
11 |
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mine_cmip_output |
|
19 |
19 |
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| mddb_workflow / analyses / energies.py |
compute_new_grid |
|
14 |
14 |
0 |
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0% |
| mddb_workflow / analyses / energies.py |
format_data |
|
42 |
42 |
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28 |
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helical_parameters |
|
28 |
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hydrogen_bonds |
|
17 |
2 |
0 |
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hydrogen_bonds.renumber_dat_file |
|
16 |
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0 |
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hydrogen_bonds.compress_dat_to_bin |
|
39 |
3 |
0 |
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terminal_execution |
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28 |
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send_files |
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19 |
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get_stiffness |
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16 |
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transform |
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26 |
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get_stiffness_seq |
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17 |
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get_subunit_stiffness |
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23 |
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get_subunit_stiffness.circ_avg |
|
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checking |
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5 |
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checking2 |
|
7 |
7 |
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read_series |
|
7 |
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57% |
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flow_files_average |
|
23 |
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0 |
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average_std |
|
6 |
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average_std_intra |
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6 |
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|
24 |
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sugar_puckering |
|
9 |
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fix_angles |
|
3 |
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0 |
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cpuck |
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7 |
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canonical_alphagamma |
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18 |
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fix_angles2 |
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4 |
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check_alpgamm |
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7 |
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bi_populations |
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20 |
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angles_diff_ze |
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5 |
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bi_pop |
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3 |
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flow_files_timeseries |
|
22 |
22 |
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| mddb_workflow / analyses / helical_parameters.py |
time_series |
|
10 |
10 |
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| mddb_workflow / analyses / helical_parameters.py |
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|
54 |
0 |
0 |
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100% |
| mddb_workflow / analyses / hydrogen_bonds.py |
hydrogen_bonds |
|
84 |
10 |
0 |
|
88% |
| mddb_workflow / analyses / hydrogen_bonds.py |
hydrogen_bonds.pytraj_residue_number_2_residue |
|
12 |
4 |
0 |
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| mddb_workflow / analyses / hydrogen_bonds.py |
hydrogen_bonds.get_populated_value |
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0 |
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9 |
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0 |
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| mddb_workflow / analyses / lipid_interactions.py |
lipid_interactions |
|
10 |
1 |
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aa_lipid_interactions |
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19 |
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0 |
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cg_lipid_interactions |
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26 |
26 |
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plot_lipid_interactions |
|
12 |
12 |
0 |
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10 |
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| mddb_workflow / analyses / lipid_order.py |
lipid_order |
|
34 |
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0 |
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get_all_acyl_chains |
|
13 |
0 |
0 |
|
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| mddb_workflow / analyses / lipid_order.py |
get_all_acyl_chains.explore_carbon_group |
|
14 |
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0 |
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| mddb_workflow / analyses / lipid_order.py |
find_CH_bonds |
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natural_sort_key |
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0 |
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| mddb_workflow / analyses / lipid_order.py |
plot_lipid_order |
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18 |
18 |
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11 |
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0 |
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| mddb_workflow / analyses / markov.py |
markov |
|
53 |
50 |
0 |
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7 |
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0 |
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| mddb_workflow / analyses / markov_2.py |
markov |
|
45 |
45 |
0 |
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5 |
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0% |
| mddb_workflow / analyses / nassa.py |
BasePairCorrelation.__init__ |
|
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0 |
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0% |
| mddb_workflow / analyses / nassa.py |
BasePairCorrelation.extract |
|
20 |
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0 |
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| mddb_workflow / analyses / nassa.py |
BasePairCorrelation.extraer_tetramero_central |
|
1 |
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| mddb_workflow / analyses / nassa.py |
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12 |
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BasePairCorrelation.iterate_trajectory |
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15 |
15 |
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| mddb_workflow / analyses / nassa.py |
BasePairCorrelation.get_correlation |
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12 |
12 |
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BasePairCorrelation.get_corr_by_method |
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BasePairCorrelation.circular |
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7 |
7 |
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BasePairCorrelation.circlineal |
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12 |
12 |
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BasePairCorrelation.make_tables |
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1 |
1 |
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| mddb_workflow / analyses / nassa.py |
BasePairCorrelation.make_plots |
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1 |
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BConformations.__init__ |
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7 |
7 |
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| mddb_workflow / analyses / nassa.py |
BConformations.extract |
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20 |
20 |
0 |
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| mddb_workflow / analyses / nassa.py |
BConformations.transform |
|
17 |
17 |
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BConformations.get_angles_difference |
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17 |
17 |
0 |
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BConformations.get_angles_difference.fix_angle_range |
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5 |
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| mddb_workflow / analyses / nassa.py |
BConformations.make_tables |
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4 |
4 |
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| mddb_workflow / analyses / nassa.py |
BConformations.make_plots |
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4 |
4 |
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| mddb_workflow / analyses / nassa.py |
CoordinateCorrelation.__init__ |
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1 |
1 |
0 |
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0% |
| mddb_workflow / analyses / nassa.py |
CoordinateCorrelation.extract |
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20 |
20 |
0 |
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| mddb_workflow / analyses / nassa.py |
CoordinateCorrelation.transform |
|
7 |
7 |
0 |
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| mddb_workflow / analyses / nassa.py |
CoordinateCorrelation.iterate_trajectory |
|
24 |
24 |
0 |
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| mddb_workflow / analyses / nassa.py |
CoordinateCorrelation.get_corr_method |
|
8 |
8 |
0 |
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0% |
| mddb_workflow / analyses / nassa.py |
CoordinateCorrelation.circular |
|
7 |
7 |
0 |
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0% |
| mddb_workflow / analyses / nassa.py |
CoordinateCorrelation.circlineal |
|
10 |
10 |
0 |
|
0% |
| mddb_workflow / analyses / nassa.py |
CoordinateCorrelation.make_tables |
|
8 |
8 |
0 |
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| mddb_workflow / analyses / nassa.py |
CoordinateCorrelation.make_plots |
|
4 |
4 |
0 |
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0% |
| mddb_workflow / analyses / nassa.py |
CoordinateDistributions.__init__ |
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5 |
5 |
0 |
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0% |
| mddb_workflow / analyses / nassa.py |
CoordinateDistributions.extract |
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20 |
20 |
0 |
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| mddb_workflow / analyses / nassa.py |
CoordinateDistributions.transform |
|
8 |
8 |
0 |
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0% |
| mddb_workflow / analyses / nassa.py |
CoordinateDistributions.coordinate_iteration |
|
9 |
9 |
0 |
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0% |
| mddb_workflow / analyses / nassa.py |
CoordinateDistributions.duplicate_trajectory_iteration |
|
23 |
23 |
0 |
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0% |
| mddb_workflow / analyses / nassa.py |
CoordinateDistributions.trajectory_iteration |
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23 |
23 |
0 |
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| mddb_workflow / analyses / nassa.py |
CoordinateDistributions.subunit_iteration |
|
5 |
5 |
0 |
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0% |
| mddb_workflow / analyses / nassa.py |
CoordinateDistributions.add_modality_labels |
|
15 |
15 |
0 |
|
0% |
| mddb_workflow / analyses / nassa.py |
CoordinateDistributions.make_tables |
|
2 |
2 |
0 |
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0% |
| mddb_workflow / analyses / nassa.py |
CoordinateDistributions.make_plots |
|
5 |
5 |
0 |
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0% |
| mddb_workflow / analyses / nassa.py |
StiffnessDistributions.__init__ |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / analyses / nassa.py |
StiffnessDistributions.extract |
|
23 |
23 |
0 |
|
0% |
| mddb_workflow / analyses / nassa.py |
StiffnessDistributions.transform |
|
13 |
13 |
0 |
|
0% |
| mddb_workflow / analyses / nassa.py |
StiffnessDistributions.get_stiffness |
|
18 |
18 |
0 |
|
0% |
| mddb_workflow / analyses / nassa.py |
StiffnessDistributions.get_subunit_stiffness |
|
35 |
35 |
0 |
|
0% |
| mddb_workflow / analyses / nassa.py |
StiffnessDistributions.circ_avg |
|
5 |
5 |
0 |
|
0% |
| mddb_workflow / analyses / nassa.py |
StiffnessDistributions.unimod_labels |
|
8 |
8 |
0 |
|
0% |
| mddb_workflow / analyses / nassa.py |
StiffnessDistributions.make_tables |
|
10 |
10 |
0 |
|
0% |
| mddb_workflow / analyses / nassa.py |
StiffnessDistributions.make_plots |
|
11 |
11 |
0 |
|
0% |
| mddb_workflow / analyses / nassa.py |
run_nassa |
|
23 |
23 |
0 |
|
0% |
| mddb_workflow / analyses / nassa.py |
workflow_nassa |
|
94 |
94 |
0 |
|
0% |
| mddb_workflow / analyses / nassa.py |
(no function) |
|
77 |
0 |
0 |
|
100% |
| mddb_workflow / analyses / pca.py |
pca |
|
61 |
8 |
0 |
|
87% |
| mddb_workflow / analyses / pca.py |
get_closer_value_index |
|
2 |
0 |
0 |
|
100% |
| mddb_workflow / analyses / pca.py |
(no function) |
|
9 |
0 |
0 |
|
100% |
| mddb_workflow / analyses / pca_contacts.py |
pytraj_residue_pairs |
|
2 |
2 |
0 |
|
0% |
| mddb_workflow / analyses / pca_contacts.py |
mdtraj_residue_pairs |
|
2 |
2 |
0 |
|
0% |
| mddb_workflow / analyses / pca_contacts.py |
pytraj_distances |
|
3 |
3 |
0 |
|
0% |
| mddb_workflow / analyses / pca_contacts.py |
mdtraj_distances |
|
2 |
2 |
0 |
|
0% |
| mddb_workflow / analyses / pca_contacts.py |
get_most_frequent_pairs |
|
6 |
6 |
0 |
|
0% |
| mddb_workflow / analyses / pca_contacts.py |
sigmoid |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / analyses / pca_contacts.py |
pca_contacts |
|
33 |
33 |
0 |
|
0% |
| mddb_workflow / analyses / pca_contacts.py |
(no function) |
|
13 |
13 |
0 |
|
0% |
| mddb_workflow / analyses / pockets.py |
pockets |
|
189 |
20 |
0 |
|
89% |
| mddb_workflow / analyses / pockets.py |
pockets.get_index |
|
2 |
0 |
0 |
|
100% |
| mddb_workflow / analyses / pockets.py |
pockets.get_colliding_points |
|
15 |
6 |
0 |
|
60% |
| mddb_workflow / analyses / pockets.py |
pockets.set_pocket |
|
14 |
0 |
0 |
|
100% |
| mddb_workflow / analyses / pockets.py |
pockets.is_pocket_base |
|
7 |
0 |
0 |
|
100% |
| mddb_workflow / analyses / pockets.py |
pockets.get_coordinates |
|
3 |
0 |
0 |
|
100% |
| mddb_workflow / analyses / pockets.py |
(no function) |
|
17 |
0 |
0 |
|
100% |
| mddb_workflow / analyses / rgyr.py |
rgyr |
|
17 |
2 |
0 |
|
88% |
| mddb_workflow / analyses / rgyr.py |
(no function) |
|
10 |
0 |
0 |
|
100% |
| mddb_workflow / analyses / rmsd_check.py |
check_trajectory_integrity |
|
100 |
55 |
0 |
|
45% |
| mddb_workflow / analyses / rmsd_check.py |
display_rmsd_jumps_graph |
|
12 |
12 |
0 |
|
0% |
| mddb_workflow / analyses / rmsd_check.py |
check_trajectory_integrity_per_residue |
|
98 |
98 |
0 |
|
0% |
| mddb_workflow / analyses / rmsd_check.py |
(no function) |
|
16 |
0 |
0 |
|
100% |
| mddb_workflow / analyses / rmsd_pairwise.py |
rmsd_pairwise |
|
41 |
8 |
0 |
|
80% |
| mddb_workflow / analyses / rmsd_pairwise.py |
(no function) |
|
8 |
0 |
0 |
|
100% |
| mddb_workflow / analyses / rmsd_per_residue.py |
rmsd_per_residue |
|
25 |
2 |
0 |
|
92% |
| mddb_workflow / analyses / rmsd_per_residue.py |
(no function) |
|
7 |
0 |
0 |
|
100% |
| mddb_workflow / analyses / rmsds.py |
rmsds |
|
41 |
2 |
0 |
|
95% |
| mddb_workflow / analyses / rmsds.py |
rmsd |
|
7 |
0 |
0 |
|
100% |
| mddb_workflow / analyses / rmsds.py |
(no function) |
|
9 |
0 |
0 |
|
100% |
| mddb_workflow / analyses / rmsf.py |
rmsf |
|
12 |
3 |
0 |
|
75% |
| mddb_workflow / analyses / rmsf.py |
(no function) |
|
7 |
0 |
0 |
|
100% |
| mddb_workflow / analyses / sasa.py |
sasa |
|
58 |
7 |
0 |
|
88% |
| mddb_workflow / analyses / sasa.py |
(no function) |
|
10 |
0 |
0 |
|
100% |
| mddb_workflow / analyses / thickness.py |
thickness |
|
24 |
0 |
0 |
|
100% |
| mddb_workflow / analyses / thickness.py |
plot_thickness |
|
20 |
20 |
0 |
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0% |
| mddb_workflow / analyses / thickness.py |
(no function) |
|
9 |
0 |
0 |
|
100% |
| mddb_workflow / analyses / tmscores.py |
_tm_score_no_filter |
|
3 |
0 |
0 |
|
100% |
| mddb_workflow / analyses / tmscores.py |
tmscores |
|
34 |
2 |
0 |
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94% |
| mddb_workflow / analyses / tmscores.py |
(no function) |
|
10 |
0 |
0 |
|
100% |
| mddb_workflow / console.py |
CustomHelpFormatter.__init__ |
|
1 |
0 |
0 |
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100% |
| mddb_workflow / console.py |
CustomHelpFormatter._get_help_string |
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8 |
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0 |
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CustomHelpFormatter._split_lines |
|
7 |
0 |
0 |
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CustomHelpFormatter._format_usage |
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13 |
0 |
0 |
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CustomHelpFormatter._format_action_invocation |
|
14 |
1 |
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93% |
| mddb_workflow / console.py |
CustomArgumentParser.error |
|
16 |
0 |
0 |
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100% |
| mddb_workflow / console.py |
parse_docstring_for_help |
|
17 |
3 |
0 |
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82% |
| mddb_workflow / console.py |
pretty_list |
|
8 |
1 |
0 |
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88% |
| mddb_workflow / console.py |
custom.__call__ |
|
3 |
3 |
0 |
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0% |
| mddb_workflow / console.py |
main |
|
117 |
67 |
0 |
|
43% |
| mddb_workflow / console.py |
(no function) |
|
116 |
0 |
0 |
|
100% |
| mddb_workflow / core / dataset.py |
Dataset.__init__ |
|
5 |
5 |
0 |
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0% |
| mddb_workflow / core / dataset.py |
Dataset._resolve_directory_patterns |
|
12 |
12 |
0 |
|
0% |
| mddb_workflow / core / dataset.py |
Dataset.get_project_directories |
|
6 |
6 |
0 |
|
0% |
| mddb_workflow / core / dataset.py |
Dataset.get_groups |
|
4 |
4 |
0 |
|
0% |
| mddb_workflow / core / dataset.py |
Dataset.generate_inputs_yaml |
|
16 |
16 |
0 |
|
0% |
| mddb_workflow / core / dataset.py |
Dataset.status |
|
43 |
43 |
0 |
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0% |
| mddb_workflow / core / dataset.py |
Dataset.show_groups |
|
13 |
13 |
0 |
|
0% |
| mddb_workflow / core / dataset.py |
Dataset.status_with_links |
|
7 |
7 |
0 |
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0% |
| mddb_workflow / core / dataset.py |
Dataset.status_with_links.make_out_link |
|
6 |
6 |
0 |
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0% |
| mddb_workflow / core / dataset.py |
Dataset.status_with_links.make_error_link |
|
6 |
6 |
0 |
|
0% |
| mddb_workflow / core / dataset.py |
Dataset.display_status_with_links |
|
6 |
6 |
0 |
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0% |
| mddb_workflow / core / dataset.py |
Dataset.launch_workflow |
|
44 |
44 |
0 |
|
0% |
| mddb_workflow / core / dataset.py |
(no function) |
|
20 |
0 |
0 |
|
100% |
| mddb_workflow / mwf.py |
MD.__init__ |
|
41 |
4 |
0 |
|
90% |
| mddb_workflow / mwf.py |
MD.__repr__ |
|
1 |
1 |
0 |
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0% |
| mddb_workflow / mwf.py |
MD.pathify |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / mwf.py |
MD.get_input_structure_filepath |
|
15 |
4 |
0 |
|
73% |
| mddb_workflow / mwf.py |
MD.get_input_structure_filepath.relativize_and_parse_paths |
|
37 |
20 |
0 |
|
46% |
| mddb_workflow / mwf.py |
MD.get_input_structure_file |
|
16 |
3 |
0 |
|
81% |
| mddb_workflow / mwf.py |
MD.get_input_trajectory_filepaths |
|
13 |
2 |
0 |
|
85% |
| mddb_workflow / mwf.py |
MD.get_input_trajectory_filepaths.relativize_and_parse_paths |
|
47 |
19 |
0 |
|
60% |
| mddb_workflow / mwf.py |
MD.get_input_trajectory_filepaths.relativize_and_parse_paths.parse_all_glob |
|
4 |
0 |
0 |
|
100% |
| mddb_workflow / mwf.py |
MD.get_input_trajectory_files |
|
33 |
9 |
0 |
|
73% |
| mddb_workflow / mwf.py |
MD.get_md_inputs |
|
19 |
6 |
0 |
|
68% |
| mddb_workflow / mwf.py |
MD.get_input |
|
4 |
1 |
0 |
|
75% |
| mddb_workflow / mwf.py |
MD.get_file |
|
8 |
4 |
0 |
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50% |
| mddb_workflow / mwf.py |
MD.print_tests_summary |
|
15 |
4 |
0 |
|
73% |
| mddb_workflow / mwf.py |
MD._issue_required_test_warnings |
|
11 |
9 |
0 |
|
18% |
| mddb_workflow / mwf.py |
MD.get_topology_filepath |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / mwf.py |
MD.get_topology_file |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / mwf.py |
MD.get_reference_bonds |
|
1 |
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0 |
|
100% |
| mddb_workflow / mwf.py |
MD.get_structure |
|
10 |
1 |
0 |
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90% |
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|
2 |
0 |
0 |
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100% |
| mddb_workflow / mwf.py |
MD.input_getter.getter |
|
4 |
1 |
0 |
|
75% |
| mddb_workflow / mwf.py |
MD._set_pbc_selection |
|
29 |
9 |
0 |
|
69% |
| mddb_workflow / mwf.py |
MD.get_pbc_selection |
|
4 |
0 |
0 |
|
100% |
| mddb_workflow / mwf.py |
MD.get_pbc_residues |
|
8 |
4 |
0 |
|
50% |
| mddb_workflow / mwf.py |
MD._set_cg_selection |
|
23 |
8 |
0 |
|
65% |
| mddb_workflow / mwf.py |
MD.get_cg_selection |
|
4 |
1 |
0 |
|
75% |
| mddb_workflow / mwf.py |
MD.get_cg_residues |
|
8 |
4 |
0 |
|
50% |
| mddb_workflow / mwf.py |
MD.get_populations |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / mwf.py |
MD.get_transitions |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / mwf.py |
MD.get_protein_map |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / mwf.py |
MD.get_charges |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / mwf.py |
MD.is_trajectory_integral |
|
4 |
1 |
0 |
|
75% |
| mddb_workflow / mwf.py |
MD.get_warnings |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / mwf.py |
Project.__init__ |
|
114 |
28 |
0 |
|
75% |
| mddb_workflow / mwf.py |
Project.__repr__ |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / mwf.py |
Project.pathify |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / mwf.py |
Project.check_md_directories |
|
4 |
2 |
0 |
|
50% |
| mddb_workflow / mwf.py |
Project.get_md_directories |
|
21 |
8 |
0 |
|
62% |
| mddb_workflow / mwf.py |
Project.get_reference_md_index |
|
8 |
1 |
0 |
|
88% |
| mddb_workflow / mwf.py |
Project.get_reference_md |
|
4 |
0 |
0 |
|
100% |
| mddb_workflow / mwf.py |
Project.get_mds |
|
20 |
0 |
0 |
|
100% |
| mddb_workflow / mwf.py |
Project.is_inputs_file_available |
|
7 |
1 |
0 |
|
86% |
| mddb_workflow / mwf.py |
Project.get_inputs_file |
|
8 |
1 |
0 |
|
88% |
| mddb_workflow / mwf.py |
Project.get_input_topology_filepath |
|
20 |
4 |
0 |
|
80% |
| mddb_workflow / mwf.py |
Project.get_input_topology_filepath.parse |
|
14 |
8 |
0 |
|
43% |
| mddb_workflow / mwf.py |
Project.get_input_topology_file |
|
27 |
9 |
0 |
|
67% |
| mddb_workflow / mwf.py |
Project.get_input_structure_file |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / mwf.py |
Project.get_input_trajectory_files |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / mwf.py |
Project.get_populations_file |
|
3 |
1 |
0 |
|
67% |
| mddb_workflow / mwf.py |
Project.get_transitions_file |
|
3 |
1 |
0 |
|
67% |
| mddb_workflow / mwf.py |
Project.get_aiida_data_file |
|
3 |
2 |
0 |
|
33% |
| mddb_workflow / mwf.py |
Project.get_file |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / mwf.py |
Project.get_inputs |
|
16 |
3 |
0 |
|
81% |
| mddb_workflow / mwf.py |
Project.update_inputs |
|
11 |
2 |
0 |
|
82% |
| mddb_workflow / mwf.py |
Project.get_input |
|
8 |
1 |
0 |
|
88% |
| mddb_workflow / mwf.py |
Project.input_property |
|
2 |
0 |
0 |
|
100% |
| mddb_workflow / mwf.py |
Project.input_property.getter |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / mwf.py |
Project.get_input_pbc_selection |
|
6 |
1 |
0 |
|
83% |
| mddb_workflow / mwf.py |
Project.get_input_cg_selection |
|
6 |
1 |
0 |
|
83% |
| mddb_workflow / mwf.py |
Project.check_is_time_dependent |
|
5 |
3 |
0 |
|
40% |
| mddb_workflow / mwf.py |
Project.inherit_topology_filename |
|
8 |
1 |
0 |
|
88% |
| mddb_workflow / mwf.py |
Project.get_topology_filepath |
|
7 |
1 |
0 |
|
86% |
| mddb_workflow / mwf.py |
Project.get_topology_file |
|
2 |
0 |
0 |
|
100% |
| mddb_workflow / mwf.py |
Project.get_structure_file |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / mwf.py |
Project.get_trajectory_file |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / mwf.py |
Project.get_structure |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / mwf.py |
Project.get_pbc_residues |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / mwf.py |
Project.get_cg_residues |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / mwf.py |
Project.get_snapshots |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / mwf.py |
Project.get_universe |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / mwf.py |
Project.get_processed_interactions |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / mwf.py |
Project.get_check_stable_bonds |
|
4 |
4 |
0 |
|
0% |
| mddb_workflow / mwf.py |
Project.get_topology_reader |
|
3 |
0 |
0 |
|
100% |
| mddb_workflow / mwf.py |
Project.get_dihedrals |
|
3 |
0 |
0 |
|
100% |
| mddb_workflow / mwf.py |
Project.get_populations |
|
6 |
3 |
0 |
|
50% |
| mddb_workflow / mwf.py |
Project.get_transitions |
|
6 |
6 |
0 |
|
0% |
| mddb_workflow / mwf.py |
Project.get_pdb_ids |
|
14 |
2 |
0 |
|
86% |
| mddb_workflow / mwf.py |
Project.get_warnings |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / mwf.py |
read_file |
|
5 |
5 |
0 |
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0% |
| mddb_workflow / mwf.py |
name_2_directory |
|
4 |
0 |
0 |
|
100% |
| mddb_workflow / mwf.py |
check_directory |
|
4 |
1 |
0 |
|
75% |
| mddb_workflow / mwf.py |
directory_2_name |
|
2 |
2 |
0 |
|
0% |
| mddb_workflow / mwf.py |
workflow |
|
69 |
18 |
0 |
|
74% |
| mddb_workflow / mwf.py |
(no function) |
|
324 |
2 |
0 |
|
99% |
| mddb_workflow / resources / covid_variants.py |
(no function) |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / tools / __init__.py |
(no function) |
|
2 |
0 |
0 |
|
100% |
| mddb_workflow / tools / chains.py |
request_interpsocan |
|
13 |
13 |
0 |
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0% |
| mddb_workflow / tools / chains.py |
check_interproscan_status |
|
12 |
12 |
0 |
|
0% |
| mddb_workflow / tools / chains.py |
check_interproscan_result |
|
14 |
14 |
0 |
|
0% |
| mddb_workflow / tools / chains.py |
get_protein_parsed_chains |
|
13 |
0 |
0 |
|
100% |
| mddb_workflow / tools / chains.py |
import_chains |
|
6 |
6 |
0 |
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0% |
| mddb_workflow / tools / chains.py |
prepare_chain_references |
|
24 |
5 |
0 |
|
79% |
| mddb_workflow / tools / chains.py |
get_interproscan_results |
|
28 |
24 |
0 |
|
14% |
| mddb_workflow / tools / chains.py |
(no function) |
|
17 |
0 |
0 |
|
100% |
| mddb_workflow / tools / check_inputs.py |
check_inputs |
|
49 |
30 |
0 |
|
39% |
| mddb_workflow / tools / check_inputs.py |
get_topology_and_trajectory_atoms_pytraj |
|
10 |
10 |
0 |
|
0% |
| mddb_workflow / tools / check_inputs.py |
get_topology_and_trajectory_atoms |
|
57 |
25 |
0 |
|
56% |
| mddb_workflow / tools / check_inputs.py |
get_structure_atoms |
|
4 |
1 |
0 |
|
75% |
| mddb_workflow / tools / check_inputs.py |
get_structure_and_trajectory_atoms |
|
6 |
0 |
0 |
|
100% |
| mddb_workflow / tools / check_inputs.py |
(no function) |
|
31 |
0 |
0 |
|
100% |
| mddb_workflow / tools / conversions.py |
convert |
|
36 |
7 |
0 |
|
81% |
| mddb_workflow / tools / conversions.py |
convert.convert_structure |
|
18 |
6 |
0 |
|
67% |
| mddb_workflow / tools / conversions.py |
convert.convert_trajectory |
|
22 |
6 |
0 |
|
73% |
| mddb_workflow / tools / conversions.py |
(no function) |
|
15 |
0 |
0 |
|
100% |
| mddb_workflow / tools / filter_atoms.py |
filter_atoms |
|
65 |
30 |
0 |
|
54% |
| mddb_workflow / tools / filter_atoms.py |
standard_topology_filter |
|
50 |
50 |
0 |
|
0% |
| mddb_workflow / tools / filter_atoms.py |
standard_topology_filter.filter_by_indices |
|
3 |
3 |
0 |
|
0% |
| mddb_workflow / tools / filter_atoms.py |
(no function) |
|
14 |
0 |
0 |
|
100% |
| mddb_workflow / tools / fix_gromacs_masses.py |
fix_gromacs_masses |
|
5 |
0 |
0 |
|
100% |
| mddb_workflow / tools / fix_gromacs_masses.py |
(no function) |
|
3 |
0 |
0 |
|
100% |
| mddb_workflow / tools / generate_map.py |
add_leading_and_trailing_gaps |
|
10 |
0 |
0 |
|
100% |
| mddb_workflow / tools / generate_map.py |
generate_protein_mapping |
|
91 |
41 |
0 |
|
55% |
| mddb_workflow / tools / generate_map.py |
generate_protein_mapping.get_reference |
|
8 |
3 |
0 |
|
62% |
| mddb_workflow / tools / generate_map.py |
generate_protein_mapping.match_sequences |
|
73 |
15 |
0 |
|
79% |
| mddb_workflow / tools / generate_map.py |
export_references |
|
15 |
2 |
0 |
|
87% |
| mddb_workflow / tools / generate_map.py |
import_references |
|
7 |
0 |
0 |
|
100% |
| mddb_workflow / tools / generate_map.py |
get_parsed_chains |
|
13 |
0 |
0 |
|
100% |
| mddb_workflow / tools / generate_map.py |
align |
|
31 |
6 |
0 |
|
81% |
| mddb_workflow / tools / generate_map.py |
blast |
|
22 |
22 |
0 |
|
0% |
| mddb_workflow / tools / generate_map.py |
get_uniprot_reference |
|
74 |
74 |
0 |
|
0% |
| mddb_workflow / tools / generate_map.py |
pdb_to_uniprot |
|
48 |
27 |
0 |
|
44% |
| mddb_workflow / tools / generate_map.py |
get_sequence_metadata |
|
66 |
23 |
0 |
|
65% |
| mddb_workflow / tools / generate_map.py |
get_sequence_metadata.in_range |
|
4 |
0 |
0 |
|
100% |
| mddb_workflow / tools / generate_map.py |
(no function) |
|
31 |
0 |
0 |
|
100% |
| mddb_workflow / tools / generate_metadata.py |
prepare_project_metadata |
|
68 |
18 |
0 |
|
74% |
| mddb_workflow / tools / generate_metadata.py |
generate_md_metadata |
|
17 |
0 |
0 |
|
100% |
| mddb_workflow / tools / generate_metadata.py |
(no function) |
|
10 |
0 |
0 |
|
100% |
| mddb_workflow / tools / generate_pdb_references.py |
prepare_pdb_references |
|
15 |
6 |
0 |
|
60% |
| mddb_workflow / tools / generate_pdb_references.py |
get_pdb_reference |
|
32 |
5 |
0 |
|
84% |
| mddb_workflow / tools / generate_pdb_references.py |
DEPRECATED_download_pdb_data |
|
30 |
30 |
0 |
|
0% |
| mddb_workflow / tools / generate_pdb_references.py |
(no function) |
|
8 |
0 |
0 |
|
100% |
| mddb_workflow / tools / generate_topology.py |
generate_topology |
|
40 |
4 |
0 |
|
90% |
| mddb_workflow / tools / generate_topology.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| mddb_workflow / tools / get_atoms_count.py |
get_atoms_count |
|
37 |
0 |
0 |
|
100% |
| mddb_workflow / tools / get_atoms_count.py |
(no function) |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / tools / get_bonds.py |
get_excluded_atoms_selection |
|
3 |
0 |
0 |
|
100% |
| mddb_workflow / tools / get_bonds.py |
do_bonds_match |
|
26 |
6 |
0 |
|
77% |
| mddb_workflow / tools / get_bonds.py |
get_most_stable_bonds |
|
22 |
0 |
0 |
|
100% |
| mddb_workflow / tools / get_bonds.py |
get_bonds_reference_frame |
|
29 |
13 |
0 |
|
55% |
| mddb_workflow / tools / get_bonds.py |
get_bonds_reference_frame.format_row |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / tools / get_bonds.py |
mine_topology_bonds |
|
31 |
4 |
0 |
|
87% |
| mddb_workflow / tools / get_bonds.py |
get_tpr_bonds |
|
12 |
9 |
0 |
|
25% |
| mddb_workflow / tools / get_bonds.py |
sort_bonds |
|
6 |
0 |
0 |
|
100% |
| mddb_workflow / tools / get_bonds.py |
find_safe_bonds |
|
27 |
12 |
0 |
|
56% |
| mddb_workflow / tools / get_bonds.py |
discard_coarse_grain_bonds |
|
2 |
1 |
0 |
|
50% |
| mddb_workflow / tools / get_bonds.py |
(no function) |
|
21 |
0 |
0 |
|
100% |
| mddb_workflow / tools / get_box_size.py |
get_box_size |
|
11 |
0 |
0 |
|
100% |
| mddb_workflow / tools / get_box_size.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| mddb_workflow / tools / get_charges.py |
get_charges |
|
20 |
4 |
0 |
|
80% |
| mddb_workflow / tools / get_charges.py |
get_topology_charges |
|
7 |
4 |
0 |
|
43% |
| mddb_workflow / tools / get_charges.py |
get_topology_charges_pytraj |
|
3 |
0 |
0 |
|
100% |
| mddb_workflow / tools / get_charges.py |
get_topology_charges_mdanalysis |
|
4 |
4 |
0 |
|
0% |
| mddb_workflow / tools / get_charges.py |
generate_raw_energies_file |
|
3 |
3 |
0 |
|
0% |
| mddb_workflow / tools / get_charges.py |
get_raw_charges |
|
6 |
6 |
0 |
|
0% |
| mddb_workflow / tools / get_charges.py |
get_tpr_charges |
|
6 |
3 |
0 |
|
50% |
| mddb_workflow / tools / get_charges.py |
get_tpr_charges_mdanalysis |
|
4 |
0 |
0 |
|
100% |
| mddb_workflow / tools / get_charges.py |
(no function) |
|
16 |
0 |
0 |
|
100% |
| mddb_workflow / tools / get_first_frame.py |
get_first_frame |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / tools / get_first_frame.py |
(no function) |
|
3 |
0 |
0 |
|
100% |
| mddb_workflow / tools / get_inchi_keys.py |
InChIKeyData.load_cache |
|
9 |
9 |
0 |
|
0% |
| mddb_workflow / tools / get_inchi_keys.py |
is_ferroheme |
|
16 |
16 |
0 |
|
0% |
| mddb_workflow / tools / get_inchi_keys.py |
residue_to_inchi |
|
18 |
18 |
0 |
|
0% |
| mddb_workflow / tools / get_inchi_keys.py |
generate_inchikeys |
|
54 |
9 |
0 |
|
83% |
| mddb_workflow / tools / get_inchi_keys.py |
generate_inchi_references |
|
13 |
0 |
0 |
|
100% |
| mddb_workflow / tools / get_inchi_keys.py |
(no function) |
|
28 |
0 |
0 |
|
100% |
| mddb_workflow / tools / get_ligands.py |
record_pubchem_match |
|
7 |
0 |
0 |
|
100% |
| mddb_workflow / tools / get_ligands.py |
generate_ligand_references |
|
115 |
51 |
0 |
|
56% |
| mddb_workflow / tools / get_ligands.py |
pdb_ligand_2_prd |
|
11 |
5 |
0 |
|
55% |
| mddb_workflow / tools / get_ligands.py |
get_pdb_ligand_codes |
|
15 |
1 |
0 |
|
93% |
| mddb_workflow / tools / get_ligands.py |
pdb_ligand_2_pubchem |
|
7 |
3 |
0 |
|
57% |
| mddb_workflow / tools / get_ligands.py |
pdb_ligand_2_pubchem_RAW |
|
17 |
8 |
0 |
|
53% |
| mddb_workflow / tools / get_ligands.py |
pdb_ligand_2_pubchem_RAW_RAW |
|
18 |
6 |
0 |
|
67% |
| mddb_workflow / tools / get_ligands.py |
pdb_2_pubchem |
|
15 |
2 |
0 |
|
87% |
| mddb_workflow / tools / get_ligands.py |
pdbs_2_pubchems |
|
19 |
4 |
0 |
|
79% |
| mddb_workflow / tools / get_ligands.py |
handle_http_request |
|
9 |
6 |
0 |
|
33% |
| mddb_workflow / tools / get_ligands.py |
get_pubchem_data |
|
88 |
28 |
0 |
|
68% |
| mddb_workflow / tools / get_ligands.py |
drugbank_2_pubchem |
|
6 |
6 |
0 |
|
0% |
| mddb_workflow / tools / get_ligands.py |
chembl_2_pubchem |
|
6 |
6 |
0 |
|
0% |
| mddb_workflow / tools / get_ligands.py |
obtain_mordred_morgan_descriptors |
|
16 |
0 |
0 |
|
100% |
| mddb_workflow / tools / get_ligands.py |
tanimoto_similarity |
|
8 |
2 |
0 |
|
75% |
| mddb_workflow / tools / get_ligands.py |
obtain_pubchem_data_from_input |
|
15 |
8 |
0 |
|
47% |
| mddb_workflow / tools / get_ligands.py |
inchikey_2_pubchem |
|
9 |
1 |
0 |
|
89% |
| mddb_workflow / tools / get_ligands.py |
pubchem_standardization |
|
17 |
2 |
0 |
|
88% |
| mddb_workflow / tools / get_ligands.py |
(no function) |
|
36 |
0 |
0 |
|
100% |
| mddb_workflow / tools / get_lipids.py |
generate_lipid_references |
|
17 |
5 |
0 |
|
71% |
| mddb_workflow / tools / get_lipids.py |
is_in_LIPID_MAPS |
|
10 |
1 |
0 |
|
90% |
| mddb_workflow / tools / get_lipids.py |
get_swisslipids_info |
|
6 |
1 |
0 |
|
83% |
| mddb_workflow / tools / get_lipids.py |
is_in_swisslipids |
|
10 |
0 |
0 |
|
100% |
| mddb_workflow / tools / get_lipids.py |
(no function) |
|
10 |
0 |
0 |
|
100% |
| mddb_workflow / tools / get_pdb_frames.py |
get_pdb_frames |
|
5 |
0 |
0 |
|
100% |
| mddb_workflow / tools / get_pdb_frames.py |
get_pdb_frames.frames_generator |
|
13 |
0 |
0 |
|
100% |
| mddb_workflow / tools / get_pdb_frames.py |
get_pdb_frame |
|
5 |
0 |
0 |
|
100% |
| mddb_workflow / tools / get_pdb_frames.py |
(no function) |
|
8 |
0 |
0 |
|
100% |
| mddb_workflow / tools / get_reduced_trajectory.py |
calculate_frame_step |
|
3 |
0 |
0 |
|
100% |
| mddb_workflow / tools / get_reduced_trajectory.py |
get_reduced_trajectory |
|
14 |
9 |
0 |
|
36% |
| mddb_workflow / tools / get_reduced_trajectory.py |
(no function) |
|
6 |
0 |
0 |
|
100% |
| mddb_workflow / tools / get_screenshot.py |
get_screenshot |
|
163 |
19 |
0 |
|
88% |
| mddb_workflow / tools / get_screenshot.py |
get_screenshot.display_vector |
|
6 |
6 |
0 |
|
0% |
| mddb_workflow / tools / get_screenshot.py |
tuple_to_vmd |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / tools / get_screenshot.py |
rotate_vector |
|
9 |
0 |
0 |
|
100% |
| mddb_workflow / tools / get_screenshot.py |
calculate_distance |
|
6 |
0 |
0 |
|
100% |
| mddb_workflow / tools / get_screenshot.py |
point_adds_vector |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / tools / get_screenshot.py |
multiply_vector |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / tools / get_screenshot.py |
(no function) |
|
19 |
0 |
0 |
|
100% |
| mddb_workflow / tools / guess_and_filter.py |
guess_and_filter_topology |
|
29 |
29 |
0 |
|
0% |
| mddb_workflow / tools / guess_and_filter.py |
(no function) |
|
11 |
0 |
0 |
|
100% |
| mddb_workflow / tools / image_and_fit.py |
get_chains |
|
3 |
3 |
0 |
|
0% |
| mddb_workflow / tools / image_and_fit.py |
set_chains |
|
3 |
3 |
0 |
|
0% |
| mddb_workflow / tools / image_and_fit.py |
image_and_fit |
|
48 |
48 |
0 |
|
0% |
| mddb_workflow / tools / image_and_fit.py |
reset_structure |
|
2 |
2 |
0 |
|
0% |
| mddb_workflow / tools / image_and_fit.py |
(no function) |
|
10 |
0 |
0 |
|
100% |
| mddb_workflow / tools / membrane_mapping.py |
generate_membrane_mapping |
|
8 |
0 |
0 |
|
100% |
| mddb_workflow / tools / membrane_mapping.py |
all_atom_membranes |
|
56 |
10 |
0 |
|
82% |
| mddb_workflow / tools / membrane_mapping.py |
coarse_grain_membranes |
|
30 |
0 |
0 |
|
100% |
| mddb_workflow / tools / membrane_mapping.py |
display_membrane_mapping |
|
15 |
15 |
0 |
|
0% |
| mddb_workflow / tools / membrane_mapping.py |
(no function) |
|
11 |
0 |
0 |
|
100% |
| mddb_workflow / tools / nassa_base.py |
Base.__init__ |
|
21 |
21 |
0 |
|
0% |
| mddb_workflow / tools / nassa_base.py |
Base.extract |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / tools / nassa_base.py |
Base.transform |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / tools / nassa_base.py |
Base.make_tables |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / tools / nassa_base.py |
Base.make_plots |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / tools / nassa_base.py |
Base.load |
|
2 |
2 |
0 |
|
0% |
| mddb_workflow / tools / nassa_base.py |
Base.run |
|
10 |
10 |
0 |
|
0% |
| mddb_workflow / tools / nassa_base.py |
Base.save_path |
|
11 |
11 |
0 |
|
0% |
| mddb_workflow / tools / nassa_base.py |
Base.create_logger |
|
7 |
7 |
0 |
|
0% |
| mddb_workflow / tools / nassa_base.py |
(no function) |
|
20 |
0 |
0 |
|
100% |
| mddb_workflow / tools / nassa_loaders.py |
load_sequence |
|
10 |
10 |
0 |
|
0% |
| mddb_workflow / tools / nassa_loaders.py |
load_sequence2 |
|
11 |
5 |
0 |
|
55% |
| mddb_workflow / tools / nassa_loaders.py |
reverse_sequence |
|
8 |
1 |
0 |
|
88% |
| mddb_workflow / tools / nassa_loaders.py |
write_sequence |
|
3 |
3 |
0 |
|
0% |
| mddb_workflow / tools / nassa_loaders.py |
load_serfile |
|
10 |
2 |
0 |
|
80% |
| mddb_workflow / tools / nassa_loaders.py |
write_serfile |
|
10 |
10 |
0 |
|
0% |
| mddb_workflow / tools / nassa_loaders.py |
(no function) |
|
10 |
0 |
0 |
|
100% |
| mddb_workflow / tools / process_input_files.py |
is_amber_top |
|
11 |
9 |
0 |
|
18% |
| mddb_workflow / tools / process_input_files.py |
process_input_files |
|
154 |
49 |
0 |
|
68% |
| mddb_workflow / tools / process_input_files.py |
(no function) |
|
20 |
0 |
0 |
|
100% |
| mddb_workflow / tools / process_interactions.py |
process_interactions |
|
120 |
40 |
0 |
|
67% |
| mddb_workflow / tools / process_interactions.py |
add_residues_indices |
|
7 |
0 |
0 |
|
100% |
| mddb_workflow / tools / process_interactions.py |
(no function) |
|
12 |
0 |
0 |
|
100% |
| mddb_workflow / tools / provenance.py |
produce_provenance |
|
22 |
19 |
0 |
|
14% |
| mddb_workflow / tools / provenance.py |
(no function) |
|
6 |
0 |
0 |
|
100% |
| mddb_workflow / tools / remove_trash.py |
remove_trash |
|
6 |
0 |
0 |
|
100% |
| mddb_workflow / tools / remove_trash.py |
(no function) |
|
4 |
0 |
0 |
|
100% |
| mddb_workflow / tools / residue_mapping.py |
generate_residue_mapping |
|
59 |
14 |
0 |
|
76% |
| mddb_workflow / tools / residue_mapping.py |
(no function) |
|
3 |
0 |
0 |
|
100% |
| mddb_workflow / tools / structure_corrector.py |
structure_corrector |
|
116 |
54 |
0 |
|
53% |
| mddb_workflow / tools / structure_corrector.py |
structure_corrector.check_stable_bonds |
|
29 |
7 |
0 |
|
76% |
| mddb_workflow / tools / structure_corrector.py |
(no function) |
|
11 |
0 |
0 |
|
100% |
| mddb_workflow / tools / xvg_parse.py |
xvg_parse |
|
14 |
0 |
0 |
|
100% |
| mddb_workflow / tools / xvg_parse.py |
(no function) |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / __init__.py |
(no function) |
|
0 |
0 |
0 |
|
100% |
| mddb_workflow / utils / arg_cksum.py |
get_cksum_id |
|
27 |
5 |
0 |
|
81% |
| mddb_workflow / utils / arg_cksum.py |
(no function) |
|
12 |
0 |
0 |
|
100% |
| mddb_workflow / utils / auxiliar.py |
is_imported |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / auxiliar.py |
NoReferableException.__str__ |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / auxiliar.py |
NoReferableException.__repr__ |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / auxiliar.py |
NoReferableException.get_sequence |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / utils / auxiliar.py |
custom_excepthook |
|
4 |
4 |
0 |
|
0% |
| mddb_workflow / utils / auxiliar.py |
get_new_letter |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / utils / auxiliar.py |
all_cases |
|
7 |
0 |
0 |
|
100% |
| mddb_workflow / utils / auxiliar.py |
residue_name_to_letter |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / auxiliar.py |
protein_residue_name_to_letter |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / auxiliar.py |
recursive_transformer |
|
14 |
1 |
0 |
|
93% |
| mddb_workflow / utils / auxiliar.py |
json_serializer |
|
3 |
0 |
0 |
|
100% |
| mddb_workflow / utils / auxiliar.py |
json_serializer.serializer |
|
8 |
0 |
0 |
|
100% |
| mddb_workflow / utils / auxiliar.py |
json_deserializer |
|
3 |
0 |
0 |
|
100% |
| mddb_workflow / utils / auxiliar.py |
json_deserializer.deserializer |
|
7 |
5 |
0 |
|
29% |
| mddb_workflow / utils / auxiliar.py |
load_json |
|
11 |
4 |
0 |
|
64% |
| mddb_workflow / utils / auxiliar.py |
save_json |
|
7 |
3 |
0 |
|
57% |
| mddb_workflow / utils / auxiliar.py |
load_yaml |
|
12 |
3 |
0 |
|
75% |
| mddb_workflow / utils / auxiliar.py |
save_yaml |
|
2 |
0 |
0 |
|
100% |
| mddb_workflow / utils / auxiliar.py |
delete_previous_log |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / auxiliar.py |
reprint |
|
2 |
0 |
0 |
|
100% |
| mddb_workflow / utils / auxiliar.py |
warn |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / auxiliar.py |
mean |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / utils / auxiliar.py |
round_to_hundredths |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / utils / auxiliar.py |
round_to_thousandths |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / auxiliar.py |
ranger |
|
25 |
1 |
0 |
|
96% |
| mddb_workflow / utils / auxiliar.py |
otherwise |
|
3 |
0 |
0 |
|
100% |
| mddb_workflow / utils / auxiliar.py |
list_files |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / utils / auxiliar.py |
is_directory_empty |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / utils / auxiliar.py |
is_glob |
|
9 |
5 |
0 |
|
44% |
| mddb_workflow / utils / auxiliar.py |
parse_glob |
|
4 |
2 |
0 |
|
50% |
| mddb_workflow / utils / auxiliar.py |
is_url |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / auxiliar.py |
url_to_source_filename |
|
2 |
0 |
0 |
|
100% |
| mddb_workflow / utils / auxiliar.py |
download_file |
|
7 |
7 |
0 |
|
0% |
| mddb_workflow / utils / auxiliar.py |
is_standard_topology |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / auxiliar.py |
store_binary_data |
|
8 |
8 |
0 |
|
0% |
| mddb_workflow / utils / auxiliar.py |
CaptureOutput.__init__ |
|
6 |
6 |
0 |
|
0% |
| mddb_workflow / utils / auxiliar.py |
CaptureOutput.__enter__ |
|
4 |
4 |
0 |
|
0% |
| mddb_workflow / utils / auxiliar.py |
CaptureOutput.__exit__ |
|
7 |
7 |
0 |
|
0% |
| mddb_workflow / utils / auxiliar.py |
CaptureOutput.readOutput |
|
5 |
5 |
0 |
|
0% |
| mddb_workflow / utils / auxiliar.py |
request_pdb_data |
|
16 |
7 |
0 |
|
56% |
| mddb_workflow / utils / auxiliar.py |
request_replaced_pdb |
|
9 |
9 |
0 |
|
0% |
| mddb_workflow / utils / auxiliar.py |
numerate_filename |
|
3 |
0 |
0 |
|
100% |
| mddb_workflow / utils / auxiliar.py |
glob_filename |
|
3 |
3 |
0 |
|
0% |
| mddb_workflow / utils / auxiliar.py |
purge_glob |
|
4 |
4 |
0 |
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0% |
| mddb_workflow / utils / auxiliar.py |
get_analysis_name |
|
4 |
1 |
0 |
|
75% |
| mddb_workflow / utils / auxiliar.py |
safe_hasattr |
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1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / auxiliar.py |
safe_getattr |
|
2 |
0 |
0 |
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100% |
| mddb_workflow / utils / auxiliar.py |
read_ndict |
|
11 |
0 |
0 |
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100% |
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write_ndict |
|
16 |
2 |
0 |
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88% |
| mddb_workflow / utils / auxiliar.py |
get_git_version |
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3 |
0 |
0 |
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100% |
| mddb_workflow / utils / auxiliar.py |
(no function) |
|
95 |
0 |
0 |
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100% |
| mddb_workflow / utils / bibitransformer_nassa.py |
BiBiTransformer.__init__ |
|
4 |
4 |
0 |
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0% |
| mddb_workflow / utils / bibitransformer_nassa.py |
BiBiTransformer.GMM_models |
|
3 |
3 |
0 |
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| mddb_workflow / utils / bibitransformer_nassa.py |
BiBiTransformer.fit |
|
3 |
3 |
0 |
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| mddb_workflow / utils / bibitransformer_nassa.py |
BiBiTransformer.transform |
|
31 |
31 |
0 |
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| mddb_workflow / utils / bibitransformer_nassa.py |
BiBiTransformer.bayes_factor_criteria |
|
11 |
11 |
0 |
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| mddb_workflow / utils / bibitransformer_nassa.py |
BiBiTransformer.is_unimodal |
|
4 |
4 |
0 |
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0% |
| mddb_workflow / utils / bibitransformer_nassa.py |
(no function) |
|
10 |
0 |
0 |
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100% |
| mddb_workflow / utils / cache.py |
Cache.__init__ |
|
5 |
0 |
0 |
|
100% |
| mddb_workflow / utils / cache.py |
Cache.retrieve |
|
1 |
0 |
0 |
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100% |
| mddb_workflow / utils / cache.py |
Cache.update |
|
2 |
0 |
0 |
|
100% |
| mddb_workflow / utils / cache.py |
Cache.delete |
|
3 |
3 |
0 |
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0% |
| mddb_workflow / utils / cache.py |
Cache.reset |
|
2 |
2 |
0 |
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0% |
| mddb_workflow / utils / cache.py |
Cache.load |
|
4 |
3 |
0 |
|
25% |
| mddb_workflow / utils / cache.py |
Cache.save |
|
2 |
0 |
0 |
|
100% |
| mddb_workflow / utils / cache.py |
(no function) |
|
11 |
0 |
0 |
|
100% |
| mddb_workflow / utils / constants.py |
(no function) |
|
159 |
8 |
0 |
|
95% |
| mddb_workflow / utils / database.py |
Remote.__init__ |
|
6 |
0 |
0 |
|
100% |
| mddb_workflow / utils / database.py |
Remote.get_project_data |
|
16 |
10 |
0 |
|
38% |
| mddb_workflow / utils / database.py |
Remote.get_snaphsots |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / database.py |
Remote.get_available_files |
|
9 |
2 |
0 |
|
78% |
| mddb_workflow / utils / database.py |
Remote.download_file |
|
13 |
4 |
0 |
|
69% |
| mddb_workflow / utils / database.py |
Remote.download_standard_topology |
|
8 |
2 |
0 |
|
75% |
| mddb_workflow / utils / database.py |
Remote.download_standard_structure |
|
8 |
2 |
0 |
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75% |
| mddb_workflow / utils / database.py |
Remote.download_trajectory |
|
27 |
4 |
0 |
|
85% |
| mddb_workflow / utils / database.py |
Remote.download_inputs_file |
|
14 |
5 |
0 |
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64% |
| mddb_workflow / utils / database.py |
Remote.download_analysis_data |
|
10 |
10 |
0 |
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0% |
| mddb_workflow / utils / database.py |
Database.__init__ |
|
4 |
1 |
0 |
|
75% |
| mddb_workflow / utils / database.py |
Database.__str__ |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / database.py |
Database.is_alive |
|
19 |
15 |
0 |
|
21% |
| mddb_workflow / utils / database.py |
Database.get_remote_project |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / database.py |
Database.get_reference_data |
|
11 |
6 |
0 |
|
45% |
| mddb_workflow / utils / database.py |
(no function) |
|
32 |
0 |
0 |
|
100% |
| mddb_workflow / utils / file.py |
File.__init__ |
|
26 |
2 |
0 |
|
92% |
| mddb_workflow / utils / file.py |
File.__repr__ |
|
4 |
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|
75% |
| mddb_workflow / utils / file.py |
File.__str__ |
|
1 |
1 |
0 |
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| mddb_workflow / utils / file.py |
File.__hash__ |
|
1 |
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| mddb_workflow / utils / file.py |
File.__bool__ |
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| mddb_workflow / utils / file.py |
File.__eq__ |
|
3 |
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| mddb_workflow / utils / file.py |
File.check_existence |
|
1 |
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0 |
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100% |
| mddb_workflow / utils / file.py |
File.get_format |
|
6 |
2 |
0 |
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67% |
| mddb_workflow / utils / file.py |
File.get_mtime |
|
2 |
2 |
0 |
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0% |
| mddb_workflow / utils / file.py |
File.get_size |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / file.py |
File.get_cksum |
|
15 |
3 |
0 |
|
80% |
| mddb_workflow / utils / file.py |
File.is_pytraj_supported |
|
1 |
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0 |
|
100% |
| mddb_workflow / utils / file.py |
File.get_pytraj_parm_format |
|
1 |
1 |
0 |
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0% |
| mddb_workflow / utils / file.py |
File.remove |
|
1 |
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0 |
|
100% |
| mddb_workflow / utils / file.py |
File.get_standard_file |
|
3 |
1 |
0 |
|
67% |
| mddb_workflow / utils / file.py |
File.reformat |
|
5 |
0 |
0 |
|
100% |
| mddb_workflow / utils / file.py |
File.get_prefixed_file |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / file.py |
File.get_neighbour_file |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / utils / file.py |
File.get_symlink |
|
4 |
4 |
0 |
|
0% |
| mddb_workflow / utils / file.py |
File.set_symlink_to |
|
8 |
3 |
0 |
|
62% |
| mddb_workflow / utils / file.py |
File.is_symlink |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / file.py |
File.copy_to |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / file.py |
File.rename_to |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / file.py |
(no function) |
|
40 |
0 |
0 |
|
100% |
| mddb_workflow / utils / filters.py |
filter_atoms |
|
73 |
34 |
0 |
|
53% |
| mddb_workflow / utils / filters.py |
(no function) |
|
13 |
0 |
0 |
|
100% |
| mddb_workflow / utils / formats.py |
get_format |
|
3 |
1 |
0 |
|
67% |
| mddb_workflow / utils / formats.py |
get_format_set_suitable_function |
|
17 |
1 |
0 |
|
94% |
| mddb_workflow / utils / formats.py |
get_common_argument_formats |
|
17 |
3 |
0 |
|
82% |
| mddb_workflow / utils / formats.py |
check_format_sets_compability |
|
25 |
8 |
0 |
|
68% |
| mddb_workflow / utils / formats.py |
get_format_set_suitable_combination |
|
9 |
0 |
0 |
|
100% |
| mddb_workflow / utils / formats.py |
get_format_set_suitable_combination.get_combinations |
|
26 |
2 |
0 |
|
92% |
| mddb_workflow / utils / formats.py |
get_format_set_suitable_combination.combined_function |
|
57 |
12 |
0 |
|
79% |
| mddb_workflow / utils / formats.py |
is_pdb |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / utils / formats.py |
is_psf |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / utils / formats.py |
is_tpr |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / utils / formats.py |
is_gro |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / utils / formats.py |
is_prmtop |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / utils / formats.py |
is_top |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / utils / formats.py |
is_xtc |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / utils / formats.py |
is_dcd |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / utils / formats.py |
is_netcdf |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / utils / formats.py |
are_xtc |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / utils / formats.py |
are_dcd |
|
1 |
1 |
0 |
|
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| mddb_workflow / utils / formats.py |
are_netcdf |
|
1 |
1 |
0 |
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| mddb_workflow / utils / formats.py |
is_pytraj_supported |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / utils / formats.py |
get_pytraj_parm_format |
|
9 |
9 |
0 |
|
0% |
| mddb_workflow / utils / formats.py |
(no function) |
|
22 |
0 |
0 |
|
100% |
| mddb_workflow / utils / gmx_spells.py |
run_gromacs |
|
28 |
5 |
0 |
|
82% |
| mddb_workflow / utils / gmx_spells.py |
get_first_frame |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / gmx_spells.py |
get_structure |
|
1 |
1 |
0 |
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| mddb_workflow / utils / gmx_spells.py |
get_structure_alone |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / gmx_spells.py |
merge_and_convert_trajectories |
|
15 |
15 |
0 |
|
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| mddb_workflow / utils / gmx_spells.py |
get_trajectory_subset |
|
5 |
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0 |
|
100% |
| mddb_workflow / utils / gmx_spells.py |
filter_structure |
|
7 |
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0 |
|
100% |
| mddb_workflow / utils / gmx_spells.py |
filter_trajectory |
|
7 |
0 |
0 |
|
100% |
| mddb_workflow / utils / gmx_spells.py |
mine_system_atoms_count |
|
5 |
2 |
0 |
|
60% |
| mddb_workflow / utils / gmx_spells.py |
get_tpr_atom_count |
|
5 |
1 |
0 |
|
80% |
| mddb_workflow / utils / gmx_spells.py |
read_and_parse_tpr |
|
5 |
0 |
0 |
|
100% |
| mddb_workflow / utils / gmx_spells.py |
get_tpr_content |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / utils / gmx_spells.py |
get_tpr_charges |
|
9 |
9 |
0 |
|
0% |
| mddb_workflow / utils / gmx_spells.py |
get_tpr_bonds |
|
6 |
0 |
0 |
|
100% |
| mddb_workflow / utils / gmx_spells.py |
filter_tpr |
|
7 |
7 |
0 |
|
0% |
| mddb_workflow / utils / gmx_spells.py |
merge_xtc_files |
|
4 |
4 |
0 |
|
0% |
| mddb_workflow / utils / gmx_spells.py |
generate_frames_ndx |
|
11 |
2 |
0 |
|
82% |
| mddb_workflow / utils / gmx_spells.py |
parse_xpm |
|
34 |
34 |
0 |
|
0% |
| mddb_workflow / utils / gmx_spells.py |
pdb_filter |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / gmx_spells.py |
xtc_filter |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / gmx_spells.py |
tpr_filter |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / gmx_spells.py |
make_index |
|
5 |
5 |
0 |
|
0% |
| mddb_workflow / utils / gmx_spells.py |
read_ndx |
|
18 |
18 |
0 |
|
0% |
| mddb_workflow / utils / gmx_spells.py |
get_atom_count |
|
4 |
4 |
0 |
|
0% |
| mddb_workflow / utils / gmx_spells.py |
(no function) |
|
48 |
0 |
0 |
|
100% |
| mddb_workflow / utils / heatmaps_nassa.py |
get_axes |
|
26 |
26 |
0 |
|
0% |
| mddb_workflow / utils / heatmaps_nassa.py |
reorder_labels_rotated_plot |
|
50 |
50 |
0 |
|
0% |
| mddb_workflow / utils / heatmaps_nassa.py |
reorder_labels_straight_plot |
|
50 |
50 |
0 |
|
0% |
| mddb_workflow / utils / heatmaps_nassa.py |
arlequin_plot |
|
78 |
78 |
0 |
|
0% |
| mddb_workflow / utils / heatmaps_nassa.py |
bconf_heatmap |
|
46 |
46 |
0 |
|
0% |
| mddb_workflow / utils / heatmaps_nassa.py |
correlation_plot |
|
36 |
36 |
0 |
|
0% |
| mddb_workflow / utils / heatmaps_nassa.py |
basepair_plot |
|
35 |
35 |
0 |
|
0% |
| mddb_workflow / utils / heatmaps_nassa.py |
(no function) |
|
16 |
0 |
0 |
|
100% |
| mddb_workflow / utils / httpsf.py |
FileHandler.__init__ |
|
8 |
8 |
0 |
|
0% |
| mddb_workflow / utils / httpsf.py |
FileHandler.__init__.create_whistleblower |
|
2 |
2 |
0 |
|
0% |
| mddb_workflow / utils / httpsf.py |
FileHandler.__init__.create_whistleblower.whistleblower |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / utils / httpsf.py |
FileHandler.__call__ |
|
2 |
2 |
0 |
|
0% |
| mddb_workflow / utils / httpsf.py |
FileHandler._get_file_size |
|
4 |
4 |
0 |
|
0% |
| mddb_workflow / utils / httpsf.py |
FileHandler._fetch_file_content |
|
2 |
2 |
0 |
|
0% |
| mddb_workflow / utils / httpsf.py |
FileHandler.getattr |
|
5 |
5 |
0 |
|
0% |
| mddb_workflow / utils / httpsf.py |
FileHandler.open |
|
3 |
3 |
0 |
|
0% |
| mddb_workflow / utils / httpsf.py |
FileHandler.read |
|
3 |
3 |
0 |
|
0% |
| mddb_workflow / utils / httpsf.py |
FileHandler.destroy |
|
2 |
2 |
0 |
|
0% |
| mddb_workflow / utils / httpsf.py |
mount |
|
4 |
4 |
0 |
|
0% |
| mddb_workflow / utils / httpsf.py |
(no function) |
|
25 |
25 |
0 |
|
0% |
| mddb_workflow / utils / mda_spells.py |
to_MDAnalysis_topology |
|
14 |
14 |
0 |
|
0% |
| mddb_workflow / utils / mda_spells.py |
get_mda_universe_from_stopology |
|
2 |
2 |
0 |
|
0% |
| mddb_workflow / utils / mda_spells.py |
get_mda_universe |
|
13 |
0 |
0 |
|
100% |
| mddb_workflow / utils / mda_spells.py |
get_mda_universe_cksum |
|
2 |
0 |
0 |
|
100% |
| mddb_workflow / utils / mda_spells.py |
get_tpr_bonds_mdanalysis |
|
4 |
4 |
0 |
|
0% |
| mddb_workflow / utils / mda_spells.py |
(no function) |
|
15 |
0 |
0 |
|
100% |
| mddb_workflow / utils / mdt_spells.py |
merge_and_convert_trajectories |
|
7 |
2 |
0 |
|
71% |
| mddb_workflow / utils / mdt_spells.py |
merge_and_convert_trajectories_alternative |
|
25 |
25 |
0 |
|
0% |
| mddb_workflow / utils / mdt_spells.py |
merge_and_convert_trajectories_unefficient |
|
11 |
11 |
0 |
|
0% |
| mddb_workflow / utils / mdt_spells.py |
get_trajectory_subset |
|
38 |
38 |
0 |
|
0% |
| mddb_workflow / utils / mdt_spells.py |
get_first_frame |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / utils / mdt_spells.py |
split_merged_trajectories |
|
24 |
24 |
0 |
|
0% |
| mddb_workflow / utils / mdt_spells.py |
sort_trajectory_atoms |
|
24 |
24 |
0 |
|
0% |
| mddb_workflow / utils / mdt_spells.py |
(no function) |
|
28 |
0 |
0 |
|
100% |
| mddb_workflow / utils / nassa_file.py |
generate_nassa_config |
|
69 |
69 |
0 |
|
0% |
| mddb_workflow / utils / nassa_file.py |
(no function) |
|
8 |
0 |
0 |
|
100% |
| mddb_workflow / utils / nucleicacid.py |
NucleicAcid.__init__ |
|
13 |
3 |
0 |
|
77% |
| mddb_workflow / utils / nucleicacid.py |
NucleicAcid.__len__ |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / utils / nucleicacid.py |
NucleicAcid.__repr__ |
|
5 |
5 |
0 |
|
0% |
| mddb_workflow / utils / nucleicacid.py |
NucleicAcid.size |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / nucleicacid.py |
NucleicAcid.bases |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / utils / nucleicacid.py |
NucleicAcid.baselen |
|
4 |
1 |
0 |
|
75% |
| mddb_workflow / utils / nucleicacid.py |
NucleicAcid.flanksize |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / nucleicacid.py |
NucleicAcid.ic_sequence |
|
3 |
3 |
0 |
|
0% |
| mddb_workflow / utils / nucleicacid.py |
NucleicAcid._adenine_complement |
|
9 |
4 |
0 |
|
56% |
| mddb_workflow / utils / nucleicacid.py |
NucleicAcid.inverse_complement |
|
2 |
0 |
0 |
|
100% |
| mddb_workflow / utils / nucleicacid.py |
NucleicAcid.get_subunit |
|
2 |
0 |
0 |
|
100% |
| mddb_workflow / utils / nucleicacid.py |
NucleicAcid.get_all_subunits |
|
2 |
0 |
0 |
|
100% |
| mddb_workflow / utils / nucleicacid.py |
NucleicAcid.get_all_ic_subunits |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / nucleicacid.py |
NucleicAcid.search_subunit |
|
8 |
8 |
0 |
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0% |
| mddb_workflow / utils / nucleicacid.py |
(no function) |
|
20 |
0 |
0 |
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100% |
| mddb_workflow / utils / pyt_spells.py |
get_pytraj_trajectory |
|
14 |
9 |
0 |
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36% |
| mddb_workflow / utils / pyt_spells.py |
get_reduced_pytraj_trajectory |
|
7 |
3 |
0 |
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57% |
| mddb_workflow / utils / pyt_spells.py |
get_frames_count |
|
11 |
3 |
0 |
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73% |
| mddb_workflow / utils / pyt_spells.py |
filter_topology |
|
6 |
6 |
0 |
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0% |
| mddb_workflow / utils / pyt_spells.py |
find_first_corrupted_frame |
|
9 |
9 |
0 |
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| mddb_workflow / utils / pyt_spells.py |
get_average_structure |
|
5 |
0 |
0 |
|
100% |
| mddb_workflow / utils / pyt_spells.py |
(no function) |
|
18 |
0 |
0 |
|
100% |
| mddb_workflow / utils / register.py |
Register.__init__ |
|
18 |
8 |
0 |
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56% |
| mddb_workflow / utils / register.py |
Register.__repr__ |
|
1 |
1 |
0 |
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Register.to_dict |
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2 |
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100% |
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Register.update_test |
|
2 |
0 |
0 |
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100% |
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Register.get_warnings |
|
1 |
1 |
0 |
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0% |
| mddb_workflow / utils / register.py |
Register.add_warning |
|
6 |
6 |
0 |
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0% |
| mddb_workflow / utils / register.py |
Register.remove_warnings |
|
5 |
1 |
0 |
|
80% |
| mddb_workflow / utils / register.py |
Register.save |
|
4 |
1 |
0 |
|
75% |
| mddb_workflow / utils / register.py |
(no function) |
|
15 |
0 |
0 |
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100% |
| mddb_workflow / utils / selections.py |
Selection.__init__ |
|
1 |
0 |
0 |
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100% |
| mddb_workflow / utils / selections.py |
Selection.__repr__ |
|
1 |
1 |
0 |
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0% |
| mddb_workflow / utils / selections.py |
Selection.__hash__ |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / selections.py |
Selection.__len__ |
|
1 |
0 |
0 |
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100% |
| mddb_workflow / utils / selections.py |
Selection.__bool__ |
|
1 |
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| mddb_workflow / utils / selections.py |
Selection.__eq__ |
|
3 |
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Selection.__add__ |
|
1 |
0 |
0 |
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100% |
| mddb_workflow / utils / selections.py |
Selection.__sub__ |
|
1 |
0 |
0 |
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100% |
| mddb_workflow / utils / selections.py |
Selection.__and__ |
|
1 |
0 |
0 |
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100% |
| mddb_workflow / utils / selections.py |
Selection.__or__ |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / utils / selections.py |
Selection.merge |
|
4 |
0 |
0 |
|
100% |
| mddb_workflow / utils / selections.py |
Selection.substract |
|
4 |
0 |
0 |
|
100% |
| mddb_workflow / utils / selections.py |
Selection.intersection |
|
6 |
0 |
0 |
|
100% |
| mddb_workflow / utils / selections.py |
Selection.to_mdanalysis |
|
2 |
2 |
0 |
|
0% |
| mddb_workflow / utils / selections.py |
Selection.to_pytraj |
|
3 |
0 |
0 |
|
100% |
| mddb_workflow / utils / selections.py |
Selection.to_ngl |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / utils / selections.py |
Selection.to_list |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / selections.py |
Selection.to_bash |
|
4 |
4 |
0 |
|
0% |
| mddb_workflow / utils / selections.py |
Selection.to_vmd |
|
2 |
0 |
0 |
|
100% |
| mddb_workflow / utils / selections.py |
Selection.to_ndx |
|
13 |
1 |
0 |
|
92% |
| mddb_workflow / utils / selections.py |
Selection.to_ndx_file |
|
3 |
0 |
0 |
|
100% |
| mddb_workflow / utils / selections.py |
(no function) |
|
24 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Atom.__init__ |
|
6 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Atom.__repr__ |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Atom.__eq__ |
|
3 |
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100% |
| mddb_workflow / utils / structures.py |
Atom.__hash__ |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / utils / structures.py |
Atom.get_structure |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Atom.get_index |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Atom.get_residue_index |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Atom.set_residue_index |
|
7 |
1 |
0 |
|
86% |
| mddb_workflow / utils / structures.py |
Atom.get_residue |
|
3 |
1 |
0 |
|
67% |
| mddb_workflow / utils / structures.py |
Atom.set_residue |
|
4 |
1 |
0 |
|
75% |
| mddb_workflow / utils / structures.py |
Atom.get_chain_index |
|
3 |
1 |
0 |
|
67% |
| mddb_workflow / utils / structures.py |
Atom.get_chain |
|
3 |
1 |
0 |
|
67% |
| mddb_workflow / utils / structures.py |
Atom.get_bonds |
|
10 |
2 |
0 |
|
80% |
| mddb_workflow / utils / structures.py |
Atom.get_bonded_atoms |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Atom.get_selection |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Atom.copy |
|
5 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Atom.is_fatty_candidate |
|
9 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Atom.is_carbohydrate_candidate |
|
12 |
7 |
0 |
|
42% |
| mddb_workflow / utils / structures.py |
Atom.is_ion |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / utils / structures.py |
Atom.guess_element |
|
14 |
4 |
0 |
|
71% |
| mddb_workflow / utils / structures.py |
Atom.get_name_suggested_element |
|
21 |
2 |
0 |
|
90% |
| mddb_workflow / utils / structures.py |
Atom.get_label |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Atom.is_cg |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Residue.__init__ |
|
8 |
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0 |
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100% |
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Residue.__repr__ |
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1 |
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3 |
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Residue.__hash__ |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Residue.get_structure |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Residue.get_index |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Residue.set_index |
|
5 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Residue.get_atom_indices |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Residue.set_atom_indices |
|
9 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Residue.get_atoms |
|
4 |
1 |
0 |
|
75% |
| mddb_workflow / utils / structures.py |
Residue.set_atoms |
|
7 |
1 |
0 |
|
86% |
| mddb_workflow / utils / structures.py |
Residue.get_atom_count |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Residue.add_atom |
|
6 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Residue.remove_atom |
|
4 |
1 |
0 |
|
75% |
| mddb_workflow / utils / structures.py |
Residue.get_chain_index |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Residue.set_chain_index |
|
9 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Residue.get_chain |
|
3 |
1 |
0 |
|
67% |
| mddb_workflow / utils / structures.py |
Residue.set_chain |
|
13 |
2 |
0 |
|
85% |
| mddb_workflow / utils / structures.py |
Residue.get_bonded_atom_indices |
|
5 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Residue.get_bonded_atoms |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Residue.get_bonded_residue_indices |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Residue.get_bonded_residues |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Residue.is_bonded_with_residue |
|
3 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Residue.is_missing_any_bonds |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Residue.is_coherent |
|
6 |
1 |
0 |
|
83% |
| mddb_workflow / utils / structures.py |
Residue.get_classification |
|
72 |
10 |
0 |
|
86% |
| mddb_workflow / utils / structures.py |
Residue.get_classification.get_bonded_fatty_atoms_recursive |
|
11 |
2 |
0 |
|
82% |
| mddb_workflow / utils / structures.py |
Residue.get_classification_by_name |
|
17 |
9 |
0 |
|
47% |
| mddb_workflow / utils / structures.py |
Residue.get_selection |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Residue.copy |
|
6 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Residue.get_letter |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / utils / structures.py |
Residue.get_formula |
|
8 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Residue.find_rings |
|
5 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Residue.split |
|
25 |
7 |
0 |
|
72% |
| mddb_workflow / utils / structures.py |
Residue.split_by_atom_names |
|
11 |
5 |
0 |
|
55% |
| mddb_workflow / utils / structures.py |
Residue.get_atom_by_name |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Residue.get_label |
|
2 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Residue.is_cg |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Chain.__init__ |
|
5 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Chain.__repr__ |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Chain.__eq__ |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Chain.__hash__ |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Chain.get_structure |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Chain.get_index |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Chain.set_index |
|
3 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Chain.get_residue_indices |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Chain.set_residue_indices |
|
11 |
1 |
0 |
|
91% |
| mddb_workflow / utils / structures.py |
Chain.get_residues |
|
4 |
1 |
0 |
|
75% |
| mddb_workflow / utils / structures.py |
Chain.set_residues |
|
9 |
1 |
0 |
|
89% |
| mddb_workflow / utils / structures.py |
Chain.add_residue |
|
3 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Chain.remove_residue |
|
4 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Chain.get_atom_indices |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Chain.get_atoms |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Chain.get_atom_count |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Chain.get_residue_count |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / utils / structures.py |
Chain.get_classification |
|
4 |
1 |
0 |
|
75% |
| mddb_workflow / utils / structures.py |
Chain.set_classification |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Chain.get_sequence |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Chain.get_selection |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Chain.copy |
|
5 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Chain.has_cg |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Chain.is_missing_any_bonds |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Chain.find_residue |
|
4 |
4 |
0 |
|
0% |
| mddb_workflow / utils / structures.py |
Structure.__init__ |
|
17 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Structure.__repr__ |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Structure.get_bonds |
|
4 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Structure.set_bonds |
|
2 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Structure.get_fragments |
|
4 |
4 |
0 |
|
0% |
| mddb_workflow / utils / structures.py |
Structure.find_fragments |
|
35 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Structure.find_whole_fragments |
|
3 |
3 |
0 |
|
0% |
| mddb_workflow / utils / structures.py |
Structure.name_selection |
|
14 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Structure.set_new_atom |
|
4 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Structure.set_new_residue |
|
7 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Structure.purge_residue |
|
9 |
9 |
0 |
|
0% |
| mddb_workflow / utils / structures.py |
Structure.set_new_chain |
|
7 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Structure.purge_chain |
|
8 |
2 |
0 |
|
75% |
| mddb_workflow / utils / structures.py |
Structure.from_pdb |
|
71 |
10 |
0 |
|
86% |
| mddb_workflow / utils / structures.py |
Structure.from_pdb_file |
|
9 |
2 |
0 |
|
78% |
| mddb_workflow / utils / structures.py |
Structure.from_mmcif |
|
47 |
6 |
0 |
|
87% |
| mddb_workflow / utils / structures.py |
Structure.from_mmcif_file |
|
9 |
2 |
0 |
|
78% |
| mddb_workflow / utils / structures.py |
Structure.from_mdanalysis |
|
32 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Structure.from_prmtop_file |
|
11 |
3 |
0 |
|
73% |
| mddb_workflow / utils / structures.py |
Structure.from_tpr_file |
|
11 |
3 |
0 |
|
73% |
| mddb_workflow / utils / structures.py |
Structure.from_file |
|
10 |
1 |
0 |
|
90% |
| mddb_workflow / utils / structures.py |
Structure.get_atom_count |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Structure.get_residue_count |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Structure.get_chain_count |
|
1 |
1 |
0 |
|
0% |
| mddb_workflow / utils / structures.py |
Structure.fix_atom_elements |
|
26 |
4 |
0 |
|
85% |
| mddb_workflow / utils / structures.py |
Structure.set_new_coordinates |
|
4 |
1 |
0 |
|
75% |
| mddb_workflow / utils / structures.py |
Structure.get_ion_atom_indices |
|
8 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Structure.get_dummy_atom_indices |
|
8 |
1 |
0 |
|
88% |
| mddb_workflow / utils / structures.py |
Structure.generate_pdb |
|
21 |
2 |
0 |
|
90% |
| mddb_workflow / utils / structures.py |
Structure.generate_pdb_file |
|
3 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Structure.get_pytraj_topology |
|
7 |
1 |
0 |
|
86% |
| mddb_workflow / utils / structures.py |
Structure.select |
|
35 |
20 |
0 |
|
43% |
| mddb_workflow / utils / structures.py |
Structure.select_atom_indices |
|
5 |
1 |
0 |
|
80% |
| mddb_workflow / utils / structures.py |
Structure.select_residue_indices |
|
4 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Structure.select_all |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Structure.select_by_classification |
|
5 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Structure.select_water |
|
1 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Structure.select_ions |
|
1 |
0 |
0 |
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100% |
| mddb_workflow / utils / structures.py |
Structure.select_counter_ions |
|
14 |
2 |
0 |
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86% |
| mddb_workflow / utils / structures.py |
Structure.select_water_and_counter_ions |
|
1 |
1 |
0 |
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0% |
| mddb_workflow / utils / structures.py |
Structure.select_heavy_atoms |
|
5 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Structure.select_protein |
|
1 |
0 |
0 |
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100% |
| mddb_workflow / utils / structures.py |
Structure.select_nucleic |
|
1 |
0 |
0 |
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100% |
| mddb_workflow / utils / structures.py |
Structure.select_lipids |
|
1 |
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0 |
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100% |
| mddb_workflow / utils / structures.py |
Structure.select_carbohydrates |
|
1 |
0 |
0 |
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100% |
| mddb_workflow / utils / structures.py |
Structure.select_pbc_guess |
|
1 |
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0 |
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100% |
| mddb_workflow / utils / structures.py |
Structure.select_cg |
|
1 |
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0 |
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100% |
| mddb_workflow / utils / structures.py |
Structure.select_missing_bonds |
|
1 |
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0 |
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100% |
| mddb_workflow / utils / structures.py |
Structure.select_cartoon |
|
13 |
1 |
0 |
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92% |
| mddb_workflow / utils / structures.py |
Structure.invert_selection |
|
4 |
0 |
0 |
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100% |
| mddb_workflow / utils / structures.py |
Structure.get_selection_residue_indices |
|
1 |
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0 |
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100% |
| mddb_workflow / utils / structures.py |
Structure.get_selection_residues |
|
2 |
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0 |
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| mddb_workflow / utils / structures.py |
Structure.get_selection_chain_indices |
|
1 |
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0 |
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100% |
| mddb_workflow / utils / structures.py |
Structure.get_selection_chains |
|
2 |
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0 |
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100% |
| mddb_workflow / utils / structures.py |
Structure.get_selection_classification |
|
30 |
16 |
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47% |
| mddb_workflow / utils / structures.py |
Structure.filter |
|
52 |
0 |
0 |
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100% |
| mddb_workflow / utils / structures.py |
Structure.chainer |
|
10 |
0 |
0 |
|
100% |
| mddb_workflow / utils / structures.py |
Structure.auto_chainer |
|
21 |
0 |
0 |
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100% |
| mddb_workflow / utils / structures.py |
Structure.raw_protein_chainer |
|
12 |
2 |
0 |
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83% |
| mddb_workflow / utils / structures.py |
Structure.set_selection_chain_name |
|
8 |
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0 |
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100% |
| mddb_workflow / utils / structures.py |
Structure.check_available_chains |
|
4 |
1 |
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75% |
| mddb_workflow / utils / structures.py |
Structure.get_available_chain_name |
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4 |
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| mddb_workflow / utils / structures.py |
Structure.get_next_available_chain_name |
|
14 |
5 |
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64% |
| mddb_workflow / utils / structures.py |
Structure.get_chain_by_name |
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1 |
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| mddb_workflow / utils / structures.py |
Structure.find_residue |
|
3 |
3 |
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| mddb_workflow / utils / structures.py |
Structure.display_summary |
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6 |
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0 |
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| mddb_workflow / utils / structures.py |
Structure.check_repeated_chains |
|
45 |
15 |
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| mddb_workflow / utils / structures.py |
Structure.check_splitted_chains |
|
30 |
15 |
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50% |
| mddb_workflow / utils / structures.py |
Structure.sort_residues |
|
5 |
5 |
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0% |
| mddb_workflow / utils / structures.py |
Structure.sort_residues.by_first_atom_index |
|
1 |
1 |
0 |
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0% |
| mddb_workflow / utils / structures.py |
Structure.check_merged_residues |
|
20 |
12 |
0 |
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40% |
| mddb_workflow / utils / structures.py |
Structure.check_repeated_residues |
|
104 |
25 |
0 |
|
76% |
| mddb_workflow / utils / structures.py |
Structure.check_repeated_residues.trajectory_atom_sorter |
|
1 |
1 |
0 |
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0% |
| mddb_workflow / utils / structures.py |
Structure.check_repeated_atoms |
|
31 |
3 |
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|
90% |
| mddb_workflow / utils / structures.py |
Structure.is_missing_any_bonds |
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0 |
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100% |
| mddb_workflow / utils / structures.py |
Structure.check_incoherent_bonds |
|
27 |
3 |
0 |
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89% |
| mddb_workflow / utils / structures.py |
Structure.get_covalent_bonds |
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8 |
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0 |
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| mddb_workflow / utils / structures.py |
Structure.copy_bonds |
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7 |
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71% |
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Structure.copy |
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6 |
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0 |
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Structure.merge |
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23 |
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0 |
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Structure.find_rings |
|
2 |
2 |
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Structure.get_selection_outer_bonds |
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6 |
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| mddb_workflow / utils / structures.py |
Structure.find_ptms |
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Structure.has_cg |
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calculate_distance |
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calculate_angle |
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calculate_torsion |
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13 |
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get_next_letter |
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first_cap_only |
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5 |
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get_lower_numbers |
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filter_model |
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17 |
17 |
0 |
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(no function) |
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253 |
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| mddb_workflow / utils / subsets.py |
get_trajectory_subset |
|
25 |
9 |
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64% |
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(no function) |
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9 |
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| mddb_workflow / utils / tasks.py |
Task.__init__ |
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14 |
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Task._get_parent_output |
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Task._set_parent_output |
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Task._get_parent_output_file |
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Task._set_parent_output_file |
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Task.get_output |
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3 |
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Task.get_output_file_getter |
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Task.get_output_file_getter.get_output_file |
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Task.__repr__ |
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Task.__call__ |
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Task._run |
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88 |
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Task._find_arg_value |
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11 |
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Task._get_changed_inputs |
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14 |
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Task.prefill |
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4 |
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(no function) |
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28 |
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| mddb_workflow / utils / topologies.py |
Topology.__init__ |
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4 |
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Topology.read_raw_content |
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Topology.get_flag_summary |
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20 |
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Topology.mine_amber_flag |
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Topology.get_dihedrals_data |
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Topology._get_dihedrals_data_amber |
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52 |
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98% |
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(no function) |
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15 |
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(no function) |
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3 |
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10 |
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| mddb_workflow / utils / vmd_spells.py |
escape_tcl_selection |
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4 |
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| mddb_workflow / utils / vmd_spells.py |
vmd_to_pdb |
|
17 |
17 |
0 |
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| mddb_workflow / utils / vmd_spells.py |
chainer |
|
29 |
29 |
0 |
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0% |
| mddb_workflow / utils / vmd_spells.py |
merge_and_convert_trajectories |
|
16 |
3 |
0 |
|
81% |
| mddb_workflow / utils / vmd_spells.py |
get_vmd_selection_atom_indices |
|
19 |
2 |
0 |
|
89% |
| mddb_workflow / utils / vmd_spells.py |
get_covalent_bonds |
|
47 |
3 |
0 |
|
94% |
| mddb_workflow / utils / vmd_spells.py |
get_covalent_bonds_between |
|
70 |
6 |
0 |
|
91% |
| mddb_workflow / utils / vmd_spells.py |
get_interface_atom_indices |
|
66 |
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0 |
|
97% |
| mddb_workflow / utils / vmd_spells.py |
get_interface_atom_indices.process_vmd_output |
|
3 |
0 |
0 |
|
100% |
| mddb_workflow / utils / vmd_spells.py |
(no function) |
|
21 |
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0 |
|
100% |