| biobb_gromacs/__init__.py |
(no function) |
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4 |
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0 |
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15 |
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get_gromacs_version |
|
29 |
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gmx_check |
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gmx_rms |
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14 |
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read_mdp |
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10 |
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mdp_preset |
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89 |
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write_mdp |
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create_mdp |
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clean_key |
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(no function) |
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14 |
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ConvertTpr.__init__ |
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20 |
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ConvertTpr.launch |
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convert_tpr |
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(no function) |
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15 |
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Editconf.__init__ |
|
20 |
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Editconf.launch |
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editconf |
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(no function) |
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15 |
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Genion.__init__ |
|
22 |
0 |
0 |
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Genion.launch |
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genion |
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(no function) |
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16 |
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| biobb_gromacs/gromacs/genrestr.py |
Genrestr.__init__ |
|
18 |
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0 |
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Genrestr.launch |
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25 |
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genrestr |
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(no function) |
|
15 |
1 |
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| biobb_gromacs/gromacs/gmxselect.py |
Gmxselect.__init__ |
|
18 |
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0 |
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Gmxselect.launch |
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31 |
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gmxselect |
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1 |
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(no function) |
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15 |
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| biobb_gromacs/gromacs/grompp.py |
Grompp.__init__ |
|
24 |
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Grompp.launch |
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grompp |
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(no function) |
|
17 |
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| biobb_gromacs/gromacs/grompp_mdrun.py |
GromppMdrun.__init__ |
|
31 |
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0 |
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GromppMdrun.launch |
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grompp_mdrun |
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(no function) |
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16 |
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| biobb_gromacs/gromacs/make_ndx.py |
MakeNdx.__init__ |
|
17 |
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0 |
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MakeNdx.launch |
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23 |
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make_ndx |
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1 |
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(no function) |
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15 |
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| biobb_gromacs/gromacs/mdrun.py |
Mdrun.__init__ |
|
7 |
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0 |
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Mdrun.launch |
|
32 |
12 |
0 |
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mdrun |
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1 |
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0 |
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(no function) |
|
13 |
1 |
0 |
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92% |
| biobb_gromacs/gromacs/mdrun_base.py |
MdrunBase._init_common_properties |
|
22 |
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0 |
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| biobb_gromacs/gromacs/mdrun_base.py |
MdrunBase._get_working_dir |
|
3 |
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| biobb_gromacs/gromacs/mdrun_base.py |
MdrunBase._prepend_mpi_runner |
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8 |
7 |
0 |
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| biobb_gromacs/gromacs/mdrun_base.py |
MdrunBase._append_gmx_runtime_flags |
|
31 |
19 |
0 |
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MdrunBase._apply_noappend_renaming |
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18 |
16 |
0 |
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MdrunBase._apply_noappend_renaming.capture_part_pattern |
|
2 |
2 |
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| biobb_gromacs/gromacs/mdrun_base.py |
MdrunBase._extra_copy_to_host |
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0 |
0 |
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MdrunBase.copy_to_host |
|
3 |
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| biobb_gromacs/gromacs/mdrun_base.py |
(no function) |
|
13 |
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0 |
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100% |
| biobb_gromacs/gromacs/mdrun_multidir.py |
MdrunMultidir.__init__ |
|
8 |
8 |
0 |
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0% |
| biobb_gromacs/gromacs/mdrun_multidir.py |
MdrunMultidir.launch |
|
19 |
19 |
0 |
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mdrun_multidir |
|
1 |
1 |
0 |
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| biobb_gromacs/gromacs/mdrun_multidir.py |
(no function) |
|
15 |
15 |
0 |
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| biobb_gromacs/gromacs/mdrun_plumed.py |
MdrunPlumed.__init__ |
|
7 |
0 |
0 |
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| biobb_gromacs/gromacs/mdrun_plumed.py |
MdrunPlumed.launch |
|
35 |
14 |
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MdrunPlumed.stage_files |
|
12 |
9 |
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| biobb_gromacs/gromacs/mdrun_plumed.py |
MdrunPlumed._extra_copy_to_host |
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15 |
14 |
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mdrun_plumed |
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1 |
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0 |
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(no function) |
|
18 |
1 |
0 |
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94% |
| biobb_gromacs/gromacs/pdb2gmx.py |
Pdb2gmx.__init__ |
|
41 |
5 |
0 |
|
88% |
| biobb_gromacs/gromacs/pdb2gmx.py |
Pdb2gmx.launch |
|
57 |
16 |
0 |
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72% |
| biobb_gromacs/gromacs/pdb2gmx.py |
Pdb2gmx.check_lengths |
|
6 |
1 |
0 |
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| biobb_gromacs/gromacs/pdb2gmx.py |
Pdb2gmx.find_length |
|
4 |
1 |
0 |
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| biobb_gromacs/gromacs/pdb2gmx.py |
pdb2gmx |
|
1 |
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0 |
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| biobb_gromacs/gromacs/pdb2gmx.py |
(no function) |
|
17 |
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94% |
| biobb_gromacs/gromacs/solvate.py |
Solvate.__init__ |
|
20 |
0 |
0 |
|
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| biobb_gromacs/gromacs/solvate.py |
Solvate.launch |
|
26 |
8 |
0 |
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solvate |
|
1 |
0 |
0 |
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| biobb_gromacs/gromacs/solvate.py |
(no function) |
|
16 |
1 |
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| biobb_gromacs/gromacs/trjcat.py |
Trjcat.__init__ |
|
18 |
0 |
0 |
|
100% |
| biobb_gromacs/gromacs/trjcat.py |
Trjcat.launch |
|
19 |
3 |
0 |
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trjcat |
|
1 |
0 |
0 |
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(no function) |
|
15 |
1 |
0 |
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93% |
| biobb_gromacs/gromacs_extra/__init__.py |
(no function) |
|
4 |
0 |
0 |
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| biobb_gromacs/gromacs_extra/append_ligand.py |
AppendLigand.__init__ |
|
7 |
0 |
0 |
|
100% |
| biobb_gromacs/gromacs_extra/append_ligand.py |
AppendLigand.launch |
|
99 |
34 |
0 |
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append_ligand |
|
1 |
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0 |
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| biobb_gromacs/gromacs_extra/append_ligand.py |
(no function) |
|
16 |
1 |
0 |
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94% |
| biobb_gromacs/gromacs_extra/ndx2resttop.py |
Ndx2resttop.__init__ |
|
9 |
0 |
0 |
|
100% |
| biobb_gromacs/gromacs_extra/ndx2resttop.py |
Ndx2resttop._parse_ndx_groups |
|
16 |
1 |
0 |
|
94% |
| biobb_gromacs/gromacs_extra/ndx2resttop.py |
Ndx2resttop._read_ndx_atoms |
|
6 |
0 |
0 |
|
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| biobb_gromacs/gromacs_extra/ndx2resttop.py |
Ndx2resttop._write_posre_itp |
|
6 |
0 |
0 |
|
100% |
| biobb_gromacs/gromacs_extra/ndx2resttop.py |
Ndx2resttop._insert_posres_in_top |
|
32 |
32 |
0 |
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0% |
| biobb_gromacs/gromacs_extra/ndx2resttop.py |
Ndx2resttop.launch |
|
47 |
4 |
0 |
|
91% |
| biobb_gromacs/gromacs_extra/ndx2resttop.py |
ndx2resttop |
|
1 |
1 |
0 |
|
0% |
| biobb_gromacs/gromacs_extra/ndx2resttop.py |
(no function) |
|
20 |
1 |
0 |
|
95% |
| biobb_gromacs/test/__init__.py |
(no function) |
|
0 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_convert_tpr.py |
TestConvertTpr.setup_class |
|
1 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_convert_tpr.py |
TestConvertTpr.teardown_class |
|
1 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_convert_tpr.py |
TestConvertTpr.test_convert_tpr |
|
2 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_convert_tpr.py |
(no function) |
|
6 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_editconf.py |
TestEditconf.setup_class |
|
1 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_editconf.py |
TestEditconf.teardown_class |
|
1 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_editconf.py |
TestEditconf.test_editconf |
|
3 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_editconf.py |
(no function) |
|
6 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_genion.py |
TestGenion.setup_class |
|
1 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_genion.py |
TestGenion.teardown_class |
|
1 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_genion.py |
TestGenion.test_genion |
|
4 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_genion.py |
(no function) |
|
6 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_genrestr.py |
TestGenrestr.setup_class |
|
1 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_genrestr.py |
TestGenrestr.teardown_class |
|
1 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_genrestr.py |
TestGenrestr.test_genrestr |
|
4 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_genrestr.py |
TestGenrestr.test_genrestr_noNDX |
|
5 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_genrestr.py |
(no function) |
|
7 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_gmxselect.py |
TestGmxselect.setup_class |
|
1 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_gmxselect.py |
TestGmxselect.teardown_class |
|
1 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_gmxselect.py |
TestGmxselect.test_select |
|
4 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_gmxselect.py |
(no function) |
|
6 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_grompp.py |
TestGrompp.setup_class |
|
1 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_grompp.py |
TestGrompp.teardown_class |
|
1 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_grompp.py |
TestGrompp.test_grompp |
|
4 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_grompp.py |
(no function) |
|
7 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_grompp_mdrun.py |
TestGromppMdrun.setup_class |
|
1 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_grompp_mdrun.py |
TestGromppMdrun.teardown_class |
|
1 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_grompp_mdrun.py |
TestGromppMdrun.test_grompp_mdrun |
|
7 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_grompp_mdrun.py |
(no function) |
|
7 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_make_ndx.py |
TestMakeNdx.setup_class |
|
1 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_make_ndx.py |
TestMakeNdx.teardown_class |
|
1 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_make_ndx.py |
TestMakeNdx.test_make_ndx |
|
4 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_make_ndx.py |
(no function) |
|
6 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_mdrun.py |
TestMdrun.setup_class |
|
1 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_mdrun.py |
TestMdrun.teardown_class |
|
1 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_mdrun.py |
TestMdrun.test_mdrun |
|
7 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_mdrun.py |
(no function) |
|
7 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_mdrun_plumed.py |
TestMdrunPlumed.setup_class |
|
1 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_mdrun_plumed.py |
TestMdrunPlumed.teardown_class |
|
1 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_mdrun_plumed.py |
TestMdrunPlumed.test_mdrun_plumed |
|
7 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_mdrun_plumed.py |
(no function) |
|
7 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_pdb2gmx.py |
TestPdb2gmx.setup_class |
|
1 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_pdb2gmx.py |
TestPdb2gmx.teardown_class |
|
1 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_pdb2gmx.py |
TestPdb2gmx.test_pdb2gmx |
|
6 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_pdb2gmx.py |
(no function) |
|
6 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_solvate.py |
TestSolvate.setup_class |
|
1 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_solvate.py |
TestSolvate.teardown_class |
|
1 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_solvate.py |
TestSolvate.test_solvate |
|
6 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_solvate.py |
(no function) |
|
6 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_trjcat.py |
TestSolvate.setup_class |
|
1 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_trjcat.py |
TestSolvate.teardown_class |
|
1 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_trjcat.py |
TestSolvate.test_solvate |
|
4 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs/test_trjcat.py |
(no function) |
|
6 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs_extra/test_append_ligand.py |
TestAppendLigand.setup_class |
|
1 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs_extra/test_append_ligand.py |
TestAppendLigand.teardown_class |
|
1 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs_extra/test_append_ligand.py |
TestAppendLigand.test_append_ligand |
|
4 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs_extra/test_append_ligand.py |
(no function) |
|
6 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs_extra/test_ndx2resttop.py |
TestNdx2resttop.setup_class |
|
1 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs_extra/test_ndx2resttop.py |
TestNdx2resttop.teardown_class |
|
1 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs_extra/test_ndx2resttop.py |
TestNdx2resttop.test_ndx2resttop |
|
3 |
0 |
0 |
|
100% |
| biobb_gromacs/test/unitests/test_gromacs_extra/test_ndx2resttop.py |
(no function) |
|
6 |
0 |
0 |
|
100% |