Révision 9fd1daa6
| b/examples/dockonsurf.inp | ||
|---|---|---|
| 16 | 16 |
molec_file = tests/acetic.xyz # run_type-dependent |
| 17 | 17 |
cluster_magns = energy MOI |
| 18 | 18 |
num_conformers = 100 |
| 19 |
num_prom_cand = 5 |
|
| 20 |
iso_rmsd = 0.1 |
|
| 21 | 19 |
min_confs = False |
| 22 | 20 |
|
| 23 | 21 |
[Screening] |
| ... | ... | |
| 27 | 25 |
try_disso = True |
| 28 | 26 |
sample_points_per_angle = 4 |
| 29 | 27 |
collision_threshold = 0.9 |
| 30 |
screen_rmsd = 0.1 |
|
| 31 | 28 |
collision_bottom_z = 5.2 |
| 32 | 29 |
|
| 33 | 30 |
[Refinement] |
| b/modules/dos_input.py | ||
|---|---|---|
| 581 | 581 |
# Facultative options (Default/Fallback value present) |
| 582 | 582 |
return_vars['cluster_magns'] = get_cluster_magns() |
| 583 | 583 |
return_vars['num_conformers'] = get_num_conformers() |
| 584 |
return_vars['num_prom_cand'] = get_num_prom_cand() |
|
| 585 |
return_vars['iso_rmsd'] = get_iso_rmsd() |
|
| 584 |
# return_vars['num_prom_cand'] = get_num_prom_cand()
|
|
| 585 |
# return_vars['iso_rmsd'] = get_iso_rmsd()
|
|
| 586 | 586 |
return_vars['min_confs'] = get_min_confs() |
| 587 | 587 |
|
| 588 | 588 |
# Screening |
| ... | ... | |
| 605 | 605 |
return_vars['try_disso'] = get_try_disso() |
| 606 | 606 |
return_vars['sample_points_per_angle'] = get_pts_per_angle() |
| 607 | 607 |
return_vars['collision_threshold'] = get_coll_thrsld() |
| 608 |
return_vars['screen_rmsd'] = get_screen_rmsd() |
|
| 608 |
# return_vars['screen_rmsd'] = get_screen_rmsd()
|
|
| 609 | 609 |
return_vars['collision_bottom_z'] = get_coll_bottom_z() |
| 610 | 610 |
|
| 611 | 611 |
# Refinement |
| b/tests/good.inp | ||
|---|---|---|
| 16 | 16 |
molec_file = acetic.xyz # run_type-dependent |
| 17 | 17 |
cluster_magns = energy MOI |
| 18 | 18 |
num_conformers = 100 |
| 19 |
num_prom_cand = 5 |
|
| 20 |
iso_rmsd = 0.1 |
|
| 21 | 19 |
min_confs = False |
| 22 | 20 |
|
| 23 | 21 |
[Screening] |
| ... | ... | |
| 27 | 25 |
try_disso = True |
| 28 | 26 |
sample_points_per_angle = 4 |
| 29 | 27 |
collision_threshold = 0.9 |
| 30 |
screen_rmsd = 0.1 |
|
| 31 | 28 |
collision_bottom_z = 5.2 |
| 32 | 29 |
|
| 33 | 30 |
[Refinement] |
| b/tests/test_dos_input.py | ||
|---|---|---|
| 22 | 22 |
read_input('good.inp')
|
| 23 | 23 |
|
| 24 | 24 |
def test_all_good(self): |
| 25 |
exp_dict = {'isolated': True,
|
|
| 25 |
exp_dict = {'project_name': 'example',
|
|
| 26 |
'isolated': True, |
|
| 26 | 27 |
'screening': True, |
| 27 | 28 |
'refinement': True, |
| 28 | 29 |
'code': 'cp2k', |
| 29 | 30 |
'batch_q_sys': 'sge', |
| 31 |
'subm_script': 'cp2k.sub', |
|
| 30 | 32 |
'relaunch_err': 'geo_not_conv', |
| 31 | 33 |
'max_qw': 5, |
| 32 | 34 |
'special_atoms': [('Fe1', 'Fe'), ('Fe2', 'Fe'),
|
| ... | ... | |
| 35 | 37 |
'molec_file': 'acetic.xyz', |
| 36 | 38 |
'cluster_magns': ['energy', 'moi'], |
| 37 | 39 |
'num_conformers': 100, |
| 38 |
'num_prom_cand': 5, |
|
| 39 |
'iso_rmsd': 0.1, |
|
| 40 | 40 |
'min_confs': False, |
| 41 | 41 |
'screen_inp_file': 'screen.inp', |
| 42 | 42 |
'sites': [128, [135, 138, 141]], |
| ... | ... | |
| 44 | 44 |
'try_disso': True, |
| 45 | 45 |
'sample_points_per_angle': 4, |
| 46 | 46 |
'collision_threshold': 0.9, |
| 47 |
'screen_rmsd': 0.1, |
|
| 48 | 47 |
'collision_bottom_z': 5.2, |
| 49 | 48 |
'refine_inp_file': 'refine.inp', |
| 50 | 49 |
'energy_cutoff': 1.0 |
| 51 | 50 |
} |
| 52 | 51 |
self.assertEqual(read_input('good.inp'), exp_dict)
|
| 53 | 52 |
|
| 53 |
# TODO add single tests for subm_script and project_name |
|
| 54 |
|
|
| 54 | 55 |
def test_run_type(self): |
| 55 | 56 |
self.assertEqual(get_run_type(), (True, True, True)) |
| 56 | 57 |
|
| ... | ... | |
| 83 | 84 |
def test_num_conformers(self): |
| 84 | 85 |
self.assertEqual(get_num_conformers(), 100) |
| 85 | 86 |
|
| 86 |
def test_num_prom_cand(self): |
|
| 87 |
self.assertEqual(get_num_prom_cand(), 5) |
|
| 88 |
|
|
| 89 |
def test_iso_rmsd(self): |
|
| 90 |
self.assertEqual(get_iso_rmsd(), 0.1) |
|
| 91 |
|
|
| 92 | 87 |
def test_min_confs(self): |
| 93 | 88 |
self.assertEqual(get_min_confs(), False) |
| 94 | 89 |
|
| ... | ... | |
| 110 | 105 |
def test_coll_thrsld(self): |
| 111 | 106 |
self.assertEqual(get_coll_thrsld(), 0.9) |
| 112 | 107 |
|
| 113 |
def test_screen_rmsd(self): |
|
| 114 |
self.assertEqual(get_screen_rmsd(), 0.1) |
|
| 115 |
|
|
| 116 | 108 |
def test_coll_bottom_z(self): |
| 117 | 109 |
self.assertEqual(get_coll_bottom_z(), 5.2) |
| 118 | 110 |
|
| ... | ... | |
| 153 | 145 |
def test_num_conformers(self): |
| 154 | 146 |
self.assertRaises(ValueError, get_num_conformers) |
| 155 | 147 |
|
| 156 |
def test_num_prom_cand(self): |
|
| 157 |
self.assertRaises(ValueError, get_num_prom_cand) |
|
| 158 |
|
|
| 159 |
def test_iso_rmsd(self): |
|
| 160 |
self.assertRaises(ValueError, get_iso_rmsd) |
|
| 161 |
|
|
| 162 | 148 |
def test_min_confs(self): |
| 163 | 149 |
self.assertRaises(ValueError, get_min_confs) |
| 164 | 150 |
|
| ... | ... | |
| 180 | 166 |
def test_coll_thrsld(self): |
| 181 | 167 |
self.assertRaises(ValueError, get_coll_thrsld) |
| 182 | 168 |
|
| 183 |
def test_screen_rmsd(self): |
|
| 184 |
self.assertRaises(ValueError, get_screen_rmsd) |
|
| 185 |
|
|
| 186 | 169 |
def test_coll_bottom_z(self): |
| 187 | 170 |
self.assertRaises(ValueError, get_coll_bottom_z) |
| 188 | 171 |
|
| b/tests/wrong.inp | ||
|---|---|---|
| 17 | 17 |
molec_file = qweqwe.xyz # run_type-dependent |
| 18 | 18 |
cluster_magns = Perseus |
| 19 | 19 |
num_conformers = -3/2 |
| 20 |
num_prom_cand = i dunno |
|
| 21 |
iso_rmsd = pi? |
|
| 22 | 20 |
min_confs = flash? |
| 23 | 21 |
|
| 24 | 22 |
[Screening] # run_type-dependent |
| ... | ... | |
| 28 | 26 |
try_disso = No drugs, thanks |
| 29 | 27 |
sample_points_per_angle = which points? what angle? who am I? |
| 30 | 28 |
collision_threshold = don't have a collision insurance, sorry |
| 31 |
screen_rmsd = rmsd? Real Madrid Sudden Defeat, probably. |
|
| 32 | 29 |
collision_bottom_z = this must be twerking |
| 33 | 30 |
|
| 34 | 31 |
[Refinement] |
Formats disponibles : Unified diff