def test_launch(self):
output_trr_path = opj(self.properties['path'],
self.properties['output_trr_path'])
output_gro_path = opj(self.properties['path'],
self.properties['output_gro_path'])
returncode = Mdrun(input_tpr_path=opj(
self.data_dir, self.properties['input_tpr_path']),
output_trr_path=output_trr_path,
output_gro_path=output_gro_path,
properties=self.properties).launch()
assert fx.exe_success(returncode)
assert fx.not_empty(output_trr_path)
assert fx.not_empty(output_gro_path)
def test_launch(self):
output_gro_path = opj(self.properties['path'],
self.properties['output_gro_path'])
output_top_zip_path = opj(self.properties['path'],
self.properties['output_top_zip_path'])
returncode = Pdb2gmx(input_structure_pdb_path=opj(
self.data_dir, self.properties['input_structure_pdb_path']),
output_gro_path=output_gro_path,
output_top_zip_path=output_top_zip_path,
properties=self.properties).launch()
assert fx.exe_success(returncode)
assert fx.not_empty(output_gro_path)
assert fx.not_empty(output_top_zip_path)
def test_launch(self):
output_gro_path = opj(self.properties['path'],
self.properties['output_gro_path'])
output_top_zip_path = opj(self.properties['path'],
self.properties['output_top_zip_path'])
returncode = Solvate(input_solute_gro_path=opj(
self.data_dir, self.properties['input_solute_gro_path']),
output_gro_path=output_gro_path,
input_top_zip_path=opj(
self.data_dir,
self.properties['input_top_zip_path']),
output_top_zip_path=output_top_zip_path,
properties=self.properties).launch()
assert fx.exe_success(returncode)
assert fx.not_empty(output_gro_path)
assert fx.not_empty(output_top_zip_path)
def test_launch(self):
output_ndx_path = opj(self.properties['path'], self.properties['output_ndx_path'])
returncode = MakeNdx(input_structure_path=opj(self.data_dir, self.properties['input_structure_path']),
output_ndx_path=output_ndx_path,
properties=self.properties).launch()
assert fx.exe_success(returncode)
assert fx.not_empty(output_ndx_path)
def test_launch(self):
output_pdb_path=opj(self.properties['path'], self.properties['output_pdb_path'])
returncode = Scwrl4(input_pdb_path=opj(self.data_dir, self.properties['input_pdb_path']),
output_pdb_path=output_pdb_path,
properties=self.properties).launch()
assert fx.exe_success(returncode)
assert fx.not_empty(output_pdb_path)
def test_launch(self):
output_pdb_path=opj(self.properties['path'], self.properties['output_pdb_path'])
Box(input_pdb_path = opj(self.data_dir, self.properties['input_pdb_path']),
resid_pdb_path = opj(self.data_dir, self.properties['resid_pdb_path']),
output_pdb_path = opj(self.properties['path'], self.properties['output_pdb_path']),
properties = self.properties).launch()
assert fx.not_empty(output_pdb_path)
def test_launch(self):
output_xvg_path = opj(self.properties['path'],
self.properties['output_xvg_path'])
Rms(input_gro_path=opj(self.data_dir,
self.properties['input_gro_path']),
input_trr_path=opj(self.data_dir,
self.properties['input_trr_path']),
output_xvg_path=output_xvg_path,
properties=self.properties).launch()
assert fx.not_empty(output_xvg_path)
def test_launch(self):
output_png_path = opj(self.properties['path'],
self.properties['output_png_path'])
returncode = Gnuplot(input_xvg_path_dict={
u'A.Lys58Glu':
np.array([[0., 2.3958132], [1., 2.4249675]]),
u'A.Thr74Ala':
np.array([[0., 2.4072435], [1., 2.4521089]])
},
output_png_path=output_png_path,
properties=self.properties).launch()
assert fx.exe_success(returncode)
assert fx.not_empty(output_png_path)
def test_launch(self):
out_log, _ = fu.get_logs(path=self.properties['path'], console=True)
self.properties['global_log'] = out_log
output_tpr_path = opj(self.properties['path'],
self.properties['output_tpr_path'])
returncode = Grompp(
input_gro_path=opj(self.data_dir,
self.properties['input_gro_path']),
input_top_zip_path=opj(self.data_dir,
self.properties['input_top_zip_path']),
input_cpt_path=opj(self.data_dir,
self.properties['input_cpt_path']),
output_tpr_path=output_tpr_path,
properties=self.properties).launch()
assert fx.exe_success(returncode)
assert fx.not_empty(output_tpr_path)
def test_launch(self):
output_sdf_path=opj(self.properties['path'], self.properties['output_sdf_path'])
Dude(output_sdf_path=output_sdf_path, properties=self.properties).get_decoys_from_pdb()
assert fx.not_empty(output_sdf_path)