def test_launch(self):
output_gro_path = opj(self.properties['path'], self.properties['output_gro_path'])
returncode = Editconf(input_gro_path=opj(self.data_dir, self.properties['input_gro_path']),
output_gro_path=output_gro_path,
properties=self.properties).launch()
assert fx.exe_success(returncode)
assert fx.not_empty(output_gro_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_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):
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):
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)
