def test_str_check_add_hydrogens(self):
str_check_add_hydrogens(properties=self.properties, **self.paths)
assert fx.not_empty(self.paths['output_structure_path'])
assert fx.equal(self.paths['output_structure_path'],
self.paths['reference_output_structure_path'])
def test_trjconv_str_singularity(self):
gmx_trjconv_str(properties=self.properties, **self.paths)
assert fx.not_empty(self.paths['output_str_path'])
assert fx.equal(self.paths['output_str_path'],
self.paths['ref_output_str_path'])
def test_grompp(self):
returncode = grompp(properties=self.properties, **self.paths)
assert fx.not_empty(self.paths['output_tpr_path'])
assert gmx_check(self.paths['output_tpr_path'], self.paths['ref_output_tpr_path'], gmx=self.properties.get('gmx_path','gmx'))
assert fx.exe_success(returncode)
def test_pls_components(self):
pls_components(properties=self.properties, **self.paths)
assert fx.not_empty(self.paths['output_results_path'])
assert fx.equal(self.paths['output_results_path'], self.paths['ref_output_results_path'])
assert fx.not_empty(self.paths['output_plot_path'])
assert fx.equal(self.paths['output_plot_path'], self.paths['ref_output_plot_path'])
def test_box_residues(self):
box_residues(properties=self.properties, **self.paths)
assert fx.not_empty(self.paths['output_pdb_path'])
assert fx.equal_txt(self.paths['output_pdb_path'],
self.paths['ref_output_pdb_path'])
def test_memprotmd_sim(self):
memprotmd_sim(properties=self.properties, **self.paths)
assert fx.not_empty(self.paths['output_simulation'])
def test_launch(self):
extract_model(properties=self.properties, **self.paths)
assert fx.not_empty(self.paths['output_structure_path'])
assert fx.equal(self.paths['output_structure_path'], self.paths['reference_output_structure_path'])
def test_cluster_singularity(self):
gmx_energy(properties=self.properties, **self.paths)
assert fx.not_empty(self.paths['output_xvg_path'])
assert fx.equal(self.paths['output_xvg_path'],
self.paths['ref_output_xvg_path'])
def test_editconf_docker(self):
editconf(properties=self.properties, **self.paths)
assert fx.not_empty(self.paths['output_gro_path'])
assert fx.equal(self.paths['output_gro_path'],
self.paths['ref_output_gro_path'])
def test_fpocket(self):
fpocket(properties=self.properties, **self.paths)
assert fx.not_empty(self.paths['output_pockets_zip'])
#assert fx.equal(self.paths['output_pockets_zip'], self.paths['ref_output_pockets_zip'])
assert fx.not_empty(self.paths['output_summary'])
def test_bfactor_experimental_singularity(self):
cpptraj_bfactor(properties=self.properties, **self.paths)
assert fx.not_empty(self.paths['output_cpptraj_path'])
assert fx.equal(self.paths['output_cpptraj_path'],
self.paths['ref_output_cpptraj_path'])
def test_bfactor_average_docker(self):
cpptraj_bfactor(properties=self.properties, **self.paths)
assert fx.not_empty(self.paths['output_cpptraj_path'])
assert fx.equal(self.paths['output_cpptraj_path'],
self.paths['ref_output_cpptraj_path'])
def test_rms_docker(self):
gmx_rms(properties=self.properties, **self.paths)
assert fx.not_empty(self.paths['output_xvg_path'])
assert fx.equal(self.paths['output_xvg_path'],
self.paths['ref_output_xvg_path'])
def test_make_ndx(self):
returncode = MakeNdx(properties=self.properties, **self.paths).launch()
assert fx.not_empty(self.paths['output_ndx_path'])
assert fx.equal(self.paths['output_ndx_path'],
self.paths['ref_output_ndx_path'])
assert fx.exe_success(returncode)
def test_launch(self):
fix_chirality(properties=self.properties, **self.paths)
assert fx.not_empty(self.paths['output_pdb_path'])
assert fx.equal(self.paths['output_pdb_path'],
self.paths['reference_output_pdb_path'])