def test_grompp_singulariy(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_template_singularity(self):
returncode = TemplateContainer(properties=self.properties,
**self.paths).launch()
assert fx.not_empty(self.paths['output_file_path'])
assert fx.equal(self.paths['output_file_path'],
self.paths['ref_output_file_path'])
assert fx.exe_success(returncode)
def test_genrestr_noNDX(self):
self.paths.pop('input_ndx_path')
returncode = genrestr(properties=self.properties, **self.paths)
assert fx.not_empty(self.paths['output_itp_path'])
assert fx.equal(self.paths['output_itp_path'],
self.paths['ref_output_itp_noNDX_path'])
assert fx.exe_success(returncode)
def test_genrestr(self):
returncode = Genrestr(properties=self.properties,
**self.paths).launch()
assert fx.not_empty(self.paths['output_itp_path'])
assert fx.equal(self.paths['output_itp_path'],
self.paths['ref_output_itp_path'])
assert fx.exe_success(returncode)
def test_append_ligand(self):
returncode = AppendLigand(properties=self.properties,
**self.paths).launch()
assert fx.not_empty(self.paths['output_top_zip_path'])
assert fx.equal(self.paths['output_top_zip_path'],
self.paths['ref_output_top_zip_path'])
assert fx.exe_success(returncode)
def test_select(self):
returncode = Gmxselect(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_genion_docker(self):
returncode = genion(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'])
assert fx.not_empty(self.paths['output_top_zip_path'])
assert fx.equal(self.paths['output_top_zip_path'], self.paths['ref_output_top_zip_path'])
assert fx.exe_success(returncode)
def test_grompp_mdrun(self):
returncode = grompp_mdrun(properties=self.properties, **self.paths)
assert fx.not_empty(self.paths['output_trr_path'])
assert gmx_rms(self.paths['output_trr_path'], self.paths['ref_output_trr_path'], self.paths['input_gro_path'], self.properties.get('gmx_path','gmx'))
assert fx.not_empty(self.paths['output_gro_path'])
assert fx.not_empty(self.paths['output_edr_path'])
assert fx.not_empty(self.paths['output_log_path'])
assert fx.exe_success(returncode)
def test_solvate(self):
returncode = Solvate(properties=self.properties, **self.paths).launch()
assert fx.not_empty(self.paths['output_gro_path'])
assert fx.equal(self.paths['output_gro_path'],
self.paths['ref_output_gro_path'])
assert fx.not_empty(self.paths['output_top_zip_path'])
assert fx.equal(self.paths['output_top_zip_path'],
self.paths['ref_output_top_zip_path'])
assert fx.exe_success(returncode)
def test_pdb2gmx_singularity(self):
returncode = pdb2gmx(properties=self.properties, **self.paths)
assert fx.not_empty(self.paths['output_top_zip_path'])
assert fx.equal(self.paths['output_top_zip_path'],
self.paths['ref_output_top_zip_path'])
assert fx.not_empty(self.paths['output_gro_path'])
assert fx.equal(self.paths['output_gro_path'],
self.paths['ref_output_gro_path'])
assert fx.exe_success(returncode)
def test_make_ndx(self):
returncode = make_ndx(properties=self.properties, **self.paths)
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_template_docker(self):
returncode= template_container(properties=self.properties, **self.paths)
assert fx.not_empty(self.paths['output_file_path'])
assert fx.equal(self.paths['output_file_path'], self.paths['ref_output_file_path'])
assert fx.exe_success(returncode)
def test_ndx2resttop(self):
returncode= Ndx2resttop(properties=self.properties, **self.paths).launch()
assert fx.not_empty(self.paths['output_top_zip_path'])
assert fx.equal(self.paths['output_top_zip_path'], self.paths['ref_output_top_zip_path'])
assert fx.exe_success(returncode)
def test_genion_singularity(self):
returncode = genion(properties=self.properties, **self.paths)
assert fx.not_empty(self.paths['output_itp_path'])
assert fx.equal(self.paths['output_itp_path'],
self.paths['ref_output_itp_path'])
assert fx.exe_success(returncode)
