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_decision_tree(self):
decision_tree(properties=self.properties, **self.paths)
assert fx.not_empty(self.paths['output_model_path'])
assert fx.equal(self.paths['output_model_path'], self.paths['ref_output_model_path'])
assert fx.not_empty(self.paths['output_test_table_path'])
assert fx.equal(self.paths['output_test_table_path'], self.paths['ref_output_test_table_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_neural_network_decode(self):
neural_network_decode(properties=self.properties, **self.paths)
assert fx.not_empty(self.paths['output_decode_path'])
assert fx.equal(self.paths['output_decode_path'],
self.paths['ref_output_decode_path'])
assert fx.not_empty(self.paths['output_predict_path'])
assert fx.equal(self.paths['output_predict_path'],
self.paths['ref_output_predict_path'])
def test_k_neighbors_coefficient(self):
k_neighbors_coefficient(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_params_gmx_opls(self):
AcpypeParamsGMXOPLS(properties=self.properties, **self.paths).launch()
assert fx.not_empty(self.paths['output_path_itp'])
assert fx.not_empty(self.paths['output_path_top'])
assert fx.equal(self.paths['output_path_itp'],
self.paths['ref_output_acpype_path_itp'])
assert fx.equal(self.paths['output_path_top'],
self.paths['ref_output_acpype_path_top'])
def test_principal_component(self):
principal_component(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_k_neighbors(self):
k_neighbors(properties=self.properties, **self.paths)
assert fx.not_empty(self.paths['output_model_path'])
assert fx.equal(self.paths['output_model_path'], self.paths['ref_output_model_path'])
assert fx.not_empty(self.paths['output_test_table_path'])
assert fx.equal(self.paths['output_test_table_path'], self.paths['ref_output_test_table_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_dbscan(self):
dbscan(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_cmip_mip_singularity(self):
cmip(properties=self.properties, **self.paths)
assert fx.not_empty(self.paths['output_cube_path'])
assert fx.not_empty(self.paths['output_grd_path'])
assert fx.equal(self.paths['output_grd_path'],
self.paths['ref_output_cmip_mip_grd_path'])
assert fx.equal(self.paths['output_cube_path'],
self.paths['ref_output_cmip_mip_cube_path'])
def test_agglomerative_coefficient(self):
agglomerative_coefficient(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_linear_regression(self):
linear_regression(properties=self.properties, **self.paths)
assert fx.not_empty(self.paths['output_model_path'])
assert fx.equal(self.paths['output_model_path'], self.paths['ref_output_model_path'])
assert fx.not_empty(self.paths['output_test_table_path'])
assert fx.equal(self.paths['output_test_table_path'], self.paths['ref_output_test_table_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_launch(self):
renumber_structure(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_stucture_path'])
assert fx.not_empty(self.paths['output_mapping_json_path'])
assert fx.equal(self.paths['output_mapping_json_path'],
self.paths['reference_output_mapping_json_path'])
def test_params_gmx_opls(self):
acpype_params_gmx_opls(properties=self.properties, **self.paths)
#assert fx.not_empty(self.paths['output_path_itp'])
assert fx.not_empty(self.paths['output_path_top'])
assert fx.equal(self.paths['output_path_itp'],
self.paths['ref_output_acpype_path_itp'])
assert fx.equal(self.paths['output_path_top'],
self.paths['ref_output_acpype_path_top'])
def test_fpocket_select(self):
fpocket_select(properties=self.properties, **self.paths)
assert fx.not_empty(self.paths['output_pocket_pdb'])
assert fx.equal(self.paths['output_pocket_pdb'],
self.paths['ref_output_pocket_pdb'])
assert fx.not_empty(self.paths['output_pocket_pqr'])
assert fx.equal(self.paths['output_pocket_pqr'],
self.paths['ref_output_pocket_pqr'])
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_params_ac_singularity(self):
acpype_params_ac(properties=self.properties, **self.paths)
assert fx.not_empty(self.paths['output_path_frcmod'])
assert fx.not_empty(self.paths['output_path_inpcrd'])
assert fx.not_empty(self.paths['output_path_lib'])
assert fx.not_empty(self.paths['output_path_prmtop'])
assert fx.equal(self.paths['output_path_frcmod'],
self.paths['ref_output_acpype_path_frcmod'])
assert fx.equal(self.paths['output_path_inpcrd'],
self.paths['ref_output_acpype_path_inpcrd'])
def test_params_cns(self):
AcpypeParamsCNS(properties=self.properties, **self.paths).launch()
assert fx.not_empty(self.paths['output_path_par'])
assert fx.not_empty(self.paths['output_path_inp'])
assert fx.not_empty(self.paths['output_path_top'])
#assert fx.equal(self.paths['output_path_par'], self.paths['ref_output_acpype_path_par'])
assert fx.equal(self.paths['output_path_inp'],
self.paths['ref_output_acpype_path_inp'])
assert fx.equal(self.paths['output_path_top'],
self.paths['ref_output_acpype_path_top'])
def test_leap_gen_top(self):
leap_gen_top(properties=self.properties, **self.paths)
assert fx.not_empty(self.paths['output_pdb_path'])
assert fx.not_empty(self.paths['output_top_path'])
assert fx.not_empty(self.paths['output_crd_path'])
assert fx.equal(self.paths['output_pdb_path'],
self.paths['ref_output_pdb_path'])
assert fx.equal(self.paths['output_top_path'],
self.paths['ref_output_top_path'])
assert fx.equal(self.paths['output_crd_path'],
self.paths['ref_output_crd_path'])
def test_random_forest_regressor(self):
random_forest_regressor(properties=self.properties, **self.paths)
assert fx.not_empty(self.paths['output_model_path'])
assert fx.equal(self.paths['output_model_path'],
self.paths['ref_output_model_path'])
assert fx.not_empty(self.paths['output_test_table_path'])
assert fx.equal(self.paths['output_test_table_path'],
self.paths['ref_output_test_table_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_params_ac(self):
AcpypeParamsAC(properties=self.properties, **self.paths).launch()
assert fx.not_empty(self.paths['output_path_frcmod'])
assert fx.not_empty(self.paths['output_path_inpcrd'])
assert fx.not_empty(self.paths['output_path_lib'])
assert fx.not_empty(self.paths['output_path_prmtop'])
assert fx.equal(self.paths['output_path_frcmod'],
self.paths['ref_output_acpype_path_frcmod'])
assert fx.equal(self.paths['output_path_inpcrd'],
self.paths['ref_output_acpype_path_inpcrd'])
assert fx.equal(self.paths['output_path_lib'],
self.paths['ref_output_acpype_path_lib'])
assert fx.equal(self.paths['output_path_prmtop'],
self.paths['ref_output_acpype_path_prmtop'])
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_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_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_prepare_structureTopology(self):
prepare_structure(properties=self.properties, **self.paths)
assert fx.not_empty(self.paths['output_pdb_path'])
assert fx.equal(
self.paths['output_pdb_path'],
self.paths['ref_output_prepare_structure_topology_path'],
remove_hetatm=False)
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_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_cmip_docking(self):
cmip(properties=self.properties, **self.paths)
assert fx.not_empty(self.paths['output_pdb_path'])
assert fx.not_empty(self.paths['output_grd_path'])
assert fx.not_empty(self.paths['output_rst_path'])
assert fx.equal(self.paths['output_pdb_path'],
self.paths['ref_output_cmip_docking_pdb_path'],
remove_hetatm=False)
#assert fx.equal(self.paths['output_grd_path'], self.paths['ref_output_cmip_docking_grd_path'])
#assert fx.equal(self.paths['output_rst_path'], self.paths['ref_output_cmip_docking_rst_path'])
# class TestCmipEnergy():
# def setUp(self):
# fx.test_setup(self, 'cmip_energy')
#
# def tearDown(self):
# #pass
# fx.test_teardown(self)
#
# def test_cmip_mip(self):
# cmip(properties=self.properties, **self.paths)
# assert fx.not_empty(self.paths['output_cube_path'])
# assert fx.not_empty(self.paths['output_grd_path'])
# assert fx.equal(self.paths['output_grd_path'], self.paths['ref_output_cmip_mip_grd_path'])
# assert fx.equal(self.paths['output_cube_path'], self.paths['ref_output_cmip_mip_cube_path'])
#
# class TestCmipSolvation():
# def setUp(self):
# fx.test_setup(self, 'cmip_solvation')
#
# def tearDown(self):
# #pass
# fx.test_teardown(self)
#
# def test_cmip_mip(self):
# cmip(properties=self.properties, **self.paths)
# assert fx.not_empty(self.paths['output_cube_path'])
# assert fx.not_empty(self.paths['output_grd_path'])
# assert fx.equal(self.paths['output_grd_path'], self.paths['ref_output_cmip_mip_grd_path'])
# assert fx.equal(self.paths['output_cube_path'], self.paths['ref_output_cmip_mip_cube_path'])
def test_dry_singularity(self):
cpptraj_dry(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_launch(self):
sort_gro_residues(properties=self.properties, **self.paths)
assert fx.not_empty(self.paths['output_gro_path'])
assert fx.equal(self.paths['output_gro_path'],
self.paths['reference_output_gro_path'])
