Coverage report: 81%

Files Functions Classes

coverage.py v7.6.12, created at 2025-03-12 09:28 +0000

File function statements missing excluded coverage
biobb_chemistry/__init__.py (no function) 4 0 0 100%
biobb_chemistry/acpype/__init__.py (no function) 7 0 0 100%
biobb_chemistry/acpype/acpype_convert_amber_to_gmx.py AcpypeConvertAMBERtoGMX.__init__ 9 0 0 100%
biobb_chemistry/acpype/acpype_convert_amber_to_gmx.py AcpypeConvertAMBERtoGMX.check_data_params 3 0 0 100%
biobb_chemistry/acpype/acpype_convert_amber_to_gmx.py AcpypeConvertAMBERtoGMX.create_cmd 12 1 0 92%
biobb_chemistry/acpype/acpype_convert_amber_to_gmx.py AcpypeConvertAMBERtoGMX.launch 14 2 0 86%
biobb_chemistry/acpype/acpype_convert_amber_to_gmx.py acpype_convert_amber_to_gmx 2 1 0 50%
biobb_chemistry/acpype/acpype_convert_amber_to_gmx.py main 11 11 0 0%
biobb_chemistry/acpype/acpype_convert_amber_to_gmx.py (no function) 16 1 0 94%
biobb_chemistry/acpype/acpype_params_ac.py AcpypeParamsAC.__init__ 10 0 0 100%
biobb_chemistry/acpype/acpype_params_ac.py AcpypeParamsAC.check_data_params 6 0 0 100%
biobb_chemistry/acpype/acpype_params_ac.py AcpypeParamsAC.create_cmd 14 1 0 93%
biobb_chemistry/acpype/acpype_params_ac.py AcpypeParamsAC.launch 15 2 0 87%
biobb_chemistry/acpype/acpype_params_ac.py acpype_params_ac 2 1 0 50%
biobb_chemistry/acpype/acpype_params_ac.py main 12 12 0 0%
biobb_chemistry/acpype/acpype_params_ac.py (no function) 16 1 0 94%
biobb_chemistry/acpype/acpype_params_cns.py AcpypeParamsCNS.__init__ 10 0 0 100%
biobb_chemistry/acpype/acpype_params_cns.py AcpypeParamsCNS.check_data_params 6 0 0 100%
biobb_chemistry/acpype/acpype_params_cns.py AcpypeParamsCNS.create_cmd 14 1 0 93%
biobb_chemistry/acpype/acpype_params_cns.py AcpypeParamsCNS.launch 15 2 0 87%
biobb_chemistry/acpype/acpype_params_cns.py acpype_params_cns 2 1 0 50%
biobb_chemistry/acpype/acpype_params_cns.py main 12 12 0 0%
biobb_chemistry/acpype/acpype_params_cns.py (no function) 16 1 0 94%
biobb_chemistry/acpype/acpype_params_gmx.py AcpypeParamsGMX.__init__ 10 0 0 100%
biobb_chemistry/acpype/acpype_params_gmx.py AcpypeParamsGMX.check_data_params 5 0 0 100%
biobb_chemistry/acpype/acpype_params_gmx.py AcpypeParamsGMX.create_cmd 14 1 0 93%
biobb_chemistry/acpype/acpype_params_gmx.py AcpypeParamsGMX.launch 15 2 0 87%
biobb_chemistry/acpype/acpype_params_gmx.py acpype_params_gmx 2 1 0 50%
biobb_chemistry/acpype/acpype_params_gmx.py main 11 11 0 0%
biobb_chemistry/acpype/acpype_params_gmx.py (no function) 16 1 0 94%
biobb_chemistry/acpype/acpype_params_gmx_opls.py AcpypeParamsGMXOPLS.__init__ 10 0 0 100%
biobb_chemistry/acpype/acpype_params_gmx_opls.py AcpypeParamsGMXOPLS.check_data_params 4 0 0 100%
biobb_chemistry/acpype/acpype_params_gmx_opls.py AcpypeParamsGMXOPLS.create_cmd 14 1 0 93%
biobb_chemistry/acpype/acpype_params_gmx_opls.py AcpypeParamsGMXOPLS.launch 15 2 0 87%
biobb_chemistry/acpype/acpype_params_gmx_opls.py acpype_params_gmx_opls 2 1 0 50%
biobb_chemistry/acpype/acpype_params_gmx_opls.py main 10 10 0 0%
biobb_chemistry/acpype/acpype_params_gmx_opls.py (no function) 16 1 0 94%
biobb_chemistry/acpype/common.py check_input_path 10 5 0 50%
biobb_chemistry/acpype/common.py check_output_path 8 4 0 50%
biobb_chemistry/acpype/common.py get_binary_path 1 0 0 100%
biobb_chemistry/acpype/common.py get_basename 5 2 0 60%
biobb_chemistry/acpype/common.py get_charge 8 4 0 50%
biobb_chemistry/acpype/common.py create_unique_name 1 0 0 100%
biobb_chemistry/acpype/common.py get_default_value 2 0 0 100%
biobb_chemistry/acpype/common.py is_valid_input 2 0 0 100%
biobb_chemistry/acpype/common.py process_output 14 0 0 100%
biobb_chemistry/acpype/common.py process_output_gmx 16 0 0 100%
biobb_chemistry/acpype/common.py process_output_cns 23 0 0 100%
biobb_chemistry/acpype/common.py (no function) 18 0 0 100%
biobb_chemistry/ambertools/__init__.py (no function) 4 0 0 100%
biobb_chemistry/ambertools/common.py check_input_path 10 5 0 50%
biobb_chemistry/ambertools/common.py check_output_path 8 4 0 50%
biobb_chemistry/ambertools/common.py get_binary_path 1 0 0 100%
biobb_chemistry/ambertools/common.py get_default_value 2 0 0 100%
biobb_chemistry/ambertools/common.py is_valid_reduce 2 0 0 100%
biobb_chemistry/ambertools/common.py (no function) 7 0 0 100%
biobb_chemistry/ambertools/reduce_add_hydrogens.py ReduceAddHydrogens.__init__ 27 0 0 100%
biobb_chemistry/ambertools/reduce_add_hydrogens.py ReduceAddHydrogens.check_data_params 2 0 0 100%
biobb_chemistry/ambertools/reduce_add_hydrogens.py ReduceAddHydrogens.create_cmd 44 15 0 66%
biobb_chemistry/ambertools/reduce_add_hydrogens.py ReduceAddHydrogens.launch 10 1 0 90%
biobb_chemistry/ambertools/reduce_add_hydrogens.py reduce_add_hydrogens 2 1 0 50%
biobb_chemistry/ambertools/reduce_add_hydrogens.py main 9 9 0 0%
biobb_chemistry/ambertools/reduce_add_hydrogens.py (no function) 16 1 0 94%
biobb_chemistry/ambertools/reduce_remove_hydrogens.py ReduceRemoveHydrogens.__init__ 8 0 0 100%
biobb_chemistry/ambertools/reduce_remove_hydrogens.py ReduceRemoveHydrogens.check_data_params 2 0 0 100%
biobb_chemistry/ambertools/reduce_remove_hydrogens.py ReduceRemoveHydrogens.create_cmd 7 0 0 100%
biobb_chemistry/ambertools/reduce_remove_hydrogens.py ReduceRemoveHydrogens.launch 10 1 0 90%
biobb_chemistry/ambertools/reduce_remove_hydrogens.py reduce_remove_hydrogens 2 1 0 50%
biobb_chemistry/ambertools/reduce_remove_hydrogens.py main 9 9 0 0%
biobb_chemistry/ambertools/reduce_remove_hydrogens.py (no function) 16 1 0 94%
biobb_chemistry/babelm/__init__.py (no function) 6 0 0 100%
biobb_chemistry/babelm/babel_add_hydrogens.py BabelAddHydrogens.__init__ 15 0 0 100%
biobb_chemistry/babelm/babel_add_hydrogens.py BabelAddHydrogens.check_data_params 2 0 0 100%
biobb_chemistry/babelm/babel_add_hydrogens.py BabelAddHydrogens.create_cmd 33 2 0 94%
biobb_chemistry/babelm/babel_add_hydrogens.py BabelAddHydrogens.launch 10 1 0 90%
biobb_chemistry/babelm/babel_add_hydrogens.py babel_add_hydrogens 2 1 0 50%
biobb_chemistry/babelm/babel_add_hydrogens.py main 9 9 0 0%
biobb_chemistry/babelm/babel_add_hydrogens.py (no function) 16 1 0 94%
biobb_chemistry/babelm/babel_convert.py BabelConvert.__init__ 16 0 0 100%
biobb_chemistry/babelm/babel_convert.py BabelConvert.check_data_params 2 0 0 100%
biobb_chemistry/babelm/babel_convert.py BabelConvert.create_cmd 35 3 0 91%
biobb_chemistry/babelm/babel_convert.py BabelConvert.launch 10 1 0 90%
biobb_chemistry/babelm/babel_convert.py babel_convert 2 1 0 50%
biobb_chemistry/babelm/babel_convert.py main 9 9 0 0%
biobb_chemistry/babelm/babel_convert.py (no function) 16 1 0 94%
biobb_chemistry/babelm/babel_minimize.py BabelMinimize.__init__ 17 0 0 100%
biobb_chemistry/babelm/babel_minimize.py BabelMinimize.check_data_params 2 0 0 100%
biobb_chemistry/babelm/babel_minimize.py BabelMinimize.create_cmd 27 0 0 100%
biobb_chemistry/babelm/babel_minimize.py BabelMinimize.launch 10 1 0 90%
biobb_chemistry/babelm/babel_minimize.py babel_minimize 2 1 0 50%
biobb_chemistry/babelm/babel_minimize.py main 9 9 0 0%
biobb_chemistry/babelm/babel_minimize.py (no function) 17 1 0 94%
biobb_chemistry/babelm/babel_remove_hydrogens.py BabelRemoveHydrogens.__init__ 15 0 0 100%
biobb_chemistry/babelm/babel_remove_hydrogens.py BabelRemoveHydrogens.check_data_params 2 0 0 100%
biobb_chemistry/babelm/babel_remove_hydrogens.py BabelRemoveHydrogens.create_cmd 33 2 0 94%
biobb_chemistry/babelm/babel_remove_hydrogens.py BabelRemoveHydrogens.launch 10 1 0 90%
biobb_chemistry/babelm/babel_remove_hydrogens.py babel_remove_hydrogens 2 1 0 50%
biobb_chemistry/babelm/babel_remove_hydrogens.py main 9 9 0 0%
biobb_chemistry/babelm/babel_remove_hydrogens.py (no function) 16 1 0 94%
biobb_chemistry/babelm/common.py check_input_path 10 5 0 50%
biobb_chemistry/babelm/common.py check_output_path 8 4 0 50%
biobb_chemistry/babelm/common.py check_input_path_minimize 10 5 0 50%
biobb_chemistry/babelm/common.py check_output_path_minimize 8 4 0 50%
biobb_chemistry/babelm/common.py get_binary_path 1 1 0 0%
biobb_chemistry/babelm/common.py get_input_format 6 3 0 50%
biobb_chemistry/babelm/common.py check_minimize_property 42 14 0 67%
biobb_chemistry/babelm/common.py get_output_format 6 3 0 50%
biobb_chemistry/babelm/common.py get_coordinates 5 2 0 60%
biobb_chemistry/babelm/common.py get_ph 5 2 0 60%
biobb_chemistry/babelm/common.py get_default_value 2 2 0 0%
biobb_chemistry/babelm/common.py is_valid_input 2 0 0 100%
biobb_chemistry/babelm/common.py is_valid_output 2 0 0 100%
biobb_chemistry/babelm/common.py is_valid_input_minimize 2 0 0 100%
biobb_chemistry/babelm/common.py is_valid_output_minimize 2 2 0 0%
biobb_chemistry/babelm/common.py _from_string_to_list 8 4 0 50%
biobb_chemistry/babelm/common.py (no function) 20 0 0 100%
biobb_chemistry/test/__init__.py (no function) 0 0 0 100%
biobb_chemistry/test/unitests/test_acpype/test_acpype_amber2gmx.py TestAcpypeAmber2GMX.setup_class 1 0 0 100%
biobb_chemistry/test/unitests/test_acpype/test_acpype_amber2gmx.py TestAcpypeAmber2GMX.teardown_class 2 0 0 100%
biobb_chemistry/test/unitests/test_acpype/test_acpype_amber2gmx.py TestAcpypeAmber2GMX.test_amber2gmx 5 0 0 100%
biobb_chemistry/test/unitests/test_acpype/test_acpype_amber2gmx.py (no function) 6 0 0 100%
biobb_chemistry/test/unitests/test_acpype/test_acpype_params_ac.py TestAcpypeParamsAC.setup_class 1 0 0 100%
biobb_chemistry/test/unitests/test_acpype/test_acpype_params_ac.py TestAcpypeParamsAC.teardown_class 1 0 0 100%
biobb_chemistry/test/unitests/test_acpype/test_acpype_params_ac.py TestAcpypeParamsAC.test_params_ac 7 0 0 100%
biobb_chemistry/test/unitests/test_acpype/test_acpype_params_ac.py (no function) 6 0 0 100%
biobb_chemistry/test/unitests/test_acpype/test_acpype_params_cns.py TestAcpypeParamsCNS.setup_class 1 0 0 100%
biobb_chemistry/test/unitests/test_acpype/test_acpype_params_cns.py TestAcpypeParamsCNS.teardown_class 1 0 0 100%
biobb_chemistry/test/unitests/test_acpype/test_acpype_params_cns.py TestAcpypeParamsCNS.test_params_cns 4 0 0 100%
biobb_chemistry/test/unitests/test_acpype/test_acpype_params_cns.py (no function) 6 0 0 100%
biobb_chemistry/test/unitests/test_acpype/test_acpype_params_gmx.py TestAcpypeParamsGMX.setup_class 1 0 0 100%
biobb_chemistry/test/unitests/test_acpype/test_acpype_params_gmx.py TestAcpypeParamsGMX.teardown_class 2 0 0 100%
biobb_chemistry/test/unitests/test_acpype/test_acpype_params_gmx.py TestAcpypeParamsGMX.test_params_gmx 6 0 0 100%
biobb_chemistry/test/unitests/test_acpype/test_acpype_params_gmx.py (no function) 6 0 0 100%
biobb_chemistry/test/unitests/test_acpype/test_acpype_params_gmx_opls.py TestAcpypeParamsGMXOPLS.setup_class 1 0 0 100%
biobb_chemistry/test/unitests/test_acpype/test_acpype_params_gmx_opls.py TestAcpypeParamsGMXOPLS.teardown_class 1 0 0 100%
biobb_chemistry/test/unitests/test_acpype/test_acpype_params_gmx_opls.py TestAcpypeParamsGMXOPLS.test_params_gmx_opls 4 0 0 100%
biobb_chemistry/test/unitests/test_acpype/test_acpype_params_gmx_opls.py (no function) 6 0 0 100%
biobb_chemistry/test/unitests/test_ambertools/test_reduce_add_hydrogens.py TestReduceAddHydrogens.setup_class 1 0 0 100%
biobb_chemistry/test/unitests/test_ambertools/test_reduce_add_hydrogens.py TestReduceAddHydrogens.teardown_class 2 0 0 100%
biobb_chemistry/test/unitests/test_ambertools/test_reduce_add_hydrogens.py TestReduceAddHydrogens.test_add_hydrogens 2 0 0 100%
biobb_chemistry/test/unitests/test_ambertools/test_reduce_add_hydrogens.py (no function) 6 0 0 100%
biobb_chemistry/test/unitests/test_ambertools/test_reduce_remove_hydrogens.py TestReduceRemoveHydrogens.setup_class 1 0 0 100%
biobb_chemistry/test/unitests/test_ambertools/test_reduce_remove_hydrogens.py TestReduceRemoveHydrogens.teardown_class 2 0 0 100%
biobb_chemistry/test/unitests/test_ambertools/test_reduce_remove_hydrogens.py TestReduceRemoveHydrogens.test_remove_hydrogens 2 0 0 100%
biobb_chemistry/test/unitests/test_ambertools/test_reduce_remove_hydrogens.py (no function) 6 0 0 100%
biobb_chemistry/test/unitests/test_babel/test_babel_add_hydrogens.py TestBabelAddHydrogens.setup_class 1 0 0 100%
biobb_chemistry/test/unitests/test_babel/test_babel_add_hydrogens.py TestBabelAddHydrogens.teardown_class 2 0 0 100%
biobb_chemistry/test/unitests/test_babel/test_babel_add_hydrogens.py TestBabelAddHydrogens.test_add_hydrogens 2 0 0 100%
biobb_chemistry/test/unitests/test_babel/test_babel_add_hydrogens.py (no function) 6 0 0 100%
biobb_chemistry/test/unitests/test_babel/test_babel_convert.py TestBabelConvert.setup_class 1 0 0 100%
biobb_chemistry/test/unitests/test_babel/test_babel_convert.py TestBabelConvert.teardown_class 2 0 0 100%
biobb_chemistry/test/unitests/test_babel/test_babel_convert.py TestBabelConvert.test_convert 2 0 0 100%
biobb_chemistry/test/unitests/test_babel/test_babel_convert.py (no function) 6 0 0 100%
biobb_chemistry/test/unitests/test_babel/test_babel_minimize.py TestBabelMinimize.setup_class 1 0 0 100%
biobb_chemistry/test/unitests/test_babel/test_babel_minimize.py TestBabelMinimize.teardown_class 2 0 0 100%
biobb_chemistry/test/unitests/test_babel/test_babel_minimize.py TestBabelMinimize.test_minimize 3 0 0 100%
biobb_chemistry/test/unitests/test_babel/test_babel_minimize.py (no function) 6 0 0 100%
biobb_chemistry/test/unitests/test_babel/test_babel_remove_hydrogens.py TestBabelRemoveHydrogens.setup_class 1 0 0 100%
biobb_chemistry/test/unitests/test_babel/test_babel_remove_hydrogens.py TestBabelRemoveHydrogens.teardown_class 2 0 0 100%
biobb_chemistry/test/unitests/test_babel/test_babel_remove_hydrogens.py TestBabelRemoveHydrogens.test_remove_hydrogens 2 0 0 100%
biobb_chemistry/test/unitests/test_babel/test_babel_remove_hydrogens.py (no function) 6 0 0 100%
Total   1306 250 0 81%

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