Coverage report: 89%

Files Functions Classes

coverage.py v7.14.1, created at 2026-05-29 07:52 +0000

File function   statements missing excluded   coverage
biobb_structure_utils/__init__.py (no function)   4 0 0   100%
biobb_structure_utils/gro_lib/__init__.py (no function)   0 0 0   100%
biobb_structure_utils/gro_lib/gro.py Gro.__init__   13 0 0   100%
biobb_structure_utils/gro_lib/gro.py Gro.read_gro_file   27 0 0   100%
biobb_structure_utils/gro_lib/gro.py Gro.write_gro_file   10 2 0   80%
biobb_structure_utils/gro_lib/gro.py Gro.rename_atoms   6 6 0   0%
biobb_structure_utils/gro_lib/gro.py Gro.rename_residues   6 6 0   0%
biobb_structure_utils/gro_lib/gro.py Gro.renumber_atoms   27 1 0   96%
biobb_structure_utils/gro_lib/gro.py Gro.replace_atom_entry   10 10 0   0%
biobb_structure_utils/gro_lib/gro.py Gro.sort_residues   10 10 0   0%
biobb_structure_utils/gro_lib/gro.py Gro.sort_residues2   13 0 0   100%
biobb_structure_utils/gro_lib/gro.py Gro.copy_atom_entry   11 0 0   100%
biobb_structure_utils/gro_lib/gro.py Gro.copy_residue_entry   3 3 0   0%
biobb_structure_utils/gro_lib/gro.py Gro.copy_atoms   5 5 0   0%
biobb_structure_utils/gro_lib/gro.py Gro.copy_residues   5 0 0   100%
biobb_structure_utils/gro_lib/gro.py Gro.remove_atom_entry   11 0 0   100%
biobb_structure_utils/gro_lib/gro.py Gro.remove_residue_entry   7 7 0   0%
biobb_structure_utils/gro_lib/gro.py Gro.remove_atoms   9 9 0   0%
biobb_structure_utils/gro_lib/gro.py Gro.select_atoms   7 0 0   100%
biobb_structure_utils/gro_lib/gro.py Gro.remove_residues   9 0 0   100%
biobb_structure_utils/gro_lib/gro.py (no function)   21 0 0   100%
biobb_structure_utils/test/__init__.py (no function)   0 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_cat_pdb.py TestCatPDB.setup_class   1 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_cat_pdb.py TestCatPDB.teardown_class   2 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_cat_pdb.py TestCatPDB.test_launch   3 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_cat_pdb.py (no function)   6 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_closest_residues.py TestClosestResidues.setup_class   1 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_closest_residues.py TestClosestResidues.teardown_class   2 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_closest_residues.py TestClosestResidues.test_launch   3 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_closest_residues.py (no function)   6 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_extract_atoms_gro.py TestExtractAtomsGRO.setup_class   1 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_extract_atoms_gro.py TestExtractAtomsGRO.teardown_class   2 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_extract_atoms_gro.py TestExtractAtomsGRO.test_launch   3 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_extract_atoms_gro.py (no function)   6 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_extract_atoms_pdb.py TestExtractAtomsPDB.setup_class   1 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_extract_atoms_pdb.py TestExtractAtomsPDB.teardown_class   2 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_extract_atoms_pdb.py TestExtractAtomsPDB.test_launch   3 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_extract_atoms_pdb.py (no function)   6 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_extract_chain.py TestExtractChain.setup_class   1 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_extract_chain.py TestExtractChain.teardown_class   2 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_extract_chain.py TestExtractChain.test_launch   3 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_extract_chain.py (no function)   6 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_extract_heteroatom.py TestExtractHeteroAtoms.setup_class   1 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_extract_heteroatom.py TestExtractHeteroAtoms.teardown_class   2 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_extract_heteroatom.py TestExtractHeteroAtoms.test_launch   3 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_extract_heteroatom.py (no function)   6 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_extract_model.py TestExtractModel.setup_class   1 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_extract_model.py TestExtractModel.teardown_class   1 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_extract_model.py TestExtractModel.test_launch   3 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_extract_model.py (no function)   6 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_extract_molecule.py TestExtractMolecule.setup_class   1 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_extract_molecule.py TestExtractMolecule.teardown_class   2 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_extract_molecule.py TestExtractMolecule.test_launch   3 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_extract_molecule.py (no function)   6 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_extract_residues.py TestExtractResidues.setup_class   1 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_extract_residues.py TestExtractResidues.teardown_class   2 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_extract_residues.py TestExtractResidues.test_launch   3 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_extract_residues.py (no function)   6 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_remove_ligand_gro.py TestRemoveLigandGro.setup_class   1 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_remove_ligand_gro.py TestRemoveLigandGro.teardown_class   2 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_remove_ligand_gro.py TestRemoveLigandGro.test_launch   3 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_remove_ligand_gro.py (no function)   6 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_remove_ligand_pdb.py TestRemoveLigandPDB.setup_class   1 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_remove_ligand_pdb.py TestRemoveLigandPDB.teardown_class   2 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_remove_ligand_pdb.py TestRemoveLigandPDB.test_launch   3 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_remove_ligand_pdb.py (no function)   6 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_remove_molecules.py TestRemoveMolecules.setup_class   1 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_remove_molecules.py TestRemoveMolecules.teardown_class   2 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_remove_molecules.py TestRemoveMolecules.test_launch   3 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_remove_molecules.py (no function)   6 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_remove_pdb_water.py TestRemovePDBWater.setup_class   1 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_remove_pdb_water.py TestRemovePDBWater.teardown_class   2 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_remove_pdb_water.py TestRemovePDBWater.test_launch   3 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_remove_pdb_water.py (no function)   6 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_2vgb.py TestRenumberStructure2VGB.setup_class   1 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_2vgb.py TestRenumberStructure2VGB.teardown_class   2 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_2vgb.py TestRenumberStructure2VGB.test_launch   5 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_2vgb.py (no function)   6 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_gro.py TestRenumberStructureGRO.setup_class   1 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_gro.py TestRenumberStructureGRO.teardown_class   2 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_gro.py TestRenumberStructureGRO.test_launch   5 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_gro.py (no function)   6 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_pdb.py TestRenumberStructurePDB.setup_class   1 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_pdb.py TestRenumberStructurePDB.teardown_class   2 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_pdb.py TestRenumberStructurePDB.test_launch   5 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_pdb.py (no function)   6 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_smallgro.py TestRenumberStructureSMALLGRO.setup_class   1 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_smallgro.py TestRenumberStructureSMALLGRO.teardown_class   2 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_smallgro.py TestRenumberStructureSMALLGRO.test_launch   5 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_renumber_structure_smallgro.py (no function)   6 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_sort_gro_residues.py TestSortGroResidues.setup_class   1 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_sort_gro_residues.py TestSortGroResidues.teardown_class   2 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_sort_gro_residues.py TestSortGroResidues.test_launch   3 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_sort_gro_residues.py (no function)   6 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_str_check_add_hydrogens.py TestStrCheckAddHydrogens.setup_class   1 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_str_check_add_hydrogens.py TestStrCheckAddHydrogens.teardown_class   2 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_str_check_add_hydrogens.py TestStrCheckAddHydrogens.test_str_check_add_hydrogens   2 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_str_check_add_hydrogens.py (no function)   6 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_structure_check.py TestStructureCheck.setup_class   1 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_structure_check.py TestStructureCheck.teardown_class   2 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_structure_check.py TestStructureCheck.test_launch   2 0 0   100%
biobb_structure_utils/test/unitests/test_utils/test_structure_check.py (no function)   6 0 0   100%
biobb_structure_utils/utils/__init__.py (no function)   3 0 0   100%
biobb_structure_utils/utils/cat_pdb.py CatPDB.__init__   7 0 0   100%
biobb_structure_utils/utils/cat_pdb.py CatPDB.launch   26 1 0   96%
biobb_structure_utils/utils/cat_pdb.py cat_pdb   1 0 0   100%
biobb_structure_utils/utils/cat_pdb.py (no function)   13 1 0   92%
biobb_structure_utils/utils/closest_residues.py ClosestResidues.__init__   10 0 0   100%
biobb_structure_utils/utils/closest_residues.py ClosestResidues.launch   48 7 0   85%
biobb_structure_utils/utils/closest_residues.py closest_residues   1 0 0   100%
biobb_structure_utils/utils/closest_residues.py (no function)   15 1 0   93%
biobb_structure_utils/utils/common.py check_input_path   10 5 0   50%
biobb_structure_utils/utils/common.py check_output_path   8 4 0   50%
biobb_structure_utils/utils/common.py check_output_path_pdbqt   8 4 0   50%
biobb_structure_utils/utils/common.py check_output_path_json   8 4 0   50%
biobb_structure_utils/utils/common.py is_valid_pdb   2 0 0   100%
biobb_structure_utils/utils/common.py is_valid_pdbqt   2 0 0   100%
biobb_structure_utils/utils/common.py is_valid_json   2 0 0   100%
biobb_structure_utils/utils/common.py check_output_end   10 0 0   100%
biobb_structure_utils/utils/common.py create_output_file   28 1 0   96%
biobb_structure_utils/utils/common.py create_biopython_residue   1 0 0   100%
biobb_structure_utils/utils/common.py create_residues_list   20 3 0   85%
biobb_structure_utils/utils/common.py check_format_heteroatoms   17 3 0   82%
biobb_structure_utils/utils/common.py _from_string_to_list   8 5 0   38%
biobb_structure_utils/utils/common.py (no function)   20 0 0   100%
biobb_structure_utils/utils/extract_atoms.py ExtractAtoms.__init__   7 0 0   100%
biobb_structure_utils/utils/extract_atoms.py ExtractAtoms.launch   32 4 0   88%
biobb_structure_utils/utils/extract_atoms.py extract_atoms   1 0 0   100%
biobb_structure_utils/utils/extract_atoms.py (no function)   17 1 0   94%
biobb_structure_utils/utils/extract_chain.py ExtractChain.__init__   10 0 0   100%
biobb_structure_utils/utils/extract_chain.py ExtractChain.launch   22 4 0   82%
biobb_structure_utils/utils/extract_chain.py check_format_chains   7 4 0   43%
biobb_structure_utils/utils/extract_chain.py extract_chain   1 0 0   100%
biobb_structure_utils/utils/extract_chain.py (no function)   16 1 0   94%
biobb_structure_utils/utils/extract_heteroatoms.py ExtractHeteroAtoms.__init__   9 0 0   100%
biobb_structure_utils/utils/extract_heteroatoms.py ExtractHeteroAtoms.launch   33 7 0   79%
biobb_structure_utils/utils/extract_heteroatoms.py extract_heteroatoms   1 0 0   100%
biobb_structure_utils/utils/extract_heteroatoms.py (no function)   15 1 0   93%
biobb_structure_utils/utils/extract_model.py ExtractModel.__init__   9 0 0   100%
biobb_structure_utils/utils/extract_model.py ExtractModel.launch   30 3 0   90%
biobb_structure_utils/utils/extract_model.py check_format_models   7 4 0   43%
biobb_structure_utils/utils/extract_model.py extract_model   1 0 0   100%
biobb_structure_utils/utils/extract_model.py (no function)   16 1 0   94%
biobb_structure_utils/utils/extract_molecule.py ExtractMolecule.__init__   10 0 0   100%
biobb_structure_utils/utils/extract_molecule.py ExtractMolecule.create_command_list   9 3 0   67%
biobb_structure_utils/utils/extract_molecule.py ExtractMolecule.launch   15 1 0   93%
biobb_structure_utils/utils/extract_molecule.py extract_molecule   1 0 0   100%
biobb_structure_utils/utils/extract_molecule.py (no function)   15 1 0   93%
biobb_structure_utils/utils/extract_residues.py ExtractResidues.__init__   8 0 0   100%
biobb_structure_utils/utils/extract_residues.py ExtractResidues.launch   29 4 0   86%
biobb_structure_utils/utils/extract_residues.py extract_residues   1 0 0   100%
biobb_structure_utils/utils/extract_residues.py (no function)   15 1 0   93%
biobb_structure_utils/utils/remove_ligand.py RemoveLigand.__init__   7 0 0   100%
biobb_structure_utils/utils/remove_ligand.py RemoveLigand.launch   21 1 0   95%
biobb_structure_utils/utils/remove_ligand.py remove_ligand   1 0 0   100%
biobb_structure_utils/utils/remove_ligand.py (no function)   15 1 0   93%
biobb_structure_utils/utils/remove_molecules.py RemoveMolecules.__init__   8 0 0   100%
biobb_structure_utils/utils/remove_molecules.py RemoveMolecules.launch   32 4 0   88%
biobb_structure_utils/utils/remove_molecules.py remove_molecules   1 0 0   100%
biobb_structure_utils/utils/remove_molecules.py (no function)   15 1 0   93%
biobb_structure_utils/utils/remove_pdb_water.py RemovePdbWater.__init__   7 0 0   100%
biobb_structure_utils/utils/remove_pdb_water.py RemovePdbWater.launch   9 1 0   89%
biobb_structure_utils/utils/remove_pdb_water.py remove_pdb_water   1 0 0   100%
biobb_structure_utils/utils/remove_pdb_water.py (no function)   12 1 0   92%
biobb_structure_utils/utils/renumber_structure.py RenumberStructure.__init__   15 0 0   100%
biobb_structure_utils/utils/renumber_structure.py RenumberStructure.launch   43 1 0   98%
biobb_structure_utils/utils/renumber_structure.py renumber_structure   1 0 0   100%
biobb_structure_utils/utils/renumber_structure.py (no function)   17 1 0   94%
biobb_structure_utils/utils/sort_gro_residues.py SortGroResidues.__init__   7 0 0   100%
biobb_structure_utils/utils/sort_gro_residues.py SortGroResidues.launch   12 1 0   92%
biobb_structure_utils/utils/sort_gro_residues.py sort_gro_residues   1 0 0   100%
biobb_structure_utils/utils/sort_gro_residues.py (no function)   14 1 0   93%
biobb_structure_utils/utils/str_check_add_hydrogens.py StrCheckAddHydrogens.__init__   13 0 0   100%
biobb_structure_utils/utils/str_check_add_hydrogens.py StrCheckAddHydrogens.launch   26 4 0   85%
biobb_structure_utils/utils/str_check_add_hydrogens.py str_check_add_hydrogens   1 0 0   100%
biobb_structure_utils/utils/str_check_add_hydrogens.py (no function)   13 1 0   92%
biobb_structure_utils/utils/structure_check.py StructureCheck.__init__   9 0 0   100%
biobb_structure_utils/utils/structure_check.py StructureCheck.launch   23 3 0   87%
biobb_structure_utils/utils/structure_check.py structure_check   1 0 0   100%
biobb_structure_utils/utils/structure_check.py (no function)   14 1 0   93%
Total     1403 160 0   89%

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