Coverage report: 97%

Files Functions Classes

coverage.py v7.16.2, created at 2026-10-16 00:10 +0000

File function   statements missing excluded   coverage
cvpack/__init__.py (no function)   29 2 0   93%
cvpack/angle.py Angle.__init__   4 0 0   100%
cvpack/angle.py (no function)   6 0 0   100%
cvpack/atomic_function.py AtomicFunction.__init__   11 1 0   91%
cvpack/atomic_function.py AtomicFunction._fromCustomForce   34 5 0   85%
cvpack/atomic_function.py AtomicFunction._fromHarmonicBondForce   8 0 0   100%
cvpack/atomic_function.py AtomicFunction._fromHarmonicAngleForce   8 0 0   100%
cvpack/atomic_function.py AtomicFunction._fromPeriodicTorsionForce   9 0 0   100%
cvpack/atomic_function.py AtomicFunction.fromOpenMMForce   15 1 0   93%
cvpack/atomic_function.py (no function)   20 0 0   100%
cvpack/attraction_strength.py _cutoff_distance   3 0 0   100%
cvpack/attraction_strength.py _lennard_jones_switch   4 0 0   100%
cvpack/attraction_strength.py AttractionStrength.__init__   40 1 0   98%
cvpack/attraction_strength.py (no function)   14 0 0   100%
cvpack/base_custom_function.py BaseCustomFunction._extractParameters   11 0 0   100%
cvpack/base_custom_function.py BaseCustomFunction._addParameters   7 0 0   100%
cvpack/base_custom_function.py (no function)   7 0 0   100%
cvpack/base_path_cv.py BasePathCV.__init__   18 0 0   100%
cvpack/base_path_cv.py BasePathCV._generateName   5 1 0   80%
cvpack/base_path_cv.py (no function)   8 0 0   100%
cvpack/base_radius_of_gyration.py BaseRadiusOfGyration.__init__   10 0 0   100%
cvpack/base_radius_of_gyration.py (no function)   6 0 0   100%
cvpack/base_rmsd.py BaseRMSD._getDefinedCoords   4 0 0   100%
cvpack/base_rmsd.py BaseRMSD._getAllCoords   4 0 0   100%
cvpack/base_rmsd.py (no function)   7 0 0   100%
cvpack/base_rmsd_content.py BaseRMSDContent.__init__   21 1 0   95%
cvpack/base_rmsd_content.py BaseRMSDContent.__init__.get_expression   12 0 0   100%
cvpack/base_rmsd_content.py BaseRMSDContent._loadPositions   2 0 0   100%
cvpack/base_rmsd_content.py BaseRMSDContent._getAtomList   17 0 0   100%
cvpack/base_rmsd_content.py BaseRMSDContent.getNumResidueBlocks   1 0 0   100%
cvpack/base_rmsd_content.py (no function)   18 0 0   100%
cvpack/centroid_function.py CentroidFunction.__init__   17 3 0   82%
cvpack/centroid_function.py (no function)   11 0 0   100%
cvpack/collective_variable.py CollectiveVariable.__getstate__   1 0 0   100%
cvpack/collective_variable.py CollectiveVariable.__setstate__   1 0 0   100%
cvpack/collective_variable.py CollectiveVariable.__copy__   1 0 0   100%
cvpack/collective_variable.py CollectiveVariable.__deepcopy__   1 0 0   100%
cvpack/collective_variable.py CollectiveVariable._registerCV   7 0 0   100%
cvpack/collective_variable.py CollectiveVariable._registerPeriodicBounds   5 0 0   100%
cvpack/collective_variable.py CollectiveVariable._setUnusedForceGroup   3 0 0   100%
cvpack/collective_variable.py CollectiveVariable.getName   1 0 0   100%
cvpack/collective_variable.py CollectiveVariable.getUnit   1 0 0   100%
cvpack/collective_variable.py CollectiveVariable.getMassUnit   1 0 0   100%
cvpack/collective_variable.py CollectiveVariable.getPeriodicBounds   1 0 0   100%
cvpack/collective_variable.py CollectiveVariable.addToSystem   3 0 0   100%
cvpack/collective_variable.py CollectiveVariable.getValue   3 0 0   100%
cvpack/collective_variable.py CollectiveVariable.getEffectiveMass   1 0 0   100%
cvpack/collective_variable.py (no function)   29 0 0   100%
cvpack/composite_rmsd.py _stub   3 0 0   100%
cvpack/composite_rmsd.py _stub.Stub.__init__   1 0 0   100%
cvpack/composite_rmsd.py _get_force_class   10 0 0   100%
cvpack/composite_rmsd.py CompositeRMSD.__init__   12 3 0   75%
cvpack/composite_rmsd.py (no function)   12 0 0   100%
cvpack/distance.py Distance.__init__   4 0 0   100%
cvpack/distance.py (no function)   6 0 0   100%
cvpack/helix_angle_content.py HelixAngleContent.__init__   17 0 0   100%
cvpack/helix_angle_content.py HelixAngleContent.__init__.find_alpha_carbon   4 0 0   100%
cvpack/helix_angle_content.py (no function)   11 0 0   100%
cvpack/helix_hbond_content.py HelixHBondContent.__init__   19 1 0   95%
cvpack/helix_hbond_content.py HelixHBondContent.__init__.find_atom   4 1 0   75%
cvpack/helix_hbond_content.py (no function)   12 0 0   100%
cvpack/helix_rmsd_content.py HelixRMSDContent.__init__   5 0 0   100%
cvpack/helix_rmsd_content.py (no function)   11 0 0   100%
cvpack/helix_torsion_content.py HelixTorsionContent.__init__   16 0 0   100%
cvpack/helix_torsion_content.py HelixTorsionContent.__init__.find_atom   4 0 0   100%
cvpack/helix_torsion_content.py (no function)   12 0 0   100%
cvpack/meta_collective_variable.py MetaCollectiveVariable.__init__   15 1 0   93%
cvpack/meta_collective_variable.py MetaCollectiveVariable.getInnerVariables   1 0 0   100%
cvpack/meta_collective_variable.py MetaCollectiveVariable.getInnerValues   2 0 0   100%
cvpack/meta_collective_variable.py MetaCollectiveVariable.getInnerEffectiveMasses   9 0 0   100%
cvpack/meta_collective_variable.py MetaCollectiveVariable._getContextWithVirtualSites   13 0 0   100%
cvpack/meta_collective_variable.py MetaCollectiveVariable._createContextWithVirtualSites   8 0 0   100%
cvpack/meta_collective_variable.py MetaCollectiveVariable.getParameterDefaultValues   1 0 0   100%
cvpack/meta_collective_variable.py MetaCollectiveVariable.getParameterValues   1 0 0   100%
cvpack/meta_collective_variable.py MetaCollectiveVariable.getParameterDerivatives   3 0 0   100%
cvpack/meta_collective_variable.py (no function)   20 0 0   100%
cvpack/number_of_contacts.py NumberOfContacts.__init__   26 0 0   100%
cvpack/number_of_contacts.py (no function)   10 0 0   100%
cvpack/openmm_force_wrapper.py OpenMMForceWrapper.__init__   8 0 0   100%
cvpack/openmm_force_wrapper.py OpenMMForceWrapper.__getattr__   5 0 0   100%
cvpack/openmm_force_wrapper.py OpenMMForceWrapper.__getattr__._wrapped_method   1 0 0   100%
cvpack/openmm_force_wrapper.py (no function)   10 0 0   100%
cvpack/path/__init__.py (no function)   1 0 0   100%
cvpack/path/path.py Metric.__init__   1 0 0   100%
cvpack/path/path.py Metric.__repr__   1 1 0   0%
cvpack/path/path.py Metric.__eq__   1 0 0   100%
cvpack/path/path.py Metric.__hash__   1 1 0   0%
cvpack/path/path.py Metric.__getstate__   1 0 0   100%
cvpack/path/path.py Metric.__setstate__   1 0 0   100%
cvpack/path/path.py (no function)   12 0 0   100%
cvpack/path_in_cv_space.py _milestone_values   3 0 0   100%
cvpack/path_in_cv_space.py PathInCVSpace.__init__   28 2 0   93%
cvpack/path_in_cv_space.py (no function)   13 0 0   100%
cvpack/path_in_rmsd_space.py PathInRMSDSpace.__init__   10 1 0   90%
cvpack/path_in_rmsd_space.py (no function)   10 0 0   100%
cvpack/radius_of_gyration.py RadiusOfGyration.__init__   3 0 0   100%
cvpack/radius_of_gyration.py (no function)   6 0 0   100%
cvpack/radius_of_gyration_sq.py RadiusOfGyrationSq.__init__   3 0 0   100%
cvpack/radius_of_gyration_sq.py (no function)   6 0 0   100%
cvpack/reporting/__init__.py (no function)   4 0 0   100%
cvpack/reporting/custom_writer.py CustomWriter.getHeaders   1 1 0   0%
cvpack/reporting/custom_writer.py CustomWriter.getValues   1 1 0   0%
cvpack/reporting/custom_writer.py (no function)   6 0 0   100%
cvpack/reporting/cv_writer.py CVWriter.__init__   8 2 0   75%
cvpack/reporting/cv_writer.py CVWriter.getHeaders   6 0 0   100%
cvpack/reporting/cv_writer.py CVWriter.getValues   9 0 0   100%
cvpack/reporting/cv_writer.py (no function)   7 0 0   100%
cvpack/reporting/meta_cv_writer.py MetaCVWriter.__init__   9 0 0   100%
cvpack/reporting/meta_cv_writer.py MetaCVWriter.__init__.select   4 0 0   100%
cvpack/reporting/meta_cv_writer.py MetaCVWriter.getHeaders   11 0 0   100%
cvpack/reporting/meta_cv_writer.py MetaCVWriter.getHeaders.add_header   1 0 0   100%
cvpack/reporting/meta_cv_writer.py MetaCVWriter.getValues   19 0 0   100%
cvpack/reporting/meta_cv_writer.py (no function)   9 0 0   100%
cvpack/reporting/state_data_reporter.py StateDataReporter.__init__   6 1 0   83%
cvpack/reporting/state_data_reporter.py StateDataReporter._expand   2 0 0   100%
cvpack/reporting/state_data_reporter.py StateDataReporter._initializeConstants   4 1 0   75%
cvpack/reporting/state_data_reporter.py StateDataReporter._constructHeaders   1 0 0   100%
cvpack/reporting/state_data_reporter.py StateDataReporter._constructReportValues   1 0 0   100%
cvpack/reporting/state_data_reporter.py (no function)   11 0 0   100%
cvpack/residue_coordination.py ResidueCoordination.__init__   20 0 0   100%
cvpack/residue_coordination.py ResidueCoordination.__getstate__   1 0 0   100%
cvpack/residue_coordination.py ResidueCoordination.__setstate__   5 0 0   100%
cvpack/residue_coordination.py ResidueCoordination.getReferenceValue   1 0 0   100%
cvpack/residue_coordination.py ResidueCoordination.setReferenceValue   4 0 0   100%
cvpack/residue_coordination.py (no function)   14 0 0   100%
cvpack/rmsd.py RMSD.__init__   10 0 0   100%
cvpack/rmsd.py RMSD.getNullBondForce   5 0 0   100%
cvpack/rmsd.py (no function)   10 0 0   100%
cvpack/serialization/__init__.py (no function)   1 0 0   100%
cvpack/serialization/serialization.py Serializable.registerTag   3 0 0   100%
cvpack/serialization/serialization.py SerializableAtom.__init__   8 2 0   75%
cvpack/serialization/serialization.py SerializableAtom.__getstate__   1 0 0   100%
cvpack/serialization/serialization.py SerializableAtom.__setstate__   1 0 0   100%
cvpack/serialization/serialization.py SerializableAtom.element   3 0 0   100%
cvpack/serialization/serialization.py SerializableResidue.__init__   7 1 0   86%
cvpack/serialization/serialization.py SerializableResidue.__getstate__   1 0 0   100%
cvpack/serialization/serialization.py SerializableResidue.__setstate__   1 0 0   100%
cvpack/serialization/serialization.py SerializableResidue.__len__   1 1 0   0%
cvpack/serialization/serialization.py SerializableResidue.atoms   1 0 0   100%
cvpack/serialization/serialization.py SerializableForce.__init__   2 0 0   100%
cvpack/serialization/serialization.py SerializableForce.__getattr__   1 0 0   100%
cvpack/serialization/serialization.py SerializableForce.__getstate__   1 0 0   100%
cvpack/serialization/serialization.py SerializableForce.__setstate__   1 0 0   100%
cvpack/serialization/serialization.py serialize   1 0 0   100%
cvpack/serialization/serialization.py deserialize   1 0 0   100%
cvpack/serialization/serialization.py (no function)   29 0 0   100%
cvpack/sheet_rmsd_content.py SheetRMSDContent.__init__   13 1 0   92%
cvpack/sheet_rmsd_content.py (no function)   14 0 0   100%
cvpack/shortest_distance.py ShortestDistance.__init__   35 0 0   100%
cvpack/shortest_distance.py (no function)   12 0 0   100%
cvpack/torsion.py Torsion.__init__   5 0 0   100%
cvpack/torsion.py (no function)   7 0 0   100%
cvpack/torsion_similarity.py TorsionSimilarity.__init__   11 0 0   100%
cvpack/torsion_similarity.py (no function)   9 0 0   100%
cvpack/units/__init__.py (no function)   1 0 0   100%
cvpack/units/units.py _to_builtin   7 1 0   86%
cvpack/units/units.py _unit_names   10 0 0   100%
cvpack/units/units.py _evaluate_unit_node   20 0 0   100%
cvpack/units/units.py _parse_unit   11 2 0   82%
cvpack/units/units.py Unit.__init__   5 0 0   100%
cvpack/units/units.py Unit.__repr__   1 1 0   0%
cvpack/units/units.py Unit.__getstate__   9 1 0   89%
cvpack/units/units.py Unit.__setstate__   1 0 0   100%
cvpack/units/units.py Quantity.__init__   3 0 0   100%
cvpack/units/units.py Quantity.__repr__   1 0 0   100%
cvpack/units/units.py Quantity.__getstate__   1 0 0   100%
cvpack/units/units.py Quantity.__setstate__   1 0 0   100%
cvpack/units/units.py Quantity.value   1 0 0   100%
cvpack/units/units.py Quantity.in_md_units   1 1 0   0%
cvpack/units/units.py _md_exponents   7 0 0   100%
cvpack/units/units.py _md_unit   12 0 0   100%
cvpack/units/units.py in_md_units   11 1 0   91%
cvpack/units/units.py value_in_md_units   3 0 0   100%
cvpack/units/units.py (no function)   38 0 0   100%
cvpack/utils.py evaluate_in_context   24 1 0   96%
cvpack/utils.py convert_to_matrix   5 1 0   80%
cvpack/utils.py check_contiguous_residues   4 0 0   100%
cvpack/utils.py check_contiguous_residues.chain_index   3 0 0   100%
cvpack/utils.py find_unused_force_group   5 1 0   80%
cvpack/utils.py get_single_force_state   16 0 0   100%
cvpack/utils.py compute_effective_mass   10 1 0   90%
cvpack/utils.py preprocess_args   5 0 0   100%
cvpack/utils.py preprocess_args.convert   22 1 0   95%
cvpack/utils.py preprocess_args.wrapper   4 0 0   100%
cvpack/utils.py (no function)   19 0 0   100%
Total     1468 49 0   97%

No items found using the specified filter.