Coverage report: 44%

Files Functions Classes

coverage.py v7.13.0, created at 2025-12-13 01:26 -0600

File function   statements missing excluded   coverage
src / molecular_simulations / __init__.py (no function)   1 0 0   100%
src / molecular_simulations / analysis / __init__.py (no function)   6 0 0   100%
src / molecular_simulations / analysis / autocluster.py GenericDataloader.__init__   2 0 0   100%
src / molecular_simulations / analysis / autocluster.py GenericDataloader.load_data   13 0 0   100%
src / molecular_simulations / analysis / autocluster.py GenericDataloader.data   1 0 0   100%
src / molecular_simulations / analysis / autocluster.py GenericDataloader.shape   3 0 0   100%
src / molecular_simulations / analysis / autocluster.py PeriodicDataloader.__init__   1 0 0   100%
src / molecular_simulations / analysis / autocluster.py PeriodicDataloader.load_data   7 0 0   100%
src / molecular_simulations / analysis / autocluster.py PeriodicDataloader.remove_periodicity   6 0 0   100%
src / molecular_simulations / analysis / autocluster.py AutoKMeans.__init__   7 0 0   100%
src / molecular_simulations / analysis / autocluster.py AutoKMeans.run   5 5 0   0%
src / molecular_simulations / analysis / autocluster.py AutoKMeans.reduce_dimensionality   1 0 0   100%
src / molecular_simulations / analysis / autocluster.py AutoKMeans.sweep_n_clusters   13 0 0   100%
src / molecular_simulations / analysis / autocluster.py AutoKMeans.map_centers_to_frames   10 0 0   100%
src / molecular_simulations / analysis / autocluster.py AutoKMeans.save_centers   2 0 0   100%
src / molecular_simulations / analysis / autocluster.py AutoKMeans.save_labels   10 1 0   90%
src / molecular_simulations / analysis / autocluster.py Decomposition.__init__   2 0 0   100%
src / molecular_simulations / analysis / autocluster.py Decomposition.fit   1 0 0   100%
src / molecular_simulations / analysis / autocluster.py Decomposition.transform   1 0 0   100%
src / molecular_simulations / analysis / autocluster.py Decomposition.fit_transform   1 0 0   100%
src / molecular_simulations / analysis / autocluster.py (no function)   35 0 0   100%
src / molecular_simulations / analysis / constant_pH_analysis.py UWHAMSolver.__init__   4 0 0   100%
src / molecular_simulations / analysis / constant_pH_analysis.py UWHAMSolver.load_data   26 0 0   100%
src / molecular_simulations / analysis / constant_pH_analysis.py UWHAMSolver.solve   44 3 0   93%
src / molecular_simulations / analysis / constant_pH_analysis.py UWHAMSolver.compute_log_weights   12 0 0   100%
src / molecular_simulations / analysis / constant_pH_analysis.py UWHAMSolver.compute_expectation_at_pH   4 0 0   100%
src / molecular_simulations / analysis / constant_pH_analysis.py UWHAMSolver.get_occupancy_for_resid   1 0 0   100%
src / molecular_simulations / analysis / constant_pH_analysis.py TitrationCurve.__init__   14 0 0   100%
src / molecular_simulations / analysis / constant_pH_analysis.py TitrationCurve.parse_log   25 0 0   100%
src / molecular_simulations / analysis / constant_pH_analysis.py TitrationCurve.prepare   10 1 0   90%
src / molecular_simulations / analysis / constant_pH_analysis.py TitrationCurve.compute_titrations_curvefit   22 5 0   77%
src / molecular_simulations / analysis / constant_pH_analysis.py TitrationCurve.compute_titrations_weighted   29 29 0   0%
src / molecular_simulations / analysis / constant_pH_analysis.py TitrationCurve.compute_titrations_bootstrap   41 41 0   0%
src / molecular_simulations / analysis / constant_pH_analysis.py TitrationCurve.compute_titrations   7 7 0   0%
src / molecular_simulations / analysis / constant_pH_analysis.py TitrationCurve.postprocess   15 15 0   0%
src / molecular_simulations / analysis / constant_pH_analysis.py TitrationCurve.plot   1 1 0   0%
src / molecular_simulations / analysis / constant_pH_analysis.py TitrationCurve.diagnose_residue   25 25 0   0%
src / molecular_simulations / analysis / constant_pH_analysis.py TitrationCurve.hill_equation   1 0 0   100%
src / molecular_simulations / analysis / constant_pH_analysis.py TitrationCurve.protonation_mapping   1 0 0   100%
src / molecular_simulations / analysis / constant_pH_analysis.py TitrationCurve.canonical_resname   1 0 0   100%
src / molecular_simulations / analysis / constant_pH_analysis.py TitrationCurve.compare_methods   7 7 0   0%
src / molecular_simulations / analysis / constant_pH_analysis.py TitrationAnalyzer.__init__   14 0 0   100%
src / molecular_simulations / analysis / constant_pH_analysis.py TitrationAnalyzer.run   48 31 0   35%
src / molecular_simulations / analysis / constant_pH_analysis.py TitrationAnalyzer._generate_comparison   1 1 0   0%
src / molecular_simulations / analysis / constant_pH_analysis.py TitrationAnalyzer.summary   32 32 0   0%
src / molecular_simulations / analysis / constant_pH_analysis.py TitrationAnalyzer.get_results   9 7 0   22%
src / molecular_simulations / analysis / constant_pH_analysis.py TitrationAnalyzer.plot_residue   47 47 0   0%
src / molecular_simulations / analysis / constant_pH_analysis.py TitrationAnalyzer.plot_all   21 21 0   0%
src / molecular_simulations / analysis / constant_pH_analysis.py TitrationAnalyzer.plot_summary   39 39 0   0%
src / molecular_simulations / analysis / constant_pH_analysis.py TitrationAnalyzer.save_results   15 3 0   80%
src / molecular_simulations / analysis / constant_pH_analysis.py TitrationAnalyzer.save_results.save_df   9 4 0   56%
src / molecular_simulations / analysis / constant_pH_analysis.py TitrationAnalyzer.diagnose   3 3 0   0%
src / molecular_simulations / analysis / constant_pH_analysis.py TitrationAnalyzer.recommend_protonation   73 73 0   0%
src / molecular_simulations / analysis / constant_pH_analysis.py TitrationAnalyzer.get_protonation_string   5 5 0   0%
src / molecular_simulations / analysis / constant_pH_analysis.py TitrationAnalyzer.export_protonation_states   18 18 0   0%
src / molecular_simulations / analysis / constant_pH_analysis.py TitrationAnalyzer.plot_protonation_summary   40 40 0   0%
src / molecular_simulations / analysis / constant_pH_analysis.py TitrationAnalyzer.__repr__   2 0 0   100%
src / molecular_simulations / analysis / constant_pH_analysis.py analyze_cph   13 8 0   38%
src / molecular_simulations / analysis / constant_pH_analysis.py (no function)   75 21 2   72%
src / molecular_simulations / analysis / cov_ppi.py PPInteractions.__init__   11 0 0   100%
src / molecular_simulations / analysis / cov_ppi.py PPInteractions.run   12 12 0   0%
src / molecular_simulations / analysis / cov_ppi.py PPInteractions.compute_interactions   10 10 0   0%
src / molecular_simulations / analysis / cov_ppi.py PPInteractions.get_covariance   31 31 0   0%
src / molecular_simulations / analysis / cov_ppi.py PPInteractions.res_map   6 0 0   100%
src / molecular_simulations / analysis / cov_ppi.py PPInteractions.interpret_covariance   20 0 0   100%
src / molecular_simulations / analysis / cov_ppi.py PPInteractions.identify_interaction_type   11 0 0   100%
src / molecular_simulations / analysis / cov_ppi.py PPInteractions.analyze_saltbridge   27 27 0   0%
src / molecular_simulations / analysis / cov_ppi.py PPInteractions.analyze_hbond   5 5 0   0%
src / molecular_simulations / analysis / cov_ppi.py PPInteractions.analyze_hydrophobic   14 0 0   100%
src / molecular_simulations / analysis / cov_ppi.py PPInteractions.survey_donors_acceptors   17 17 0   0%
src / molecular_simulations / analysis / cov_ppi.py PPInteractions.evaluate_hbond   14 1 0   93%
src / molecular_simulations / analysis / cov_ppi.py PPInteractions.save   2 0 0   100%
src / molecular_simulations / analysis / cov_ppi.py PPInteractions.plot_results   10 10 0   0%
src / molecular_simulations / analysis / cov_ppi.py PPInteractions.parse_results   7 0 0   100%
src / molecular_simulations / analysis / cov_ppi.py PPInteractions.make_plot   9 9 0   0%
src / molecular_simulations / analysis / cov_ppi.py (no function)   31 0 0   100%
src / molecular_simulations / analysis / fingerprinter.py unravel_index   5 5 0   0%
src / molecular_simulations / analysis / fingerprinter.py _dist_mat   10 10 0   0%
src / molecular_simulations / analysis / fingerprinter.py dist_mat   3 3 0   0%
src / molecular_simulations / analysis / fingerprinter.py electrostatic   10 10 0   0%
src / molecular_simulations / analysis / fingerprinter.py electrostatic_sum   7 7 0   0%
src / molecular_simulations / analysis / fingerprinter.py lennard_jones   9 9 0   0%
src / molecular_simulations / analysis / fingerprinter.py lennard_jones_sum   7 7 0   0%
src / molecular_simulations / analysis / fingerprinter.py fingerprints   8 8 0   0%
src / molecular_simulations / analysis / fingerprinter.py Fingerprinter.__init__   12 2 0   83%
src / molecular_simulations / analysis / fingerprinter.py Fingerprinter.assign_nonbonded_params   10 10 0   0%
src / molecular_simulations / analysis / fingerprinter.py Fingerprinter.load_pdb   8 4 0   50%
src / molecular_simulations / analysis / fingerprinter.py Fingerprinter.assign_residue_mapping   6 6 0   0%
src / molecular_simulations / analysis / fingerprinter.py Fingerprinter.iterate_frames   4 4 0   0%
src / molecular_simulations / analysis / fingerprinter.py Fingerprinter.calculate_fingerprints   3 3 0   0%
src / molecular_simulations / analysis / fingerprinter.py Fingerprinter.run   4 4 0   0%
src / molecular_simulations / analysis / fingerprinter.py Fingerprinter.save   1 1 0   0%
src / molecular_simulations / analysis / fingerprinter.py (no function)   34 0 0   100%
src / molecular_simulations / analysis / interaction_energy.py InteractionEnergy.__init__   1 1 0   0%
src / molecular_simulations / analysis / interaction_energy.py InteractionEnergy.compute   1 1 0   0%
src / molecular_simulations / analysis / interaction_energy.py InteractionEnergy.energy   1 1 0   0%
src / molecular_simulations / analysis / interaction_energy.py InteractionEnergy.get_selection   1 1 0   0%
src / molecular_simulations / analysis / interaction_energy.py StaticInteractionEnergy.__init__   5 0 0   100%
src / molecular_simulations / analysis / interaction_energy.py StaticInteractionEnergy.get_system   11 11 0   0%
src / molecular_simulations / analysis / interaction_energy.py StaticInteractionEnergy.compute   37 37 0   0%
src / molecular_simulations / analysis / interaction_energy.py StaticInteractionEnergy.get_selection   8 0 0   100%
src / molecular_simulations / analysis / interaction_energy.py StaticInteractionEnergy.fix_pdb   6 0 0   100%
src / molecular_simulations / analysis / interaction_energy.py StaticInteractionEnergy.interactions   1 0 0   100%
src / molecular_simulations / analysis / interaction_energy.py StaticInteractionEnergy.energy   5 0 0   100%
src / molecular_simulations / analysis / interaction_energy.py InteractionEnergyFrame.__init__   3 0 0   100%
src / molecular_simulations / analysis / interaction_energy.py InteractionEnergyFrame.get_system   2 0 0   100%
src / molecular_simulations / analysis / interaction_energy.py DynamicInteractionEnergy.__init__   7 0 0   100%
src / molecular_simulations / analysis / interaction_energy.py DynamicInteractionEnergy.compute_energies   13 13 0   0%
src / molecular_simulations / analysis / interaction_energy.py DynamicInteractionEnergy.build_system   10 0 0   100%
src / molecular_simulations / analysis / interaction_energy.py DynamicInteractionEnergy.load_traj   1 0 0   100%
src / molecular_simulations / analysis / interaction_energy.py DynamicInteractionEnergy.setup_pbar   1 1 0   0%
src / molecular_simulations / analysis / interaction_energy.py (no function)   44 0 0   100%
src / molecular_simulations / analysis / ipSAE.py ipSAE.__init__   5 0 0   100%
src / molecular_simulations / analysis / ipSAE.py ipSAE.parse_structure_file   4 0 0   100%
src / molecular_simulations / analysis / ipSAE.py ipSAE.prepare_scorer   4 0 0   100%
src / molecular_simulations / analysis / ipSAE.py ipSAE.run   9 9 0   0%
src / molecular_simulations / analysis / ipSAE.py ipSAE.save_scores   1 0 0   100%
src / molecular_simulations / analysis / ipSAE.py ipSAE.load_pLDDT_file   3 0 0   100%
src / molecular_simulations / analysis / ipSAE.py ipSAE.load_PAE_file   2 0 0   100%
src / molecular_simulations / analysis / ipSAE.py ScoreCalculator.__init__   8 0 0   100%
src / molecular_simulations / analysis / ipSAE.py ScoreCalculator.compute_scores   11 0 0   100%
src / molecular_simulations / analysis / ipSAE.py ScoreCalculator.compute_pDockQ_scores   26 0 0   100%
src / molecular_simulations / analysis / ipSAE.py ScoreCalculator.compute_LIS   10 0 0   100%
src / molecular_simulations / analysis / ipSAE.py ScoreCalculator.compute_ipTM_ipSAE   19 1 0   95%
src / molecular_simulations / analysis / ipSAE.py ScoreCalculator.get_max_values   11 0 0   100%
src / molecular_simulations / analysis / ipSAE.py ScoreCalculator.permute_chains   6 0 0   100%
src / molecular_simulations / analysis / ipSAE.py ScoreCalculator.pDockQ_score   1 0 0   100%
src / molecular_simulations / analysis / ipSAE.py ScoreCalculator.pDockQ2_score   1 0 0   100%
src / molecular_simulations / analysis / ipSAE.py ScoreCalculator.compute_pTM   1 0 0   100%
src / molecular_simulations / analysis / ipSAE.py ScoreCalculator.compute_d0   5 0 0   100%
src / molecular_simulations / analysis / ipSAE.py ModelParser.__init__   5 0 0   100%
src / molecular_simulations / analysis / ipSAE.py ModelParser.parse_structure_file   26 7 0   73%
src / molecular_simulations / analysis / ipSAE.py ModelParser.classify_chains   8 0 0   100%
src / molecular_simulations / analysis / ipSAE.py ModelParser.nucleic_acids   1 0 0   100%
src / molecular_simulations / analysis / ipSAE.py ModelParser.parse_pdb_line   9 0 0   100%
src / molecular_simulations / analysis / ipSAE.py ModelParser.parse_cif_line   12 0 0   100%
src / molecular_simulations / analysis / ipSAE.py ModelParser.package_line   1 0 0   100%
src / molecular_simulations / analysis / ipSAE.py (no function)   45 0 0   100%
src / molecular_simulations / analysis / sasa.py SASA.__init__   14 0 0   100%
src / molecular_simulations / analysis / sasa.py SASA.get_sphere   11 0 0   100%
src / molecular_simulations / analysis / sasa.py SASA.measure_sasa   14 0 0   100%
src / molecular_simulations / analysis / sasa.py SASA._prepare   2 0 0   100%
src / molecular_simulations / analysis / sasa.py SASA._single_frame   5 0 0   100%
src / molecular_simulations / analysis / sasa.py SASA._conclude   2 0 0   100%
src / molecular_simulations / analysis / sasa.py RelativeSASA.__init__   3 0 0   100%
src / molecular_simulations / analysis / sasa.py RelativeSASA._prepare   3 0 0   100%
src / molecular_simulations / analysis / sasa.py RelativeSASA._single_frame   14 1 0   93%
src / molecular_simulations / analysis / sasa.py RelativeSASA._conclude   3 0 0   100%
src / molecular_simulations / analysis / sasa.py (no function)   20 0 0   100%
src / molecular_simulations / analysis / utils.py EmbedData.__init__   4 0 0   100%
src / molecular_simulations / analysis / utils.py EmbedData.embed   3 0 0   100%
src / molecular_simulations / analysis / utils.py EmbedData.embed_selection   3 0 0   100%
src / molecular_simulations / analysis / utils.py EmbedData.write_new_pdb   5 0 0   100%
src / molecular_simulations / analysis / utils.py EmbedEnergyData.__init__   2 0 0   100%
src / molecular_simulations / analysis / utils.py EmbedEnergyData.preprocess   12 0 0   100%
src / molecular_simulations / analysis / utils.py EmbedEnergyData.sanitize_data   5 0 0   100%
src / molecular_simulations / analysis / utils.py (no function)   16 0 0   100%
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src / molecular_simulations / build / __init__.py (no function)   12 0 0   100%
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src / molecular_simulations / build / build_amber.py ImplicitSolvent.tleap_it   3 0 0   100%
src / molecular_simulations / build / build_amber.py ImplicitSolvent.write_leap   4 0 0   100%
src / molecular_simulations / build / build_amber.py ImplicitSolvent.temp_tleap   5 0 0   100%
src / molecular_simulations / build / build_amber.py ExplicitSolvent.__init__   8 0 0   100%
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src / molecular_simulations / build / build_amber.py (no function)   25 0 0   100%
src / molecular_simulations / build / build_calvados.py CGBuilder.__init__   23 0 0   100%
src / molecular_simulations / build / build_calvados.py CGBuilder.from_dict   26 0 0   100%
src / molecular_simulations / build / build_calvados.py CGBuilder.build   2 0 0   100%
src / molecular_simulations / build / build_calvados.py CGBuilder.write_config   3 0 0   100%
src / molecular_simulations / build / build_calvados.py CGBuilder.write_components   4 0 0   100%
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src / molecular_simulations / logging_config.py (no function)   7 0 0   100%
src / molecular_simulations / simulate / __init__.py (no function)   2 0 0   100%
src / molecular_simulations / simulate / mmpbsa.py _run_energy_calculation   24 24 0   0%
src / molecular_simulations / simulate / mmpbsa.py _run_sasa_calculation   31 31 0   0%
src / molecular_simulations / simulate / mmpbsa.py MMPBSA.__init__   21 21 0   0%
src / molecular_simulations / simulate / mmpbsa.py MMPBSA.run   8 8 0   0%
src / molecular_simulations / simulate / mmpbsa.py MMPBSA._run_serial   5 5 0   0%
src / molecular_simulations / simulate / mmpbsa.py MMPBSA._run_frame_parallel   50 50 0   0%
src / molecular_simulations / simulate / mmpbsa.py MMPBSA._write_sasa_script   5 5 0   0%
src / molecular_simulations / simulate / mmpbsa.py MMPBSA._combine_sasa_chunks   16 16 0   0%
src / molecular_simulations / simulate / mmpbsa.py MMPBSA._combine_sasa_chunks.extract_chunk_idx   2 2 0   0%
src / molecular_simulations / simulate / mmpbsa.py MMPBSA._combine_energy_chunks   15 15 0   0%
src / molecular_simulations / simulate / mmpbsa.py MMPBSA._combine_energy_chunks.extract_chunk_idx   2 2 0   0%
src / molecular_simulations / simulate / mmpbsa.py MMPBSA.calculate_sasa   5 5 0   0%
src / molecular_simulations / simulate / mmpbsa.py MMPBSA.calculate_energy   2 2 0   0%
src / molecular_simulations / simulate / mmpbsa.py MMPBSA.write_mdins   7 7 0   0%
src / molecular_simulations / simulate / mmpbsa.py MMPBSA._verify_combined_outputs   32 32 0   0%
src / molecular_simulations / simulate / mmpbsa.py OutputAnalyzer.__init__   9 9 0   0%
src / molecular_simulations / simulate / mmpbsa.py OutputAnalyzer.parse_outputs   14 14 0   0%
src / molecular_simulations / simulate / mmpbsa.py OutputAnalyzer.read_sasa   3 3 0   0%
src / molecular_simulations / simulate / mmpbsa.py OutputAnalyzer.read_GB   4 4 0   0%
src / molecular_simulations / simulate / mmpbsa.py OutputAnalyzer.read_PB   4 4 0   0%
src / molecular_simulations / simulate / mmpbsa.py OutputAnalyzer.parse_energy_file   9 9 0   0%
src / molecular_simulations / simulate / mmpbsa.py OutputAnalyzer.parse_energy_file_OLD   15 15 0   0%
src / molecular_simulations / simulate / mmpbsa.py OutputAnalyzer.check_bonded_terms   16 16 0   0%
src / molecular_simulations / simulate / mmpbsa.py OutputAnalyzer.generate_summary   17 17 0   0%
src / molecular_simulations / simulate / mmpbsa.py OutputAnalyzer.compute_dG   26 26 0   0%
src / molecular_simulations / simulate / mmpbsa.py OutputAnalyzer.pretty_print   24 24 0   0%
src / molecular_simulations / simulate / mmpbsa.py OutputAnalyzer.parse_line   10 10 0   0%
src / molecular_simulations / simulate / mmpbsa.py FileHandler.__init__   17 17 0   0%
src / molecular_simulations / simulate / mmpbsa.py FileHandler.prepare_topologies   6 6 0   0%
src / molecular_simulations / simulate / mmpbsa.py FileHandler.prepare_trajectories   13 13 0   0%
src / molecular_simulations / simulate / mmpbsa.py FileHandler._count_frames   16 16 0   0%
src / molecular_simulations / simulate / mmpbsa.py FileHandler._estimate_frames   11 11 0   0%
src / molecular_simulations / simulate / mmpbsa.py FileHandler._split_trajectories   19 19 0   0%
src / molecular_simulations / simulate / mmpbsa.py FileHandler.files   2 2 0   0%
src / molecular_simulations / simulate / mmpbsa.py FileHandler.files_chunked   6 6 0   0%
src / molecular_simulations / simulate / mmpbsa.py FileHandler.write_file   4 4 0   0%
src / molecular_simulations / simulate / mmpbsa.py (no function)   73 0 0   100%
src / molecular_simulations / simulate / multires_simulator.py sander_min_defaults.__init__   1 0 0   100%
src / molecular_simulations / simulate / multires_simulator.py sander_minimize   11 0 0   100%
src / molecular_simulations / simulate / multires_simulator.py MultiResolutionSimulator.__init__   8 0 0   100%
src / molecular_simulations / simulate / multires_simulator.py MultiResolutionSimulator.from_toml   18 0 0   100%
src / molecular_simulations / simulate / multires_simulator.py MultiResolutionSimulator.strip_solvent   5 0 0   100%
src / molecular_simulations / simulate / multires_simulator.py MultiResolutionSimulator.run_rounds   47 47 0   0%
src / molecular_simulations / simulate / multires_simulator.py (no function)   39 0 0   100%
src / molecular_simulations / simulate / omm_simulator.py Simulator.__init__   29 29 0   0%
src / molecular_simulations / simulate / omm_simulator.py Simulator.setup_barostat   6 6 0   0%
src / molecular_simulations / simulate / omm_simulator.py Simulator.load_system   8 8 0   0%
src / molecular_simulations / simulate / omm_simulator.py Simulator.load_amber_files   5 5 0   0%
src / molecular_simulations / simulate / omm_simulator.py Simulator.load_charmm_files   10 10 0   0%
src / molecular_simulations / simulate / omm_simulator.py Simulator.setup_sim   3 3 0   0%
src / molecular_simulations / simulate / omm_simulator.py Simulator.run   12 12 0   0%
src / molecular_simulations / simulate / omm_simulator.py Simulator.equilibrate   10 10 0   0%
src / molecular_simulations / simulate / omm_simulator.py Simulator.production   10 10 0   0%
src / molecular_simulations / simulate / omm_simulator.py Simulator.load_checkpoint   7 7 0   0%
src / molecular_simulations / simulate / omm_simulator.py Simulator.attach_reporters   2 2 0   0%
src / molecular_simulations / simulate / omm_simulator.py Simulator._heating   14 14 0   0%
src / molecular_simulations / simulate / omm_simulator.py Simulator._equilibrate   15 15 0   0%
src / molecular_simulations / simulate / omm_simulator.py Simulator._production   4 4 0   0%
src / molecular_simulations / simulate / omm_simulator.py Simulator.get_restraint_indices   5 5 0   0%
src / molecular_simulations / simulate / omm_simulator.py Simulator.check_num_steps_left   24 24 0   0%
src / molecular_simulations / simulate / omm_simulator.py Simulator.add_backbone_posres   12 12 0   0%
src / molecular_simulations / simulate / omm_simulator.py ImplicitSimulator.__init__   5 5 0   0%
src / molecular_simulations / simulate / omm_simulator.py ImplicitSimulator.load_amber_files   5 5 0   0%
src / molecular_simulations / simulate / omm_simulator.py ImplicitSimulator.equilibrate   14 14 0   0%
src / molecular_simulations / simulate / omm_simulator.py ImplicitSimulator.production   9 9 0   0%
src / molecular_simulations / simulate / omm_simulator.py CustomForcesSimulator.__init__   2 2 0   0%
src / molecular_simulations / simulate / omm_simulator.py CustomForcesSimulator.load_amber_files   8 8 0   0%
src / molecular_simulations / simulate / omm_simulator.py CustomForcesSimulator.add_forces   3 3 0   0%
src / molecular_simulations / simulate / omm_simulator.py Minimizer.__init__   8 0 0   100%
src / molecular_simulations / simulate / omm_simulator.py Minimizer.minimize   8 8 0   0%
src / molecular_simulations / simulate / omm_simulator.py Minimizer.load_files   8 8 0   0%
src / molecular_simulations / simulate / omm_simulator.py Minimizer.load_amber   4 4 0   0%
src / molecular_simulations / simulate / omm_simulator.py Minimizer.load_gromacs   5 5 0   0%
src / molecular_simulations / simulate / omm_simulator.py Minimizer.load_pdb   5 5 0   0%
src / molecular_simulations / simulate / omm_simulator.py (no function)   48 0 0   100%
src / molecular_simulations / utils / __init__.py (no function)   5 0 0   100%
src / molecular_simulations / utils / amber_utils.py assign_chainids   11 0 0   100%
src / molecular_simulations / utils / amber_utils.py assign_chainids.get_chain_label   5 0 0   100%
src / molecular_simulations / utils / amber_utils.py (no function)   3 0 0   100%
src / molecular_simulations / utils / mda_utils.py trim_trajectory   16 16 0   0%
src / molecular_simulations / utils / mda_utils.py (no function)   5 5 0   0%
src / molecular_simulations / utils / parsl_settings.py BaseSettings.dump_yaml   2 0 0   100%
src / molecular_simulations / utils / parsl_settings.py BaseSettings.from_yaml   3 0 0   100%
src / molecular_simulations / utils / parsl_settings.py BaseComputeSettings.config_factory   0 0 0   100%
src / molecular_simulations / utils / parsl_settings.py LocalSettings.config_factory   1 0 0   100%
src / molecular_simulations / utils / parsl_settings.py PolarisSettings.config_factory   1 0 0   100%
src / molecular_simulations / utils / parsl_settings.py AuroraSettings.config_factory   1 0 0   100%
src / molecular_simulations / utils / parsl_settings.py (no function)   52 0 0   100%
Total     3475 1956 2   44%

No items found using the specified filter.