Method dictionary¶
Scan the public Python API by name. Each entry jumps to the heading on the hand-written module page. Examples live in tests/<module>_examples/ and are included on those pages.
Regenerate with python scripts/gen_api_dictionary.py.
Structure Manager¶
assign_secondary_structure_mapparse_pdbStructureManager.__init__StructureManager.align_to_axisStructureManager.apply_mempro_orientationStructureManager.assign_secondary_structureStructureManager.auto_detect_moleculesStructureManager.center_atomsStructureManager.delete_atomsStructureManager.get_chainsStructureManager.get_residuesStructureManager.get_secondary_structure_summaryStructureManager.get_structure_infoStructureManager.load_from_pdb_idStructureManager.load_structureStructureManager.rename_chainStructureManager.rename_chain_by_indicesStructureManager.rename_residuesStructureManager.rename_residues_by_indicesStructureManager.renumber_residuesStructureManager.renumber_residues_by_indicesStructureManager.rotate_atomsStructureManager.save_pdbStructureManager.select_atomsStructureManager.select_by_criteriaStructureManager.translate_atoms
Structure checker¶
Biological assembly¶
Preparation¶
complete_missing_heavy_atomscount_protein_hydrogensextract_summary_sectionmodify_pdb_based_on_summaryparse_summary_sectionPreparationManager.__init__PreparationManager.apply_disulfide_bondsPreparationManager.apply_protonation_statesPreparationManager.build_titration_figurePreparationManager.complete_missing_heavy_atomsPreparationManager.detect_disulfide_bondsPreparationManager.extract_summaryPreparationManager.get_available_statesPreparationManager.get_default_protonation_statePreparationManager.get_ph_titration_curvePreparationManager.get_residue_statisticsPreparationManager.parse_summaryPreparationManager.restore_original_residue_numbersPreparationManager.run_analysisPreparationManager.run_pdb4amber_with_cap_fixrun_propkastrip_protein_hydrogens
Residue mapping¶
Protein capping¶
cap_proteindetect_terminal_capsis_already_cappedProteinCapper.__init__ProteinCapper.remove_hydrogens_and_cap
Builder¶
Builder.__init__Builder.cancel_preparationBuilder.generate_preparation_inputsBuilder.modify_residue_names_for_propkaBuilder.prepare_systemBuilder.prepare_system_stage1_for_propkaBuilder.prepare_system_stage2_for_propkaBuilder.run_preparationBuilder.set_configurationBuilder.validate_system_inputsBuilder.wait_for_completion
Job monitor¶
JobMonitor.__init__JobMonitor.cleanup_stale_jobsJobMonitor.export_job_summaryJobMonitor.get_active_jobsJobMonitor.get_completed_jobsJobMonitor.get_jobJobMonitor.get_job_statisticsJobMonitor.refresh_jobJobMonitor.remove_jobJobMonitor.scan_for_jobsJobMonitor.set_working_directory
Force fields¶
ForceFieldManager.__init__ForceFieldManager.get_available_anionsForceFieldManager.get_available_cationsForceFieldManager.get_available_lipidsForceFieldManager.get_force_field_infoForceFieldManager.get_lipid_catalogForceFieldManager.get_lipid_force_fieldsForceFieldManager.get_protein_force_fieldsForceFieldManager.get_recommendationsForceFieldManager.get_water_modelsForceFieldManager.validate_combinationForceFieldManager.validate_ionForceFieldManager.validate_lipid
MemPrO¶
apply_orientation_transformcompute_orientation_transformMemPrO.__init__MemPrO.build_commandMemPrO.get_oriented_pdbMemPrO.is_availableMemPrO.parse_resultsMemPrO.run
Hydration¶
build_hydrate_inp_textcheck_packmol_availabledetect_hydrogen_statusestimate_cavity_volumehydrate_cavityprepare_hydration_jobpreview_hydrate_inprun_custom_packmol
Equilibration¶
adjust_protocol_for_missing_proteinAmberEquilibrationManager.__init__AmberEquilibrationManager.build_group_restraint_blockAmberEquilibrationManager.ensure_inpcrd_boxAmberEquilibrationManager.ensure_prmtop_boxAmberEquilibrationManager.find_system_filesAmberEquilibrationManager.generate_input_fileAmberEquilibrationManager.generate_mdin_fileAmberEquilibrationManager.generate_run_scriptAmberEquilibrationManager.get_default_selectionsAmberEquilibrationManager.get_default_stage_paramsAmberEquilibrationManager.setup_amber_equilibrationEquilibrationStage.replaceEquilibrationStage.to_dictGROMACSEquilibrationManager.__init__GROMACSEquilibrationManager.convert_from_amberGROMACSEquilibrationManager.find_system_filesGROMACSEquilibrationManager.generate_com_colvars_configGROMACSEquilibrationManager.generate_index_ndxGROMACSEquilibrationManager.generate_mdp_fileGROMACSEquilibrationManager.generate_posres_itpGROMACSEquilibrationManager.generate_run_scriptGROMACSEquilibrationManager.get_default_selectionsGROMACSEquilibrationManager.get_default_stage_paramsGROMACSEquilibrationManager.setup_gromacs_equilibrationNAMDEquilibrationManager.__init__NAMDEquilibrationManager.count_all_selectionsNAMDEquilibrationManager.count_selection_atomsNAMDEquilibrationManager.find_system_filesNAMDEquilibrationManager.generate_bilayer_thickness_colvarNAMDEquilibrationManager.generate_charmm_gui_config_fileNAMDEquilibrationManager.generate_colvars_fileNAMDEquilibrationManager.generate_com_colvars_configNAMDEquilibrationManager.generate_config_fileNAMDEquilibrationManager.generate_restraints_fileNAMDEquilibrationManager.generate_restraints_file_mdaNAMDEquilibrationManager.generate_run_scriptNAMDEquilibrationManager.get_default_selectionsNAMDEquilibrationManager.get_default_stage_paramsNAMDEquilibrationManager.load_charmm_gui_templateNAMDEquilibrationManager.run_equilibrationNAMDEquilibrationManager.setup_namd_equilibrationOpenMMEquilibrationManager.__init__OpenMMEquilibrationManager.find_system_filesOpenMMEquilibrationManager.generate_openmm_configOpenMMEquilibrationManager.generate_openmm_restraint_filesOpenMMEquilibrationManager.generate_run_scriptOpenMMEquilibrationManager.get_default_selectionsOpenMMEquilibrationManager.get_default_stage_paramsOpenMMEquilibrationManager.setup_openmm_equilibrationpdb_has_protein
Equilibration extras¶
NAMD / energy analysis¶
EnergyAnalyzer.__init__EnergyAnalyzer.get_available_propertiesEnergyAnalyzer.get_statisticsEnergyAnalyzer.plot_energyEnergyAnalyzer.plot_propertiesparse_namd_logrun_energetic_analysis
Trajectory analysis¶
prepare_structural_inputsrun_structural_analysisTrajectoryAnalyzer.__init__TrajectoryAnalyzer.calculate_distancesTrajectoryAnalyzer.calculate_radius_of_gyrationTrajectoryAnalyzer.calculate_rmsdTrajectoryAnalyzer.calculate_rmsfTrajectoryAnalyzer.clear_analysis_cacheTrajectoryAnalyzer.plot_distancesTrajectoryAnalyzer.plot_radius_of_gyrationTrajectoryAnalyzer.plot_rmsdTrajectoryAnalyzer.plot_rmsfTrajectoryAnalyzer.plot_summaryTrajectoryAnalyzer.time_array_for_analysis
Bilayer analysis¶
BilayerTrajectoryAnalyzer.__init__BilayerTrajectoryAnalyzer.calculate_area_per_lipidBilayerTrajectoryAnalyzer.calculate_membrane_thicknessBilayerTrajectoryAnalyzer.plot_area_per_lipidBilayerTrajectoryAnalyzer.plot_membrane_thicknessBilayerTrajectoryAnalyzer.universerun_bilayer_analysis
OpenMM analysis¶
OpenMMLogAnalyzer.__init__OpenMMLogAnalyzer.get_statisticsOpenMMLogAnalyzer.plot_energyOpenMMLogAnalyzer.plot_propertiesrun_openmm_energetic_analysis
GROMACS analysis¶
GROMACSLogEnergyAnalyzer.__init__GROMACSLogEnergyAnalyzer.get_available_propertiesGROMACSLogEnergyAnalyzer.get_statistics
Amber analysis¶
AmberLogEnergyAnalyzer.__init__AmberLogEnergyAnalyzer.get_available_propertiesrun_amber_energetic_analysis