Dynamic Module Documentation
Contents
- pyCADD.Dynamic package
- Submodules
- pyCADD.Dynamic.analysis module
- pyCADD.Dynamic.cli module
- pyCADD.Dynamic.common module
ProcessorProcessor.work_dirProcessor.apoProcessor.pro_fileProcessor.mol2_fileProcessor.frcmod_fileProcessor.comsolvate_topfileProcessor.comsolvate_crdfileProcessor.comsolvate_pdbfileProcessor.com_topfileProcessor.pro_topfileProcessor.lig_topfileProcessor.md_process_listProcessor.__init__()Processor.protein_prepare()Processor.molecule_prepare()Processor.load_processed_profile()Processor.load_processed_molfile()Processor.load_frcmod_file()Processor.leap_prepare()Processor.set_prepared_file()Processor.get_water_resnum()Processor.create_minimize_input()Processor.create_heat_input()Processor.create_nvt_input()Processor.create_npt_input()Processor.add_process()Processor.add_minimize_process()Processor.add_nvt_process()Processor.add_heat_process()Processor.add_npt_process()
SimulatorAnalyzerAnalyzer.traj_file_pathAnalyzer.traj_fileAnalyzer.trajAnalyzer.top_file_pathAnalyzer.top_fileAnalyzer.__init__()Analyzer.load_traj()Analyzer.load_mdout()Analyzer.load_topfile()Analyzer.calc_rmsd()Analyzer.calc_rmsf()Analyzer.calc_hbond()Analyzer.trace_distance()Analyzer.trace_angle()Analyzer.extract_frame()Analyzer.extract_frames()Analyzer.extract_lowest_energy_st()Analyzer.create_energy_inputfile()Analyzer.run_energy_calc()
- pyCADD.Dynamic.constant module
- pyCADD.Dynamic.core module
protein_prepare()molecule_prepare()leap_prepare()BaseProcessMDProcessMDProcess.control_cfgMDProcess.is_minimizeMDProcess.is_restrainedMDProcess.is_productionMDProcess.total_stepMDProcess.step_sizeMDProcess.cmdMDProcess.topology_fileMDProcess.inpcrd_fileMDProcess.mdout_file_pathMDProcess.mdcrd_file_pathMDProcess.mdrst_file_pathMDProcess.__init__()MDProcess.run()
MinimizeProcessNPTProcessNVTProcessrun_simulation()create_energy_inputfile()run_energy_calculation()
- pyCADD.Dynamic.template module
BaseConstructorBaseConstructor._state_dictBaseConstructor._state_keysBaseConstructor.__init__()BaseConstructor.get_state_dict()BaseConstructor.to_string()BaseConstructor.to_str()BaseConstructor.to_dict()BaseConstructor.save()BaseConstructor.add_attr()BaseConstructor.get_attr()BaseConstructor.set_attr()BaseConstructor.del_attr()
LeapConstructorSimulationConstructorAnalysisConstructorMultiConstructorManagerLeapInputMinimizeInputRestrainedMinimizeInputNVTInputHeatInputNPTInputMMGBSAInput
- pyCADD.Dynamic.utils module
- Module contents
- Dynamic User Guide