Python Module Index

p


	p
	`pygromos`
	`pygromos.analysis`
	`pygromos.analysis.coordinate_analysis`
	`pygromos.analysis.energy_analysis`
	`pygromos.analysis.error_estimate`
	`pygromos.analysis.free_energy_calculation`
	`pygromos.data`
	`pygromos.data.ene_ana_libs`
	`pygromos.data.ff`
	`pygromos.data.ff.addAtomType`
	`pygromos.data.ff.atomType`
	`pygromos.data.ff.Gromos2016H66`
	`pygromos.data.ff.Gromos54A7`
	`pygromos.data.ff.MixHexGromos54A7`
	`pygromos.data.simulation_parameters_templates`
	`pygromos.data.solvent_coordinates`
	`pygromos.data.topology_templates`
	`pygromos.files`
	`pygromos.files.blocks`
	`pygromos.files.blocks.coord_blocks`
	`pygromos.files.blocks.imd_blocks`
	`pygromos.files.blocks.miscBlocks`
	`pygromos.files.blocks.mtb_blocks`
	`pygromos.files.blocks.pertubation_blocks`
	`pygromos.files.blocks.qmmm_blocks`
	`pygromos.files.blocks.replica_exchange_blocks`
	`pygromos.files.blocks.topology_blocks`
	`pygromos.files.coord`
	`pygromos.files.coord.cnf`
	`pygromos.files.coord.posres`
	`pygromos.files.coord.refpos`
	`pygromos.files.forcefield`
	`pygromos.files.forcefield.amber`
	`pygromos.files.forcefield.amber.amberff`
	`pygromos.files.forcefield.gromos`
	`pygromos.files.forcefield.gromos.gromosff`
	`pygromos.files.forcefield.openff`
	`pygromos.files.forcefield.openff.openff`
	`pygromos.files.forcefield.serenityff`
	`pygromos.files.forcefield.serenityff.serenityff`
	`pygromos.files.forcefield.serenityff.serenityff_data`
	`pygromos.files.gromos_system`
	`pygromos.files.gromos_system.gromos_system`
	`pygromos.files.otherfiles`
	`pygromos.files.otherfiles.new_repdat`
	`pygromos.files.otherfiles.noe_output`
	`pygromos.files.otherfiles.repdat`
	`pygromos.files.otherfiles.residue_library`
	`pygromos.files.qmmm`
	`pygromos.files.qmmm.qmmm`
	`pygromos.files.simulation_parameters`
	`pygromos.files.simulation_parameters.imd`
	`pygromos.files.topology`
	`pygromos.files.topology.disres`
	`pygromos.files.topology.ifp`
	`pygromos.files.topology.mtb`
	`pygromos.files.topology.ptp`
	`pygromos.files.topology.top`
	`pygromos.files.trajectory`
	`pygromos.files.trajectory.blocks`
	`pygromos.files.trajectory.blocks.energy_trajectory_subblock`
	`pygromos.files.trajectory.blocks.trajectory_blocks`
	`pygromos.files.trajectory.trc`
	`pygromos.files.trajectory.tre`
	`pygromos.files.trajectory.tre_field_libs`
	`pygromos.files.trajectory.tre_field_libs.ene_fields`
	`pygromos.files.trajectory.trg`
	`pygromos.gromos`
	`pygromos.gromos.compile_gromos`
	`pygromos.gromos.gromosBashSyntaxParser`
	`pygromos.gromos.gromosPP`
	`pygromos.gromos.gromosXX`
	`pygromos.gromos.pyGromosPP`
	`pygromos.gromos.pyGromosPP.com_top`
	`pygromos.gromos.pyGromosPP.ran_box`
	`pygromos.pygromos`
	`pygromos.simulations`
	`pygromos.simulations.approaches`
	`pygromos.simulations.approaches.hvap_calculation`
	`pygromos.simulations.approaches.hvap_calculation.hvap_calculation`
	`pygromos.simulations.approaches.hvap_calculation.hvap_input_files`
	`pygromos.simulations.hpc_queuing`
	`pygromos.simulations.hpc_queuing.job_scheduling`
	`pygromos.simulations.hpc_queuing.job_scheduling.file_management`
	`pygromos.simulations.hpc_queuing.job_scheduling.module_functions`
	`pygromos.simulations.hpc_queuing.job_scheduling.schedulers`
	`pygromos.simulations.hpc_queuing.job_scheduling.schedulers.scheduler_functions`
	`pygromos.simulations.hpc_queuing.job_scheduling.schedulers.simulation_scheduler`
	`pygromos.simulations.hpc_queuing.job_scheduling.workers`
	`pygromos.simulations.hpc_queuing.job_scheduling.workers.analysis_workers`
	`pygromos.simulations.hpc_queuing.job_scheduling.workers.analysis_workers.simulation_analysis`
	`pygromos.simulations.hpc_queuing.job_scheduling.workers.simulation_workers`
	`pygromos.simulations.hpc_queuing.job_scheduling.workers.simulation_workers.clean_up_simulation_files`
	`pygromos.simulations.hpc_queuing.job_scheduling.workers.simulation_workers.simulation_run_worker`
	`pygromos.simulations.hpc_queuing.submission_systems`
	`pygromos.simulations.hpc_queuing.submission_systems.dummy`
	`pygromos.simulations.hpc_queuing.submission_systems.local`
	`pygromos.simulations.hpc_queuing.submission_systems.lsf`
	`pygromos.simulations.hpc_queuing.submission_systems.submission_job`
	`pygromos.simulations.modules`
	`pygromos.simulations.modules.general_analysis_modules`
	`pygromos.simulations.modules.general_simulation_modules`
	`pygromos.simulations.modules.preset_simulation_modules`
	`pygromos.simulations.modules.ti_modules`
	`pygromos.tests`
	`pygromos.tests.in_testfiles`
	`pygromos.tests.out_testresults`
	`pygromos.tests.test_analysis`
	`pygromos.tests.test_analysis.test_error_estimate`
	`pygromos.tests.test_analysis.test_freeEnergy`
	`pygromos.tests.test_approaches`
	`pygromos.tests.test_approaches.test_solvation_free_ernergy`
	`pygromos.tests.test_files`
	`pygromos.tests.test_files.general_file_functions`
	`pygromos.tests.test_files.test_cnf_funcs`
	`pygromos.tests.test_files.test_disres`
	`pygromos.tests.test_files.test_disres_file`
	`pygromos.tests.test_files.test_gromosSystem`
	`pygromos.tests.test_files.test_gromosSystem_forcefields`
	`pygromos.tests.test_files.test_imd`
	`pygromos.tests.test_files.test_imd_block`
	`pygromos.tests.test_files.test_mtb`
	`pygromos.tests.test_files.test_ptp`
	`pygromos.tests.test_files.test_qmmm`
	`pygromos.tests.test_files.test_repdat`
	`pygromos.tests.test_files.test_resnlib`
	`pygromos.tests.test_files.test_top`
	`pygromos.tests.test_files.test_trajectory`
	`pygromos.tests.test_pygromos`
	`pygromos.tests.test_simulation_blocks`
	`pygromos.tests.test_simulation_blocks.test_simulation_runner_blocks`
	`pygromos.tests.test_submission`
	`pygromos.tests.test_submission.test_hpc_queuing_submission_job`
	`pygromos.tests.test_submission.test_hpc_queuing_submission_scheduling`
	`pygromos.tests.test_submission.test_hpc_queuing_submission_systems`
	`pygromos.utils`
	`pygromos.utils.amino_acids`
	`pygromos.utils.bash`
	`pygromos.utils.compiledProgram`
	`pygromos.utils.pdb`
	`pygromos.utils.typing`
	`pygromos.utils.utils`
	`pygromos.visualization`
	`pygromos.visualization.coordinates_visualization`