topo¶ topo package Subpackages topo.analysis package Submodules topo.analysis.native_contacts module Module contents topo.core package Submodules topo.core.geometry module topo.csp package Submodules topo.csp.core module topo.csp.cylinder module topo.csp.kinetics module topo.csp.movie module topo.csp.protocol module topo.csp.ribosome module Module contents topo.mdrun package Submodules topo.mdrun.mdrun module topo.mdrun.protocol module Module contents topo.optimize package Submodules topo.optimize.optimize module Module contents topo.utils package Submodules topo.utils.config module topo.utils.multichain module topo.utils.nonbonded module topo.utils.read_parms module topo.utils.runinfo module Module contents Submodules topo.engine module BuiltSystem BuiltSystem.cgModel BuiltSystem.positions BuiltSystem.system BuiltSystem.topology RunContext RunContext.checkpoint RunContext.done_steps RunContext.restart_active RunContext.runinfo_path RunContext.simulation attach_reporters() build_system() finalize_simulation() setup_simulation()