Reference

• Full Python API Reference
  • meld.test_install
    • meld.test_install.test_install
      • test_install()
  • meld.system
    • meld.system.amber
      • meld.system.amber.CrdReader
        • CrdReader
          • CrdReader.__init__()
          • CrdReader.get_box_vectors()
          • CrdReader.get_coordinates()
      • meld.system.amber.ParmTopReader
        • ParmTopReader
          • ParmTopReader.__init__()
          • ParmTopReader.get_atom_map()
          • ParmTopReader.get_atom_names()
          • ParmTopReader.get_bonds()
          • ParmTopReader.get_residue_names()
          • ParmTopReader.get_residue_numbers()
    • meld.system.builders
      • meld.system.builders.amber
        • meld.system.builders.amber.amap
          • meld.system.builders.amber.amap.add_amap
          • meld.system.builders.amber.amap.CMAPResidue
        • meld.system.builders.amber.builder
          • meld.system.builders.amber.builder.AmberOptions
          • meld.system.builders.amber.builder.AmberSystemBuilder
        • meld.system.builders.amber.subsystem
          • meld.system.builders.amber.subsystem.AmberSubSystemFromPdbFile
          • meld.system.builders.amber.subsystem.AmberSubSystemFromSequence
      • meld.system.builders.build_elastic_network_restraints
        • meld.system.builders.build_elastic_network_restraints.add_elastic_network_restraints
          • add_elastic_network_restraints()
        • meld.system.builders.build_elastic_network_restraints.create_elastic_network_restraints
          • create_elastic_network_restraints()
      • meld.system.builders.martini
      • meld.system.builders.spec
        • meld.system.builders.spec.SystemSpec
          • SystemSpec
    • meld.system.density
      • meld.system.density.DensityManager
        • DensityManager
          • DensityManager.__init__()
      • meld.system.density.DensityMap
        • DensityMap
          • DensityMap.__init__()
    • meld.system.indexing
      • meld.system.indexing.setup_indexing
        • setup_indexing()
      • meld.system.indexing.AtomIndex
        • AtomIndex
          • AtomIndex.__init__()
      • meld.system.indexing.Indexer
        • Indexer
          • Indexer.__init__()
          • Indexer.atom()
          • Indexer.residue()
      • meld.system.indexing.ResidueIndex
        • ResidueIndex
          • ResidueIndex.__init__()
    • meld.system.mapping
      • meld.system.mapping.PeakMapManager
        • PeakMapManager
          • PeakMapManager.__init__()
      • meld.system.mapping.PeakMapper
        • PeakMapper
          • PeakMapper.__init__()
      • meld.system.mapping.PeakMapping
        • PeakMapping
          • PeakMapping.__init__()
          • PeakMapping.atom_name
          • PeakMapping.map_name
          • PeakMapping.peak_id
    • meld.system.meld_system
      • meld.system.meld_system.System
        • System
          • System.__init__()
          • System.add_extra_angle()
          • System.add_extra_bond()
          • System.add_extra_torsion()
          • System.atom_names
          • System.barostat
          • System.density
          • System.get_pdb_writer()
          • System.get_state_template()
          • System.index
          • System.integrator
          • System.mapper
          • System.n_atoms
          • System.num_alignments
          • System.omm_system
          • System.param_sampler
          • System.residue_names
          • System.residue_numbers
          • System.restraints
          • System.solvation
          • System.temperature_scaler
          • System.template_box_vectors
          • System.template_coordinates
          • System.template_velocities
          • System.topology
    • meld.system.montecarlo
      • meld.system.montecarlo.DoubleTorsionMover
        • DoubleTorsionMover
          • DoubleTorsionMover.__init__()
          • DoubleTorsionMover.trial()
      • meld.system.montecarlo.MonteCarloScheduler
        • MonteCarloScheduler
          • MonteCarloScheduler.__init__()
          • MonteCarloScheduler.update()
      • meld.system.montecarlo.Mover
        • Mover
          • Mover.__init__()
      • meld.system.montecarlo.RandomTorsionMover
        • RandomTorsionMover
          • RandomTorsionMover.__init__()
          • RandomTorsionMover.trial()
      • meld.system.montecarlo.TranslationMover
        • TranslationMover
          • TranslationMover.__init__()
          • TranslationMover.trial()
    • meld.system.options
      • meld.system.options.RunOptions
        • RunOptions
          • RunOptions.__init__()
    • meld.system.param_sampling
      • meld.system.param_sampling.ContinuousParameter
        • ContinuousParameter
          • ContinuousParameter.__init__()
      • meld.system.param_sampling.ContinuousPrior
        • ContinuousPrior
          • ContinuousPrior.__init__()
      • meld.system.param_sampling.ContinuousSampler
        • ContinuousSampler
          • ContinuousSampler.__init__()
      • meld.system.param_sampling.DiscreteParameter
        • DiscreteParameter
          • DiscreteParameter.__init__()
      • meld.system.param_sampling.DiscretePrior
        • DiscretePrior
          • DiscretePrior.__init__()
      • meld.system.param_sampling.DiscreteSampler
        • DiscreteSampler
          • DiscreteSampler.__init__()
      • meld.system.param_sampling.ExponentialContinuousPrior
        • ExponentialContinuousPrior
          • ExponentialContinuousPrior.__init__()
      • meld.system.param_sampling.ExponentialDiscretePrior
        • ExponentialDiscretePrior
          • ExponentialDiscretePrior.__init__()
      • meld.system.param_sampling.Parameter
        • Parameter
          • Parameter.__init__()
      • meld.system.param_sampling.ParameterManager
        • ParameterManager
          • ParameterManager.__init__()
      • meld.system.param_sampling.ParameterState
        • ParameterState
          • ParameterState.__init__()
          • ParameterState.continuous
          • ParameterState.discrete
      • meld.system.param_sampling.Prior
        • Prior
          • Prior.__init__()
      • meld.system.param_sampling.Sampler
        • Sampler
          • Sampler.__init__()
      • meld.system.param_sampling.ScaledExponentialDiscretePrior
        • ScaledExponentialDiscretePrior
          • ScaledExponentialDiscretePrior.__init__()
      • meld.system.param_sampling.UniformContinuousPrior
        • UniformContinuousPrior
          • UniformContinuousPrior.__init__()
      • meld.system.param_sampling.UniformDiscretePrior
        • UniformDiscretePrior
          • UniformDiscretePrior.__init__()
    • meld.system.patchers
      • meld.system.patchers.freeze
        • meld.system.patchers.freeze.freeze_atoms
          • freeze_atoms()
      • meld.system.patchers.potential
        • meld.system.patchers.potential.remove_potential
          • remove_potential()
      • meld.system.patchers.rdc_alignment
        • meld.system.patchers.rdc_alignment.add_rdc_alignment
          • add_rdc_alignment()
      • meld.system.patchers.rdc_integrator
        • meld.system.patchers.rdc_integrator.CustomRDCIntegrator
          • CustomRDCIntegrator
      • meld.system.patchers.spin_label
        • meld.system.patchers.spin_label.add_virtual_spin_label
          • add_virtual_spin_label()
    • meld.system.pdb_writer
      • meld.system.pdb_writer.PDBWriter
        • PDBWriter
          • PDBWriter.__init__()
          • PDBWriter.get_pdb_string()
    • meld.system.restraints
      • Restraints
      • Groups
      • Collections
      • Scalers
      • Ramps
      • Positioners
      • Restraint Manager
      • meld.system.restraints.AbsoluteCOMRestraint
        • AbsoluteCOMRestraint
          • AbsoluteCOMRestraint.__init__()
      • meld.system.restraints.AlwaysActiveCollection
        • AlwaysActiveCollection
          • AlwaysActiveCollection.__init__()
          • AlwaysActiveCollection.add_restraint()
      • meld.system.restraints.COMRestraint
        • COMRestraint
          • COMRestraint.__init__()
      • meld.system.restraints.CartesianRestraint
        • CartesianRestraint
          • CartesianRestraint.__init__()
      • meld.system.restraints.ConfinementRestraint
        • ConfinementRestraint
          • ConfinementRestraint.__init__()
      • meld.system.restraints.DensityRestraint
        • DensityRestraint
          • DensityRestraint.__init__()
      • meld.system.restraints.DistProfileRestraint
        • DistProfileRestraint
          • DistProfileRestraint.__init__()
      • meld.system.restraints.DistanceRestraint
        • DistanceRestraint
          • DistanceRestraint.__init__()
      • meld.system.restraints.GMMDistanceRestraint
        • GMMDistanceRestraint
          • GMMDistanceRestraint.__init__()
          • GMMDistanceRestraint.from_params()
      • meld.system.restraints.GMMParams
        • GMMParams
          • GMMParams.__init__()
          • GMMParams.atoms
          • GMMParams.means
          • GMMParams.n_components
          • GMMParams.n_distances
          • GMMParams.precisions
          • GMMParams.weights
      • meld.system.restraints.HyperbolicDistanceRestraint
        • HyperbolicDistanceRestraint
          • HyperbolicDistanceRestraint.__init__()
      • meld.system.restraints.NonSelectableRestraint
        • NonSelectableRestraint
          • NonSelectableRestraint.__init__()
      • meld.system.restraints.RdcRestraint
        • RdcRestraint
          • RdcRestraint.__init__()
      • meld.system.restraints.Restraint
        • Restraint
          • Restraint.__init__()
      • meld.system.restraints.RestraintGroup
        • RestraintGroup
          • RestraintGroup.__init__()
          • RestraintGroup.num_active
          • RestraintGroup.restraints
      • meld.system.restraints.RestraintManager
        • RestraintManager
          • RestraintManager.__init__()
          • RestraintManager.add_as_always_active()
          • RestraintManager.add_as_always_active_list()
          • RestraintManager.add_selectively_active_collection()
          • RestraintManager.always_active
          • RestraintManager.create_restraint()
          • RestraintManager.create_restraint_group()
          • RestraintManager.create_scaler()
          • RestraintManager.selectively_active_collections
      • meld.system.restraints.SelectableRestraint
        • SelectableRestraint
          • SelectableRestraint.__init__()
      • meld.system.restraints.SelectivelyActiveCollection
        • SelectivelyActiveCollection
          • SelectivelyActiveCollection.__init__()
          • SelectivelyActiveCollection.groups
          • SelectivelyActiveCollection.num_active
      • meld.system.restraints.TorsProfileRestraint
        • TorsProfileRestraint
          • TorsProfileRestraint.__init__()
      • meld.system.restraints.TorsionRestraint
        • TorsionRestraint
          • TorsionRestraint.__init__()
      • meld.system.restraints.YZCartesianRestraint
        • YZCartesianRestraint
          • YZCartesianRestraint.__init__()
    • meld.system.scalers
      • meld.system.scalers.AlphaMapper
        • AlphaMapper
          • AlphaMapper.__init__()
      • meld.system.scalers.BlurScaler
        • BlurScaler
          • BlurScaler.__init__()
      • meld.system.scalers.ConstantBlurScaler
        • ConstantBlurScaler
          • ConstantBlurScaler.__init__()
      • meld.system.scalers.ConstantPositioner
        • ConstantPositioner
          • ConstantPositioner.__init__()
      • meld.system.scalers.ConstantRamp
        • ConstantRamp
          • ConstantRamp.__init__()
      • meld.system.scalers.ConstantScaler
        • ConstantScaler
          • ConstantScaler.__init__()
      • meld.system.scalers.GeometricScaler
        • GeometricScaler
          • GeometricScaler.__init__()
      • meld.system.scalers.LinearBlurScaler
        • LinearBlurScaler
          • LinearBlurScaler.__init__()
      • meld.system.scalers.LinearPositioner
        • LinearPositioner
          • LinearPositioner.__init__()
      • meld.system.scalers.LinearRamp
        • LinearRamp
          • LinearRamp.__init__()
      • meld.system.scalers.LinearScaler
        • LinearScaler
          • LinearScaler.__init__()
      • meld.system.scalers.NonLinearRamp
        • NonLinearRamp
          • NonLinearRamp.__init__()
      • meld.system.scalers.NonLinearScaler
        • NonLinearScaler
          • NonLinearScaler.__init__()
      • meld.system.scalers.PlateauLinearScaler
        • PlateauLinearScaler
          • PlateauLinearScaler.__init__()
      • meld.system.scalers.PlateauNonLinearScaler
        • PlateauNonLinearScaler
          • PlateauNonLinearScaler.__init__()
      • meld.system.scalers.PlateauSmoothScaler
        • PlateauSmoothScaler
          • PlateauSmoothScaler.__init__()
      • meld.system.scalers.Positioner
        • Positioner
          • Positioner.__init__()
      • meld.system.scalers.RestraintScaler
        • RestraintScaler
          • RestraintScaler.__init__()
      • meld.system.scalers.ScalerRegistry
        • ScalerRegistry
          • ScalerRegistry.__init__()
          • ScalerRegistry.get_constructor_for_key()
      • meld.system.scalers.TimeRamp
        • TimeRamp
          • TimeRamp.__init__()
      • meld.system.scalers.TimeRampSwitcher
        • TimeRampSwitcher
          • TimeRampSwitcher.__init__()
    • meld.system.state
      • meld.system.state.SystemState
        • SystemState
          • SystemState.__init__()
    • meld.system.temperature
      • meld.system.temperature.ConstantTemperatureScaler
        • ConstantTemperatureScaler
          • ConstantTemperatureScaler.__init__()
      • meld.system.temperature.GeometricTemperatureScaler
        • GeometricTemperatureScaler
          • GeometricTemperatureScaler.__init__()
      • meld.system.temperature.LinearTemperatureScaler
        • LinearTemperatureScaler
          • LinearTemperatureScaler.__init__()
      • meld.system.temperature.REST2Scaler
        • REST2Scaler
          • REST2Scaler.__init__()
      • meld.system.temperature.TemperatureScaler
        • TemperatureScaler
          • TemperatureScaler.__init__()
  • meld.remd
    • meld.remd.adaptor
      • meld.remd.adaptor.AdaptationPolicy
        • AdaptationPolicy
          • AdaptationPolicy.__init__()
          • AdaptationPolicy.should_adapt()
      • meld.remd.adaptor.AdaptationRequired
        • AdaptationRequired
          • AdaptationRequired.__init__()
          • AdaptationRequired.adapt_now
          • AdaptationRequired.reset_now
      • meld.remd.adaptor.EqualAcceptanceAdaptor
        • EqualAcceptanceAdaptor
          • EqualAcceptanceAdaptor.__init__()
          • EqualAcceptanceAdaptor.adapt()
          • EqualAcceptanceAdaptor.reset()
          • EqualAcceptanceAdaptor.update()
      • meld.remd.adaptor.NullAdaptor
        • NullAdaptor
          • NullAdaptor.__init__()
          • NullAdaptor.reset()
          • NullAdaptor.update()
      • meld.remd.adaptor.SwitchingCompositeAdaptor
        • SwitchingCompositeAdaptor
          • SwitchingCompositeAdaptor.__init__()
          • SwitchingCompositeAdaptor.adapt()
          • SwitchingCompositeAdaptor.reset()
          • SwitchingCompositeAdaptor.update()
    • meld.remd.ladder
      • meld.remd.ladder.NearestNeighborLadder
        • NearestNeighborLadder
          • NearestNeighborLadder.__init__()
          • NearestNeighborLadder.compute_exchanges()
    • meld.remd.launch
      • meld.remd.launch.launch
        • launch()
      • meld.remd.launch.log_versions
        • log_versions()
    • meld.remd.leader
      • meld.remd.leader.LeaderReplicaExchangeRunner
        • LeaderReplicaExchangeRunner
          • LeaderReplicaExchangeRunner.__init__()
          • LeaderReplicaExchangeRunner.alphas
          • LeaderReplicaExchangeRunner.max_steps
          • LeaderReplicaExchangeRunner.n_replicas
          • LeaderReplicaExchangeRunner.run()
          • LeaderReplicaExchangeRunner.step
          • LeaderReplicaExchangeRunner.to_worker()
    • meld.remd.permute
      • meld.remd.permute.permute_states
        • permute_states()
    • meld.remd.worker
      • meld.remd.worker.WorkerReplicaExchangeRunner
        • WorkerReplicaExchangeRunner
          • WorkerReplicaExchangeRunner.__init__()
          • WorkerReplicaExchangeRunner.max_steps
          • WorkerReplicaExchangeRunner.run()
          • WorkerReplicaExchangeRunner.step
  • meld.comm
    • meld.comm.HostInfo
      • HostInfo
        • HostInfo.__init__()
        • HostInfo.devices
        • HostInfo.host_name
    • meld.comm.MPICommunicator
      • MPICommunicator
        • MPICommunicator.__init__()
        • MPICommunicator.barrier()
        • MPICommunicator.broadcast_all_states_to_workers()
        • MPICommunicator.distribute_alphas_to_workers()
        • MPICommunicator.distribute_states_to_workers()
        • MPICommunicator.gather_energies_from_workers()
        • MPICommunicator.gather_states_from_workers()
        • MPICommunicator.initialize()
        • MPICommunicator.is_leader()
        • MPICommunicator.n_atoms
        • MPICommunicator.n_replicas
        • MPICommunicator.n_workers
        • MPICommunicator.negotiate_device_id()
        • MPICommunicator.rank
        • MPICommunicator.receive_all_states_from_leader()
        • MPICommunicator.receive_alphas_from_leader()
        • MPICommunicator.receive_states_from_leader()
        • MPICommunicator.send_energies_to_leader()
        • MPICommunicator.send_states_to_leader()
  • meld.parse
    • meld.parse.get_rdc_restraints
      • get_rdc_restraints()
    • meld.parse.get_secondary_structure_restraints
      • get_secondary_structure_restraints()
    • meld.parse.get_sequence_from_AA1
      • get_sequence_from_AA1()
    • meld.parse.get_sequence_from_AA3
      • get_sequence_from_AA3()
  • meld.vault
    • meld.vault.DataStore
      • DataStore
        • DataStore.__init__()
        • DataStore.append_traj()
        • DataStore.backup()
        • DataStore.close()
        • DataStore.initialize()
        • DataStore.iterate_box_vectors()
        • DataStore.iterate_permutation_vectors()
        • DataStore.iterate_positions()
        • DataStore.load_acceptance_probabilities()
        • DataStore.load_all_acceptance_probabilities()
        • DataStore.load_all_alphas()
        • DataStore.load_all_box_vectors()
        • DataStore.load_all_energies()
        • DataStore.load_all_energy_matrices()
        • DataStore.load_all_permutation_vectors()
        • DataStore.load_all_positions()
        • DataStore.load_all_velocities()
        • DataStore.load_alphas()
        • DataStore.load_box_vectors()
        • DataStore.load_communicator()
        • DataStore.load_data_store()
        • DataStore.load_energies()
        • DataStore.load_energy_matrix()
        • DataStore.load_permutation_vector()
        • DataStore.load_positions()
        • DataStore.load_positions_random_access()
        • DataStore.load_remd_runner()
        • DataStore.load_run_options()
        • DataStore.load_states()
        • DataStore.load_system()
        • DataStore.load_velocities()
        • DataStore.log_dir
        • DataStore.max_safe_block
        • DataStore.max_safe_frame
        • DataStore.n_atoms
        • DataStore.n_replicas
        • DataStore.save_acceptance_probabilities()
        • DataStore.save_alphas()
        • DataStore.save_box_vectors()
        • DataStore.save_communicator()
        • DataStore.save_data_store()
        • DataStore.save_energies()
        • DataStore.save_energy_matrix()
        • DataStore.save_permutation_vector()
        • DataStore.save_positions()
        • DataStore.save_remd_runner()
        • DataStore.save_run_options()
        • DataStore.save_states()
        • DataStore.save_system()
        • DataStore.save_velocities()
  • meld.util
    • meld.util.in_temp_dir
      • in_temp_dir()
    • meld.util.log_timing
      • log_timing()
    • meld.util.strip_unit
      • strip_unit()
    • meld.util.HostNameContextFilter
      • HostNameContextFilter
        • HostNameContextFilter.__init__()
        • HostNameContextFilter.filter()
  • meld.runner
    • meld.runner.get_runner
      • get_runner()
    • meld.runner.fake_runner
      • meld.runner.fake_runner.FakeSystemRunner
        • FakeSystemRunner
          • FakeSystemRunner.__init__()
    • meld.runner.openmm_runner
      • meld.runner.openmm_runner.OpenMMRunner
        • OpenMMRunner
          • OpenMMRunner.__init__()
    • meld.runner.transform
      • meld.runner.transform.TransformerBase
        • TransformerBase
          • TransformerBase.__init__()
          • TransformerBase.add_interactions()
          • TransformerBase.finalize()
          • TransformerBase.update()
      • meld.runner.transform.rest2
        • meld.runner.transform.rest2.REST2Transformer
          • REST2Transformer
      • meld.runner.transform.restraints
        • meld.runner.transform.restraints.cartesian
          • meld.runner.transform.restraints.cartesian.CartesianRestraintTransformer
          • meld.runner.transform.restraints.cartesian.YZCartesianTransformer
        • meld.runner.transform.restraints.com
          • meld.runner.transform.restraints.com.AbsoluteCOMRestraintTransformer
          • meld.runner.transform.restraints.com.COMRestraintTransformer
        • meld.runner.transform.restraints.confinement
          • meld.runner.transform.restraints.confinement.ConfinementRestraintTransformer
        • meld.runner.transform.restraints.meld
          • meld.runner.transform.restraints.meld.meld
          • meld.runner.transform.restraints.meld.tracker
        • meld.runner.transform.restraints.util
  • meld.interfaces
    • meld.interfaces.ExtraAngleParam
      • ExtraAngleParam
        • ExtraAngleParam.__init__()
        • ExtraAngleParam.angle
        • ExtraAngleParam.force_constant
        • ExtraAngleParam.i
        • ExtraAngleParam.j
        • ExtraAngleParam.k
    • meld.interfaces.ExtraBondParam
      • ExtraBondParam
        • ExtraBondParam.__init__()
        • ExtraBondParam.force_constant
        • ExtraBondParam.i
        • ExtraBondParam.j
        • ExtraBondParam.length
    • meld.interfaces.ExtraTorsParam
      • ExtraTorsParam
        • ExtraTorsParam.__init__()
        • ExtraTorsParam.energy
        • ExtraTorsParam.i
        • ExtraTorsParam.j
        • ExtraTorsParam.k
        • ExtraTorsParam.l
        • ExtraTorsParam.multiplicity
        • ExtraTorsParam.phase
    • meld.interfaces.ICommunicator
      • ICommunicator
        • ICommunicator.__init__()
        • ICommunicator.barrier()
        • ICommunicator.broadcast_all_states_to_workers()
        • ICommunicator.distribute_alphas_to_workers()
        • ICommunicator.distribute_states_to_workers()
        • ICommunicator.gather_energies_from_workers()
        • ICommunicator.gather_states_from_workers()
        • ICommunicator.initialize()
        • ICommunicator.is_leader()
        • ICommunicator.n_atoms
        • ICommunicator.n_replicas
        • ICommunicator.n_workers
        • ICommunicator.negotiate_device_id()
        • ICommunicator.rank
        • ICommunicator.receive_all_states_from_leader()
        • ICommunicator.receive_alphas_from_leader()
        • ICommunicator.receive_states_from_leader()
        • ICommunicator.send_energies_to_leader()
        • ICommunicator.send_states_to_leader()
    • meld.interfaces.IRunner
      • IRunner
        • IRunner.__init__()
    • meld.interfaces.IState
      • IState
        • IState.__init__()
    • meld.interfaces.ISystem
      • ISystem
        • ISystem.__init__()
        • ISystem.add_extra_angle()
        • ISystem.add_extra_bond()
        • ISystem.add_extra_torsion()
        • ISystem.atom_names
        • ISystem.barostat
        • ISystem.get_pdb_writer()
        • ISystem.get_state_template()
        • ISystem.integrator
        • ISystem.n_atoms
        • ISystem.num_alignments
        • ISystem.omm_system
        • ISystem.residue_names
        • ISystem.residue_numbers
        • ISystem.solvation
        • ISystem.template_box_vectors
        • ISystem.template_coordinates
        • ISystem.template_velocities
        • ISystem.topology
  • meld.helpers
    • meld.helpers.setup_data_store
      • setup_data_store()
    • meld.helpers.setup_replica_exchange
      • setup_replica_exchange()
    • meld.helpers.REMDInfo
      • REMDInfo
        • REMDInfo.__init__()
        • REMDInfo.communicator
        • REMDInfo.n_replicas
        • REMDInfo.remd_runner
• C++ API Reference