CodeEntropy.levels package

Subpackages

• CodeEntropy.levels.dihedrals package
  • Submodules
    • CodeEntropy.levels.dihedrals.angle_observations module
      • ConformationChunkTask
      • DihedralAngleCollector
      • DihedralAngleObservable
    • CodeEntropy.levels.dihedrals.conformational_state_builder module
      • ConformationStateBuilder
    • CodeEntropy.levels.dihedrals.kernels module
      • assign_peak_labels_and_count_flexible()
      • histogram_counts_by_dihedral()
      • wrap_degrees_positive()
    • CodeEntropy.levels.dihedrals.peak_detection module
      • ConformationPeakDetector
      • DihedralHistogramData
      • DihedralPeakData
    • CodeEntropy.levels.dihedrals.state_assignment module
      • ConformationStateAssigner
      • ConformationStateData
      • ConformationStatePartial
    • CodeEntropy.levels.dihedrals.topology module
      • DihedralTopologyDiscovery
      • MoleculeDihedralTopology
  • Module contents
• CodeEntropy.levels.execution package
  • Submodules
    • CodeEntropy.levels.execution.chunks module
      • chunk_frame_indices()
    • CodeEntropy.levels.execution.policy module
      • ExecutionPolicy
    • CodeEntropy.levels.execution.reducers module
      • CovarianceReducer
      • NeighborReducer
      • incremental_mean()
      • merge_means()
      • stable_keys()
    • CodeEntropy.levels.execution.scheduler module
      • FrameScheduler
    • CodeEntropy.levels.execution.tasks module
      • CovarianceChunkPartial
      • FrameChunkResult
      • FrameChunkTask
      • execute_frame_chunk_worker()
      • execute_frame_map_output()
      • get_worker_frame_universe()
      • incremental_mean_value()
      • make_frame_worker_shared_data()
      • reduce_frame_covariance_into_partial()
  • Module contents
• CodeEntropy.levels.graph package
  • Submodules
    • CodeEntropy.levels.graph.conformation_dag module
      • ConformationDAG
    • CodeEntropy.levels.graph.frame_dag module
      • FrameGraph
    • CodeEntropy.levels.graph.level_dag module
      • LevelDAG
  • Module contents
• CodeEntropy.levels.nodes package
  • Submodules
    • CodeEntropy.levels.nodes.accumulators module
      • CovarianceAccumulators
      • GroupIndex
      • InitCovarianceAccumulatorsNode
    • CodeEntropy.levels.nodes.axes_topology module
      • AxesTopology
      • BuildAxesTopologyNode
      • ResidueAxesTopology
      • UAAxesTopology
    • CodeEntropy.levels.nodes.beads module
      • BuildBeadsNode
      • UnitedAtomBead
    • CodeEntropy.levels.nodes.covariance module
      • FrameCovarianceNode
    • CodeEntropy.levels.nodes.detect_levels module
      • DetectLevelsNode
    • CodeEntropy.levels.nodes.detect_molecules module
      • DetectMoleculesNode
  • Module contents

Submodules

• CodeEntropy.levels.axes module
  • AxesCalculator
    • AxesCalculator.find_bonded_atoms()
    • AxesCalculator.get_UA_axes()
    • AxesCalculator.get_UA_axes_from_topology()
    • AxesCalculator.get_UA_masses()
    • AxesCalculator.get_bonded_axes()
    • AxesCalculator.get_bonded_axes_from_topology()
    • AxesCalculator.get_custom_axes()
    • AxesCalculator.get_custom_moment_of_inertia()
    • AxesCalculator.get_custom_principal_axes()
    • AxesCalculator.get_flipped_axes()
    • AxesCalculator.get_moment_of_inertia_tensor()
    • AxesCalculator.get_residue_axes()
    • AxesCalculator.get_residue_axes_from_topology()
    • AxesCalculator.get_vanilla_axes()
    • AxesCalculator.get_vector()
• CodeEntropy.levels.forces module
  • ForceTorqueCalculator
    • ForceTorqueCalculator.compute_frame_covariance()
    • ForceTorqueCalculator.get_weighted_forces()
    • ForceTorqueCalculator.get_weighted_torques()
  • TorqueInputs
    • TorqueInputs.axes_manager
    • TorqueInputs.box
    • TorqueInputs.center
    • TorqueInputs.force_partitioning
    • TorqueInputs.moment_of_inertia
    • TorqueInputs.rot_axes
• CodeEntropy.levels.hierarchy module
  • HierarchyBuilder
    • HierarchyBuilder.get_beads()
    • HierarchyBuilder.select_levels()
• CodeEntropy.levels.linalg module
  • MatrixUtils
    • MatrixUtils.create_submatrix()
    • MatrixUtils.filter_zero_rows_columns()
• CodeEntropy.levels.neighbors module
  • Neighbors
    • Neighbors.get_frame_neighbor_counts()
    • Neighbors.get_symmetry()
• CodeEntropy.levels.search module
  • Search
    • Search.get_RAD_neighbors()
    • Search.get_grid_neighbors()

Module contents