Generated API from Docstrings ============================== .. note:: This page is generated during the Sphinx build by scanning the ``pyar`` package. Add or update Python docstrings when adding, moving, or refactoring modules; the developer API documentation will then update automatically on the next documentation build. Aimnet2 ------- pyar.AIMNet2 ~~~~~~~~~~~~ .. automodule:: pyar.AIMNet2 :no-index: :members: :undoc-members: :show-inheritance: Molecule -------- pyar.Molecule ~~~~~~~~~~~~~ .. automodule:: pyar.Molecule :no-index: :members: :undoc-members: :show-inheritance: Afir ---- pyar.afir ~~~~~~~~~ .. automodule:: pyar.afir :no-index: :members: :undoc-members: :show-inheritance: pyar.afir.restraints ~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.afir.restraints :no-index: :members: :undoc-members: :show-inheritance: pyar.afir.utils ~~~~~~~~~~~~~~~ .. automodule:: pyar.afir.utils :no-index: :members: :undoc-members: :show-inheritance: Aggregate State --------------- pyar.aggregate_state ~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.aggregate_state :no-index: :members: :undoc-members: :show-inheritance: Aggregator ---------- pyar.aggregator ~~~~~~~~~~~~~~~ .. automodule:: pyar.aggregator :no-index: :members: :undoc-members: :show-inheritance: Backend Capabilities -------------------- pyar.backend_capabilities ~~~~~~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.backend_capabilities :no-index: :members: :undoc-members: :show-inheritance: Backends -------- pyar.backends ~~~~~~~~~~~~~ .. automodule:: pyar.backends :no-index: :members: :undoc-members: :show-inheritance: Biases ------ pyar.biases ~~~~~~~~~~~ .. automodule:: pyar.biases :no-index: :members: :undoc-members: :show-inheritance: pyar.biases.afir ~~~~~~~~~~~~~~~~ .. automodule:: pyar.biases.afir :no-index: :members: :undoc-members: :show-inheritance: Cli --- pyar.cli ~~~~~~~~ .. automodule:: pyar.cli :no-index: :members: :undoc-members: :show-inheritance: Core ---- pyar.core ~~~~~~~~~ .. automodule:: pyar.core :no-index: :members: :undoc-members: :show-inheritance: pyar.core.geometry ~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.core.geometry :no-index: :members: :undoc-members: :show-inheritance: pyar.core.molecule ~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.core.molecule :no-index: :members: :undoc-members: :show-inheritance: Data ---- pyar.data ~~~~~~~~~ .. automodule:: pyar.data :no-index: :members: :undoc-members: :show-inheritance: pyar.data.atomic_data ~~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.data.atomic_data :no-index: :members: :undoc-members: :show-inheritance: pyar.data.defualt_parameters ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.data.defualt_parameters :no-index: :members: :undoc-members: :show-inheritance: pyar.data.new_atomic_data ~~~~~~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.data.new_atomic_data :no-index: :members: :undoc-members: :show-inheritance: pyar.data.units ~~~~~~~~~~~~~~~ .. automodule:: pyar.data.units :no-index: :members: :undoc-members: :show-inheritance: Data Analysis ------------- pyar.data_analysis ~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.data_analysis :no-index: :members: :undoc-members: :show-inheritance: pyar.data_analysis.clustering ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.data_analysis.clustering :no-index: :members: :undoc-members: :show-inheritance: Energy Gradient Providers ------------------------- pyar.energy_gradient_providers ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.energy_gradient_providers :no-index: :members: :undoc-members: :show-inheritance: File Manager ------------ pyar.file_manager ~~~~~~~~~~~~~~~~~ .. automodule:: pyar.file_manager :no-index: :members: :undoc-members: :show-inheritance: Interface --------- pyar.interface ~~~~~~~~~~~~~~ .. automodule:: pyar.interface :no-index: :members: :undoc-members: :show-inheritance: Io -- pyar.io ~~~~~~~ .. automodule:: pyar.io :no-index: :members: :undoc-members: :show-inheritance: pyar.io.results ~~~~~~~~~~~~~~~ .. automodule:: pyar.io.results :no-index: :members: :undoc-members: :show-inheritance: pyar.io.xyz ~~~~~~~~~~~ .. automodule:: pyar.io.xyz :no-index: :members: :undoc-members: :show-inheritance: Mlatom ------ pyar.mlatom ~~~~~~~~~~~ .. automodule:: pyar.mlatom :no-index: :members: :undoc-members: :show-inheritance: Molecule Geometry ----------------- pyar.molecule_geometry ~~~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.molecule_geometry :no-index: :members: :undoc-members: :show-inheritance: Molecule Io ----------- pyar.molecule_io ~~~~~~~~~~~~~~~~ .. automodule:: pyar.molecule_io :no-index: :members: :undoc-members: :show-inheritance: Molecule Merge -------------- pyar.molecule_merge ~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.molecule_merge :no-index: :members: :undoc-members: :show-inheritance: Optimiser --------- pyar.optimiser ~~~~~~~~~~~~~~ .. automodule:: pyar.optimiser :no-index: :members: :undoc-members: :show-inheritance: Optional Dependencies --------------------- pyar.optional_dependencies ~~~~~~~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.optional_dependencies :no-index: :members: :undoc-members: :show-inheritance: Orientation Sampling -------------------- pyar.orientation_sampling ~~~~~~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.orientation_sampling :no-index: :members: :undoc-members: :show-inheritance: Property -------- pyar.property ~~~~~~~~~~~~~ .. automodule:: pyar.property :no-index: :members: :undoc-members: :show-inheritance: Reaction Analysis ----------------- pyar.reaction_analysis ~~~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.reaction_analysis :no-index: :members: :undoc-members: :show-inheritance: Reaction Identity ----------------- pyar.reaction_identity ~~~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.reaction_identity :no-index: :members: :undoc-members: :show-inheritance: Reaction State -------------- pyar.reaction_state ~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.reaction_state :no-index: :members: :undoc-members: :show-inheritance: Reaction Trace -------------- pyar.reaction_trace ~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.reaction_trace :no-index: :members: :undoc-members: :show-inheritance: Reactor ------- pyar.reactor ~~~~~~~~~~~~ .. automodule:: pyar.reactor :no-index: :members: :undoc-members: :show-inheritance: Representations --------------- pyar.representations ~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.representations :no-index: :members: :undoc-members: :show-inheritance: Sampling -------- pyar.sampling ~~~~~~~~~~~~~ .. automodule:: pyar.sampling :no-index: :members: :undoc-members: :show-inheritance: pyar.sampling.metrics ~~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.sampling.metrics :no-index: :members: :undoc-members: :show-inheritance: pyar.sampling.rotation ~~~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.sampling.rotation :no-index: :members: :undoc-members: :show-inheritance: pyar.sampling.sphere ~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.sampling.sphere :no-index: :members: :undoc-members: :show-inheritance: pyar.sampling.trial_generator ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.sampling.trial_generator :no-index: :members: :undoc-members: :show-inheritance: Scan ---- pyar.scan ~~~~~~~~~ .. automodule:: pyar.scan :no-index: :members: :undoc-members: :show-inheritance: Scripts ------- pyar.scripts ~~~~~~~~~~~~ .. automodule:: pyar.scripts :no-index: :members: :undoc-members: :show-inheritance: pyar.scripts.benchmark_clustering ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.scripts.benchmark_clustering :no-index: :members: :undoc-members: :show-inheritance: pyar.scripts.benchmark_orientations ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.scripts.benchmark_orientations :no-index: :members: :undoc-members: :show-inheritance: pyar.scripts.clustering ~~~~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.scripts.clustering :no-index: :members: :undoc-members: :show-inheritance: pyar.scripts.descriptor ~~~~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.scripts.descriptor :no-index: :members: :undoc-members: :show-inheritance: pyar.scripts.energy_table ~~~~~~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.scripts.energy_table :no-index: :members: :undoc-members: :show-inheritance: pyar.scripts.explore ~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.scripts.explore :no-index: :members: :undoc-members: :show-inheritance: pyar.scripts.optimiser ~~~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.scripts.optimiser :no-index: :members: :undoc-members: :show-inheritance: pyar.scripts.react ~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.scripts.react :no-index: :members: :undoc-members: :show-inheritance: pyar.scripts.reaction_trace ~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.scripts.reaction_trace :no-index: :members: :undoc-members: :show-inheritance: pyar.scripts.similarity ~~~~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.scripts.similarity :no-index: :members: :undoc-members: :show-inheritance: pyar.scripts.trial_generation ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.scripts.trial_generation :no-index: :members: :undoc-members: :show-inheritance: Selection --------- pyar.selection ~~~~~~~~~~~~~~ .. automodule:: pyar.selection :no-index: :members: :undoc-members: :show-inheritance: pyar.selection.basin_memory ~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.selection.basin_memory :no-index: :members: :undoc-members: :show-inheritance: pyar.selection.clustering ~~~~~~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.selection.clustering :no-index: :members: :undoc-members: :show-inheritance: pyar.selection.deduplication ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.selection.deduplication :no-index: :members: :undoc-members: :show-inheritance: pyar.selection.diversity ~~~~~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.selection.diversity :no-index: :members: :undoc-members: :show-inheritance: Similarity ---------- pyar.similarity ~~~~~~~~~~~~~~~ .. automodule:: pyar.similarity :no-index: :members: :undoc-members: :show-inheritance: Solvation State --------------- pyar.solvation_state ~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.solvation_state :no-index: :members: :undoc-members: :show-inheritance: State ----- pyar.state ~~~~~~~~~~ .. automodule:: pyar.state :no-index: :members: :undoc-members: :show-inheritance: pyar.state.aggregate ~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.state.aggregate :no-index: :members: :undoc-members: :show-inheritance: pyar.state.reaction ~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.state.reaction :no-index: :members: :undoc-members: :show-inheritance: pyar.state.solvation ~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.state.solvation :no-index: :members: :undoc-members: :show-inheritance: Trial Generation ---------------- pyar.trial_generation ~~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.trial_generation :no-index: :members: :undoc-members: :show-inheritance: Workflow Results ---------------- pyar.workflow_results ~~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.workflow_results :no-index: :members: :undoc-members: :show-inheritance: Workflows --------- pyar.workflows ~~~~~~~~~~~~~~ .. automodule:: pyar.workflows :no-index: :members: :undoc-members: :show-inheritance: pyar.workflows._growth ~~~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.workflows._growth :no-index: :members: :undoc-members: :show-inheritance: pyar.workflows.aggregate ~~~~~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.workflows.aggregate :no-index: :members: :undoc-members: :show-inheritance: pyar.workflows.reaction ~~~~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.workflows.reaction :no-index: :members: :undoc-members: :show-inheritance: pyar.workflows.solvation ~~~~~~~~~~~~~~~~~~~~~~~~ .. automodule:: pyar.workflows.solvation :no-index: :members: :undoc-members: :show-inheritance: