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Getting Started
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API Documentation
Developer Guide
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enerzyme.bond
enerzyme.bond.bond
enerzyme.bond.bond.bond_with_template
enerzyme.bond.bond.get_atom_map
enerzyme.bond.bond.pdb2mol
enerzyme.data
enerzyme.data.datahub
enerzyme.data.datahub.array_padding
enerzyme.data.datahub.load_from_pickle
enerzyme.data.datahub.DataHub
enerzyme.data.datahub.FieldDataset
enerzyme.data.datahub.SingleDataHub
enerzyme.data.datatype
enerzyme.data.datatype.is_int
enerzyme.data.datatype.is_rounded
enerzyme.data.datatype.is_atomic
enerzyme.data.datatype.requires_grad
enerzyme.data.datatype.is_idx
enerzyme.data.datatype.get_tensor_rank
enerzyme.data.datatype.is_target
enerzyme.data.datatype.is_target_uq
enerzyme.data.datatype.register_data_type
enerzyme.data.datatype.is_grad
enerzyme.data.neighbor_list
enerzyme.data.neighbor_list.full_neighbor_list
enerzyme.data.supplier
enerzyme.data.supplier.get_supplier
enerzyme.data.supplier.PickleSupplier
enerzyme.data.supplier.SDFSupplier
enerzyme.data.supplier.Supplier
enerzyme.data.transform
enerzyme.data.transform.load_atomic_energy
enerzyme.data.transform.parse_Za
enerzyme.data.transform.AtomicEnergyTransform
enerzyme.data.transform.BaseTransform
enerzyme.data.transform.NegativeGradientTransform
enerzyme.data.transform.TotalEnergyNormalization
enerzyme.data.transform.Transform
enerzyme.models
enerzyme.models.activation
enerzyme.models.activation.get_activation_fn
enerzyme.models.activation.BaseScaledTemperedActivation
enerzyme.models.activation.ShiftedSoftplus
enerzyme.models.activation.Swish
enerzyme.models.blocks
enerzyme.models.blocks.attention
enerzyme.models.blocks.attention.Attention
enerzyme.models.blocks.mlp
enerzyme.models.blocks.mlp.DenseLayer
enerzyme.models.blocks.mlp.NeuronLayer
enerzyme.models.blocks.mlp.ResidualLayer
enerzyme.models.blocks.mlp.ResidualMLP
enerzyme.models.blocks.mlp.ResidualStack
enerzyme.models.cutoff
enerzyme.models.cutoff.bump_transition
enerzyme.models.cutoff.polynomial_transition
enerzyme.models.cutoff.scale
enerzyme.models.cutoff.smooth_transition
enerzyme.models.ff
enerzyme.models.ff.build_layer
enerzyme.models.ff.build_model
enerzyme.models.ff.get_ff_core
enerzyme.models.ff.BaseFFLauncher
enerzyme.models.ff.FFDataset
enerzyme.models.ff.FF_committee
enerzyme.models.ff.FF_single
enerzyme.models.ff.MetaStateDict
enerzyme.models.functional
enerzyme.models.functional.gather_nd
enerzyme.models.functional.segment_sum_coo
enerzyme.models.functional.softplus_inverse
enerzyme.models.init
enerzyme.models.init.semi_orthogonal_glorot_weights
enerzyme.models.init.semi_orthogonal_matrix
enerzyme.models.init.square_orthogonal_matrix
enerzyme.models.irreps_tools
enerzyme.models.irreps_tools.U_matrix_real
enerzyme.models.irreps_tools.linear_out_irreps
enerzyme.models.irreps_tools.tp_out_irreps_with_instructions
enerzyme.models.irreps_tools.reshape_irreps
enerzyme.models.layers
enerzyme.models.layers.atom_embedding
enerzyme.models.layers.atom_embedding.BaseAtomEmbedding
enerzyme.models.layers.atom_embedding.NuclearEmbedding
enerzyme.models.layers.atom_embedding.RandomAtomEmbedding
enerzyme.models.layers.denormalize
enerzyme.models.layers.denormalize.AtomicAffineLayer
enerzyme.models.layers.dispersion
enerzyme.models.layers.dispersion.grimme_d3
enerzyme.models.layers.dispersion.grimme_d4
enerzyme.models.layers.electron_embedding
enerzyme.models.layers.electron_embedding.ResidualMLP
enerzyme.models.layers.electron_embedding.BaseElectronEmbedding
enerzyme.models.layers.electron_embedding.ElectronicEmbedding
enerzyme.models.layers.electron_embedding.NonlinearElectronicEmbedding
enerzyme.models.layers.electrostatics
enerzyme.models.layers.electrostatics.AtomicCharge2DipoleLayer
enerzyme.models.layers.electrostatics.ChargeConservationLayer
enerzyme.models.layers.electrostatics.ElectrostaticEnergyLayer
enerzyme.models.layers.gather_embedding
enerzyme.models.layers.gather_embedding.GatherAtomEmbedding
enerzyme.models.layers.geometry
enerzyme.models.layers.geometry.DistanceLayer
enerzyme.models.layers.geometry.RadiusGraphLayer
enerzyme.models.layers.geometry.RangeSeparationLayer
enerzyme.models.layers.gradient
enerzyme.models.layers.gradient.EnergyVarianceGradientLayer
enerzyme.models.layers.gradient.ForceLayer
enerzyme.models.layers.rbf
enerzyme.models.layers.rbf.BaseRBF
enerzyme.models.layers.rbf.BernsteinRBFLayer
enerzyme.models.layers.rbf.BesselRBFLayer
enerzyme.models.layers.rbf.ExponentialBernsteinRBFLayer
enerzyme.models.layers.rbf.ExponentialGaussianRBFLayer
enerzyme.models.layers.rbf.ExponentialRBF
enerzyme.models.layers.rbf.GaussianRBFLayer
enerzyme.models.layers.rbf.GaussianSmearing
enerzyme.models.layers.rbf.SincRBFLayer
enerzyme.models.layers.reduce
enerzyme.models.layers.reduce.EnergyReduceLayer
enerzyme.models.layers.reduce.ShallowEnsembleReduceLayer
enerzyme.models.layers.scalar_embedding
enerzyme.models.layers.scalar_embedding.ScalarDenseEmbedding
enerzyme.models.layers.scalar_embedding.ScalarEmbedding
enerzyme.models.layers.scalar_embedding.ScalarResidualMLPEmbedding
enerzyme.models.layers.zbl
enerzyme.models.layers.zbl.ZBLRepulsionEnergyLayer
enerzyme.models.leftnet
enerzyme.models.leftnet.core
enerzyme.models.leftnet.core.check_and_reshape_cell
enerzyme.models.leftnet.core.get_max_neighbors_mask
enerzyme.models.leftnet.core.get_pbc_distances
enerzyme.models.leftnet.core.print_fingerprint
enerzyme.models.leftnet.core.radius_graph_pbc
enerzyme.models.leftnet.core.swish
enerzyme.models.leftnet.core.EquiMessagePassing
enerzyme.models.leftnet.core.EquiOutput
enerzyme.models.leftnet.core.FTE
enerzyme.models.leftnet.core.GatedEquivariantBlock
enerzyme.models.leftnet.core.LEFTNet
enerzyme.models.leftnet.core.NeighborEmb
enerzyme.models.leftnet.core.S_vector
enerzyme.models.leftnet.core.aggregate_pos
enerzyme.models.leftnet.core.rbf_emb
enerzyme.models.loss
enerzyme.models.loss.CRPSLoss
enerzyme.models.loss.L2Penalty
enerzyme.models.loss.MAELoss
enerzyme.models.loss.MSELoss
enerzyme.models.loss.NLLLoss
enerzyme.models.loss.NLLLossVarOnly
enerzyme.models.loss.RMSELoss
enerzyme.models.loss.WeightedLoss
enerzyme.models.mace
enerzyme.models.mace.core
enerzyme.models.mace.core.MACECore
enerzyme.models.mace.core.MACEWrapper
enerzyme.models.mace.interaction
enerzyme.models.mace.interaction.AgnosticNonlinearInteractionBlock
enerzyme.models.mace.interaction.AgnosticResidualNonlinearInteractionBlock
enerzyme.models.mace.interaction.Contraction
enerzyme.models.mace.interaction.EquivariantProductBasisBlock
enerzyme.models.mace.interaction.InteractionBlock
enerzyme.models.mace.interaction.LinearReadoutBlock
enerzyme.models.mace.interaction.NonLinearReadoutBlock
enerzyme.models.mace.interaction.RealAgnosticAttResidualInteractionBlock
enerzyme.models.mace.interaction.RealAgnosticInteractionBlock
enerzyme.models.mace.interaction.RealAgnosticResidualInteractionBlock
enerzyme.models.mace.interaction.ResidualElementDependentInteractionBlock
enerzyme.models.mace.interaction.SymmetricContraction
enerzyme.models.mace.interaction.TensorProductWeightsBlock
enerzyme.models.modelhub
enerzyme.models.modelhub.compare_path
enerzyme.models.modelhub.get_all_possible_paths
enerzyme.models.modelhub.get_all_possible_paths_with_rank
enerzyme.models.modelhub.get_model_str
enerzyme.models.modelhub.get_pretrain_path
enerzyme.models.modelhub.path_resolve
enerzyme.models.modelhub.ModelHub
enerzyme.models.nequip
enerzyme.models.nequip.core
enerzyme.models.nequip.core.NequIPWrapper
enerzyme.models.physnet
enerzyme.models.physnet.core
enerzyme.models.physnet.core.PhysNetCore
enerzyme.models.physnet.interaction
enerzyme.models.physnet.interaction.DenseLayer
enerzyme.models.physnet.interaction.OutputBlock
enerzyme.models.physnet.interaction.ResidualStack
enerzyme.models.physnet.interaction.bias_default
enerzyme.models.physnet.interaction.weight_default
enerzyme.models.physnet.interaction.InteractionBlock
enerzyme.models.physnet.interaction.InteractionLayer
enerzyme.models.physnet.loss
enerzyme.models.physnet.loss.NHLoss
enerzyme.models.schnet
enerzyme.models.schnet.core
enerzyme.models.schnet.core.SchNetCore
enerzyme.models.schnet.interaction
enerzyme.models.schnet.interaction.CFConv
enerzyme.models.schnet.interaction.InteractionBlock
enerzyme.models.special
enerzyme.models.special.get_berstein_coefficient
enerzyme.models.special.sinc
enerzyme.models.spookynet
enerzyme.models.spookynet.core
enerzyme.models.spookynet.core.SpookyNetCore
enerzyme.models.spookynet.interaction
enerzyme.models.spookynet.interaction.ResidualStack
enerzyme.models.spookynet.interaction.InteractionModule
enerzyme.models.spookynet.interaction.LocalInteraction
enerzyme.models.spookynet.interaction.NonlocalInteraction
enerzyme.models.xpainn
enerzyme.models.xpainn.core
enerzyme.models.xpainn.core.XPaiNNWrapper
enerzyme.qm
enerzyme.qm.qm_driver
enerzyme.qm.qm_driver.ORCADriver
enerzyme.qm.qm_driver.Psi4Driver
enerzyme.qm.qm_driver.PySCFDriver
enerzyme.qm.qm_driver.QMDriver
enerzyme.qm.qm_driver.TeraChemDriver
enerzyme.tasks
enerzyme.tasks.batch
enerzyme.tasks.calculator
enerzyme.tasks.calculator.get_calculator
enerzyme.tasks.calculator.ASECalculator
enerzyme.tasks.extractor
enerzyme.tasks.extractor.extract_submol
enerzyme.tasks.extractor.extract_submol_with_center
enerzyme.tasks.extractor.get_bond_lengths
enerzyme.tasks.extractor.make_xyz_block
enerzyme.tasks.extractor.Extractor
enerzyme.tasks.lightning_utils
enerzyme.tasks.lightning_utils.CollectOutputCallback
enerzyme.tasks.lightning_utils.EMACallback
enerzyme.tasks.lightning_utils.LightningModel
enerzyme.tasks.lightning_utils.MonitorCallback
enerzyme.tasks.metrics
enerzyme.tasks.metrics.build_single_metric
enerzyme.tasks.metrics.Metrics
enerzyme.tasks.monitor
enerzyme.tasks.monitor.Monitor
enerzyme.tasks.optimizer
enerzyme.tasks.optimizer.get_optimizer
enerzyme.tasks.optimizer.get_optimizer_config
enerzyme.tasks.picker
enerzyme.tasks.picker.build_Fa_picking
enerzyme.tasks.picker.random_picking
enerzyme.tasks.server
enerzyme.tasks.server.Server
enerzyme.tasks.simulator
enerzyme.tasks.simulator.get_optimizer
enerzyme.tasks.simulator.Simulation
enerzyme.tasks.splitter
enerzyme.tasks.splitter.RandomSplit
enerzyme.tasks.splitter.Splitter
enerzyme.tasks.trainer
enerzyme.tasks.trainer.Trainer
enerzyme.utils
enerzyme.utils.base_logger
enerzyme.utils.base_logger.Logger
enerzyme.utils.base_logger.PackagePathFilter
enerzyme.utils.config_handler
enerzyme.utils.config_handler.addict2dict
enerzyme.utils.config_handler.YamlHandler
enerzyme.utils.util
enerzyme.utils.util.hash_model_name
enerzyme.utils.util.model_name_generation
API Documentation
enerzyme.data
enerzyme.data.datatype
enerzyme.data.datatype.requires_grad
enerzyme.data.datatype.requires_grad
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