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Enerzyme documentation

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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.models
  • enerzyme.models.modelhub

enerzyme.models.modelhub#

Functions

compare_path(path1, path2[, preference, ...])

Compare two paths in the order of

get_all_possible_paths(pretrain_path, prefix)

get_all_possible_paths_with_rank(pretrain_path)

get_model_str(model_id, model_params)

get_pretrain_path([pretrain_path, ...])

path_resolve(path[, target_preference, ...])

Classes

ModelHub(datahub, trainer, **params)

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