maml package

Subpackages

maml.apps package
- Subpackages
  - maml.apps.bowsr package
    - Subpackages
      - maml.apps.bowsr.model package
        
        EnergyModel
        
        maml.apps.bowsr.model.base module
        
        maml.apps.bowsr.model.cgcnn module
        
        maml.apps.bowsr.model.dft module
        
        maml.apps.bowsr.model.megnet module
    - maml.apps.bowsr.acquisition module
      - AcquisitionFunction
        
        AcquisitionFunction._ei()
        
        AcquisitionFunction._gpucb()
        
        AcquisitionFunction._poi()
        
        AcquisitionFunction._ucb()
        
        AcquisitionFunction.calculate()
      - _trunc()
      - ensure_rng()
      - lhs_sample()
      - predict_mean_std()
      - propose_query_point()
    - maml.apps.bowsr.optimizer module
      - BayesianOptimizer
        
        BayesianOptimizer.add_query()
        
        BayesianOptimizer.as_dict()
        
        BayesianOptimizer.from_dict()
        
        BayesianOptimizer.get_derived_structure()
        
        BayesianOptimizer.get_formation_energy()
        
        BayesianOptimizer.get_optimized_structure_and_energy()
        
        BayesianOptimizer.gpr
        
        BayesianOptimizer.optimize()
        
        BayesianOptimizer.propose()
        
        BayesianOptimizer.set_bounds()
        
        BayesianOptimizer.set_gpr_params()
        
        BayesianOptimizer.set_space_empty()
        
        BayesianOptimizer.space
      - atoms_crowded()
      - struct2perturbation()
    - maml.apps.bowsr.perturbation module
      - LatticePerturbation
        
        LatticePerturbation.abc
        
        LatticePerturbation.fit_lattice
        
        LatticePerturbation.lattice
        
        LatticePerturbation.sanity_check()
      - WyckoffPerturbation
        
        WyckoffPerturbation.fit_site
        
        WyckoffPerturbation.get_orbit()
        
        WyckoffPerturbation.sanity_check()
        
        WyckoffPerturbation.site
        
        WyckoffPerturbation.standardize()
      - crystal_system()
      - get_standardized_structure()
      - perturbation_mapping()
    - maml.apps.bowsr.preprocessing module
      - DummyScaler
        
        DummyScaler.as_dict()
        
        DummyScaler.fit()
        
        DummyScaler.from_dict()
        
        DummyScaler.inverse_transform()
        
        DummyScaler.transform()
      - StandardScaler
        
        StandardScaler.as_dict()
        
        StandardScaler.fit()
        
        StandardScaler.from_dict()
        
        StandardScaler.inverse_transform()
        
        StandardScaler.transform()
    - maml.apps.bowsr.target_space module
      - TargetSpace
        
        TargetSpace.bounds
        
        TargetSpace.lhs_sample()
        
        TargetSpace.params
        
        TargetSpace.probe()
        
        TargetSpace.register()
        
        TargetSpace.set_bounds()
        
        TargetSpace.set_empty()
        
        TargetSpace.target
        
        TargetSpace.uniform_sample()
      - _hashable()
  - maml.apps.gbe package
    - maml.apps.gbe.describer module
      - GBBond
        
        GBBond.NNDict
        
        GBBond._get_bond_mat()
        
        GBBond.as_dict()
        
        GBBond.bond_matrix
        
        GBBond.from_dict()
        
        GBBond.get_breakbond_ratio()
        
        GBBond.get_mean_bl_chg()
        
        GBBond.max_bl
        
        GBBond.min_bl
      - GBDescriber
        
        GBDescriber._abc_impl
        
        GBDescriber._sklearn_auto_wrap_output_keys
        
        GBDescriber.generate_bulk_ref()
        
        GBDescriber.transform_one()
      - convert_hcp_direction()
      - convert_hcp_plane()
      - get_elemental_feature()
      - get_structural_feature()
    - maml.apps.gbe.presetfeatures module
      - my_quant
        
        my_quant.latex
        
        my_quant.name
        
        my_quant.unit
    - maml.apps.gbe.utils module
      - load_b0_dict()
      - load_data()
      - load_mean_delta_bl_dict()
      - update_b0_dict()
  - maml.apps.pes package
    - DefectFormation
      - DefectFormation._parse()
      - DefectFormation._sanity_check()
      - DefectFormation._setup()
      - DefectFormation.calculate()
      - DefectFormation.get_unit_cell()
    - ElasticConstant
      - ElasticConstant._RESTART_CONFIG
      - ElasticConstant._parse()
      - ElasticConstant._sanity_check()
      - ElasticConstant._setup()
    - EnergyForceStress
      - EnergyForceStress._parse()
      - EnergyForceStress._rotate_force_stress()
      - EnergyForceStress._sanity_check()
      - EnergyForceStress._setup()
      - EnergyForceStress.calculate()
    - GAPotential
      - GAPotential._abc_impl
      - GAPotential._line_up()
      - GAPotential.evaluate()
      - GAPotential.from_config()
      - GAPotential.pair_coeff
      - GAPotential.pair_style
      - GAPotential.read_cfgs()
      - GAPotential.save()
      - GAPotential.train()
      - GAPotential.write_cfgs()
      - GAPotential.write_param()
    - LMPStaticCalculator
      - LMPStaticCalculator._COMMON_CMDS
      - LMPStaticCalculator._parse()
      - LMPStaticCalculator._sanity_check()
      - LMPStaticCalculator._setup()
      - LMPStaticCalculator.allowed_kwargs
      - LMPStaticCalculator.calculate()
      - LMPStaticCalculator.set_lmp_exe()
    - LatticeConstant
      - LatticeConstant.calculate()
    - MTPotential
      - MTPotential._abc_impl
      - MTPotential._line_up()
      - MTPotential.evaluate()
      - MTPotential.from_config()
      - MTPotential.pair_coeff
      - MTPotential.pair_style
      - MTPotential.read_cfgs()
      - MTPotential.train()
      - MTPotential.write_cfg()
      - MTPotential.write_ini()
      - MTPotential.write_param()
    - NNPotential
      - NNPotential._abc_impl
      - NNPotential._line_up()
      - NNPotential.bohr_to_angstrom
      - NNPotential.eV_to_Ha
      - NNPotential.evaluate()
      - NNPotential.from_config()
      - NNPotential.load_input()
      - NNPotential.load_scaler()
      - NNPotential.load_weights()
      - NNPotential.pair_coeff
      - NNPotential.pair_style
      - NNPotential.read_cfgs()
      - NNPotential.train()
      - NNPotential.write_cfgs()
      - NNPotential.write_input()
      - NNPotential.write_param()
    - NudgedElasticBand
      - NudgedElasticBand._parse()
      - NudgedElasticBand._sanity_check()
      - NudgedElasticBand._setup()
      - NudgedElasticBand.calculate()
      - NudgedElasticBand.get_unit_cell()
    - Potential
    - SNAPotential
      - SNAPotential._abc_impl
      - SNAPotential.evaluate()
      - SNAPotential.from_config()
      - SNAPotential.pair_coeff
      - SNAPotential.pair_style
      - SNAPotential.train()
      - SNAPotential.write_param()
    - SpectralNeighborAnalysis
      - SpectralNeighborAnalysis._CMDS
      - SpectralNeighborAnalysis._parse()
      - SpectralNeighborAnalysis._sanity_check()
      - SpectralNeighborAnalysis._setup()
      - SpectralNeighborAnalysis.get_bs_subscripts()
      - SpectralNeighborAnalysis.n_bs
    - get_default_lmp_exe()
    - maml.apps.pes._base module
      - Potential
      - PotentialMixin
        
        PotentialMixin.evaluate()
        
        PotentialMixin.from_config()
        
        PotentialMixin.predict_efs()
        
        PotentialMixin.train()
        
        PotentialMixin.write_param()
    - maml.apps.pes._gap module
      - GAPotential
        
        GAPotential._abc_impl
        
        GAPotential._line_up()
        
        GAPotential.evaluate()
        
        GAPotential.from_config()
        
        GAPotential.pair_coeff
        
        GAPotential.pair_style
        
        GAPotential.read_cfgs()
        
        GAPotential.save()
        
        GAPotential.train()
        
        GAPotential.write_cfgs()
        
        GAPotential.write_param()
    - maml.apps.pes._lammps module
      - DefectFormation
        
        DefectFormation._parse()
        
        DefectFormation._sanity_check()
        
        DefectFormation._setup()
        
        DefectFormation.calculate()
        
        DefectFormation.get_unit_cell()
      - ElasticConstant
        
        ElasticConstant._RESTART_CONFIG
        
        ElasticConstant._parse()
        
        ElasticConstant._sanity_check()
        
        ElasticConstant._setup()
      - EnergyForceStress
        
        EnergyForceStress._parse()
        
        EnergyForceStress._rotate_force_stress()
        
        EnergyForceStress._sanity_check()
        
        EnergyForceStress._setup()
        
        EnergyForceStress.calculate()
      - LMPRelaxationCalculator
        
        LMPRelaxationCalculator._parse()
        
        LMPRelaxationCalculator._sanity_check()
        
        LMPRelaxationCalculator._setup()
      - LMPStaticCalculator
        
        LMPStaticCalculator._COMMON_CMDS
        
        LMPStaticCalculator._parse()
        
        LMPStaticCalculator._sanity_check()
        
        LMPStaticCalculator._setup()
        
        LMPStaticCalculator.allowed_kwargs
        
        LMPStaticCalculator.calculate()
        
        LMPStaticCalculator.set_lmp_exe()
      - LammpsPotential
        
        LammpsPotential._abc_impl
        
        LammpsPotential.predict_efs()
      - LatticeConstant
        
        LatticeConstant.calculate()
      - NudgedElasticBand
        
        NudgedElasticBand._parse()
        
        NudgedElasticBand._sanity_check()
        
        NudgedElasticBand._setup()
        
        NudgedElasticBand.calculate()
        
        NudgedElasticBand.get_unit_cell()
      - SpectralNeighborAnalysis
        
        SpectralNeighborAnalysis._CMDS
        
        SpectralNeighborAnalysis._parse()
        
        SpectralNeighborAnalysis._sanity_check()
        
        SpectralNeighborAnalysis._setup()
        
        SpectralNeighborAnalysis.get_bs_subscripts()
        
        SpectralNeighborAnalysis.n_bs
      - SurfaceEnergy
        
        SurfaceEnergy.calculate()
      - _pretty_input()
      - _read_dump()
      - get_default_lmp_exe()
    - maml.apps.pes._mtp module
      - MTPotential
        
        MTPotential._abc_impl
        
        MTPotential._line_up()
        
        MTPotential.evaluate()
        
        MTPotential.from_config()
        
        MTPotential.pair_coeff
        
        MTPotential.pair_style
        
        MTPotential.read_cfgs()
        
        MTPotential.train()
        
        MTPotential.write_cfg()
        
        MTPotential.write_ini()
        
        MTPotential.write_param()
      - feed()
    - maml.apps.pes._nnp module
      - NNPotential
        
        NNPotential._abc_impl
        
        NNPotential._line_up()
        
        NNPotential.bohr_to_angstrom
        
        NNPotential.eV_to_Ha
        
        NNPotential.evaluate()
        
        NNPotential.from_config()
        
        NNPotential.load_input()
        
        NNPotential.load_scaler()
        
        NNPotential.load_weights()
        
        NNPotential.pair_coeff
        
        NNPotential.pair_style
        
        NNPotential.read_cfgs()
        
        NNPotential.train()
        
        NNPotential.write_cfgs()
        
        NNPotential.write_input()
        
        NNPotential.write_param()
    - maml.apps.pes._snap module
      - SNAPotential
        
        SNAPotential._abc_impl
        
        SNAPotential.evaluate()
        
        SNAPotential.from_config()
        
        SNAPotential.pair_coeff
        
        SNAPotential.pair_style
        
        SNAPotential.train()
        
        SNAPotential.write_param()
  - maml.apps.symbolic package
    - AdaptiveLasso
      - AdaptiveLasso._penalty_jac()
      - AdaptiveLasso.get_w()
      - AdaptiveLasso.penalty()
      - AdaptiveLasso.select()
    - DantzigSelector
      - DantzigSelector.construct_constraints()
      - DantzigSelector.construct_jac()
      - DantzigSelector.construct_loss()
    - FeatureGenerator
      - FeatureGenerator.augment()
    - ISIS
      - ISIS.evaluate()
      - ISIS.run()
    - L0BrutalForce
      - L0BrutalForce.select()
    - Lasso
      - Lasso._penalty_jac()
      - Lasso.penalty()
    - Operator
      - Operator.compute()
      - Operator.from_str()
      - Operator.gen_name()
      - Operator.is_binary
      - Operator.is_commutative
      - Operator.is_unary
      - Operator.support_op_rep
    - SCAD
      - SCAD._penalty_jac()
      - SCAD.penalty()
    - SIS
      - SIS.compute_residual()
      - SIS.run()
      - SIS.screen()
      - SIS.select()
      - SIS.set_gamma()
      - SIS.set_selector()
      - SIS.update_gamma()
    - maml.apps.symbolic._feature_generator module
      - FeatureGenerator
        
        FeatureGenerator.augment()
      - Operator
        
        Operator.compute()
        
        Operator.from_str()
        
        Operator.gen_name()
        
        Operator.is_binary
        
        Operator.is_commutative
        
        Operator.is_unary
        
        Operator.support_op_rep
      - _my_abs_diff()
      - _my_abs_log10()
      - _my_abs_sqrt()
      - _my_abs_sum()
      - _my_diff()
      - _my_div()
      - _my_exp()
      - _my_exp_power_2()
      - _my_exp_power_3()
      - _my_mul()
      - _my_power()
      - _my_sum()
      - _my_sum_exp()
      - _my_sum_power_2()
      - _my_sum_power_3()
      - _update_df()
      - generate_feature()
    - maml.apps.symbolic._selectors module
      - AdaptiveLasso
        
        AdaptiveLasso._penalty_jac()
        
        AdaptiveLasso.get_w()
        
        AdaptiveLasso.penalty()
        
        AdaptiveLasso.select()
      - BaseSelector
        
        BaseSelector._get_param_names()
        
        BaseSelector.compute_residual()
        
        BaseSelector.construct_constraints()
        
        BaseSelector.construct_jac()
        
        BaseSelector.construct_loss()
        
        BaseSelector.evaluate()
        
        BaseSelector.get_coef()
        
        BaseSelector.get_feature_indices()
        
        BaseSelector.get_params()
        
        BaseSelector.predict()
        
        BaseSelector.select()
        
        BaseSelector.set_params()
      - DantzigSelector
        
        DantzigSelector.construct_constraints()
        
        DantzigSelector.construct_jac()
        
        DantzigSelector.construct_loss()
      - L0BrutalForce
        
        L0BrutalForce.select()
      - Lasso
        
        Lasso._penalty_jac()
        
        Lasso.penalty()
      - PenalizedLeastSquares
        
        PenalizedLeastSquares._penalty_jac()
        
        PenalizedLeastSquares._sse_jac()
        
        PenalizedLeastSquares.construct_constraints()
        
        PenalizedLeastSquares.construct_jac()
        
        PenalizedLeastSquares.construct_loss()
        
        PenalizedLeastSquares.penalty()
      - SCAD
        
        SCAD._penalty_jac()
        
        SCAD.penalty()
    - maml.apps.symbolic._selectors_cvxpy module
      - AdaptiveLassoCP
        
        AdaptiveLassoCP.get_w()
        
        AdaptiveLassoCP.penalty()
        
        AdaptiveLassoCP.select()
      - BaseSelectorCP
        
        BaseSelectorCP.construct_constraints()
        
        BaseSelectorCP.construct_loss()
        
        BaseSelectorCP.select()
      - DantzigSelectorCP
        
        DantzigSelectorCP.construct_constraints()
        
        DantzigSelectorCP.construct_loss()
      - LassoCP
        
        LassoCP.penalty()
      - PenalizedLeastSquaresCP
        
        PenalizedLeastSquaresCP.construct_loss()
        
        PenalizedLeastSquaresCP.penalty()
    - maml.apps.symbolic._sis module
      - ISIS
        
        ISIS.evaluate()
        
        ISIS.run()
      - SIS
        
        SIS.compute_residual()
        
        SIS.run()
        
        SIS.screen()
        
        SIS.select()
        
        SIS.set_gamma()
        
        SIS.set_selector()
        
        SIS.update_gamma()
      - _best_combination()
      - _eval()
      - _get_coeff()
maml.base package
- BaseDataSource
  - BaseDataSource.get()
- BaseDescriber
  - BaseDescriber._abc_impl
  - BaseDescriber._is_multi_output()
  - BaseDescriber._sklearn_auto_wrap_output_keys
  - BaseDescriber.clear_cache()
  - BaseDescriber.feature_dim
  - BaseDescriber.fit()
  - BaseDescriber.transform()
  - BaseDescriber.transform_one()
- BaseModel
  - BaseModel._predict()
  - BaseModel.fit()
  - BaseModel.predict_objs()
  - BaseModel.train()
- DummyDescriber
  - DummyDescriber._abc_impl
  - DummyDescriber._sklearn_auto_wrap_output_keys
  - DummyDescriber.transform_one()
- KerasModel
  - KerasModel._get_validation_data()
  - KerasModel.fit()
- SKLModel
- SequentialDescriber
  - SequentialDescriber._abc_impl
  - SequentialDescriber.steps
- TargetScalerMixin
  - TargetScalerMixin.predict_objs()
  - TargetScalerMixin.train()
- describer_type()
- get_feature_batch()
- is_keras_model()
- is_sklearn_model()
- maml.base._data module
  - BaseDataSource
    - BaseDataSource.get()
- maml.base._describer module
  - BaseDescriber
    - BaseDescriber._abc_impl
    - BaseDescriber._is_multi_output()
    - BaseDescriber._sklearn_auto_wrap_output_keys
    - BaseDescriber.clear_cache()
    - BaseDescriber.feature_dim
    - BaseDescriber.fit()
    - BaseDescriber.transform()
    - BaseDescriber.transform_one()
  - DummyDescriber
    - DummyDescriber._abc_impl
    - DummyDescriber._sklearn_auto_wrap_output_keys
    - DummyDescriber.transform_one()
  - SequentialDescriber
    - SequentialDescriber._abc_impl
    - SequentialDescriber.steps
  - _transform_one()
  - describer_type()
- maml.base._feature_batch module
  - get_feature_batch()
  - no_action()
  - pandas_concat()
  - stack_first_dim()
  - stack_padded()
- maml.base._mixin module
  - TargetScalerMixin
    - TargetScalerMixin.predict_objs()
    - TargetScalerMixin.train()
- maml.base._model module
  - BaseModel
    - BaseModel._predict()
    - BaseModel.fit()
    - BaseModel.predict_objs()
    - BaseModel.train()
  - KerasMixin
    - KerasMixin.evaluate()
    - KerasMixin.from_file()
    - KerasMixin.get_input_dim()
    - KerasMixin.load()
    - KerasMixin.save()
  - KerasModel
    - KerasModel._get_validation_data()
    - KerasModel.fit()
  - SKLModel
  - SklearnMixin
    - SklearnMixin.evaluate()
    - SklearnMixin.from_file()
    - SklearnMixin.load()
    - SklearnMixin.save()
  - is_keras_model()
  - is_sklearn_model()
maml.data package
- MaterialsProject
  - MaterialsProject.get()
- URLSource
  - URLSource.get()
- maml.data._mp module
  - MaterialsProject
    - MaterialsProject.get()
- maml.data._url module
  - FigshareSource
    - FigshareSource.get()
  - URLSource
    - URLSource.get()
maml.describers package
- BPSymmetryFunctions
  - BPSymmetryFunctions._abc_impl
  - BPSymmetryFunctions._fc()
  - BPSymmetryFunctions._sklearn_auto_wrap_output_keys
  - BPSymmetryFunctions.describer_type
  - BPSymmetryFunctions.transform_one()
- BispectrumCoefficients
  - BispectrumCoefficients._abc_impl
  - BispectrumCoefficients._sklearn_auto_wrap_output_keys
  - BispectrumCoefficients.describer_type
  - BispectrumCoefficients.feature_dim
  - BispectrumCoefficients.subscripts
  - BispectrumCoefficients.transform_one()
- CoulombEigenSpectrum
  - CoulombEigenSpectrum._abc_impl
  - CoulombEigenSpectrum._sklearn_auto_wrap_output_keys
  - CoulombEigenSpectrum.describer_type
  - CoulombEigenSpectrum.transform_one()
- CoulombMatrix
  - CoulombMatrix._abc_impl
  - CoulombMatrix._get_columb_mat()
  - CoulombMatrix._sklearn_auto_wrap_output_keys
  - CoulombMatrix.describer_type
  - CoulombMatrix.get_coulomb_mat()
  - CoulombMatrix.transform_one()
- DistinctSiteProperty
  - DistinctSiteProperty._abc_impl
  - DistinctSiteProperty._sklearn_auto_wrap_output_keys
  - DistinctSiteProperty.describer_type
  - DistinctSiteProperty.supported_properties
  - DistinctSiteProperty.transform_one()
- ElementProperty
  - ElementProperty._abc_impl
  - ElementProperty._get_param_names()
  - ElementProperty._sklearn_auto_wrap_output_keys
  - ElementProperty.describer_type
  - ElementProperty.from_preset()
  - ElementProperty.get_params()
  - ElementProperty.transform_one()
- ElementStats
  - ElementStats.ALLOWED_STATS
  - ElementStats.AVAILABLE_DATA
  - ElementStats._abc_impl
  - ElementStats._reduce_dimension()
  - ElementStats._sklearn_auto_wrap_output_keys
  - ElementStats.describer_type
  - ElementStats.from_data()
  - ElementStats.from_file()
  - ElementStats.transform_one()
- M3GNetStructure
  - M3GNetStructure._abc_impl
  - M3GNetStructure._sklearn_auto_wrap_output_keys
  - M3GNetStructure.transform_one()
- MEGNetSite
  - MEGNetSite._abc_impl
  - MEGNetSite._sklearn_auto_wrap_output_keys
  - MEGNetSite.describer_type
  - MEGNetSite.transform_one()
- MEGNetStructure
  - MEGNetStructure._abc_impl
  - MEGNetStructure._sklearn_auto_wrap_output_keys
  - MEGNetStructure.describer_type
  - MEGNetStructure.transform_one()
- RadialDistributionFunction
  - RadialDistributionFunction._get_specie_density()
  - RadialDistributionFunction.get_site_coordination()
  - RadialDistributionFunction.get_site_rdf()
  - RadialDistributionFunction.get_species_coordination()
  - RadialDistributionFunction.get_species_rdf()
- RandomizedCoulombMatrix
  - RandomizedCoulombMatrix._abc_impl
  - RandomizedCoulombMatrix._sklearn_auto_wrap_output_keys
  - RandomizedCoulombMatrix.describer_type
  - RandomizedCoulombMatrix.get_randomized_coulomb_mat()
  - RandomizedCoulombMatrix.transform_one()
- SiteElementProperty
  - SiteElementProperty._abc_impl
  - SiteElementProperty._get_keys()
  - SiteElementProperty._sklearn_auto_wrap_output_keys
  - SiteElementProperty.describer_type
  - SiteElementProperty.feature_dim
  - SiteElementProperty.transform_one()
- SmoothOverlapAtomicPosition
  - SmoothOverlapAtomicPosition._abc_impl
  - SmoothOverlapAtomicPosition._sklearn_auto_wrap_output_keys
  - SmoothOverlapAtomicPosition.describer_type
  - SmoothOverlapAtomicPosition.transform_one()
- SortedCoulombMatrix
  - SortedCoulombMatrix._abc_impl
  - SortedCoulombMatrix._sklearn_auto_wrap_output_keys
  - SortedCoulombMatrix.describer_type
  - SortedCoulombMatrix.get_sorted_coulomb_mat()
  - SortedCoulombMatrix.transform_one()
- wrap_matminer_describer()
- maml.describers._composition module
  - ElementStats
    - ElementStats.ALLOWED_STATS
    - ElementStats.AVAILABLE_DATA
    - ElementStats._abc_impl
    - ElementStats._reduce_dimension()
    - ElementStats._sklearn_auto_wrap_output_keys
    - ElementStats.describer_type
    - ElementStats.from_data()
    - ElementStats.from_file()
    - ElementStats.transform_one()
  - _is_element_or_specie()
  - _keys_are_elements()
- maml.describers._m3gnet module
  - M3GNetStructure
    - M3GNetStructure._abc_impl
    - M3GNetStructure._sklearn_auto_wrap_output_keys
    - M3GNetStructure.transform_one()
- maml.describers._matminer module
  - wrap_matminer_describer()
- maml.describers._megnet module
  - MEGNetNotFound
  - MEGNetSite
    - MEGNetSite._abc_impl
    - MEGNetSite._sklearn_auto_wrap_output_keys
    - MEGNetSite.describer_type
    - MEGNetSite.transform_one()
  - MEGNetStructure
    - MEGNetStructure._abc_impl
    - MEGNetStructure._sklearn_auto_wrap_output_keys
    - MEGNetStructure.describer_type
    - MEGNetStructure.transform_one()
  - _load_model()
- maml.describers._rdf module
  - RadialDistributionFunction
    - RadialDistributionFunction._get_specie_density()
    - RadialDistributionFunction.get_site_coordination()
    - RadialDistributionFunction.get_site_rdf()
    - RadialDistributionFunction.get_species_coordination()
    - RadialDistributionFunction.get_species_rdf()
  - _dist_to_counts()
  - get_pair_distances()
- maml.describers._site module
  - BPSymmetryFunctions
    - BPSymmetryFunctions._abc_impl
    - BPSymmetryFunctions._fc()
    - BPSymmetryFunctions._sklearn_auto_wrap_output_keys
    - BPSymmetryFunctions.describer_type
    - BPSymmetryFunctions.transform_one()
  - BispectrumCoefficients
    - BispectrumCoefficients._abc_impl
    - BispectrumCoefficients._sklearn_auto_wrap_output_keys
    - BispectrumCoefficients.describer_type
    - BispectrumCoefficients.feature_dim
    - BispectrumCoefficients.subscripts
    - BispectrumCoefficients.transform_one()
  - MEGNetSite
    - MEGNetSite._abc_impl
    - MEGNetSite._sklearn_auto_wrap_output_keys
    - MEGNetSite.describer_type
    - MEGNetSite.transform_one()
  - SiteElementProperty
    - SiteElementProperty._abc_impl
    - SiteElementProperty._get_keys()
    - SiteElementProperty._sklearn_auto_wrap_output_keys
    - SiteElementProperty.describer_type
    - SiteElementProperty.feature_dim
    - SiteElementProperty.transform_one()
  - SmoothOverlapAtomicPosition
    - SmoothOverlapAtomicPosition._abc_impl
    - SmoothOverlapAtomicPosition._sklearn_auto_wrap_output_keys
    - SmoothOverlapAtomicPosition.describer_type
    - SmoothOverlapAtomicPosition.transform_one()
- maml.describers._spectrum module
- maml.describers._structure module
  - CoulombEigenSpectrum
    - CoulombEigenSpectrum._abc_impl
    - CoulombEigenSpectrum._sklearn_auto_wrap_output_keys
    - CoulombEigenSpectrum.describer_type
    - CoulombEigenSpectrum.transform_one()
  - CoulombMatrix
    - CoulombMatrix._abc_impl
    - CoulombMatrix._get_columb_mat()
    - CoulombMatrix._sklearn_auto_wrap_output_keys
    - CoulombMatrix.describer_type
    - CoulombMatrix.get_coulomb_mat()
    - CoulombMatrix.transform_one()
  - DistinctSiteProperty
    - DistinctSiteProperty._abc_impl
    - DistinctSiteProperty._sklearn_auto_wrap_output_keys
    - DistinctSiteProperty.describer_type
    - DistinctSiteProperty.supported_properties
    - DistinctSiteProperty.transform_one()
  - RandomizedCoulombMatrix
    - RandomizedCoulombMatrix._abc_impl
    - RandomizedCoulombMatrix._sklearn_auto_wrap_output_keys
    - RandomizedCoulombMatrix.describer_type
    - RandomizedCoulombMatrix.get_randomized_coulomb_mat()
    - RandomizedCoulombMatrix.transform_one()
  - SortedCoulombMatrix
    - SortedCoulombMatrix._abc_impl
    - SortedCoulombMatrix._sklearn_auto_wrap_output_keys
    - SortedCoulombMatrix.describer_type
    - SortedCoulombMatrix.get_sorted_coulomb_mat()
    - SortedCoulombMatrix.transform_one()
maml.models package
- AtomSets
  - AtomSets._get_data_generator()
  - AtomSets._predict()
  - AtomSets.evaluate()
  - AtomSets.fit()
  - AtomSets.from_dir()
  - AtomSets.save()
- KerasModel
  - KerasModel._get_validation_data()
  - KerasModel.fit()
- MLP
- SKLModel
- WeightedAverageLayer
  - WeightedAverageLayer.build()
  - WeightedAverageLayer.call()
  - WeightedAverageLayer.compute_output_shape()
  - WeightedAverageLayer.get_config()
  - WeightedAverageLayer.reduce_sum()
- WeightedSet2Set
  - WeightedSet2Set._lstm()
  - WeightedSet2Set.build()
  - WeightedSet2Set.call()
  - WeightedSet2Set.compute_output_shape()
  - WeightedSet2Set.get_config()
- Subpackages
  - maml.models.dl package
    - AtomSets
      - AtomSets._get_data_generator()
      - AtomSets._predict()
      - AtomSets.evaluate()
      - AtomSets.fit()
      - AtomSets.from_dir()
      - AtomSets.save()
    - MLP
    - WeightedAverageLayer
      - WeightedAverageLayer.build()
      - WeightedAverageLayer.call()
      - WeightedAverageLayer.compute_output_shape()
      - WeightedAverageLayer.get_config()
      - WeightedAverageLayer.reduce_sum()
    - WeightedSet2Set
      - WeightedSet2Set._lstm()
      - WeightedSet2Set.build()
      - WeightedSet2Set.call()
      - WeightedSet2Set.compute_output_shape()
      - WeightedSet2Set.get_config()
    - maml.models.dl._atomsets module
      - AtomSets
        
        AtomSets._get_data_generator()
        
        AtomSets._predict()
        
        AtomSets.evaluate()
        
        AtomSets.fit()
        
        AtomSets.from_dir()
        
        AtomSets.save()
      - construct_atom_sets()
    - maml.models.dl._keras_utils module
      - deserialize_keras_activation()
      - deserialize_keras_optimizer()
    - maml.models.dl._layers module
      - WeightedAverageLayer
        
        WeightedAverageLayer.build()
        
        WeightedAverageLayer.call()
        
        WeightedAverageLayer.compute_output_shape()
        
        WeightedAverageLayer.get_config()
        
        WeightedAverageLayer.reduce_sum()
      - WeightedSet2Set
        
        WeightedSet2Set._lstm()
        
        WeightedSet2Set.build()
        
        WeightedSet2Set.call()
        
        WeightedSet2Set.compute_output_shape()
        
        WeightedSet2Set.get_config()
    - maml.models.dl._mlp module
      - MLP
      - construct_mlp()
maml.sampling package
- maml.sampling.clustering module
  - BirchClustering
    - BirchClustering._sklearn_auto_wrap_output_keys
    - BirchClustering.fit()
    - BirchClustering.transform()
- maml.sampling.direct module
- maml.sampling.pca module
  - PrincipalComponentAnalysis
    - PrincipalComponentAnalysis._sklearn_auto_wrap_output_keys
    - PrincipalComponentAnalysis.fit()
    - PrincipalComponentAnalysis.transform()
- maml.sampling.stratified_sampling module
  - SelectKFromClusters
    - SelectKFromClusters._sklearn_auto_wrap_output_keys
    - SelectKFromClusters.fit()
    - SelectKFromClusters.transform()
maml.utils package
- ConstantValue
  - ConstantValue.get_value()
- DataSplitter
  - DataSplitter.split()
- DummyScaler
  - DummyScaler.from_training_data()
  - DummyScaler.inverse_transform()
  - DummyScaler.transform()
- LinearProfile
  - LinearProfile.get_value()
- MultiScratchDir
  - MultiScratchDir.SCR_LINK
- Scaler
  - Scaler.inverse_transform()
  - Scaler.transform()
- ShuffleSplitter
  - ShuffleSplitter.split()
- StandardScaler
  - StandardScaler.from_training_data()
  - StandardScaler.inverse_transform()
  - StandardScaler.transform()
- Stats
  - Stats.allowed_stats
  - Stats.average()
  - Stats.geometric_mean()
  - Stats.harmonic_mean()
  - Stats.inverse_mean()
  - Stats.kurtosis()
  - Stats.max()
  - Stats.mean()
  - Stats.mean_absolute_deviation()
  - Stats.mean_absolute_error()
  - Stats.min()
  - Stats.mode()
  - Stats.moment()
  - Stats.power_mean()
  - Stats.range()
  - Stats.shifted_geometric_mean()
  - Stats.skewness()
  - Stats.std()
- ValueProfile
  - ValueProfile.get_value()
  - ValueProfile.get_value()
  - ValueProfile.increment_step()
- check_structures_forces_stresses()
- convert_docs()
- cwt()
- feature_dim_from_test_system()
- fft_magnitude()
- get_describer_dummy_obj()
- get_full_args()
- get_full_stats_and_funcs()
- get_lammps_lattice_and_rotation()
- get_sp_method()
- njit()
- pool_from()
- spectrogram()
- stats_list_conversion()
- stress_format_change()
- stress_list_to_matrix()
- stress_matrix_to_list()
- to_array()
- to_composition()
- write_data_from_structure()
- wvd()
- maml.utils._data_conversion module
  - convert_docs()
  - doc_from()
  - pool_from()
  - to_array()
- maml.utils._data_split module
  - DataSplitter
    - DataSplitter.split()
  - ShuffleSplitter
    - ShuffleSplitter.split()
- maml.utils._dummy module
  - feature_dim_from_test_system()
  - get_describer_dummy_obj()
- maml.utils._inspect module
  - get_full_args()
  - get_param_types()
- maml.utils._jit module
  - njit()
- maml.utils._lammps module
  - _get_atomic_mass()
  - _get_charge()
  - check_structures_forces_stresses()
  - get_lammps_lattice_and_rotation()
  - stress_format_change()
  - stress_list_to_matrix()
  - stress_matrix_to_list()
  - write_data_from_structure()
- maml.utils._material module
  - to_composition()
- maml.utils._preprocessing module
  - DummyScaler
    - DummyScaler.from_training_data()
    - DummyScaler.inverse_transform()
    - DummyScaler.transform()
  - Scaler
    - Scaler.inverse_transform()
    - Scaler.transform()
  - StandardScaler
    - StandardScaler.from_training_data()
    - StandardScaler.inverse_transform()
    - StandardScaler.transform()
- maml.utils._signal_processing module
  - cwt()
  - fft_magnitude()
  - get_sp_method()
  - spectrogram()
  - wvd()
- maml.utils._stats module
  - Stats
    - Stats.allowed_stats
    - Stats.average()
    - Stats.geometric_mean()
    - Stats.harmonic_mean()
    - Stats.inverse_mean()
    - Stats.kurtosis()
    - Stats.max()
    - Stats.mean()
    - Stats.mean_absolute_deviation()
    - Stats.mean_absolute_error()
    - Stats.min()
    - Stats.mode()
    - Stats.moment()
    - Stats.power_mean()
    - Stats.range()
    - Stats.shifted_geometric_mean()
    - Stats.skewness()
    - Stats.std()
  - _add_allowed_stats()
  - _convert_a_or_b()
  - _moment_symbol_conversion()
  - _root_moment()
  - get_full_stats_and_funcs()
  - stats_list_conversion()
- maml.utils._tempfile module
  - MultiScratchDir
    - MultiScratchDir.SCR_LINK
    - MultiScratchDir.tempdirs
  - _copy_r_with_suffix()
- maml.utils._typing module
- maml.utils._value_profile module
  - ConstantValue
    - ConstantValue.get_value()
  - LinearProfile
    - LinearProfile.get_value()
  - ValueProfile
    - ValueProfile.get_value()
    - ValueProfile.get_value()
    - ValueProfile.increment_step()