README.md
setup.py
benchmol/__init__.py
benchmol.egg-info/PKG-INFO
benchmol.egg-info/SOURCES.txt
benchmol.egg-info/dependency_links.txt
benchmol.egg-info/top_level.txt
benchmol/configs/StructureNet_params.py
benchmol/configs/__init__.py
benchmol/configs/model_params.py
benchmol/data_process/__init__.py
benchmol/data_process/molecules/__init__.py
benchmol/data_process/molecules/fingerprints.py
benchmol/data_process/molecules/generate_3d_graph_data_from_csv.py
benchmol/data_process/molecules/generate_3d_images_pymol.py
benchmol/data_process/molecules/generate_StructureNet.py
benchmol/data_process/molecules/generate_graph_data_from_csv.py
benchmol/data_process/molecules/generate_images_rdkit.py
benchmol/data_process/molecules/get_fp_features.py
benchmol/data_process/molecules/geometry_helpers/__init__.py
benchmol/data_process/molecules/geometry_helpers/data_utils.py
benchmol/data_process/molecules/graph_helpers/__init__.py
benchmol/data_process/molecules/graph_helpers/mol2_3dgraph.py
benchmol/data_process/molecules/graph_helpers/mol2graph.py
benchmol/data_process/molecules/ogb_helpers/__init__.py
benchmol/data_process/molecules/ogb_helpers/mol.py
benchmol/data_process/molecules/ogb_helpers/mol_sdf2_3dgraph.py
benchmol/dataloader/__init__.py
benchmol/dataloader/collater.py
benchmol/dataloader/data_utils.py
benchmol/dataloader/feat_dataset.py
benchmol/dataloader/geometry_dataset.py
benchmol/dataloader/graph_dataset.py
benchmol/dataloader/image_dataset.py
benchmol/dataloader/sequence_dataset.py
benchmol/feature_extraction/__init__.py
benchmol/feature_extraction/feature_extractor.py
benchmol/metrics/__init__.py
benchmol/metrics/metric.py
benchmol/model_pools/__init__.py
benchmol/model_pools/base_utils.py
benchmol/model_pools/geometry_factory.py
benchmol/model_pools/graph_factory.py
benchmol/model_pools/image_factory.py
benchmol/model_pools/smiles_factory.py
benchmol/model_pools/geom3d/AWARE.py
benchmol/model_pools/geom3d/AutoEncoder.py
benchmol/model_pools/geom3d/BERT.py
benchmol/model_pools/geom3d/CDConv.py
benchmol/model_pools/geom3d/CNN.py
benchmol/model_pools/geom3d/ClofNet.py
benchmol/model_pools/geom3d/DMPNN.py
benchmol/model_pools/geom3d/DimeNet.py
benchmol/model_pools/geom3d/DimeNetPlusPlus.py
benchmol/model_pools/geom3d/DimeNet_utils.py
benchmol/model_pools/geom3d/EGNN.py
benchmol/model_pools/geom3d/ENN.py
benchmol/model_pools/geom3d/GEM.py
benchmol/model_pools/geom3d/GPS.py
benchmol/model_pools/geom3d/GPS_layer.py
benchmol/model_pools/geom3d/GVP.py
benchmol/model_pools/geom3d/GearNet.py
benchmol/model_pools/geom3d/GearNet_layer.py
benchmol/model_pools/geom3d/GeoSSL_DDM.py
benchmol/model_pools/geom3d/GeoSSL_PDM.py
benchmol/model_pools/geom3d/MLP.py
benchmol/model_pools/geom3d/PaiNN.py
benchmol/model_pools/geom3d/PaiNN_utils.py
benchmol/model_pools/geom3d/SE3_Transformer.py
benchmol/model_pools/geom3d/SE3_Transformer_utils.py
benchmol/model_pools/geom3d/SchNet.py
benchmol/model_pools/geom3d/SphereNet.py
benchmol/model_pools/geom3d/SphereNet_periodic.py
benchmol/model_pools/geom3d/SphereNet_utils.py
benchmol/model_pools/geom3d/TFN.py
benchmol/model_pools/geom3d/TFN_utils.py
benchmol/model_pools/geom3d/__init__.py
benchmol/model_pools/geom3d/fibers.py
benchmol/model_pools/geom3d/molecule_gnn_model.py
benchmol/model_pools/geom3d/molecule_gnn_model_simplified.py
benchmol/model_pools/geom3d/unimol.py
benchmol/model_pools/geom3d/utils.py
benchmol/model_pools/geom3d/Allegro/__init__.py
benchmol/model_pools/geom3d/Allegro/_keys.py
benchmol/model_pools/geom3d/Allegro/model/Allegro.py
benchmol/model_pools/geom3d/Allegro/model/__init__.py
benchmol/model_pools/geom3d/Allegro/nn/__init__.py
benchmol/model_pools/geom3d/Allegro/nn/_allegro.py
benchmol/model_pools/geom3d/Allegro/nn/_edgewise.py
benchmol/model_pools/geom3d/Allegro/nn/_fc.py
benchmol/model_pools/geom3d/Allegro/nn/_norm_basis.py
benchmol/model_pools/geom3d/Allegro/nn/cutoffs.py
benchmol/model_pools/geom3d/Allegro/nn/_strided/__init__.py
benchmol/model_pools/geom3d/Allegro/nn/_strided/_channels.py
benchmol/model_pools/geom3d/Allegro/nn/_strided/_contract.py
benchmol/model_pools/geom3d/Allegro/nn/_strided/_layout.py
benchmol/model_pools/geom3d/Allegro/nn/_strided/_linear.py
benchmol/model_pools/geom3d/Allegro/nn/_strided/_spmm.py
benchmol/model_pools/geom3d/Equiformer/__init__.py
benchmol/model_pools/geom3d/Equiformer/drop.py
benchmol/model_pools/geom3d/Equiformer/equiformer_type_0.py
benchmol/model_pools/geom3d/Equiformer/equiformer_type_01.py
benchmol/model_pools/geom3d/Equiformer/equiformer_type_0_periodic.py
benchmol/model_pools/geom3d/Equiformer/expnorm_rbf.py
benchmol/model_pools/geom3d/Equiformer/fast_activation.py
benchmol/model_pools/geom3d/Equiformer/fast_layer_norm.py
benchmol/model_pools/geom3d/Equiformer/gaussian_rbf.py
benchmol/model_pools/geom3d/Equiformer/graph_norm.py
benchmol/model_pools/geom3d/Equiformer/instance_norm.py
benchmol/model_pools/geom3d/Equiformer/layer_norm.py
benchmol/model_pools/geom3d/Equiformer/radial_basis.py
benchmol/model_pools/geom3d/Equiformer/radial_func.py
benchmol/model_pools/geom3d/Equiformer/tensor_product_rescale.py
benchmol/model_pools/geom3d/GemNet/GemNet.py
benchmol/model_pools/geom3d/GemNet/__init__.py
benchmol/model_pools/geom3d/GemNet/initializers.py
benchmol/model_pools/geom3d/GemNet/utils.py
benchmol/model_pools/geom3d/Graphormer/__init__.py
benchmol/model_pools/geom3d/Graphormer/graphormer.py
benchmol/model_pools/geom3d/Graphormer/graphormer_graph_encoder.py
benchmol/model_pools/geom3d/Graphormer/layers/__init__.py
benchmol/model_pools/geom3d/Graphormer/layers/graphormer_graph_encoder_layer.py
benchmol/model_pools/geom3d/Graphormer/layers/graphormer_layers.py
benchmol/model_pools/geom3d/Graphormer/layers/multihead_attention.py
benchmol/model_pools/geom3d/Graphormer/modules/__init__.py
benchmol/model_pools/geom3d/Graphormer/modules/fairseq_dropout.py
benchmol/model_pools/geom3d/Graphormer/modules/layer_drop.py
benchmol/model_pools/geom3d/Graphormer/modules/layer_norm.py
benchmol/model_pools/geom3d/Graphormer/modules/quant_noise.py
benchmol/model_pools/geom3d/Graphormer/modules/utils.py
benchmol/model_pools/geom3d/NequIP/__init__.py
benchmol/model_pools/geom3d/NequIP/data/AtomicData.py
benchmol/model_pools/geom3d/NequIP/data/AtomicDataDict.py
benchmol/model_pools/geom3d/NequIP/data/__init__.py
benchmol/model_pools/geom3d/NequIP/data/_build.py
benchmol/model_pools/geom3d/NequIP/data/_keys.py
benchmol/model_pools/geom3d/NequIP/data/_test_data.py
benchmol/model_pools/geom3d/NequIP/data/_util.py
benchmol/model_pools/geom3d/NequIP/data/dataloader.py
benchmol/model_pools/geom3d/NequIP/data/dataset.py
benchmol/model_pools/geom3d/NequIP/data/transforms.py
benchmol/model_pools/geom3d/NequIP/model/__init__.py
benchmol/model_pools/geom3d/NequIP/model/_build.py
benchmol/model_pools/geom3d/NequIP/model/_eng.py
benchmol/model_pools/geom3d/NequIP/model/_grads.py
benchmol/model_pools/geom3d/NequIP/model/_scaling.py
benchmol/model_pools/geom3d/NequIP/model/_weight_init.py
benchmol/model_pools/geom3d/NequIP/model/builder_utils.py
benchmol/model_pools/geom3d/NequIP/nn/__init__.py
benchmol/model_pools/geom3d/NequIP/nn/_atomwise.py
benchmol/model_pools/geom3d/NequIP/nn/_concat.py
benchmol/model_pools/geom3d/NequIP/nn/_convnetlayer.py
benchmol/model_pools/geom3d/NequIP/nn/_grad_output.py
benchmol/model_pools/geom3d/NequIP/nn/_graph_mixin.py
benchmol/model_pools/geom3d/NequIP/nn/_interaction_block.py
benchmol/model_pools/geom3d/NequIP/nn/_rescale.py
benchmol/model_pools/geom3d/NequIP/nn/_util.py
benchmol/model_pools/geom3d/NequIP/nn/cutoffs.py
benchmol/model_pools/geom3d/NequIP/nn/nonlinearities.py
benchmol/model_pools/geom3d/NequIP/nn/radial_basis.py
benchmol/model_pools/geom3d/NequIP/nn/embedding/__init__.py
benchmol/model_pools/geom3d/NequIP/nn/embedding/_edge.py
benchmol/model_pools/geom3d/NequIP/nn/embedding/_one_hot.py
benchmol/model_pools/geom3d/NequIP/scripts/__init__.py
benchmol/model_pools/geom3d/NequIP/scripts/_logger.py
benchmol/model_pools/geom3d/NequIP/scripts/benchmark.py
benchmol/model_pools/geom3d/NequIP/scripts/deploy.py
benchmol/model_pools/geom3d/NequIP/scripts/evaluate.py
benchmol/model_pools/geom3d/NequIP/scripts/run_md.py
benchmol/model_pools/geom3d/NequIP/scripts/train.py
benchmol/model_pools/geom3d/NequIP/utils/__init__.py
benchmol/model_pools/geom3d/NequIP/utils/_global_options.py
benchmol/model_pools/geom3d/NequIP/utils/auto_init.py
benchmol/model_pools/geom3d/NequIP/utils/batch_ops.py
benchmol/model_pools/geom3d/NequIP/utils/config.py
benchmol/model_pools/geom3d/NequIP/utils/git.py
benchmol/model_pools/geom3d/NequIP/utils/misc.py
benchmol/model_pools/geom3d/NequIP/utils/modules.py
benchmol/model_pools/geom3d/NequIP/utils/multiprocessing.py
benchmol/model_pools/geom3d/NequIP/utils/output.py
benchmol/model_pools/geom3d/NequIP/utils/regressor.py
benchmol/model_pools/geom3d/NequIP/utils/savenload.py
benchmol/model_pools/geom3d/NequIP/utils/scatter.py
benchmol/model_pools/geom3d/NequIP/utils/test.py
benchmol/model_pools/geom3d/NequIP/utils/tp_utils.py
benchmol/model_pools/geom3d/NequIP/utils/versions.py
benchmol/model_pools/geom3d/NequIP/utils/wandb.py
benchmol/model_pools/geom3d/PNA/PNA.py
benchmol/model_pools/geom3d/PNA/__init__.py
benchmol/model_pools/geom3d/PNA/aggregators.py
benchmol/model_pools/geom3d/PNA/scalers.py
benchmol/model_pools/geom3d/ProNet/ProNet.py
benchmol/model_pools/geom3d/ProNet/__init__.py
benchmol/model_pools/geom3d/ProNet/features.py
benchmol/model_pools/geom3d/SEGNN/SEGNN.py
benchmol/model_pools/geom3d/SEGNN/__init__.py
benchmol/model_pools/geom3d/SEGNN/balanced_irreps.py
benchmol/model_pools/geom3d/SEGNN/instance_norm.py
benchmol/model_pools/geom3d/SEGNN/node_attribute_network.py
benchmol/model_pools/geom3d/SEGNN/o3_building_blocks.py
benchmol/model_pools/geom3d/TransformerM/__init__.py
benchmol/model_pools/geom3d/TransformerM/transformer_m.py
benchmol/model_pools/geom3d/TransformerM/transformer_m_encoder.py
benchmol/model_pools/geom3d/TransformerM/layers/__init__.py
benchmol/model_pools/geom3d/TransformerM/layers/multihead_attention.py
benchmol/model_pools/geom3d/TransformerM/layers/transformer_m_encoder_layer.py
benchmol/model_pools/geom3d/TransformerM/layers/transformer_m_layers.py
benchmol/model_pools/geom3d/TransformerM/modules/__init__.py
benchmol/model_pools/geom3d/TransformerM/modules/droppath.py
benchmol/model_pools/geom3d/TransformerM/modules/fairseq_dropout.py
benchmol/model_pools/geom3d/TransformerM/modules/layer_drop.py
benchmol/model_pools/geom3d/TransformerM/modules/layer_norm.py
benchmol/model_pools/geom3d/TransformerM/modules/quant_noise.py
benchmol/model_pools/geom3d/TransformerM/modules/utils.py
benchmol/model_pools/geom3d/UniMol/__init__.py
benchmol/model_pools/geom3d/UniMol/unimol_tools/__init__.py
benchmol/model_pools/geom3d/UniMol/unimol_tools/predict.py
benchmol/model_pools/geom3d/UniMol/unimol_tools/predictor.py
benchmol/model_pools/geom3d/UniMol/unimol_tools/train.py
benchmol/model_pools/geom3d/UniMol/unimol_tools/config/__init__.py
benchmol/model_pools/geom3d/UniMol/unimol_tools/config/model_config.py
benchmol/model_pools/geom3d/UniMol/unimol_tools/data/__init__.py
benchmol/model_pools/geom3d/UniMol/unimol_tools/data/conformer.py
benchmol/model_pools/geom3d/UniMol/unimol_tools/data/datahub.py
benchmol/model_pools/geom3d/UniMol/unimol_tools/data/datareader.py
benchmol/model_pools/geom3d/UniMol/unimol_tools/data/datascaler.py
benchmol/model_pools/geom3d/UniMol/unimol_tools/data/dictionary.py
benchmol/model_pools/geom3d/UniMol/unimol_tools/models/__init__.py
benchmol/model_pools/geom3d/UniMol/unimol_tools/models/loss.py
benchmol/model_pools/geom3d/UniMol/unimol_tools/models/nnmodel.py
benchmol/model_pools/geom3d/UniMol/unimol_tools/models/transformers.py
benchmol/model_pools/geom3d/UniMol/unimol_tools/models/unimol.py
benchmol/model_pools/geom3d/UniMol/unimol_tools/tasks/__init__.py
benchmol/model_pools/geom3d/UniMol/unimol_tools/tasks/split.py
benchmol/model_pools/geom3d/UniMol/unimol_tools/tasks/trainer.py
benchmol/model_pools/geom3d/UniMol/unimol_tools/utils/__init__.py
benchmol/model_pools/geom3d/UniMol/unimol_tools/utils/base_logger.py
benchmol/model_pools/geom3d/UniMol/unimol_tools/utils/config_handler.py
benchmol/model_pools/geom3d/UniMol/unimol_tools/utils/metrics.py
benchmol/model_pools/geom3d/UniMol/unimol_tools/utils/util.py
benchmol/model_pools/geom3d/UniMol/unimol_tools/weights/__init__.py
benchmol/model_pools/geom3d/UniMol/unimol_tools/weights/weighthub.py
benchmol/model_pools/geom3d/from_se3cnn/SO3.py
benchmol/model_pools/geom3d/from_se3cnn/__init__.py
benchmol/model_pools/geom3d/from_se3cnn/cache_file.py
benchmol/model_pools/geom3d/from_se3cnn/representations.py
benchmol/model_pools/geom3d/from_se3cnn/utils_steerable.py
benchmol/model_pools/graph/__init__.py
benchmol/model_pools/graph/cgip.py
benchmol/model_pools/graph/cgip_helper.py
benchmol/model_pools/graph/deepergcn.py
benchmol/model_pools/graph/gnns.py
benchmol/model_pools/graph/gnns_graphmvp.py
benchmol/model_pools/graph/gnns_graphmvp_helper.py
benchmol/model_pools/graph/gnns_molebert.py
benchmol/model_pools/image/__init__.py
benchmol/model_pools/smiles/__init__.py
benchmol/model_pools/smiles/abc_smiles.py
benchmol/model_pools/smiles/chembert.py
benchmol/model_pools/smiles/molformer.py
benchmol/model_pools/smiles/chembert_helper/__init__.py
benchmol/model_pools/smiles/chembert_helper/dataset.py
benchmol/model_pools/smiles/chembert_helper/model_component.py
benchmol/model_pools/smiles/molformer_helper/__init__.py
benchmol/trainer/__init__.py
benchmol/trainer/trainer.py
benchmol/utils/__init__.py
benchmol/utils/evaluate.py
benchmol/utils/graph_utils.py
benchmol/utils/logger.py
benchmol/utils/public_utils.py
benchmol/utils/splitter.py