Python Module Index

b | d | g | m | p


	b
	`bapred`
	`bapred.data`
	`bapred.data.atom_feature`
	`bapred.data.data`
	`bapred.data.utils`
	`bapred.inference`
	`bapred.model`
	`bapred.model.GatedGCNLSPE`
	`bapred.model.GraphGPS`
	`bapred.model.MHA`
	`bapred.model.model`
	`bindingrmsd`
	`bindingrmsd.data`
	`bindingrmsd.data.data`
	`bindingrmsd.data.data_bck`
	`bindingrmsd.data.ligand_atom_feature`
	`bindingrmsd.data.protein_atom_feature`
	`bindingrmsd.data.utils`
	`bindingrmsd.inference`
	`bindingrmsd.model`
	`bindingrmsd.model.GatedGCNLSPE`
	`bindingrmsd.model.model`
	`bis_protein_structure`
	`bis_protein_structure.CROSSLINK`
	`bis_protein_structure.DATAGEN`
	`bis_protein_structure.DISULFIDE`
	`bis_protein_structure.MMEVAL`
	`bis_protein_structure.residue_constants`
	`bis_protein_structure.SOLVENTACC`
	`bis_protein_structure.split_pdb`
	`bis_protein_structure.TORSION2`
	`bsitep`
	`bsitep.proteindata`
	`bsitep.seresnet`
	`bsitep.utils`
	`bsitep.utils.data_utils`
	`bsitep.utils.model_utils`
	`bsitep.utils.pocket_utils`

	d
	`deepfold`
	`deepfold.common`
	`deepfold.common.protein`
	`deepfold.common.residue_constants`
	`deepfold.config`
	`deepfold.data`
	`deepfold.data.errors`
	`deepfold.data.modules`
	`deepfold.data.modules.dataloaders`
	`deepfold.data.modules.mmcif_dataset`
	`deepfold.data.modules.samplers`
	`deepfold.data.modules.single_dataset`
	`deepfold.data.monomer`
	`deepfold.data.multimer`
	`deepfold.data.multimer.input_features`
	`deepfold.data.multimer.msa_pairing`
	`deepfold.data.pdbio`
	`deepfold.data.pdbx_parsing`
	`deepfold.data.search`
	`deepfold.data.search.crfalign`
	`deepfold.data.search.input_features`
	`deepfold.data.search.mmcif`
	`deepfold.data.search.msa_identifiers`
	`deepfold.data.search.parsers`
	`deepfold.data.search.templates`
	`deepfold.data.tools`
	`deepfold.data.tools.hhblits`
	`deepfold.data.tools.hhsearch`
	`deepfold.data.tools.hmmbuild`
	`deepfold.data.tools.hmmsearch`
	`deepfold.data.tools.jackhmmer`
	`deepfold.data.tools.kalign`
	`deepfold.data.tools.utils`
	`deepfold.distributed`
	`deepfold.distributed.model_parallel`
	`deepfold.distributed.utils`
	`deepfold.eval`
	`deepfold.eval.cell_lists`
	`deepfold.eval.contact`
	`deepfold.eval.distogram`
	`deepfold.eval.msa`
	`deepfold.eval.plot`
	`deepfold.eval.pseudo_3d`
	`deepfold.loss`
	`deepfold.losses`
	`deepfold.losses.auxillary`
	`deepfold.losses.confidence`
	`deepfold.losses.geometry`
	`deepfold.losses.masked_msa`
	`deepfold.losses.procrustes`
	`deepfold.losses.utils`
	`deepfold.losses.violation`
	`deepfold.modules`
	`deepfold.modules.alphafold`
	`deepfold.modules.angle_resnet`
	`deepfold.modules.attention`
	`deepfold.modules.auxiliary_heads`
	`deepfold.modules.backbone_update`
	`deepfold.modules.dropout`
	`deepfold.modules.evoformer_block`
	`deepfold.modules.evoformer_block_pair_core`
	`deepfold.modules.evoformer_stack`
	`deepfold.modules.extra_msa_block`
	`deepfold.modules.extra_msa_embedder`
	`deepfold.modules.extra_msa_stack`
	`deepfold.modules.global_attention`
	`deepfold.modules.inductor`
	`deepfold.modules.input_embedder`
	`deepfold.modules.invariant_point_attention`
	`deepfold.modules.layer_norm`
	`deepfold.modules.linear`
	`deepfold.modules.msa_column_attention`
	`deepfold.modules.msa_column_global_attention`
	`deepfold.modules.msa_row_attention_with_pair_bias`
	`deepfold.modules.msa_transition`
	`deepfold.modules.outer_product_mean`
	`deepfold.modules.pair_transition`
	`deepfold.modules.recycling_embedder`
	`deepfold.modules.single_transition`
	`deepfold.modules.structure_module`
	`deepfold.modules.template_angle_embedder`
	`deepfold.modules.template_pair_block`
	`deepfold.modules.template_pair_embedder`
	`deepfold.modules.template_pair_stack`
	`deepfold.modules.template_pointwise_attention`
	`deepfold.modules.template_projection`
	`deepfold.modules.triangular_attention`
	`deepfold.modules.triangular_multiplicative_update`
	`deepfold.modules.tweaks`
	`deepfold.modules.tweaks.evo_attn`
	`deepfold.ops`
	`deepfold.ops.evoformer_attention`
	`deepfold.package_info`
	`deepfold.relax`
	`deepfold.relax.amber_minimize`
	`deepfold.relax.cleanup`
	`deepfold.relax.relax`
	`deepfold.relax.utils`
	`deepfold.runner`
	`deepfold.runner.config_utils`
	`deepfold.runner.parser`
	`deepfold.runner.utils`
	`deepfold.testing`
	`deepfold.testing.common`
	`deepfold.testing.utils`
	`deepfold.train`
	`deepfold.train.gradient_clipping`
	`deepfold.train.lr_scheduler`
	`deepfold.train.validation_metrics`
	`deepfold.utils`
	`deepfold.utils.checkpoint_utils`
	`deepfold.utils.chunk_utils`
	`deepfold.utils.crop_utils`
	`deepfold.utils.datetime_utils`
	`deepfold.utils.dist_utils`
	`deepfold.utils.feats_utils`
	`deepfold.utils.file_utils`
	`deepfold.utils.geometry`
	`deepfold.utils.geometry.quat_rigid`
	`deepfold.utils.geometry.rigid_matrix_vector`
	`deepfold.utils.geometry.rotation_matrix`
	`deepfold.utils.geometry.utils`
	`deepfold.utils.geometry.vector`
	`deepfold.utils.hash_utils`
	`deepfold.utils.import_utils`
	`deepfold.utils.iter_utils`
	`deepfold.utils.log_utils`
	`deepfold.utils.precision`
	`deepfold.utils.random`
	`deepfold.utils.rigid_utils`
	`deepfold.utils.script_utils`
	`deepfold.utils.swa_utils`
	`deepfold.utils.tensor_utils`
	`diffalign`
	`diffalign.models`
	`diffalign.models.common`
	`diffalign.models.encoder`
	`diffalign.models.encoder.edge`
	`diffalign.models.encoder.egnn`
	`diffalign.models.epsnet`
	`diffalign.models.epsnet.diffusion`
	`diffalign.train`
	`diffalign.utils`
	`diffalign.utils.chem`
	`diffalign.utils.common`
	`diffalign.utils.dataloader`
	`diffalign.utils.datasets`
	`diffalign.utils.evaluation`
	`diffalign.utils.evaluation.covmat`
	`diffalign.utils.misc`
	`diffalign.utils.transforms`
	`diffalign.utils.visualize`

	g
	`gd_dl`
	`gd_dl.data`
	`gd_dl.data.all_ML_rerank`
	`gd_dl.data.ML_inference`
	`gd_dl.data.ML_rerank`
	`gd_dl.data.single_ML_rerank`
	`gd_dl.lib_pdb_mol2`
	`gd_dl.models`
	`gd_dl.path_setting`
	`gd_dl.rerank_model`
	`gd_dl.utils`

	m
	`miniworld`
	`miniworld.feature`
	`miniworld.feature.MiniWorld_featuring_species`
	`miniworld.MiniWorld_train_multi_deep_v1_5_use_interaction`
	`miniworld.models_MiniWorld_v1_5_use_interaction`
	`miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module`
	`miniworld.models_MiniWorld_v1_5_use_interaction.AuxiliaryPredictor`
	`miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings`
	`miniworld.models_MiniWorld_v1_5_use_interaction.MiniWorld`
	`miniworld.models_MiniWorld_v1_5_use_interaction.Track_module`
	`miniworld.models_MiniWorld_v1_5_use_interaction.value_network`
	`miniworld.utils`
	`miniworld.utils.arguments_MiniWorld`
	`miniworld.utils.chemical`
	`miniworld.utils.data_refactoring`
	`miniworld.utils.DataClass`
	`miniworld.utils.ffindex`
	`miniworld.utils.hhpred_parser`
	`miniworld.utils.kalign_mapping`
	`miniworld.utils.kinematics`
	`miniworld.utils.My_mistake`
	`miniworld.utils.output_visualize`
	`miniworld.utils.parser_util`
	`miniworld.utils.ProteinClass`
	`miniworld.utils.template_parser`
	`miniworld.utils.util`
	`miniworld.utils.util_module`

	p
	`promptbind`
	`promptbind.data`
	`promptbind.data.data`
	`promptbind.data.inference_preprocess_mol_confs`
	`promptbind.data.inference_preprocess_protein`
	`promptbind.models`
	`promptbind.models.att_model`
	`promptbind.models.cross_att`
	`promptbind.models.egnn`
	`promptbind.models.model`
	`promptbind.models.model_utils`
	`promptbind.test_promptbind`
	`promptbind.train_promptbind`
	`promptbind.utils`
	`promptbind.utils.fabind_inference_dataset`
	`promptbind.utils.feature_utils`
	`promptbind.utils.generation_utils`
	`promptbind.utils.inference_mol_utils`
	`promptbind.utils.inference_pdb_utils`
	`promptbind.utils.logging_utils`
	`promptbind.utils.metrics`
	`promptbind.utils.metrics_to_tsb`
	`promptbind.utils.post_optim_utils`
	`promptbind.utils.utils`
	`promptbind.visualize_prompt_components`