Backbone Models

• DeepFold
  • deepfold
    • deepfold.common
      • deepfold.common.protein
      • deepfold.common.residue_constants
    • deepfold.config
      • deepfold.config.AlphaFoldConfig
      • deepfold.config.AuxiliaryHeadsConfig
      • deepfold.config.CenterOfMassConfig
      • deepfold.config.DistogramHeadConfig
      • deepfold.config.DistogramLossConfig
      • deepfold.config.EvoformerStackConfig
      • deepfold.config.ExperimentallyResolvedHeadConfig
      • deepfold.config.ExperimentallyResolvedLossConfig
      • deepfold.config.ExtraMSAEmbedderConfig
      • deepfold.config.ExtraMSAStackConfig
      • deepfold.config.FAPELossConfig
      • deepfold.config.FeaturePipelineConfig
      • deepfold.config.InputEmbedderConfig
      • deepfold.config.LossConfig
      • deepfold.config.MaskedMSAHeadConfig
      • deepfold.config.MaskedMSALossConfig
      • deepfold.config.PLDDTLossConfig
      • deepfold.config.PerResidueLDDTCaPredictorConfig
      • deepfold.config.RecyclingEmbedderConfig
      • deepfold.config.StructureModuleConfig
      • deepfold.config.SupervisedChiLossConfig
      • deepfold.config.TMLossConfig
      • deepfold.config.TMScoreHeadConfig
      • deepfold.config.TemplateAngleEmbedderConfig
      • deepfold.config.TemplatePairEmbedderConfig
      • deepfold.config.TemplatePairStackConfig
      • deepfold.config.TemplatePointwiseAttentionConfig
      • deepfold.config.TemplateProjectionConfig
      • deepfold.config.TrainingConfig
      • deepfold.config.ViolationLossConfig
    • deepfold.data
      • deepfold.data.errors
      • deepfold.data.modules
      • deepfold.data.monomer
      • deepfold.data.multimer
      • deepfold.data.pdbio
      • deepfold.data.pdbx_parsing
      • deepfold.data.search
      • deepfold.data.tools
    • 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.loss.AlphaFoldLoss
    • 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.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.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
• MiniWorld
  • miniworld
    • miniworld.MiniWorld_train_multi_deep_v1_5_use_interaction
      • miniworld.MiniWorld_train_multi_deep_v1_5_use_interaction.a3m_parse
      • miniworld.MiniWorld_train_multi_deep_v1_5_use_interaction.add_weight_decay
      • miniworld.MiniWorld_train_multi_deep_v1_5_use_interaction.count_parameters
      • miniworld.MiniWorld_train_multi_deep_v1_5_use_interaction.visualize_2D_tensor
      • miniworld.MiniWorld_train_multi_deep_v1_5_use_interaction.EMA
      • miniworld.MiniWorld_train_multi_deep_v1_5_use_interaction.ModelVisulizer
    • miniworld.feature
      • miniworld.feature.MiniWorld_featuring_species
    • 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.DataClass
      • miniworld.utils.My_mistake
      • miniworld.utils.ProteinClass
      • miniworld.utils.arguments_MiniWorld
      • miniworld.utils.chemical
      • miniworld.utils.data_refactoring
      • miniworld.utils.ffindex
      • miniworld.utils.hhpred_parser
      • miniworld.utils.kalign_mapping
      • miniworld.utils.kinematics
      • miniworld.utils.output_visualize
      • miniworld.utils.parser_util
      • miniworld.utils.template_parser
      • miniworld.utils.util
      • miniworld.utils.util_module
• RoseTTAFold2