Backbone Models

• 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
• miniworld
  • miniworld.MiniWorld_train_multi_deep_v1_5_use_interaction
  • 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