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AI toolkits for prediction of structure-based protein interaction 0.0.3 documentation
AI toolkits for prediction of structure-based protein interaction 0.0.3 documentation

Table of Contents

  • Backbone Models
    • DeepFold
      • deepfold
        • deepfold.common
          • deepfold.common.protein
            • deepfold.common.protein.add_pdb_headers
            • deepfold.common.protein.from_pdb_string
            • deepfold.common.protein.from_prediction
            • deepfold.common.protein.from_relaxation
            • deepfold.common.protein.get_pdb_headers
            • deepfold.common.protein.ideal_atom_mask
            • deepfold.common.protein.to_modelcif
            • deepfold.common.protein.to_pdb
            • deepfold.common.protein.Protein
          • deepfold.common.residue_constants
            • deepfold.common.residue_constants.aatype_to_str_sequence
            • deepfold.common.residue_constants.chi_angle_atom
            • deepfold.common.residue_constants.load_stereo_chemical_props
            • deepfold.common.residue_constants.make_atom14_dists_bounds
            • deepfold.common.residue_constants.map_structure_with_atom_order
            • deepfold.common.residue_constants.sequence_to_onehot
            • deepfold.common.residue_constants.Bond
            • deepfold.common.residue_constants.BondAngle
        • 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.modules.dataloaders
            • deepfold.data.modules.mmcif_dataset
            • deepfold.data.modules.samplers
            • deepfold.data.modules.single_dataset
          • deepfold.data.monomer
            • deepfold.data.monomer.build_atom_map
            • deepfold.data.monomer.fetch_ligand
            • deepfold.data.monomer.get_ligand
            • deepfold.data.monomer.read_ligand
            • deepfold.data.monomer.AtomMap
            • deepfold.data.monomer.Ligand
          • deepfold.data.multimer
            • deepfold.data.multimer.input_features
              • deepfold.data.multimer.input_features.add_assembly_features
              • deepfold.data.multimer.input_features.convert_monomer_features
              • deepfold.data.multimer.input_features.create_all_seq_msa_features
              • deepfold.data.multimer.input_features.create_all_seq_msa_features_from_a3m
              • deepfold.data.multimer.input_features.create_multimer_features
              • deepfold.data.multimer.input_features.crop_chains
              • deepfold.data.multimer.input_features.int_id_to_str_id
              • deepfold.data.multimer.input_features.pad_msa
              • deepfold.data.multimer.input_features.pair_and_merge
              • deepfold.data.multimer.input_features.process_final
              • deepfold.data.multimer.input_features.process_multimer_features
              • deepfold.data.multimer.input_features.process_single_chain
              • deepfold.data.multimer.input_features.process_unmerged_features
              • deepfold.data.multimer.input_features.ComplexInfo
            • deepfold.data.multimer.msa_pairing
              • deepfold.data.multimer.msa_pairing.block_diag
              • deepfold.data.multimer.msa_pairing.create_paired_features
              • deepfold.data.multimer.msa_pairing.deduplicate_unpaired_sequences
              • deepfold.data.multimer.msa_pairing.merge_chain_features
              • deepfold.data.multimer.msa_pairing.pad_features
              • deepfold.data.multimer.msa_pairing.pair_sequences
              • deepfold.data.multimer.msa_pairing.reorder_paired_rows
          • deepfold.data.pdbio
            • deepfold.data.pdbio.IO
            • deepfold.data.pdbio.PDBIO
          • deepfold.data.pdbx_parsing
            • deepfold.data.pdbx_parsing.fetch_mmcif
            • deepfold.data.pdbx_parsing.get_assemblies
            • deepfold.data.pdbx_parsing.get_chain_features
            • deepfold.data.pdbx_parsing.get_fasta
            • deepfold.data.pdbx_parsing.loop_to_dict
            • deepfold.data.pdbx_parsing.loop_to_list
            • deepfold.data.pdbx_parsing.print_amap
            • deepfold.data.pdbx_parsing.print_chain_features
            • deepfold.data.pdbx_parsing.read_mmcif
            • deepfold.data.pdbx_parsing.AssemblyGenerator
            • deepfold.data.pdbx_parsing.AtomSite
            • deepfold.data.pdbx_parsing.ModResidue
            • deepfold.data.pdbx_parsing.Monomer
            • deepfold.data.pdbx_parsing.Op
            • deepfold.data.pdbx_parsing.PDBxHeader
            • deepfold.data.pdbx_parsing.PDBxObject
            • deepfold.data.pdbx_parsing.PDBxParser
            • deepfold.data.pdbx_parsing.ParsingResult
            • deepfold.data.pdbx_parsing.ResidueAtPosition
            • deepfold.data.pdbx_parsing.ResiduePosition
          • deepfold.data.search
            • deepfold.data.search.crfalign
              • deepfold.data.search.crfalign.parse_crf
              • deepfold.data.search.crfalign.parse_pir
            • deepfold.data.search.input_features
              • deepfold.data.search.input_features.create_mmcif_features
              • deepfold.data.search.input_features.create_msa_features
              • deepfold.data.search.input_features.create_pdb_features
              • deepfold.data.search.input_features.create_protein_features
              • deepfold.data.search.input_features.create_sequence_features
              • deepfold.data.search.input_features.create_template_features
              • deepfold.data.search.input_features.create_template_features_from_hhr_string
              • deepfold.data.search.input_features.create_template_features_from_hmmsearch_sto_string
            • deepfold.data.search.mmcif
              • deepfold.data.search.mmcif.load_mmcif_file
              • deepfold.data.search.mmcif.parse_mmcif_string
              • deepfold.data.search.mmcif.zero_center_atom_positions
            • deepfold.data.search.msa_identifiers
              • deepfold.data.search.msa_identifiers.get_identifiers
            • deepfold.data.search.parsers
              • deepfold.data.search.parsers.convert_stockholm_to_a3m
              • deepfold.data.search.parsers.deduplicate_stockholm_msa
              • deepfold.data.search.parsers.parse_a3m
              • deepfold.data.search.parsers.parse_e_values_from_tblout
              • deepfold.data.search.parsers.parse_fasta
              • deepfold.data.search.parsers.parse_hhr
              • deepfold.data.search.parsers.parse_hmmsearch_a3m
              • deepfold.data.search.parsers.parse_hmmsearch_sto
              • deepfold.data.search.parsers.parse_stockholm
              • deepfold.data.search.parsers.remove_empty_columns_from_stockholm_msa
              • deepfold.data.search.parsers.truncate_stockholm_msa
              • deepfold.data.search.parsers.HitMetadata
              • deepfold.data.search.parsers.TemplateHit
            • deepfold.data.search.templates
              • deepfold.data.search.templates.build_query_to_hit_index_mapping
              • deepfold.data.search.templates.create_empty_template_feats
              • deepfold.data.search.templates.extract_template_features
              • deepfold.data.search.templates.get_atom_positions
              • deepfold.data.search.templates.load_mmcif_dict
              • deepfold.data.search.templates.load_pdb_obsolete_mapping
              • deepfold.data.search.templates.TemplateFeaturesResult
              • deepfold.data.search.templates.TemplateHitFeaturizer
          • deepfold.data.tools
            • deepfold.data.tools.hhblits
              • deepfold.data.tools.hhblits.HHBlits
            • deepfold.data.tools.hhsearch
              • deepfold.data.tools.hhsearch.HHSearch
            • deepfold.data.tools.hmmbuild
              • deepfold.data.tools.hmmbuild.Hmmbuild
            • deepfold.data.tools.hmmsearch
              • deepfold.data.tools.hmmsearch.Hmmsearch
            • deepfold.data.tools.jackhmmer
              • deepfold.data.tools.jackhmmer.Jackhmmer
            • deepfold.data.tools.kalign
              • deepfold.data.tools.kalign.Kalign
            • deepfold.data.tools.utils
              • deepfold.data.tools.utils.timing
              • deepfold.data.tools.utils.tmpdir_manager
              • deepfold.data.tools.utils.to_date
        • deepfold.distributed
          • deepfold.distributed.model_parallel
            • deepfold.distributed.model_parallel.all_to_all
            • deepfold.distributed.model_parallel.broadcast
            • deepfold.distributed.model_parallel.broadcast_on_model_parallel_region
            • deepfold.distributed.model_parallel.col_to_row
            • deepfold.distributed.model_parallel.copy_to_model_parallel_reigon
            • deepfold.distributed.model_parallel.disable
            • deepfold.distributed.model_parallel.enable
            • deepfold.distributed.model_parallel.gather
            • deepfold.distributed.model_parallel.gather_from_model_parallel_region
            • deepfold.distributed.model_parallel.group
            • deepfold.distributed.model_parallel.group_rank
            • deepfold.distributed.model_parallel.initialize
            • deepfold.distributed.model_parallel.is_enabled
            • deepfold.distributed.model_parallel.is_initialized
            • deepfold.distributed.model_parallel.rank
            • deepfold.distributed.model_parallel.reduce
            • deepfold.distributed.model_parallel.reduce_from_model_parallel_region
            • deepfold.distributed.model_parallel.row_to_col
            • deepfold.distributed.model_parallel.scatter
            • deepfold.distributed.model_parallel.scatter_to_model_parallel_region
            • deepfold.distributed.model_parallel.size
            • deepfold.distributed.model_parallel.transpose_on_model_parallel_region
            • deepfold.distributed.model_parallel.Disable
            • deepfold.distributed.model_parallel.Enable
          • deepfold.distributed.utils
            • deepfold.distributed.utils.assert_viewless_tensor
            • deepfold.distributed.utils.divide
            • deepfold.distributed.utils.ensure_divisibility
            • deepfold.distributed.utils.safely_set_viewless_tensor_data
            • deepfold.distributed.utils.GlobalMemoryBuffer
        • deepfold.eval
          • deepfold.eval.cell_lists
            • deepfold.eval.cell_lists.CellLists
            • deepfold.eval.cell_lists.Particle
          • deepfold.eval.contact
            • deepfold.eval.contact.contact_map
            • deepfold.eval.contact.Atom
          • deepfold.eval.distogram
            • deepfold.eval.distogram.bin_edges_np
            • deepfold.eval.distogram.calculate_bin_centers_np
            • deepfold.eval.distogram.compute_distogram
            • deepfold.eval.distogram.compute_predicted_distogram
            • deepfold.eval.distogram.undigitize
          • deepfold.eval.msa
            • deepfold.eval.msa.compute_neff_v1
            • deepfold.eval.msa.compute_neff_v2
          • deepfold.eval.plot
            • deepfold.eval.plot.find_cluster_boundaries
            • deepfold.eval.plot.plot_distogram
            • deepfold.eval.plot.plot_msa
            • deepfold.eval.plot.plot_plddt
            • deepfold.eval.plot.plot_predicted_alignment_error
          • deepfold.eval.pseudo_3d
            • deepfold.eval.pseudo_3d.kabsch
            • deepfold.eval.pseudo_3d.plot_protein
            • deepfold.eval.pseudo_3d.plot_protein_bb
        • deepfold.loss
          • deepfold.loss.AlphaFoldLoss
        • deepfold.losses
          • deepfold.losses.auxillary
            • deepfold.losses.auxillary.chain_centre_mass_loss
            • deepfold.losses.auxillary.experimentally_resolved_loss
            • deepfold.losses.auxillary.get_asym_mask
            • deepfold.losses.auxillary.repr_norm_loss
          • deepfold.losses.confidence
            • deepfold.losses.confidence.compute_plddt
            • deepfold.losses.confidence.compute_predicted_aligned_error
            • deepfold.losses.confidence.compute_tm
            • deepfold.losses.confidence.lddt
            • deepfold.losses.confidence.lddt_ca
            • deepfold.losses.confidence.plddt_loss
            • deepfold.losses.confidence.tm_loss
          • deepfold.losses.geometry
            • deepfold.losses.geometry.backbone_loss
            • deepfold.losses.geometry.compute_distogram
            • deepfold.losses.geometry.compute_fape
            • deepfold.losses.geometry.compute_renamed_ground_truth
            • deepfold.losses.geometry.distogram_loss
            • deepfold.losses.geometry.fape_loss
            • deepfold.losses.geometry.get_optimal_transform
            • deepfold.losses.geometry.kabsch_rmsd
            • deepfold.losses.geometry.sidechain_loss
            • deepfold.losses.geometry.superimpose
            • deepfold.losses.geometry.supervised_chi_loss
          • deepfold.losses.masked_msa
            • deepfold.losses.masked_msa.masked_msa_loss
          • deepfold.losses.procrustes
            • deepfold.losses.procrustes.flatten_batch_dims
            • deepfold.losses.procrustes.kabsch
            • deepfold.losses.procrustes.procrustes
            • deepfold.losses.procrustes.rigid_points_registration
            • deepfold.losses.procrustes.rigid_vectors_registration
            • deepfold.losses.procrustes.speical_procrustes
            • deepfold.losses.procrustes.svd
            • deepfold.losses.procrustes.unflatten_batch_dims
            • deepfold.losses.procrustes.Procrustes
          • deepfold.losses.utils
            • deepfold.losses.utils.calculate_bin_centers
            • deepfold.losses.utils.sigmoid_cross_entropy
            • deepfold.losses.utils.softmax_cross_entropy
          • deepfold.losses.violation
            • deepfold.losses.violation.between_residue_bond_loss
            • deepfold.losses.violation.between_residue_clash_loss
            • deepfold.losses.violation.compute_violation_metrics
            • deepfold.losses.violation.compute_violation_metrics_np
            • deepfold.losses.violation.extreme_ca_ca_distance_violations
            • deepfold.losses.violation.find_structural_violations
            • deepfold.losses.violation.find_structural_violations_np
            • deepfold.losses.violation.violation_loss
            • deepfold.losses.violation.within_residue_violations
        • deepfold.modules
          • deepfold.modules.alphafold
            • deepfold.modules.alphafold.AlphaFold
          • deepfold.modules.angle_resnet
            • deepfold.modules.angle_resnet.AngleResnet
            • deepfold.modules.angle_resnet.AngleResnetBlock
          • deepfold.modules.attention
            • deepfold.modules.attention.CrossAttentionNoGate
            • deepfold.modules.attention.SelfAttentionWithGate
          • deepfold.modules.auxiliary_heads
            • deepfold.modules.auxiliary_heads.AuxiliaryHeads
            • deepfold.modules.auxiliary_heads.DistogramHead
            • deepfold.modules.auxiliary_heads.ExperimentallyResolvedHead
            • deepfold.modules.auxiliary_heads.MaskedMSAHead
            • deepfold.modules.auxiliary_heads.PerResidueLDDTCaPredictor
            • deepfold.modules.auxiliary_heads.TMScoreHead
          • deepfold.modules.backbone_update
            • deepfold.modules.backbone_update.BackboneUpdate
          • deepfold.modules.dropout
            • deepfold.modules.dropout.Dropout
            • deepfold.modules.dropout.DropoutColumnwise
            • deepfold.modules.dropout.DropoutRowwise
          • deepfold.modules.evoformer_block
            • deepfold.modules.evoformer_block.EvoformerBlock
          • deepfold.modules.evoformer_block_pair_core
            • deepfold.modules.evoformer_block_pair_core.EvoformerBlockPairCore
          • deepfold.modules.evoformer_stack
            • deepfold.modules.evoformer_stack.EvoformerStack
          • deepfold.modules.extra_msa_block
            • deepfold.modules.extra_msa_block.ExtraMSABlock
          • deepfold.modules.extra_msa_embedder
            • deepfold.modules.extra_msa_embedder.ExtraMSAEmbedder
          • deepfold.modules.extra_msa_stack
            • deepfold.modules.extra_msa_stack.ExtraMSAStack
          • deepfold.modules.global_attention
            • deepfold.modules.global_attention.GlobalAttention
          • deepfold.modules.inductor
            • deepfold.modules.inductor.disable
            • deepfold.modules.inductor.enable
            • deepfold.modules.inductor.is_enabled
            • deepfold.modules.inductor.is_enabled_and_autograd_off
          • deepfold.modules.input_embedder
            • deepfold.modules.input_embedder.InputEmbedder
            • deepfold.modules.input_embedder.InputEmbedderMultimer
          • deepfold.modules.invariant_point_attention
            • deepfold.modules.invariant_point_attention.ipa_point_weights_init_
            • deepfold.modules.invariant_point_attention.InvariantPointAttention
            • deepfold.modules.invariant_point_attention.InvariantPointAttentionMultimer
            • deepfold.modules.invariant_point_attention.PointProjection
          • deepfold.modules.layer_norm
            • deepfold.modules.layer_norm.LayerNorm
          • deepfold.modules.linear
            • deepfold.modules.linear.final_init_
            • deepfold.modules.linear.gating_init_
            • deepfold.modules.linear.glorot_uniform_init_
            • deepfold.modules.linear.he_normal_init_
            • deepfold.modules.linear.lecun_normal_init_
            • deepfold.modules.linear.normal_init_
            • deepfold.modules.linear.trunc_normal_init_
            • deepfold.modules.linear.Linear
          • deepfold.modules.msa_column_attention
            • deepfold.modules.msa_column_attention.MSAColumnAttention
          • deepfold.modules.msa_column_global_attention
            • deepfold.modules.msa_column_global_attention.MSAColumnGlobalAttention
          • deepfold.modules.msa_row_attention_with_pair_bias
            • deepfold.modules.msa_row_attention_with_pair_bias.MSARowAttentionWithPairBias
          • deepfold.modules.msa_transition
            • deepfold.modules.msa_transition.MSATransition
          • deepfold.modules.outer_product_mean
            • deepfold.modules.outer_product_mean.OuterProductMean
          • deepfold.modules.pair_transition
            • deepfold.modules.pair_transition.PairTransition
          • deepfold.modules.recycling_embedder
            • deepfold.modules.recycling_embedder.RecyclingEmbedder
          • deepfold.modules.single_transition
            • deepfold.modules.single_transition.SingleTransition
          • deepfold.modules.structure_module
            • deepfold.modules.structure_module.StructureModule
          • deepfold.modules.template_angle_embedder
            • deepfold.modules.template_angle_embedder.TemplateAngleEmbedder
          • deepfold.modules.template_pair_block
            • deepfold.modules.template_pair_block.TemplatePairBlock
          • deepfold.modules.template_pair_embedder
            • deepfold.modules.template_pair_embedder.TemplatePairEmbedder
            • deepfold.modules.template_pair_embedder.TemplatePairEmbedderMultimer
          • deepfold.modules.template_pair_stack
            • deepfold.modules.template_pair_stack.TemplatePairStack
          • deepfold.modules.template_pointwise_attention
            • deepfold.modules.template_pointwise_attention.TemplatePointwiseAttention
          • deepfold.modules.template_projection
            • deepfold.modules.template_projection.TemplateProjection
          • deepfold.modules.triangular_attention
            • deepfold.modules.triangular_attention.TriangleAttention
            • deepfold.modules.triangular_attention.TriangleAttentionEndingNode
            • deepfold.modules.triangular_attention.TriangleAttentionStartingNode
          • deepfold.modules.triangular_multiplicative_update
            • deepfold.modules.triangular_multiplicative_update.TriangleMultiplicationIncoming
            • deepfold.modules.triangular_multiplicative_update.TriangleMultiplicationOutgoing
            • deepfold.modules.triangular_multiplicative_update.TriangleMultiplicativeUpdate
          • deepfold.modules.tweaks
            • deepfold.modules.tweaks.evo_attn
              • deepfold.modules.tweaks.evo_attn.disable
              • deepfold.modules.tweaks.evo_attn.enable
              • deepfold.modules.tweaks.evo_attn.is_enabled
        • deepfold.ops
          • deepfold.ops.evoformer_attention
            • deepfold.ops.evoformer_attention.deepspeed_evo_attn
        • deepfold.package_info
        • deepfold.relax
          • deepfold.relax.amber_minimize
            • deepfold.relax.amber_minimize.clean_protein
            • deepfold.relax.amber_minimize.find_violations
            • deepfold.relax.amber_minimize.get_violation_metrics
            • deepfold.relax.amber_minimize.make_atom14_positions
            • deepfold.relax.amber_minimize.run_pipeline
            • deepfold.relax.amber_minimize.will_restrain
          • deepfold.relax.cleanup
            • deepfold.relax.cleanup.clean_structure
            • deepfold.relax.cleanup.fix_pdb
          • deepfold.relax.relax
            • deepfold.relax.relax.AmberRelaxation
          • deepfold.relax.utils
            • deepfold.relax.utils.assert_equal_nonterminal_atom_types
            • deepfold.relax.utils.overwrite_b_factors
            • deepfold.relax.utils.overwrite_pdb_coordinates
        • deepfold.runner
          • deepfold.runner.config_utils
            • deepfold.runner.config_utils.load
          • deepfold.runner.parser
            • deepfold.runner.parser.Lexer
            • deepfold.runner.parser.Parser
          • deepfold.runner.utils
            • deepfold.runner.utils.safe_filename
        • deepfold.testing
          • deepfold.testing.common
            • deepfold.testing.common.skip_if_lt_x_gpu
            • deepfold.testing.common.skip_if_no_gpu
            • deepfold.testing.common.with_nccl_blocking_wait
            • deepfold.testing.common.MultiProcessTestCase
          • deepfold.testing.utils
            • deepfold.testing.utils.find_free_port
        • deepfold.train
          • deepfold.train.gradient_clipping
            • deepfold.train.gradient_clipping.update_norm_from_buckets
            • deepfold.train.gradient_clipping.AsyncGradientClipping
          • deepfold.train.lr_scheduler
            • deepfold.train.lr_scheduler.get_learning_rate
            • deepfold.train.lr_scheduler.set_learning_rate
            • deepfold.train.lr_scheduler.AlphaFoldLRScheduler
            • deepfold.train.lr_scheduler.OpenFoldBenchmarkLRScheduler
          • deepfold.train.validation_metrics
            • deepfold.train.validation_metrics.compute_validation_metrics
            • deepfold.train.validation_metrics.drmsd
            • deepfold.train.validation_metrics.gdt
            • deepfold.train.validation_metrics.gdt_ha
            • deepfold.train.validation_metrics.gdt_ts
        • deepfold.utils
          • deepfold.utils.checkpoint_utils
            • deepfold.utils.checkpoint_utils.map_init_state_dicts
            • deepfold.utils.checkpoint_utils.resume_checkpoint
            • deepfold.utils.checkpoint_utils.resume_from_latest_checkpoint
            • deepfold.utils.checkpoint_utils.save_checkpoint
            • deepfold.utils.checkpoint_utils.save_last_checkpoint
            • deepfold.utils.checkpoint_utils.save_val_checkpoint
          • deepfold.utils.chunk_utils
            • deepfold.utils.chunk_utils.chunk_layer
          • deepfold.utils.crop_utils
            • deepfold.utils.crop_utils.unpad_to_schema_shape_
          • deepfold.utils.datetime_utils
            • deepfold.utils.datetime_utils.datetime_from_string
            • deepfold.utils.datetime_utils.datetime_to_string
            • deepfold.utils.datetime_utils.get_timestamp_string
          • deepfold.utils.dist_utils
            • deepfold.utils.dist_utils.get_pad_size
            • deepfold.utils.dist_utils.pad_tensor
          • deepfold.utils.feats_utils
            • deepfold.utils.feats_utils.crop_a3m_string
            • deepfold.utils.feats_utils.crop_features
          • deepfold.utils.file_utils
            • deepfold.utils.file_utils.dump_pickle
            • deepfold.utils.file_utils.find_paths
            • deepfold.utils.file_utils.get_file_content_and_extension
            • deepfold.utils.file_utils.load_pickle
            • deepfold.utils.file_utils.read_text
            • deepfold.utils.file_utils.restore_wrapper
          • deepfold.utils.geometry
            • deepfold.utils.geometry.quat_rigid
              • deepfold.utils.geometry.quat_rigid.QuatRigid
            • deepfold.utils.geometry.rigid_matrix_vector
              • deepfold.utils.geometry.rigid_matrix_vector.Rigid3Array
            • deepfold.utils.geometry.rotation_matrix
              • deepfold.utils.geometry.rotation_matrix.Rot3Array
            • deepfold.utils.geometry.utils
              • deepfold.utils.geometry.utils.get_field_names
            • deepfold.utils.geometry.vector
              • deepfold.utils.geometry.vector.cross
              • deepfold.utils.geometry.vector.dihedral_angle
              • deepfold.utils.geometry.vector.dot
              • deepfold.utils.geometry.vector.euclidean_distance
              • deepfold.utils.geometry.vector.norm
              • deepfold.utils.geometry.vector.normalized
              • deepfold.utils.geometry.vector.square_euclidean_distance
              • deepfold.utils.geometry.vector.Vec3Array
          • deepfold.utils.hash_utils
            • deepfold.utils.hash_utils.hash_string_into_number
          • deepfold.utils.import_utils
            • deepfold.utils.import_utils.assign
            • deepfold.utils.import_utils.import_jax_weights_
            • deepfold.utils.import_utils.reshape_weight
            • deepfold.utils.import_utils.stacked
            • deepfold.utils.import_utils.Param
            • deepfold.utils.import_utils.ParamType
          • deepfold.utils.iter_utils
            • deepfold.utils.iter_utils.all_equal
            • deepfold.utils.iter_utils.flatten_dict
            • deepfold.utils.iter_utils.list_zip
            • deepfold.utils.iter_utils.map_dict_values
            • deepfold.utils.iter_utils.slice_generator
          • deepfold.utils.log_utils
            • deepfold.utils.log_utils.read_logs
            • deepfold.utils.log_utils.save_logs
            • deepfold.utils.log_utils.setup_logging
            • deepfold.utils.log_utils.TqdmHandler
          • deepfold.utils.precision
            • deepfold.utils.precision.is_fp16_enabled
          • deepfold.utils.random
            • deepfold.utils.random.get_seed_from_string
            • deepfold.utils.random.get_seed_randomly
            • deepfold.utils.random.numpy_seed
            • deepfold.utils.random.str_hash
          • deepfold.utils.rigid_utils
            • deepfold.utils.rigid_utils.identity_quats
            • deepfold.utils.rigid_utils.identity_rot_mats
            • deepfold.utils.rigid_utils.identity_trans
            • deepfold.utils.rigid_utils.invert_quat
            • deepfold.utils.rigid_utils.invert_rot_mat
            • deepfold.utils.rigid_utils.quat_multiply
            • deepfold.utils.rigid_utils.quat_multiply_by_vec
            • deepfold.utils.rigid_utils.quat_to_rot
            • deepfold.utils.rigid_utils.rot_matmul
            • deepfold.utils.rigid_utils.rot_to_quat
            • deepfold.utils.rigid_utils.rot_vec_mul
            • deepfold.utils.rigid_utils.Rigid
            • deepfold.utils.rigid_utils.Rotation
          • deepfold.utils.script_utils
            • deepfold.utils.script_utils.get_basename
            • deepfold.utils.script_utils.make_output_directory
            • deepfold.utils.script_utils.parse_fasta
          • deepfold.utils.swa_utils
            • deepfold.utils.swa_utils.AlphaFoldSWA
            • deepfold.utils.swa_utils.swa_avg_fn
          • deepfold.utils.tensor_utils
            • deepfold.utils.tensor_utils.add
            • deepfold.utils.tensor_utils.batched_gather
            • deepfold.utils.tensor_utils.collate
            • deepfold.utils.tensor_utils.dict_map
            • deepfold.utils.tensor_utils.dict_multimap
            • deepfold.utils.tensor_utils.flatten_final_dims
            • deepfold.utils.tensor_utils.masked_mean
            • deepfold.utils.tensor_utils.one_hot
            • deepfold.utils.tensor_utils.permute_final_dims
            • deepfold.utils.tensor_utils.pts_to_distogram
            • deepfold.utils.tensor_utils.tree_map
    • 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.feature.MiniWorld_featuring_species.MSA_block_deletion
            • miniworld.feature.MiniWorld_featuring_species.MSA_featurize_wo_statistics
            • miniworld.feature.MiniWorld_featuring_species.MSA_featurize_wo_statistics_by_chain
            • miniworld.feature.MiniWorld_featuring_species.center_and_realign_missing
            • miniworld.feature.MiniWorld_featuring_species.chain_break_cropping
            • miniworld.feature.MiniWorld_featuring_species.cluster_sum
            • miniworld.feature.MiniWorld_featuring_species.cutoff_chain_num
            • miniworld.feature.MiniWorld_featuring_species.display_top
            • miniworld.feature.MiniWorld_featuring_species.find_chain_combinations
            • miniworld.feature.MiniWorld_featuring_species.generate_combinations
            • miniworld.feature.MiniWorld_featuring_species.get_STRING_crop
            • miniworld.feature.MiniWorld_featuring_species.get_complex_crop
            • miniworld.feature.MiniWorld_featuring_species.get_crop
            • miniworld.feature.MiniWorld_featuring_species.get_same_crop_idx
            • miniworld.feature.MiniWorld_featuring_species.get_spatial_crop
            • miniworld.feature.MiniWorld_featuring_species.getsize
            • miniworld.feature.MiniWorld_featuring_species.permute_label
            • miniworld.feature.MiniWorld_featuring_species.random_split
            • miniworld.feature.MiniWorld_featuring_species.template_featurize
        • miniworld.models_MiniWorld_v1_5_use_interaction
          • miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module
            • miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module.Attention
            • miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module.AttentionWithBias
            • miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module.BiasedAxialAttention
            • miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module.FeedForwardLayer
            • miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module.GraphTriangleAttention
            • miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module.MSAColAttention
            • miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module.MSAColGlobalAttention
            • miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module.MSARowAttentionWithBias
            • miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module.SequenceWeight
            • miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module.StateAttentionGate
            • miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module.TriangleMultiplication
          • miniworld.models_MiniWorld_v1_5_use_interaction.AuxiliaryPredictor
            • miniworld.models_MiniWorld_v1_5_use_interaction.AuxiliaryPredictor.BinderNetwork
            • miniworld.models_MiniWorld_v1_5_use_interaction.AuxiliaryPredictor.DistanceNetwork
            • miniworld.models_MiniWorld_v1_5_use_interaction.AuxiliaryPredictor.ExpResolvedNetwork
            • miniworld.models_MiniWorld_v1_5_use_interaction.AuxiliaryPredictor.LDDTNetwork
            • miniworld.models_MiniWorld_v1_5_use_interaction.AuxiliaryPredictor.MaskedTokenNetwork
            • miniworld.models_MiniWorld_v1_5_use_interaction.AuxiliaryPredictor.PAENetwork
          • miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings
            • miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings.Extra_emb
            • miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings.InteractionEmb
            • miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings.MSA_emb
            • miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings.PositionalEncoding2D
            • miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings.Recycling
            • miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings.Species_emb
            • miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings.Templ_emb
            • miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings.TemplatePairStack
            • miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings.TemplateTorsionStack
          • miniworld.models_MiniWorld_v1_5_use_interaction.MiniWorld
            • miniworld.models_MiniWorld_v1_5_use_interaction.MiniWorld.MiniWorldModule
          • miniworld.models_MiniWorld_v1_5_use_interaction.Track_module
            • miniworld.models_MiniWorld_v1_5_use_interaction.Track_module.update_symm_Rs
            • miniworld.models_MiniWorld_v1_5_use_interaction.Track_module.update_symm_subs
            • miniworld.models_MiniWorld_v1_5_use_interaction.Track_module.IPA
            • miniworld.models_MiniWorld_v1_5_use_interaction.Track_module.IterBlock
            • miniworld.models_MiniWorld_v1_5_use_interaction.Track_module.IterativeSimulator
            • miniworld.models_MiniWorld_v1_5_use_interaction.Track_module.MSA2Pair
            • miniworld.models_MiniWorld_v1_5_use_interaction.Track_module.MSAPairStr2MSA
            • miniworld.models_MiniWorld_v1_5_use_interaction.Track_module.PairStr2Pair
            • miniworld.models_MiniWorld_v1_5_use_interaction.Track_module.SCPred
            • miniworld.models_MiniWorld_v1_5_use_interaction.Track_module.SeqSep
            • miniworld.models_MiniWorld_v1_5_use_interaction.Track_module.Str2Chain_IPA
            • miniworld.models_MiniWorld_v1_5_use_interaction.Track_module.Str2Residue_IPA
            • miniworld.models_MiniWorld_v1_5_use_interaction.Track_module.UpdatePairByValue
          • miniworld.models_MiniWorld_v1_5_use_interaction.value_network
            • miniworld.models_MiniWorld_v1_5_use_interaction.value_network.cat_neighbors_nodes
            • miniworld.models_MiniWorld_v1_5_use_interaction.value_network.gather_edges
            • miniworld.models_MiniWorld_v1_5_use_interaction.value_network.gather_nodes
            • miniworld.models_MiniWorld_v1_5_use_interaction.value_network.MPNN_block
            • miniworld.models_MiniWorld_v1_5_use_interaction.value_network.PositionWiseFeedForward
            • miniworld.models_MiniWorld_v1_5_use_interaction.value_network.StrSeqValueNet
        • miniworld.utils
          • miniworld.utils.DataClass
            • miniworld.utils.DataClass.MiniWorldBatchedDataClass
            • miniworld.utils.DataClass.MiniWorldDataClass
            • miniworld.utils.DataClass.MiniWorldLabelClass
            • miniworld.utils.DataClass.MiniWorldMSAClass
            • miniworld.utils.DataClass.MiniWorldTemplateClass
            • miniworld.utils.DataClass.MiniWorldWrongDataClass
          • miniworld.utils.My_mistake
            • miniworld.utils.My_mistake.MSA_change_idx
            • miniworld.utils.My_mistake.MSA_change_idx_v2
          • miniworld.utils.ProteinClass
            • miniworld.utils.ProteinClass.PDB_parsing
            • miniworld.utils.ProteinClass.Protein
            • miniworld.utils.ProteinClass.ProteinMSA
            • miniworld.utils.ProteinClass.ProteinSequence
            • miniworld.utils.ProteinClass.ProteinStructure
            • miniworld.utils.ProteinClass.ProteinTemplate
            • miniworld.utils.ProteinClass.ProteinTemplates
          • miniworld.utils.arguments_MiniWorld
            • miniworld.utils.arguments_MiniWorld.get_args
          • miniworld.utils.chemical
          • miniworld.utils.data_refactoring
            • miniworld.utils.data_refactoring.AF_Results_filtering
            • miniworld.utils.data_refactoring.AF_Results_json_filtering
            • miniworld.utils.data_refactoring.AF_Results_json_viewer
            • miniworld.utils.data_refactoring.PDB_parsing_from_pt
            • miniworld.utils.data_refactoring.STRING_refactoring
            • miniworld.utils.data_refactoring.a3m_pickling
            • miniworld.utils.data_refactoring.check_hhr_loaded
            • miniworld.utils.data_refactoring.get_ID_to_source_dict
            • miniworld.utils.data_refactoring.get_csv
            • miniworld.utils.data_refactoring.get_hash_dict
            • miniworld.utils.data_refactoring.get_query_from_a3m
            • miniworld.utils.data_refactoring.gzip_files
            • miniworld.utils.data_refactoring.hhr_dir_rerefactoring
            • miniworld.utils.data_refactoring.hhr_file_rerefactoring
            • miniworld.utils.data_refactoring.hhr_refactoring
            • miniworld.utils.data_refactoring.mmcif_Full_sequence_parsing
            • miniworld.utils.data_refactoring.mmcif_full_sequence
            • miniworld.utils.data_refactoring.mmcif_line_parser
            • miniworld.utils.data_refactoring.mmcif_loop_parser
            • miniworld.utils.data_refactoring.mmcif_parsing
            • miniworld.utils.data_refactoring.mmcif_pickling
            • miniworld.utils.data_refactoring.pdb_Sampling
            • miniworld.utils.data_refactoring.pdb_pickling
            • miniworld.utils.data_refactoring.print_hhr_pt
            • miniworld.utils.data_refactoring.protein_to_template
            • miniworld.utils.data_refactoring.refactoring_hhr_file
            • miniworld.utils.data_refactoring.test_a3m
            • miniworld.utils.data_refactoring.test_a3m_file
          • miniworld.utils.ffindex
            • miniworld.utils.ffindex.finish_db
            • miniworld.utils.ffindex.get_entry_by_name
            • miniworld.utils.ffindex.read_data
            • miniworld.utils.ffindex.read_entry_data
            • miniworld.utils.ffindex.read_entry_lines
            • miniworld.utils.ffindex.read_index
            • miniworld.utils.ffindex.write_entries_to_db
            • miniworld.utils.ffindex.write_entry
            • miniworld.utils.ffindex.write_entry_with_file
            • miniworld.utils.ffindex.FFindexEntry
          • miniworld.utils.hhpred_parser
            • miniworld.utils.hhpred_parser.hhpred_parser
            • miniworld.utils.hhpred_parser.parse_segment
          • miniworld.utils.kalign_mapping
            • miniworld.utils.kalign_mapping.kalign_mapping
          • miniworld.utils.kinematics
            • miniworld.utils.kinematics.Qs2Rs
            • miniworld.utils.kinematics.Rs2Qs
            • miniworld.utils.kinematics.avgQ
            • miniworld.utils.kinematics.c6d_to_bins
            • miniworld.utils.kinematics.c6d_to_bins2
            • miniworld.utils.kinematics.dist_to_bins
            • miniworld.utils.kinematics.dist_to_onehot
            • miniworld.utils.kinematics.get_ang
            • miniworld.utils.kinematics.get_dih
            • miniworld.utils.kinematics.get_pair_dist
            • miniworld.utils.kinematics.normQ
            • miniworld.utils.kinematics.xyz_to_bbtor
            • miniworld.utils.kinematics.xyz_to_c6d
            • miniworld.utils.kinematics.xyz_to_chi1
            • miniworld.utils.kinematics.xyz_to_t2d
          • miniworld.utils.output_visualize
            • miniworld.utils.output_visualize.TMalign
            • miniworld.utils.output_visualize.align_two_protein
            • miniworld.utils.output_visualize.atom_to_pdb_line
            • miniworld.utils.output_visualize.output_to_pdb
            • miniworld.utils.output_visualize.protein_to_pdb
            • miniworld.utils.output_visualize.tensor_to_pdb
            • miniworld.utils.output_visualize.visualize_2D_heatmap
            • miniworld.utils.output_visualize.visualize_2D_heatmaps
            • miniworld.utils.output_visualize.visualize_2D_tensor
            • miniworld.utils.output_visualize.visualize_t_map
          • miniworld.utils.parser_util
            • miniworld.utils.parser_util.center_and_realign_missing
            • miniworld.utils.parser_util.cross_product_matrix
            • miniworld.utils.parser_util.donorHs
            • miniworld.utils.parser_util.get_Cb
            • miniworld.utils.parser_util.make_frame
            • miniworld.utils.parser_util.random_rot_trans
            • miniworld.utils.parser_util.rigid_from_3_points
            • miniworld.utils.parser_util.th_ang_v
            • miniworld.utils.parser_util.th_dih
            • miniworld.utils.parser_util.th_dih_v
            • miniworld.utils.parser_util.writepdb
          • miniworld.utils.template_parser
            • miniworld.utils.template_parser.get_args
            • miniworld.utils.template_parser.parse_a3m
            • miniworld.utils.template_parser.parse_pdb
            • miniworld.utils.template_parser.parse_pdb_lines
            • miniworld.utils.template_parser.parse_pdb_lines_w_seq
            • miniworld.utils.template_parser.parse_pdb_w_seq
            • miniworld.utils.template_parser.parse_templates_raw
            • miniworld.utils.template_parser.read_template_pdb
            • miniworld.utils.template_parser.read_templates
          • miniworld.utils.util
            • miniworld.utils.util.cal_integrated_frame
            • miniworld.utils.util.center_and_realign_missing
            • miniworld.utils.util.centering_RT
            • miniworld.utils.util.cross_product_matrix
            • miniworld.utils.util.donorHs
            • miniworld.utils.util.draw_attn
            • miniworld.utils.util.draw_attn_multirow
            • miniworld.utils.util.draw_pae
            • miniworld.utils.util.extract_tip_atom_xyz
            • miniworld.utils.util.generate_initial_xyz
            • miniworld.utils.util.generate_random_xyz
            • miniworld.utils.util.generate_symmetric_operation
            • miniworld.utils.util.generate_symmetric_xyz
            • miniworld.utils.util.get_Cb
            • miniworld.utils.util.get_train_valid_data_dir_dictionary
            • miniworld.utils.util.make_frame
            • miniworld.utils.util.random_rot_trans
            • miniworld.utils.util.rigid_from_3_points
            • miniworld.utils.util.rigid_from_3_points_v2
            • miniworld.utils.util.th_ang_v
            • miniworld.utils.util.th_dih
            • miniworld.utils.util.th_dih_v
            • miniworld.utils.util.writepdb
          • miniworld.utils.util_module
            • miniworld.utils.util_module.create_custom_forward
            • miniworld.utils.util_module.get_clones
            • miniworld.utils.util_module.get_seqsep
            • miniworld.utils.util_module.get_topk
            • miniworld.utils.util_module.init_lecun_normal
            • miniworld.utils.util_module.init_lecun_normal_param
            • miniworld.utils.util_module.make_rotX
            • miniworld.utils.util_module.make_rotZ
            • miniworld.utils.util_module.make_rot_axis
            • miniworld.utils.util_module.rbf
            • miniworld.utils.util_module.ComputeAllAtomCoords
            • miniworld.utils.util_module.Dropout
            • miniworld.utils.util_module.XYZConverter
    • RoseTTAFold2
  • Tools
    • BAPred
      • bapred
        • bapred.cli
          • bapred.cli.main
        • bapred.data
          • bapred.data.atom_feature
            • bapred.data.atom_feature.atom_feature
            • bapred.data.atom_feature.bond_feature
            • bapred.data.atom_feature.get_atom_feature
            • bapred.data.atom_feature.get_bond_feature
            • bapred.data.atom_feature.get_distance_feature
            • bapred.data.atom_feature.get_indices
            • bapred.data.atom_feature.get_indices_sparse
            • bapred.data.atom_feature.get_interact_feature
            • bapred.data.atom_feature.get_mol_coordinate
            • bapred.data.atom_feature.get_smarts_feature
          • bapred.data.data
            • bapred.data.data.load_ligands
            • bapred.data.data.process_ligand_file
            • bapred.data.data.BAPredDataset
          • bapred.data.utils
            • bapred.data.utils.calculate_pair_distance
            • bapred.data.utils.is_one
            • bapred.data.utils.load_obj
            • bapred.data.utils.one_hot
            • bapred.data.utils.save_obj
        • bapred.inference
          • bapred.inference.inference
        • bapred.logger
          • bapred.logger.setup_logger
        • bapred.model
          • bapred.model.GatedGCNLSPE
            • bapred.model.GatedGCNLSPE.GatedGCNLSPELayer
          • bapred.model.GraphGPS
            • bapred.model.GraphGPS.GraphGPS
          • bapred.model.MHA
            • bapred.model.MHA.MultiHeadAttention
          • bapred.model.model
            • bapred.model.model.PredictionPKD
    • BindingRMSD
      • bindingrmsd
        • bindingrmsd.data
          • bindingrmsd.data.data
            • bindingrmsd.data.data.load_ligands
            • bindingrmsd.data.data.process_ligand_file
            • bindingrmsd.data.data.PoseSelectionDataset
          • bindingrmsd.data.data_bck
            • bindingrmsd.data.data_bck.load_ligands
            • bindingrmsd.data.data_bck.process_dlg
            • bindingrmsd.data.data_bck.process_ligand_file
            • bindingrmsd.data.data_bck.PoseSelectionDataset
          • bindingrmsd.data.ligand_atom_feature
            • bindingrmsd.data.ligand_atom_feature.atom_feature
            • bindingrmsd.data.ligand_atom_feature.bond_feature
            • bindingrmsd.data.ligand_atom_feature.calculate_pair_distance
            • bindingrmsd.data.ligand_atom_feature.get_atom_feature
            • bindingrmsd.data.ligand_atom_feature.get_bond_feature
            • bindingrmsd.data.ligand_atom_feature.get_distance_feature
            • bindingrmsd.data.ligand_atom_feature.get_indices
            • bindingrmsd.data.ligand_atom_feature.get_indices_sparse
            • bindingrmsd.data.ligand_atom_feature.get_interact_feature
            • bindingrmsd.data.ligand_atom_feature.get_mol_coordinate
            • bindingrmsd.data.ligand_atom_feature.get_smarts_feature
            • bindingrmsd.data.ligand_atom_feature.is_one
            • bindingrmsd.data.ligand_atom_feature.load_obj
            • bindingrmsd.data.ligand_atom_feature.mol_to_graph
            • bindingrmsd.data.ligand_atom_feature.one_hot
            • bindingrmsd.data.ligand_atom_feature.save_obj
          • bindingrmsd.data.protein_atom_feature
            • bindingrmsd.data.protein_atom_feature.get_all_graph
            • bindingrmsd.data.protein_atom_feature.pl_to_c_graph
            • bindingrmsd.data.protein_atom_feature.prot_to_graph
            • bindingrmsd.data.protein_atom_feature.scaler
          • bindingrmsd.data.utils
            • bindingrmsd.data.utils.is_one
            • bindingrmsd.data.utils.load_obj
            • bindingrmsd.data.utils.one_hot
            • bindingrmsd.data.utils.save_obj
        • bindingrmsd.inference
          • bindingrmsd.inference.inference
          • bindingrmsd.inference.main
        • bindingrmsd.model
          • bindingrmsd.model.GatedGCNLSPE
            • bindingrmsd.model.GatedGCNLSPE.GatedGCNLSPELayer
          • bindingrmsd.model.model
            • bindingrmsd.model.model.PredictionRMSD
    • BIS Protein Structure
      • bis_protein_structure
        • bis_protein_structure.CROSSLINK
          • bis_protein_structure.CROSSLINK.calculate_calpha_distogram
          • bis_protein_structure.CROSSLINK.calculate_lys_leu_map
          • bis_protein_structure.CROSSLINK.calculate_sa_map
          • bis_protein_structure.CROSSLINK.calculate_tryptic_map
          • bis_protein_structure.CROSSLINK.load_list_from_file
          • bis_protein_structure.CROSSLINK.plot_cross_link
          • bis_protein_structure.CROSSLINK.readMMCIF
          • bis_protein_structure.CROSSLINK.readPDB
        • bis_protein_structure.DATAGEN
          • bis_protein_structure.DATAGEN.create_structure_from_feature
          • bis_protein_structure.DATAGEN.generate_feature_dict
          • bis_protein_structure.DATAGEN.mmcif_to_pdbs
          • bis_protein_structure.DATAGEN.parallel_processing
          • bis_protein_structure.DATAGEN.parse_fasta
          • bis_protein_structure.DATAGEN.parse_mmcif
          • bis_protein_structure.DATAGEN.process_mmcif_to_pdbs
          • bis_protein_structure.DATAGEN.read_fasta
          • bis_protein_structure.DATAGEN.AllResiduesSelector
        • bis_protein_structure.DISULFIDE
          • bis_protein_structure.DISULFIDE.get_SS_ver5
          • bis_protein_structure.DISULFIDE.readMMCIF_label
        • bis_protein_structure.MMEVAL
          • bis_protein_structure.MMEVAL.convert_string
          • bis_protein_structure.MMEVAL.eval_interface
          • bis_protein_structure.MMEVAL.get_ICS
          • bis_protein_structure.MMEVAL.get_IPS
          • bis_protein_structure.MMEVAL.get_contact
          • bis_protein_structure.MMEVAL.readPDB
          • bis_protein_structure.MMEVAL.restype_refer_atoms
        • bis_protein_structure.SOLVENTACC
          • bis_protein_structure.SOLVENTACC.contains_non_numeric
          • bis_protein_structure.SOLVENTACC.convert_mmcif_to_dssp
          • bis_protein_structure.SOLVENTACC.convert_mmcif_to_dssp_parallel
          • bis_protein_structure.SOLVENTACC.convert_pdb_to_dssp
          • bis_protein_structure.SOLVENTACC.create_structure_from_feature
          • bis_protein_structure.SOLVENTACC.extract_coords_from_pdb
          • bis_protein_structure.SOLVENTACC.getTMscore
          • bis_protein_structure.SOLVENTACC.load_pickle_file
        • bis_protein_structure.TORSION2
          • bis_protein_structure.TORSION2.angles_to_sincos
          • bis_protein_structure.TORSION2.getDistogram
          • bis_protein_structure.TORSION2.getTorsion_acc
          • bis_protein_structure.TORSION2.get_bondangle
          • bis_protein_structure.TORSION2.get_coordinates
          • bis_protein_structure.TORSION2.get_refer_atoms
          • bis_protein_structure.TORSION2.get_torsion
          • bis_protein_structure.TORSION2.new_dihedral
          • bis_protein_structure.TORSION2.readPDB
          • bis_protein_structure.TORSION2.restype_refer_atoms
          • bis_protein_structure.TORSION2.sidechain_sym_angle
          • bis_protein_structure.TORSION2.torsion_angle_loss
        • bis_protein_structure.residue_constants
          • bis_protein_structure.residue_constants.chi_angle_atom
          • bis_protein_structure.residue_constants.load_stereo_chemical_props
          • bis_protein_structure.residue_constants.make_atom14_dists_bounds
          • bis_protein_structure.residue_constants.sequence_to_onehot
          • bis_protein_structure.residue_constants.Bond
          • bis_protein_structure.residue_constants.BondAngle
        • bis_protein_structure.split_pdb
          • bis_protein_structure.split_pdb.extract
          • bis_protein_structure.split_pdb.split_the_pdb
    • SwinSite
    • DiffAlign
      • diffalign
        • diffalign.models
          • diffalign.models.common
            • diffalign.models.common.extend_graph_order_radius
            • diffalign.models.common.extend_to_cross_attention
            • diffalign.models.common.MultiLayerPerceptron
          • diffalign.models.encoder
            • diffalign.models.encoder.cross_attention
              • diffalign.models.encoder.cross_attention.CrossAttention
              • diffalign.models.encoder.cross_attention.CrossGraphAligner
            • diffalign.models.encoder.edge
              • diffalign.models.encoder.edge.MLPEdgeEncoder
            • diffalign.models.encoder.egnn
              • diffalign.models.encoder.egnn.unsorted_segment_sum
              • diffalign.models.encoder.egnn.EGNN
              • diffalign.models.encoder.egnn.E_GCL
          • diffalign.models.epsnet
            • diffalign.models.epsnet.diffusion
              • diffalign.models.epsnet.diffusion.cosine_beta_schedule
              • diffalign.models.epsnet.diffusion.get_distance
              • diffalign.models.epsnet.diffusion.linear_beta_schedule
              • diffalign.models.epsnet.diffusion.merge_graphs_in_batch
              • diffalign.models.epsnet.diffusion.DDPMTimeEncoder
              • diffalign.models.epsnet.diffusion.DiffAlign
              • diffalign.models.epsnet.diffusion.SinusoidalPosEmb
        • diffalign.utils
          • diffalign.utils.chem
            • diffalign.utils.chem.bond_type_to_int
            • diffalign.utils.chem.draw_mol_svg
            • diffalign.utils.chem.get_2D_mol
            • diffalign.utils.chem.get_atom_symbol
            • diffalign.utils.chem.get_atoms_in_ring
            • diffalign.utils.chem.get_best_rmsd
            • diffalign.utils.chem.mol_to_graph_data_obj
            • diffalign.utils.chem.mol_to_smiles
            • diffalign.utils.chem.mol_to_smiles_without_Hs
            • diffalign.utils.chem.remove_duplicate_mols
            • diffalign.utils.chem.set_conformer_positions
            • diffalign.utils.chem.set_rdmol_positions
            • diffalign.utils.chem.set_rdmol_positions_
            • diffalign.utils.chem.update_data_pos_from_rdmol
            • diffalign.utils.chem.update_data_rdmol_positions
    • GalaxyDock DL
      • gd_dl
        • gd_dl.data
          • gd_dl.data.ML_inference
            • gd_dl.data.ML_inference.calc_e
            • gd_dl.data.ML_inference.calculate_energy
            • gd_dl.data.ML_inference.get_ref_vec
            • gd_dl.data.ML_inference.load_files
            • gd_dl.data.ML_inference.main
          • gd_dl.data.ML_rerank
            • gd_dl.data.ML_rerank.calc_e
            • gd_dl.data.ML_rerank.main
          • gd_dl.data.all_ML_rerank
            • gd_dl.data.all_ML_rerank.calc_e
            • gd_dl.data.all_ML_rerank.main
          • gd_dl.data.single_ML_rerank
            • gd_dl.data.single_ML_rerank.calc_e
            • gd_dl.data.single_ML_rerank.main
        • gd_dl.lib_pdb_mol2
          • gd_dl.lib_pdb_mol2.Atom
          • gd_dl.lib_pdb_mol2.MOL2
          • gd_dl.lib_pdb_mol2.MOL2_UNIT
          • gd_dl.lib_pdb_mol2.Model
          • gd_dl.lib_pdb_mol2.PDB
          • gd_dl.lib_pdb_mol2.PDBline
          • gd_dl.lib_pdb_mol2.Residue
        • gd_dl.models
          • gd_dl.models.Cgc_block
          • gd_dl.models.Rerank_model
          • gd_dl.models.Weight_CGConv
        • gd_dl.path_setting
        • gd_dl.rerank_model
          • gd_dl.rerank_model.Cgc_block
          • gd_dl.rerank_model.Rerank_model
          • gd_dl.rerank_model.Weight_CGConv
        • gd_dl.utils
          • gd_dl.utils.set_prep
          • gd_dl.utils.str2bool
    • PromptBind
      • promptbind
        • promptbind.data
          • promptbind.data.data
            • promptbind.data.data.get_data
            • promptbind.data.data.FABindDataSet
          • promptbind.data.inference_preprocess_mol_confs
            • promptbind.data.inference_preprocess_mol_confs.get_mol_info
          • promptbind.data.inference_preprocess_protein
        • promptbind.models
          • promptbind.models.att_model
            • promptbind.models.att_model.sequential_and
            • promptbind.models.att_model.sequential_or
            • promptbind.models.att_model.ComplexGraph
            • promptbind.models.att_model.EfficientMCAttModel
          • promptbind.models.cross_att
            • promptbind.models.cross_att.CrossAttentionModule
            • promptbind.models.cross_att.RowAttentionBlock
            • promptbind.models.cross_att.RowTriangleAttentionBlock
          • promptbind.models.egnn
            • promptbind.models.egnn.coord2radial
            • promptbind.models.egnn.get_edges
            • promptbind.models.egnn.get_edges_batch
            • promptbind.models.egnn.unsorted_segment_mean
            • promptbind.models.egnn.unsorted_segment_sum
            • promptbind.models.egnn.MCAttEGNN
            • promptbind.models.egnn.MC_Att_L
            • promptbind.models.egnn.MC_E_GCL
            • promptbind.models.egnn.MC_E_GCL_Prompt
          • promptbind.models.model
            • promptbind.models.model.get_model
            • promptbind.models.model.IaBNet_mean_and_pocket_prediction_cls_coords_dependent
            • promptbind.models.model.Transition_diff_out_dim
          • promptbind.models.model_utils
            • promptbind.models.model_utils.flatten_final_dims
            • promptbind.models.model_utils.permute_final_dims
            • promptbind.models.model_utils.Attention
            • promptbind.models.model_utils.GaussianSmearing
            • promptbind.models.model_utils.InteractionModule
            • promptbind.models.model_utils.RBFDistanceModule
            • promptbind.models.model_utils.Transition
        • promptbind.test_promptbind
          • promptbind.test_promptbind.PromptBindInference
        • promptbind.train_promptbind
          • promptbind.train_promptbind.Seed_everything
        • promptbind.utils
          • promptbind.utils.fabind_inference_dataset
            • promptbind.utils.fabind_inference_dataset.InferenceDataset
          • promptbind.utils.feature_utils
            • promptbind.utils.feature_utils.Seed_everything
            • promptbind.utils.feature_utils.binarize
            • promptbind.utils.feature_utils.extract_torchdrug_feature_from_mol
            • promptbind.utils.feature_utils.extract_torchdrug_feature_from_mol_E3Bind
            • promptbind.utils.feature_utils.generate_and_write_sdf_from_smiles_using_rdkit_E3Bind
            • promptbind.utils.feature_utils.generate_conformation
            • promptbind.utils.feature_utils.generate_rdkit_conformation_v2
            • promptbind.utils.feature_utils.generate_sdf_from_smiles_using_rdkit
            • promptbind.utils.feature_utils.generate_sdf_from_smiles_using_rdkit_E3Bind
            • promptbind.utils.feature_utils.get_LAS_distance_constraint_mask
            • promptbind.utils.feature_utils.get_canonical_smiles
            • promptbind.utils.feature_utils.get_clean_res_list
            • promptbind.utils.feature_utils.get_compound_pair_dis_distribution
            • promptbind.utils.feature_utils.get_protein_feature
            • promptbind.utils.feature_utils.get_res_unique_id
            • promptbind.utils.feature_utils.n_hops_adj
            • promptbind.utils.feature_utils.read_mol
            • promptbind.utils.feature_utils.remove_hetero_and_extract_ligand
            • promptbind.utils.feature_utils.save_cleaned_protein
            • promptbind.utils.feature_utils.select_chain_within_cutoff_to_ligand_v2
            • promptbind.utils.feature_utils.split_protein_and_ligand
            • promptbind.utils.feature_utils.write_renumbered_sdf
            • promptbind.utils.feature_utils.write_with_new_coords
          • promptbind.utils.generation_utils
            • promptbind.utils.generation_utils.binarize
            • promptbind.utils.generation_utils.compute_RMSD
            • promptbind.utils.generation_utils.distance_loss_function
            • promptbind.utils.generation_utils.distance_optimize_compound_coords
            • promptbind.utils.generation_utils.get_LAS_distance_constraint_mask
            • promptbind.utils.generation_utils.get_info_pred_distance
            • promptbind.utils.generation_utils.n_hops_adj
            • promptbind.utils.generation_utils.read_mol
            • promptbind.utils.generation_utils.write_with_new_coords
          • promptbind.utils.inference_mol_utils
            • promptbind.utils.inference_mol_utils.binarize
            • promptbind.utils.inference_mol_utils.extract_torchdrug_feature_from_mol
            • promptbind.utils.inference_mol_utils.generate_conformation
            • promptbind.utils.inference_mol_utils.get_LAS_distance_constraint_mask
            • promptbind.utils.inference_mol_utils.get_compound_pair_dis_distribution
            • promptbind.utils.inference_mol_utils.n_hops_adj
            • promptbind.utils.inference_mol_utils.read_mol_and_renumber
            • promptbind.utils.inference_mol_utils.read_smiles
            • promptbind.utils.inference_mol_utils.write_mol
          • promptbind.utils.inference_pdb_utils
            • promptbind.utils.inference_pdb_utils.extract_esm_feature
            • promptbind.utils.inference_pdb_utils.extract_protein_structure
            • promptbind.utils.inference_pdb_utils.get_clean_res_list
            • promptbind.utils.inference_pdb_utils.get_protein_structure
          • promptbind.utils.logging_utils
            • promptbind.utils.logging_utils.Logger
          • promptbind.utils.metrics
            • promptbind.utils.metrics.affinity_metrics
            • promptbind.utils.metrics.cls_metric
            • promptbind.utils.metrics.compute_individual_metrics
            • promptbind.utils.metrics.myMetric
            • promptbind.utils.metrics.pocket_direct_metrics
            • promptbind.utils.metrics.pocket_metrics
            • promptbind.utils.metrics.print_metrics
          • promptbind.utils.metrics_to_tsb
            • promptbind.utils.metrics_to_tsb.metrics_runtime_no_prefix
          • promptbind.utils.post_optim_utils
            • promptbind.utils.post_optim_utils.compute_RMSD
            • promptbind.utils.post_optim_utils.post_optimize_compound_coords
            • promptbind.utils.post_optim_utils.post_optimize_compound_coords_lbfgs
            • promptbind.utils.post_optim_utils.post_optimize_loss_function
            • promptbind.utils.post_optim_utils.read_molecule
            • promptbind.utils.post_optim_utils.write_mol
          • promptbind.utils.utils
            • promptbind.utils.utils.SetDihedral
            • promptbind.utils.utils.compute_dis_between_two_vector
            • promptbind.utils.utils.compute_dis_between_two_vector_tensor
            • promptbind.utils.utils.construct_data_from_graph_gvp_mean
            • promptbind.utils.utils.evaluate_mean_pocket_cls_coord_multi_task
            • promptbind.utils.utils.evaluate_mean_pocket_cls_coord_pocket_pred
            • promptbind.utils.utils.get_keepNode
            • promptbind.utils.utils.get_keepNode_tensor
            • promptbind.utils.utils.get_protein_edge_features_and_index
            • promptbind.utils.utils.get_torsions
            • promptbind.utils.utils.gumbel_softmax_no_random
            • promptbind.utils.utils.post_optim_mol
            • promptbind.utils.utils.read_mol
            • promptbind.utils.utils.read_pdbbind_data
            • promptbind.utils.utils.uniform_random_rotation
        • promptbind.visualize_prompt_components
          • promptbind.visualize_prompt_components.main
  • Examples
    • EGFR-antibody interaction analysis
      • Section 2: Finding binding pockets for EGFR KD using “BsiteP”
    • EGFR-ligand interaction analysis
      • Tips and Instructions
    • EGFR-ligand interaction analysis
      • Section 2: Finding binding pockets for a given protein (EGFR) using “BsiteP”
      • Section 4: Re-scoring GDDL docking results using BindingRMSD.
      • 4-1. Re-scoring for Docked Protein-Ligand Complex
      • 4-2. 3D Visualization: Crystal Structure vs Docked Poses
      • 4-3. Crystal Ligand Pose vs Docked Ligand Pose: RMSD and Prediction Comparison
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Tools¶

Contents:

  • BAPred
    • bapred
  • BindingRMSD
    • bindingrmsd
  • BIS Protein Structure
    • bis_protein_structure
  • SwinSite
  • DiffAlign
    • diffalign
  • GalaxyDock DL
    • gd_dl
  • PromptBind
    • promptbind
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