Hide navigation sidebar

Hide table of contents sidebar

Skip to content

Toggle site navigation sidebar

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

Toggle table of contents sidebar

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

Table of Contents

Backbone Models
Toggle navigation of Backbone Models
- DeepFold
  Toggle navigation of DeepFold
  - deepfold
    Toggle navigation of deepfold
    - deepfold.common
      Toggle navigation of deepfold.common
      - deepfold.common.protein
        Toggle navigation of 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
        Toggle navigation of 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
      Toggle navigation of deepfold.config
    - deepfold.data
      Toggle navigation of deepfold.data
      - deepfold.data.errors
      - deepfold.data.modules
        Toggle navigation of deepfold.data.modules
        
        deepfold.data.modules.dataloaders
        
        deepfold.data.modules.mmcif_dataset
        
        deepfold.data.modules.samplers
        
        deepfold.data.modules.single_dataset
      - deepfold.data.monomer
        Toggle navigation of 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
        Toggle navigation of deepfold.data.multimer
        
        deepfold.data.multimer.input_features
        Toggle navigation of 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
        Toggle navigation of 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
        Toggle navigation of deepfold.data.pdbio
        
        deepfold.data.pdbio.IO
        
        deepfold.data.pdbio.PDBIO
      - deepfold.data.pdbx_parsing
        Toggle navigation of 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
        Toggle navigation of deepfold.data.search
        
        deepfold.data.search.crfalign
        Toggle navigation of deepfold.data.search.crfalign
        
        deepfold.data.search.crfalign.parse_crf
        
        deepfold.data.search.crfalign.parse_pir
        
        deepfold.data.search.input_features
        Toggle navigation of 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
        Toggle navigation of 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
        Toggle navigation of deepfold.data.search.msa_identifiers
        
        deepfold.data.search.msa_identifiers.get_identifiers
        
        deepfold.data.search.parsers
        Toggle navigation of 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
        Toggle navigation of 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
        Toggle navigation of deepfold.data.tools
        
        deepfold.data.tools.hhblits
        Toggle navigation of deepfold.data.tools.hhblits
        
        deepfold.data.tools.hhblits.HHBlits
        
        deepfold.data.tools.hhsearch
        Toggle navigation of deepfold.data.tools.hhsearch
        
        deepfold.data.tools.hhsearch.HHSearch
        
        deepfold.data.tools.hmmbuild
        Toggle navigation of deepfold.data.tools.hmmbuild
        
        deepfold.data.tools.hmmbuild.Hmmbuild
        
        deepfold.data.tools.hmmsearch
        Toggle navigation of deepfold.data.tools.hmmsearch
        
        deepfold.data.tools.hmmsearch.Hmmsearch
        
        deepfold.data.tools.jackhmmer
        Toggle navigation of deepfold.data.tools.jackhmmer
        
        deepfold.data.tools.jackhmmer.Jackhmmer
        
        deepfold.data.tools.kalign
        Toggle navigation of deepfold.data.tools.kalign
        
        deepfold.data.tools.kalign.Kalign
        
        deepfold.data.tools.utils
        Toggle navigation of deepfold.data.tools.utils
        
        deepfold.data.tools.utils.timing
        
        deepfold.data.tools.utils.tmpdir_manager
        
        deepfold.data.tools.utils.to_date
    - deepfold.distributed
      Toggle navigation of deepfold.distributed
      - deepfold.distributed.model_parallel
        Toggle navigation of 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
        Toggle navigation of 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
      Toggle navigation of deepfold.eval
      - deepfold.eval.cell_lists
        Toggle navigation of deepfold.eval.cell_lists
        
        deepfold.eval.cell_lists.CellLists
        
        deepfold.eval.cell_lists.Particle
      - deepfold.eval.contact
        Toggle navigation of deepfold.eval.contact
        
        deepfold.eval.contact.contact_map
        
        deepfold.eval.contact.Atom
      - deepfold.eval.distogram
        Toggle navigation of 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
        Toggle navigation of deepfold.eval.msa
        
        deepfold.eval.msa.compute_neff_v1
        
        deepfold.eval.msa.compute_neff_v2
      - deepfold.eval.plot
        Toggle navigation of 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
        Toggle navigation of deepfold.eval.pseudo_3d
        
        deepfold.eval.pseudo_3d.kabsch
        
        deepfold.eval.pseudo_3d.plot_protein
        
        deepfold.eval.pseudo_3d.plot_protein_bb
    - deepfold.loss
      Toggle navigation of deepfold.loss
      - deepfold.loss.AlphaFoldLoss
    - deepfold.losses
      Toggle navigation of deepfold.losses
      - deepfold.losses.auxillary
        Toggle navigation of 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
        Toggle navigation of 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
        Toggle navigation of 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
        Toggle navigation of deepfold.losses.masked_msa
        
        deepfold.losses.masked_msa.masked_msa_loss
      - deepfold.losses.procrustes
        Toggle navigation of 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
        Toggle navigation of deepfold.losses.utils
        
        deepfold.losses.utils.calculate_bin_centers
        
        deepfold.losses.utils.sigmoid_cross_entropy
        
        deepfold.losses.utils.softmax_cross_entropy
      - deepfold.losses.violation
        Toggle navigation of 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
      Toggle navigation of deepfold.modules
      - deepfold.modules.alphafold
        Toggle navigation of deepfold.modules.alphafold
        
        deepfold.modules.alphafold.AlphaFold
      - deepfold.modules.angle_resnet
        Toggle navigation of deepfold.modules.angle_resnet
        
        deepfold.modules.angle_resnet.AngleResnet
        
        deepfold.modules.angle_resnet.AngleResnetBlock
      - deepfold.modules.attention
        Toggle navigation of deepfold.modules.attention
        
        deepfold.modules.attention.CrossAttentionNoGate
        
        deepfold.modules.attention.SelfAttentionWithGate
      - deepfold.modules.auxiliary_heads
        Toggle navigation of 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
        Toggle navigation of deepfold.modules.backbone_update
        
        deepfold.modules.backbone_update.BackboneUpdate
      - deepfold.modules.dropout
        Toggle navigation of deepfold.modules.dropout
        
        deepfold.modules.dropout.Dropout
        
        deepfold.modules.dropout.DropoutColumnwise
        
        deepfold.modules.dropout.DropoutRowwise
      - deepfold.modules.evoformer_block
        Toggle navigation of deepfold.modules.evoformer_block
        
        deepfold.modules.evoformer_block.EvoformerBlock
      - deepfold.modules.evoformer_block_pair_core
        Toggle navigation of deepfold.modules.evoformer_block_pair_core
        
        deepfold.modules.evoformer_block_pair_core.EvoformerBlockPairCore
      - deepfold.modules.evoformer_stack
        Toggle navigation of deepfold.modules.evoformer_stack
        
        deepfold.modules.evoformer_stack.EvoformerStack
      - deepfold.modules.extra_msa_block
        Toggle navigation of deepfold.modules.extra_msa_block
        
        deepfold.modules.extra_msa_block.ExtraMSABlock
      - deepfold.modules.extra_msa_embedder
        Toggle navigation of deepfold.modules.extra_msa_embedder
        
        deepfold.modules.extra_msa_embedder.ExtraMSAEmbedder
      - deepfold.modules.extra_msa_stack
        Toggle navigation of deepfold.modules.extra_msa_stack
        
        deepfold.modules.extra_msa_stack.ExtraMSAStack
      - deepfold.modules.global_attention
        Toggle navigation of deepfold.modules.global_attention
        
        deepfold.modules.global_attention.GlobalAttention
      - deepfold.modules.inductor
        Toggle navigation of 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
        Toggle navigation of deepfold.modules.input_embedder
        
        deepfold.modules.input_embedder.InputEmbedder
        
        deepfold.modules.input_embedder.InputEmbedderMultimer
      - deepfold.modules.invariant_point_attention
        Toggle navigation of 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
        Toggle navigation of deepfold.modules.layer_norm
        
        deepfold.modules.layer_norm.LayerNorm
      - deepfold.modules.linear
        Toggle navigation of 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
        Toggle navigation of deepfold.modules.msa_column_attention
        
        deepfold.modules.msa_column_attention.MSAColumnAttention
      - deepfold.modules.msa_column_global_attention
        Toggle navigation of deepfold.modules.msa_column_global_attention
        
        deepfold.modules.msa_column_global_attention.MSAColumnGlobalAttention
      - deepfold.modules.msa_row_attention_with_pair_bias
        Toggle navigation of deepfold.modules.msa_row_attention_with_pair_bias
        
        deepfold.modules.msa_row_attention_with_pair_bias.MSARowAttentionWithPairBias
      - deepfold.modules.msa_transition
        Toggle navigation of deepfold.modules.msa_transition
        
        deepfold.modules.msa_transition.MSATransition
      - deepfold.modules.outer_product_mean
        Toggle navigation of deepfold.modules.outer_product_mean
        
        deepfold.modules.outer_product_mean.OuterProductMean
      - deepfold.modules.pair_transition
        Toggle navigation of deepfold.modules.pair_transition
        
        deepfold.modules.pair_transition.PairTransition
      - deepfold.modules.recycling_embedder
        Toggle navigation of deepfold.modules.recycling_embedder
        
        deepfold.modules.recycling_embedder.RecyclingEmbedder
      - deepfold.modules.single_transition
        Toggle navigation of deepfold.modules.single_transition
        
        deepfold.modules.single_transition.SingleTransition
      - deepfold.modules.structure_module
        Toggle navigation of deepfold.modules.structure_module
        
        deepfold.modules.structure_module.StructureModule
      - deepfold.modules.template_angle_embedder
        Toggle navigation of deepfold.modules.template_angle_embedder
        
        deepfold.modules.template_angle_embedder.TemplateAngleEmbedder
      - deepfold.modules.template_pair_block
        Toggle navigation of deepfold.modules.template_pair_block
        
        deepfold.modules.template_pair_block.TemplatePairBlock
      - deepfold.modules.template_pair_embedder
        Toggle navigation of deepfold.modules.template_pair_embedder
        
        deepfold.modules.template_pair_embedder.TemplatePairEmbedder
        
        deepfold.modules.template_pair_embedder.TemplatePairEmbedderMultimer
      - deepfold.modules.template_pair_stack
        Toggle navigation of deepfold.modules.template_pair_stack
        
        deepfold.modules.template_pair_stack.TemplatePairStack
      - deepfold.modules.template_pointwise_attention
        Toggle navigation of deepfold.modules.template_pointwise_attention
        
        deepfold.modules.template_pointwise_attention.TemplatePointwiseAttention
      - deepfold.modules.template_projection
        Toggle navigation of deepfold.modules.template_projection
        
        deepfold.modules.template_projection.TemplateProjection
      - deepfold.modules.triangular_attention
        Toggle navigation of deepfold.modules.triangular_attention
        
        deepfold.modules.triangular_attention.TriangleAttention
        
        deepfold.modules.triangular_attention.TriangleAttentionEndingNode
        
        deepfold.modules.triangular_attention.TriangleAttentionStartingNode
      - deepfold.modules.triangular_multiplicative_update
        Toggle navigation of 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
        Toggle navigation of deepfold.modules.tweaks
        
        deepfold.modules.tweaks.evo_attn
        Toggle navigation of 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
      Toggle navigation of deepfold.ops
      - deepfold.ops.evoformer_attention
        Toggle navigation of deepfold.ops.evoformer_attention
        
        deepfold.ops.evoformer_attention.deepspeed_evo_attn
    - deepfold.package_info
    - deepfold.relax
      Toggle navigation of deepfold.relax
      - deepfold.relax.amber_minimize
        Toggle navigation of 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
        Toggle navigation of deepfold.relax.cleanup
        
        deepfold.relax.cleanup.clean_structure
        
        deepfold.relax.cleanup.fix_pdb
      - deepfold.relax.relax
        Toggle navigation of deepfold.relax.relax
        
        deepfold.relax.relax.AmberRelaxation
      - deepfold.relax.utils
        Toggle navigation of 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
      Toggle navigation of deepfold.runner
      - deepfold.runner.config_utils
        Toggle navigation of deepfold.runner.config_utils
        
        deepfold.runner.config_utils.load
      - deepfold.runner.parser
        Toggle navigation of deepfold.runner.parser
        
        deepfold.runner.parser.Lexer
        
        deepfold.runner.parser.Parser
      - deepfold.runner.utils
        Toggle navigation of deepfold.runner.utils
        
        deepfold.runner.utils.safe_filename
    - deepfold.testing
      Toggle navigation of deepfold.testing
      - deepfold.testing.common
        Toggle navigation of 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
        Toggle navigation of deepfold.testing.utils
        
        deepfold.testing.utils.find_free_port
    - deepfold.train
      Toggle navigation of deepfold.train
      - deepfold.train.gradient_clipping
        Toggle navigation of deepfold.train.gradient_clipping
        
        deepfold.train.gradient_clipping.update_norm_from_buckets
        
        deepfold.train.gradient_clipping.AsyncGradientClipping
      - deepfold.train.lr_scheduler
        Toggle navigation of 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
        Toggle navigation of 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
      Toggle navigation of deepfold.utils
      - deepfold.utils.checkpoint_utils
        Toggle navigation of 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
        Toggle navigation of deepfold.utils.chunk_utils
        
        deepfold.utils.chunk_utils.chunk_layer
      - deepfold.utils.crop_utils
        Toggle navigation of deepfold.utils.crop_utils
        
        deepfold.utils.crop_utils.unpad_to_schema_shape_
      - deepfold.utils.datetime_utils
        Toggle navigation of 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
        Toggle navigation of deepfold.utils.dist_utils
        
        deepfold.utils.dist_utils.get_pad_size
        
        deepfold.utils.dist_utils.pad_tensor
      - deepfold.utils.feats_utils
        Toggle navigation of deepfold.utils.feats_utils
        
        deepfold.utils.feats_utils.crop_a3m_string
        
        deepfold.utils.feats_utils.crop_features
      - deepfold.utils.file_utils
        Toggle navigation of 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
        Toggle navigation of deepfold.utils.geometry
        
        deepfold.utils.geometry.quat_rigid
        Toggle navigation of deepfold.utils.geometry.quat_rigid
        
        deepfold.utils.geometry.quat_rigid.QuatRigid
        
        deepfold.utils.geometry.rigid_matrix_vector
        Toggle navigation of deepfold.utils.geometry.rigid_matrix_vector
        
        deepfold.utils.geometry.rigid_matrix_vector.Rigid3Array
        
        deepfold.utils.geometry.rotation_matrix
        Toggle navigation of deepfold.utils.geometry.rotation_matrix
        
        deepfold.utils.geometry.rotation_matrix.Rot3Array
        
        deepfold.utils.geometry.utils
        Toggle navigation of deepfold.utils.geometry.utils
        
        deepfold.utils.geometry.utils.get_field_names
        
        deepfold.utils.geometry.vector
        Toggle navigation of 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
        Toggle navigation of deepfold.utils.hash_utils
        
        deepfold.utils.hash_utils.hash_string_into_number
      - deepfold.utils.import_utils
        Toggle navigation of 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
        Toggle navigation of 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
        Toggle navigation of 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
        Toggle navigation of deepfold.utils.precision
        
        deepfold.utils.precision.is_fp16_enabled
      - deepfold.utils.random
        Toggle navigation of 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
        Toggle navigation of 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
        Toggle navigation of 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
        Toggle navigation of deepfold.utils.swa_utils
        
        deepfold.utils.swa_utils.AlphaFoldSWA
        
        deepfold.utils.swa_utils.swa_avg_fn
      - deepfold.utils.tensor_utils
        Toggle navigation of 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
  Toggle navigation of MiniWorld
  - miniworld
    Toggle navigation of miniworld
- RoseTTAFold2
Tools
Toggle navigation of Tools
- bapred
  Toggle navigation of bapred
  - bapred.cli
    Toggle navigation of bapred.cli
    - bapred.cli.main
  - bapred.data
    Toggle navigation of bapred.data
    - bapred.data.atom_feature
      Toggle navigation of bapred.data.atom_feature
    - bapred.data.data
      Toggle navigation of bapred.data.data
    - bapred.data.utils
      Toggle navigation of bapred.data.utils
  - bapred.inference
    Toggle navigation of bapred.inference
    - bapred.inference.inference
  - bapred.logger
    Toggle navigation of bapred.logger
    - bapred.logger.setup_logger
  - bapred.model
    Toggle navigation of bapred.model
    - bapred.model.GatedGCNLSPE
      Toggle navigation of bapred.model.GatedGCNLSPE
      - bapred.model.GatedGCNLSPE.GatedGCNLSPELayer
    - bapred.model.GraphGPS
      Toggle navigation of bapred.model.GraphGPS
      - bapred.model.GraphGPS.GraphGPS
    - bapred.model.MHA
      Toggle navigation of bapred.model.MHA
      - bapred.model.MHA.MultiHeadAttention
    - bapred.model.model
      Toggle navigation of bapred.model.model
      - bapred.model.model.PredictionPKD
- bindingrmsd
  Toggle navigation of bindingrmsd
  - bindingrmsd.data
    Toggle navigation of bindingrmsd.data
    - bindingrmsd.data.data
      Toggle navigation of bindingrmsd.data.data
    - bindingrmsd.data.data_bck
      Toggle navigation of bindingrmsd.data.data_bck
    - bindingrmsd.data.ligand_atom_feature
      Toggle navigation of bindingrmsd.data.ligand_atom_feature
    - bindingrmsd.data.protein_atom_feature
      Toggle navigation of bindingrmsd.data.protein_atom_feature
    - bindingrmsd.data.utils
      Toggle navigation of bindingrmsd.data.utils
  - bindingrmsd.inference
    Toggle navigation of bindingrmsd.inference
    - bindingrmsd.inference.inference
    - bindingrmsd.inference.main
  - bindingrmsd.model
    Toggle navigation of bindingrmsd.model
    - bindingrmsd.model.GatedGCNLSPE
      Toggle navigation of bindingrmsd.model.GatedGCNLSPE
      - bindingrmsd.model.GatedGCNLSPE.GatedGCNLSPELayer
    - bindingrmsd.model.model
      Toggle navigation of bindingrmsd.model.model
      - bindingrmsd.model.model.PredictionRMSD
- bis_protein_structure
  Toggle navigation of bis_protein_structure
  - bis_protein_structure.CROSSLINK
    Toggle navigation of bis_protein_structure.CROSSLINK
  - bis_protein_structure.DATAGEN
    Toggle navigation of bis_protein_structure.DATAGEN
  - bis_protein_structure.DISULFIDE
    Toggle navigation of bis_protein_structure.DISULFIDE
    - bis_protein_structure.DISULFIDE.get_SS_ver5
    - bis_protein_structure.DISULFIDE.readMMCIF_label
  - bis_protein_structure.MMEVAL
    Toggle navigation of bis_protein_structure.MMEVAL
  - bis_protein_structure.SOLVENTACC
    Toggle navigation of bis_protein_structure.SOLVENTACC
  - bis_protein_structure.TORSION2
    Toggle navigation of bis_protein_structure.TORSION2
  - bis_protein_structure.residue_constants
    Toggle navigation of bis_protein_structure.residue_constants
  - bis_protein_structure.split_pdb
    Toggle navigation of bis_protein_structure.split_pdb
    - bis_protein_structure.split_pdb.extract
    - bis_protein_structure.split_pdb.split_the_pdb
- diffalign
  Toggle navigation of diffalign
  - diffalign.models
    Toggle navigation of diffalign.models
    - diffalign.models.common
      Toggle navigation of diffalign.models.common
    - diffalign.models.encoder
      Toggle navigation of diffalign.models.encoder
      - diffalign.models.encoder.cross_attention
        Toggle navigation of diffalign.models.encoder.cross_attention
        
        diffalign.models.encoder.cross_attention.CrossAttention
        
        diffalign.models.encoder.cross_attention.CrossGraphAligner
      - diffalign.models.encoder.edge
        Toggle navigation of diffalign.models.encoder.edge
        
        diffalign.models.encoder.edge.MLPEdgeEncoder
      - diffalign.models.encoder.egnn
        Toggle navigation of 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
      Toggle navigation of diffalign.models.epsnet
      - diffalign.models.epsnet.diffusion
        Toggle navigation of 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
    Toggle navigation of diffalign.utils
    - diffalign.utils.chem
      Toggle navigation of diffalign.utils.chem
- gd_dl
  Toggle navigation of gd_dl
  - gd_dl.data
    Toggle navigation of gd_dl.data
    - gd_dl.data.ML_inference
      Toggle navigation of gd_dl.data.ML_inference
    - gd_dl.data.ML_rerank
      Toggle navigation of gd_dl.data.ML_rerank
      - gd_dl.data.ML_rerank.calc_e
      - gd_dl.data.ML_rerank.main
    - gd_dl.data.all_ML_rerank
      Toggle navigation of 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
      Toggle navigation of 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
    Toggle navigation of gd_dl.lib_pdb_mol2
  - gd_dl.models
    Toggle navigation of gd_dl.models
  - gd_dl.path_setting
  - gd_dl.rerank_model
    Toggle navigation of gd_dl.rerank_model
  - gd_dl.utils
    Toggle navigation of gd_dl.utils
    - gd_dl.utils.set_prep
    - gd_dl.utils.str2bool
- promptbind
  Toggle navigation of promptbind
  - promptbind.data
    Toggle navigation of promptbind.data
    - promptbind.data.data
      Toggle navigation of promptbind.data.data
      - promptbind.data.data.get_data
      - promptbind.data.data.FABindDataSet
    - promptbind.data.inference_preprocess_mol_confs
      Toggle navigation of promptbind.data.inference_preprocess_mol_confs
      - promptbind.data.inference_preprocess_mol_confs.get_mol_info
    - promptbind.data.inference_preprocess_protein
  - promptbind.models
    Toggle navigation of promptbind.models
    - promptbind.models.att_model
      Toggle navigation of promptbind.models.att_model
    - promptbind.models.cross_att
      Toggle navigation of promptbind.models.cross_att
    - promptbind.models.egnn
      Toggle navigation of promptbind.models.egnn
    - promptbind.models.model
      Toggle navigation of promptbind.models.model
    - promptbind.models.model_utils
      Toggle navigation of promptbind.models.model_utils
  - promptbind.test_promptbind
    Toggle navigation of promptbind.test_promptbind
    - promptbind.test_promptbind.PromptBindInference
  - promptbind.train_promptbind
    Toggle navigation of promptbind.train_promptbind
    - promptbind.train_promptbind.Seed_everything
  - promptbind.utils
    Toggle navigation of promptbind.utils
  - promptbind.visualize_prompt_components
    Toggle navigation of promptbind.visualize_prompt_components
    - promptbind.visualize_prompt_components.main
Examples
Toggle navigation of Examples
- EGFR-antibody interaction analysis
  Toggle navigation of EGFR-antibody interaction analysis
  - Section 2: Finding binding pockets for EGFR KD using “BsiteP”
- EGFR-ligand interaction analysis
  Toggle navigation of EGFR-ligand interaction analysis
  - Tips and Instructions
- EGFR-ligand interaction analysis
  Toggle navigation of EGFR-ligand interaction analysis

Toggle table of contents sidebar

miniworld.utils.util.extract_tip_atom_xyz¶

miniworld.utils.util.extract_tip_atom_xyz(query_sequence, xyz, extract_atom_number=1)[source]¶

miniworld.utils.util.generate_initial_xyz

miniworld.utils.util.draw_pae

Copyright © 2025, PPI.

Made with Sphinx and @pradyunsg's Furo

On this page

miniworld.utils.util.extract_tip_atom_xyz
- extract_tip_atom_xyz()