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

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

Table of Contents

Backbone Models
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- deepfold
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  - deepfold.common
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    - deepfold.common.protein
    - deepfold.common.residue_constants
  - deepfold.config
  - deepfold.data
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    - deepfold.data.errors
    - deepfold.data.modules
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    - deepfold.data.monomer
    - deepfold.data.multimer
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      - deepfold.data.multimer.input_features
      - deepfold.data.multimer.msa_pairing
    - deepfold.data.pdbio
    - deepfold.data.pdbx_parsing
    - deepfold.data.search
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    - deepfold.data.tools
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  - deepfold.distributed
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    - deepfold.distributed.model_parallel
    - deepfold.distributed.utils
  - deepfold.eval
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  - deepfold.loss
  - deepfold.losses
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  - deepfold.modules
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  - deepfold.ops
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    - deepfold.ops.evoformer_attention
  - deepfold.package_info
  - deepfold.relax
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  - deepfold.runner
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  - deepfold.testing
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    - deepfold.testing.common
    - deepfold.testing.utils
  - deepfold.train
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  - deepfold.utils
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- miniworld
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  - miniworld.MiniWorld_train_multi_deep_v1_5_use_interaction
  - miniworld.feature
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    - miniworld.feature.MiniWorld_featuring_species
  - miniworld.models_MiniWorld_v1_5_use_interaction
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  - miniworld.utils
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Tools
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- bapred
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  - bapred.data
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  - bapred.inference
  - bapred.model
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- bindingrmsd
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  - bindingrmsd.data
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  - bindingrmsd.inference
  - bindingrmsd.model
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    - bindingrmsd.model.GatedGCNLSPE
    - bindingrmsd.model.model
- bis_protein_structure
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- bsitep
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  - bsitep.proteindata
  - bsitep.seresnet
  - bsitep.utils
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- diffalign
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  - diffalign.models
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    - diffalign.models.common
    - diffalign.models.encoder
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      - diffalign.models.encoder.edge
      - diffalign.models.encoder.egnn
    - diffalign.models.epsnet
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      - diffalign.models.epsnet.diffusion
  - diffalign.train
  - diffalign.utils
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    - diffalign.utils.chem
    - diffalign.utils.common
    - diffalign.utils.dataloader
    - diffalign.utils.datasets
    - diffalign.utils.evaluation
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      - diffalign.utils.evaluation.covmat
    - diffalign.utils.misc
    - diffalign.utils.transforms
    - diffalign.utils.visualize
- gd_dl
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  - gd_dl.data
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  - gd_dl.lib_pdb_mol2
  - gd_dl.models
  - gd_dl.path_setting
  - gd_dl.rerank_model
  - gd_dl.utils
- promptbind
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  - promptbind.data
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  - promptbind.models
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  - promptbind.test_promptbind
  - promptbind.train_promptbind
  - promptbind.utils
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  - promptbind.visualize_prompt_components
Examples
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- EGFR-antibody interaction analysis
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  - Section 2: Finding binding pockets for EGFR KD using “BsiteP”
- EGFR-ligand interaction analysis
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  - Tips and Instructions
- EGFR-ligand interaction analysis
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deepfold.utils.swa_utils¶

Classes

`AlphaFoldSWA`(alphafold, enabled, decay_rate)	Weight averaging wrapper.
`swa_avg_fn`(decay_rate)	Averaging function for EMA with configurable decay rate.

deepfold.utils.tensor_utils

deepfold.utils.script_utils

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