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ToDo Lists

1. AlphaFold2 Source Code Review

alphafold

common

  • confidence.py
  • protein.py
  • protein_test.py
  • residue_constants.py
  • residue_constants_test.py

data

  • mmcif_parsing.py
  • parsers.py
  • pipeline.py
  • templates.py

tools

  • hhblits.py
  • hhsearch.py
  • hmmbuild.py
  • hmmsearch.py
  • jackhmmer.py
  • kalign.py
  • utils.py

model

  • all_atom.py
  • all_atom_test.py
  • common_modules.py
  • config.py
  • data.py
  • features.py
  • folding.py
  • layer_stack.py
  • layer_stack_test.py
  • lddt.py
  • lddt_test.py
  • mapping.py
  • model.py
  • modules.py
  • prng.py
  • prng_test.py
  • quat_affine.py
  • quat_affine_test.py
  • r3.py
  • utils.py

tf

  • data_transforms.py
  • input_pipeline.py
  • protein_features.py
  • protein_features_test.py
  • proteins_dataset.py
  • shape_helpers.py
  • shape_helpers_test.py
  • shape_placeholders.py
  • utils.py

relax

  • amber_minimize.py
  • amber_minimize_test.py
  • cleanup.py
  • cleanup_test.py
  • relax.py
  • relax_test.py

2. Create Unit Test for 32 Algorithms

Function Name (Algorithms) Instruction CheckBox
MSABlockDeletion MSA block deletion [ ]
Inference AlphaFold Model Inference [ ]
InputEmbedder Embeddings for initial representations [ ]
relpos Relative position encoding [ ]
one_hot One-hot encoding with nearest bin [ ]
EvoformerStack Evoformer stack [ ]
MSARowAttentionWithPairBias MSA row-wise gated self-attention with pair bias [ ]
MSAColumnAttention MSA column-wise gated self-attention [ ]
MSATransition Transition layer in the MSA stack [ ]
OuterProductMean Outer product mean [ ]
TriangleMultiplicationOutgoing Triangular multiplicative update using “outgoing” edges [ ]
TriangleMultiplicationIncoming Triangular multiplicative update using “incoming” edges [ ]
TriangleAttentionStartingNode Triangular gated self-attention around starting node [ ]
TriangleAttentionEndingNode Triangular gated self-attention around ending node [ ]
PairTransition Transition layer in the pair stack [ ]
TemplatePairStack Template pair stack [ ]
TemplatePointwiseAttention Template pointwise attention [ ]
ExtraMsaStack Extra MSA stack [ ]
MSAColumnGlobalAttention MSA global column-wise gated self-attention [ ]
StructureModule Structure module [ ]
rigidFrom3Points Rigid from 3 points using the Gram–Schmidt process [ ]
InvariantPointAttention Invariant point attention(IPA) [ ]
BackboneUpdate Backbone update [ ]
computeAllAtomCoordinates Compute all atom coordinates [ ]
makeRotX Make a transformation that rotates around the x-axis [ ]
renameSymmetricGroundTruthAtoms Rename symmetric ground truth atoms [ ]
torsionAngleLoss Side chain and backbone torsion angle loss [ ]
computeFAPE Compute the Frame aligned point error [ ]
predictPerResidueLDDT Predict model confidence pLDDT [ ]
RecyclingInference Generic recycling inference procedure [ ]
RecyclingTraining Generic recycling training procedure [ ]
RecyclingEmbedder Embedding of Evoformer and Structure module outputs for recycling [ ]