Ecosyste.ms: Issues

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GitHub / lucidrains/alphafold3-pytorch issues and pull requests

#319 - Inference time scaling (wip)

Pull Request - State: open - Opened by lucidrains 11 days ago

#318 - How to train AF3?

Issue - State: open - Opened by Thoudam-A 2 months ago

#317 - Has this been tested with V100 GPUs?

Issue - State: open - Opened by Twim17 2 months ago

#316 - G-quadruplex (G4) DNA

Issue - State: closed - Opened by ZhuLvs 3 months ago - 3 comments

#314 - Support for Deepmind's Alphafold 3 checkpoints?

Issue - State: open - Opened by virgo777 3 months ago

#312 - value residual learning

Pull Request - State: closed - Opened by lucidrains 3 months ago

#312 - value residual learning

Pull Request - State: closed - Opened by lucidrains 3 months ago

#311 - OSError: out of pty devices

Issue - State: open - Opened by miaohao0309 4 months ago

#310 - Fix pAE-related bugs

Pull Request - State: closed - Opened by qiaoqiaoLF 4 months ago - 1 comment

#309 - about the distillation data mentioned in alphafold3

Issue - State: open - Opened by yh-pengtu 4 months ago

#308 - is there pretrained models for alphafold3?

Issue - State: open - Opened by nibingwei123 4 months ago - 2 comments

#307 - Questions about the chain/interface clustering files

Issue - State: open - Opened by zqcai19 4 months ago - 3 comments

#306 - Change placeholder `expansion_factor` value

Pull Request - State: closed - Opened by amorehead 4 months ago

#305 - Remove an extra residual connection in `DiffusionTransformer`

Pull Request - State: closed - Opened by amorehead 4 months ago - 2 comments

#304 - Remove zero init and constant biasing for `to_gate`

Pull Request - State: closed - Opened by amorehead 4 months ago

#303 - Remove zero initialization for `adaln_zero_gamma_linear`

Pull Request - State: closed - Opened by amorehead 4 months ago - 1 comment

#301 - Set `bias=False` for both `LayerNorms` in `AdaptiveLayerNorm`

Pull Request - State: closed - Opened by amorehead 4 months ago - 3 comments

#221 - Designing a GUI using Gradio

Issue - State: open - Opened by vandrw 5 months ago - 12 comments

#102 - Differentiate RNA from DNA chains in `cluster_pdb_mmcifs.py`

Pull Request - State: closed - Opened by amorehead 6 months ago

#100 - slim down af3 model in tests

Pull Request - State: closed - Opened by lucidrains 7 months ago - 1 comment

#99 - Create outline of how to do cropping with `Biomolecule` objects

Pull Request - State: closed - Opened by amorehead 7 months ago - 1 comment

#98 - Correct interface chain IDs curated in `weighted_pdb_sampler.py`

Pull Request - State: closed - Opened by amorehead 7 months ago

#97 - Fix cluster ID arrangement for chains

Pull Request - State: closed - Opened by vandrw 7 months ago - 4 comments

#94 - Do not use mmCIF training bond inputs if symmetry is mismatched

Pull Request - State: closed - Opened by amorehead 7 months ago

#93 - Add `WeightedSamplerPDB`

Pull Request - State: closed - Opened by vandrw 7 months ago - 12 comments

#92 - Make training detection more robust for mmCIF bond insertion

Pull Request - State: closed - Opened by amorehead 7 months ago

#91 - Add small fix to `inputs.py`

Pull Request - State: closed - Opened by amorehead 7 months ago

#89 - Add missing function to `utils.py`

Pull Request - State: closed - Opened by amorehead 7 months ago - 1 comment

#88 - Add `test_pdbinput_input` unit test

Pull Request - State: closed - Opened by amorehead 7 months ago - 1 comment

#87 - Wrong shape of `missing_atom_indices` after calling `pad_sequence`

Issue - State: closed - Opened by amorehead 7 months ago - 6 comments

#86 - Incorrect token molecule IDs?

Issue - State: closed - Opened by amorehead 7 months ago - 2 comments

#85 - The PairformerStack in TemplateEmbedder

Issue - State: closed - Opened by fuxuliu 7 months ago - 4 comments

#84 - Add updated template indices for distograms and token center atoms in `life.py`

Pull Request - State: closed - Opened by amorehead 7 months ago - 1 comment

#83 - Fix return type in `cluster_pdb_mmcifs.py`

Pull Request - State: closed - Opened by amorehead 7 months ago

#82 - (WIP) Simplify `life.py` by switching to template residue SMILES strings

Pull Request - State: closed - Opened by amorehead 7 months ago - 9 comments

#81 - Incorrect tracking of each token's center atom?

Issue - State: closed - Opened by amorehead 7 months ago - 22 comments

#80 - Add standardized (template) SMILES strings for each residue

Pull Request - State: closed - Opened by amorehead 7 months ago - 1 comment

#76 - Fix a new source of crashes in cluster_pdb_mmcifs.py

Pull Request - State: closed - Opened by amorehead 7 months ago

#73 - bias init to -2.0?

Issue - State: closed - Opened by luwei0917 7 months ago - 1 comment

#70 - Default to downloading the PDB from its `20240101` AWS snapshot

Pull Request - State: closed - Opened by amorehead 7 months ago

#68 - loss_weight discrepancy. EDM and AF3

Issue - State: closed - Opened by luwei0917 7 months ago - 5 comments

#67 - need a coord_mask when center the coordinates.

Issue - State: closed - Opened by luwei0917 7 months ago - 1 comment

#65 - Add date range arguments to `filter_pdb_mmcifs.py`

Pull Request - State: closed - Opened by amorehead 7 months ago

#64 - Finish new (faster) PDB dataset clustering implementation

Pull Request - State: closed - Opened by amorehead 7 months ago

#61 - Remove (now-unused) PDB dataset caching script

Pull Request - State: closed - Opened by amorehead 7 months ago

#60 - Change default number of workers used in `cluster_pdb_mmcifs.py`

Pull Request - State: closed - Opened by amorehead 7 months ago

#59 - Speed up `cluster_pdb_mmcifs.py`

Pull Request - State: closed - Opened by amorehead 7 months ago

#58 - Handle a few edge cases in `cluster_pdb_mmcifs.py`

Pull Request - State: closed - Opened by amorehead 7 months ago

#57 - Bug Report: Unused Parameter in flash_attn Function

Issue - State: closed - Opened by 1120172175 7 months ago - 1 comment

#56 - The alignment error should be a pairwise error.

Pull Request - State: closed - Opened by gitabtion 7 months ago - 5 comments

#55 - check if Chem.GetDistanceMatrix is fixed

Pull Request - State: closed - Opened by lucidrains 7 months ago - 1 comment

#54 - Correct two bugs affecting filtered mmCIF files

Pull Request - State: closed - Opened by amorehead 7 months ago

#53 - Fix version import in `mmcif_metadata.py`

Pull Request - State: closed - Opened by amorehead 7 months ago

#52 - Add bug fix and update `README.md` for new PDB clustering script

Pull Request - State: closed - Opened by amorehead 7 months ago

#51 - Finish new version of `cluster_pdb_mmcifs.py`

Pull Request - State: closed - Opened by amorehead 7 months ago

#49 - Position/token masking feature

Issue - State: closed - Opened by thomashopf 7 months ago - 2 comments

#48 - [fix] collate_af3_inputs function should return an instence of BatchedAtomInput

Pull Request - State: closed - Opened by gitabtion 7 months ago - 1 comment

#46 - Returning tokens from token_transformer

Pull Request - State: closed - Opened by dirkcodes 7 months ago - 1 comment

#44 - [fix bug] make molecule_atom_indices to correct global indices

Pull Request - State: closed - Opened by gitabtion 8 months ago - 1 comment

#43 - Fixes issue 42: Editing the readme to fix the output_dir type

Pull Request - State: closed - Opened by Mo379 8 months ago - 1 comment

#42 - Typo in one of the data related commands

Issue - State: closed - Opened by Mo379 8 months ago

#41 - fixes issue 40: Here I renamed the alphafold3_pytorch/typing.py file …

Pull Request - State: closed - Opened by Mo379 8 months ago - 1 comment

#40 - A minor circular import issue due to the custom typing file

Issue - State: closed - Opened by Mo379 8 months ago

#39 - set expansion_factor=2 to be the same as the AF3.

Issue - State: closed - Opened by luwei0917 8 months ago - 3 comments

#38 - Specify RDKit version in pyproject.toml

Pull Request - State: closed - Opened by amorehead 8 months ago

#37 - Add rdkit to pyproject.toml (for data preparation)

Pull Request - State: closed - Opened by colbyford 8 months ago

#36 - Add rdkit

Pull Request - State: closed - Opened by colbyford 8 months ago

#34 - Fix context manager bug in `pdb_dataset_curation.py`

Pull Request - State: closed - Opened by amorehead 8 months ago - 1 comment

#33 - Update Dockerfile to accept build arguments

Pull Request - State: closed - Opened by colbyford 8 months ago

#32 - Add timeout decorator to pdb_dataset_curation.py

Pull Request - State: closed - Opened by amorehead 8 months ago - 1 comment

#31 - Describe AF3 PDB dataset preparation in README.md

Pull Request - State: closed - Opened by amorehead 8 months ago

#30 - Support AlphaFold 3 PDB dataset curation

Pull Request - State: closed - Opened by amorehead 8 months ago - 1 comment

#29 - Fix syntax typo in `attention.py`

Pull Request - State: closed - Opened by amorehead 8 months ago - 1 comment

#28 - Add assert to new test in `test_af3.py`

Pull Request - State: closed - Opened by amorehead 8 months ago

#27 - rollout pos should be named denoised_atom_pos

Pull Request - State: closed - Opened by gitabtion 8 months ago