lucidrains/alphafold2 issues and pull requests

#110 - The Alphafold2 class does not have the parameter XXX.

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

#109 - How to adjust the recycling times in model?

Issue - State: open - Opened by Syaoran036 almost 2 years ago

#106 - CVE-2007-4559 Patch

Pull Request - State: open - Opened by TrellixVulnTeam over 2 years ago

#105 - Failed to build mdtraj proDy ERROR: Could not build wheels for mdtraj, proDy, which is required to install pyproject.toml-based projects

Issue - State: open - Opened by Mather10 almost 3 years ago

#104 - read me dimensions are off. Example to run alpha fold 2 msa, and seq lengths should be the same. One is 128, the other is 120.

Issue - State: open - Opened by ofTarradiddle over 3 years ago

#103 - How can I get the coordinates of all the atoms?

Issue - State: open - Opened by RayTang88 over 3 years ago

#102 - outerMean module question

Issue - State: open - Opened by ifromeast over 3 years ago - 1 comment

#101 - init() got an unexpected keyword argument 'structure_module_type'

Issue - State: open - Opened by ifromeast over 3 years ago - 4 comments

#98 - Can AlphaFold2 predict the structure of cyclic peptides?

Issue - State: open - Opened by JustinDoIt over 3 years ago - 1 comment

#97 - [todo] ensembling

Issue - State: open - Opened by lucidrains over 3 years ago

#96 - Make sure random_tokens is on correct device

Pull Request - State: closed - Opened by aced125 over 3 years ago

#95 - Typo?

Issue - State: closed - Opened by CiaoHe over 3 years ago - 3 comments

#94 - Example script of an end-to-end prediction from FASTA sequence to 3D pdb

Issue - State: closed - Opened by h-midlothian over 3 years ago - 2 comments

#93 - [todo] structure module

Issue - State: open - Opened by lucidrains over 3 years ago - 3 comments
Labels: enhancement

#92 - Missing adding the `relpos` to pairwise-repr `x`

Issue - State: closed - Opened by CiaoHe over 3 years ago - 1 comment

#91 - Maybe duplicate residual addition

Issue - State: closed - Opened by CiaoHe over 3 years ago - 1 comment

#90 - Should be first MSA-attention then Pairwise-Attention

Issue - State: closed - Opened by CiaoHe over 3 years ago - 1 comment

#89 - pairwise_repr should be used in rowAttention

Issue - State: closed - Opened by CiaoHe over 3 years ago - 1 comment

#88 - Maybe Inverse of the outgoing-attention and ingoing-attention here

Issue - State: closed - Opened by CiaoHe over 3 years ago - 1 comment

#87 - TypeError: init() got an unexpected keyword argument 'num_backbone_atoms'

Issue - State: open - Opened by jackli777 over 3 years ago - 3 comments

#86 - OuterMean block's typo

Issue - State: closed - Opened by CiaoHe over 3 years ago - 4 comments

#85 - The definition of row-wise attention and col-wise attention

Issue - State: closed - Opened by CiaoHe over 3 years ago - 1 comment

#84 - MSA attention gated problem

Issue - State: closed - Opened by CiaoHe over 3 years ago - 1 comment

#83 - ModuleNotFoundError: No module named 'invariant_point_attention'

Issue - State: closed - Opened by jackli777 over 3 years ago - 2 comments

#82 - [todo] positional encoding

Issue - State: closed - Opened by lucidrains over 3 years ago - 1 comment

#81 - [todo] checkpointing

Issue - State: open - Opened by lucidrains over 3 years ago - 3 comments
Labels: enhancement

#80 - [todo] BERT loss on MSA

Issue - State: open - Opened by lucidrains over 3 years ago - 4 comments
Labels: enhancement

#79 - [todo] FAPE loss

Issue - State: closed - Opened by lucidrains over 3 years ago - 2 comments
Labels: enhancement

#78 - [todo] recycling

Issue - State: closed - Opened by lucidrains over 3 years ago - 1 comment
Labels: enhancement

#77 - [todo] embeddings

Issue - State: closed - Opened by lucidrains over 3 years ago - 1 comment
Labels: enhancement

#76 - problem with alphafold2/train_pre.py

Issue - State: open - Opened by jackli777 over 3 years ago

#75 - Dev

Pull Request - State: closed - Opened by CiaoHe over 3 years ago

#74 - Add simple training script

Pull Request - State: open - Opened by superantichrist over 3 years ago - 2 comments

#73 - no coords_3d in train_end2end.py

Issue - State: closed - Opened by moonblue333 over 3 years ago - 2 comments

#72 - Integrate newest changes

Pull Request - State: closed - Opened by hypnopump over 3 years ago - 1 comment

#71 - the dimensions of coordinates in CASP12

Issue - State: closed - Opened by zhangyi-taotao almost 4 years ago - 3 comments

#70 - demonstrate sidechain

Pull Request - State: closed - Opened by hypnopump almost 4 years ago - 1 comment

#69 - Fix utils for better training

Pull Request - State: closed - Opened by hypnopump almost 4 years ago - 2 comments

#68 - solve mds problems?

Pull Request - State: closed - Opened by hypnopump almost 4 years ago - 5 comments

#67 - MDScaling isn't working right!

Issue - State: closed - Opened by xiongzhp almost 4 years ago - 3 comments

#66 - add new results from @lhatsk

Pull Request - State: closed - Opened by lucidrains almost 4 years ago

#65 - fix tests

Pull Request - State: closed - Opened by lucidrains almost 4 years ago

#64 - solving adjmat and a couple issues in utils

Pull Request - State: closed - Opened by hypnopump almost 4 years ago

#63 - fix row scaling dtype

Pull Request - State: closed - Opened by lucidrains almost 4 years ago

#62 - allow for tied row attention with uneven number of MSAs per sequence …

Pull Request - State: closed - Opened by lucidrains almost 4 years ago - 2 comments

#61 - Basic pretrained models + quickstart instructions?

Issue - State: open - Opened by TylerBalsam almost 4 years ago - 1 comment

#60 - fix mds tensors not in same device

Pull Request - State: closed - Opened by hypnopump almost 4 years ago - 1 comment

#59 - Add PL Lightning to Enable Distributed Training and Deep Speed

Issue - State: open - Opened by aribornstein almost 4 years ago - 3 comments

#58 - Add trrosetta dataset

Pull Request - State: closed - Opened by blazingsiyan almost 4 years ago - 4 comments

#57 - test error in utils

Issue - State: closed - Opened by lucidrains almost 4 years ago - 1 comment

#56 - MSA tensor format

Issue - State: open - Opened by panganqi almost 4 years ago - 5 comments

#55 - fix embeddings with esm + msa mask

Pull Request - State: closed - Opened by hypnopump almost 4 years ago

#54 - add LDDT predictor for confidence if arg is passed

Pull Request - State: closed - Opened by hypnopump almost 4 years ago

#53 - fix so tests pass

Pull Request - State: closed - Opened by hypnopump almost 4 years ago

#52 - How to use casp13 dataset & covid-13 protein sequence on this project.

Issue - State: closed - Opened by Planet-KIM almost 4 years ago - 3 comments

#51 - the sidechainnet pkg updates, the load function doesnot has parameter return_masks and the format of casp12 data from scn has changed, which is not compatible with train_end2end.py

Issue - State: open - Opened by ditannan almost 4 years ago - 1 comment

#50 - AttributeError : Constant object has no attribute ‘kind’

Issue - State: closed - Opened by Planet-KIM almost 4 years ago - 7 comments

#49 - CUBLAS ERROR while running example

Issue - State: closed - Opened by ychuhp almost 4 years ago - 9 comments

#48 - I want use casp13 dataset.

Issue - State: closed - Opened by Planet-KIM almost 4 years ago

#47 - Link to discord?

Issue - State: closed - Opened by ychuhp almost 4 years ago - 1 comment

#46 - add util to calculate lddt

Pull Request - State: closed - Opened by hypnopump almost 4 years ago

#45 - Question: Why are lengths of seq and msa same and different?

Issue - State: closed - Opened by ychuhp almost 4 years ago - 2 comments

#44 - Predicting sidechain now

Pull Request - State: closed - Opened by hypnopump almost 4 years ago

#43 - try to get scn cloud mask working

Pull Request - State: closed - Opened by lucidrains almost 4 years ago - 2 comments

#42 - try again to fix tests

Pull Request - State: closed - Opened by lucidrains almost 4 years ago

#41 - try to fix sidechainnet needed for tests

Pull Request - State: closed - Opened by lucidrains almost 4 years ago

#40 - solved problems in se3-mds. also solved hidden issues in utils

Pull Request - State: closed - Opened by hypnopump almost 4 years ago - 2 comments

#39 - Better utils. Adapt for cbeta. Example of how to link things

Pull Request - State: closed - Opened by hypnopump almost 4 years ago

#38 - Output pdb file

Issue - State: closed - Opened by 227BaronChen almost 4 years ago - 3 comments

#37 - clean more masked_fills

Pull Request - State: closed - Opened by hypnopump almost 4 years ago - 9 comments

#36 - fix PreNormCross norm

Pull Request - State: closed - Opened by blazingsiyan almost 4 years ago - 1 comment

#35 - gets rid of mirrors for mds -> faster and can do batched folding

Pull Request - State: closed - Opened by hypnopump about 4 years ago - 4 comments

#34 - [WIP] [Do-Not-Merge] mini experiment for predicting secondary structure using seq and msa

Pull Request - State: open - Opened by nilbot about 4 years ago - 1 comment

#33 - try to fix sidechainnet for tests

Pull Request - State: closed - Opened by lucidrains about 4 years ago

#32 - solves distogram median and int2char

Pull Request - State: closed - Opened by hypnopump about 4 years ago - 4 comments

#31 - Solved various things [list]

Pull Request - State: closed - Opened by hypnopump about 4 years ago - 5 comments

#30 - How

Issue - State: closed - Opened by ErenBalatkan about 4 years ago - 2 comments

#29 - solved median issue

Pull Request - State: closed - Opened by hypnopump about 4 years ago - 1 comment

#28 - fix typo + replace constant by dynamic guess

Pull Request - State: closed - Opened by hypnopump about 4 years ago - 3 comments

#27 - fix typo. should be ready for test

Pull Request - State: closed - Opened by hypnopump about 4 years ago

#26 - center_distogram_torch with center = 'median' breaks when tensors are on CUDA device

Issue - State: closed - Opened by lucidrains about 4 years ago - 12 comments

#25 - center_distogram_torch breaks with center = 'median'

Issue - State: closed - Opened by lucidrains about 4 years ago

#24 - move utils into package

Pull Request - State: closed - Opened by lucidrains about 4 years ago

#23 - cleaning up utils

Pull Request - State: closed - Opened by lucidrains about 4 years ago

#22 - Fixes esm model name, Adds se3 , wrapper for sidechain, input elongation

Pull Request - State: closed - Opened by hypnopump about 4 years ago

#21 - Update train_end2end.py

Pull Request - State: closed - Opened by aced125 about 4 years ago - 1 comment

#20 - Adds point cloud utils

Pull Request - State: closed - Opened by hypnopump about 4 years ago

#19 - Add attn embedding

Pull Request - State: closed - Opened by hypnopump about 4 years ago - 3 comments

#18 - Solves searchsorted shape issues

Pull Request - State: closed - Opened by hypnopump about 4 years ago

#17 - A bug……

Issue - State: closed - Opened by 227BaronChen about 4 years ago - 17 comments

#16 - MDS supports batched calculation of mirrors for better parallelization

Pull Request - State: closed - Opened by hypnopump about 4 years ago

#15 - faster distogram -> threshold conversion for "median" + adjust weights for "IGNORE_INDEX" class

Pull Request - State: closed - Opened by hypnopump about 4 years ago

#14 - faster distances. add proto end2end loop. detach rotation matrix

Pull Request - State: closed - Opened by hypnopump about 4 years ago

#13 - cool weights

Pull Request - State: closed - Opened by hypnopump about 4 years ago

#12 - Add distogram -> distance constraint + weights function (median)

Pull Request - State: closed - Opened by hypnopump about 4 years ago

#11 - Minor typo bug-fix for shape call

Pull Request - State: closed - Opened by nilbot about 4 years ago - 1 comment

#10 - Requirement fixes and pyrosetta links

Pull Request - State: closed - Opened by hypnopump about 4 years ago - 1 comment

#9 - Fix mirror selection - right 3d match

Pull Request - State: closed - Opened by hypnopump about 4 years ago

#8 - Corrects 3d generation

Pull Request - State: closed - Opened by hypnopump about 4 years ago

#7 - Algorithm corrections. Distogram -> 3d and Tests/Examples

Pull Request - State: closed - Opened by hypnopump about 4 years ago

GitHub / lucidrains/alphafold2 issues and pull requests