foldcomp

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Multi-chain pdb

1

Hi, just came across this repo, very nice project. I was thinking about the feasibility of supporting multi-chain structures, an option could maybe be storing the offset coordinates for each...

Marc-commits

Hello! I've tried using `highquality_clust30` as a reference and identified the following issue. The database has around 200k repeated entries, they appear to be fragmented proteins split on `X` aminoacid....

valentynbez

https://github.com/steineggerlab/foldcomp/blob/b97c193e3029d861b6ca6b7c2970b562b779a4de/foldcomp/foldcomp.cxx#L333-L434 # Current behaviour Currently, there is no way to programmatically capture missing ids via Python interface. The missing ids are printed into non-capturable `stderr` .This would be a useful...

valentynbez

Advice for installation with pip

3

Hi! I used "pip install foldcomp" to install it in my system (WSL2 with conda as well as google colab). However it looks like foldcomp is not recognized because when...

miangoar

Pip install from pypi doesn't work when using Python3.12 but does work using pip install with a local version of the git repo. Error on pip install from pypi [error.txt](https://github.com/steineggerlab/foldcomp/files/14773102/error.txt)...

chasemc

When I extract `FASTA` from `highquality_clust30` I receive the following headers. ``` >ESMFOLD V0 PREDICTION FOR MGYP000138429313 >ESMFOLD V0 PREDICTION FOR MGYP001595280761 ... ``` I use `FoldComp` for a downstream...

valentynbez

Extraction of `FASTA` adds unnecessary `.pdb` extension if absent, which leads to inconsistensies

2

I.e., when I extract FASTA from `afdb_swissprot_v4`: ``` foldcomp_id = AF-B1YUJ2-F1-model_v4 fasta_header = AF-B1YUJ2-F1-model_v4.pdb ``` When I extract FASTA from my personal db: ``` foldcomp_id = MIP_00183643.pdb fasta_header = MIP_00183643.pdb...

valentynbez

foldcomp compress breaks input pdb file into multiple output files

2

Hi! When using foldcomp compress on this file: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/proteomics/pdb/1tim.pdb it breaks into 4 parts: 1tim.pdbA_0.fcz, 1tim.pdbA_1.fcz, 1tim.pdbB_0.fcz and 1tim.pdbB_1fcz Is this functionality desired? How to decompress into one pdb file...

vagkaratzas

Database extraction failed

2

Probably related to #39 I used the command from the issue to subset a database: ``` f"{foldcomp_binary} decompress -t 64 --db --id-list {txt_representatives} {full_af_db} {output_foldcomp}" ``` Now when I run...

valentynbez

Dealing with nested subdirectories

2

I have a lot of data to compress, and they are stored in nested subdirectories (e.g. /Data/Protein/Mutation/...pdb). Default behavior of "foldcomp compress -r" seems to be to create an output...

jomimc