mirror of
https://github.com/KosinskiLab/AlphaPulldown.git
synced 2026-06-04 14:14:24 +08:00
4d802be7d6
* symmetrical refactoring to support both af2 and af3 data pipelines * Clean tests * Keep GPU tests in place * Reverted accidentally deleted templates * Add AlphaFold3 feature creation pipeline and per-chain input generation - Implement `create_pipeline_af3` to construct the AlphaFold3 data pipeline with correct database and binary paths. - Add `create_af3_individual_features` to generate AlphaFold3 input features for each chain in a FASTA, handling protein, RNA, and DNA sequences. - Integrate new AF3 logic into the main entry point, dispatching to AF2 or AF3 as appropriate. - Ensure output directory creation and error handling for missing dependencies or invalid sequences. * Convert template dates to datetime for af3 * First check for nucleotides, then for amino-acids * Skip existing features json if --skip_existing=true * Check if DNA before RNA * Bump 2.1.0 * Git ignore build/ dir
6 lines
232 B
Plaintext
6 lines
232 B
Plaintext
>PROTEIN_CHAIN
|
|
MESAIAEGGASRFSASSGGGGSRGAPQHYPKTAGNSEFLGKTPGQNAQKWIPARSTRRDDNSAA
|
|
>DNA_CHAIN
|
|
ATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCG
|
|
>RNA_CHAIN
|
|
AUCGAUCGAUCGAUCGAUCGAUCGAUCGAUCGAUCGAUCGAUCGAUCGAUCGAUCGAUCGAUCG |