simplefold

SimpleFold wrapper.

Installation

pip install git+https://github.com/apple/ml-simplefold
pip install git+https://github.com/BejaLab/run_simplefold

simplefold_init

usage: simplefold_init [-h] -D DATA_DIR [-m {simplefold_100M,simplefold_360M,simplefold_700M,simplefold_1.1B,simplefold_1.6B,simplefold_3B}]

SimpleFold wrapper: Initialize

options:
  -h, --help            show this help message and exit
  -D DATA_DIR, --data-dir DATA_DIR
                        Base directory for data
  -m {simplefold_100M,simplefold_360M,simplefold_700M,simplefold_1.1B,simplefold_1.6B,simplefold_3B}, --model {simplefold_100M,simplefold_360M,simplefold_700M,simplefold_1.1B,simplefold_1.6B,simplefold_3B}
                        Model name (optional)

simplefold_run

usage: simplefold_run [-h] -i INPUT -O OUTPUT -D DATA_DIR -m {simplefold_100M,simplefold_360M,simplefold_700M,simplefold_1.1B,simplefold_1.6B,simplefold_3B} [-g GPUS] [-s SEED]
                      [-b BATCH] [-l LOG] [--tau TAU] [--steps STEPS]

SimpleFold wrapper: Run

options:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        Path to input sequences
  -O OUTPUT, --output OUTPUT
                        Output directory
  -D DATA_DIR, --data-dir DATA_DIR
                        Base directory for data
  -m simplefold_{100M,360M,700M,1.1B,1.6B,3B}, --model simplefold_{100M,360M,700M,1.1B,1.6B,3B}
                        Model name to use for inference
  -g GPUS, --gpus GPUS  GPU indices to use
  -s SEED, --seed SEED  Seed
  -b BATCH, --batch BATCH
                        Batch size
  -l LOG, --log LOG     Raw log file
  --tau TAU
  --steps STEPS

simplefold_select

usage: simplefold_select [-h] -I INPUT -O OUTPUT [-l] [--no-seed-suffix]

SimpleFold wrapper: Select

options:
  -h, --help            show this help message and exit
  -I INPUT, --input INPUT
                        Directory containing 'run' outputs
  -O OUTPUT, --output OUTPUT
                        Output directory for the best models
  -l, --soft-link       Soft link instead of hard copy
  --no-seed-suffix      The input files do not contain the seed as the suffix