本家様 https://github.com/jwohlwend/boltz

source /apps/pyenv/versions/anaconda3-2024.10-1/etc/profile.d/conda.sh
 
 
conda create -n Boltz-1 pip python=3.9 -c conda-forge
 
conda activate Boltz-1
 
cd /apps
 
git clone https://github.com/jwohlwend/boltz.git
 
cd boltz
 
pip install -e .
 

「/apps/modulefiles/boltz」

#%Module
set          root /apps/pyenv/versions/anaconda3-2024.10-1/envs/Boltz-1
prepend-path PATH $root/bin

「boltz --help」

Usage: boltz [OPTIONS] COMMAND [ARGS]...
 
  Boltz1.
 
Options:
  --help  Show this message and exit.
 
Commands:
  predict  Run predictions with Boltz-1.

「boltz predict --help」

Usage: boltz predict [OPTIONS] DATA
 
  Run predictions with Boltz-1.
 
Options:
  --out_dir PATH               The path where to save the predictions.
  --cache PATH                 The directory where to download the data and
                               model. Default is ~/.boltz.
  --checkpoint PATH            An optional checkpoint, will use the provided
                               Boltz-1 model by default.
  --devices INTEGER            The number of devices to use for prediction.
                               Default is 1.
  --accelerator [gpu|cpu|tpu]  The accelerator to use for prediction. Default
                               is gpu.
  --recycling_steps INTEGER    The number of recycling steps to use for
                               prediction. Default is 3.
  --sampling_steps INTEGER     The number of sampling steps to use for
                               prediction. Default is 200.
  --diffusion_samples INTEGER  The number of diffusion samples to use for
                               prediction. Default is 1.
  --step_scale FLOAT           The step size is related to the temperature at
                               which the diffusion process samples the
                               distribution.The lower the higher the diversity
                               among samples (recommended between 1 and 2).
                               Default is 1.638.
  --write_full_pae             Whether to dump the pae into a npz file.
                               Default is True.
  --write_full_pde             Whether to dump the pde into a npz file.
                               Default is False.
  --output_format [pdb|mmcif]  The output format to use for the predictions.
                               Default is mmcif.
  --num_workers INTEGER        The number of dataloader workers to use for
                               prediction. Default is 2.
  --override                   Whether to override existing found predictions.
                               Default is False.
  --seed INTEGER               Seed to use for random number generator.
                               Default is None (no seeding).
  --use_msa_server             Whether to use the MMSeqs2 server for MSA
                               generation. Default is False.
  --msa_server_url TEXT        MSA server url. Used only if --use_msa_server
                               is set.
  --msa_pairing_strategy TEXT  Pairing strategy to use. Used only if
                               --use_msa_server is set. Options are 'greedy'
                               and 'complete'
  --help                       Show this message and exit.
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Last-modified: 2025-01-20 (月) 21:40:35