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.