| |
| source ${ROCM_PATH}/cuda/env.sh |
| export LD_LIBRARY_PATH="$CONDA_PREFIX/lib:$LD_LIBRARY_PATH" |
| export LD_LIBRARY_PATH="$CONDA_PREFIX/lib/python3.11/site-packages/fastpt/torch/lib:$LD_LIBRARY_PATH" |
|
|
|
|
| SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)" |
| PROJECT_ROOT="$(cd "${SCRIPT_DIR}/../../.." && pwd)" |
|
|
| echo "ONESCIENCE_PATH:" $PROJECT_ROOT |
|
|
| |
| echo ${ONESCIENCE_DATASETS_DIR} |
| echo ${ONESCIENCE_MODELS_DIR} |
|
|
| |
| export PYTHONPATH=${PROJECT_ROOT}/src:$(pwd):$PYTHONPATH |
|
|
| if [[ $# -gt 0 && "$1" != --* ]]; then |
| CONFIG_PATH=$1 |
| CONFIG_OVERRIDES=("${@:2}") |
| else |
| CONFIG_PATH=configs/prop/pdbbind_general_egnn.yml |
| CONFIG_OVERRIDES=("$@") |
| fi |
|
|
| PDBBIND_SOURCE=${PDBBIND_SOURCE:-${ONESCIENCE_DATASETS_DIR}/targetdiff/data/pdbbind_v2020} |
| CORESET_PATH=${CORESET_PATH:-${ONESCIENCE_DATASETS_DIR}/targetdiff/data/pdbbind_v2016/coreset} |
| PROCESSED_ROOT=${PROCESSED_ROOT:-${ONESCIENCE_DATASETS_DIR}/targetdiff/data/pdbbind_v2020_processed} |
| POCKET_ROOT=${PROCESSED_ROOT}/pocket_10_refined |
| INDEX_PATH=${POCKET_ROOT}/index.pkl |
| SPLIT_PATH=${POCKET_ROOT}/split.pt |
|
|
| mkdir -p ${PROCESSED_ROOT} |
|
|
| |
| python scripts/property_prediction/extract_pockets.py \ |
| --source ${PDBBIND_SOURCE} \ |
| --dest ${PROCESSED_ROOT} \ |
| --subset refined \ |
| --num_workers 16 |
|
|
| |
| python scripts/property_prediction/pdbbind_split.py \ |
| --split_mode coreset \ |
| --index_path ${INDEX_PATH} \ |
| --test_path ${CORESET_PATH} \ |
| --save_path ${SPLIT_PATH} |
|
|
| |
| python scripts/property_prediction/train_prop.py ${CONFIG_PATH} \ |
| --device cuda \ |
| --logdir ./logs_prop \ |
| --tag targetdiff_prop_train \ |
| --dataset.path ${POCKET_ROOT} \ |
| --dataset.split ${SPLIT_PATH} \ |
| --dataset.name pdbbind \ |
| --dataset.heavy_only true \ |
| --train.seed 2021 \ |
| --train.batch_size 4 \ |
| --train.num_workers 4 \ |
| --train.max_epochs 200 \ |
| --train.report_iter 200 \ |
| --train.val_freq 1 \ |
| --train.pos_noise_std 0.1 \ |
| --train.max_grad_norm 10. \ |
| --train.optimizer.type adam \ |
| --train.optimizer.lr 1.e-4 \ |
| --train.optimizer.weight_decay 0 \ |
| --train.optimizer.beta1 0.99 \ |
| --train.optimizer.beta2 0.999 \ |
| --train.scheduler.type plateau \ |
| --train.scheduler.factor 0.6 \ |
| --train.scheduler.patience 10 \ |
| --train.scheduler.min_lr 1.e-5 \ |
| "${CONFIG_OVERRIDES[@]}" |
|
|
