File size: 2,033 Bytes
d766458 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 | # Copyright 2025 ByteDance and/or its affiliates.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
dtype=fp32
use_deepspeed_evo_attention=false
export LAYERNORM_TYPE=fast_layernorm
export USE_DEEPSPEED_EVO_ATTENTION=${use_deepspeed_evo_attention}
export TOOL_WEIGHTS_ROOT="$(pwd)/tool_weights"
# ===============================
# Tool Weights Sanity Check
# ===============================
ROOT="${TOOL_WEIGHTS_ROOT}"
declare -a REQUIRED_FILES=(
# ---- AF2 ----
"$ROOT/af2/params_model_1.npz"
"$ROOT/af2/params_model_1_ptm.npz"
)
echo "Checking tool weights in: $ROOT"
for f in "${REQUIRED_FILES[@]}"; do
if [[ ! -f "$f" ]]; then
echo -e "\nMissing required tool weight:"
echo " $f"
echo -e "\nPlease run:"
echo " bash download_tool_weights.sh"
exit 1
fi
done
# ===============================
# Main
# ===============================
input_dir="./examples/binder"
dump_dir="./output/binder"
binder_chains="B0"
is_mmcif=true
N_seqs=2
mpnn_temp=0.0001
python3 ./pxdbench/run.py \
--data_dir ${input_dir} \
--dump_dir ${dump_dir} \
--is_mmcif ${is_mmcif} \
--seed 2025 \
--orig_seqs_json ./examples/orig_seqs_test.json \
--binder.num_seqs ${N_seqs} \
--binder.tools.mpnn.temperature ${mpnn_temp} \
--binder.tools.af2.use_binder_template true \
--binder.tools.ptx_mini.dtype ${dtype} \
--binder.tools.ptx_mini.use_deepspeed_evo_attention ${use_deepspeed_evo_attention} \
--binder_chains ${binder_chains} \
--binder.use_gt_seq false
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