Adds Soloseq parameter download script.

README.md

@@ -114,7 +114,13 @@ the model, consult `run_pretrained_openfold.py`.
 ### Inference
 
 To run inference on a sequence or multiple sequences using a set of DeepMind's 
-pretrained parameters, run e.g.:
+pretrained parameters, first download the OpenFold weights e.g.:
+
+```bash 
+bash scripts/download_openfold_params.sh openfold/resources
+```
+
+then run e.g.:
 
 ```bash
 python3 run_pretrained_openfold.py \
@@ -225,6 +231,14 @@ python scripts/precompute_embeddings.py fasta_dir/ embeddings_output_dir/
 
 In the same per-label subdirectories inside `embeddings_output_dir`, you can also place `*.hhr` files (outputs from HHSearch), which can contain the details about the structures that you want to use as templates. If you do not place any such file, templates will not be used and only the ESM-1b embeddings will be used to predict the structure. If you want to use templates, you need to pass the PDB MMCIF dataset to the command.
 
+Then download the SoloSeq model weights, e.g.:
+
+
+```bash 
+bash scripts/download_openfold_soloseq_params.sh openfold/resources
+```
+
+
 Now, you are ready to run inference:
 ```bash
 python run_pretrained_openfold.py \
@@ -234,7 +248,7 @@ python run_pretrained_openfold.py \
     --output_dir ./ \
     --model_device "cuda:0" \
     --config_preset "seq_model_esm1b_ptm" \
-    --openfold_checkpoint_path openfold/resources/openfold_params/seq_model_esm1b_ptm.pt
+    --openfold_checkpoint_path openfold/resources/openfold_soloseq_params/seq_model_esm1b_ptm.pt
 ```
 
 For generating the embeddings during inference, skip the `--use_precomputed_alignments` argument. The `*.hhr` files will be generated as well if you pass the paths to the relevant databases and tools, as specified in the command below. If you skip the database and tool arguments, HHSearch will not be used to find templates and only generated ESM-1b embeddings will be used to predict the structure.

scripts/download_openfold_soloseq_params.sh

@@ -0,0 +1,34 @@
+#!/bin/bash
+#
+# Copyright 2021 DeepMind Technologies Limited
+#
+# 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.
+#
+# Downloads OpenFold parameters.
+#
+# Usage: bash download_openfold_params_huggingface.sh /path/to/download/directory
+set -e
+
+if [[ $# -eq 0 ]]; then
+    echo "Error: download directory must be provided as an input argument."
+    exit 1
+fi
+
+if ! command -v aws &> /dev/null ; then
+    echo "Error: aws could not be found. Please install aws."
+    exit 1
+fi
+
+DOWNLOAD_DIR="${1}/openfold_soloseq_params"
+mkdir -p "${DOWNLOAD_DIR}"
+aws s3 cp --no-sign-request --region us-east-1 s3://openfold/openfold_soloseq_params/ "${DOWNLOAD_DIR}" --recursive