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| # Copyright Generate Biomedicines, Inc. | |
| # | |
| # 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. | |
| """Functions to retrieve information from external databases via their API; Uniprot and RCSB are the primary databases included here. | |
| """ | |
| import requests | |
| def _download_file(url, out_file): | |
| try: | |
| with requests.get(url, stream=True) as r: | |
| r.raise_for_status() | |
| with open(out_file, "wb") as f: | |
| for chunk in r.iter_content(chunk_size=8192): | |
| if chunk: | |
| f.write(chunk) | |
| return True | |
| except requests.HTTPError: | |
| return False | |
| def RCSB_file_download(pdb_id, ext, local_filename): | |
| """Downloads a file from the RCSB files section. | |
| Args: | |
| pdb_id (str) : 4-letter pdb id, case-insensitive | |
| ext (str) : Extension of file. E.g. ".pdb" or ".pdb1" | |
| local_filename (str) : Name for downloaded file. | |
| Returns: | |
| None | |
| """ | |
| url = f"https://files.rcsb.org/view/{pdb_id.upper()}{ext}" | |
| return _download_file(url, local_filename) | |