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iwatobipen/make_peptide.ipynb

Created March 19, 2022 08:22
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@cthoyt
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cthoyt commented Mar 19, 2022 •
edited

You can replace

tree = etree.parse('./chembl_30_monomer_library.xml')
root = tree.getroot()

with the following code using chembl-downloader to make this notebook automatically download the latest ChEMBL data (or pin with version="30":

import chembl_downloader

# Option 1: Always get the latest
root = chembl_downloader.get_monomer_library_root()

# Option 2: Pin to a specific version
root = chembl_downloader.get_monomer_library_root(version="30")

This has the added benefit that anyone can re-run your notebook without messing around with wget and making sure the file paths are all correct. I demonstrated this works on my fork of this gist at https://gist.github.com/cthoyt/a48376238cabf1d368401550f5f3e5ee.

@charlesxu90
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Another alternative is to update the FTP link in wget download to the following:

! wget https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_30/chembl_30_monomer_library.xml

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