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Merge branch 'run-from-anywhere' of github.com:CyrusBiotechnology/RoseTTAFold-All-Atom into run-from-anywhere

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Brandon Frenz 2024-10-07 10:50:36 -07:00
commit fe4cefafc1
2 changed files with 4 additions and 3 deletions
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5
README.md
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@ -70,12 +70,13 @@ wget https://bfd.mmseqs.com/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted
mkdir -p bfd mkdir -p bfd
tar xfz bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gz -C ./bfd tar xfz bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gz -C ./bfd
# structure templates (including *_a3m.ffdata, *_a3m.ffindex) # structure templates [81G] (including *_a3m.ffdata, *_a3m.ffindex)
wget https://files.ipd.uw.edu/pub/RoseTTAFold/pdb100_2021Mar03.tar.gz wget https://files.ipd.uw.edu/pub/RoseTTAFold/pdb100_2021Mar03.tar.gz
tar xfz pdb100_2021Mar03.tar.gz tar xfz pdb100_2021Mar03.tar.gz
``` ```
8. Download BLAST 8. Download BLAST [39M]
``` ```
wget https://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/2.2.26/blast-2.2.26-x64-linux.tar.gz wget https://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/2.2.26/blast-2.2.26-x64-linux.tar.gz
mkdir -p blast-2.2.26 mkdir -p blast-2.2.26

2
rf2aa/data/parsers.py
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@ -227,7 +227,7 @@ def parse_multichain_fasta(filename, maxseq=10000, rna_alphabet=False, dna_alph
# convert letters into numbers # convert letters into numbers
if rna_alphabet: if rna_alphabet:
alphabet = np.array(list("00000000000000000000-000000ACGTN"), dtype='|S1').view(np.uint8) alphabet = np.array(list("00000000000000000000-000000ACGUN"), dtype='|S1').view(np.uint8)
elif dna_alphabet: elif dna_alphabet:
alphabet = np.array(list("00000000000000000000-0ACGTD00000"), dtype='|S1').view(np.uint8) alphabet = np.array(list("00000000000000000000-0ACGTD00000"), dtype='|S1').view(np.uint8)
else: else: