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Commit 02cb7711 authored by Jennifer's avatar Jennifer
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updates Bio.PDBData call and environment.yml

parent c4cccb6b
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Showing with 6 additions and 7 deletions
environment.yml
View file @ 02cb7711
...@@ -10,11 +10,10 @@ dependencies: ...@@ -10,11 +10,10 @@ dependencies:
- pip - pip
- openmm=7.7 - openmm=7.7
- pdbfixer - pdbfixer
- cudatoolkit==11.3.* - pytorch-lightning
- pytorch-lightning==2.0.9 - biopython
- biopython==1.79 - numpy
- numpy==1.21 - pandas
- pandas==2.0
- PyYAML==5.4.1 - PyYAML==5.4.1
- requests - requests
- scipy==1.7 - scipy==1.7
......
openfold/data/mmcif_parsing.py
View file @ 02cb7711
...@@ -24,7 +24,7 @@ import os ...@@ -24,7 +24,7 @@ import os
from typing import Any, Mapping, Optional, Sequence, Tuple from typing import Any, Mapping, Optional, Sequence, Tuple
from Bio import PDB from Bio import PDB
from Bio.Data import SCOPData from Bio.Data import PDBData
import numpy as np import numpy as np
from openfold.data.errors import MultipleChainsError from openfold.data.errors import MultipleChainsError
...@@ -283,7 +283,7 @@ def parse( ...@@ -283,7 +283,7 @@ def parse(
author_chain = mmcif_to_author_chain_id[chain_id] author_chain = mmcif_to_author_chain_id[chain_id]
seq = [] seq = []
for monomer in seq_info: for monomer in seq_info:
code = SCOPData.protein_letters_3to1.get(monomer.id, "X") code = PDBData.protein_letters_3to1.get(monomer.id, "X")
seq.append(code if len(code) == 1 else "X") seq.append(code if len(code) == 1 else "X")
seq = "".join(seq) seq = "".join(seq)
author_chain_to_sequence[author_chain] = seq author_chain_to_sequence[author_chain] = seq
......
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