Jared Adolf-Bryfogle
Jared Adolf-Bryfogle
### Setup I am reporting a problem with Biopython version, Python version, and operating system as follows: ```python import sys; print(sys.version) import platform; print(platform.python_implementation()); print(platform.platform()) import Bio; print(Bio.__version__) ``` [GCC...
Notebook 15.1 - accounting for the lipid membrane is failing in master with a timeout. We can put a debug statement around creating the bilayer, but perhaps there is a...
Great work, but I don't see any documentation for the inference script or even an ArgumentParser/etc. I think I can figure it out from the code, but but it would...
Ch2: First code we see is torch vision. This is missing from the requirements file. Since it's not compatible with pytorch 1.7.1, the requirements should probably have this updated.
Hello! Hope you are well! When I run inference on the included example, I get the following error: ``` ImportError: cannot import name 'DglPCQM4MDataset' from 'ogb.lsc' ``` obg is installed...
Fix bug in using ANARCI that sometimes puts '-' in the middle of CDRs that are shorter.
Hello! Awesome code base and docs! I’m trying to inpaint a small domain into a loop that of a TM protein that faces the cytosol. However, I keep getting helices...
Trying to build in presence of a receptor as such: `contigs='A219-585,5-10,A588-735,0,R144-237'` The 5-10 loop is rebuilt, but RFDesign is trying to build between the first and second chain. It outputs...
Doing some tests on a different structure with a receptor. Contigs are: 'A219-585,5-10,A588-735,0,R144-237' I'm writing 5 structures. These are PDB numbers as it seems that they are OK to use?...
Leaving this issue here, since there is no issue page on the protein_seq_des main. When running with a the --resfile option, the run fails. Also, the documentation states that it...