Protein Comparison via Model Overlaying using TM Align #192
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ansengarvin
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xnought
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Mar 10, 2024
backend/src/tmalign.py
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| # stdout = bash_cmd(cmd) | ||
| # log.warn(stdout) |
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Seems like you accidentally commented out the lines that actually run TMalign
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One way to get around the TMaligns creating files issue is to create a new directory every time. Then run TMalign, read in the file stream as bytes into RAM, and returning that to the user. See the FASTA endpoint for how to return bytes as a file. Then since we read in the file as bytes we are free to remove the files from the file system. I can help out on this. |
xnought
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Mar 10, 2024
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Real good work! I'll merge stuff in. Make sure to create an issue on the TMalgin file generation issue so we can revise that next term @ansengarvin.
Overall, very nice.
xnought
approved these changes
Mar 10, 2024
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Added ability to compare protein models by overlaying, aligning, and coloring their models. Accomplished by merging the two PDB files into a single PDB file using TM Align. This can be done with the new API endpoint /proteins/pdb/:proteinA/:proteinB
Created a rudimentary web page for comparing proteins, at compare/ProteinA/ProteinB:
Protein Comparison:
Added "compare" links to the computed insights field, to allow the user to quickly compare similar proteins:
Added two new shell commands to install and remove TM Align in docker:
