Python script to calculate distance between amino acids C-alpha atoms using PDB file. Works with AlphaFold models.
Takes "csv file" as input and outputs a "tsv file" containing distance information
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| ACC_ID | residue1 | residue2 |
| --------|------------|----------|
| O00571 | 46 | 320 |
| O00571 | 100 | 125 |
| P02545 | 235 | 240 |
| P02545 | 116 | 200 |
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python CAdist_AF.py -i "input filename" -o "output filename" -p1 "residue1" -p2 "residue 2" -a "protein ID"
-i,--ifile infile name with extension
-o,--ofile outfile name with extension
-a,--acc column index of protein accession in infile
-p1, --pos1 column index for first residue in infile
-p2,--pos2 column index for the second residue in infile
-h, --help show this help message and exit
python CAdist_AF.py -i example.txt -o exampleout.txt -a 0 -p1 1 -p2 2
Results will be wirtten as tab delimited to the specified outfile name.
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| ACC_ID | residue1 | residue2 | CAdist(A) |
| --------|------------|----------|-----------|
| O00571 | 46 | 320 | 47.2576 |
| O00571 | 100 | 125 | 52.6169 |
| P02545 | 235 | 240 | 8.4829 |
| P02545 | 116 | 200 | 123.6562 |
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