C-alphaDist

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

Infile example

  ----------------------------------
 | ACC_ID  | residue1   | residue2 |
 | --------|------------|----------|
 | O00571  |     46     |    320   |
 | O00571  |    100     |    125   | 
 | P02545  |    235     |    240   |
 | P02545  |    116     |    200   |
  ----------------------------------

Usage

python CAdist_AF.py  -i "input filename" -o "output filename" -p1 "residue1" -p2 "residue 2" -a "protein ID"

Description

-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

example

python CAdist_AF.py  -i example.txt -o exampleout.txt -a 0 -p1 1 -p2 2 

Information written to outfile

Results will be wirtten as tab delimited to the specified outfile name.

  ----------------------------------------------
 | 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 |
  ---------------------------------------------