python实现pdb转fasta

import sys

if len(sys.argv) <= 1:
    print('python pdb2fasta.py desgin_3.txt > desgin_3.fasta')
    exit()

input_file = open(sys.argv[1])

letters = {'ALA': 'A', 'ARG': 'R', 'ASN': 'N', 'ASP': 'D', 'CYS': 'C', 'GLU': 'E', 'GLN': 'Q', 'GLY': 'G', 'HIS': 'H',
           'ILE': 'I', 'LEU': 'L', 'LYS': 'K', 'MET': 'M', 'PHE': 'F', 'PRO': 'P', 'SER': 'S', 'THR': 'T', 'TRP': 'W',
           'TYR': 'Y', 'VAL': 'V'}
name = (sys.argv[1].split('.', 1)[0])
name = '>' + name;
print(name)
# print '>',name[0:len(name)]
prev = '-1'
for line in input_file:
    toks = line.split()
    if len(toks) < 1: continue
    if toks[0] != 'ATOM': continue
    if toks[5] != prev:
        sys.stdout.write('%c' % letters[toks[3]])
    prev = toks[5]

sys.stdout.write('\n')
input_file.close()

打开cmd,输入

python pdb2fasta.py desgin_3.txt > desgin_3.fasta