模块化编程1

＃　如何识别PDB文件中的特定氨基酸残基

1.PDB文件格式

ATOM   1604  C   ILE A 242      20.705 -26.318  26.653  1.00 14.92           C  
ATOM   1605  O   ILE A 242      20.152 -26.942  27.574  1.00 14.92           O  
ATOM   1606  CB  ILE A 242      19.560 -24.197  25.856  1.00 14.92           C  
ATOM   1607  CG1 ILE A 242      19.299 -22.702  26.128  1.00 24.76           C  
ATOM   1608  CG2 ILE A 242      18.303 -25.064  25.876  1.00 24.76           C  
ATOM   1609  CD1 ILE A 242      18.131 -22.226  25.235  1.00 24.76           C  
ATOM   1610  N   ALA A 243      21.439 -26.905  25.725  1.00 17.24           N  
ATOM   1611  CA  ALA A 243      21.400 -28.376  25.564  1.00 17.24           C  
ATOM   1612  C   ALA A 243      22.118 -29.051  26.721  1.00 17.24           C  
ATOM   1613  O   ALA A 243      21.805 -30.211  27.060  1.00 17.24           O  
ATOM   1614  CB  ALA A 243      22.110 -28.691  24.252  1.00 17.24           C  
ATOM   1615  N   SER A 244      22.931 -28.273  27.410  1.00 21.20           N  
ATOM   1616  CA  SER A 244      23.624 -28.860  28.537  1.00 21.20           C  
ATOM   1617  C   SER A 244      23.069 -28.457  29.888  1.00 21.20           C  
ATOM   1618  O   SER A 244      23.749 -28.808  30.883  1.00 21.20           O  
ATOM   1619  CB  SER A 244      25.120 -28.570  28.588  1.00 21.20           C  
ATOM   1620  OG  SER A 244      25.568 -27.755  27.532  1.00 37.03           O  
ATOM   1621  N   ASN A 245      22.014 -27.634  29.956  1.00 23.26           N  
ATOM   1622  CA  ASN A 245      21.491 -27.139  31.253  1.00 23.26           C  
ATOM   1623  C   ASN A 245      20.002 -27.388  31.492  1.00 23.26           C  
ATOM   1624  O   ASN A 245      19.486 -26.996  32.563  1.00 23.26           O  
ATOM   1625  CB  ASN A 245      21.630 -25.625  31.399  1.00 23.26           C  
ATOM   1626  CG  ASN A 245      23.052 -25.304  31.799  1.00 20.44           C  
ATOM   1627  OD1 ASN A 245      23.456 -25.717  32.901  1.00 20.44           O  
ATOM   1628  ND2 ASN A 245      23.863 -25.089  30.809  1.00 20.44           N  
ATOM   1629  OXT ASN A 245      19.369 -28.189  30.785  1.00 27.82           O

pdb文件说明：

2. python3版本

import struct
pdb_format = '6s5s1s4s1s3s1s1s4s1s3s8s8s8s6s6s10s2s3s'

def main(pdb_file,out_file,residues):
    pdb = open(pdb_file)
    out_file = open(out_file,'w')
    for line in pdb:
        if line[0:4] == 'ATOM':
            res_data = get_ATOM_line(line)
            res_type = bytes.decode(res_data[1])
            res_num = bytes.decode(res_data[2])
            for aa,num in residues:  ##Python3中s的Python type是bytes类型，所以当进行条件判断时需要进行decode解码。
                if res_type == aa and res_num == num:
                    out_file.write(line)
    out_file.close()


def get_ATOM_line(line):
    tmp = struct.unpack(pdb_format,bytes(line.encode('utf-8')))  ##注意struct模块是将字符串转换成元组，输出是tuple
    atom = tmp[3].strip()
    res_type = tmp[5].strip()
    chain = tmp[7].strip()
    res_num = tmp[8].strip()
    x = float(tmp[11].strip())
    y = float(tmp[12].strip())
    z = float(tmp[13].strip())
    return chain, res_type, res_num, atom, x, y, z
residues = [('ASP', '102'), ('HIS', '57'), ('SER', '195')]
main("C:\\shiyan\\honghua\\1tld.pdb", "trypsin_triad.pdb", residues)

3. python2版本

import struct
pdb_format = '6s5s1s4s1s3s1s1s4s1s3s8s8s8s6s6s10s2s3s'

def get_atom_line(line):
    '''return an ATOM line parsed to a tuple'''
    tmp = struct.unpack(pdb_format, line)
    atom = tmp[3].strip()
    res_type = tmp[5].strip()
    res_num = tmp[8].strip()
    chain = tmp[7].strip()
    x = float(tmp[11].strip())
    y = float(tmp[12].strip())
    z = float(tmp[13].strip())
    return chain, res_type, res_num, atom, x, y, z

def main(pdb_file, outfile, residues):
    '''writes residues from a PDB file to an output file'''
    pdb = open(pdb_file)
    outfile = open(outfile, "w")
    for line in pdb:
        if line.startswith('ATOM'):
            res_data = get_atom_line(line)
            for aa,num in residues:
                if res_data[1] == aa and res_data[2] == num:
                    outfile.write(line)
    outfile.close()

residues = [('ASP', '102'), ('HIS', '57'), ('SER', '195')]
main("1TLD.pdb", "trypsin_triad.pdb", residues)