x_pdb_modif_resid.py

#!/usr/bin/env python3

import sys,os,re

##########################################################################
#
#   Peter M.U. Ung @ MSSM
#
#   v1.   18.08.15
#   v2.   20.02.18 - remove disordered atoms but keep the "A" variant

#   replace modified PDB residues with the standard AA, and remove disordered
#   atoms while keeping the "A" variant. The modified  residues are hidden 
#   with REMARK
#
##########################################################################

def ReplacePDBModifiedAA( in_pdb, out_pdb ):
  name  = in_pdb.split('.pdb')[0]
  with open(in_pdb, 'r') as fi:
    Lines = [ l for l in fi ]

  Edited = []
  for l in Lines:

    ### If found atoms with alternate conformation, keep "A" only
    if re.search('^ATOM|^HETATM|^ANISOU', l) and l[16] != ' ':
      if l[16] == 'A':
        l = l[:16]+' '+l[17:]
      else:
        Edited.append('REMARK  CON '+l)
        continue

##################

    ### If found hetero-group, check
    if not re.search(r'HETATM', l):
      Edited.append(l)
    else:
      ## Replace phospho- residues (Ser, Thr, Tyr, His)
      if re.search(r'SEP|TPO|T8L|PTR|NEP', l):
        Edited.append('REMARK  HET '+l)
        m = re.sub('HETATM', 'ATOM  ', l)
        if re.search(r'SEP', l):
          n = re.sub('SEP', 'SER', m)
        if re.search(r'TPO|T8L', l):
          n = re.sub('TPO|T8L', 'THR', m)
        if re.search(r'PTR', m):
          n = re.sub('PTR', 'TYR', m)
        if re.search(r'NEP', l):
          n = re.sub('NEP', 'HIS', m)
        if not re.search(r' P  |O1P|O2P|O3P| S1 ', n):
          Edited.append(n)
      ## Replace MSE with MET
      elif re.search(r'MSE|MHO', l):
        Edited.append('REMARK  HET '+l)
        m = re.sub('HETATM', 'ATOM  ', l)
        n = re.sub(r'MSE|MHO', 'MET', m)
        o = re.sub('SE ', ' SD', n)
        if not re.search(r'OD1', o):
          Edited.append(o)
      ## Replace modified CYS
      elif re.search(r'CSO|OCS|CSX|CSD|2CO|CME|CSS', l):
        Edited.append('REMARK  HET '+l)
        m = re.sub('HETATM', 'ATOM  ', l)
        n = re.sub(r'CSO|OCS|CSX|CSD|2CO|CME|CSS', 'CYS', m)
        if not re.search(r' OD|OD1|OD2|OD3| OE| SD| CE| CZ| OH', n):
          Edited.append(n)
      ## Replace modified LYS
      elif re.search(r'KCX|ALY|MLY', l):
        Edited.append('REMARK  HET '+l)
        m = re.sub('HETATM', 'ATOM  ', l)
        n = re.sub(r'KCX|ALY|MLY', 'LYS', m)
        if not re.search(r'CX |OQ1|OQ2|CH3|CH |OH |CH1|CH2', n):
          Edited.append(n)
      ## Replace modified ARG
      elif re.search(r'NMM', l):
        Edited.append('REMARK  HET '+l)
        m = re.sub('HETATM', 'ATOM  ', l)
        n = re.sub(r'NMM', 'ARG', m)
        if not re.search(r'CAA', m):
          Edited.append(n)
      else:
        Edited.append(l)


  with open(out_pdb, 'w') as fo:
    for l in Edited:
      fo.write(l)

########################################################################