Add pdb_atom2hetatm.py

pdb_atom2hetatm.py

@@ -0,0 +1,109 @@
+#!/usr/bin/env python
+
+"""
+Transform all the non-standard aminoacid residue records into HETATM.
+
+HADDOCK formatted PDB files have allthe HETATM renamed to ATOM which sometimes
+causes problem with downstream analysis programs (eg PROFIT). This  script will
+only print the ATOM lines whose resname is one of the standard aminoacids. The
+non-ATOM/HETATM lines will not be affected.
+
+usage: python pdb_atom2hetatm.py <pdb file>
+
+Author: {0} ({1})
+
+This program is part of the PDB tools distributed with HADDOCK
+or with the HADDOCK tutorial. The utilities in this package
+can be used to quickly manipulate PDB files, with the benefit
+of 'piping' several different commands. This is a rewrite of old
+FORTRAN77 code that was taking too much effort to compile. RIP.
+"""
+
+import os
+import re
+import sys
+
+__author__ = "Joao Rodrigues"
+__email__ = "[email protected]"
+
+USAGE = __doc__.format(__author__, __email__)
+
+RESNAMES = (
+    'ALA',
+    'ARG',
+    'ASN',
+    'ASP',
+    'CYS',
+    'GLN',
+    'GLU',
+    'GLY',
+    'HIS',
+    'ILE',
+    'LEU',
+    'LYS',
+    'MET',
+    'PHE',
+    'PRO',
+    'SER',
+    'THR',
+    'TRP',
+    'TYR',
+    'VAL'
+)
+
+def check_input(args):
+    """Checks whether to read from stdin/file and validates user input/options."""
+
+    if not len(args):
+        # No chain, from pipe
+        if not sys.stdin.isatty():
+            pdbfh = sys.stdin
+        else:
+            sys.stderr.write(USAGE)
+            sys.exit(1)
+    elif len(args) == 1:
+        # File
+        if not os.path.isfile(args[0]):
+            sys.stderr.write('File not found: ' + args[0] + '\n')
+            sys.stderr.write(USAGE)
+            sys.exit(1)
+        pdbfh = open(args[0], 'r')
+    else:
+        sys.stderr.write(USAGE)
+        sys.exit(1)
+
+    return pdbfh
+
+def _slice_pdb(fhandle):
+    """Enclosing logic in a function to speed up a bit"""
+
+    for line in fhandle:
+        if line.startswith(('ATOM', 'HETATM')):
+            if line[17:20] in RESNAMES:
+                yield line
+            else:
+                yield "HETATM" + line[6:]
+        else:
+            yield line
+
+if __name__ == '__main__':
+
+    # Check Input
+    pdbfh = check_input(sys.argv[1:])
+
+    # Do the job
+    new_pdb = _slice_pdb(pdbfh)
+
+    try:
+        sys.stdout.write(''.join(new_pdb))
+        sys.stdout.flush()
+    except IOError:
+        # This is here to catch Broken Pipes
+        # for example to use 'head' or 'tail' without
+        # the error message showing up
+        pass
+
+    # last line of the script
+    # We can close it even if it is sys.stdin
+    pdbfh.close()
+    sys.exit(0)