add the script pdb_gethaddockterms.py

pdb_gethaddockterms.py

@@ -0,0 +1,78 @@
+#!/usr/bin/python
+"""
+Extract HADDOCK terms (Evdw, Eelec, Edesolv and BSA) from a HADDOCK-format PDB file.
+
+Usage: python pdb_gethaddockterms.py <HADDOCK PDB file>
+Example: python pdb_gethaddockterms.py cluster1_1.pdb
+
+Author: {0}
+Email: {1}
+"""
+from __future__ import print_function
+import os
+import sys
+import re
+
+__author__ = "Cunliang Geng"
+__email__ = "[email protected]"
+
+USAGE = __doc__.format(__author__, __email__)
+
+def check_input(args):
+    """Checks whether to read from stdin/file and validates user input/options."""
+
+    if not len(args):
+        # Read from pipe
+        if not sys.stdin.isatty():
+            fhandle = sys.stdin
+        else:
+            sys.stderr.write(USAGE)
+            sys.exit(1)
+    elif len(args) == 1:
+        if not os.path.isfile(args[0]):
+            sys.stderr.write('File not found: ' + args[0] + '\n')
+            sys.stderr.write(USAGE)
+            sys.exit(1)
+        fhandle = open(args[0], 'r')
+    else:
+        sys.stderr.write(USAGE)
+        sys.exit(1)
+    return fhandle
+
+
+def ExtractHaddockTerms(pdbfhandle):
+    terms = {}
+    for line in pdbfhandle:
+        if line[0:6] == 'REMARK':
+            if re.match(r'REMARK energies', line):
+                ene = line.split(',')
+                terms['Evdw'] = ene[5].strip()
+                terms['Eelec'] = ene[6].strip()
+            elif re.match(r'REMARK Desolvation energy', line):
+                terms['Edesolv'] = line.split()[3].strip()
+            elif re.match(r'REMARK buried surface area', line):
+                terms['BSA'] = line.split()[4].strip()
+            else:
+                continue
+
+    return terms
+
+
+def WriteHaddockTerms(pdbfhandle):
+    terms = ExtractHaddockTerms(pdbfhandle)
+    if terms:
+        header = ['Evdw', 'Eelec', 'Edesolv', 'BSA']
+        haddockterms = [terms[i] for i in header]
+        print("\t".join(header))
+        print("\t".join(haddockterms))
+    else:
+        sys.stderr.write("Error: Input is not a HADDOCK-format PDB file\n")
+        sys.stderr.write(USAGE)
+        sys.exit(1)
+
+
+if __name__ == "__main__":
+
+    pdbfhandle =  check_input(sys.argv[1:])
+    WriteHaddockTerms(pdbfhandle)
+    pdbfhandle.close()