added hb-select script

hb-select/hb-select.py

@@ -0,0 +1,70 @@
+#!/usr/bin/python2
+
+import argparse
+
+def readAtoms(file):
+    """function to read *gro file"""
+    atoms = {}
+    with open(file, 'r') as coordFile:
+        coordFile.readline()
+        num = int(coordFile.readline())
+        for i in range(num):
+            line = coordFile.readline()
+            resNum = int(line[0:5])
+            atomNum = int(line[15:20])
+            atoms[atomNum] = resNum
+    return atoms
+
+
+def readHb(files):
+    """function to read *.ndx file"""
+    hbs = []
+    start = False
+    for file in files:
+        with open(file, 'r') as ndxFile:
+            for line in ndxFile:
+                if (line[0:9] == "[ hbonds_"):
+                    start = True
+                    continue
+                elif (line.count('[') > 0):
+                    start = False
+                    continue
+                elif (start):
+                    donor = int(line[0:7])
+                    hydrogen = int(line[7:14])
+                    acceptor = int(line[14:21])
+                    if (hbs.count([donor, hydrogen, acceptor]) == 0):
+                        hbs.append([donor, hydrogen, acceptor])
+    return hbs
+
+
+def selectHb(atoms, hbs):
+    """funtion to select hydrogen bond"""
+    selectedHbs = []
+    for hb in hbs:
+        if ((atoms[hb[0]] - atoms[hb[2]]) > 5):
+            selectedHbs.append(hb)
+    return selectedHbs
+
+
+def printToFile(selectedHbs, file):
+    """function to print results"""
+    with open(file, 'w') as ndxFile:
+        ndxFile.write("[ sel_hbs ]\n")
+        for hb in selectedHbs:
+            ndxFile.write("%7i%7i%7i\n" % (hb[0], hb[1], hb[2]))
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description = 'Select hidrogen bond from GROMACS index file')
+    parser.add_argument('-i', '--input', dest = 'input',
+        help = '*.gro file', action = 'store')
+    parser.add_argument('-n', '--ndx', dest = 'ndx',
+        help = '*.ndx files, comma separated', action = 'store')
+    parser.add_argument('-o', '--output', dest = 'output',
+        help = 'output *.ndx file', action = 'store')
+    args = parser.parse_args()
+
+    atoms = readAtoms(args.input)
+    hbs = readHb(args.ndx.split(','))
+    selectedHbs = selectHb(atoms, hbs)
+    printToFile(selectedHbs, args.output)