#!/usr/local/bin/py

# Rajarshi Guha <rajarshi@presidency.com>
# 10/02/03
#
# Reorders a HIN file so that hydrogens are all at the end
# of the file, after the heavy atoms

import shutil, os, string, sys, tempfile, copy

if len(sys.argv) == 1:
    print """
    Usage: reorder.py FILE1 FILE2 ....

    It will reorder the HIN files specified so that hydrogens are all at
    the end. It will write the new file to the old file, wiping out the
    previous contents
    """
    sys.exit(0)

for arg in sys.argv[1:]:

    try:
        f = open(arg,'r')
    except IOError:
        print """
        Could'nt open file: %s. Skipped
        """ % (arg)
    
    llist = []
    for line in f:
        if line == '\n': continue
        if string.find(line,'mol') >= 0: continue
        llist.append(line)
    f.close()

    numatom = len(llist)

    numh = 0
    numo = 0
    
    # Now find the num of H's
    for line in llist:
        if string.find(line,'H') > 0:
            numh += 1
    numo = numatom - numh

    # make the map of old serial to new serial
    # First renumber the heavy atoms
    atommap = {}
    count = 1
    for line in llist:
        line = string.split(line,' ')
        oldserial = line[1]
        sym = line[3]
        if sym == 'H' or sym == 'h': continue
        atommap[oldserial] = str(count)
        count += 1

    # Now go through the list and renumber H's
    for line in llist:
        line = string.split(line,' ')
        oldserial = line[1]
        sym = line[3]
        if sym == 'H' or sym == 'h':
            atommap[oldserial] = str(count)
            count += 1
            
    newllist = []
    hlist = []

    for line in llist:

        line = string.split(line)
        if line[3] == 'H' or line[3] == 'h':
            line[1] = atommap[ line[1] ]
            c = copy.deepcopy(line)
            for i in c[11:]:
                if i[0] not in string.digits: continue
                line[ c[11:].index(i) + 11 ] = atommap[i]
            hlist.append(string.join(line))
            continue

        # Map the old serial's to their new values
        line[1] = atommap[ line[1] ]

        # Now transform the connection table
        c = copy.deepcopy(line)
        for i in c[11:]:
            if i[0] not in string.digits: continue
            line[ c[11:].index(i) + 11 ] = atommap[i]
        
        # Join the line and append to the new list
        newllist.append(string.join(line))
    
    # Join the 2 lists
    newllist.extend(hlist)

    # Dump the transformed hin file
    fname = tempfile.mktemp()
    f = open(fname,'w')
    f.write('mol 1 '+arg+'\n')
    for line in newllist:
        f.write(line+'\n')
    f.write('endmol 1')        
    f.close()
    shutil.copyfile(fname,arg)
    os.unlink(fname)