#calculate average structure from a trajectory, use conformations with high secondary structure content
ifbox    = 0      # if the trajectory file contain box information
begin    = 1      # from begin_th snap (included)
end      = 2      # to end_the snap    (included)
interval = 1      # do calculation on every interval steps
fstr_out = "output"  # output file to store your result
fstr_pdb  = "sample.pdb"  # specify a PDB file 
trajlist = ["sample.traj"]  # the trajectory file(s)

import sys

'''initialize a PDB instance, and count snapshot volume information'''
from tom import PDB
pdb = PDB(fstr_pdb)
natoms = pdb.numberOfAtoms()
nl,size_snap = pdb.numberOfLinesInSnap(ifbox)

fout = open(fstr_out,"w")

import Numeric as N
crd   = N.zeros((natoms*3,),N.Float)

from tom import DSSP
snaplist = []
for traj in trajlist:
    '''open trajectory file, skip the first line and the unwanted snaps'''
    trajin = open(traj)
    print "\nopen %s" %traj
    trajin.readline()
    trajin.read((begin-1)*size_snap)
    sys.stdout.write(".................................. %   0")
    for snap in range(begin,end+1,interval):
	sys.stdout.write("\b\b\b\b%4.1f" %(float(snap)/end*100))
	sys.stdout.flush()
	trajin.read((interval-1)*size_snap)              #skip unwanted (interval) snapshots
	crdstr = trajin.read(size_snap).replace('\n','')
	if(crdstr == ''):
	    trajin.close()
	    print crdstr
	    break
	pdb.newpdb(crdstr)

	dssp = DSSP("outpdb").secArray
	for i in range(0,len(dssp)):
	    fout.write("%d\t%d\t%s\n" %(snap,i+1,dssp[i]))

sys.stdout.write('\n')
fout.close()