#! /usr/bin/python

from Numeric import *
from VQT import *
from LinearAlgebra import *
from string import *
import re
import os
import sys
from string import capitalize

# read a Protein DataBank-format file
def pdbread(filename):
    atoms = zeros((0,3),Float)
    elem = []

    f=open(filename+".pdb","rU").readlines()
    
    for card in f:
        key=card[:6].lower().replace(" ", "")
        if key in ["atom", "hetatm"]:
            sym = capitalize(card[12:14].replace(" ", "").replace("_", ""))
            if sym == "X": continue
            elem += [sym]
            xyz = A([map(float, [card[30:38],card[38:46],card[46:54]])])
            atoms = concatenate((atoms,xyz),axis=0)
    return elem, atoms

def xyzwrite(fn, elem, pos):
    f=open(fn+".xyz","w")
    f.write(str(len(elem))+"\n--comment line--\n")
    for i in range(len(elem)):
        f.write(elem[i] + " %12.7f %12.7f %12.7f" % tuple(pos[i]) + "\n")


fn = sys.argv[1]
print fn+'.pdb --> '+fn+'.xyz'

el, pos = pdbread(fn)
xyzwrite(fn, el, pos)