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#! /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)
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