from xml.etree.ElementTree import Element, SubElement, Comment, tostring
from xml.dom import minidom

root = Element("Brenk2008")
root.append(Comment("Table S1. Definition of unwanted groups"))

f = open("Brenk_et_al-2008-ChemMedChem-SI.txt", "rt")
count = 0
for line in f:
    c = line.strip().split("\t")
    count += 1
    entry = SubElement(root, "group")
    entry.set("name", "(" + str(count) + ") " + c[0].strip())
    node = SubElement(entry, "SMARTS")
    node.text = c[1].strip()
f.close()


g = open("Brenk2008.xml", "wt")
coarse = tostring(root, "utf-8")
g.write(minidom.parseString(coarse).toprettyxml(indent="  "))
