Answers

This version uses the 'obvious' approach and .item(0) to obtain the first item from a set

#!/usr/bin/env python3
# https://docs.python.org/3.4/library/xml.dom.minidom.html

from xml.dom import minidom
import sys

progname = sys.argv.pop(0)
file     = sys.argv.pop(0)

doc = minidom.parse(file)

for mutant_group in doc.getElementsByTagName('mutant_group'):
   native_structure_list = mutant_group.getElementsByTagName('native_structure')
   ns = native_structure_list.item(0)
   resolution_list = ns.getElementsByTagName('resolution')
   res = resolution_list.item(0).firstChild.data

   if(float(res) <= 2.0):
       domid = mutant_group.getAttribute('native')
       print (domid, " ", res)

This version uses my preferred nested loops approach.

#!/usr/bin/env python3
# https://docs.python.org/3.4/library/xml.dom.minidom.html

from xml.dom import minidom
import sys

progname = sys.argv.pop(0)
file     = sys.argv.pop(0)

doc = minidom.parse(file)


for mutant_group in doc.getElementsByTagName('mutant_group'):
    for native_structure in mutant_group.getElementsByTagName('native_structure'):
        for resolution in native_structure.getElementsByTagName('resolution'):
            res = resolution.firstChild.data

            if(float(res) <= 2.0):
                domid = mutant_group.getAttribute('native')
                print (domid, " ", res)

This version uses the 'obvious' approach again, this time using [0] rather than .item(0) and splits the steps differently.

#!/usr/bin/env python3
# https://docs.python.org/3.4/library/xml.dom.minidom.html

from xml.dom import minidom
import sys

progname = sys.argv.pop(0)
file     = sys.argv.pop(0)

doc = minidom.parse(file)

for mutant_group in doc.getElementsByTagName('mutant_group'):
   nativeStructure = mutant_group.getElementsByTagName('native_structure')[0]
   resolution = nativeStructure.getElementsByTagName('resolution')[0]
   res = resolution.firstChild.data

   if(float(res) <= 2.0):
       domid = mutant_group.getAttribute('native')
       print (domid, " ", res)

This version uses the 'obvious' approach and .item(0) to obtain the first item from a set

#!/usr/bin/env python3
from xml.dom import minidom
import sys

progname = sys.argv.pop(0)
file     = sys.argv.pop(0)

doc  = minidom.parse(file)

for mutant_group in doc.getElementsByTagName('mutant_group'):
    native = mutant_group.getAttribute('native')
    if(native == '1eugA0'):
        for mutant in mutant_group.getElementsByTagName('mutant'):
            domid = mutant.getAttribute('domid')
            structure = mutant.getElementsByTagName('structure').item(0)
            resolution = structure.getElementsByTagName('resolution').item(0)
            res = resolution.firstChild.data
            mutation = mutant.getElementsByTagName('mutation').item(0)
            resnum = mutation.getAttribute('resnum')
            wildtype = mutation.getAttribute('wildtype')
            substitution = mutation.getAttribute('substitution')

            print ("%6s %-4s %3s %3s %.2f" % (domid, resnum, wildtype, substitution, float(res)))

This version uses my preferred nested loops approach.

#!/usr/bin/env python3
from xml.dom import minidom
import sys

progname = sys.argv.pop(0)
file     = sys.argv.pop(0)

doc = minidom.parse(file)

for mutant_group in doc.getElementsByTagName('mutant_group'):
    native = mutant_group.getAttribute('native')
    if(native == '1eugA0'):
        for mutant in mutant_group.getElementsByTagName('mutant'):
            domid = mutant.getAttribute('domid')
            for structure in mutant.getElementsByTagName('structure'):
                for resolution in structure.getElementsByTagName('resolution'):
                    res = resolution.firstChild.data

            for mutation in mutant.getElementsByTagName('mutation'):
                resnum = mutation.getAttribute('resnum')
                wildtype = mutation.getAttribute('wildtype')
                substitution = mutation.getAttribute('substitution')

            print ("%6s %-4s %3s %3s %.2f" % (domid, resnum, wildtype, substitution, float(res)))