如何在Python中删除XML元素？

Question

I am trying to remove some of element in xml file with ElementTree. Mycode doesn't give any error but it doesn't do what I want. I want to enter CHAIN_ID and RES_POSITION and when I look new written xml file I want to see this residue is deleted.

My xml file is too large so here is a sample of it:

<SEQ>
   <CHAIN>
      <CHAIN_ID>A</CHAIN_ID>
      <RESIDUE>
         <RES_POSITION>1</RES_POSITION>
         <AA_CODE>S</AA_CODE>
      </RESIDUE>
      <RESIDUE>
         <RES_POSITION>2</RES_POSITION>
         <AA_CODE>E</AA_CODE>
      </RESIDUE>
      <RESIDUE>
         <RES_POSITION>3</RES_POSITION>
         <AA_CODE>H</AA_CODE>
      </RESIDUE>

Mycode:

def deleted_residue(mychain_id, myresidue_id, file):
    mytree = ET.parse(file)
    chain = [seq for seq in mytree.findall('.//CHAIN') if seq.findtext('.//CHAIN_ID') == mychain_id]
    sequence = [res for res in mytree.findall('.//RESIDUE') if res.findtext('.//RES_POSITION') == myresidue_id]
    for seq in chain:
        for res in sequence:
            if mychain_id == "A" and myresidue_id == "2":
                seq.remove(res)
                return deleted_residue("A", "2", "pdb_one_letter.xml")

ET.tostring(SEQ, encoding='utf8').decode('utf8')
tree.write("pdb_one_letter_deleted.xml")
from xml.dom import minidom

pdbtoxml = minidom.parseString(ET.tostring(SEQ)).toprettyxml(indent="   ")
with open("pdb_one_letter_deleted.xml", "w") as pdb:
    pdb.write(pdbtoxml)

Answer 1

Your code is a little confusing; especially the list comprehension part and the use of minidom.

Based on this:

I am trying to remove some of element in xml file with ElementTree. Mycode doesn't give any error but it doesn't do what I want. I want to enter CHAIN_ID and RES_POSITION and when I look new written xml file I want to see this residue is deleted.

I think you can simplify by doing the value testing in XPath predicates ...

XML Input (test.xml)

<SEQ>
   <CHAIN>
      <CHAIN_ID>A</CHAIN_ID>
      <RESIDUE>
         <RES_POSITION>1</RES_POSITION>
         <AA_CODE>S</AA_CODE>
      </RESIDUE>
      <RESIDUE>
         <RES_POSITION>2</RES_POSITION>
         <AA_CODE>E</AA_CODE>
      </RESIDUE>
      <RESIDUE>
         <RES_POSITION>3</RES_POSITION>
         <AA_CODE>H</AA_CODE>
      </RESIDUE>
   </CHAIN>
</SEQ>

Python 3.x

import xml.etree.ElementTree as ET

def deleted_residue(mychain_id, myresidue_id, file):
    tree = ET.parse(file)
    for chain in tree.findall(f".//CHAIN[CHAIN_ID='{mychain_id}']"):
        for residue in chain.findall(f"./RESIDUE[RES_POSITION='{myresidue_id}']"):
            chain.remove(residue)
    tree.write(file)

deleted_residue("A", "2", "test.xml")

XML Output (modified test.xml)

<SEQ>
   <CHAIN>
      <CHAIN_ID>A</CHAIN_ID>
      <RESIDUE>
         <RES_POSITION>1</RES_POSITION>
         <AA_CODE>S</AA_CODE>
      </RESIDUE>
      <RESIDUE>
         <RES_POSITION>3</RES_POSITION>
         <AA_CODE>H</AA_CODE>
      </RESIDUE>
   </CHAIN>
</SEQ>

If you need to remove more than one RESIDUE , it would make more sense to parse the XML outside of the function and pass in the tree instead.

Hopefully this helps.