Objekt ist nicht definiert

Question

Ich habe ein Problem mit meinem Code. Das Programm wurde entwickelt, um die Datei zu analysieren, sie mit den Informationen auszuwählen und sie in der Liste der Objekte der Klasse zu speichern.

Aber zuerst - es speichert sie nicht richtig. Tatsächlich speichert nichts, es gibt leere Aufzeichnungen zurück.

Ich habe versucht, ein Minimum an Code vollständig zu erstellen und daran zu arbeiten. Als nächstes funktioniert es nicht. Ich kann keine Objekte anzeigen, weiß nicht, ob sie in der Klasse korrekt gespeichert werden. Ich änderte auch das XML zu einem kleineren und einem Beispiel, um zu sehen, wenn die Suche ein Fehler ist.

Ich denke darüber lange nach, mir sind die Ideen ausgegangen, ich frage nach einem Hinweis.

Mindest Code

from xml.dom import minidom 

class Prot(): 
    def __init__(self, name=''): 
     self.name = name 

    def addname(self, name): 
     for k in range(len(entry_list)): 
      names = entry_list[k].getElementsByTagName("Names") 
      for u in range(len(names)): 
       nam = names[u].getElementsByTagName("Name") 
       name.append(nam[u].firstChild.nodeValue) 
       print(nam[u].firstChild.nodeValue) 

xml = minidom.parse('RESIDUES.XML') 

entry_list = xml.getElementsByTagName("Entry") 
mod_list = [] 
for e in range(len(entry_list)): 
    m = Prot(e) 
    mod_list.append(m) 

xml - ein Datensatz

<Entry id="AA0003"> 
<Header> 
<Code>AA0003</Code> 
<Dates> 
<CreationDate>31-Mar-1995</CreationDate> 
<StrucRevDate>31-Mar-1995</StrucRevDate> 
<TextChngDate>30-Sep-2010</TextChngDate> 
</Dates> 
</Header> 
<Names> 
<Name>L-asparagine</Name> 
<AlternateName>2,4-bis(azanyl)-4-oxobutanoic acid</AlternateName> 
<AlternateName>2,4-diamino-4-oxobutanoic acid</AlternateName> 
<AlternateName>2-amino-3-carbamoylpropanoic acid</AlternateName> 
<AlternateName>2-amino-4-butanediamic acid</AlternateName> 
<AlternateName>2-aminosuccinamic acid</AlternateName> 
<AlternateName>2-aminosuccinic acid 4-amide</AlternateName> 
<AlternateName>alpha-amino-beta-carbamylpropionic acid</AlternateName> 
<AlternateName>alpha-aminosuccinamic acid</AlternateName> 
<AlternateName>aspartic acid 4-amide</AlternateName> 
<AlternateName>aspartic acid beta-amide</AlternateName> 
<AlternateName>beta-asparagine</AlternateName> 
<SystematicName>(2S)-2-amino-4-butanediamic acid</SystematicName> 
<Xref>CAS:70-47-3</Xref> 
<Xref>ChEBI:50347</Xref> 
<Xref>PDBHET:ASN</Xref> 
</Names> 
<FormulaBlock> 
<Formula>C 4 H 6 N 2 O 2</Formula> 
<Weight type="chemical">114.10</Weight> 
<Weight type="physical">114.042927</Weight> 
</FormulaBlock> 
<CorrectionBlock uids="AA0003" label="ASN"> 
<Formula>C 0 H 0 N 0 O 0</Formula> 
<Weight type="chemical">0.00</Weight> 
<Weight type="physical">0.000000</Weight> 
</CorrectionBlock> 
<CorrectionBlock uids="AA0004" label="ASP"> 
<Formula>C 0 H 1 N 1 O -1</Formula> 
<Weight type="chemical">-0.98</Weight> 
<Weight type="physical">-0.984016</Weight> 
</CorrectionBlock> 
<ReferenceBlock> 
<Authors> 
<Author>Vauquelin, L.N.</Author> 
<Author>Robiquet, P.J.</Author> 
</Authors> 
<Citation>Ann. Chim. 57, 88-93, 1806</Citation> 
<Title> 
Découverte d'un nouveau principe végétal dans les Asperges (Asparagus sativus, Linn.) [The discovery of a new plant principle in asparagus (Asparagus sativus, L.)]. 
</Title> 
<Note>article in French; isolation and naming</Note> 
</ReferenceBlock> 
<ReferenceBlock> 
<Authors> 
<Author>Drenth, J.</Author> 
<Author>Jansonius, J.N.</Author> 
<Author>Koekoek, R.</Author> 
<Author>Swen, H.M.</Author> 
<Author>Wolthers, B.G.</Author> 
</Authors> 
<Citation>Nature 218, 929-932, 1968</Citation> 
<Title>Structure of papain.</Title> 
<Xref>DOI:10.1038/218929a0</Xref> 
<Xref>PMID:5681232</Xref> 
<Note> 
asparagine as an active site residue in a thiol proteinase 
</Note> 
</ReferenceBlock> 
<ReferenceBlock> 
<Authors> 
<Anonymous/> 
<Group> 
IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN) 
</Group> 
</Authors> 
<Citation>Eur. J. Biochem. 138, 9-37, 1984</Citation> 
<Title> 
Nomenclature and symbolism for amino acids and peptides. Recommendations 1983. 
</Title> 
<Xref>DOI:10.1111/j.1432-1033.1984.tb07877.x</Xref> 
<Xref>PMID:6692818</Xref> 
<Note> 
standard three-letter and one-letter symbols, and nomenclature 
</Note> 
</ReferenceBlock> 
<ReferenceBlock> 
<Authors> 
<Author>Curnow, A.W.</Author> 
<Author>Tumbula, D.L.</Author> 
<Author>Pelaschier, J.T.</Author> 
<Author>Min, B.</Author> 
<Author>Soll, D.</Author> 
</Authors> 
<Citation> 
Proc. Natl. Acad. Sci. U.S.A. 95, 12838-12843, 1998 
</Citation> 
<Title> 
Glutamyl-tRNA(Gln) amidotransferase in Deinococcus radiodurans may be confined to asparagine biosynthesis. 
</Title> 
<Xref>DOI:10.1073/pnas.95.22.12838</Xref> 
<Xref>PMID:9789001</Xref> 
<Note> 
"mischarged" aspartyl-tRNA(Asn) is amidated by glutamyl-tRNA(Gln) amidotransferase in Deinococcus radiodurans 
</Note> 
</ReferenceBlock> 
<ReferenceBlock> 
<Authors> 
<Author>Paradisi, F.</Author> 
<Author>Dean, J.L.</Author> 
<Author>Geoghegan, K.F.</Author> 
<Author>Engel, P.C.</Author> 
</Authors> 
<Citation>Biochemistry 44, 3636-3643, 2005</Citation> 
<Title> 
Spontaneous chemical reversion of an active site mutation: deamidation of an asparagine residue replacing the catalytic aspartic acid of glutamate dehydrogenase. 
</Title> 
<Xref>DOI:10.1021/bi047679u</Xref> 
<Xref>PMID:15736973</Xref> 
<Note> 
an Asp to Asn mutation at an enzyme active site seemingly has partial activity; however, the asparagine form is shown to be inactive, and enhanced spontaneous deamidation results in the partial recovery of activity 
</Note> 
</ReferenceBlock> 
<ReferenceBlock> 
<Authors> 
<Author>Kolodkin-Gal, I.</Author> 
<Author>Hazan, R.</Author> 
<Author>Gaathon, A.</Author> 
<Author>Carmeli, S.</Author> 
<Author>Engelberg-Kulka, H.</Author> 
</Authors> 
<Citation>Science 318, 652-655, 2007</Citation> 
<Title> 
A linear pentapeptide is a quorum-sensing factor required for mazEF-mediated cell death in Escherichia coli. 
</Title> 
<Xref>DOI:10.1126/science.1147248</Xref> 
<Xref>PMID:17962566</Xref> 
<Note> 
enzymatic amidation of an aspartic acid residue in a peptide; the enzyme is currently identified by an activity that is different from the new activity 
</Note> 
</ReferenceBlock> 
<Comment> 
Some bacteria or archaea incorporate asparagine produced by the amidation of aspartyl-tRNA(Asn). 
</Comment> 
<GeneratingEnzyme> 
<EnzymeName link="ASN">aspartate--tRNA(Asn) ligase (EC 6.1.1.23)</EnzymeName> 
<EnzymeName link="ASN"> 
asparaginyl-tRNA synthase (glutamine-hydrolysing) (EC 6.3.5.6) 
</EnzymeName> 
<EnzymeName link="ASP">aspartate--ammonia ligase (EC 6.3.1.1)</EnzymeName> 
</GeneratingEnzyme> 
<SequenceCode link="ASN"> 
<SequenceSpec>N</SequenceSpec> 
<Abbreviation>Asn</Abbreviation> 
<Xref>PSI-MOD:00012</Xref> 
</SequenceCode> 
<SequenceCode link="ASP"> 
<SequenceSpec>D</SequenceSpec> 
<Xref>PSI-MOD:01185</Xref> 
</SequenceCode> 
<Source>natural</Source> 
<Features> 
<Feature type="UniProt" key="act_site____n" link="ASN">ACT_SITE</Feature> 
<Feature type="UniProt" key="mod_res__amidated aspartic acid__d" link="ASP">MOD_RES Amidated aspartic acid</Feature> 
</Features> 
<Image src="/images/AA0003.GIF" alt="DUMMY.GIF"/> 
<Model src="/models/AA0003.PDB"/> 
</Entry> 

Answer 1

Ich mag xml.etree für diese Art von Aufgabe wirklich. Ihre XML-Beispiel innerhalb eines anderen Elements hat mehrere Entry Aufzeichnungen Gesetzt, habe ich diese XML-Datei meinen Code zu testen:

<Records> 
<Entry id="AA0003"> 
<Header> 
<Code>AA0003</Code> 
</Header> 
<Names> 
<Name>L-asparagine</Name> 
<AlternateName>2,4-bis(azanyl)-4-oxobutanoic acid</AlternateName> 
<AlternateName>2,4-diamino-4-oxobutanoic acid</AlternateName> 
</Names> 
</Entry> 
<Entry id="??????"> 
<Header> 
<Code>??????</Code> 
</Header> 
<Names> 
<Name>N-Acetylglucosamine</Name> 
</Names> 
</Entry> 
</Records> 

Hier ist der Code die XML-Datei zu analysieren:

from xml.etree import ElementTree 

tree=ElementTree.parse('RESIDUES.XML') 
for entry in tree.findall('Entry'): 
    print entry.find('Names/Name').text 

Dies führt zu :

L-asparagine 
N-Acetylglucosamine