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I am unable to find the bug.

3x2m_modified.atoms.xml

<?xml version='1.0' encoding='UTF-8'?>
<pdb>
  <atom>
    <Protein>3X2M</Protein>
    <AtomSerialNo>1</AtomSerialNo>
    <AtomSymbol>N</AtomSymbol>
    <AtomPosition></AtomPosition>
    <AtomNoInTheBranch></AtomNoInTheBranch>
    <ConnectedToAtomNoInTheBranch></ConnectedToAtomNoInTheBranch>
    <AltLocIndicator>A</AltLocIndicator>
    <ResidueName>ALA</ResidueName>
    <ChainName>A</ChainName>
    <ResidueNo>1</ResidueNo>
    <InsertionCode></InsertionCode>
    <X>-3.589</X>
    <Y>-1.325</Y>
    <Z>-13.286</Z>
    <Occupancy>0.34</Occupancy>
    <TemperatureFactor>5.03</TemperatureFactor>
    <SegmentIdentifier></SegmentIdentifier>
    <SegmentIdentifierSymbol></SegmentIdentifierSymbol>
    <ChargeOfTheAtom></ChargeOfTheAtom>
  </atom>  
</pdb>

using System;
using System.Collections.Generic;
using System.IO;
using System.Linq;
using System.Xml;
using System.Xml.Serialization;

namespace PdbLib
{
    [XmlRoot("pdb")]
    public class XmlAtomList
    {
        [XmlElement("atom")]
        public List<XmlAtom> Atoms { get; set; }
    }

    public class XmlAtom
    {
        [XmlElement("Protein")]
        public string Protein { get; set; }

        [XmlElement("AtomSerialNo")]
        public int AtomSerialNo { get; set; }

        [XmlElement("AtomSymbol")]
        public string AtomSymbol { get; set; }

        [XmlElement("AtomPosition")]
        public string AtomPosition { get; set; }

        [XmlElement("AtomNoInTheBranch")]
        public int? AtomNoInTheBranch { get; set; }

        [XmlElement("ConnectedToAtomNoInTheBranch")]
        public int? ConnectedToAtomNoInTheBranch { get; set; }

        [XmlElement("AltLocIndicator")]
        public string AltLocIndicator { get; set; }

        [XmlElement("ResidueName")]
        public string ResidueName { get; set; }

        [XmlElement("ChainName")]
        public string ChainName { get; set; }

        [XmlElement("ResidueNo")]
        public int ResidueNo { get; set; }

        [XmlElement("InsertionCode")]
        public string InsertionCode { get; set; }

        [XmlElement("X")]
        public double X { get; set; }

        [XmlElement("Y")]
        public double Y { get; set; }

        [XmlElement("Z")]
        public double Z { get; set; }

        [XmlElement("Occupancy")]
        public double Occupancy { get; set; }

        [XmlElement("TemperatureFactor")]
        public double? TemperatureFactor { get; set; }

        [XmlElement("SegmentIdentifier")]
        public string SegmentIdentifier { get; set; }

        [XmlElement("SegmentIdentifierSymbol")]
        public string SegmentIdentifierSymbol { get; set; }

        [XmlElement("ChargeOfTheAtom")]
        public string ChargeOfTheAtom { get; set; }
    }

    public class XmlADTAtomReader
    {
        public static Dictionary<int, XmlAtom> Data { get; private set; }

        static XmlADTAtomReader()
        {
            XmlSerializer serializer = new XmlSerializer(typeof(XmlAtomList));

            try
            {
                string xmlString = File.ReadAllText(@"Data\3x2m_modified.atoms.xml");
                XmlAtomList xml;
                using (StringReader reader = new StringReader(xmlString))
                {
                    using (XmlReader xmlReader = XmlReader.Create(reader))
                    {
                        xml = (XmlAtomList)serializer.Deserialize(xmlReader);
                    }
                }

                // Manually handle empty elements
                foreach (var atom in xml.Atoms)
                {
                    atom.AtomNoInTheBranch = !atom.AtomNoInTheBranch.HasValue ? null : atom.AtomNoInTheBranch;
                    atom.ConnectedToAtomNoInTheBranch = !atom.ConnectedToAtomNoInTheBranch.HasValue ? null : atom.ConnectedToAtomNoInTheBranch;
                }

                Data = xml.Atoms.ToDictionary(atom => atom.AtomSerialNo, atom => atom);
            }
            catch (Exception ex)
            {
                Console.WriteLine(ex.Message);
            }
        }
    }
}

using Microsoft.VisualStudio.TestTools.UnitTesting;
using System;
using System.Collections.Generic;
using System.IO;
using System.Xml.Serialization;
using PdbLib;
using System.Linq;

namespace PdbLibTests
{
    [TestClass]
    public class XmlADTAtomReaderTests
    {
        [TestInitialize]
        public void Setup()
        {
            // Setup code here, if needed
        }

        [TestCleanup]
        public void Cleanup()
        {
            // Cleanup code here, if needed
        }

        [TestMethod]
        public void XmlADTAtomReader_Deserialize_ValidXml_Success()
        {
            var atom = XmlADTAtomReader.Data[0];

            // Assert the values
            Assert.AreEqual("3X2M", atom.Protein);
            Assert.AreEqual(1, atom.AtomSerialNo);
            Assert.AreEqual("N", atom.AtomSymbol);
            Assert.IsNull(atom.AtomPosition);
            Assert.IsNull(atom.AtomNoInTheBranch);
            Assert.IsNull(atom.ConnectedToAtomNoInTheBranch);
            Assert.AreEqual("A", atom.AltLocIndicator);
            Assert.AreEqual("ALA", atom.ResidueName);
            Assert.AreEqual("A", atom.ChainName);
            Assert.AreEqual(1, atom.ResidueNo);
            Assert.AreEqual("", atom.InsertionCode);
            Assert.AreEqual(-3.589, atom.X);
            Assert.AreEqual(-1.325, atom.Y);
            Assert.AreEqual(-13.286, atom.Z);
            Assert.AreEqual(0.34, atom.Occupancy);
            Assert.AreEqual(5.03, atom.TemperatureFactor);
            Assert.IsNull(atom.SegmentIdentifier);
            Assert.IsNull(atom.SegmentIdentifierSymbol);
            Assert.IsNull(atom.ChargeOfTheAtom);
        }
    }
}

Test Name:  XmlADTAtomReader_Deserialize_ValidXml_Success
Test FullName:  PdbLibTests.XmlADTAtomReaderTests.XmlADTAtomReader_Deserialize_ValidXml_Success
Test Source:    C:gitProteinAnalysisToolsutXmlADTAtomReader____unit_testUnitTest1.cs : line 27
Test Outcome:   Failed
Test Duration:  0:00:00.4733031

Result StackTrace:  
at System.Number.StringToNumber(String str, NumberStyles options, NumberBuffer& number, NumberFormatInfo info, Boolean parseDecimal)
   at System.Number.ParseInt32(String s, NumberStyles style, NumberFormatInfo info)
   at Microsoft.Xml.Serialization.GeneratedAssembly.XmlSerializationReaderXmlAtomList.Read1_NullableOfInt32(Boolean checkType)
   at Microsoft.Xml.Serialization.GeneratedAssembly.XmlSerializationReaderXmlAtomList.Read4_XmlAtom(Boolean isNullable, Boolean checkType)
   at Microsoft.Xml.Serialization.GeneratedAssembly.XmlSerializationReaderXmlAtomList.Read5_XmlAtomList(Boolean isNullable, Boolean checkType)
   at Microsoft.Xml.Serialization.GeneratedAssembly.XmlSerializationReaderXmlAtomList.Read6_pdb()
--- End of inner exception stack trace ---
    at System.Xml.Serialization.XmlSerializer.Deserialize(XmlReader xmlReader, String encodingStyle, XmlDeserializationEvents events)
   at System.Xml.Serialization.XmlSerializer.Deserialize(TextReader textReader)
   at PdbLib.XmlADTAtomReader..cctor() in C:gitProteinAnalysisToolsPdbLibXmlDataReaderXmlAdtAtomReader.cs:line 88
--- End of inner exception stack trace ---
    at PdbLib.XmlADTAtomReader.get_Data()
   at PdbLibTests.XmlADTAtomReaderTests.XmlADTAtomReader_Deserialize_ValidXml_Success() in C:gitProteinAnalysisToolsutXmlADTAtomReader____unit_testUnitTest1.cs:line 29
Result Message: 
Test method PdbLibTests.XmlADTAtomReaderTests.XmlADTAtomReader_Deserialize_ValidXml_Success threw exception: 
System.TypeInitializationException: The type initializer for 'PdbLib.XmlADTAtomReader' threw an exception. ---> System.InvalidOperationException: There is an error in XML document (8, 6). ---> System.FormatException: Input string was not in a correct format.

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Danh mục

I am unable to find the bug. There is an error in XML document (8, 6)