/// <summary>
/// This method returns the percentage of the given Amino Acid in the entire UniProt database.
/// </summary>
/// <param name="aminoAcidCode"></param>
/// <returns></returns>
public static decimal AminoAcidCompositionInPercent(string aminoAcidCode)
{
if (aminoAcidCode == null)
{
throw new ArgumentNullException(nameof(aminoAcidCode));
}
return(AminoAcidCompositionInPercent(AminoAcidConversions.AminoAcidNameToNumber(aminoAcidCode)));
}
public void IncrementAminoAcidCount(char aminoAcidCode, decimal incrementValue = 1)
{
if (!ParameterValidation.IsAminoAcidCodeValid(aminoAcidCode))
{
throw new ArgumentOutOfRangeException(nameof(aminoAcidCode));
}
IncrementAminoAcidCount(AminoAcidConversions.AminoAcidNameToNumber(aminoAcidCode), incrementValue);
}
public void IncrementAminoAcidCount(string aminoAcidCode, decimal incrementValue = 1)
{
if (string.IsNullOrEmpty(aminoAcidCode))
{
throw new ArgumentOutOfRangeException(nameof(aminoAcidCode));
}
IncrementAminoAcidCount(AminoAcidConversions.AminoAcidNameToNumber(aminoAcidCode), incrementValue);
}
/// <summary>
/// AminoAcidColorGroupsHeatMapTsv
/// </summary>
/// <returns></returns>
public List <SpreadsheetCell[]> SpreadsheetAminoAcidColorGroupsHeatMap(AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups enumAminoAcidGroups)
{
lock (_lockAminoAcidToAminoAcid)
{
var matrix = AminoAcidToAminoAcid[(int)enumAminoAcidGroups];
var rows = new List <List <SpreadsheetCell> >();
var headerRowStrings = new List <SpreadsheetCell> {
new SpreadsheetCell()
};
for (var columnIndex = 0; columnIndex < matrix.GetLength(1); columnIndex++)
{
if (enumAminoAcidGroups == AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.AminoAcids)
{
headerRowStrings.Add(new SpreadsheetCell(AminoAcidConversions.AminoAcidNumberToCode1L(columnIndex + 1)));
}
else
{
headerRowStrings.Add(new SpreadsheetCell(columnIndex + 1));
}
}
rows.Add(headerRowStrings);
for (var rowIndex = 0; rowIndex < matrix.GetLength(0); rowIndex++)
{
var row = new List <SpreadsheetCell>();
if (enumAminoAcidGroups == AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.AminoAcids)
{
row.Add(new SpreadsheetCell(AminoAcidConversions.AminoAcidNumberToCode1L(rowIndex + 1)));
}
else
{
row.Add(new SpreadsheetCell(rowIndex + 1));
}
for (var columnIndex = 0; columnIndex < matrix.GetLength(1); columnIndex++)
{
row.Add(new SpreadsheetCell(matrix[rowIndex, columnIndex]));
}
rows.Add(row);
}
return(rows.Select(a => a.ToArray()).ToList());
}
}
public static string FindProteinInterfaceAminoAcidCommonPropertiesMotif(List <string> proteinInterfaceSequenceList, AminoAcidPropertyMatchType aminoAcidPropertyMatchType, double matchValue = 0)
{
if (proteinInterfaceSequenceList == null)
{
throw new ArgumentNullException(nameof(proteinInterfaceSequenceList));
}
var totalProteinInterfaces = proteinInterfaceSequenceList.Count;
var proteinInterfaceLength = proteinInterfaceSequenceList.Select(a => a.Length).Max();
var aminoAcidObjects = new AminoAcidProperties <bool> [TotalAminoAcids];
for (var aaIndex = 0; aaIndex < aminoAcidObjects.Length; aaIndex++)
{
aminoAcidObjects[aaIndex] = AminoAcidConversions.AminoAcidNumberToAminoAcidObject(aaIndex + 1);
}
var aminoAcidPositionCount = new AminoAcidProperties <int> [proteinInterfaceLength];
for (var position = 0; position < aminoAcidPositionCount.Length; position++)
{
aminoAcidPositionCount[position] = new AminoAcidProperties <int>();
}
var motifs = new List <string>();
for (int positionIndex = 0; positionIndex < proteinInterfaceLength; positionIndex++)
{
string positionMotif = "";
foreach (var aaCode in proteinInterfaceSequenceList.Where(a => a.Length > positionIndex).Select(a => a[positionIndex]).Distinct().ToArray())
{
if (!char.IsLetterOrDigit(aaCode) || NonStandardAminoAcids.Contains(aaCode))
{
continue;
}
var aminoAcid = aminoAcidObjects[AminoAcidConversions.AminoAcidNameToNumber(aaCode) - 1];
var matches = AminoAcidConversions.ListAminoAcidsByProperty(aminoAcid, aminoAcidPropertyMatchType, matchValue);
positionMotif += string.Join("", matches.Where(a => !positionMotif.Contains(a) && !NonStandardAminoAcids.Contains(a)).ToArray());
}
motifs.Add(positionMotif);
}
return(MotifFormatter(motifs));
}
public static SpreadsheetCell[] SpreadsheetTitleRow()
{
var titleRow = new List <SpreadsheetCell>();
titleRow.Add(new SpreadsheetCell("Protein ID"));
titleRow.Add(new SpreadsheetCell("Chain ID"));
int totalAminoAcids = AminoAcidTotals.TotalAminoAcids();
for (int index = 0; index < totalAminoAcids; index++)
{
titleRow.Add(new SpreadsheetCell(AminoAcidConversions.AminoAcidNumberToCode1L(index + 1)));
}
titleRow.Add(new SpreadsheetCell("Total"));
return(titleRow.ToArray());
}
public SpreadsheetCell[] SpreadsheetDataRow()
{
var atomPoint1 = PointConversions.AtomPoint3D(InteractingAtomPair.Atom1);
var atomPoint2 = PointConversions.AtomPoint3D(InteractingAtomPair.Atom2);
var row = new[]
{
new SpreadsheetCell(ProteinId),
new SpreadsheetCell(InteractingAtomPair.Distance),
new SpreadsheetCell("-"),
new SpreadsheetCell(InteractingAtomPair.Atom1.chainID.FieldValue),
new SpreadsheetCell(ProteinInterfaceIdA),
new SpreadsheetCell(InteractingAtomPair.Atom1.resSeq.FieldValue),
new SpreadsheetCell(InteractingAtomPair.Atom1.name.FieldValue),
new SpreadsheetCell(AminoAcidConversions.AminoAcidNameToCode1L(InteractingAtomPair.Atom1.resName.FieldValue)),
new SpreadsheetCell(AminoAcidGroups.AminoAcidGroups.GetSubgroupColorNames(AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.Physicochemical)[AminoAcidGroups.AminoAcidGroups.ConvertAminoAcidNameCodeToSubgroupNumbers(AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.Physicochemical, InteractingAtomPair.Atom1.resName.FieldValue)[0]]),
new SpreadsheetCell(AminoAcidGroups.AminoAcidGroups.GetSubgroupColorNames(AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.Hydrophobicity)[AminoAcidGroups.AminoAcidGroups.ConvertAminoAcidNameCodeToSubgroupNumbers(AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.Hydrophobicity, InteractingAtomPair.Atom1.resName.FieldValue)[0]]),
new SpreadsheetCell(AminoAcidGroups.AminoAcidGroups.GetSubgroupColorNames(AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.PdbSum)[AminoAcidGroups.AminoAcidGroups.ConvertAminoAcidNameCodeToSubgroupNumbers(AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.PdbSum, InteractingAtomPair.Atom1.resName.FieldValue)[0]]),
new SpreadsheetCell(AminoAcidGroups.AminoAcidGroups.GetSubgroupColorNames(AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.UniProtKb)[AminoAcidGroups.AminoAcidGroups.ConvertAminoAcidNameCodeToSubgroupNumbers(AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.UniProtKb, InteractingAtomPair.Atom1.resName.FieldValue)[0]]),
new SpreadsheetCell(atomPoint1.X),
new SpreadsheetCell(atomPoint1.Y),
new SpreadsheetCell(atomPoint1.Z),
new SpreadsheetCell("<-->"),
new SpreadsheetCell(InteractingAtomPair.Atom2.chainID.FieldValue),
new SpreadsheetCell(ProteinInterfaceIdB),
new SpreadsheetCell(InteractingAtomPair.Atom2.resSeq.FieldValue),
new SpreadsheetCell(InteractingAtomPair.Atom2.name.FieldValue),
new SpreadsheetCell(AminoAcidConversions.AminoAcidNameToCode1L(InteractingAtomPair.Atom2.resName.FieldValue)),
new SpreadsheetCell(AminoAcidGroups.AminoAcidGroups.GetSubgroupColorNames(AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.Physicochemical)[AminoAcidGroups.AminoAcidGroups.ConvertAminoAcidNameCodeToSubgroupNumbers(AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.Physicochemical, InteractingAtomPair.Atom2.resName.FieldValue)[0]]),
new SpreadsheetCell(AminoAcidGroups.AminoAcidGroups.GetSubgroupColorNames(AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.Hydrophobicity)[AminoAcidGroups.AminoAcidGroups.ConvertAminoAcidNameCodeToSubgroupNumbers(AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.Hydrophobicity, InteractingAtomPair.Atom2.resName.FieldValue)[0]]),
new SpreadsheetCell(AminoAcidGroups.AminoAcidGroups.GetSubgroupColorNames(AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.PdbSum)[AminoAcidGroups.AminoAcidGroups.ConvertAminoAcidNameCodeToSubgroupNumbers(AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.PdbSum, InteractingAtomPair.Atom2.resName.FieldValue)[0]]),
new SpreadsheetCell(AminoAcidGroups.AminoAcidGroups.GetSubgroupColorNames(AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.UniProtKb)[AminoAcidGroups.AminoAcidGroups.ConvertAminoAcidNameCodeToSubgroupNumbers(AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.UniProtKb, InteractingAtomPair.Atom2.resName.FieldValue)[0]]),
new SpreadsheetCell(atomPoint2.X),
new SpreadsheetCell(atomPoint2.Y),
new SpreadsheetCell(atomPoint2.Z)
};
return(row);
}
/// <summary>
/// This method returns a spreadsheet heat map of the entire UniProt sequence database.
/// </summary>
/// <returns></returns>
public static List <SpreadsheetCell[]> UniProtHeatMapSpreadsheet()
{
var spreadsheet = new List <SpreadsheetCell[]>();
//spreadsheet.Add("HM Entire UniProt Database"); // filename / worksheet name
spreadsheet.Add(new[] { new SpreadsheetCell("Amino Acid Heat Map - Entire UniProt Database Composition (Converted To Matrix)") }); // spreadsheet title
//spreadsheet.Add(new[] {new SpreadsheetCell(string.Empty), });
//spreadsheet.Add(new[] {new SpreadsheetCell("Amino Acid Heat Map - Entire UniProt Database - A to Z") }); // section title
//spreadsheet.AddRange(AminoAcidCompositionAsMatrix().SpreadsheetAminoAcidColorGroupsHeatMap());
foreach (AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups enumAminoAcidGroups in Enum.GetValues(typeof(AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups)))
{
spreadsheet.Add(new[] { new SpreadsheetCell(string.Empty), });
spreadsheet.Add(new[] { new SpreadsheetCell("Amino Acid Heat Map - Entire UniProt Database - Acid Groups " + enumAminoAcidGroups) }); // section title
spreadsheet.AddRange(AminoAcidCompositionAsMatrix().SpreadsheetAminoAcidColorGroupsHeatMap(enumAminoAcidGroups));
}
spreadsheet.Add(new[] { new SpreadsheetCell(string.Empty), });
spreadsheet.Add(new[] { new SpreadsheetCell("Amino Acid Heat Map - Entire UniProt Database - Original Data - A to Z") }); // section title
AminoAcidChainComposition c = AminoAcidCompositionAsChain();
var chain = new List <SpreadsheetCell>();
chain.Add(new SpreadsheetCell(string.Empty));
for (int i = 0; i < AminoAcidTotals.TotalAminoAcids(); i++)
{
chain.Add(new SpreadsheetCell(AminoAcidConversions.AminoAcidNumberToCode1L(i + 1)));
}
spreadsheet.Add(chain.ToArray());
chain = new List <SpreadsheetCell>();
chain.Add(new SpreadsheetCell(string.Empty));
for (int i = 0; i < AminoAcidTotals.TotalAminoAcids(); i++)
{
chain.Add(new SpreadsheetCell(c.AminoAcidGroupsCount[(int)AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.AminoAcids][i]));
}
spreadsheet.Add(chain.ToArray());
foreach (AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups enumAminoAcidGroups in Enum.GetValues(typeof(AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups)))
{
spreadsheet.Add(new[] { new SpreadsheetCell(string.Empty), });
spreadsheet.Add(new[] { new SpreadsheetCell("Amino Acid Heat Map - Entire UniProt Database - Original Data - Acid Groups " + enumAminoAcidGroups) }); // section title
var chainGroups = new List <SpreadsheetCell>();
chainGroups.Add(new SpreadsheetCell(string.Empty));
for (int i = 0; i < AminoAcidGroups.AminoAcidGroups.GetTotalSubgroups(enumAminoAcidGroups); i++)
{
chainGroups.Add(new SpreadsheetCell((i + 1)));
}
spreadsheet.Add(chainGroups.ToArray());
chainGroups = new List <SpreadsheetCell>();
chainGroups.Add(new SpreadsheetCell(string.Empty));
for (int i = 0; i < AminoAcidGroups.AminoAcidGroups.GetTotalSubgroups(enumAminoAcidGroups); i++)
{
chainGroups.Add(new SpreadsheetCell(c.AminoAcidGroupsCount[(int)enumAminoAcidGroups][i]));
}
spreadsheet.Add(chainGroups.ToArray());
}
return(spreadsheet);
}
public void TestListAminoAcidsByProperty()
{
var x = new AminoAcidProperties<string>()
{
//Acidic = AminoAcidConversions.ListAminoAcidsByProperty(new AminoAcidProperties<bool>() {Acidic = true}),
Aliphatic = AminoAcidConversions.ListAminoAcidsByProperty(new AminoAcidProperties<bool>() {Aliphatic = true}),
Aromatic = AminoAcidConversions.ListAminoAcidsByProperty(new AminoAcidProperties<bool>() {Aromatic = true}),
Charged = AminoAcidConversions.ListAminoAcidsByProperty(new AminoAcidProperties<bool>() {Charged = true}),
Hydrophobic = AminoAcidConversions.ListAminoAcidsByProperty(new AminoAcidProperties<bool>() {Hydrophobic = true}),
Hydroxylic = AminoAcidConversions.ListAminoAcidsByProperty(new AminoAcidProperties<bool>() {Hydroxylic = true}),
Negative = AminoAcidConversions.ListAminoAcidsByProperty(new AminoAcidProperties<bool>() {Negative = true}),
Polar = AminoAcidConversions.ListAminoAcidsByProperty(new AminoAcidProperties<bool>() {Polar = true}),
Positive = AminoAcidConversions.ListAminoAcidsByProperty(new AminoAcidProperties<bool>() {Positive = true}),
Small = AminoAcidConversions.ListAminoAcidsByProperty(new AminoAcidProperties<bool>() {Small = true}),
Sulphur = AminoAcidConversions.ListAminoAcidsByProperty(new AminoAcidProperties<bool>() {Sulphur = true}),
Tiny = AminoAcidConversions.ListAminoAcidsByProperty(new AminoAcidProperties<bool>() { Tiny = true }),
};
var uncommon = AminoAcidConversions.ListAminoAcidsByProperty(new AminoAcidProperties<bool>() {}, AminoAcidPropertyMatchType.AllMatch);
var y = new AminoAcidProperties<string>()
{
};
for (var i = 0; i < AminoAcidTotals.TotalAminoAcids(); i++)
{
var aa = AminoAcidConversions.AminoAcidNumberToAminoAcidObject(i + 1);
//if (aa.Acidic) y.Acidic += aa.Code1L;
if (aa.Aliphatic) y.Aliphatic += aa.Code1L;
if (aa.Aromatic) y.Aromatic += aa.Code1L;
if (aa.Charged) y.Charged += aa.Code1L;
if (aa.Hydrophobic) y.Hydrophobic += aa.Code1L;
if (aa.Hydroxylic) y.Hydroxylic += aa.Code1L;
if (aa.Negative) y.Negative += aa.Code1L;
if (aa.Polar) y.Polar += aa.Code1L;
if (aa.Positive) y.Positive += aa.Code1L;
if (aa.Small) y.Small += aa.Code1L;
if (aa.Sulphur) y.Sulphur += aa.Code1L;
if (aa.Tiny) y.Tiny += aa.Code1L;
}
//Console.WriteLine("Acidic: " + x.Acidic);
Console.WriteLine("Aliphatic: " + x.Aliphatic);
Console.WriteLine("Aromatic: " + x.Aromatic);
Console.WriteLine("Charged: " + x.Charged);
Console.WriteLine("Hydrophobic: " + x.Hydrophobic);
Console.WriteLine("Hydroxylic: " + x.Hydroxylic);
Console.WriteLine("Negative: " + x.Negative);
Console.WriteLine("Polar: " + x.Polar);
Console.WriteLine("Positive: " + x.Positive);
Console.WriteLine("Small: " + x.Small);
Console.WriteLine("Sulphur: " + x.Sulphur);
Console.WriteLine("Tiny: " + x.Tiny);
Console.WriteLine("Others: " + uncommon);
//Assert.AreEqual(string.Join(" ", y.Acidic.OrderBy(a=>a).ToArray()), string.Join(" ", x.Acidic.OrderBy(a=>a).ToArray()));
Assert.AreEqual(string.Join(" ", y.Aliphatic.OrderBy(a=>a).ToArray()), string.Join(" ", x.Aliphatic.OrderBy(a=>a).ToArray()));
Assert.AreEqual(string.Join(" ", y.Aromatic.OrderBy(a=>a).ToArray()), string.Join(" ", x.Aromatic.OrderBy(a=>a).ToArray()));
Assert.AreEqual(string.Join(" ", y.Charged.OrderBy(a=>a).ToArray()), string.Join(" ", x.Charged.OrderBy(a=>a).ToArray()));
Assert.AreEqual(string.Join(" ", y.Hydrophobic.OrderBy(a=>a).ToArray()), string.Join(" ", x.Hydrophobic.OrderBy(a=>a).ToArray()));
Assert.AreEqual(string.Join(" ", y.Hydroxylic.OrderBy(a=>a).ToArray()), string.Join(" ", x.Hydroxylic.OrderBy(a=>a).ToArray()));
Assert.AreEqual(string.Join(" ", y.Negative.OrderBy(a=>a).ToArray()), string.Join(" ", x.Negative.OrderBy(a=>a).ToArray()));
Assert.AreEqual(string.Join(" ", y.Polar.OrderBy(a=>a).ToArray()), string.Join(" ", x.Polar.OrderBy(a=>a).ToArray()));
Assert.AreEqual(string.Join(" ", y.Positive.OrderBy(a=>a).ToArray()), string.Join(" ", x.Positive.OrderBy(a=>a).ToArray()));
Assert.AreEqual(string.Join(" ", y.Small.OrderBy(a=>a).ToArray()), string.Join(" ", x.Small.OrderBy(a=>a).ToArray()));
Assert.AreEqual(string.Join(" ", y.Sulphur.OrderBy(a=>a).ToArray()), string.Join(" ", x.Sulphur.OrderBy(a=>a).ToArray()));
Assert.AreEqual(string.Join(" ", y.Tiny.OrderBy(a=>a).ToArray()), string.Join(" ", x.Tiny.OrderBy(a=>a).ToArray()));
}
static void Main(string[] args)
{
// the indexes of data, contacts1 and contacts2 all match
var data = MultiBindingInterface.LoadAuthorData(@"c:\multibinding\multibinding.csv", @"c:\multibinding\multibinding_homolog_clusters.csv");
var contactsPartner1 =
data.Select(
a =>
{
var x = ProteinBioClass.AtomPair.LoadAtomPairList(@"C:\multibinding\contacts\contacts_pdb" +
a.InteractionChainsPdb1.ToUpperInvariant() + ".pdb")
.Where(
b =>
(b.Atom1.chainID.FieldValue.ToUpperInvariant()[0] ==
a.InteractionChainsPdb1Chain1
&&
b.Atom2.chainID.FieldValue.ToUpperInvariant()[0] ==
a.InteractionChainsPdb1Chain2)
||
(b.Atom1.chainID.FieldValue.ToUpperInvariant()[0] ==
a.InteractionChainsPdb1Chain2
&&
b.Atom2.chainID.FieldValue.ToUpperInvariant()[0] ==
a.InteractionChainsPdb1Chain1)).ToList();
x = x.Select(c =>
{
if (c.Atom1.chainID.FieldValue.ToUpperInvariant()[0] == a.InteractionChainsPdb1Chain2)
{
c.SwapAtoms();
}
return(c);
}).ToList();
return(x);
}).ToList();
var contactsPartner2 =
data.Select(
a =>
{
var x = ProteinBioClass.AtomPair.LoadAtomPairList(@"C:\multibinding\contacts\contacts_pdb" +
a.InteractionChainsPdb2.ToUpperInvariant() + ".pdb")
.Where(
b =>
(b.Atom1.chainID.FieldValue.ToUpperInvariant()[0] ==
a.InteractionChainsPdb2Chain1
&&
b.Atom2.chainID.FieldValue.ToUpperInvariant()[0] ==
a.InteractionChainsPdb2Chain2)
||
(b.Atom1.chainID.FieldValue.ToUpperInvariant()[0] ==
a.InteractionChainsPdb2Chain2
&&
b.Atom2.chainID.FieldValue.ToUpperInvariant()[0] ==
a.InteractionChainsPdb2Chain1)).ToList();
x = x.Select(c =>
{
if (c.Atom1.chainID.FieldValue.ToUpperInvariant()[0] == a.InteractionChainsPdb2Chain2)
{
c.SwapAtoms();
}
return(c);
}).ToList();
return(x);
}).ToList();
var interfacePartner1 = contactsPartner1.Select(a =>
{
var resSeqChain1 = a.Select(b => int.Parse(b.Atom1.resSeq.FieldValue)).ToList();
var resSeqChain2 = a.Select(b => int.Parse(b.Atom2.resSeq.FieldValue)).ToList();
if (resSeqChain1.Count > 0 && resSeqChain2.Count > 0)
{
return(new Tuple <int, int, int, int>(resSeqChain1.Min(), resSeqChain1.Max(), resSeqChain2.Min(),
resSeqChain2.Max()));
}
else
{
return(null);
}
}).ToList();
var interfacePartner2 = contactsPartner2.Select(a =>
{
var resSeqChain1 = a.Select(b => int.Parse(b.Atom1.resSeq.FieldValue)).ToList();
var resSeqChain2 = a.Select(b => int.Parse(b.Atom2.resSeq.FieldValue)).ToList();
if (resSeqChain1.Count > 0 && resSeqChain2.Count > 0)
{
return(new Tuple <int, int, int, int>(resSeqChain1.Min(), resSeqChain1.Max(), resSeqChain2.Min(),
resSeqChain2.Max()));
}
else
{
return(null);
}
}).ToList();
// var resultData = new List<MultiBindingInterface>();
for (int index = 0; index < data.Count; index++)
{
var d = data[index];
var cp1 = contactsPartner1[index];
var cp2 = contactsPartner2[index];
var ip1 = interfacePartner1[index];
var ip2 = interfacePartner2[index];
if (d == null || cp1 == null || cp2 == null || ip1 == null || ip2 == null)
{
continue;
}
if (cp1.Count == 0 || cp2.Count == 0)
{
continue;
}
var p1c1_pdb = ProteinBioClass.PdbAtomicChains(@"c:\multibinding\pdb" + d.InteractionChainsPdb1 + ".pdb", new char[] { d.InteractionChainsPdb1Chain1 }, -1, -1, true);
var p1c2_pdb = ProteinBioClass.PdbAtomicChains(@"c:\multibinding\pdb" + d.InteractionChainsPdb1 + ".pdb", new char[] { d.InteractionChainsPdb1Chain2 }, -1, -1, true);
var p2c1_pdb = ProteinBioClass.PdbAtomicChains(@"c:\multibinding\pdb" + d.InteractionChainsPdb2 + ".pdb", new char[] { d.InteractionChainsPdb2Chain1 }, -1, -1, true);
var p2c2_pdb = ProteinBioClass.PdbAtomicChains(@"c:\multibinding\pdb" + d.InteractionChainsPdb2 + ".pdb", new char[] { d.InteractionChainsPdb2Chain2 }, -1, -1, true);
var p1c1_res_seq = p1c1_pdb.ChainList.First().AtomList.Select(a => int.Parse(a.resSeq.FieldValue)).ToList();
var p1c2_res_seq = p1c2_pdb.ChainList.First().AtomList.Select(a => int.Parse(a.resSeq.FieldValue)).ToList();
var p2c1_res_seq = p2c1_pdb.ChainList.First().AtomList.Select(a => int.Parse(a.resSeq.FieldValue)).ToList();
var p2c2_res_seq = p2c2_pdb.ChainList.First().AtomList.Select(a => int.Parse(a.resSeq.FieldValue)).ToList();
var cp1a1_res_seq = cp1.Select(a => int.Parse(a.Atom1.resSeq.FieldValue)).ToList();
var cp1a2_res_seq = cp1.Select(a => int.Parse(a.Atom2.resSeq.FieldValue)).ToList();
var cp2a1_res_seq = cp2.Select(a => int.Parse(a.Atom1.resSeq.FieldValue)).ToList();
var cp2a2_res_seq = cp2.Select(a => int.Parse(a.Atom2.resSeq.FieldValue)).ToList();
var cp1a1_min = cp1a1_res_seq.Min();
var cp1a1_max = cp1a1_res_seq.Max();
var cp1a2_min = cp1a2_res_seq.Min();
var cp1a2_max = cp1a2_res_seq.Max();
var cp2a1_min = cp2a1_res_seq.Min();
var cp2a1_max = cp2a1_res_seq.Max();
var cp2a2_min = cp2a2_res_seq.Min();
var cp2a2_max = cp2a2_res_seq.Max();
var cp1a1_best50_min = int.MinValue;
var cp1a1_best50_max = int.MinValue;
var cp1a1_best50_interactions = int.MinValue;
var cp1a1_best50_middle_finder = new List <Tuple <int, int, int> >();
var interface_target_length = 50;
for (var x = cp1a1_min - interface_target_length; x <= cp1a1_max; x++)
{
if (Math.Abs(cp1a1_max - cp1a1_min) <= interface_target_length)
{
cp1a1_best50_min = cp1a1_min;
cp1a1_best50_max = cp1a1_max;
cp1a1_best50_interactions = cp1a1_res_seq.Count;
break;
}
var min = x;
var max = x + interface_target_length > cp1a1_max ? cp1a1_max : x + interface_target_length;
var best50 = cp1a1_res_seq.Count(a => a >= cp1a1_best50_min && a <= cp1a1_best50_max);
if (best50 == cp1a1_best50_interactions)
{
cp1a1_best50_middle_finder.Add(new Tuple <int, int, int>(min, max, best50));
}
if (cp1a1_best50_interactions == int.MinValue || best50 > cp1a1_best50_interactions)
{
cp1a1_best50_middle_finder.Clear();
cp1a1_best50_middle_finder.Add(new Tuple <int, int, int>(min, max, best50));
cp1a1_best50_min = min;
cp1a1_best50_max = max;
cp1a1_best50_interactions = best50;
}
if (x + interface_target_length >= cp1a1_max)
{
break;
}
}
if (cp1a1_best50_middle_finder.Count > 2)
{
var middle = cp1a1_best50_middle_finder[cp1a1_best50_middle_finder.Count / 2];
cp1a1_best50_min = middle.Item1;
cp1a1_best50_max = middle.Item2;
cp1a1_best50_interactions = middle.Item3;
}
var cp1a2_best50_min = int.MinValue;
var cp1a2_best50_max = int.MinValue;
var cp1a2_best50_interactions = int.MinValue;
var cp1a2_best50_middle_finder = new List <Tuple <int, int, int> >();
for (var x = cp1a2_min - interface_target_length; x <= cp1a2_max; x++)
{
if (Math.Abs(cp1a2_max - cp1a2_min) <= interface_target_length)
{
cp1a2_best50_min = cp1a2_min;
cp1a2_best50_max = cp1a2_max;
cp1a2_best50_interactions = cp1a2_res_seq.Count;
break;
}
var min = x;
var max = x + interface_target_length > cp1a2_max ? cp1a2_max : x + interface_target_length;
var best50 = cp1a2_res_seq.Count(a => a >= cp1a2_best50_min && a <= cp1a2_best50_max);
if (best50 == cp1a2_best50_interactions)
{
cp1a2_best50_middle_finder.Add(new Tuple <int, int, int>(min, max, best50));
}
if (cp1a2_best50_interactions == int.MinValue || best50 > cp1a2_best50_interactions)
{
cp1a2_best50_middle_finder.Clear();
cp1a2_best50_middle_finder.Add(new Tuple <int, int, int>(min, max, best50));
cp1a2_best50_min = min;
cp1a2_best50_max = max;
cp1a2_best50_interactions = best50;
}
if (x + interface_target_length >= cp1a2_max)
{
break;
}
}
if (cp1a2_best50_middle_finder.Count > 2)
{
var middle = cp1a2_best50_middle_finder[cp1a2_best50_middle_finder.Count / 2];
cp1a2_best50_min = middle.Item1;
cp1a2_best50_max = middle.Item2;
cp1a2_best50_interactions = middle.Item3;
}
var cp2a1_best50_min = int.MinValue;
var cp2a1_best50_max = int.MinValue;
var cp2a1_best50_interactions = int.MinValue;
var cp2a1_best50_middle_finder = new List <Tuple <int, int, int> >();
for (var x = cp2a1_min - interface_target_length; x <= cp2a1_max; x++)
{
if (Math.Abs(cp2a1_max - cp2a1_min) <= interface_target_length)
{
cp2a1_best50_min = cp2a1_min;
cp2a1_best50_max = cp2a1_max;
cp2a1_best50_interactions = cp2a1_res_seq.Count;
break;
}
var min = x;
var max = x + interface_target_length > cp2a1_max ? cp2a1_max : x + interface_target_length;
var best50 = cp2a1_res_seq.Count(a => a >= cp2a1_best50_min && a <= cp2a1_best50_max);
if (best50 == cp2a1_best50_interactions)
{
cp2a1_best50_middle_finder.Add(new Tuple <int, int, int>(min, max, best50));
}
if (cp2a1_best50_interactions == int.MinValue || best50 > cp2a1_best50_interactions)
{
cp2a1_best50_middle_finder.Clear();
cp2a1_best50_middle_finder.Add(new Tuple <int, int, int>(min, max, best50));
cp2a1_best50_min = min;
cp2a1_best50_max = max;
cp2a1_best50_interactions = best50;
}
if (x + interface_target_length >= cp2a1_max)
{
break;
}
}
if (cp2a1_best50_middle_finder.Count > 2)
{
var middle = cp2a1_best50_middle_finder[cp2a1_best50_middle_finder.Count / 2];
cp2a1_best50_min = middle.Item1;
cp2a1_best50_max = middle.Item2;
cp2a1_best50_interactions = middle.Item3;
}
var cp2a2_best50_min = int.MinValue;
var cp2a2_best50_max = int.MinValue;
var cp2a2_best50_interactions = int.MinValue;
var cp2a2_best50_middle_finder = new List <Tuple <int, int, int> >();
for (var x = cp2a2_min - interface_target_length; x <= cp2a2_max; x++)
{
if (Math.Abs(cp2a2_max - cp2a2_min) <= interface_target_length)
{
cp2a2_best50_min = cp2a2_min;
cp2a2_best50_max = cp2a2_max;
cp2a2_best50_interactions = cp2a2_res_seq.Count;
break;
}
var min = x;
var max = x + interface_target_length > cp2a2_max ? cp2a2_max : x + interface_target_length;
var best50 = cp2a2_res_seq.Count(a => a >= cp2a2_best50_min && a <= cp2a2_best50_max);
if (best50 == cp2a2_best50_interactions)
{
cp2a2_best50_middle_finder.Add(new Tuple <int, int, int>(min, max, best50));
}
if (cp2a2_best50_interactions == int.MinValue || best50 > cp2a2_best50_interactions)
{
cp2a2_best50_middle_finder.Clear();
cp2a2_best50_middle_finder.Add(new Tuple <int, int, int>(min, max, best50));
cp2a2_best50_min = min;
cp2a2_best50_max = max;
cp2a2_best50_interactions = best50;
}
if (x + interface_target_length >= cp2a2_max)
{
break;
}
}
if (cp2a2_best50_middle_finder.Count > 2)
{
var middle = cp2a2_best50_middle_finder[cp2a2_best50_middle_finder.Count / 2];
cp2a2_best50_min = middle.Item1;
cp2a2_best50_max = middle.Item2;
cp2a2_best50_interactions = middle.Item3;
}
var cp1a1_interface = string.Join("", p1c1_pdb.ChainList.First().AtomList.Where(a =>
{
var l = int.Parse(a.resSeq.FieldValue);
return(l >= cp1a1_min && l <= cp1a1_max);
}).OrderBy(c => int.Parse(c.resSeq.FieldValue)).Select(b => AminoAcidConversions.AminoAcidNameToCode1L(b.resName.FieldValue)).ToList());
var cp1a2_interface = string.Join("", p1c2_pdb.ChainList.First().AtomList.Where(a =>
{
var l = int.Parse(a.resSeq.FieldValue);
return(l >= cp1a2_min && l <= cp1a2_max);
}).OrderBy(c => int.Parse(c.resSeq.FieldValue)).Select(b => AminoAcidConversions.AminoAcidNameToCode1L(b.resName.FieldValue)).ToList());
var cp2a1_interface = string.Join("", p2c1_pdb.ChainList.First().AtomList.Where(a =>
{
var l = int.Parse(a.resSeq.FieldValue);
return(l >= cp2a1_min && l <= cp2a1_max);
}).OrderBy(c => int.Parse(c.resSeq.FieldValue)).Select(b => AminoAcidConversions.AminoAcidNameToCode1L(b.resName.FieldValue)).ToList());
var cp2a2_interface = string.Join("", p2c2_pdb.ChainList.First().AtomList.Where(a =>
{
var l = int.Parse(a.resSeq.FieldValue);
return(l >= cp2a2_min && l <= cp2a2_max);
}).OrderBy(c => int.Parse(c.resSeq.FieldValue)).Select(b => AminoAcidConversions.AminoAcidNameToCode1L(b.resName.FieldValue)).ToList());
var cp1a1_interface_interactions = new string('_', cp1a1_interface.Length);
cp1a1_interface_interactions = string.Join("", cp1a1_interface_interactions.Select((a, i) => cp1a1_res_seq.Contains(i + cp1a1_min) ? "X" : "_").ToList());
var cp1a2_interface_interactions = new string('_', cp1a2_interface.Length);
cp1a2_interface_interactions = string.Join("", cp1a2_interface_interactions.Select((a, i) => cp1a2_res_seq.Contains(i + cp1a2_min) ? "X" : "_").ToList());
var cp2a1_interface_interactions = new string('_', cp2a1_interface.Length);
cp2a1_interface_interactions = string.Join("", cp2a1_interface_interactions.Select((a, i) => cp2a1_res_seq.Contains(i + cp2a1_min) ? "X" : "_").ToList());
var cp2a2_interface_interactions = new string('_', cp2a2_interface.Length);
cp2a2_interface_interactions = string.Join("", cp2a2_interface_interactions.Select((a, i) => cp2a2_res_seq.Contains(i + cp2a2_min) ? "X" : "_").ToList());
var cp1a1_interactions = cp1a1_interface_interactions.Count(a => a == 'X');
var cp1a2_interactions = cp1a2_interface_interactions.Count(a => a == 'X');
var cp2a1_interactions = cp2a1_interface_interactions.Count(a => a == 'X');
var cp2a2_interactions = cp2a2_interface_interactions.Count(a => a == 'X');
var cp1a1_best50_interface = string.Join("", p1c1_pdb.ChainList.First().AtomList.Where(a =>
{
var l = int.Parse(a.resSeq.FieldValue);
return(l >= cp1a1_best50_min && l <= cp1a1_best50_max);
}).OrderBy(c => int.Parse(c.resSeq.FieldValue)).Select(b => AminoAcidConversions.AminoAcidNameToCode1L(b.resName.FieldValue)).ToList());
var cp1a2_best50_interface = string.Join("", p1c2_pdb.ChainList.First().AtomList.Where(a =>
{
var l = int.Parse(a.resSeq.FieldValue);
return(l >= cp1a2_best50_min && l <= cp1a2_best50_max);
}).OrderBy(c => int.Parse(c.resSeq.FieldValue)).Select(b => AminoAcidConversions.AminoAcidNameToCode1L(b.resName.FieldValue)).ToList());
var cp2a1_best50_interface = string.Join("", p2c1_pdb.ChainList.First().AtomList.Where(a =>
{
var l = int.Parse(a.resSeq.FieldValue);
return(l >= cp2a1_best50_min && l <= cp2a1_best50_max);
}).OrderBy(c => int.Parse(c.resSeq.FieldValue)).Select(b => AminoAcidConversions.AminoAcidNameToCode1L(b.resName.FieldValue)).ToList());
var cp2a2_best50_interface = string.Join("", p2c2_pdb.ChainList.First().AtomList.Where(a =>
{
var l = int.Parse(a.resSeq.FieldValue);
return(l >= cp2a2_best50_min && l <= cp2a2_best50_max);
}).OrderBy(c => int.Parse(c.resSeq.FieldValue)).Select(b => AminoAcidConversions.AminoAcidNameToCode1L(b.resName.FieldValue)).ToList());
var cp1a1_best50_interface_interactions = new string('_', cp1a1_best50_interface.Length);
cp1a1_best50_interface_interactions = string.Join("", cp1a1_best50_interface_interactions.Select((a, i) => cp1a1_res_seq.Contains(i + cp1a1_best50_min) ? "X" : "_").ToList());
var cp1a2_best50_interface_interactions = new string('_', cp1a2_best50_interface.Length);
cp1a2_best50_interface_interactions = string.Join("", cp1a2_best50_interface_interactions.Select((a, i) => cp1a2_res_seq.Contains(i + cp1a2_best50_min) ? "X" : "_").ToList());
var cp2a1_best50_interface_interactions = new string('_', cp2a1_best50_interface.Length);
cp2a1_best50_interface_interactions = string.Join("", cp2a1_best50_interface_interactions.Select((a, i) => cp2a1_res_seq.Contains(i + cp2a1_best50_min) ? "X" : "_").ToList());
var cp2a2_best50_interface_interactions = new string('_', cp2a2_best50_interface.Length);
cp2a2_best50_interface_interactions = string.Join("", cp2a2_best50_interface_interactions.Select((a, i) => cp2a2_res_seq.Contains(i + cp2a2_best50_min) ? "X" : "_").ToList());
d.Pdb1Chain1InterfaceStart = ip1.Item1;
d.Pdb1Chain1InterfaceEnd = ip1.Item2;
d.Pdb1Chain1TotalInteractions = cp1a1_interactions;
d.Pdb1Chain1InterfaceSequence = cp1a1_interface;
d.Pdb1Chain1InterfaceMask = cp1a1_interface_interactions;
d.Pdb1Chain1Best50InterfaceStart = cp1a1_best50_min;
d.Pdb1Chain1Best50InterfaceEnd = cp1a1_best50_max;
d.Pdb1Chain1Best50TotalInteractions = cp1a1_best50_interactions;
d.Pdb1Chain1Best50InterfaceSequence = cp1a1_best50_interface;
d.Pdb1Chain1Best50InterfaceMask = cp1a1_best50_interface_interactions;
d.Pdb1Chain2InterfaceStart = ip1.Item3;
d.Pdb1Chain2InterfaceEnd = ip1.Item4;
d.Pdb1Chain2TotalInteractions = cp1a2_interactions;
d.Pdb1Chain2InterfaceSequence = cp1a2_interface;
d.Pdb1Chain2InterfaceMask = cp1a2_interface_interactions;
d.Pdb1Chain2Best50InterfaceStart = cp1a2_best50_min;
d.Pdb1Chain2Best50InterfaceEnd = cp1a2_best50_max;
d.Pdb1Chain2Best50TotalInteractions = cp1a2_best50_interactions;
d.Pdb1Chain2Best50InterfaceSequence = cp1a2_best50_interface;
d.Pdb1Chain2Best50InterfaceMask = cp1a2_best50_interface_interactions;
d.Pdb2Chain1InterfaceStart = ip2.Item1;
d.Pdb2Chain1InterfaceEnd = ip2.Item2;
d.Pdb2Chain1TotalInteractions = cp2a1_interactions;
d.Pdb2Chain1InterfaceSequence = cp2a1_interface;
d.Pdb2Chain1InterfaceMask = cp2a1_interface_interactions;
d.Pdb2Chain1Best50InterfaceStart = cp2a1_best50_min;
d.Pdb2Chain1Best50InterfaceEnd = cp2a1_best50_max;
d.Pdb2Chain1Best50TotalInteractions = cp2a1_best50_interactions;
d.Pdb2Chain1Best50InterfaceSequence = cp2a1_best50_interface;
d.Pdb2Chain1Best50InterfaceMask = cp2a1_best50_interface_interactions;
d.Pdb2Chain2InterfaceStart = ip2.Item3;
d.Pdb2Chain2InterfaceEnd = ip2.Item4;
d.Pdb2Chain2TotalInteractions = cp2a2_interactions;
d.Pdb2Chain2InterfaceSequence = cp2a2_interface;
d.Pdb2Chain2InterfaceMask = cp2a2_interface_interactions;
d.Pdb2Chain2Best50InterfaceStart = cp2a2_best50_min;
d.Pdb2Chain2Best50InterfaceEnd = cp2a2_best50_max;
d.Pdb2Chain2Best50TotalInteractions = cp2a2_best50_interactions;
d.Pdb2Chain2Best50InterfaceSequence = cp2a2_best50_interface;
d.Pdb2Chain2Best50InterfaceMask = cp2a2_best50_interface_interactions;
}
var output = data.Select(a => a.ToString()).ToList();
output.Insert(0, MultiBindingInterface.Header());
File.WriteAllLines(@"c:\multibinding\MultiBinding_parsed_results.csv", output);
return;
}
static void Main(string[] args)
{
// the indexes of data, contacts1 and contacts2 all match
var data = MultiBindingInterface.Load(@"c:\pdb\new_data_set.csv");
var contactsPartner1 =
data.Select(
a =>
{
var x = FindAtomicContacts.AtomPair.LoadAtomPairList(@"C:\pdb\new_data_set\contacts\contacts_" +
a.InteractionChainsPdb1.ToLowerInvariant() + ".pdb")
.Where(
b =>
(b.Atom1.chainID.FieldValue.ToUpperInvariant() ==
a.InteractionChainsPdb1Chain1.ToUpperInvariant()
&&
b.Atom2.chainID.FieldValue.ToUpperInvariant() ==
a.InteractionChainsPdb1Chain2.ToUpperInvariant())
||
(b.Atom1.chainID.FieldValue.ToUpperInvariant() ==
a.InteractionChainsPdb1Chain2.ToUpperInvariant()
&&
b.Atom2.chainID.FieldValue.ToUpperInvariant() ==
a.InteractionChainsPdb1Chain1.ToUpperInvariant())).ToList();
x = x.Select(c =>
{
if (c.Atom1.chainID.FieldValue.ToUpperInvariant() == a.InteractionChainsPdb1Chain2.ToUpperInvariant())
{
c.SwapAtoms();
}
return(c);
}).ToList();
return(x);
}).ToList();
var contactsPartner2 =
data.Select(
a =>
{
var x = FindAtomicContacts.AtomPair.LoadAtomPairList(@"C:\pdb\new_data_set\contacts\contacts_" +
a.InteractionChainsPdb2.ToLowerInvariant() + ".pdb")
.Where(
b =>
(b.Atom1.chainID.FieldValue.ToUpperInvariant() ==
a.InteractionChainsPdb2Chain1.ToUpperInvariant()
&&
b.Atom2.chainID.FieldValue.ToUpperInvariant() ==
a.InteractionChainsPdb2Chain2.ToUpperInvariant())
||
(b.Atom1.chainID.FieldValue.ToUpperInvariant() ==
a.InteractionChainsPdb2Chain2.ToUpperInvariant()
&&
b.Atom2.chainID.FieldValue.ToUpperInvariant() ==
a.InteractionChainsPdb2Chain1.ToUpperInvariant())).ToList();
x = x.Select(c =>
{
if (c.Atom1.chainID.FieldValue.ToUpperInvariant() == a.InteractionChainsPdb2Chain2.ToUpperInvariant())
{
c.SwapAtoms();
}
return(c);
}).ToList();
return(x);
}).ToList();
var interfacePartner1 = contactsPartner1.Select(a =>
{
var resSeqChain1 = a.Select(b => int.Parse(b.Atom1.resSeq.FieldValue)).ToList();
var resSeqChain2 = a.Select(b => int.Parse(b.Atom2.resSeq.FieldValue)).ToList();
if (resSeqChain1.Count > 0 && resSeqChain2.Count > 0)
{
return(new Tuple <int, int, int, int>(resSeqChain1.Min(), resSeqChain1.Max(), resSeqChain2.Min(),
resSeqChain2.Max()));
}
else
{
return(null);
}
}).ToList();
var interfacePartner2 = contactsPartner2.Select(a =>
{
var resSeqChain1 = a.Select(b => int.Parse(b.Atom1.resSeq.FieldValue)).ToList();
var resSeqChain2 = a.Select(b => int.Parse(b.Atom2.resSeq.FieldValue)).ToList();
if (resSeqChain1.Count > 0 && resSeqChain2.Count > 0)
{
return(new Tuple <int, int, int, int>(resSeqChain1.Min(), resSeqChain1.Max(), resSeqChain2.Min(),
resSeqChain2.Max()));
}
else
{
return(null);
}
}).ToList();
var resultData = new List <string>();
for (int index = 0; index < data.Count; index++)
{
var d = data[index];
var cp1 = contactsPartner1[index];
var cp2 = contactsPartner2[index];
var ip1 = interfacePartner1[index];
var ip2 = interfacePartner2[index];
if (d == null || cp1 == null || cp2 == null || ip1 == null || ip2 == null)
{
continue;
}
if (cp1.Count == 0 || cp2.Count == 0)
{
continue;
}
var p1c1_pdb = FindAtomicContacts.PdbAtomicChains(@"c:\pdb\new_data_set\" + d.InteractionChainsPdb1 + ".pdb", new string[] { d.InteractionChainsPdb1Chain1 }, -1, -1, true);
var p1c2_pdb = FindAtomicContacts.PdbAtomicChains(@"c:\pdb\new_data_set\" + d.InteractionChainsPdb1 + ".pdb", new string[] { d.InteractionChainsPdb1Chain2 }, -1, -1, true);
var p2c1_pdb = FindAtomicContacts.PdbAtomicChains(@"c:\pdb\new_data_set\" + d.InteractionChainsPdb2 + ".pdb", new string[] { d.InteractionChainsPdb2Chain1 }, -1, -1, true);
var p2c2_pdb = FindAtomicContacts.PdbAtomicChains(@"c:\pdb\new_data_set\" + d.InteractionChainsPdb2 + ".pdb", new string[] { d.InteractionChainsPdb2Chain2 }, -1, -1, true);
var p1c1_res_seq = p1c1_pdb.ChainList.First().AtomList.Select(a => int.Parse(a.resSeq.FieldValue)).ToList();
var p1c2_res_seq = p1c2_pdb.ChainList.First().AtomList.Select(a => int.Parse(a.resSeq.FieldValue)).ToList();
var p2c1_res_seq = p2c1_pdb.ChainList.First().AtomList.Select(a => int.Parse(a.resSeq.FieldValue)).ToList();
var p2c2_res_seq = p2c2_pdb.ChainList.First().AtomList.Select(a => int.Parse(a.resSeq.FieldValue)).ToList();
var cp1a1_res_seq = cp1.Select(a => int.Parse(a.Atom1.resSeq.FieldValue)).ToList();
var cp1a2_res_seq = cp1.Select(a => int.Parse(a.Atom2.resSeq.FieldValue)).ToList();
var cp2a1_res_seq = cp2.Select(a => int.Parse(a.Atom1.resSeq.FieldValue)).ToList();
var cp2a2_res_seq = cp2.Select(a => int.Parse(a.Atom2.resSeq.FieldValue)).ToList();
var cp1a1_min = cp1a1_res_seq.Min();
var cp1a1_max = cp1a1_res_seq.Max();
var cp1a2_min = cp1a2_res_seq.Min();
var cp1a2_max = cp1a2_res_seq.Max();
var cp2a1_min = cp2a1_res_seq.Min();
var cp2a1_max = cp2a1_res_seq.Max();
var cp2a2_min = cp2a2_res_seq.Min();
var cp2a2_max = cp2a2_res_seq.Max();
var cp1a1_best50_min = int.MinValue;
var cp1a1_best50_max = int.MinValue;
var cp1a1_best50_interactions = int.MinValue;
var cp1a1_best50_middle_finder = new List <Tuple <int, int, int> >();
var interface_target_length = 50;
for (var x = cp1a1_min - interface_target_length; x <= cp1a1_max; x++)
{
if (Math.Abs(cp1a1_max - cp1a1_min) <= interface_target_length)
{
cp1a1_best50_min = cp1a1_min;
cp1a1_best50_max = cp1a1_max;
cp1a1_best50_interactions = cp1a1_res_seq.Count;
break;
}
var min = x;
var max = x + interface_target_length > cp1a1_max ? cp1a1_max : x + interface_target_length;
var best50 = cp1a1_res_seq.Count(a => a >= cp1a1_best50_min && a <= cp1a1_best50_max);
if (best50 == cp1a1_best50_interactions)
{
cp1a1_best50_middle_finder.Add(new Tuple <int, int, int>(min, max, best50));
}
if (cp1a1_best50_interactions == int.MinValue || best50 > cp1a1_best50_interactions)
{
cp1a1_best50_middle_finder.Clear();
cp1a1_best50_middle_finder.Add(new Tuple <int, int, int>(min, max, best50));
cp1a1_best50_min = min;
cp1a1_best50_max = max;
cp1a1_best50_interactions = best50;
}
if (x + interface_target_length >= cp1a1_max)
{
break;
}
}
if (cp1a1_best50_middle_finder.Count > 2)
{
var middle = cp1a1_best50_middle_finder[cp1a1_best50_middle_finder.Count / 2];
cp1a1_best50_min = middle.Item1;
cp1a1_best50_max = middle.Item2;
cp1a1_best50_interactions = middle.Item3;
}
var cp1a2_best50_min = int.MinValue;
var cp1a2_best50_max = int.MinValue;
var cp1a2_best50_interactions = int.MinValue;
var cp1a2_best50_middle_finder = new List <Tuple <int, int, int> >();
for (var x = cp1a2_min - interface_target_length; x <= cp1a2_max; x++)
{
if (Math.Abs(cp1a2_max - cp1a2_min) <= interface_target_length)
{
cp1a2_best50_min = cp1a2_min;
cp1a2_best50_max = cp1a2_max;
cp1a2_best50_interactions = cp1a2_res_seq.Count;
break;
}
var min = x;
var max = x + interface_target_length > cp1a2_max ? cp1a2_max : x + interface_target_length;
var best50 = cp1a2_res_seq.Count(a => a >= cp1a2_best50_min && a <= cp1a2_best50_max);
if (best50 == cp1a2_best50_interactions)
{
cp1a2_best50_middle_finder.Add(new Tuple <int, int, int>(min, max, best50));
}
if (cp1a2_best50_interactions == int.MinValue || best50 > cp1a2_best50_interactions)
{
cp1a2_best50_middle_finder.Clear();
cp1a2_best50_middle_finder.Add(new Tuple <int, int, int>(min, max, best50));
cp1a2_best50_min = min;
cp1a2_best50_max = max;
cp1a2_best50_interactions = best50;
}
if (x + interface_target_length >= cp1a2_max)
{
break;
}
}
if (cp1a2_best50_middle_finder.Count > 2)
{
var middle = cp1a2_best50_middle_finder[cp1a2_best50_middle_finder.Count / 2];
cp1a2_best50_min = middle.Item1;
cp1a2_best50_max = middle.Item2;
cp1a2_best50_interactions = middle.Item3;
}
var cp2a1_best50_min = int.MinValue;
var cp2a1_best50_max = int.MinValue;
var cp2a1_best50_interactions = int.MinValue;
var cp2a1_best50_middle_finder = new List <Tuple <int, int, int> >();
for (var x = cp2a1_min - interface_target_length; x <= cp2a1_max; x++)
{
if (Math.Abs(cp2a1_max - cp2a1_min) <= interface_target_length)
{
cp2a1_best50_min = cp2a1_min;
cp2a1_best50_max = cp2a1_max;
cp2a1_best50_interactions = cp2a1_res_seq.Count;
break;
}
var min = x;
var max = x + interface_target_length > cp2a1_max ? cp2a1_max : x + interface_target_length;
var best50 = cp2a1_res_seq.Count(a => a >= cp2a1_best50_min && a <= cp2a1_best50_max);
if (best50 == cp2a1_best50_interactions)
{
cp2a1_best50_middle_finder.Add(new Tuple <int, int, int>(min, max, best50));
}
if (cp2a1_best50_interactions == int.MinValue || best50 > cp2a1_best50_interactions)
{
cp2a1_best50_middle_finder.Clear();
cp2a1_best50_middle_finder.Add(new Tuple <int, int, int>(min, max, best50));
cp2a1_best50_min = min;
cp2a1_best50_max = max;
cp2a1_best50_interactions = best50;
}
if (x + interface_target_length >= cp2a1_max)
{
break;
}
}
if (cp2a1_best50_middle_finder.Count > 2)
{
var middle = cp2a1_best50_middle_finder[cp2a1_best50_middle_finder.Count / 2];
cp2a1_best50_min = middle.Item1;
cp2a1_best50_max = middle.Item2;
cp2a1_best50_interactions = middle.Item3;
}
var cp2a2_best50_min = int.MinValue;
var cp2a2_best50_max = int.MinValue;
var cp2a2_best50_interactions = int.MinValue;
var cp2a2_best50_middle_finder = new List <Tuple <int, int, int> >();
for (var x = cp2a2_min - interface_target_length; x <= cp2a2_max; x++)
{
if (Math.Abs(cp2a2_max - cp2a2_min) <= interface_target_length)
{
cp2a2_best50_min = cp2a2_min;
cp2a2_best50_max = cp2a2_max;
cp2a2_best50_interactions = cp2a2_res_seq.Count;
break;
}
var min = x;
var max = x + interface_target_length > cp2a2_max ? cp2a2_max : x + interface_target_length;
var best50 = cp2a2_res_seq.Count(a => a >= cp2a2_best50_min && a <= cp2a2_best50_max);
if (best50 == cp2a2_best50_interactions)
{
cp2a2_best50_middle_finder.Add(new Tuple <int, int, int>(min, max, best50));
}
if (cp2a2_best50_interactions == int.MinValue || best50 > cp2a2_best50_interactions)
{
cp2a2_best50_middle_finder.Clear();
cp2a2_best50_middle_finder.Add(new Tuple <int, int, int>(min, max, best50));
cp2a2_best50_min = min;
cp2a2_best50_max = max;
cp2a2_best50_interactions = best50;
}
if (x + interface_target_length >= cp2a2_max)
{
break;
}
}
if (cp2a2_best50_middle_finder.Count > 2)
{
var middle = cp2a2_best50_middle_finder[cp2a2_best50_middle_finder.Count / 2];
cp2a2_best50_min = middle.Item1;
cp2a2_best50_max = middle.Item2;
cp2a2_best50_interactions = middle.Item3;
}
var cp1a1_interface = string.Join("", p1c1_pdb.ChainList.First().AtomList.Where(a =>
{
var l = int.Parse(a.resSeq.FieldValue);
return(l >= cp1a1_best50_min && l <= cp1a1_best50_max);
}).OrderBy(c => int.Parse(c.resSeq.FieldValue)).Select(b => AminoAcidConversions.AminoAcidNameToCode1L(b.resName.FieldValue)).ToList());
var cp1a2_interface = string.Join("", p1c2_pdb.ChainList.First().AtomList.Where(a =>
{
var l = int.Parse(a.resSeq.FieldValue);
return(l >= cp1a2_best50_min && l <= cp1a2_best50_max);
}).OrderBy(c => int.Parse(c.resSeq.FieldValue)).Select(b => AminoAcidConversions.AminoAcidNameToCode1L(b.resName.FieldValue)).ToList());
var cp2a1_interface = string.Join("", p2c1_pdb.ChainList.First().AtomList.Where(a =>
{
var l = int.Parse(a.resSeq.FieldValue);
return(l >= cp2a1_best50_min && l <= cp2a1_best50_max);
}).OrderBy(c => int.Parse(c.resSeq.FieldValue)).Select(b => AminoAcidConversions.AminoAcidNameToCode1L(b.resName.FieldValue)).ToList());
var cp2a2_interface = string.Join("", p2c2_pdb.ChainList.First().AtomList.Where(a =>
{
var l = int.Parse(a.resSeq.FieldValue);
return(l >= cp2a2_best50_min && l <= cp2a2_best50_max);
}).OrderBy(c => int.Parse(c.resSeq.FieldValue)).Select(b => AminoAcidConversions.AminoAcidNameToCode1L(b.resName.FieldValue)).ToList());
var cp1a1_interface_interactions = new string('_', cp1a1_interface.Length);
cp1a1_interface_interactions = string.Join("", cp1a1_interface_interactions.Select((a, i) => cp1a1_res_seq.Contains(i + cp1a1_best50_min) ? "X" : "_").ToList());
var cp1a2_interface_interactions = new string('_', cp1a2_interface.Length);
cp1a2_interface_interactions = string.Join("", cp1a2_interface_interactions.Select((a, i) => cp1a2_res_seq.Contains(i + cp1a2_best50_min) ? "X" : "_").ToList());
var cp2a1_interface_interactions = new string('_', cp2a1_interface.Length);
cp2a1_interface_interactions = string.Join("", cp2a1_interface_interactions.Select((a, i) => cp2a1_res_seq.Contains(i + cp2a1_best50_min) ? "X" : "_").ToList());
var cp2a2_interface_interactions = new string('_', cp2a2_interface.Length);
cp2a2_interface_interactions = string.Join("", cp2a2_interface_interactions.Select((a, i) => cp2a2_res_seq.Contains(i + cp2a2_best50_min) ? "X" : "_").ToList());
resultData.Add(string.Join(",", new string[] {
d.DomainSuperFamily,
d.InteractionChainsPdb1,
d.InteractionChainsPdb1Chain1, "" + ip1.Item1, "" + ip1.Item2, "" + cp1a1_best50_min, "" + cp1a1_best50_max, "" + cp1a1_best50_interactions, cp1a1_interface, cp1a1_interface_interactions,
d.InteractionChainsPdb1Chain2, "" + ip1.Item3, "" + ip1.Item4, "" + cp1a2_best50_min, "" + cp1a2_best50_max, "" + cp1a2_best50_interactions, cp1a2_interface, cp1a2_interface_interactions,
d.InteractionChainsPdb2,
d.InteractionChainsPdb2Chain1, "" + ip2.Item1, "" + ip2.Item2, "" + cp2a1_best50_min, "" + cp2a1_best50_max, "" + cp2a1_best50_interactions, cp2a1_interface, cp2a1_interface_interactions,
d.InteractionChainsPdb2Chain2, "" + ip2.Item3, "" + ip2.Item4, "" + cp2a2_best50_min, "" + cp2a2_best50_max, "" + cp2a2_best50_interactions, cp2a2_interface, cp2a2_interface_interactions,
}));
}
resultData.Insert(0, string.Join(",", new string[] {
"super family",
"partner 1 pdb id",
"partner 1 chain id 1", "p1c1 interface start", "p1c1 interface end", "p1c1 best 50 start", "p1c1 best 50 end", "p1c1 best 50 interactions", "p1c1 interface seq", "p1c1 interface mask",
"partner 1 chain id 2", "p1c2 interface start", "p1c1 interface end", "p1c2 best 50 start", "p1c2 best 50 end", "p1c2 best 50 interactions", "p1c2 interface seq", "p1c2 interface mask",
"partner 2 pdb id",
"partner 2 chain id 1", "p2c1 interface start", "p2c1 interface end", "p2c1 best 50 start", "p2c1 best 50 end", "p2c1 best 50 interactions", "p2c1 interface seq", "p2c1 interface mask",
"partner 2 chain id 2", "p2c2 interface start", "p2c2 interface end", "p2c2 best 50 start", "p2c2 best 50 end", "p2c2 best 50 interactions", "p2c2 interface seq", "p2c2 interface mask",
}));
File.WriteAllLines(@"c:\pdb\new_data_set_results.csv", resultData);
return;
}
public static List <Sequence> LoadStructureFile(ProteinBioClass.StructureChainListContainer pdb, string pdbId = "", char[] chainIdWhiteList = null, bool padMissingBool = true, int[] startResSeq = null, int[] endResSeq = null, char outsidePaddingChar = ' ', char insidePaddingChar = 'X')
{
var result = new List <Sequence>();
List <ProteinBioClass.AtomListContainer> x = pdb.ChainList;
var zeroBased = pdb.ChainList.Any(a => a.AtomList.Any(b => Int32.Parse(b.resSeq.FieldValue) == 0));
if ((chainIdWhiteList != null && chainIdWhiteList.Length > 0) && (startResSeq != null && startResSeq.Length > 0) && (endResSeq != null && endResSeq.Length > 0))
{
for (int chainIndex = 0; chainIndex < pdb.ChainList.Count; chainIndex++)
{
var chainId = pdb.ChainList[chainIndex].ChainId;
var chainStartResSeq = startResSeq[chainIdWhiteList.ToList().FindIndex(a => a == chainId)];
var chainEndResSeq = endResSeq[chainIdWhiteList.ToList().FindIndex(a => a == chainId)];
pdb.ChainList[chainIndex].AtomList = pdb.ChainList[chainIndex].AtomList.Where(a => Int32.Parse(a.resSeq.FieldValue) >= chainStartResSeq && Int32.Parse(a.resSeq.FieldValue) <= chainEndResSeq).ToList();
}
}
for (int index = 0; index < pdb.ChainList.Count; index++)
{
var suplAtoms = new List <ATOM_Record>();
foreach (var atom in pdb.ChainList[index].AtomList)
{
if (String.IsNullOrWhiteSpace(atom.iCode.FieldValue))
{
continue;
}
var resSeq = atom.resSeq.FieldValue;
var aa = atom.resName.FieldValue;
var atomName = atom.name.FieldValue;
var matches = pdb.ChainList[index].AtomList.Where(a => a.resSeq.FieldValue == atom.resSeq.FieldValue && a.resName.FieldValue == atom.resName.FieldValue && a.name.FieldValue == atom.name.FieldValue).ToList();
if (matches.Count <= 1)
{
continue;
}
var noIcode = matches.FindIndex(a => string.IsNullOrWhiteSpace(a.iCode.FieldValue));
if (noIcode > -1)
{
suplAtoms.AddRange(matches.Where((a, i) => i != noIcode).ToList());
}
else
{
suplAtoms.AddRange(matches.Skip(1).ToList());
}
}
//pdb.ChainList[index].AtomList = pdb.ChainList[index].AtomList.Where(a => String.IsNullOrWhiteSpace(a.iCode.FieldValue)).ToList();
pdb.ChainList[index].AtomList.RemoveAll(a => suplAtoms.Contains(a));
var chain = pdb.ChainList[index];
var first = chain.AtomList.Min(a => Int32.Parse(a.resSeq.FieldValue));
var last = chain.AtomList.Max(a => Int32.Parse(a.resSeq.FieldValue));
var resSeqOffset = first < 0 ? Math.Abs(first) + 1 : 0;
var chainAa = new char[last + (zeroBased ? 1 : 0) + resSeqOffset];
var chainAaMask = new bool[last + (zeroBased ? 1 : 0) + resSeqOffset];
for (var i = 0; i < chainAa.Length; i++)
{
chainAa[i] = outsidePaddingChar;
chainAaMask[i] = false;
}
foreach (var atom in chain.AtomList)
{
var aa = atom.resName.FieldValue;
if (String.IsNullOrWhiteSpace(aa))
{
aa = "" + insidePaddingChar;
}
var res = Int32.Parse(atom.resSeq.FieldValue);
if (!zeroBased)
{
res = res - 1;
}
res += resSeqOffset;
var aa1l = AminoAcidConversions.AminoAcidNameToCode1L(aa);
chainAa[res] = aa1l[0];
chainAaMask[res] = true;
}
for (var i = first; i <= last; i++)
{
var res = i;
res += resSeqOffset;
if (!zeroBased)
{
res = res - 1;
}
if (!chainAaMask[res])
{
chainAa[res] = insidePaddingChar;
}
}
var chainAaStr = String.Join("", chainAa);
if (!padMissingBool)
{
chainAaStr = chainAaStr.Trim(outsidePaddingChar);
}
result.Add(new Sequence(">" + pdbId + ":" + chain.ChainId, chainAaStr));
}
return(result);
}
/// <summary>
/// IncrementAminoAcidCount
/// </summary>
/// <param name="aminoAcidCodeA"></param>
/// <param name="aminoAcidCodeB"></param>
/// <param name="incrementValue"></param>
public void IncrementAminoAcidCount(string aminoAcidCodeA, string aminoAcidCodeB, decimal incrementValue = 1.0m)
{
IncrementAminoAcidCount(AminoAcidConversions.AminoAcidNameToNumber(aminoAcidCodeA), AminoAcidConversions.AminoAcidNameToNumber(aminoAcidCodeB), incrementValue);
}
static void Main(string[] args)
{
var pdbFolder = @"C:\ds96ub_homologs\";
var homologClusterData = FindHomologsCluster.FindHomologsCluster.HomologClusterData.Load(@"c:\ds96ub_homologs\ds96ub_homologs_0.7.csv");
var pdbFiles = Directory.GetFiles(pdbFolder, "*.pdb", SearchOption.TopDirectoryOnly);
var pdbIdList = pdbFiles.Select(ProteinBioClass.PdbIdFromPdbFilename).ToList();
// only ca-atoms, ters and endmdls
var pdbAtomsText =
pdbFiles.Select(
a =>
File.ReadAllLines(a)
.Where(b => (b.StartsWith("ATOM ") && b[13] == 'C' && b[14] == 'A') || /*b.StartsWith("TER ") ||*/ b.StartsWith("ENDMDL "))
.ToList()).ToList();
// only first nmr model
pdbAtomsText = pdbAtomsText.Select(a =>
{
var x = a.FindIndex(b => b.StartsWith("ENDMDL "));
return(x == -1 ? a : a.GetRange(0, x - 1));
}).ToList();
var pdbAtoms = pdbAtomsText.Select(a => a.Select(b => new ATOM_Record(b)).ToList()).ToList();
// get list of unique chain ids
var pdbChainIds = pdbAtoms.Select((a, i) => a.Select(b => char.ToUpperInvariant(b.chainID.FieldValue[0])).ToList()).Distinct().ToList();
var pdbIdChainIdList = new List <Tuple <string, char> >();
for (var i = 0; i < pdbIdList.Count; i++)
{
pdbIdChainIdList.AddRange(pdbChainIds[i].Select(chainId => new Tuple <string, char>(pdbIdList[i], chainId)));
}
pdbIdChainIdList = pdbIdChainIdList.Distinct().ToList();
// for each chain
var pdbContacts =
pdbIdChainIdList.Select(a =>
{
var x =
ProteinBioClass.AtomPair.LoadAtomPairList(@"C:\ds96ub_homologs\contacts\contacts_pdb" + a.Item1.ToUpperInvariant() + ".pdb")
.Where(b => char.ToUpperInvariant(b.Atom1.chainID.FieldValue[0]) == a.Item2 || char.ToUpperInvariant(b.Atom2.chainID.FieldValue[0]) == a.Item2)
.Select(c =>
{
if (char.ToUpperInvariant(c.Atom1.chainID.FieldValue[0]) != a.Item2)
{
c.SwapAtoms();
}
return(c);
}).ToList();
return(x);
}).ToList();
// res min, res max, best min, best max, interface aa, interface mask
var pdbInterfaces = new List <Ds93UbInterface>();
var interface_target_length = 50;
for (int index = 0; index < pdbContacts.Count; index++)
{
var pdbId = pdbIdChainIdList[index].Item1;
var chainId = pdbIdChainIdList[index].Item2;
var pdbContact = pdbContacts[index];
if (pdbContact.Count == 0)
{
continue;
}
var contactChains = pdbContact.Where(a => char.ToUpperInvariant(a.Atom2.chainID.FieldValue[0]) != chainId).Select(a => char.ToUpperInvariant(a.Atom2.chainID.FieldValue[0])).Distinct().ToList();
foreach (var contactChain in contactChains)
{
var pdbContactsResSeqIds =
pdbContact.Where(a => char.ToUpperInvariant(a.Atom1.chainID.FieldValue[0]) == chainId &&
char.ToUpperInvariant(a.Atom2.chainID.FieldValue[0]) == contactChain)
.Select(a => int.Parse(a.Atom1.resSeq.FieldValue))
.ToList();
var res_seq = pdbContactsResSeqIds;
var min_res_seq = pdbContactsResSeqIds.Min();
var max_res_seq = pdbContactsResSeqIds.Max();
var best50_min = int.MinValue;
var best50_max = int.MinValue;
var best50_interactions = int.MinValue;
var best50_middle_finder = new List <Tuple <int, int, int> >();
for (var x = min_res_seq - interface_target_length; x <= max_res_seq; x++)
{
if (Math.Abs(max_res_seq - min_res_seq) <= interface_target_length)
{
best50_min = min_res_seq;
best50_max = max_res_seq;
best50_interactions = res_seq.Count;
break;
}
var min = x;
var max = x + interface_target_length > max_res_seq ? max_res_seq : x + interface_target_length;
var best50 = res_seq.Count(a => a >= best50_min && a <= best50_max);
if (best50 == best50_interactions)
{
best50_middle_finder.Add(new Tuple <int, int, int>(min, max, best50));
}
if (best50_interactions == int.MinValue || best50 > best50_interactions)
{
best50_middle_finder.Clear();
best50_middle_finder.Add(new Tuple <int, int, int>(min, max, best50));
best50_min = min;
best50_max = max;
best50_interactions = best50;
}
if (x + interface_target_length >= max)
{
break;
}
}
if (best50_middle_finder.Count > 2)
{
var middle = best50_middle_finder[best50_middle_finder.Count / 2];
best50_min = middle.Item1;
best50_max = middle.Item2;
best50_interactions = middle.Item3;
}
var best50_interface_atoms = pdbAtoms[pdbIdList.IndexOf(pdbId)].Where(a =>
{
var l = int.Parse(a.resSeq.FieldValue);
var c = char.ToUpperInvariant(a.chainID.FieldValue[0]);
return(c == chainId && l >= best50_min && l <= best50_max);
}).ToList();
best50_interface_atoms = best50_interface_atoms.OrderBy(c => int.Parse(c.resSeq.FieldValue)).ToList();
var best50_interface = string.Join("", best50_interface_atoms.Select(b => AminoAcidConversions.AminoAcidNameToCode1L(b.resName.FieldValue)).ToList());
var best50_mask = new string('_', best50_interface.Length);
best50_mask = string.Join("",
best50_mask.Select((a, i) => res_seq.Contains(i + best50_min) ? "X" : "_").ToList());
pdbInterfaces.Add(new Ds93UbInterface(pdbId, chainId, contactChain, min_res_seq, max_res_seq, best50_min,
best50_max, best50_interactions, best50_interface, best50_mask, -1, "", "", 0, -1, "", "", 0));
}
}
var homologClusterIndexes = homologClusterData.Select(a => a.ClusterIndex).Distinct().ToList();
var homologClusters = homologClusterIndexes.Select(a => homologClusterData.Where(b => b.ClusterIndex == a).ToList()).ToList();
var pdbInterfacesSorted = homologClusters.Select(a => pdbInterfaces.Where(b => a.Any(c => c.PdbId == b.PdbId && (char.ToUpperInvariant(c.ChainId) == b.ChainId1 || char.ToUpperInvariant(c.ChainId) == b.ChainId2))).ToList()).ToList();
var outputData = new List <string>();
foreach (var clusterIndex in homologClusterIndexes)
{
var cluster = pdbInterfacesSorted[clusterIndex - 1];
// currently, cluster is a list of chain1-->chain2 interfaces ... so the 'chain2' interface needs adding to the record
foreach (var inf1 in cluster)
{
var partner =
cluster.Where(a => a != inf1 && a.PdbId == inf1.PdbId && inf1.ChainId2 == a.ChainId1)
.OrderByDescending(
a => InterfaceOverlap(inf1.MinResSeq, inf1.MaxResSeq, a.MinResSeq, a.MaxResSeq))
.ToList();
var first = partner.FirstOrDefault();
if (first != null)
{
inf1.Partner1InterfaceAminoAcids = first.InterfaceAminoAcids;
inf1.Partner1InterfaceInteractionsMask = first.InterfaceInteractionsMask;
inf1.Partner1InterfaceOverlap = InterfaceOverlap(inf1.MinResSeq, inf1.MaxResSeq, first.MinResSeq, first.MaxResSeq);
}
var second = partner.ElementAtOrDefault(1);
if (second != null)
{
inf1.Partner2InterfaceAminoAcids = second.InterfaceAminoAcids;
inf1.Partner2InterfaceInteractionsMask = second.InterfaceInteractionsMask;
inf1.Partner2InterfaceOverlap = InterfaceOverlap(inf1.MinResSeq, inf1.MaxResSeq, second.MinResSeq, second.MaxResSeq);
}
}
cluster = cluster.Where(a => a.Partner1InterfaceOverlap > 0 || a.Partner2InterfaceOverlap > 0).ToList();
/*
* var partners =
* foreach (var inf2 in cluster)
* {
* if (inf1.PdbId!=inf2.PdbId) continue;
*
* if (inf1==inf2) continue;
*
* if (!(inf1.ChainId1==inf2.ChainId2 || inf1.ChainId2==inf2.ChainId1)) continue;
*
* //
* var overlap = InterfaceOverlap(inf1.MinResSeq, inf1.MaxResSeq, inf2.MinResSeq, inf2.MaxResSeq);
*
* if (overlap > 0)
* {
* if (overlap > inf1.Partner1InterfaceOverlap)
* {
* inf1.Partner1InterfaceOverlap = overlap;
* inf1.Partner1InterfaceAminoAcids = inf2.InterfaceAminoAcids;
* inf1.Partner1InterfaceInteractionsMask = inf2.InterfaceInteractionsMask;
* }
*
* if (overlap > inf2.Partner1InterfaceOverlap)
* {
* inf2.Partner1InterfaceOverlap = overlap;
* inf2.Partner1InterfaceAminoAcids = inf1.InterfaceAminoAcids;
* inf2.Partner1InterfaceInteractionsMask = inf1.InterfaceInteractionsMask;
* }
* }
* }
* }
*/
//var interfaces = cluster.Select(a => a.InterfaceAminoAcids).ToList();
//interfaces = interfaces.Where(a => interfaces.Count(b => b == a) > 1).ToList();
//cluster = cluster.Where(a => a.InterfaceAminoAcids.Length >= 5 && cluster.Count(b => b.InterfaceAminoAcids == a.InterfaceAminoAcids) > 1).ToList();
cluster = cluster.Where(a => a.InterfaceAminoAcids.Length >= 5).ToList();
var clusterInterfaces = cluster.Select(a => a.InterfaceAminoAcids).ToList();
var homologInterfaces = new List <List <string> >();
foreach (var inf1 in clusterInterfaces)
{
var highest_score = decimal.MinValue;
string highest_inf = null;
foreach (var inf2 in clusterInterfaces)
{
if (inf1 == inf2)
{
continue;
}
var score = ProteinBioClass.AlignedSequenceSimilarityPercentage(inf1, inf2, ProteinBioClass.AlignmentType.NMW);
if (score.Score > highest_score)
{
highest_score = score.Score;
highest_inf = inf2;
}
}
var y = homologInterfaces.FirstOrDefault(a => a.Contains(inf1) || a.Contains(highest_inf));
if (y != null)
{
if (!y.Contains(inf1))
{
y.Add(inf1);
}
if (!y.Contains(highest_inf))
{
y.Add(highest_inf);
}
}
else
{
var z = new List <string>();
z.Add(inf1);
z.Add(highest_inf);
homologInterfaces.Add(z);
}
}
foreach (var c in cluster)
{
c.Partner1ClusterIndex = homologInterfaces.FindIndex(b => b.Contains(c.Partner1InterfaceAminoAcids));
c.Partner2ClusterIndex = homologInterfaces.FindIndex(b => b.Contains(c.Partner2InterfaceAminoAcids));
}
for (int index = 0; index < homologInterfaces.Count; index++)
{
var homologInterface = homologInterfaces[index];
var cluster2 =
cluster.Where(a => homologInterface.Contains(a.InterfaceAminoAcids)
)
.OrderBy(a => a.Partner1ClusterIndex)
.ThenBy(a => a.Partner2ClusterIndex)
.ThenBy(a => a.InterfaceAminoAcids)
.ThenBy(a => a.Partner1InterfaceAminoAcids)
.ThenBy(a => a.Partner2InterfaceAminoAcids)
.ToList();
var partners =
cluster2.Select(
a =>
new Tuple <string, string, string>(a.InterfaceAminoAcids, a.Partner1InterfaceAminoAcids,
a.Partner2InterfaceAminoAcids)).Distinct();
cluster2 =
partners.Select(
a =>
cluster2.FirstOrDefault(
b =>
b.InterfaceAminoAcids == a.Item1 && b.Partner1InterfaceAminoAcids == a.Item2 &&
b.Partner2InterfaceAminoAcids == a.Item3)).ToList();
outputData.Add("cluster " + clusterIndex + "." + index);
outputData.AddRange(cluster2.Select(a => a.ToString()).ToList());
outputData.Add("");
}
}
File.WriteAllLines(@"c:\ds96ub_homologs\ds96ub_homologs_interfaces.csv", outputData);//pdbInterfaces.Select(a=>a.ToString()).ToList());
}
public static bool IsAminoAcidCodeValid(string aminoAcidNameOrCode)
{
int aminoAcidNumber = AminoAcidConversions.AminoAcidNameToNumber(aminoAcidNameOrCode);
return(IsAminoAcidNumberValid(aminoAcidNumber));
}
public void TestAminoAcids()
{
//int intAcidic = 0;
int intAliphatic = 0;
int intAromatic = 0;
int intCharged = 0;
int intHydrophobic = 0;
int intHydroxylic = 0;
int intNegative = 0;
int intPolar = 0;
int intPositive = 0;
int intSmall = 0;
int intSulphur = 0;
int intTiny = 0;
//string strAcidic = "";
string strAliphatic = "";
string strAromatic = "";
string strCharged = "";
string strHydrophobic = "";
string strHydroxylic = "";
string strNegative = "";
string strPolar = "";
string strPositive = "";
string strSmall = "";
string strSulphur = "";
string strTiny = "";
for (var i = 1; i <= 26; i++)
{
var x = AminoAcidConversions.AminoAcidNumberToAminoAcidObject(i);
//if (x.Acidic)
//{
//intAcidic++;
//strAcidic += x.Code1L;
//}
if (x.Aliphatic)
{
intAliphatic++;
strAliphatic += x.Code1L;
}
if (x.Aromatic)
{
intAromatic++;
strAromatic += x.Code1L;
}
if (x.Charged)
{
intCharged++;
strCharged += x.Code1L;
}
if (x.Hydrophobic)
{
intHydrophobic++;
strHydrophobic += x.Code1L;
}
if (x.Hydroxylic)
{
intHydroxylic++;
strHydroxylic += x.Code1L;
}
if (x.Negative)
{
intNegative++;
strNegative += x.Code1L;
}
if (x.Polar)
{
intPolar++;
strPolar += x.Code1L;
}
if (x.Positive)
{
intPositive++;
strPositive += x.Code1L;
}
if (x.Small)
{
intSmall++;
strSmall += x.Code1L;
}
if (x.Sulphur)
{
intSulphur++;
strSulphur += x.Code1L;
}
if (x.Tiny)
{
intTiny++;
strTiny += x.Code1L;
}
}
//Console.WriteLine("Acidic: " + intAcidic + " " + strAcidic);
Console.WriteLine("Aliphatic: " + intAliphatic + " " + strAliphatic);
Console.WriteLine("Aromatic: " + intAromatic + " " + strAromatic);
Console.WriteLine("Charged: " + intCharged + " " + strCharged);
Console.WriteLine("Hydrophobic: " + intHydrophobic + " " + strHydrophobic);
Console.WriteLine("Hydroxylic: " + intHydroxylic + " " + strHydroxylic);
Console.WriteLine("Negative: " + intNegative + " " + strNegative);
Console.WriteLine("Polar: " + intPolar + " " + strPolar);
Console.WriteLine("Positive: " + intPositive + " " + strPositive);
Console.WriteLine("Small: " + intSmall + " " + strSmall);
Console.WriteLine("Sulphur: " + intSulphur + " " + strSulphur);
Console.WriteLine("Tiny: " + intTiny + " " + strTiny);
}
public static int[] ConvertAminoAcidNameCodeToSubgroupNumbers(EnumAminoAcidGroups enumAminoAcidGroups, char aminoAcidNameCode)
{
return(ConvertAminoAcidNumberToSubgroupNumbers(enumAminoAcidGroups, AminoAcidConversions.AminoAcidNameToNumber(aminoAcidNameCode)));
}
public static string[,] Spreadsheet(List <MotifProfileSpreadsheetRecord> motifProfileSpreadsheetRecordList)
{
if (motifProfileSpreadsheetRecordList == null)
{
throw new ArgumentNullException(nameof(motifProfileSpreadsheetRecordList));
}
var result = new List <string[]>();
var totalAminoAcids = AminoAcidTotals.TotalAminoAcids();
var sheetHeader = new List <string>()
{
"Motif Name",
"Motif Source",
"Direction",
"Total Found",
//"Total Found In Heterodimers",
//"Total Found In Homodimers",
"Profile Position",
};
sheetHeader.AddRange(AminoAcidConversions.AminoAcidCodeArray1L());
result.Add(sheetHeader.ToArray());
foreach (var record in motifProfileSpreadsheetRecordList.OrderByDescending(a => ProteinDataBankFileOperations.NullableTryParseInt32(a.TotalFound)))
{
result.Add(new string[] { });
var recordHeader = new List <string>()
{
record.MotifName,
record.MotifSource,
record.Direction,
record.TotalFound,
//record.TotalFoundInHeterodimers,
//record.TotalFoundInHomodimers,
"",
};
recordHeader.AddRange(AminoAcidConversions.AminoAcidCodeArray1L());
result.Add(recordHeader.ToArray());
for (var positionIndex = 0; positionIndex < record.AminoAcidProfile.Length; positionIndex++)
{
var row = new string[sheetHeader.Count];
row[sheetHeader.IndexOf("Profile Position")] = "" + (positionIndex + 1);
for (var aaIndex = 0; aaIndex < record.AminoAcidProfile[positionIndex].Length; aaIndex++)
{
row[aaIndex + sheetHeader.IndexOf("Profile Position") + 1] = $"{record.AminoAcidProfile[positionIndex][aaIndex]:0.00}";
}
result.Add(row);
}
var rowAverage = new string[sheetHeader.Count];
rowAverage[sheetHeader.IndexOf("Profile Position")] = "Average";
for (var aaIndex = 0; aaIndex < record.AverageProfile.Length; aaIndex++)
{
rowAverage[aaIndex + sheetHeader.IndexOf("Profile Position") + 1] = $"{record.AverageProfile[aaIndex]:0.00}";
}
result.Add(rowAverage);
}
return(ConvertTypes.StringJagged2DArrayTo2DArray(result.ToArray()));
}
public static MotifProfileSpreadsheetRecord Record(List <VectorProteinInterfaceWhole> vectorProteinInterfaceWholeList)
{
if (vectorProteinInterfaceWholeList == null || vectorProteinInterfaceWholeList.Count == 0)
{
return(null);
}
var maxProteinInterfaceLength = vectorProteinInterfaceWholeList.Select(a => a.ProteinInterfaceAminoAcids1L().Length).Max();
var totalAminoAcids = AminoAcidTotals.TotalAminoAcids();
var result = new MotifProfileSpreadsheetRecord
{
AminoAcidProfile = new decimal[maxProteinInterfaceLength][],
AverageProfile = new decimal[totalAminoAcids],
TotalFound = "" + vectorProteinInterfaceWholeList.Count,
};
var directionFwd = vectorProteinInterfaceWholeList.Count(a => !a.ReversedSequence);
var directionRev = vectorProteinInterfaceWholeList.Count - directionFwd;
if (directionFwd > 0 && directionRev == 0)
{
result.Direction = "Fwd";
}
else if (directionFwd == 0 && directionRev > 0)
{
result.Direction = "Rev";
}
else
{
result.Direction = "Mix";
}
for (var positionIndex = 0; positionIndex < result.AminoAcidProfile.Length; positionIndex++)
{
result.AminoAcidProfile[positionIndex] = new decimal[totalAminoAcids];
}
foreach (var record in vectorProteinInterfaceWholeList)
{
var aminoAcidCode1L = record.ProteinInterfaceAminoAcids1L();
for (int positionIndex = 0; positionIndex < aminoAcidCode1L.Length; positionIndex++)
{
var aa = aminoAcidCode1L[positionIndex];
var aaIndex = AminoAcidConversions.AminoAcidNameToNumber(aa) - 1;
result.AminoAcidProfile[positionIndex][aaIndex]++;
result.AverageProfile[aaIndex]++;
}
}
for (var positionIndex = 0; positionIndex < result.AminoAcidProfile.Length; positionIndex++)
{
var positionTotal = result.AminoAcidProfile[positionIndex].Sum();
for (var aaIndex = 0; aaIndex < totalAminoAcids; aaIndex++)
{
result.AminoAcidProfile[positionIndex][aaIndex] = (result.AminoAcidProfile[positionIndex][aaIndex] / positionTotal) * 100;
}
}
var averageTotal = result.AverageProfile.Sum();
for (var aaIndex = 0; aaIndex < totalAminoAcids; aaIndex++)
{
result.AverageProfile[aaIndex] = averageTotal != 0 ? (result.AverageProfile[aaIndex] / averageTotal) * 100 : 0;
}
return(result);
}
/// <summary>
/// Load proteinInterface data from the PDB file based on a list of already detected proteinInterfaces.
/// The detected proteinInterfaces may be missing data such as other atoms or residues which are also in the proteinInterface but were not
/// directly interacting.
/// The positions and lengths of the proteinInterfaces are also calculated.
/// </summary>
/// <param name="pdbFilename"></param>
/// <param name="pdbFileChains"></param>
/// <param name="singularAaToAaInteractions"></param>
/// <param name="proteinInterfacesClusteringResult"></param>
/// <param name="detectedBestStages"></param>
/// <param name="interactionBetweenProteinInterfacesContainer"></param>
/// <returns></returns>
public static List <ProteinInterfaceSequenceAndPositionData> AnalyseProteinInterfacesSequenceAndPositionData(
string pdbFilename,
Dictionary <string, List <string> > pdbIdChainIdList,
ProteinChainListContainer pdbFileChains,
ProteinChainListContainer singularAaToAaInteractions,
ClusteringFullResultListContainer proteinInterfacesClusteringResult,
int[] detectedBestStages,
InteractionBetweenProteinInterfacesListContainer interactionBetweenProteinInterfacesContainer)
{
if (string.IsNullOrWhiteSpace(pdbFilename))
{
throw new ArgumentOutOfRangeException(nameof(pdbFilename));
}
if (!File.Exists(pdbFilename))
{
throw new FileNotFoundException("File not found", pdbFilename);
}
if (ParameterValidation.IsProteinChainListContainerNullOrEmpty(singularAaToAaInteractions))
{
throw new ArgumentOutOfRangeException(nameof(singularAaToAaInteractions));
}
if (ParameterValidation.IsClusteringFullResultListContainerNullOrEmpty(proteinInterfacesClusteringResult))
{
throw new ArgumentOutOfRangeException(nameof(proteinInterfacesClusteringResult));
}
if (ParameterValidation.IsIntArrayNullOrEmpty(detectedBestStages))
{
throw new ArgumentOutOfRangeException(nameof(detectedBestStages));
}
// ProteinInterfaces are clusters with non-proteinInterfaces removed.
var result = new List <ProteinInterfaceSequenceAndPositionData>();
string proteinId = ProteinDataBankFileOperations.PdbIdFromPdbFilename(pdbFilename);
int totalChains = proteinInterfacesClusteringResult.ChainList.Count;
for (int chainIndex = 0; chainIndex < totalChains; chainIndex++)
{
int stageIndex = detectedBestStages[chainIndex];
string chainIdLetter = SpreadsheetFileHandler.AlphabetLetterRollOver(chainIndex);
List <ClusteringFullResultListContainer.Chain.Stage.Cluster> proteinInterfaceList = proteinInterfacesClusteringResult.ChainList[chainIndex].StageList[stageIndex].ClusterList;
List <ClusteringFullResultListContainer.Chain.Stage.Cluster> nonEmptyProteinInterfaceList = proteinInterfaceList.Where(a => a != null && a.AtomIndexList != null && a.AtomIndexList.Count > 0).ToList();
// loop through each proteinInterface
for (int proteinInterfaceIndex = 0; proteinInterfaceIndex < nonEmptyProteinInterfaceList.Count; proteinInterfaceIndex++)
{
ClusteringFullResultListContainer.Chain.Stage.Cluster proteinInterface = nonEmptyProteinInterfaceList[proteinInterfaceIndex];
// Find min and max residue sequence index value in the proteinInterface
MinMax proteinInterfaceResidueSequenceIndexes = MinMaxResidueSequenceIndex(proteinInterface, singularAaToAaInteractions, chainIndex);
int proteinInterfaceLength = CalculateProteinInterfaceLength(proteinInterfaceResidueSequenceIndexes.Min, proteinInterfaceResidueSequenceIndexes.Max);
string proteinInterfaceIdLetter = SpreadsheetFileHandler.AlphabetLetterRollOver(proteinInterfaceIndex);
var proteinInterfacePositionData = new ProteinInterfaceSequenceAndPositionData
{
FullProteinInterfaceId = new FullProteinInterfaceId(proteinId, chainIndex, proteinInterfaceIndex, proteinInterfaceResidueSequenceIndexes.Min, proteinInterfaceResidueSequenceIndexes.Max),
ChainIdLetter = chainIdLetter,
ProteinInterfaceIdLetter = proteinInterfaceIdLetter,
StartPosition = proteinInterfaceResidueSequenceIndexes.Min,
EndPosition = proteinInterfaceResidueSequenceIndexes.Max,
ProteinInterfaceLength = CalculateProteinInterfaceLength(proteinInterfaceResidueSequenceIndexes.Min, proteinInterfaceResidueSequenceIndexes.Max)
};
proteinInterfacePositionData.AminoAcidSequenceAllResidueSequenceIndexes = new ProteinInterfaceAminoAcidMetaData[proteinInterfacePositionData.ProteinInterfaceLength];
proteinInterfacePositionData.AminoAcidSequenceAll1L = "";
proteinInterfacePositionData.AminoAcidSequenceInteractionsAll1L = "";
proteinInterfacePositionData.AminoAcidSequenceInteractionsInsideProteinInterfacesOnly1L = "";
proteinInterfacePositionData.AminoAcidSequenceInteractionsNone1L = "";
proteinInterfacePositionData.AminoAcidSequenceInteractionsOutsideProteinInterfacesOnly1L = "";
proteinInterfacePositionData.AminoAcidSequenceAll3L = "";
proteinInterfacePositionData.AminoAcidSequenceInteractionsAll3L = "";
proteinInterfacePositionData.AminoAcidSequenceInteractionsInsideProteinInterfacesOnly3L = "";
proteinInterfacePositionData.AminoAcidSequenceInteractionsNone3L = "";
proteinInterfacePositionData.AminoAcidSequenceInteractionsOutsideProteinInterfacesOnly3L = "";
//int foundAtomCount = 0;
const string placeholder1L = "_";
const string placeholder3L = "___";
for (int residueSequenceIndex = proteinInterfaceResidueSequenceIndexes.Min; residueSequenceIndex <= proteinInterfaceResidueSequenceIndexes.Max; residueSequenceIndex++)
{
/* questions
* 1. does this reside interact with another reside which is also part of a proteinInterface?
* 2. if not, does this reside interact at all?
*/
var proteinInterfaceAminoAcidMetaData = new ProteinInterfaceAminoAcidMetaData();
proteinInterfacePositionData.AminoAcidSequenceAllResidueSequenceIndexes[proteinInterfacePositionData.AminoAcidSequenceAll1L.Length] = proteinInterfaceAminoAcidMetaData;
ATOM_Record foundAtomInsidePdbFile = AtomSearchMethods.FindAtomInsidePdbFileChain(pdbFileChains, chainIndex, residueSequenceIndex);
if (foundAtomInsidePdbFile == null)
{
// Non-CA atom is loaded here in case of missing CA atom to find the AA code for the resSeq index
var chainIdList = pdbIdChainIdList != null ? (pdbIdChainIdList.ContainsKey(proteinId) ? pdbIdChainIdList[proteinId].ToArray() : null) : null;
ProteinChainListContainer pdbFileChains2 = ProteinDataBankFileOperations.PdbAtomicChains(pdbFilename, chainIdList, -1, -1, false);
foundAtomInsidePdbFile = AtomSearchMethods.FindAtomInsidePdbFileChain(pdbFileChains2, chainIndex, residueSequenceIndex);
}
proteinInterfaceAminoAcidMetaData.PdbResidueSequenceIndex = residueSequenceIndex;
proteinInterfaceAminoAcidMetaData.ArrayMemberIndex = pdbFileChains.ChainList[chainIndex].AtomList.IndexOf(foundAtomInsidePdbFile);
proteinInterfaceAminoAcidMetaData.OppoproteinInterfaceInteractions = new bool[proteinInterfaceLength];
if (foundAtomInsidePdbFile != null)
{
proteinInterfacePositionData.AminoAcidSequenceAll1L += AminoAcidConversions.AminoAcidNameToCode1L(foundAtomInsidePdbFile.resName.FieldValue);
proteinInterfacePositionData.AminoAcidSequenceAll3L += foundAtomInsidePdbFile.resName.FieldValue.PadRight(3, '_');
}
else
{
proteinInterfacePositionData.AminoAcidSequenceAll1L += placeholder1L;
proteinInterfacePositionData.AminoAcidSequenceInteractionsAll1L += placeholder1L;
proteinInterfacePositionData.AminoAcidSequenceInteractionsInsideProteinInterfacesOnly1L += placeholder1L;
proteinInterfacePositionData.AminoAcidSequenceInteractionsOutsideProteinInterfacesOnly1L += placeholder1L;
proteinInterfacePositionData.AminoAcidSequenceInteractionsNone1L += placeholder1L;
proteinInterfacePositionData.AminoAcidSequenceAll3L += placeholder3L;
proteinInterfacePositionData.AminoAcidSequenceInteractionsAll3L += placeholder3L;
proteinInterfacePositionData.AminoAcidSequenceInteractionsInsideProteinInterfacesOnly3L += placeholder3L;
proteinInterfacePositionData.AminoAcidSequenceInteractionsOutsideProteinInterfacesOnly3L += placeholder3L;
proteinInterfacePositionData.AminoAcidSequenceInteractionsNone3L += placeholder3L;
proteinInterfaceAminoAcidMetaData.ProteinInterfaceInteractionType = ProteinInterfaceInteractionType.NoInteractionFound;
proteinInterfaceAminoAcidMetaData.NonProteinInterfaceInteractionResidueNames1L += placeholder1L;
proteinInterfaceAminoAcidMetaData.NonProteinInterfaceInteractionResidueNames3L += placeholder3L;
continue;
}
List <ATOM_Record> foundAtomInteractingWithAnotherProteinInterface = AtomSearchMethods.FindAtomInteractingWithOtherProteinInterfaces(foundAtomInsidePdbFile, interactionBetweenProteinInterfacesContainer, FindAtomInteractingWithAnotherProteinInterfaceOptions.FindAtomsInteractingWithOtherProteinInterfaces);
List <ATOM_Record> foundAtomInteractingWithNonProteinInterface = AtomSearchMethods.FindAtomInteractingWithOtherProteinInterfaces(foundAtomInsidePdbFile, interactionBetweenProteinInterfacesContainer, FindAtomInteractingWithAnotherProteinInterfaceOptions.FindAtomsInteractingWithNonProteinInterfaces);
proteinInterfaceAminoAcidMetaData.OppoproteinInterfaceInteractions = AminoAcidInteractionVector(singularAaToAaInteractions, proteinInterfacesClusteringResult, detectedBestStages, interactionBetweenProteinInterfacesContainer, chainIndex, proteinInterfaceIndex, residueSequenceIndex);
proteinInterfaceAminoAcidMetaData.ResidueName1L = AminoAcidConversions.AminoAcidNameToCode1L(foundAtomInsidePdbFile.resName.FieldValue);
proteinInterfaceAminoAcidMetaData.ResidueName3L = foundAtomInsidePdbFile.resName.FieldValue.PadRight(3, '_');
if (foundAtomInteractingWithAnotherProteinInterface != null)
{
foreach (ATOM_Record atom in foundAtomInteractingWithAnotherProteinInterface)
{
proteinInterfaceAminoAcidMetaData.ProteinInterfaceInteractionResidueNames1L += AminoAcidConversions.AminoAcidNameToCode1L(atom.resName.FieldValue);
proteinInterfaceAminoAcidMetaData.ProteinInterfaceInteractionResidueNames3L += atom.resName.FieldValue.PadRight(3, '_');
}
}
if (foundAtomInteractingWithNonProteinInterface != null)
{
foreach (ATOM_Record atom in foundAtomInteractingWithNonProteinInterface)
{
proteinInterfaceAminoAcidMetaData.NonProteinInterfaceInteractionResidueNames1L += AminoAcidConversions.AminoAcidNameToCode1L(atom.resName.FieldValue);
proteinInterfaceAminoAcidMetaData.NonProteinInterfaceInteractionResidueNames3L += atom.resName.FieldValue.PadRight(3, '_');
}
}
if (foundAtomInteractingWithAnotherProteinInterface != null && foundAtomInteractingWithAnotherProteinInterface.Count > 0)
{
proteinInterfacePositionData.AminoAcidSequenceInteractionsAll1L += AminoAcidConversions.AminoAcidNameToCode1L(foundAtomInsidePdbFile.resName.FieldValue);
proteinInterfacePositionData.AminoAcidSequenceInteractionsInsideProteinInterfacesOnly1L += AminoAcidConversions.AminoAcidNameToCode1L(foundAtomInsidePdbFile.resName.FieldValue);
proteinInterfacePositionData.AminoAcidSequenceInteractionsOutsideProteinInterfacesOnly1L += placeholder1L;
proteinInterfacePositionData.AminoAcidSequenceInteractionsNone1L += placeholder1L;
proteinInterfacePositionData.AminoAcidSequenceInteractionsAll3L += foundAtomInsidePdbFile.resName.FieldValue.PadRight(3, '_');
proteinInterfacePositionData.AminoAcidSequenceInteractionsInsideProteinInterfacesOnly3L += foundAtomInsidePdbFile.resName.FieldValue.PadRight(3, '_');
proteinInterfacePositionData.AminoAcidSequenceInteractionsOutsideProteinInterfacesOnly3L += placeholder3L;
proteinInterfacePositionData.AminoAcidSequenceInteractionsNone3L += placeholder3L;
proteinInterfaceAminoAcidMetaData.ProteinInterfaceInteractionType = ProteinInterfaceInteractionType.InteractionWithAnotherProteinInterface;
if (foundAtomInteractingWithNonProteinInterface != null && foundAtomInteractingWithNonProteinInterface.Count > 0)
{
proteinInterfaceAminoAcidMetaData.ProteinInterfaceInteractionType |= ProteinInterfaceInteractionType.InteractionWithNonProteinInterface;
}
}
else if (foundAtomInteractingWithNonProteinInterface != null && foundAtomInteractingWithNonProteinInterface.Count > 0)
{
proteinInterfacePositionData.AminoAcidSequenceInteractionsAll1L += AminoAcidConversions.AminoAcidNameToCode1L(foundAtomInsidePdbFile.resName.FieldValue);
proteinInterfacePositionData.AminoAcidSequenceInteractionsInsideProteinInterfacesOnly1L += placeholder1L;
proteinInterfacePositionData.AminoAcidSequenceInteractionsOutsideProteinInterfacesOnly1L += AminoAcidConversions.AminoAcidNameToCode1L(foundAtomInsidePdbFile.resName.FieldValue);
proteinInterfacePositionData.AminoAcidSequenceInteractionsNone1L += placeholder1L;
proteinInterfacePositionData.AminoAcidSequenceInteractionsAll3L += foundAtomInsidePdbFile.resName.FieldValue.PadRight(3, '_');
proteinInterfacePositionData.AminoAcidSequenceInteractionsInsideProteinInterfacesOnly3L += placeholder3L;
proteinInterfacePositionData.AminoAcidSequenceInteractionsOutsideProteinInterfacesOnly3L += foundAtomInsidePdbFile.resName.FieldValue.PadRight(3, '_');
proteinInterfacePositionData.AminoAcidSequenceInteractionsNone3L += placeholder3L;
proteinInterfaceAminoAcidMetaData.ProteinInterfaceInteractionType = ProteinInterfaceInteractionType.InteractionWithNonProteinInterface;
}
else
{
proteinInterfacePositionData.AminoAcidSequenceInteractionsAll1L += placeholder1L;
proteinInterfacePositionData.AminoAcidSequenceInteractionsInsideProteinInterfacesOnly1L += placeholder1L;
proteinInterfacePositionData.AminoAcidSequenceInteractionsOutsideProteinInterfacesOnly1L += placeholder1L;
proteinInterfacePositionData.AminoAcidSequenceInteractionsNone1L += AminoAcidConversions.AminoAcidNameToCode1L(foundAtomInsidePdbFile.resName.FieldValue);
proteinInterfacePositionData.AminoAcidSequenceInteractionsAll3L += placeholder3L;
proteinInterfacePositionData.AminoAcidSequenceInteractionsInsideProteinInterfacesOnly3L += placeholder3L;
proteinInterfacePositionData.AminoAcidSequenceInteractionsOutsideProteinInterfacesOnly3L += placeholder3L;
proteinInterfacePositionData.AminoAcidSequenceInteractionsNone3L += foundAtomInsidePdbFile.resName.FieldValue.PadRight(3, '_');
proteinInterfaceAminoAcidMetaData.ProteinInterfaceInteractionType = ProteinInterfaceInteractionType.NoInteractionFound;
}
}
result.Add(proteinInterfacePositionData);
}
}
return(result);
}
