public static List <Sequence> LoadStructureFile(string atomsFilename, char[] chainIdWhiteList = null, bool padMissingBool = true, int[] startResSeq = null, int[] endResSeq = null, char outsidePaddingChar = ' ', char insidePaddingChar = 'X')
{
var pdb = ProteinBioClass.PdbAtomicChains(atomsFilename, chainIdWhiteList, -1, -1, true);
var pdbId = ProteinBioClass.PdbIdFromPdbFilename(atomsFilename);
return(LoadStructureFile(pdb, pdbId, chainIdWhiteList, padMissingBool, startResSeq, endResSeq,
outsidePaddingChar, insidePaddingChar));
}
public static List <Sequence> LoadStructureFile(string[] structureFileLines, string pdbId = "", char[] chainIdWhiteList = null, bool padMissingBool = true, int[] startResSeq = null, int[] endResSeq = null, char outsidePaddingChar = ' ', char insidePaddingChar = 'X')
{
var pdb = ProteinBioClass.PdbAtomicChains(structureFileLines, chainIdWhiteList, -1, -1, false);
foreach (var c in pdb.ChainList)
{
c.AtomList = c.AtomList.GroupBy(a => a.resSeq.FieldValue).OrderBy(g => int.Parse(g.Key)).Select(g => g.First()).ToList();
}
return(LoadStructureFile(pdb, pdbId, chainIdWhiteList, padMissingBool, startResSeq, endResSeq, outsidePaddingChar, insidePaddingChar));
}
public static StructureToSequenceAlignment.StructureToSequenceAlignmentResult GetSequence(string pdbId, char chainId, int first = -1, int last = -1)
{
//var chainId = pdbId[4];
pdbId = pdbId.Substring(0, 4);
var pdbFilename = @"c:\pdbe\" + pdbId + ".pdb";
var fastaFilename = @"c:\pdbe\pdb_seqres.fasta";
var fastaSequence = Sequence.LoadSequenceFile(fastaFilename, new string[] { null, "", "protein" }).First(a => a.IdSplit.PdbId.ToUpperInvariant() == pdbId.ToUpperInvariant() && a.IdSplit.ChainId == chainId);
var pdbSequence = Sequence.LoadStructureFile(pdbFilename, new[] { chainId }, true, null, null, '-', '-').First(a => a.IdSplit.PdbId.ToUpperInvariant() == pdbId.ToUpperInvariant() && a.IdSplit.ChainId == chainId);
var atoms = ProteinBioClass.PdbAtomicChains(pdbFilename, new char[] { chainId }).ChainList.First(a => a.ChainId == chainId).AtomList;
var align = StructureToSequenceAlignment.Align(atoms, fastaSequence.FullSequence, pdbSequence.FullSequence, first, last);
return(align);
}
static void Main(string[] args)
{
var parameters = new string[, ]
{
{ "[pdb_file]", "PDB ~v3.3 Protein Data Bank format file [*.pdb, *.ent]" },
{ "[interface-interface_file]", "interface-interface file" },
{ "[[chain_ids]]", "molecule chains to output [* for all]" },
{ "[[output_file]]", "optional output file. use ? for chain id. when ommitted, output to console" },
};
var maxParamLength = parameters.Cast <string>().Where((a, i) => i % 2 == 0).Max(a => a.Length);
var exeFilename = Path.GetFileName(System.Diagnostics.Process.GetCurrentProcess().MainModule.FileName);
if (args.Length == 0)
{
Console.WriteLine(exeFilename + @" is a program to extract ATOM records from a PDB file.");
Console.WriteLine();
Console.WriteLine(@"Usage:");
Console.WriteLine(ProteinBioClass.WrapConsoleText(exeFilename + @" " + String.Join(" ", parameters.Cast <string>().Where((a, i) => i % 2 == 0)), maxParamLength + 2, 1));
Console.WriteLine();
Console.WriteLine(@"Example:");
Console.WriteLine(ProteinBioClass.WrapConsoleText(exeFilename + @" ""c:\pdb_db\pdb1a12.pdb"" 8.0 ""c:\pdb_atoms\atoms1a12.pdb""", maxParamLength + 2, 1));
Console.WriteLine();
Console.WriteLine(@"Arguments:");
for (var i = 0; i < parameters.GetLength(0); i++)
{
Console.WriteLine(@" " + parameters[i, 0].PadLeft(maxParamLength, ' ') + " " + ProteinBioClass.WrapConsoleText(parameters[i, 1], maxParamLength + 2, 1, false));
}
Console.WriteLine();
return;
}
// load and echo arguments
var p = 0;
var pdbFilename = args.Length > p && args[p].Length > 0 ? args[p] : "";
pdbFilename = pdbFilename.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + pdbFilename);
p++;
var interfaceInterfaceFile = args.Length > p && args[p].Length > 0 ? args[p].ToUpperInvariant() : "";
interfaceInterfaceFile = interfaceInterfaceFile.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + interfaceInterfaceFile);
p++;
var chainIds = args.Length > p && args[p].Length > 0 ? args[p] : "";
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + chainIds);
p++;
var outputFilename = args.Length > p && args[p].Length > 0 ? args[p] : "";
outputFilename = outputFilename.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + outputFilename);
Console.WriteLine();
if (!File.Exists(pdbFilename))
{
Console.WriteLine("; File not found: " + pdbFilename);
return;
}
if (!File.Exists(interfaceInterfaceFile))
{
Console.WriteLine("; File not found: " + interfaceInterfaceFile);
return;
}
if (string.IsNullOrWhiteSpace(pdbFilename))
{
return;
}
if (chainIds.Contains('*'))
{
chainIds = null;
}
var chainIdWhiteList = !string.IsNullOrEmpty(chainIds) ? chainIds.ToUpperInvariant().Split(new char[] { ' ', ',' }, StringSplitOptions.RemoveEmptyEntries) : null;
var interfaceData = ComplexInterfaces.ComplexInterfaces.InterfaceInterfaceData.Load(interfaceInterfaceFile);
var terminatedChains = new List <string>();
var pdbfilenameShort = Path.GetFileNameWithoutExtension(pdbFilename);
var pdbId = pdbfilenameShort.Substring(pdbfilenameShort.Length - 4).ToUpperInvariant();
var lines = File.ReadAllLines(pdbFilename);
var result = new List <Tuple <string, string> >();
var interfaceDataChains = interfaceData.Select(a => a.ReceptorChainId).Distinct().ToList();
var interfaceDataStart = interfaceDataChains.Select(a => interfaceData.Where(b => b.ReceptorChainId == a).Min(b => b.ReceptorInterfaceResSeqStart)).ToList();
var interfaceDataEnd = interfaceDataChains.Select(a => interfaceData.Where(b => b.ReceptorChainId == a).Max(b => b.ReceptorInterfaceResSeqEnd)).ToList();
foreach (var line in lines)
{
if (line.Length < 22)
{
continue;
}
if (line.Substring(0, 4).ToUpperInvariant() == "TER ")
{
var chainId = ("" + line[21]).ToUpperInvariant();
terminatedChains.Add(chainId);
}
if (line.Substring(0, 5).ToUpperInvariant() == "ATOM ")
{
var chainId = ("" + line[21]).ToUpperInvariant();
if (terminatedChains.Contains(chainId))
{
continue;
}
if (chainIdWhiteList != null && chainIdWhiteList.Length > 0 && !chainIdWhiteList.Contains(chainId))
{
continue;
}
if (!interfaceDataChains.Contains(chainId[0]))
{
continue;
}
//if (caTraceOnlyBool && (line[13] != 'C' || line[14] != 'A')) continue;
var interfaceDataChainIndex = interfaceDataChains.IndexOf(chainId[0]);
var resSeq = int.Parse(line.Substring(22, 4).Trim());
if (resSeq >= interfaceDataStart[interfaceDataChainIndex] && resSeq <= interfaceDataEnd[interfaceDataChainIndex])
{
result.Add(new Tuple <string, string>(chainId, line));
}
}
}
if (!string.IsNullOrWhiteSpace(outputFilename))
{
Directory.CreateDirectory(Path.GetDirectoryName(outputFilename.Replace("?", "")));
if (!outputFilename.Contains("?"))
{
File.WriteAllLines(outputFilename, result.Select(a => a.Item2).ToList());
}
else
{
var chains = result.Select(a => a.Item1).Distinct().ToList();
foreach (var chain in chains)
{
var outputFilename2 = outputFilename.Replace("?", "");
outputFilename2 = Path.GetDirectoryName(outputFilename2) + @"\" + Path.GetFileNameWithoutExtension(outputFilename2) + chain + Path.GetExtension(outputFilename2);
File.WriteAllLines(outputFilename2, result.Where(a => a.Item1 == chain).Select(a => a.Item2).ToList());
}
}
}
else
{
foreach (var line in result)
{
Console.WriteLine(line);
}
Console.WriteLine();
}
}
public static void Main(string[] args)
{
var parameters = new string[, ]
{
{ "[pdb_or_atoms_file]", "standard crystal pdb file or output from the ComplexAtoms program" },
{ "[[pad_missing]]", "Y or N (default: Y)" },
{ "[[output_fasta_file]]", "optional output fasta file. when ommitted, output to console" },
{ "[[append_or_overwrite]]", "optional (A) append or (O) overwrite (default: overwrite)" },
};
var maxParamLength = parameters.Cast <string>().Where((a, i) => i % 2 == 0).Max(a => a.Length);
var exeFilename = Path.GetFileName(System.Diagnostics.Process.GetCurrentProcess().MainModule.FileName);
if (args.Length < 1)
{
Console.WriteLine(exeFilename + @" is a program to extract the protein amino acid fasta sequence from protein structure pdb file.");
Console.WriteLine();
Console.WriteLine(@"Usage:");
Console.WriteLine(ProteinBioClass.WrapConsoleText(exeFilename + @" " + String.Join(" ", parameters.Cast <string>().Where((a, i) => i % 2 == 0)), maxParamLength + 2, 1));
Console.WriteLine();
Console.WriteLine(@"Example:");
Console.WriteLine(ProteinBioClass.WrapConsoleText(exeFilename + @" ""c:\pdb_db\atoms\atoms1a12.pdb"" ""c:\pdb_db\fasta_from_pdb\atoms1a12.pdb.fasta""", maxParamLength + 2, 1));
Console.WriteLine();
Console.WriteLine(@"Arguments:");
for (var i = 0; i < parameters.GetLength(0); i++)
{
Console.WriteLine(@" " + parameters[i, 0].PadLeft(maxParamLength, ' ') + " " + ProteinBioClass.WrapConsoleText(parameters[i, 1], maxParamLength + 2, 1, false));
}
Console.WriteLine();
return;
}
// load arguments
var p = 0;
var atomsFilename = args.Length > p && args[p].Length > 0 ? args[p] : "";
atomsFilename = atomsFilename.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + atomsFilename);
p++;
var padMissing = args.Length > p && args[p].Length > 0 ? args[p] : "Y";
padMissing = padMissing.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + padMissing);
if (padMissing != "Y" && padMissing != "N")
{
padMissing = "Y";
}
var padMissingBool = padMissing == "Y";
p++;
var outputFastaFilename = args.Length > p && args[p].Length > 0 ? args[p] : "";
outputFastaFilename = outputFastaFilename.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + outputFastaFilename);
p++;
var appendOrOverwrite = args.Length > p && args[p].Length > 0 ? args[p] : "";
appendOrOverwrite = appendOrOverwrite.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + appendOrOverwrite);
if (!(string.IsNullOrWhiteSpace(appendOrOverwrite) || appendOrOverwrite == "O" || appendOrOverwrite == "A"))
{
return;
}
Console.WriteLine();
var sequenceList = Sequence.LoadStructureFile(atomsFilename, null, padMissingBool);// ProteinBioClass.StructureFileToAaFastaSequence(atomsFilename, null, padMissingBool);
var output = Sequence.GetAsFasta(sequenceList);
if (string.IsNullOrWhiteSpace(outputFastaFilename))
{
Console.WriteLine();
Console.WriteLine(output);
Console.WriteLine();
}
else
{
Directory.CreateDirectory(Path.GetDirectoryName(outputFastaFilename));
if (appendOrOverwrite == "A" && File.Exists(outputFastaFilename))
{
var data = File.ReadAllText(outputFastaFilename);
if (!data.EndsWith(Environment.NewLine))
{
data = data + Environment.NewLine;
}
output = data + output;
}
File.WriteAllText(outputFastaFilename, output);
}
}
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)
{
//var s1 =
// @"XXXXXXXXXXXXXXXXXXXXKKVKVSHRSHSTEPGLVLTLGQGDVGQLGLGENVMERKKPALVSIPEDVVQAEAGGMHTVCLSKSGQVYSFGCNDEGALGRDTSVEGSEMVPGKVELQEKVVQVSAGDSHTAALTDDGRVFLWGSFRDNNGVIGLLEPMKKSMVPVQVQLDVPVVKVASGNDHLVMLTADGDLYTLGCGEQGQLGRVPELFANRGGRQGLERLLVPKCVMLKSRGSRGHVRFQDAFCGAYFTFAISHEGHVYGFGLSNYHQLGTPGTESCFIPQNLTSFKNSTKSWVGFSGGQHHTVCMDSEGKAYSLGRAEYGRLGLGEGAEEKSIPTLISRLPAVSSVACGASVGYAVTKDGRVFAWGMGTNYQLGTGQDEDAWSPVEMMGKQLENRVVLSVSSGGQHTVLLVKDKEQS";
//var s2 = @"RRSPPADAIPKSKKVKVSHRSHSTEPGLVLTLGQGDVGQLGLGENVMERKKPALVSIPEDVVQAEAGGMHTVCLSKSGQVYSFGCNDEGALGRDTSVEGSEMVPGKVELQEKVVQVSAGDSHTAALTDDGRVFLWGSFRDNNGVIGLLEPMKKSMVPVQVQLDVPVVKVASGNDHLVMLTADGDLYTLGCGEQGQLGRVPELFANRGGRQGLERLLVPKCVMLKSRGSRGHVRFQDAFCGAYFTFAISHEGHVYGFGLSNYHQLGTPGTESCFIPQNLTSFKNSTKSWVGFSGGQHHTVCMDSEGKAYSLGRAEYGRLGLGEGAEEKSIPTLISRLPAVSSVACGASVGYAVTKDGRVFAWGMGTNYQLGTGQDEDAWSPVEMMGKQLENRVVLSVSSGGQHTVLLVKDKEQS";
//var x = SimpleAlignmentOffset(s1,s2);
//Console.WriteLine();
//Console.WriteLine(x.Item1);
//Console.WriteLine(x.Item2);
//Console.WriteLine();
//Console.ReadLine();
//return;
// MutateSequence example.fasta start end mutation original (will find closest to start/end in case of sequence/structure index misalignment)
var parameters = new string[, ]
{
{ "[input_fasta_file]", "fasta file with sequence to mutate" },
{ "[chain_ids]", "chain ids to mutate" },
{ "[start_positions]", "mutation start position (one based)" },
{ "[end_positions]", "mutation end position (one based)" },
{ "[offsets]", "offsets (for where pdb index doesn't match fasta sequence index) (one based)" },
{ "[mutation_sequence]", "new amino acids to overwrite with" },
{ "[[output_fasta_file]]", "optional output fasta file. when ommitted, output to console" },
};
var maxParamLength = parameters.Cast <string>().Where((a, i) => i % 2 == 0).Max(a => a.Length);
var exeFilename = Path.GetFileName(System.Diagnostics.Process.GetCurrentProcess().MainModule.FileName);
if (args.Length < 5)
{
Console.WriteLine(exeFilename +
@" is a program to mutate (substitute) a subsequence of a protein amino acid sequence within a fasta file.");
Console.WriteLine();
Console.WriteLine(@"Usage:");
Console.WriteLine(
ProteinBioClass.WrapConsoleText(
exeFilename + @" " + String.Join(" ", parameters.Cast <string>().Where((a, i) => i % 2 == 0)),
maxParamLength + 2, 1));
Console.WriteLine();
Console.WriteLine(@"Example:");
Console.WriteLine(
ProteinBioClass.WrapConsoleText(
exeFilename +
@" ""c:\pdb_db\fasta\fasta_pdb1a12.pdb.fasta"" A,B,C 10,76,100 15,77,102 GBVBGA,AA,GHG ""c:\pdb_db\fasta_mutated\mutated_pdb1a12.pdb.fasta""",
maxParamLength + 2, 1));
Console.WriteLine();
Console.WriteLine(@"Arguments:");
for (var i = 0; i < parameters.GetLength(0); i++)
{
Console.WriteLine(@" " + parameters[i, 0].PadLeft(maxParamLength, ' ') + " " +
ProteinBioClass.WrapConsoleText(parameters[i, 1], maxParamLength + 2, 1, false));
}
Console.WriteLine();
return;
}
var p = 0;
var input_fasta_file = args.Length > p && args[p].Length > 0 ? args[p] : "";
input_fasta_file = input_fasta_file.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + input_fasta_file);
p++;
var chain_ids = args.Length > p && args[p].Length > 0 ? args[p] : "";
chain_ids = chain_ids.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + chain_ids);
var chain_ids_split = chain_ids.ToUpperInvariant().Split(',');
p++;
var start_position = args.Length > p && args[p].Length > 0 ? args[p] : "";
start_position = start_position.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + start_position);
var start_position_split = start_position.Split(',').Select(int.Parse).ToArray();
p++;
var end_position = args.Length > p && args[p].Length > 0 ? args[p] : "";
end_position = end_position.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + end_position);
var end_position_split = end_position.Split(',').Select(int.Parse).ToArray();
p++;
var offset_position = args.Length > p && args[p].Length > 0 ? args[p] : "";
offset_position = offset_position.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + offset_position);
var offset_position_split = offset_position.Split(',').Select(int.Parse).ToArray();
p++;
var mutation_sequence = args.Length > p && args[p].Length > 0 ? args[p] : "";
mutation_sequence = mutation_sequence.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + mutation_sequence);
var mutation_sequence_split = mutation_sequence.Split(',');
p++;
var output_fasta_file = args.Length > p && args[p].Length > 0 ? args[p] : "";
output_fasta_file = output_fasta_file.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + output_fasta_file);
Console.WriteLine();
MutateFastaSequenceSave(input_fasta_file, chain_ids_split, start_position_split, end_position_split,
offset_position_split, mutation_sequence_split, output_fasta_file);
}
static void Main(string[] args)
{
//var requiredInterfaceLengths = new int[] { 7, 9, 11, 13, 15 };
var requiredInterfaceLengths = new int[] { 9 };
var sequenceFilename = @"C:\pdbe\pdb_seqres.fasta";
var dsspFilename = @"C:\pdbe\ss.txt";
var sequenceListFromFastaFile = Sequence.LoadSequenceFile(sequenceFilename, new string[] { null, "", "protein" });
var dsspList = Sequence.LoadSequenceFile(dsspFilename, new string[] { null, "", "protein" });
dsspList = dsspList.Where(a => a.IdSplit.Description == "secstr").ToList();
//var pdbIdList = new List<string>(); {"1a00"};
var pdbFiles = Directory.GetFiles(@"c:\pdbe\contacts_all\", "????.pdb", SearchOption.TopDirectoryOnly).ToList();
var pdbFileLengths = pdbFiles.Select(a => new Tuple <string, long>(a, new FileInfo(a).Length)).ToList();
pdbFileLengths = pdbFileLengths.Where(a => a.Item2 > 0).ToList();
pdbFileLengths = pdbFileLengths.OrderBy(a => a.Item2).ToList();
var ifList = InterfaceFragment.Load(@"c:\r\if.csv");
ifList = ifList.Where(a => requiredInterfaceLengths.Contains(a.FragmentLength)).ToList();
if (ifList.Count == 0)
{
var pdbIdList = pdbFileLengths.Select(a => a.Item1).Select(Path.GetFileNameWithoutExtension).Select(a => a.ToUpperInvariant()).ToList();
//pdbIdList = pdbIdList.GetRange(0, 100);
//var result = new List<InterfaceFragment>();
var taskList1 = new List <Task <List <InterfaceFragment> > >();
foreach (var pdbId1 in pdbIdList)
{
var pdbId = pdbId1;
Console.WriteLine(pdbId + " " + (pdbIdList.IndexOf(pdbId) + 1) + "/" + pdbIdList.Count);
while (taskList1.Count(a => !a.IsCompleted) >= Environment.ProcessorCount)
{
Task.WaitAny(taskList1.Where(a => !a.IsCompleted).ToArray <Task>());
}
taskList1.Add(Task.Run(() =>
{
var pdbResult = new List <InterfaceFragment>();
var atomsFilename = @"c:\pdbe\atoms_all\" + pdbId + ".pdb";
var contactsFilename = @"c:\pdbe\contacts_all\" + pdbId + ".pdb";
var interfaceCsv = @"c:\r\interface_9\" + pdbId + @".csv";
if (File.Exists(interfaceCsv))
{
return(InterfaceFragment.Load(interfaceCsv));
}
if (!File.Exists(atomsFilename) || !File.Exists(contactsFilename))
{
return(null); // new List<InterfaceFragment>(); // continue;
}
if (new FileInfo(atomsFilename).Length == 0 || new FileInfo(contactsFilename).Length == 0)
{
return(null); //new List<InterfaceFragment>(); // continue;
}
var contacts = ProteinBioClass.AtomPair.LoadAtomPairList(contactsFilename);
var contactChainIds = contacts.SelectMany(a => new char[] { a.Atom1.chainID.FieldValue[0], a.Atom2.chainID.FieldValue[0] }).Distinct().ToList();
var proteinFileChains = ProteinBioClass.PdbAtomicChains(atomsFilename, contactChainIds.ToArray(), -1, -1, false);
var sequenceListFromPdbFile = proteinFileChains.ChainList.Select(pdbChain => Sequence.LoadStructureFile(atomsFilename, new[] { pdbChain.ChainId }, true, null, null, '-', '-')).ToList();
var dsspFromFastaFile = proteinFileChains.ChainList.Select(pdbChain => dsspList.FirstOrDefault(a => a.IdSplit.PdbId.ToUpperInvariant() == pdbId.Substring(0, a.IdSplit.PdbId.Length).ToUpperInvariant() && a.IdSplit.ChainId == pdbChain.ChainId)?.FullSequence).ToList();
var sequenceFromFastaFile = proteinFileChains.ChainList.Select(pdbChain => sequenceListFromFastaFile.FirstOrDefault(a => a.IdSplit.PdbId.ToUpperInvariant() == pdbId.Substring(0, a.IdSplit.PdbId.Length).ToUpperInvariant() && a.IdSplit.ChainId == pdbChain.ChainId)?.FullSequence).ToList();
var sequenceFromPdbFile = proteinFileChains.ChainList.Select((pdbChain, i) => sequenceListFromPdbFile[i].FirstOrDefault(a => (string.IsNullOrWhiteSpace(a.IdSplit.PdbId) || a.IdSplit.PdbId.ToUpperInvariant() == pdbId.Substring(0, a.IdSplit.PdbId.Length).ToUpperInvariant()) && a.IdSplit.ChainId == pdbChain.ChainId)?.FullSequence).ToList();
var structureToSequenceAlignmentResult = proteinFileChains.ChainList.Select((pdbChain, i) => ProteinBioClass.StructureToSequenceAlignment.Align(pdbChain.AtomList, sequenceFromFastaFile[i], sequenceFromPdbFile[i])).ToList();
if (structureToSequenceAlignmentResult.Any(a => a == null))
{
return(null);
}
for (var chainIndex3 = 0; chainIndex3 < proteinFileChains.ChainList.Count; chainIndex3++)
{
for (var i = 0; i < structureToSequenceAlignmentResult[chainIndex3].FastaSequenceAligned.Length; i++)
{
if (structureToSequenceAlignmentResult[chainIndex3].FastaSequenceAligned[i] == '-')
{
dsspFromFastaFile[chainIndex3] = dsspFromFastaFile[chainIndex3].Insert(i, "-");
}
}
}
foreach (var contactChainId1 in contactChainIds)
{
var chainIndex1 = proteinFileChains.ChainList.FindIndex(g => g.ChainId == contactChainId1);
if (structureToSequenceAlignmentResult[chainIndex1] == null)
{
continue;
}
if (string.IsNullOrWhiteSpace(sequenceFromPdbFile[chainIndex1]) || string.IsNullOrWhiteSpace(sequenceFromFastaFile[chainIndex1]) || string.IsNullOrWhiteSpace(dsspFromFastaFile[chainIndex1]))
{
continue;
}
var chainResult = new List <InterfaceFragment>();
//var pdbChain = proteinFileChains.ChainList.First(a => a.ChainId == contactChainId).AtomList;
var chainContacts = contacts.Where(a => a.Atom1.chainID.FieldValue[0] == contactChainId1 || a.Atom2.chainID.FieldValue[0] == contactChainId1).Select(a => a.Atom1.chainID.FieldValue[0] == contactChainId1 ? a : a.SwapAtoms()).ToList();
//chainContacts = chainContacts.GroupBy(a => int.Parse(a.resSeq.FieldValue)).ToList().Select(a => a.First()).ToList();
//chainContacts = chainContacts.Distinct().ToList();
chainContacts = chainContacts.OrderBy(a => int.Parse(a.Atom1.resSeq.FieldValue)).ThenBy(a => int.Parse(a.Atom1.serial.FieldValue)).ToList();
foreach (var atomPair in chainContacts)
{
foreach (var requiredInterfaceLength in requiredInterfaceLengths)
{
var contactChainId2 = atomPair.Atom2.chainID.FieldValue[0];
var chainIndex2 = proteinFileChains.ChainList.FindIndex(g => g.ChainId == contactChainId2);
if (structureToSequenceAlignmentResult[chainIndex2] == null)
{
continue;
}
if (string.IsNullOrWhiteSpace(sequenceFromPdbFile[chainIndex2]) || string.IsNullOrWhiteSpace(sequenceFromFastaFile[chainIndex2]) || string.IsNullOrWhiteSpace(dsspFromFastaFile[chainIndex2]))
{
continue;
}
var interfaceLength1 = requiredInterfaceLength;
var interfaceLength2 = requiredInterfaceLength;
var resSeq1 = int.Parse(atomPair.Atom1.resSeq.FieldValue);
var resSeq2 = int.Parse(atomPair.Atom2.resSeq.FieldValue);
var resSeqIndex1a = structureToSequenceAlignmentResult[chainIndex1].AlignmentMap.ToList().FindIndex(a => a == resSeq1);
var resSeqIndex2a = structureToSequenceAlignmentResult[chainIndex2].AlignmentMap.ToList().FindIndex(a => a == resSeq2);
if (structureToSequenceAlignmentResult[chainIndex1].FastaSequenceAligned.Length < interfaceLength1)
{
interfaceLength1 = structureToSequenceAlignmentResult[chainIndex1].FastaSequenceAligned.Length;
}
if (structureToSequenceAlignmentResult[chainIndex2].FastaSequenceAligned.Length < interfaceLength2)
{
interfaceLength2 = structureToSequenceAlignmentResult[chainIndex2].FastaSequenceAligned.Length;
}
var resSeqIndex1 = resSeqIndex1a - (interfaceLength1 / 2);
var resSeqIndex2 = resSeqIndex2a - (interfaceLength2 / 2);
if (resSeqIndex1 < 0)
{
resSeqIndex1 = 0;
}
if (resSeqIndex2 < 0)
{
resSeqIndex2 = 0;
}
if (resSeqIndex1 + interfaceLength1 > structureToSequenceAlignmentResult[chainIndex1].FastaSequenceAligned.Length)
{
resSeqIndex1 = (structureToSequenceAlignmentResult[chainIndex1].FastaSequenceAligned.Length - interfaceLength1);
}
if (resSeqIndex2 + interfaceLength2 > structureToSequenceAlignmentResult[chainIndex2].FastaSequenceAligned.Length)
{
resSeqIndex2 = (structureToSequenceAlignmentResult[chainIndex2].FastaSequenceAligned.Length - interfaceLength2);
}
var interfaceSuper1 = structureToSequenceAlignmentResult[chainIndex1].FastaSequenceAligned.Substring(resSeqIndex1, interfaceLength1);
var interfaceSuper2 = structureToSequenceAlignmentResult[chainIndex2].FastaSequenceAligned.Substring(resSeqIndex2, interfaceLength2);
var dsspSuper1 = dsspFromFastaFile[chainIndex1].Substring(resSeqIndex1, interfaceLength1);
var dsspSuper2 = dsspFromFastaFile[chainIndex2].Substring(resSeqIndex2, interfaceLength2);
if (interfaceSuper1.Length != requiredInterfaceLength || dsspSuper1.Length != requiredInterfaceLength)
{
continue;
}
if (interfaceSuper2.Length != requiredInterfaceLength || dsspSuper2.Length != requiredInterfaceLength)
{
continue;
}
var interfaceFragment = new InterfaceFragment()
{
FragmentLength = requiredInterfaceLength,
PdbId = pdbId,
ReceptorChainId = contactChainId1,
ReceptorResSeq = resSeq1,
ReceptorIndex = resSeqIndex1a,
ReceptorAminoAcidSequence = interfaceSuper1,
ReceptorSecondaryStructure = dsspSuper1,
LigandChainId = contactChainId2,
LigandResSeq = resSeq2,
LigandIndex = resSeqIndex2a,
LigandAminoAcidSequence = interfaceSuper2,
LigandSecondaryStructure = dsspSuper2
};
chainResult.Add(interfaceFragment);
}
}
pdbResult.AddRange(chainResult);
}
InterfaceFragment.Save(interfaceCsv, pdbResult.Distinct().ToList());
return(null); // return pdbResult;
}));
//result.AddRange(pdbResult);
}
//try
//{
Task.WaitAll(taskList1.ToArray <Task>());
//}
//catch (AggregateException ae)
//{
// throw ae.Flatten();
//}
ifList = taskList1.Where(a => a.Result != null).SelectMany(a => a.Result).ToList();
ifList = ifList.Distinct().ToList();
InterfaceFragment.Save(@"c:\r\if.csv", ifList);
}
var pairs1 = ifList.Select(a => new Tuple <string, string>(a.ReceptorAminoAcidSequence, a.ReceptorSecondaryStructure)).Distinct().ToList();
sequenceFilename = null;
dsspFilename = null;
sequenceListFromFastaFile.Clear(); sequenceListFromFastaFile = null;
dsspList.Clear(); dsspList = null;
pdbFiles.Clear(); pdbFiles = null;
pdbFileLengths.Clear(); pdbFileLengths = null;
//ifList.Clear(); ifList = null;
var similarAA = new string[] { "LAGVIP", "DE", "ST", "RKH", "FYW", "NQ", "CM", "BJOUXZ", "-" };
var simAaList = similarAA.SelectMany(a => a.ToList()).ToList();
var simAaDict = new Dictionary <char, string>();
foreach (var s in simAaList)
{
simAaDict.Add(s, similarAA.First(a => a.Contains(s)));
}
DateTime startTime = DateTime.Now;
var simList = new List <Tuple <string, string, string, string, decimal, decimal, decimal> >(); // aa, ss, aa-sim, aa-evo-sim, ss-sim
// compare without alignments, as aligments takes too long, also allow for insertion/deletions with index pos -1/+1.
for (int i = 0; i < pairs1.Count; i++)
{
TimeSpan timeRemaining = TimeSpan.FromTicks(DateTime.Now.Subtract(startTime).Ticks *(pairs1.Count - (i + 1)) / (i + 1));
Console.WriteLine((i + 1) + " / " + pairs1.Count + " " + timeRemaining.ToString("d'd 'h'h 'm'm 's's'"));
var a = pairs1[i];
for (int j = 0; j < pairs1.Count; j++)
{
if (j <= i)
{
continue;
}
var b = pairs1[j];
if (a.Item1.Length != b.Item1.Length)
{
continue;
}
var scoreAa = 0;
var scoreSs = 0;
var scoreAaEvo = 0;
for (var x = 0; x < a.Item1.Length; x++)
{
if (a.Item1[x] == b.Item1[x])
{
scoreAa++;
}
else if (x > 0 && (a.Item1[x - 1] == b.Item1[x] || a.Item1[x] == b.Item1[x - 1]))
{
scoreAa++;
}
else if (x < a.Item1.Length - 1 && (a.Item1[x + 1] == b.Item1[x] || a.Item1[x] == b.Item1[x + 1]))
{
scoreAa++;
}
if (simAaDict[a.Item1[x]].Contains(b.Item1[x]))
{
scoreAaEvo++;
}
else if (x > 0 && (simAaDict[a.Item1[x - 1]].Contains(b.Item1[x]) || simAaDict[a.Item1[x]].Contains(b.Item1[x - 1])))
{
scoreAaEvo++;
}
else if (x < a.Item1.Length - 1 && (simAaDict[a.Item1[x + 1]].Contains(b.Item1[x]) || simAaDict[a.Item1[x]].Contains(b.Item1[x + 1])))
{
scoreAaEvo++;
}
if (a.Item2[x] == b.Item2[x])
{
scoreSs++;
}
else if (x > 0 && (a.Item2[x - 1] == b.Item2[x] || a.Item2[x] == b.Item2[x - 1]))
{
scoreSs++;
}
else if (x < a.Item2.Length - 1 && (a.Item2[x + 1] == b.Item2[x] || a.Item2[x] == b.Item2[x + 1]))
{
scoreSs++;
}
}
decimal scoreAaPct = (decimal)scoreAa / (decimal)a.Item1.Length;
decimal scoreAaEvoPct = (decimal)scoreAaEvo / (decimal)a.Item1.Length;
decimal scoreSsPct = (decimal)scoreSs / (decimal)a.Item2.Length;
simList.Add(new Tuple <string, string, string, string, decimal, decimal, decimal>(a.Item1, a.Item2, b.Item1, b.Item2, scoreAaPct, scoreAaEvoPct, scoreSsPct));
//simList.Add(new Tuple<string, string, string, string, decimal, decimal, decimal>(b.AminoAcidSequence, b.SecondaryStructure, a.AminoAcidSequence, a.SecondaryStructure, scoreAaPct, scoreAaEvoPct, scoreSsPct));
}
}
//var if2 = simList.SelectMany(a => new List<string>() { string.Join(",", new string[] { a.Item1, a.Item2, a.Item3, a.Item4, "" + a.Item5, "" + a.Item6, "" + a.Item7 }) /*,
// string.Join(",", new string[] { a.Item3, a.Item4, a.Item1, a.Item2, "" + a.Item5, "" + a.Item6, "" + a.Item7 })*/ }).ToList();
var taskList3 = new List <Task>();
for (int i = 0; i < pairs1.Count; i++)
{
TimeSpan timeRemaining = TimeSpan.FromTicks(DateTime.Now.Subtract(startTime).Ticks *(pairs1.Count - (i + 1)) / (i + 1));
Console.WriteLine((i + 1) + " / " + pairs1.Count + " " + timeRemaining.ToString("d'd 'h'h 'm'm 's's'"));
while (taskList3.Count(a => !a.IsCompleted) >= Environment.ProcessorCount)
{
Task.WaitAny(taskList3.Where(a => !a.IsCompleted).ToArray <Task>());
}
var i1 = i;
var t = Task.Run(() =>
{
var a = pairs1[i1];
// find all instances of this pair with good simple alignment
var cluster = simList.Where(c => (c.Item1 == a.Item1 || c.Item3 == a.Item1) && (c.Item2 == a.Item2 || c.Item4 == a.Item2) && (c.Item5 >= 0.4m && c.Item6 >= 0.8m && c.Item7 >= 0.9m) && (c.Item5 < 1.0m /*&& c.Item6 < 1.0m && c.Item7 < 1.0m*/)).ToList();
if (cluster.Count < 5)
{
return;
}
var clusterPdbs = ifList.Where(c => cluster.Any(d => (d.Item1 == c.ReceptorAminoAcidSequence || d.Item3 == c.ReceptorAminoAcidSequence) && (d.Item2 == c.ReceptorSecondaryStructure || d.Item4 == c.ReceptorSecondaryStructure))).Select(e => new Tuple <string, char>(e.PdbId, e.ReceptorChainId)).ToList();
if (clusterPdbs.Count < 5)
{
return;
}
List <string> o = new List <string>();
o.Add("delete *");
o.AddRange(clusterPdbs.Select(e => @"load c:\pdbe\" + e.Item1 + ".pdb").ToList());
o.Add("hide all");
o.Add("show cartoon");
o.AddRange(clusterPdbs.Select((e, w) => w == 0 ? "" : @"super /" + e.Item1 + @"//" + e.Item2 + @", /" + clusterPdbs[0].Item1 + @"//" + clusterPdbs[0].Item2).ToList());
File.WriteAllLines(@"c:\r\cluster_" + (i1 + 1) + ".txt", o);
});
taskList3.Add(t);
}
Task.WaitAll(taskList3.ToArray <Task>());
//File.WriteAllLines(@"c:\r\if2.csv", if2);
Console.WriteLine("Calculating aa/ss sequence identities - part 1");
var taskList2 = new List <Task <InterfaceFragmentData> >();
//var interfaceFragmentLengths = new int[] { 15, 13, 11, 9, 7, 5, 3 };
//var interfaceFragmentLengths = new int[] { requiredInterfaceLengths[0] };
var interfaceFragmentLengths = new int[] { 11 };
for (int index = 0; index < interfaceFragmentLengths.Length; index++)
{
var index1 = index;
var interfaceFragmentLength = interfaceFragmentLengths[index1];
taskList2.Add(Task.Run(() =>
{
var pairs = ifList.Where(a => a.FragmentLength == interfaceFragmentLength).Select(a => new Tuple <string, string>(a.ReceptorAminoAcidSequence.Substring(index1, interfaceFragmentLength), a.ReceptorSecondaryStructure.Substring(index1, interfaceFragmentLength))).Distinct().ToList();
var aassList = new List <Tuple <string, string, string, string, decimal, decimal, decimal> >();
var aaSequenceList = pairs.Select(a => a.Item1).Distinct().ToList();
var aaAlignmentList = Align(aaSequenceList);
var ssSequenceList = pairs.Select(a => a.Item2).Distinct().ToList();
var ssAlignmentList = Align(ssSequenceList);
for (int i = 0; i < pairs.Count; i++)
{
Console.WriteLine((i + 1) + " / " + pairs.Count);
var pair1 = pairs[i];
for (int j = 0; j < pairs.Count; j++)
{
if (j < i)
{
continue;
}
var pair2 = pairs[j];
var aaSid = aaAlignmentList.First(alignment => alignment.Item1 == pair1.Item1 && alignment.Item2 == pair2.Item1).Item3;
var ssSid = ssAlignmentList.First(alignment => alignment.Item1 == pair1.Item2 && alignment.Item2 == pair2.Item2).Item3;
var weighted = (aaSid * 0.5m) + (ssSid * 0.5m);
aassList.Add(new Tuple <string, string, string, string, decimal, decimal, decimal>(pair1.Item1, pair1.Item2, pair2.Item1, pair2.Item2, aaSid, ssSid, weighted));
aassList.Add(new Tuple <string, string, string, string, decimal, decimal, decimal>(pair2.Item1, pair2.Item2, pair1.Item1, pair1.Item2, aaSid, ssSid, weighted));
}
}
var r = new InterfaceFragmentData();
r.AaSsData = aassList;
r.AaData = aaAlignmentList;
r.SsData = ssAlignmentList;
return(r);
}));
}
Task.WaitAll(taskList2.ToArray <Task>());
Console.WriteLine("Calculating aa/ss sequence identities - part 2");
var sids = new decimal[] { 1.0m, 0.9m, 0.8m, 0.7m, 0.6m, 0.5m, 0.4m, 0.3m, 0.2m, 0.1m, 0.0m };
//aa count non-transivity clusters
var aaData = taskList2.SelectMany(a => a.Result.AaData).ToList();
var aaDistinct = aaData.Select(a => a.Item1).Distinct().ToList();
var aaNeighbours = new List <Tuple <string, decimal, decimal> >();
foreach (var aa in aaDistinct)
{
var subset = aaData.Where(a => a.Item1 == aa).ToList();
foreach (var sid in sids)
{
aaNeighbours.Add(new Tuple <string, decimal, decimal>(aa, sid, subset.Count(b => b.Item3 >= sid)));
}
}
File.WriteAllLines(@"c:\r\aa.csv", aaData.Select(a => string.Join(",", new string[] { "" + a.Item1.Length, a.Item1, a.Item2, "" + a.Item3 })));
File.WriteAllLines(@"c:\r\aa-clusters-1.csv", aaDistinct.Select(a => a + "," + string.Join(",", aaNeighbours.Where(d => d.Item1 == a).Select(d => "" + d.Item3).ToArray())));
//ss count non-transivity clusters
var ssData = taskList2.SelectMany(a => a.Result.SsData).ToList();
var ssDistinct = ssData.Select(a => a.Item1).Distinct().ToList();
var ssNeighbours = new List <Tuple <string, decimal, decimal> >();
foreach (var ss in ssDistinct)
{
var subset = ssData.Where(a => a.Item1 == ss).ToList();
foreach (var sid in sids)
{
ssNeighbours.Add(new Tuple <string, decimal, decimal>(ss, sid, subset.Count(b => b.Item3 >= sid)));
}
}
File.WriteAllLines(@"c:\r\ss.csv", ssData.Select(a => string.Join(",", new string[] { "" + a.Item1.Length, a.Item1, a.Item2, "" + a.Item3 })));
File.WriteAllLines(@"c:\r\ss-clusters-1.csv", ssDistinct.Select(a => a + "," + string.Join(",", ssNeighbours.Where(d => d.Item1 == a).Select(d => "" + d.Item3).ToList())));
//aa-ss count non-transivity clusters
var aaSsData = taskList2.SelectMany(a => a.Result.AaSsData).ToList();
var aaSsDistinct = aaSsData.Select(a => new Tuple <string, string>(a.Item1, a.Item2)).Distinct().ToList();
var aaSsNeighbours = new List <Tuple <string, string, decimal, decimal> >();
foreach (var aaSs in aaSsDistinct)
{
var subset = aaSsData.Where(a => a.Item1 == aaSs.Item1 && a.Item2 == aaSs.Item2).ToList();
foreach (var sid in sids)
{
aaSsNeighbours.Add(new Tuple <string, string, decimal, decimal>(aaSs.Item1, aaSs.Item2, sid, subset.Count(b => b.Item5 >= sid)));
}
}
File.WriteAllLines(@"c:\r\aa-ss.csv", aaSsData.Select(a => string.Join(",", new string[] { "" + a.Item1.Length, a.Item1, a.Item2, a.Item3, a.Item4, "" + a.Item5, "" + a.Item6, "" + a.Item7 })));
File.WriteAllLines(@"c:\r\aa-ss-clusters-1.csv", aaSsDistinct.Select(a => a.Item1 + "," + a.Item2 + "," + string.Join(",", aaSsNeighbours.Where(d => d.Item1 == a.Item1 && d.Item2 == a.Item2).Select(d => "" + d.Item4).ToList())));
// cluster by transivity
//var aaSsPairList = aaSsData.Select(a => new Tuple<string, string>(a.Item1, a.Item2)).Distinct().ToList();
var aaSsPairClusters = aaSsData.Select(a => new Tuple <string, string>(a.Item1, a.Item2)).Distinct().Select(a => new List <Tuple <string, string> >()
{
a
}).ToList();
var aaClusters = aaSsData.Select(a => a.Item1).Distinct().Select(a => new List <string>()
{
a
}).ToList();
var ssClusters = aaSsData.Select(a => a.Item2).Distinct().Select(a => new List <string>()
{
a
}).ToList();
decimal minTransivitySid = 0.3m;
foreach (var x in aaSsDistinct)
{
foreach (var y in aaSsDistinct)
{
if (x == y)
{
continue;
}
if (x.Item1.Length != y.Item1.Length)
{
continue; //items have not been sequence aligned if not the same length
}
var z = aaSsData.First(a => a.Item1 == x.Item1 && a.Item2 == x.Item2 && a.Item3 == y.Item1 && a.Item4 == y.Item2);
if (z.Item5 >= minTransivitySid)
{
var c1 = aaClusters.First(a => a.Any(b => b == x.Item1));
var c2 = aaClusters.First(a => a.Any(b => b == y.Item1));
if (c1 != c2)
{
c1.AddRange(c2);
aaClusters.Remove(c2);
}
}
if (z.Item6 >= minTransivitySid)
{
var c1 = ssClusters.First(a => a.Any(b => b == x.Item2));
var c2 = ssClusters.First(a => a.Any(b => b == y.Item2));
if (c1 != c2)
{
c1.AddRange(c2);
ssClusters.Remove(c2);
}
}
if (z.Item7 >= minTransivitySid)
{
var c1 = aaSsPairClusters.First(a => a.Any(b => b.Item1 == x.Item1 && b.Item2 == x.Item2));
var c2 = aaSsPairClusters.First(a => a.Any(b => b.Item1 == y.Item1 && b.Item2 == y.Item2));
if (c1 != c2)
{
c1.AddRange(c2);
aaSsPairClusters.Remove(c2);
}
}
}
}
var aaSsPairClusters2 = aaSsPairClusters.SelectMany((a, i) => a.Select(b => new Tuple <int, string, string>(i + 1, b.Item1, b.Item2))).ToList();
aaSsPairClusters2 = aaSsPairClusters2.OrderByDescending(a => aaSsPairClusters2.Count(b => b.Item1 == a.Item1)).ToList();
File.WriteAllLines(@"c:\r\aa-ss-clusters-2.csv", aaSsPairClusters2.Select(a => string.Join(",", new string[] { "" + a.Item1, a.Item2, a.Item3 })));
var aaClusters2 = aaClusters.SelectMany((a, i) => a.Select(b => new Tuple <int, string>(i + 1, b))).ToList();
aaClusters2 = aaClusters2.OrderByDescending(a => aaClusters2.Count(b => b.Item1 == a.Item1)).ToList();
File.WriteAllLines(@"c:\r\aa-clusters-2.csv", aaClusters2.Select(a => string.Join(",", new string[] { "" + a.Item1, a.Item2 })));
var ssClusters2 = ssClusters.SelectMany((a, i) => a.Select(b => new Tuple <int, string>(i + 1, b))).ToList();
ssClusters2 = ssClusters2.OrderByDescending(a => ssClusters2.Count(b => b.Item1 == a.Item1)).ToList();
File.WriteAllLines(@"c:\r\ss-clusters-2.csv", ssClusters2.Select(a => string.Join(",", new string[] { "" + a.Item1, a.Item2 })));
//File.WriteAllLines(@"c:\r\clusters-ss.csv", ssClusters2.Select(a => string.Join(",", new string[] { "" + a.Item1, a.Item2 })));
// clusters by aa sid, ss sid, aa-ss sid
}
private static void Main(string[] args)
{
// this program will load the homolog list in csv format and for homologs of X sequence distance return a list of all partners
// however, some partners may be duplicates, which cannot initially be removed, since they may bind differently in other instances
// then, because of such cases, unique id to describe each protein must be created... this is slightly problematic because
// close target homologs of proteins are also considered to be the same protein as the query protein
// which means that they could exist for more than one query protein
// FindHomologsCluster.exe c:\pdb\ds96ub_homologs\ c:\pdb\pdb_seqres.fasta 0.9 0.9 > ds96ub_homologs.csv
var homolog_csv_folder = args[0];
var sequence_file = args[1];
var min_similarity_str = args[2];
var min_similarity_evo_str = args[3];
var min_similarity = decimal.Parse(min_similarity_str);
var min_similarity_evo = decimal.Parse(min_similarity_evo_str);
var seqList = Sequence.LoadSequenceFile(sequence_file, new[] { null, "", "protein" });
var homologCsvFiles = Directory.GetFiles(homolog_csv_folder, "homologs_?????.csv");
var parsedData = FindHomologs.FindHomologs.HomologChain.Load(homologCsvFiles);
Array.Clear(homologCsvFiles, 0, homologCsvFiles.Length);
//var query_pdb_list = parsed_data.Select(a => new Tuple<string, string>(a.query_pdb_id, a.query_chainid)).ToList();
//var target_pdb_list = parsed_data.Select(a => new Tuple<string, string>(a.target_pdb_id, a.target_chainid)).ToList();
//var query_alignments = new List<homolog_csv>();
var homologs_clustered = new List <List <Tuple <string, char> > >();
//var min_similarity = 0.9m;
foreach (var rec in parsedData)
{
if (rec.AlignmentScore >= min_similarity && rec.AlignmentScoreEvo >= min_similarity_evo)
{
//var query_group = homologs_clustered.FirstOrDefault(a => a.FirstOrDefault(b => b.Item1 == rec.query_pdb_id && b.Item2 == rec.query_chainid) != null);
//var target_group = homologs_clustered.FirstOrDefault(a => a.FirstOrDefault(b => b.Item1 == rec.target_pdb_id && b.Item2 == rec.target_chainid) != null);
List <Tuple <string, char> > query_group = null;
List <Tuple <string, char> > target_group = null;
foreach (var cluster in homologs_clustered)
{
var xq = cluster.FirstOrDefault(b => b.Item1.ToUpperInvariant() == rec.QueryPdbId.ToUpperInvariant() && b.Item2 == rec.QueryChainId);
if (xq == null)
{
continue;
}
query_group = cluster;
break;
}
foreach (var cluster in homologs_clustered)
{
var xt =
cluster.FirstOrDefault(b => b.Item1.ToUpperInvariant() == rec.TargetPdbId.ToUpperInvariant() && b.Item2 == rec.TargetChainId);
if (xt == null)
{
continue;
}
target_group = cluster;
break;
}
var new_group = new List <Tuple <string, char> >();
if (query_group != null)
{
new_group.AddRange(query_group);
homologs_clustered.Remove(query_group);
query_group.Clear();
}
else
{
new_group.Add(new Tuple <string, char>(rec.QueryPdbId, rec.QueryChainId));
}
if (target_group != null)
{
new_group.AddRange(target_group);
homologs_clustered.Remove(target_group);
target_group.Clear();
}
else
{
new_group.Add(new Tuple <string, char>(rec.TargetPdbId, rec.TargetChainId));
}
new_group = new_group.Distinct().ToList(); // try without distinct?
new_group = new_group.OrderBy(a => a.Item1).ThenBy(a => a.Item2).ToList();
homologs_clustered.Add(new_group);
}
}
var seq_list_ids = seqList.Select(a => new ProteinBioClass.SequenceId(a.Id)).ToList();
var wd2 = new WorkDivision(homologs_clustered.Count);
for (var thread2 = 0; thread2 < wd2.ThreadCount; thread2++)
{
var lti2 = thread2;
wd2.TaskList.Add(Task.Run(() =>
{
var result2 = new List <string>();
for (var index2 = wd2.ThreadFirstIndex[lti2]; index2 <= wd2.ThreadLastIndex[lti2]; index2++)
{
var cluster2 = homologs_clustered[index2];
var wd3 = new WorkDivision(cluster2.Count);
for (var thread3 = 0; thread3 < wd3.ThreadCount; thread3++)
{
var lti3 = thread3;
var cluster3 = cluster2;
var index4 = index2;
wd3.TaskList.Add(Task.Run(() =>
{
var result = new List <HomologClusterData>();
for (var index3 = wd3.ThreadFirstIndex[lti3]; index3 <= wd3.ThreadLastIndex[lti3]; index3++)
{
var item = cluster3[index3];
Sequence s = null;
for (var j = 0; j < seqList.Count; j++)
{
if (seq_list_ids[j].PdbId.ToUpperInvariant() == item.Item1.ToUpperInvariant() && seq_list_ids[j].ChainId == item.Item2)
{
s = seqList[j];
break;
}
}
if (s == null)
{
throw new Exception("sequence not found for " + item.Item1 + ":" + item.Item2);
}
var complexChains = seq_list_ids.Count(a => a.PdbId.ToUpperInvariant() == item.Item1.ToUpperInvariant());
var minAlignmentScore = -1m;
var maxAlignmentScore = -1m;
var minAlignmentScoreEvo = -1m;
var maxAlignmentScoreEvo = -1m;
foreach (var item2 in cluster3)
{
if (ReferenceEquals(item, item2))
{
continue;
}
Sequence s2 = null;
for (var j2 = 0; j2 < seqList.Count; j2++)
{
if (seq_list_ids[j2].PdbId.ToUpperInvariant() == item2.Item1.ToUpperInvariant() &&
seq_list_ids[j2].ChainId == item2.Item2)
{
s2 = seqList[j2];
break;
}
}
if (s2 == null)
{
continue;
}
var alignmentScore = ProteinBioClass.AlignedSequenceSimilarityPercentage(s,
s2,
ProteinBioClass.AlignmentType.NMW);
if (alignmentScore.Score > maxAlignmentScore || maxAlignmentScore == -1m)
{
maxAlignmentScore = alignmentScore.Score;
}
if (alignmentScore.Score < minAlignmentScore || minAlignmentScore == -1m)
{
minAlignmentScore = alignmentScore.Score;
}
if (alignmentScore.ScoreEvo > maxAlignmentScoreEvo || maxAlignmentScoreEvo == -1m)
{
maxAlignmentScoreEvo = alignmentScore.ScoreEvo;
}
if (alignmentScore.ScoreEvo < minAlignmentScoreEvo || minAlignmentScoreEvo == -1m)
{
minAlignmentScoreEvo = alignmentScore.ScoreEvo;
}
}
var r = new HomologClusterData(index4 + 1, index3 + 1, item.Item1, item.Item2, complexChains, Convert.ToInt32(s.Count()), minAlignmentScore, maxAlignmentScore, minAlignmentScoreEvo, maxAlignmentScoreEvo, s.FullSequence);
result.Add(r);
}
return(result);
}));
}
wd3.WaitAllTasks();
result2.Add("; Cluster # " + (index2 + 1) + " with " + wd3.ItemsToProcess + " protein chains");
result2.Add("cluster index,item index,pdb id,chain id,complex chains,seq len,min clstr sid,max clstr sid,min evo clstr sid,max evo clstr sid,sequence");
foreach (var task in wd3.TaskList)
{
//if (task.IsFaulted || task.IsCanceled) continue;
var tr = task as Task <List <HomologClusterData> >;
if (tr == null || tr.Result == null)
{
continue;
}
result2.AddRange(tr.Result.Select(a => a.ToString()).ToList());
}
result2.Add("");
}
return(result2);
}));
//wd2.TaskList.Add(task2);
}
wd2.WaitAllTasks();
var result1 = new List <string>();
foreach (var task in wd2.TaskList)
{
//if (task.IsFaulted || task.IsCanceled) continue;
var tr = task as Task <List <string> >;
if (tr == null || tr.Result == null)
{
continue;
}
result1.AddRange(tr.Result);
}
foreach (var line in result1)
{
Console.WriteLine(line);
}
// partners may have other interfaces, should those also be considered?
}
public static void Main(string[] args)
{
//var logResultsFolder = @"c:\r\r\";
//var logResultsFolder = @"c:\r-some modelled\";
//var logResultsFolder = @"c:\r\" ; //args[0];
//var saveFile = args[1];
//var logResultsFolder = @"c:\pdbe_split\models\" ; //args[0];
//var logResultsFolder = @"C:\pdbe_split\manual\sw_1SBNI_2SICI_4GI3C\"; //args[0];
//var logResultsFolder = @"C:\pdbe_split\manual\sw_1OYVI_1R0RI_1SBNI_1V5IB_2SICI_3BX1C_4GI3C_4LVNP\"; //args[0];
var logResultsFolder = @"C:\pdbe_split\manual\sw_3BX1C\"; //args[0];
//C:\pdbe_split\manual\sw_1H1VG_1KXPD_1RGIG_1T44G_3JBIV_4EAHA_4PKHB_5AFUb
var seq = ProteinBioinformaticsSharedLibrary.Sequence.LoadSequenceFile(logResultsFolder + "sequences.fasta");
var inf = ProteinBioinformaticsSharedLibrary.Sequence.LoadSequenceFile(logResultsFolder + "interfaces_fixed_length.fasta");
foreach (var s1 in seq)
{
var r = new List <Tuple <string, ProteinBioClass.AlignmentScore> >();
foreach (var s2 in seq)
{
//if (s1==s2) continue;
var nmw = new NeedlemanWunsch(s1.FullSequence, s2.FullSequence);
var a = nmw.getAlignment();
ProteinBioClass.AlignmentScore s = ProteinBioClass.SequenceSimilarityPercentage(a[0], a[1], ProteinBioClass.AlignmentIdentityOption.MinimumSequenceLength);
//r.Add(s1.Id.Substring(1, 5) + " " + s2.Id.Substring(1, 5) + " " + s.Score + " " + s.ScoreEvo);
r.Add(new Tuple <string, ProteinBioClass.AlignmentScore>(s1.Id.Substring(1, 5) + "," + s2.Id.Substring(1, 5), s));
}
r = r.OrderByDescending(a => a.Item2.Score).ThenByDescending(a => a.Item2.ScoreEvo).ToList();
var e = r.Select(a => a.Item1 + "," + string.Format("{0:0.00}", Math.Round(a.Item2.Score, 2)) + "," + string.Format("{0:0.00}", Math.Round(a.Item2.ScoreEvo, 2))).ToList();
e.Insert(0, "Sequence Alignment");
e.Insert(1, "ID1,ID2,Match%,Physicochemical%");
e = e.Select(a => a.Replace(",", "\t")).ToList();
File.WriteAllLines(logResultsFolder + "score_all_" + s1.Id.Substring(1, 5) + ".txt", e);
}
foreach (var s1 in inf)
{
var r = new List <Tuple <string, ProteinBioClass.AlignmentScore> >();
foreach (var s2 in inf)
{
//if (s1==s2) continue;
var nmw = new NeedlemanWunsch(s1.FullSequence, s2.FullSequence);
var a = nmw.getAlignment();
ProteinBioClass.AlignmentScore s = ProteinBioClass.SequenceSimilarityPercentage(a[0], a[1], ProteinBioClass.AlignmentIdentityOption.MinimumSequenceLength);
//r.Add(s1.Id.Substring(1, 5) + " " + s2.Id.Substring(1, 5) + " " + s.Score + " " + s.ScoreEvo);
r.Add(new Tuple <string, ProteinBioClass.AlignmentScore>(s1.Id.Substring(1, 5) + "," + s2.Id.Substring(1, 5), s));
}
r = r.OrderByDescending(a => a.Item2.Score).ThenByDescending(a => a.Item2.ScoreEvo).ToList();
var e = r.Select(a => a.Item1 + "," + string.Format("{0:0.00}", Math.Round(a.Item2.Score, 2)) + "," + string.Format("{0:0.00}", Math.Round(a.Item2.ScoreEvo, 2))).ToList();
e.Insert(0, "Interface Alignment");
e.Insert(1, "ID1,ID2,Match%,Physicochemical%");
e.Insert(0, "");
e = e.Select(a => a.Replace(",", "\t")).ToList();
File.AppendAllLines(logResultsFolder + "score_all_" + s1.Id.Substring(1, 5) + ".txt", e);
}
//return;
//r-some modelled
//var pdbFileNames = Directory.GetFiles(logResultsFolder, "*.pdb", SearchOption.AllDirectories).Select(a=>Path.GetFileName(a).ToLowerInvariant()).Distinct().ToList();
var modellerLogFiles = Directory.GetFiles(logResultsFolder, "modeller_monomer_assessment.log", SearchOption.AllDirectories).ToList();
//modellerLogFiles = modellerLogFiles.Where(a => a.StartsWith(logResultsFolder + @"sw2\")).ToList();
//var dimerModellerLogFiles = Directory.GetFiles(logResultsFolder, "modeller_dimer_assessment.log", SearchOption.AllDirectories).ToList();
//var pisaLogFiles = Directory.GetFiles(logResultsFolder, "pisa_monomer_assessment.log", SearchOption.AllDirectories).ToList();
var data = new List <List <string> >();
var nats = new List <List <string> >();
var rowlen = 0;
var scores = modellerLogFiles.SelectMany(m => ParseModellerLog(m)).ToList();
foreach (var scoreGroup in scores.GroupBy(a =>
{
var structureFolderSplit = a.StructureFolder.Split('\\');
// \ -4 \ -3 \ -2 \ -1 \
// \sw_1OYVI_1R0RI_1SBNI_1V5IB_2SICI_3BX1C_4GI3C_4LVNP\1V5IB\1V5IB\all_0016_0026_1_1\
return(structureFolderSplit[structureFolderSplit.Length - 1].Substring(0, 3) + '_' + structureFolderSplit[structureFolderSplit.Length - 3] + '_' + structureFolderSplit[structureFolderSplit.Length - 2]);
}))
{
var group = scoreGroup.ToList();
group = group.OrderBy(a => a.StructureFolder).ToList();
var natives1 = group.Where(a => a.StructureFolder.Contains("_native")).ToList();
foreach (var n in natives1)
{
nats.Add(new List <string>()
{
"nat_" + scoreGroup.Key.Substring(4), n.ModellerDope
});
}
//data.Add(group.Select(a => a.ModellerDope).ToList());
if (!scoreGroup.Key.StartsWith("nat"))
{
// make index line
if (scoreGroup.Key.Substring(4, 5) == scoreGroup.Key.Substring(10, 5))
{
//data.Add(new List<string>());
data.Add(group.Select(a => a.StructureFolder.Split('\\').Last().Substring(4)).ToList());
rowlen = data[data.Count - 1].Count;
data[data.Count - 1].Insert(0, scoreGroup.Key + "_index");
}
}
data.Add(group.Select(a => a.ModellerDope).ToList());
data[data.Count - 1].Insert(0, scoreGroup.Key + "_energy");
}
var output = new List <string>();
var nats2 = nats.Select(a => string.Join(",", a)).Distinct().OrderBy(a => a[0]).ToList();
//nats = nats.Distinct().OrderBy(a => a[0]).ToList();
foreach (var g in data.GroupBy(a => a[0].Substring(0, 3 + 1 + 5)))
{
var gi = g.ToList();
var index = gi.First(a => a[0].Contains("_index"));
var len = index.Count - 1;
var main = gi.First(a => a != index && a[0].Substring(4, 5) == a[0].Substring(10, 5));
var others = gi.Where(a => a != index && a != main).OrderBy(a => a[0]).ToList();
var natives = nats2.Where(a => a.Substring(4, 5) == index[0].Substring(4, 5)).OrderBy(a => a[0]).ToList();
natives = natives.Select(a =>
{
var b = a.Split(',');
var r = b[0];
for (var j = 0; j < len; j++)
{
r = r + ',' + string.Join(",", b.Skip(1).ToList());
}
return(r);
}).ToList();
var nativemain = natives.First(a => a.Substring(4, 5) == a.Substring(10, 5));
natives.Remove(nativemain);
output.Add(string.Join(",", index));
output.Add(string.Join(",", main));
others.ForEach(a => output.Add(string.Join(",", a)));
output.Add(string.Join(",", nativemain));
natives.ForEach(a => output.Add(string.Join(",", a)));
output.Add("");
}
//var output = data.Select(a => string.Join(",", a))
// .Distinct()
// .OrderByDescending(a => a.Substring(4, 5))
// .ThenBy(a => a.Substring(0, 3))
// .ThenByDescending(a => a.Substring(4, 5) == a.Substring(10, 5))
// .ThenByDescending(a => a.Contains("_index"))
// .ToList();
//for (var j = output.Count - 1; j >= 0; j--)
//{
// if (output[j].Contains("_index"))
// output.Insert(j, "");
//}
File.WriteAllLines(logResultsFolder + Environment.MachineName + "_energy.csv", output);
}
static void Main(string[] args)
{
const int atom_chain = 21;
const int atom_chain_len = 1;
const int atom_icode = 26;
const int atom_icode_len = 1;
const int atom_type = 14;
const int atom_type_len = 3;
const int atom_resseq = 22;
const int atom_resseq_len = 4;
var parameters = new string[, ]
{
{ "[pdb_file]", "PDB ~v3.3 Protein Data Bank format file [*.pdb, *.ent]" },
{ "[[subset]]", "-, mc, sc, ca" },
{ "[[chain_ids]]", "molecule chains to output [2 formats: - for all, ABC, or A,1,50,B,2,40,C,5,200]" },
{ "[[output_file]]", "optional output file. use ? for chain id. when ommitted, output to console" },
};
var maxParamLength = parameters.Cast <string>().Where((a, i) => i % 2 == 0).Max(a => a.Length);
var exeFilename = Path.GetFileName(System.Diagnostics.Process.GetCurrentProcess().MainModule.FileName);
if (args.Length == 0)
{
Console.WriteLine(exeFilename + @" is a program to extract ATOM records from a PDB file.");
Console.WriteLine();
Console.WriteLine(@"Usage:");
Console.WriteLine(ProteinBioClass.WrapConsoleText(exeFilename + @" " + String.Join(" ", parameters.Cast <string>().Where((a, i) => i % 2 == 0)), maxParamLength + 2, 1));
Console.WriteLine();
Console.WriteLine(@"Example:");
Console.WriteLine(ProteinBioClass.WrapConsoleText(exeFilename + @" ""c:\pdb_db\pdb1a12.pdb"" 8.0 ""c:\pdb_atoms\atoms1a12.pdb""", maxParamLength + 2, 1));
Console.WriteLine();
Console.WriteLine(@"Arguments:");
for (var i = 0; i < parameters.GetLength(0); i++)
{
Console.WriteLine(@" " + parameters[i, 0].PadLeft(maxParamLength, ' ') + " " + ProteinBioClass.WrapConsoleText(parameters[i, 1], maxParamLength + 2, 1, false));
}
Console.WriteLine();
return;
}
// load and echo arguments
var p = 0;
var pdbFilename = args.Length > p && args[p].Length > 0 ? args[p] : "";
pdbFilename = pdbFilename.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + pdbFilename);
p++;
var subset = args.Length > p && args[p].Length > 0 ? args[p].ToUpperInvariant() : "";
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + subset);
p++;
var chainIds = args.Length > p && args[p].Length > 0 ? args[p] : "";
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + chainIds);
p++;
var outputFilename = args.Length > p && args[p].Length > 0 ? args[p] : "";
outputFilename = outputFilename.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + outputFilename);
Console.WriteLine();
if (string.IsNullOrWhiteSpace(pdbFilename))
{
return;
}
if (!File.Exists(pdbFilename))
{
return;
}
if (chainIds.Contains('-'))
{
chainIds = null;
}
var chainStartEnd = new List <Tuple <char, int, int> >();
var chainIdsSplit = chainIds?.Split(',').ToList();
char[] chainIdWhiteList;
if (chainIdsSplit?.Count > 1)
{
if (chainIdsSplit.Count % 3 != 0)
{
return;
}
for (var i = 0; i < chainIdsSplit.Count; i += 3)
{
var id = chainIdsSplit[i + 0][0];
var start = chainIdsSplit[i + 1];
if (string.IsNullOrWhiteSpace(start))
{
start = "-1";
}
var end = chainIdsSplit[i + 2];
if (string.IsNullOrWhiteSpace(end))
{
end = "-1";
}
chainStartEnd.Add(new Tuple <char, int, int>(id, int.Parse(start), int.Parse(end)));
}
chainIdWhiteList = chainStartEnd.Select(a => a.Item1).Distinct().ToArray();
}
else
{
chainIdWhiteList = chainIds?.Where(char.IsLetter).Distinct().ToArray();//!string.IsNullOrEmpty(chainIds) ? chainIds.ToUpperInvariant().Split(new char[] { ' ', ',' },StringSplitOptions.RemoveEmptyEntries) : null;
}
var terminatedChains = new List <char>();
var pdbfilenameShort = Path.GetFileNameWithoutExtension(pdbFilename);
var pdbId = pdbfilenameShort.Substring(pdbfilenameShort.Length - 4).ToUpperInvariant();
var lines = File.ReadAllLines(pdbFilename);
var result = new List <Tuple <char, string> >();
string[] ca = new string[] { "CA" };
string[] bb = new[] { "N", "CA", "C", "O" };
foreach (var line in lines)
{
if (line.Length < 22)
{
continue;
}
if (line.Substring(0, 4).ToUpperInvariant() == "TER ")
{
var chainId = line[21];//).ToUpperInvariant();
terminatedChains.Add(chainId);
}
if (line.Substring(0, 5).ToUpperInvariant() == "ATOM ")
{
var chainId = line[21];//).ToUpperInvariant();
if (terminatedChains.Contains(chainId))
{
continue;
}
if (chainIdWhiteList != null && chainIdWhiteList.Length > 0 && !chainIdWhiteList.Contains(chainId))
{
continue;
}
//if (subset == "ca" || subset == "sc") && (line[13] != 'C' || line[14] != 'A')) continue;
var add = false;
var atom_type_s = line.Substring(13, 3).Trim();
if (atom_type_s[0] != 'C' && atom_type_s[0] != 'N' && atom_type_s[0] != 'O')
{
continue;
}
// check chainIdsSplit
var resId = int.Parse(line.Substring(atom_resseq, atom_resseq_len));
var chainStartEndItem = chainStartEnd.FirstOrDefault(a => a.Item1 == chainId);
if (chainStartEndItem != null)
{
if (!((chainStartEndItem.Item2 == -1 || resId >= chainStartEndItem.Item2) && (chainStartEndItem.Item3 == -1 || resId <= chainStartEndItem.Item3)))
{
continue;
}
}
if (subset == "-")
{
add = true;
}
else if (subset == "CA" && ca.Contains(atom_type_s))
{
add = true;
}
else if (subset == "MC" && bb.Contains(atom_type_s))
{
add = true;
}
else if (subset == "SC" && !bb.Contains(atom_type_s))
{
add = true;
}
if (add)
{
result.Add(new Tuple <char, string>(chainId, line));
}
}
}
if (!string.IsNullOrWhiteSpace(outputFilename))
{
var outputFilename2 = outputFilename.Replace("?", "");
Directory.CreateDirectory(Path.GetDirectoryName(outputFilename2));
if (!outputFilename.Contains("?"))
{
File.WriteAllLines(outputFilename, result.Select(a => a.Item2).ToList());
}
else if (outputFilename.Contains("??"))
{
var chains = new string(result.Select(a => a.Item1).Where(char.IsLetter).Distinct().OrderBy(a => a).ToArray());
outputFilename2 = Path.GetDirectoryName(outputFilename2) + @"\" + Path.GetFileNameWithoutExtension(outputFilename2) + chains + Path.GetExtension(outputFilename2);
File.WriteAllLines(outputFilename2, result.Select(a => a.Item2).ToList());
}
else if (outputFilename.Contains("?"))
{
var chains = result.Select(a => a.Item1).Distinct().ToList();
foreach (var chain in chains)
{
outputFilename2 = outputFilename.Replace("?", "");
outputFilename2 = Path.GetDirectoryName(outputFilename2) + @"\" + Path.GetFileNameWithoutExtension(outputFilename2) + chain + Path.GetExtension(outputFilename2);
File.WriteAllLines(outputFilename2, result.Where(a => a.Item1 == chain).Select(a => a.Item2).ToList());
}
}
}
else
{
foreach (var line in result)
{
Console.WriteLine(line);
}
Console.WriteLine();
}
}
static void Main(string[] args)
{
//var crystals = new List<Tuple<string, char, char>>();
//crystals.Add(new Tuple<string, char, char>("2SIC", 'E', 'I'));
//crystals.Add(new Tuple<string, char, char>("3BX1", 'A', 'C'));
//crystals.Add(new Tuple<string, char, char>("1RGI", 'A', 'G'));
//MakeCrystalTemplates(crystals);
//return;
// uncomment one of the options below or add a new one
//var pdbSumInterfaceIdFirstLastList = @"
//3JBIV 990 1001
//1T44G 95 110
//4PKHB 114 137
//5AFUb 52 60
//1RGIAG 95 110
//1H1VG 473 488
//4EAHA 641 653
//1KXPD 196 210
//1M8QA 529 544
//3JBIAV 990 1001
//1T44AG 95 110
//4PKHAB 114 137
//1RGIAG 95 110
//1H1VAG 473 488
//4EAHHA 641 653
//1KXPAD 196 210
//var pdbSumInterfaceIdFirstLastList = @"
//4GI3AC 22 29
//2SICEI 65 74
//1SBNEI 35 53
//4LVNAP 207 216
//1OYVBI 54 64
//1V5IAB 68 76
//1R0REI 11 20
//3BX1AC 84 94
//";
// receptor ligand lig-inf-start lig-inf-end
/*
* var ligandSiblingInterfaceList = @"
* 1RGIAG 95 110
* 3JBIAV 990 1001
* 4PKHAB 114 137
* 1H1VAG 473 488
* 4EAHHA 641 653
* 1KXPAD 196 210
* ";
*/
var ligandSiblingInterfaceList = @"
4GI3AC 22 29
2SICEI 65 74
1SBNEI 35 53
4LVNAP 207 216
1OYVBI 54 64
1V5IAB 68 76
1R0REI 11 20
3BX1AC 84 94
";
/*
* 2SICEI 65 74
* 3BX1AC 84 94
* 1RGIAG 95 110
*/
var recLigInfoList = ligandSiblingInterfaceList.Trim().Split(new char[] { '\r', '\n' }, StringSplitOptions.RemoveEmptyEntries)
.Select(a =>
{
var b = a.Trim().Split(new char[] { ' ', '\t' }, StringSplitOptions.RemoveEmptyEntries);
var pdbId = b[0].Substring(0, 4);
var recChainId = b[0][4];
var recInfStart = -1;
var recInfEnd = -1;
var recSequenceAlignment = GetSequence(pdbId, recChainId);
var recSequence = recSequenceAlignment.SuperSequence;
var recInfSequence = "";
var recInfPosInRecSeq = -1;
var ligChainId = b[0][5];
var ligInfStart = int.Parse(b[1]);
var ligInfEnd = int.Parse(b[2]);
var ligSequenceAlignment = GetSequence(pdbId, ligChainId);
var ligSequence = ligSequenceAlignment.SuperSequence;
var ligInfSequenceAlignment = GetSequence(pdbId, ligChainId, ligInfStart, ligInfEnd);
var ligInfSequence = ligInfSequenceAlignment.SuperSequence;
var ligInfPosInLigSeq = ligSequence.IndexOf(ligInfSequence);
return(new RecLigInfo()
{
PdbId = pdbId,
RecChainId = recChainId,
RecInfStart = recInfStart,
RecInfEnd = recInfEnd,
RecSequence = recSequence,
RecInfSequence = recInfSequence,
RecInfPosInRecSeq = recInfPosInRecSeq,
RecSequenceAlignment = recSequenceAlignment,
RecInfSequenceAlignment = null,
LigChainId = ligChainId,
LigInfStart = ligInfStart,
LigInfEnd = ligInfEnd,
LigSequence = ligSequence,
LigInfSequence = ligInfSequence,
LigInfPosInLigSeq = ligInfPosInLigSeq,
LigSequenceAlignment = ligSequenceAlignment,
LigInfSequenceAlignment = ligInfSequenceAlignment,
});
}).ToList();
var allSequenceIds = recLigInfoList.Select(a => a.PdbId + a.RecChainId + a.LigChainId).Distinct().OrderBy(a => a).ToList();
var rootFolder = @"C:\pdbe_split_4\sw_" + string.Join("_", allSequenceIds) + @"\";
Directory.CreateDirectory(rootFolder);
//var rootFolderSubDirs = Directory.GetDirectories(rootFolder, "*", SearchOption.AllDirectories).ToList();
//rootFolderSubDirs.Remove(Path.GetDirectoryName(rootFolder));
if (recLigInfoList.Any(a => string.IsNullOrWhiteSpace(a.LigInfSequence)))
{
Console.WriteLine("Error: empty interface");
return;
}
if (recLigInfoList.Any(a => string.IsNullOrWhiteSpace(a.LigSequence) || a.LigSequence.Length < 50))
{
Console.WriteLine("Error: empty/short sequence");
return;
}
var fastaSequences = recLigInfoList.Select(a => ">" + a.PdbId + a.LigChainId + "_pdb\r\n" + a.LigSequence).ToList();
var fastaInfSequences = recLigInfoList.Select(a => ">" + a.PdbId + a.LigChainId + "_interface\r\n" + a.LigInfSequence).ToList();
File.WriteAllLines(rootFolder + "sequences.fasta", fastaSequences);
File.WriteAllLines(rootFolder + "interfaces_pdbsum.fasta", fastaInfSequences);
if (recLigInfoList.Any(a => a.LigSequence.IndexOf(a.LigInfSequence) != a.LigSequence.LastIndexOf(a.LigInfSequence)))
{
Console.WriteLine("More than one interface match in the sequence");
return;
}
var folders = new List <string>();
foreach (var template in recLigInfoList.Where(a => (new List <string>()
{
"1RGI", "3BX1", "2SIC"
}).Contains(a.PdbId)))
{
/*
* // replacement with direct overwrite of interface
* foreach (var templateForSiblingInterface in recLigInfoList)
* {
* var superOffset = templateForSiblingInterface.LigSequenceAlignment.SuperSequenceStartIndex;
*
* var siblingInterfaceToFit = InterfaceSubsequence(templateForSiblingInterface.LigSequence, templateForSiblingInterface.LigInfStart - superOffset, templateForSiblingInterface.LigInfEnd - superOffset, templateForModelling.LigInfSequence.Length).InterfaceSequence;
*
* var substitutionDescription = "sibling_" + templateForSiblingInterface.PdbId + templateForSiblingInterface.RecChainId + templateForSiblingInterface.LigChainId;
*
* var templateFolder = rootFolder + templateForModelling.PdbId + templateForModelling.RecChainId + templateForModelling.LigChainId + @"\" + templateForSiblingInterface.PdbId + templateForSiblingInterface.RecChainId + templateForSiblingInterface.LigChainId + @"\";
* var currentFolder = rootFolder + templateForModelling.PdbId + templateForModelling.RecChainId + templateForModelling.LigChainId + @"\" + templateForSiblingInterface.PdbId + templateForSiblingInterface.RecChainId + templateForSiblingInterface.LigChainId + @"\" + substitutionDescription + @"\";
* Directory.CreateDirectory(Path.GetDirectoryName(currentFolder));
* rootFolderSubDirs.Remove(Path.GetDirectoryName(currentFolder));
*
* var ligSeqModified = templateForModelling.LigSequence.Remove(templateForModelling.LigInfPosInLigSeq, siblingInterfaceToFit.Length).Insert(templateForModelling.LigInfPosInLigSeq, siblingInterfaceToFit);
*
* var file = currentFolder + "template_ligand_after_substitution.ali";
* var seqModPir = Pir(new List<string>() { templateForModelling.RecSequence, ligSeqModified });
*
* File.WriteAllText(file, seqModPir);
* folders.Add(currentFolder);
*
* //DimerTemplate(, templateForModelling.RecChainId, templateForModelling.LigChainId);
*
* var templateSrc = @"c:\pdb_templates\repaired_crystal_and_repaired_model\" + templateForModelling.PdbId + templateForModelling.RecChainId + templateForModelling.LigChainId + ".pdb"; //@"c:\pdbe\" + templateForModelling.PdbId + ".pdb";
* var templateDest = templateFolder + "template_ligand_all.pdb";
* File.Copy(templateSrc, templateDest, true);
*
* if (templateForModelling.PdbId == templateForSiblingInterface.PdbId)
* {
* Debug.WriteLine("");
* }
* }
*/
// replacements with sliding window method
foreach (var sibling in recLigInfoList /*.Where(a => a == templateForModelling).ToList()*/)//.Where(a => a.PdbId == templateForModelling.PdbId && a.RecChainId == templateForModelling.RecChainId))
{
if (template != sibling && (template.LigInfSequence.Contains(sibling.LigInfSequence) || sibling.LigInfSequence.Contains(template.LigInfSequence)))
{
Debug.WriteLine("template and sibling have matching interface");
continue;
}
var currentFolder = rootFolder + template.PdbId + template.RecChainId + template.LigChainId + @"\" + sibling.PdbId + sibling.RecChainId + sibling.LigChainId + @"\";
Directory.CreateDirectory(Path.GetDirectoryName(currentFolder));
var templateSrc = @"c:\pdb_templates\repaired_crystal_and_repaired_model\" + template.PdbId + template.RecChainId + template.LigChainId + ".pdb"; //@"c:\pdbe\" + templateForModelling.PdbId + ".pdb";
var templateDest = currentFolder + "template_ligand_all.pdb";
File.Copy(templateSrc, templateDest, true);
// 1. slide sibling interface over template interface (if bigger, try each possible)
// 2. best alignments?
// 3.
// 1. ignore size difference (sibling can be same size, longer or shorter, still copied as-is)
//Debug.WriteLine("Template: " + template.LigInfSequence + " " + template.LigInfSequence.Length);
//Debug.WriteLine("Sibling: " + sibling.LigInfSequence + " " + sibling.LigInfSequence.Length);
//part 0 - random sequence tests
if (template == sibling)
{
var firstPosition = template.LigInfPosInLigSeq - 50;// (template.LigInfSequence.Length - 1);
if (firstPosition < 0)
{
firstPosition = 0;
}
var lastPosition = template.LigInfPosInLigSeq + template.LigInfSequence.Length + 50;
if (lastPosition + (template.LigInfSequence.Length - 1) > template.LigSequence.Length)
{
lastPosition = template.LigSequence.Length - sibling.LigInfSequence.Length;
}
var substitutionMode = "0";
for (var i = firstPosition; i <= lastPosition; i++)
{
var overlap = ProteinBioClass.InterfaceOverlapPercentage(i, (i + template.LigInfSequence.Length) - 1, template.LigInfPosInLigSeq, (template.LigInfPosInLigSeq + template.LigInfSequence.Length) - 1); overlap = Math.Round(overlap, 2);
var random = template.LigSequence.Substring(i, template.LigInfSequence.Length);
var ligSeqMod = template.LigSequence.Remove(template.LigInfPosInLigSeq, template.LigInfSequence.Length).Insert(template.LigInfPosInLigSeq, random);
currentFolder = rootFolder + template.PdbId + template.RecChainId + template.LigChainId + @"\" +
template.PdbId + template.RecChainId + template.LigChainId + @"\" +
substitutionMode + "_" + (i + 1).ToString().PadLeft(4, '0') + "_" + (template.LigInfSequence.Length + 1).ToString().PadLeft(4, '0') + "_" + (sibling.LigInfSequence.Length + 1).ToString().PadLeft(4, '0') + "_" + (overlap) + @"\";
Directory.CreateDirectory(Path.GetDirectoryName(currentFolder));
var file = currentFolder + "template_ligand_after_substitution.ali";
var seqModPir = Pir(new List <string>()
{
template.RecSequence, ligSeqMod
});
if (!File.Exists(file))
{
if (!folders.Contains(currentFolder))
{
folders.Add(currentFolder);
}
File.WriteAllText(file, seqModPir);
}
}
}
continue;
{
//Debug.WriteLine("Part 1");
var firstPosition = template.LigInfPosInLigSeq - (sibling.LigInfSequence.Length - 1);
if (firstPosition < 0)
{
firstPosition = 0;
}
var lastPosition = template.LigInfPosInLigSeq + (template.LigInfSequence.Length - 1);
if (lastPosition + (sibling.LigInfSequence.Length - 1) > template.LigSequence.Length)
{
lastPosition = template.LigSequence.Length - sibling.LigInfSequence.Length;
}
for (var i = firstPosition; i <= lastPosition; i++)
{
var substitutionMode = "1";
var overlap = ProteinBioClass.InterfaceOverlapPercentage(i, (i + sibling.LigInfSequence.Length) - 1, template.LigInfPosInLigSeq, (template.LigInfPosInLigSeq + template.LigInfSequence.Length) - 1); overlap = Math.Round(overlap, 2);
var ligSeqMod = template.LigSequence.Remove(i, sibling.LigInfSequence.Length).Insert(i, sibling.LigInfSequence);
currentFolder = rootFolder + template.PdbId + template.RecChainId + template.LigChainId + @"\" +
sibling.PdbId + sibling.RecChainId + sibling.LigChainId + @"\" +
substitutionMode + "_" + (i + 1).ToString().PadLeft(4, '0') + "_" + (template.LigInfSequence.Length + 1).ToString().PadLeft(4, '0') + "_" + (sibling.LigInfSequence.Length + 1).ToString().PadLeft(4, '0') + "_" + (overlap) + @"\";
if (!folders.Contains(currentFolder))
{
folders.Add(currentFolder);
}
Directory.CreateDirectory(Path.GetDirectoryName(currentFolder));
var file = currentFolder + "template_ligand_after_substitution.ali";
var seqModPir = Pir(new List <string>()
{
template.RecSequence, ligSeqMod
});
File.WriteAllText(file, seqModPir);
// Debug.WriteLine(io + " " + ligSeqMod);
//Debug.WriteLine("");
}
}
// 2. keep longer sibling interface the same size as template interface
if (sibling.LigInfSequence.Length > template.LigInfSequence.Length)
{
//Debug.WriteLine("Part 2");
var firstPosition = template.LigInfPosInLigSeq - (template.LigInfSequence.Length - 1);
var lastPosition = template.LigInfPosInLigSeq + (template.LigInfSequence.Length - 1);
for (var i = firstPosition; i <= lastPosition; i++)
{
for (var j = 0; j <= sibling.LigInfSequence.Length - template.LigInfSequence.Length; j++)
{
var ligSeqMod = template.LigSequence.Remove(i, template.LigInfSequence.Length).Insert(i, sibling.LigInfSequence.Substring(j, template.LigInfSequence.Length));
var substitutionMode = "2";
var overlap = ProteinBioClass.InterfaceOverlapPercentage(i, (i + template.LigInfSequence.Length) - 1, template.LigInfPosInLigSeq, (template.LigInfPosInLigSeq + template.LigInfSequence.Length) - 1);
overlap = Math.Round(overlap, 2);
currentFolder = rootFolder + template.PdbId + template.RecChainId + template.LigChainId + @"\" +
sibling.PdbId + sibling.RecChainId + sibling.LigChainId + @"\" +
substitutionMode + "_" + (i + 1).ToString().PadLeft(4, '0') + "_" + (j + 1).ToString().PadLeft(4, '0') + "_" + (overlap) + @"\";
if (!folders.Contains(currentFolder))
{
folders.Add(currentFolder);
}
Directory.CreateDirectory(Path.GetDirectoryName(currentFolder));
var file = currentFolder + "template_ligand_after_substitution.ali";
var seqModPir = Pir(new List <string>()
{
template.RecSequence, ligSeqMod
});
File.WriteAllText(file, seqModPir);
}
}
//Debug.WriteLine("");
}
// 3. delete original template interface, insert sibling interface (will already be in part 1 if size is equal)
if (sibling.LigInfSequence.Length != template.LigInfSequence.Length)
{
Debug.WriteLine("Part 3");
var ligSeqMod = template.LigSequence.Remove(template.LigInfPosInLigSeq, template.LigInfSequence.Length).Insert(template.LigInfPosInLigSeq, sibling.LigInfSequence);
var substitutionMode = "3";
currentFolder = rootFolder + template.PdbId + template.RecChainId + template.LigChainId + @"\" +
sibling.PdbId + sibling.RecChainId + sibling.LigChainId + @"\" +
substitutionMode + "_" + "delete-insert" + @"\";
if (!folders.Contains(currentFolder))
{
folders.Add(currentFolder);
}
Directory.CreateDirectory(Path.GetDirectoryName(currentFolder));
var file = currentFolder + "template_ligand_after_substitution.ali";
var seqModPir = Pir(new List <string>()
{
template.RecSequence, ligSeqMod
});
File.WriteAllText(file, seqModPir);
Debug.WriteLine("");
}
/*
* continue;
*
* var firstBound = -1;
* var lastBound = -1;
* var resolution = -1;
* var substitutionDescription = "";
*
* var interfaceLengthDifference = template.LigInfSequence.Length - sibling.LigInfSequence.Length; // positive=replacement is shorter, negative=replacement is longer, zero=the same
*
* const int flank = 10;
* firstBound = sibling.LigInfPosInLigSeq - flank;
* lastBound = (firstBound + sibling.LigInfSequence.Length + (flank * 2)) - 1;
*
* resolution = 1;
* substitutionDescription = "inf";
*
*
* if (firstBound < 0) firstBound = 0;
* if (lastBound > sibling.LigSequence.Length - 1) lastBound = sibling.LigSequence.Length - 1;
*
* var totalPossibleInterfaceOverlapPositions = 1;
*
*
* if (interfaceLengthDifference < 0)
* {
* totalPossibleInterfaceOverlapPositions = Math.Abs(interfaceLengthDifference) + 1;
* }
*
*
*
* var lastPossibleSubPos = (lastBound - (interfaceLengthDifference > 0 ? sibling.LigInfSequence.Length : template.LigInfSequence.Length)) + 1;
*
* for (var substitutionSourcePos = firstBound; substitutionSourcePos <= lastBound && substitutionSourcePos <= lastPossibleSubPos; substitutionSourcePos += resolution)
* {
* for (var interfaceOverlapPosition = 0; interfaceOverlapPosition < totalPossibleInterfaceOverlapPositions; interfaceOverlapPosition++)
* {
* var replacementInterfaceSubsequence = sibling.LigSequence.Substring(substitutionSourcePos, sibling.LigInfSequence.Length);
*
* if (sibling.LigInfSequence.Length > template.LigInfSequence.Length)
* {
* replacementInterfaceSubsequence = replacementInterfaceSubsequence.Substring(interfaceOverlapPosition, template.LigInfSequence.Length);
* }
*
* var ligSeqModified = template.LigSequence.Remove(template.LigInfPosInLigSeq, replacementInterfaceSubsequence.Length).Insert(template.LigInfPosInLigSeq, replacementInterfaceSubsequence);
*
* if (ligSeqModified.Length != template.LigSequence.Length)
* {
* throw new Exception("Wrong sub pos or len");
* }
*
* var native = (substitutionSourcePos >= sibling.LigInfPosInLigSeq && substitutionSourcePos + replacementInterfaceSubsequence.Length <= sibling.LigInfPosInLigSeq + sibling.LigInfSequence.Length);
* if (native)
* {
* Console.WriteLine("");
* }
* currentFolder = rootFolder + template.PdbId + template.RecChainId + template.LigChainId + @"\" + sibling.PdbId + sibling.RecChainId + sibling.LigChainId + @"\" + substitutionDescription + "_" + (substitutionSourcePos + 1).ToString().PadLeft(4, '0') + "_" + (substitutionSourcePos + replacementInterfaceSubsequence.Length).ToString().PadLeft(4, '0') + "_" + (interfaceOverlapPosition + 1) + "_" + totalPossibleInterfaceOverlapPositions + (native ? "_native" : "") + @"\";
* Directory.CreateDirectory(Path.GetDirectoryName(currentFolder));
* //rootFolderSubDirs.Remove(Path.GetDirectoryName(currentFolder));
*
* var file = currentFolder + "template_ligand_after_substitution.ali";
* var seqModPir = Pir(new List<string>() { template.RecSequence, ligSeqModified });
* File.WriteAllText(file, seqModPir);
* }
* }
*/
}
}
//File.WriteAllLines(rootFolder + "obsolete_dirs.txt", rootFolderSubDirs);
if (folders.Count > 0)
{
var scripts = new List <string> {
"modeller_monomer.bat", "foldx_dimer.bat"
}; //, "pisa_dimer.bat" };
int div = folders.Count / Environment.ProcessorCount;
var batch = new List <string>();
var c = 0;
while (folders.Count > 0)
{
c++;
batch.Add(@"@echo off");
batch.Add(@"set HDF5_DISABLE_VERSION_CHECK=2");
batch.Add(@"set THIS_DIR=%cd%");
batch.Add(@"set PATH=%PATH%;c:\modeller_scripts;");
var t = folders.Count >= div * 2 ? div : folders.Count;
folders.Take(t).ToList().ForEach(a =>
{
batch.Add(@"echo " + a);
batch.Add(@"cd " + a);
batch.Add(@"CALL %script1%");
batch.Add(@"CALL %script2%");
});
folders = folders.Skip(t).ToList();
batch.Add(@"pause");
var d = batch /*.Select(a => a.Replace("%script%", script))*/.ToList();
var n = "";
for (var i = 0; i < scripts.Count; i++)
{
var script = scripts[i];
d = d.Select(a => a.Replace("%script" + (i + 1).ToString() + "%", script)).ToList();
n = n + Path.GetFileNameWithoutExtension(script) + "_";
}
File.WriteAllLines(rootFolder + @"r_" + c + "_" + n + DateTime.Now.Ticks + @".bat", d);
batch.Clear();
}
}
}
public static List <SequenceIdentityClusterMember> ClusterSequenceByAlignedSequenceIdentity(List <Sequence> seqList, ProteinBioClass.AlignmentIdentityOption alignmentIdentityOption, decimal mininumClusterPairwiseSimilarity = 0.3m, decimal mininumEvoClusterPairwiseSimilarity = 0.3m)
{
var allsequences = seqList.Select(a => new Tuple <string, char, string>(new ProteinBioClass.SequenceId(a.Id).PdbId, new ProteinBioClass.SequenceId(a.Id).ChainId, Sequence.EscapeAminoAcidSequence(a.FullSequence))).ToList();
var sequences = allsequences.Select(a => a.Item3).Distinct().ToList();
var sequenceIds = sequences.Select(a => allsequences.Where(b => b.Item3 == a).ToList()).ToList();
var seqClusters = new List <List <string> >();
for (int x = 0; x < sequences.Count; x++)
{
var seq1 = sequences[x];
var newCluster = new List <string>();
newCluster.Add(seq1);
seqClusters.Add(newCluster);
}
for (int indexX = 0; indexX < sequences.Count; indexX++)
{
Console.WriteLine("Aligning sequence " + indexX);
var seqX = sequences[indexX];
//List<decimal> scoreList = new List<decimal>();
//List<decimal> scoreEvoList = new List<decimal>();
for (int indexY = 0; indexY < sequences.Count; indexY++)
{
if (indexY <= indexX)
{
continue;
}
var seqY = sequences[indexY];
if ((decimal)Math.Min(seqX.Length, seqY.Length) / (decimal)Math.Max(seqX.Length, seqY.Length) < mininumClusterPairwiseSimilarity)
{
continue;
}
var cluster1 = seqClusters.FirstOrDefault(a => a.Contains(seqX));
var cluster2 = seqClusters.FirstOrDefault(a => a.Contains(seqY));
if (cluster1 != null && cluster2 != null && cluster1 == cluster2)
{
continue;
}
var score = ProteinBioClass.AlignedSequenceSimilarityPercentage(seqX, seqY, ProteinBioClass.AlignmentType.NON, alignmentIdentityOption);
Console.WriteLine("1: " + seqX);
Console.WriteLine("2: " + seqY);
Console.WriteLine("Score1: " + score.Score);
Console.WriteLine("Score2: " + score.ScoreEvo);
if (score.Score < mininumClusterPairwiseSimilarity || score.ScoreEvo < mininumEvoClusterPairwiseSimilarity)
{
var x = ProteinBioClass.AlignedSequenceSimilarityPercentage(seqX, seqY, ProteinBioClass.AlignmentType.SIM, alignmentIdentityOption);
if (x.Score > score.Score)
{
score.Score = x.Score;
}
if (x.ScoreEvo > score.ScoreEvo)
{
score.ScoreEvo = x.ScoreEvo;
}
}
if (score.Score < mininumClusterPairwiseSimilarity || score.ScoreEvo < mininumEvoClusterPairwiseSimilarity)
{
var x = ProteinBioClass.AlignedSequenceSimilarityPercentage(seqX, seqY, ProteinBioClass.AlignmentType.NMW, alignmentIdentityOption);
if (x.Score > score.Score)
{
score = x;
}
if (x.ScoreEvo > score.ScoreEvo)
{
score.ScoreEvo = x.ScoreEvo;
}
}
if (score.Score >= mininumClusterPairwiseSimilarity && score.ScoreEvo >= mininumEvoClusterPairwiseSimilarity)
{
var newCluster = new List <string>();
newCluster.AddRange(cluster1);
newCluster.AddRange(cluster2);
seqClusters.Remove(cluster1);
seqClusters.Remove(cluster2);
seqClusters.Add(newCluster);
}
//scoreList.Add(score.Score);
//scoreEvoList.Add(score.ScoreEvo);
}
//Console.WriteLine("[" + string.Join(", ", scoreList.Select(a => String.Format("{0:0.00}", a)).ToList()) + "]");
//Console.WriteLine("[" + string.Join(", ", scoreEvoList.Select(a => String.Format("{0:0.00}", a)).ToList()) + "]");
}
seqClusters = seqClusters.OrderBy(a => a.Count).ToList();
var output = new List <SequenceIdentityClusterMember>();
for (var index = 0; index < seqClusters.Count; index++)
{
var seqCluster = seqClusters[index];
foreach (var item in seqCluster)
{
var indexIds = sequences.IndexOf(item);
var ids = sequenceIds[indexIds];
foreach (var id in ids)
{
output.Add(new SequenceIdentityClusterMember(index + 1, ProteinBioClass.PdbIdFromPdbFilename(id.Item1), id.Item2, id.Item3));
}
}
}
return(output);
}
static void Main(string[] args)
{
// this program takes a fasta or pdb file and finds all matching homologs
// FindHomologs.exe "c:\ds96ub\ds96ub.fasta" * "c:\pdb\pdb_seqres.fasta" NMW Y 0.3 75 c:\pdb\
// alignment_type = (n)one, (s)imple, NMW, SWM
var query_sequence_file = args[0]; //query.fasta
var query_id_chain = args[1]; //1A2G:B
var target_sequence_file = args[2]; //targets.fasta
var alignment_type_str = args[3]; //NMW,SWM,SIM,NON
if (alignment_type_str == "*")
{
alignment_type_str = "NMW,SWM,SIM,NON";
}
var alignment_type_str_split = alignment_type_str.ToUpperInvariant().Split(new char[] { ',', ';', ' ', '\t' });
var compare_physicochemically = args[4]; //Y/N
var compare_physicochemically_bool = compare_physicochemically == "Y";
var min_similarity_str = args[5]; // 0.3
var max_len_difference = args[6];
var max_len_difference_int = int.Parse(max_len_difference);
var output_folder = args[7];
var minSimilarity = decimal.Parse(min_similarity_str);
var alignmentTypes = new List <ProteinBioClass.AlignmentType>();
if (alignment_type_str_split.Contains("NMW"))
{
alignmentTypes.Add(ProteinBioClass.AlignmentType.NMW);
}
if (alignment_type_str_split.Contains("SWM"))
{
alignmentTypes.Add(ProteinBioClass.AlignmentType.SWM);
}
if (alignment_type_str_split.Contains("SIM"))
{
alignmentTypes.Add(ProteinBioClass.AlignmentType.SIM);
}
if (alignment_type_str_split.Contains("NON") || alignmentTypes.Count == 0)
{
alignmentTypes.Add(ProteinBioClass.AlignmentType.NON);
}
if (alignmentTypes.Count < alignment_type_str_split.Length)
{
Console.WriteLine("; unknown alignment type");
return;
}
// load list of query sequences
var queryPdbid = query_id_chain.Split(new char[] { ':' })[0];
var queryChainid = (query_id_chain.Contains(":") ? query_id_chain.Split(new char[] { ':' })[1] : "*")[0];
var querySeq = Sequence.LoadSequenceFile(query_sequence_file, null);
var queryResults = querySeq.Where(a =>
{
var id = new ProteinBioClass.SequenceId(a.Id);
return((queryPdbid == "*" || id.PdbId.ToUpperInvariant() == queryPdbid.ToUpperInvariant()) &&
(queryChainid == '*' || id.ChainId == queryChainid));
}).ToList();
if (queryResults.Count == 0)
{
Console.WriteLine("; the query pdbids/chainids were not found");
return;
}
// load list of target sequences
var targetSeq = Sequence.LoadSequenceFile(target_sequence_file, new string[] { null, "", "protein" });
targetSeq = targetSeq.Where(a => a.Count() >= 50).ToList();
Console.WriteLine("; aligning " + queryResults.Count + " query sequences to " + targetSeq.Count + " target sequences");
// perform alignment
//var startTime = DateTime.Now;
//var progress = 0;
//var progressLock = new object();
//var tasks = new List<Task<StringBuilder>>();
var queryPdbIds = queryResults.Select(a => new ProteinBioClass.SequenceId(a.Id).PdbId);
var targetPdbIds = targetSeq.Select(a => new ProteinBioClass.SequenceId(a.Id).PdbId);
var queryPdbIdCounts = new Dictionary <string, int>();
foreach (var x in queryPdbIds)
{
if (!queryPdbIdCounts.ContainsKey(x))
{
queryPdbIdCounts.Add(x, 1);
}
else
{
queryPdbIdCounts[x]++;
}
}
var targetPdbIdCounts = new Dictionary <string, int>();
foreach (var x in targetPdbIds)
{
if (!targetPdbIdCounts.ContainsKey(x))
{
targetPdbIdCounts.Add(x, 1);
}
else
{
targetPdbIdCounts[x]++;
}
}
foreach (var _query in queryResults)
{
var _queryId = new ProteinBioClass.SequenceId(_query.Id);
var filename = (new DirectoryInfo(output_folder).FullName) + @"\homologs_" + _queryId.PdbId + _queryId.ChainId + @".csv";
// skip if already processed
if (File.Exists(filename) && new FileInfo(filename).Length > 0)
{
continue;
}
var totalQueryPdbIdChains = queryPdbIdCounts[_queryId.PdbId];
WorkDivision wd = new WorkDivision(targetSeq.Count);
for (var thread = 0; thread < wd.ThreadCount; thread++)
{
var query = _query;
var queryId = _queryId;
var lti = thread;
wd.TaskList.Add(Task.Run(() =>
{
var result = new List <HomologChain>();
for (var target = wd.ThreadFirstIndex[lti]; target <= wd.ThreadLastIndex[lti]; target++)
{
var targetobj = targetSeq[target];
if (max_len_difference_int != -1 && Math.Abs(targetobj.Count() - query.Count()) > max_len_difference_int)
{
continue;
}
var targetId = new ProteinBioClass.SequenceId(targetobj.Id);
//var totalTargetPdbIdChains = targetSeq.Count(a => FindAtomicContacts.SequenceIdToPdbIdAndChainId(a.ID).PdbId.ToUpperInvariant() == targetId.PdbId.ToUpperInvariant());
//var timeRemaining =
// TimeSpan.FromTicks(DateTime.Now.Subtract(startTime).Ticks *
// ((targetSeq.Count * queryResults.Count) - (progress + 1)) /
// (progress + 1));
foreach (var alignmentType in alignmentTypes)
{
var scores = ProteinBioClass.AlignedSequenceSimilarityPercentage(query, targetobj, alignmentType /*,
* compare_physicochemically_bool*/);
decimal percentSimilar;
if (compare_physicochemically_bool)
{
percentSimilar = scores.ScoreEvo;
}
else
{
percentSimilar = scores.Score;
}
if (percentSimilar >= minSimilarity)
{
result.Add(new HomologChain(
queryId.PdbId, queryId.ChainId, totalQueryPdbIdChains,
targetId.PdbId, targetId.ChainId, targetPdbIdCounts[targetId.PdbId],
alignmentType.ToString(),
scores.Score,
scores.ScoreEvo));
}
}
//if (progress % 20 == 0)
// Console.Write("\r{0}% eta {1} ",
// Math.Round((decimal)(progress + 1) / (decimal)(targetSeq.Count * queryResults.Count),
// 2)
// .ToString(CultureInfo.InvariantCulture),
// timeRemaining.ToString(@"d\d\:h\h\:m\m\:s\s",
// CultureInfo.InvariantCulture));
//lock (progressLock)
// progress++;
}
return(result);
}));
}
wd.WaitAllTasks();
var mergedlist = new List <string>();
mergedlist.Add("; " + _queryId.PdbId + ":" + _queryId.ChainId);
mergedlist.Add(String.Join(",",
new string[]
{
"query pdb id", "query chain id", "query chains",
"target pdb id", "target chain id", "target chains",
"alignment method", "sequence similarity", "sequence evo similarity"
}));
foreach (var t in wd.TaskList)
{
var tc = t as Task <List <HomologChain> >;
if (tc == null)
{
throw new Exception("task in tasklist was null");
}
mergedlist.AddRange(tc.Result.Select(a => a.ToString()).ToList());
}
if (string.IsNullOrWhiteSpace(output_folder))
{
Console.WriteLine(String.Join(Environment.NewLine, mergedlist));
}
else
{
File.WriteAllLines(filename, mergedlist);
}
}
}
static void Main(string[] args)
{
var parameters = new string[, ]
{
{ "[pdb_or_atoms_file]", "output from the ComplexAtoms program" },
{ "[max_distance]", "maximum allowed contact distance in angstroms [i.e. 5.0 or 8.0]" },
{ "[[output_file]]", "optional output file. when ommitted, output to console" },
{ "[[overwrite]]", "overwrite if output file exists" }
};
var maxParamLength = parameters.Cast <string>().Where((a, i) => i % 2 == 0).Max(a => a.Length);
var exeFilename = Path.GetFileName(System.Diagnostics.Process.GetCurrentProcess().MainModule.FileName);
if (args.Length == 0)
{
Console.WriteLine(exeFilename + @" is a program to list atomic contacts for a PDB file ATOM records.");
Console.WriteLine();
Console.WriteLine(@"Usage:");
Console.WriteLine(ProteinBioClass.WrapConsoleText(exeFilename + @" " + String.Join(" ", parameters.Cast <string>().Where((a, i) => i % 2 == 0)), maxParamLength + 2, 1));
Console.WriteLine();
Console.WriteLine(@"Example:");
Console.WriteLine(ProteinBioClass.WrapConsoleText(exeFilename + @" ""c:\pdb_db\pdb1a12.pdb"" 8.0 ""c:\pdb_atoms\atoms1a12.pdb""", maxParamLength + 2, 1));
Console.WriteLine();
Console.WriteLine(@"Arguments:");
for (var i = 0; i < parameters.GetLength(0); i++)
{
Console.WriteLine(@" " + parameters[i, 0].PadLeft(maxParamLength, ' ') + " " + ProteinBioClass.WrapConsoleText(parameters[i, 1], maxParamLength + 2, 1, false));
}
Console.WriteLine();
//return;
}
// load arguments
var p = 0;
var atomsFilename = args.Length > p && args[p].Length > 0 ? args[p] : "";
atomsFilename = atomsFilename.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + atomsFilename);
p++;
var maxDistance = args.Length > p && args[p].Length > 0 ? Decimal.Parse(args[p]) : 0.0m;
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + maxDistance);
p++;
var outputFilename = args.Length > p && args[p].Length > 0 ? args[p] : "";
outputFilename = outputFilename.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + outputFilename);
p++;
var overwrite = args.Length > p && args[p].Length > 0 ? args[p] : "";
overwrite = overwrite.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + overwrite);
if (!string.IsNullOrWhiteSpace(overwrite) && overwrite.ToUpperInvariant() != "Y" && File.Exists(outputFilename))
{
Console.Write("; File exists, skipping.");
return;
}
Console.WriteLine();
if (!File.Exists(atomsFilename))
{
return;
}
var interactions = ProteinBioClass.FindInteractions(CancellationToken.None, maxDistance, atomsFilename, new Dictionary <string, List <char> >());
if (!string.IsNullOrWhiteSpace(outputFilename))
{
ProteinBioClass.AtomPair.SaveAtomPairList(outputFilename, interactions);
}
else
{
//Console.WriteLine("; Atom pairs with contacts: " + interactions.Count);
foreach (var a in interactions.Select(a => a.ToString()).ToList())
{
Console.WriteLine(a);
}
}
}
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());
}
static void Main(string[] args)
{
var parameters = new string[, ]
{
{ "[pdb_or_atoms_file]", "input structure for sequence" },
{ "[fasta_file]", "input sequence for structure" },
{ "[[output_file]]", "optional output file" },
};
var maxParamLength = parameters.Cast <string>().Where((a, i) => i % 2 == 0).Max(a => a.Length);
var exeFilename = Path.GetFileName(Process.GetCurrentProcess().MainModule.FileName);
if (args.Length < 1)
{
Console.WriteLine(exeFilename + @" is a program to calculate offset between the sequence and structure.");
Console.WriteLine();
Console.WriteLine(@"Usage:");
Console.WriteLine(ProteinBioClass.WrapConsoleText(exeFilename + @" " + String.Join(" ", parameters.Cast <string>().Where((a, i) => i % 2 == 0)), maxParamLength + 2, 1));
Console.WriteLine();
Console.WriteLine(@"Example:");
Console.WriteLine(ProteinBioClass.WrapConsoleText(exeFilename + @" ""c:\pdb_db\atoms\atoms1a12.pdb"" ""c:\pdb_db\fasta\atoms1a12.fasta""", maxParamLength + 2, 1));
Console.WriteLine();
Console.WriteLine(@"Arguments:");
for (var i = 0; i < parameters.GetLength(0); i++)
{
Console.WriteLine(@" " + parameters[i, 0].PadLeft(maxParamLength, ' ') + " " + ProteinBioClass.WrapConsoleText(parameters[i, 1], maxParamLength + 2, 1, false));
}
Console.WriteLine();
return;
}
// load arguments
var p = 0;
var atomsFilename = args.Length > p && args[p].Length > 0 ? args[p] : "";
atomsFilename = atomsFilename.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + atomsFilename);
p++;
var inputFastaFilename = args.Length > p && args[p].Length > 0 ? args[p] : "";
inputFastaFilename = inputFastaFilename.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + inputFastaFilename);
p++;
var outputDataFilename = args.Length > p && args[p].Length > 0 ? args[p] : "";
outputDataFilename = outputDataFilename.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + outputDataFilename);
Console.WriteLine();
var struct_seq = ProteinBioinformaticsSharedLibrary.ProteinBioClass.StructureFileToAaSequence(atomsFilename, null,
false);
//foreach (var s in struct_seq)
//Console.WriteLine(s);
//var fasta = File.ReadAllLines(inputFastaFilename);
//foreach (var line in fasta)
//{
// if (string.IsNullOrWhiteSpace(line))continue;
// if (line[0] == '>')
// {
// if (line.Contains())
// }
//}
/// not finished!
}
public static string LoadDsspStructureSequence(string pdbFilename, string chainId = null, int startResidueSequenceIndex = -1, int endResidueSequenceIndex = -1, bool reversedSequence = false)
{
if (string.IsNullOrWhiteSpace(pdbFilename))
{
return("");
}
var pdbId = ProteinBioClass.PdbIdFromPdbFilename(pdbFilename);
var dsspFilename = pdbFilename;
if (Path.GetExtension(dsspFilename) != ".dssp")
{
dsspFilename += ".dssp";
}
if (!File.Exists(dsspFilename))
{
return("");
}
var secondaryStructure = DsspFormatFile.LoadDsspFile(dsspFilename);
if (chainId != null && secondaryStructure.FirstOrDefault(a => a.FieldChain.FieldValue.ToUpperInvariant() == chainId.ToUpperInvariant()) == null)
{
return("");
}
if (startResidueSequenceIndex == -1)
{
startResidueSequenceIndex = secondaryStructure.Where(a => chainId == null || a.FieldChain.FieldValue.ToUpperInvariant() == chainId.ToUpperInvariant()).Min(a => int.Parse(a.FieldPdbResidueSequenceIndex.FieldValue));
}
if (endResidueSequenceIndex == -1)
{
endResidueSequenceIndex = secondaryStructure.Where(a => chainId == null || a.FieldChain.FieldValue.ToUpperInvariant() == chainId.ToUpperInvariant()).Max(a => int.Parse(a.FieldPdbResidueSequenceIndex.FieldValue));
}
// dssp specification says order may not be correct
secondaryStructure = secondaryStructure.Where(a => !string.IsNullOrWhiteSpace(a.FieldChain.FieldValue) && !string.IsNullOrWhiteSpace(a.FieldPdbResidueSequenceIndex.FieldValue)).OrderBy(a => a.FieldChain.FieldValue).ThenBy(a => NullableTryParseInt32(a.FieldPdbResidueSequenceIndex.FieldValue)).ToList();
var proteinInterfaceLen = CalculateProteinInterfaceLength(startResidueSequenceIndex, endResidueSequenceIndex);
char[] result = new char[proteinInterfaceLen];
for (int index = 0; index < result.Length; index++)
{
result[index] = '_';
}
foreach (var record in secondaryStructure.Where(a => chainId == null || a.FieldChain.FieldValue.ToUpperInvariant() == chainId.ToUpperInvariant()))
{
var resSeq = NullableTryParseInt32(record.FieldPdbResidueSequenceIndex.FieldValue);
if (resSeq == null || resSeq < startResidueSequenceIndex || resSeq > endResidueSequenceIndex)
{
continue;
}
var position = resSeq - startResidueSequenceIndex;
if (record.FieldSecondaryStructure.FieldValue.Length == 0)
{
continue;
}
result[position.Value] = record.FieldSecondaryStructure.FieldValue[0];
}
if (reversedSequence)
{
Array.Reverse(result);
}
return(new string(result));
}
