public static void LoadReceptor(string mainReceptorPdbId)
{
Debug.WriteLine(mainReceptorPdbId);
//var mainReceptorPdbId = "2SICE";
//if (mainReceptorPdbId != "1KXPA" && mainReceptorPdbId != "2SICE") return;
if (mainReceptorPdbId.Length != 5)
{
return;
}
mainReceptorPdbId = mainReceptorPdbId.ToUpperInvariant();
var pdbFile = @"c:\pdbe\" + mainReceptorPdbId.Substring(0, 4) + ".pdb";
var ibisFile = @"c:\phd\ibis\" + mainReceptorPdbId.Substring(1, 2) + @"\" + mainReceptorPdbId.Substring(0, 4) + ".txt";
var ibisData = IbisData.Load(ibisFile);
if (ibisData == null || ibisData.Count == 0)
{
return;
}
ibisData = ibisData.Where(a => a.Query.ToUpperInvariant() == mainReceptorPdbId.ToUpperInvariant()).ToList();
ibisData = ibisData.Where(a => a.Interaction_type == "PPI").ToList();
ibisData = ibisData.Where(a =>
{
var pdbEvience = a.PDB_Evidence.Trim().Split('_');
var rec = pdbEvience[0];
var lig = pdbEvience[1];
return /*pdbEvience[0]== mainReceptorPdbId ||*/ (rec.Length == 5 && lig.Length == 5 && rec != lig);
}).ToList();
// at least one matching resid?
//var mmResNos = ibisData.Select(a => a.Mmdb_Residue_No.Trim().Split(new[] {' '}, StringSplitOptions.RemoveEmptyEntries)).Select(b => b.Select(int.Parse).ToList()).ToList();
//ibisData = ibisData.Where((a, i) => mmResNos.Any(b => mmResNos.IndexOf(b) != i && b.Intersect(mmResNos[i]).Any())).ToList();
// at least one matching domain?
const int minLigands = 2;
const int maxLigands = 400;
if (ibisData.Count >= minLigands && ibisData.Count <= maxLigands)
{
Directory.CreateDirectory(@"c:\pdbe_split\receptors\" + mainReceptorPdbId + @"\");
var pdbEvidenceList = ibisData.Select(a => new Tuple <string, List <int> >(a.PDB_Evidence, a.PDB_Residue_No.Trim().Split(' ').Select(b => int.Parse(string.Join("", b.Where(c => char.IsNumber(c))))).ToList())).ToList();
var pdbsumInteractonList = pdbEvidenceList.Select(a =>
{
var origPdbFile = @"c:\pdbe\" + a.Item1.Substring(0, 4) + ".pdb";
var recChain = a.Item1[4];
var ligChain = a.Item1[10];
var outPdb = PdbRecLigFile(mainReceptorPdbId, a.Item1, -1);
//ExtractAtoms(origPdbFile, "-", evidenceChains, outPdb);
var pdbsumInteractions = TruncateDimerContacts(origPdbFile, recChain, ligChain, outPdb);
var ibisInteractions = a.Item2;
return(new Tuple <string, List <int>, List <int> >(a.Item1, pdbsumInteractions, ibisInteractions));
}).ToList();
//pdbEvidenceList = pdbEvidenceList.Where((a, i) => success[i] || a.StartsWith(mainReceptorPdbId)).ToList();
//pdbEvidenceList = pdbEvidenceList.Where((a, i) => pdbsumInteractonList[i].Item2 != null).ToList();
pdbsumInteractonList = pdbsumInteractonList.Where(a => a.Item2 != null).ToList();
File.WriteAllLines(@"c:\pdbe_split\receptors\" + mainReceptorPdbId + @"\rec_lig_list_" + mainReceptorPdbId + ".txt", pdbsumInteractonList.Select(a => string.Join("\t", new List <string>()
{
a.Item1, string.Join("+", a.Item2), string.Join("+", a.Item3)
})));
PymolAlignmentCmds(mainReceptorPdbId, pdbsumInteractonList, @"c:\pdbe_split\receptors\" + mainReceptorPdbId + @"\pymol_images.py");
var batFilename = @"c:\pdbe_split\receptors\" + mainReceptorPdbId + @"\pymol_images.bat";
var batData = File.ReadAllLines(@"c:\phd\modeller_scripts\pymol_images.bat");
for (var i = 0; i <= 4; i++)
{
File.WriteAllLines(Path.GetDirectoryName(batFilename) + @"\" + Path.GetFileNameWithoutExtension(batFilename) + "_" + i + Path.GetExtension(batFilename), batData.Select(a => a.Replace("pymol_images.py", "pymol_images_" + i + ".py").Replace("pymol -e", "pymol")).ToList());
}
var start = false;
if (start)
{
var process = new Process()
{
StartInfo = new ProcessStartInfo(batFilename)
};
process.StartInfo.WorkingDirectory = Path.GetDirectoryName(batFilename);
process.Start();
process.WaitForExit();
Thread.Sleep(1000);
}
}
}
public static void Main(string[] args)
{
var ligandInterfaceList = new List <LigandInterface>();
var proteinList = File.ReadAllLines(@"c:\phd\search_mimicry_pdb_list.txt");
if (proteinList.Any(a => a.Length != 5))
{
throw new Exception("Wrong pdb code length");
}
List <Tuple <string, decimal> > crystalToSeqQuality = new List <Tuple <string, decimal> >();
List <Tuple <string, string, decimal> > homology = new List <Tuple <string, string, decimal> >();
if (File.Exists(@"c:\phd\pdb_quality.csv"))
{
var q = File.ReadAllLines(@"c:\phd\pdb_quality.csv");
crystalToSeqQuality = q.Select(a => new Tuple <string, decimal>(a.Split(' ')[0], decimal.Parse(a.Split(' ')[1]))).ToList();
}
if (File.Exists(@"c:\phd\pdb_homology.csv"))
{
var h = File.ReadAllLines(@"c:\phd\pdb_homology.csv");
homology = h.Select(a => new Tuple <string, string, decimal>(a.Split(' ')[0], a.Split(' ')[1], decimal.Parse(a.Split(' ')[2]))).ToList();
}
foreach (var mainReceptorPdbId in proteinList)
{
Debug.WriteLine(mainReceptorPdbId);
var chain = mainReceptorPdbId[4];
var pdbFile = @"c:\pdbe\" + mainReceptorPdbId.Substring(0, 4) + ".pdb";
var ibisFile = @"c:\phd\ibis\" + mainReceptorPdbId.Substring(1, 2) + @"\" + mainReceptorPdbId.Substring(0, 4) + ".txt";
var ibisRecordList = IbisData.Load(ibisFile);
ibisRecordList = ibisRecordList.Where(a => a.Interaction_type == "PPI").ToList();
ibisRecordList = ibisRecordList.Where(a => a.Query == mainReceptorPdbId && /*a.PDB_Evidence.StartsWith(mainReceptorPdbId) &&*/ !a.PDB_Evidence.EndsWith(mainReceptorPdbId)).ToList();
ibisRecordList = ibisRecordList.Where(a => a.PDB_Evidence.Substring(0, 5) != a.PDB_Evidence.Substring(6, 5)).ToList();
var ligandPdbIds = ibisRecordList.Select(a => a.PDB_Evidence.Substring(6, 5)).Distinct().ToList();
Debug.WriteLine("B: " + string.Join(", ", ligandPdbIds));
ligandPdbIds = FilterLigandHomology(ligandPdbIds, crystalToSeqQuality, homology);
Debug.WriteLine("A: " + string.Join(", ", ligandPdbIds));
ibisRecordList = ibisRecordList.Where(a => ligandPdbIds.Any(b => a.PDB_Evidence.EndsWith(b))).ToList();
var currentLigandInterfaceList = new List <LigandInterface>();
foreach (var ibisRecord in ibisRecordList)
{
var ligandPdbId = ibisRecord.PDB_Evidence.Substring(6, 5);
// check quality
var ligandQuality = crystalToSeqQuality.FirstOrDefault(a => a.Item1 == ligandPdbId);
if (ligandQuality == null)
{
ligandQuality = new Tuple <string, decimal>(ligandPdbId, PdbStructureQuality(ligandPdbId));
crystalToSeqQuality.Add(ligandQuality);
File.WriteAllLines(@"c:\phd\pdb_quality.csv", crystalToSeqQuality.Select(a => a.Item1 + " " + a.Item2).ToList());
}
var dsspFilename = ligandPdbId.Substring(0, 4).ToLowerInvariant() + ".dssp";
var dsspFullFilename = @"c:\dssp\" + dsspFilename;
var downloadDssp = false;
if (!File.Exists(dsspFullFilename) && downloadDssp)
{
var ftpDsspFile = @"ftp://ftp.cmbi.ru.nl/pub/molbio/data/dssp/" + dsspFilename;
var client = new WebClient();
try { client.DownloadFile(ftpDsspFile, dsspFullFilename); }
catch (Exception)
{
// throw;
}
//if (File.Exists(dsspFullFilename))
{
//var data = File.ReadAllText(dsspFullFilename);
//if (!data.Contains("\r\n") && data.Contains("\n")) { data = data.Replace("\n", "\r\n"); }
//if (!data.Contains("\r\n") && data.Contains("\r")) { data = data.Replace("\r", "\r\n"); }
}
}
foreach (var ibisRecord2 in ibisRecordList)
{
if (ibisRecord == ibisRecord2)
{
continue;
}
// check homology
var ligandPdbId2 = ibisRecord2.PDB_Evidence.Substring(6, 5);
var homologyPct = homology.FirstOrDefault(a => a.Item1 == ligandPdbId && a.Item2 == ligandPdbId2);
if (homologyPct == null)
{
homologyPct = new Tuple <string, string, decimal>(ligandPdbId, ligandPdbId2, Homology(ligandPdbId, ligandPdbId2));
homology.Add(homologyPct);
File.WriteAllLines(@"c:\phd\pdb_homology.csv", homology.Select(a => a.Item1 + " " + a.Item2 + " " + a.Item3).ToList());
}
}
var contacts = ibisRecord.PDB_Residue_No.Trim().Split(' ').Select(a => int.Parse(string.Join("", a.Where(b => char.IsNumber(b)).ToList()))).ToList();
var min = contacts.Min();
var max = contacts.Max();
var groups = new List <List <int> >();
foreach (var c in contacts)
{
var g = groups.FirstOrDefault(a => a.Contains(c) || a.Any(b => Math.Abs(c - b) <= 5));
if (g == null)
{
groups.Add(new List <int>()
{
c
});
continue;
}
g.Add(c);
}
groups = groups.Where(g => g.Count >= 5 && g.Count <= 20).ToList();
var secStructs = groups.Select(g => ProteinBioinformaticsSharedLibrary.Dssp.DsspStructureSequence.LoadDsspStructureSequence(dsspFullFilename, "" + chain, g.Min(), g.Max())).ToList();
var mainSecStructs = secStructs.Select(a => a.GroupBy(i => i).OrderByDescending(grp => grp.Count()).Select(grp => grp.Key).FirstOrDefault()).ToList();
foreach (var @group in groups)
{
var index = groups.IndexOf(@group);
var r = new LigandInterface()
{
MasterReceptor = mainReceptorPdbId, Receptor = ibisRecord.PDB_Evidence.Substring(0, 5), Ligand = ibisRecord.PDB_Evidence.Substring(6, 5), ReceptorInterfaceSecStruct = secStructs[index], ReceptorInterfaceMainSecStruct = mainSecStructs[index], ReceptorInterfacePdbResSeqIndexes = @group, ReceptorInterfaceFirst = @group.Min(), ReceptorInterfaceLast = @group.Max(), InterfaceIndex = groups.IndexOf(@group) + 1,
};
currentLigandInterfaceList.Add(r);
ligandInterfaceList.Add(r);
}
}
var resSeqIndexes = currentLigandInterfaceList.SelectMany(a => a.ReceptorInterfacePdbResSeqIndexes).Distinct().OrderBy(a => a).ToList();
var currentLigandInterfaceListGroups = currentLigandInterfaceList.Select(a => new List <LigandInterface>()
{
a
}).ToList();
foreach (var index in resSeqIndexes)
{
var lists = currentLigandInterfaceListGroups.Where(a => a.Any(b => b.ReceptorInterfacePdbResSeqIndexes.Contains(index))).ToList();
currentLigandInterfaceListGroups = currentLigandInterfaceListGroups.Except(lists).ToList();
var list = lists.SelectMany(a => a).ToList();
var sslist = list.GroupBy(a => a.ReceptorInterfaceMainSecStruct).ToList();
sslist.ForEach(list2 => currentLigandInterfaceListGroups.Add(list2.ToList()));
}
foreach (var g in currentLigandInterfaceListGroups)
{
g.ForEach(a => a.ContactCluster = currentLigandInterfaceListGroups.IndexOf(g) + 1);
}
//return;
}
//File.WriteAllLines(@"c:\phd\pdb_quality.csv", crystalToSeqQuality.Select(a => a.Item1 + " " + a.Item2).ToList());
//File.WriteAllLines(@"c:\phd\pdb_homology.csv", homology.Select(a => a.Item1 + " " + a.Item2 + " " + a.Item3).ToList());
LigandInterface.Save(ligandInterfaceList);
}
