private void LogBarrel(StrandGroupMaker myStrandGroup)
{
var numberOfStrands = 0;
if (this.Success)
{
numberOfStrands = myStrandGroup.BarrelStrands.Count;
}
var chainID = "";
if (this.barrelType == "mono")
{
chainID = myStrandGroup.BarrelStrands[0].ChainName;
}
else if (this.barrelType == "poly")
{
var curChain = myStrandGroup.BarrelStrands[0].ChainName;
chainID += curChain;
foreach (Strand curStrand in myStrandGroup.BarrelStrands)
{
if (curStrand.ChainName != curChain)
{
curChain = curStrand.ChainName;
chainID += "," + curChain;
}
}
}
else
{
chainID = "NA";
}
string logFileLoc = Global.OUTPUT_DIR + "Log.txt";
using (StreamWriter log = File.AppendText(logFileLoc))
{
log.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}", this.PdbName, this.Success, this.barrelType, chainID, numberOfStrands);
}
}
//barrel constructor
public AllBarrel(ref Protein newProt)
{
this.newProt = newProt;
this.PdbName = newProt.PdbName;
this.protoBarrel = new List <List <List <int> > >();
this.Strands = new List <Strand>();
this.barrelType = "NA";
this.Success = false;
var resList = new List <Res>();
StrandGroupMaker myStrandGroup = null;
CreateStrandList(ref newProt);
SharedFunctions.writePymolScriptForStrandsRik(Strands, Global.OUTPUT_DIR, Global.DB_DIR, PdbName);
foreach (var chain in newProt.Chains)
{
foreach (var residue in chain)
{
resList.Add(residue);
}
}
#region find the barrel
var isMonoFlag = false;
var isPolyFlag = false;
var flag = true;
#region Hard code some PolyBarrels
if (new List <string>()
{
"5GAQ", "6RB9", "3W9T", "5WC3", "3ANZ", "4P1X", "5JZT"
}.Contains(PdbName))
{
flag = false;
}
#endregion
if (flag)
{
foreach (var chain in newProt.Chains)//check for each chain first
{
var monoStrands = new List <Strand>();
foreach (var strand in this.Strands)
{
if (strand.ChainName == chain.ChainName)
{
monoStrands.Add(strand);
}
}
if (monoStrands.Count != 0)
{
Console.WriteLine($"Starting strandGroupMaker for Chain {chain.ChainName}");
myStrandGroup = new StrandGroupMaker(newProt, monoStrands);
if (myStrandGroup.GroupOfGroup.Any(group => group.IsBarrel == true))
{
isMonoFlag = true;
this.Strands = myStrandGroup.BarrelStrands;
var group = myStrandGroup.GroupOfGroup.First(group => group.IsBarrel == true);
this.Ncentroid = group.Ncentroid;
this.Ccentroid = group.Ccentroid;
this.CellipseCoords = group.CellipseCoords;
this.NellipseCoords = group.NellipseCoords;
this.Axis = group.Axis;
Console.WriteLine($"Protein {PdbName} Chain {chain.ChainName} has a Mono barrel with {myStrandGroup.BarrelStrands.Count} strands");
this.barrelType = "mono";
this.Success = true;
//LogBarrel(myStrandGroup);
break;
}
}
}
}
if (isMonoFlag == false) //if all the chain comes back as negative then check for poly
{
this.Strands = new List <Strand>(); //reseting the list of strands as it gets modified by the single chain StrandGroupMaker
CreateStrandList(ref newProt);
//Console.WriteLine($"\nStarting strandGroupMaker for whole protein");
myStrandGroup = new StrandGroupMaker(newProt, Strands);
if (myStrandGroup.GroupOfGroup.Any(group => group.IsBarrel == true))
{
isPolyFlag = true;
this.Strands = myStrandGroup.BarrelStrands;
Console.WriteLine($"Protein {PdbName} has a Poly barrel with {myStrandGroup.BarrelStrands.Count} strands");
this.barrelType = "poly";
this.Success = true;
//LogBarrel(myStrandGroup);
}
}
#endregion
if (!isMonoFlag && !isPolyFlag)
{
//LogBarrel(null);
}
else
{
this.Strands = myStrandGroup.BarrelStrands;
var barrel_strand_ctr = 0;
foreach (Strand strand in this.Strands)
{
strand.StrandNum = barrel_strand_ctr++;
foreach (Res r in strand)
{
r.StrandNum = barrel_strand_ctr;
}
}
/* ---------output information from mono --------- */
this.StrandLength = SharedFunctions.getStrandLengths(this.Strands, path, this.PdbName);
//this.PrevTwists = SharedFunctions.writeTwists(this.Strands, Global.OUTPUT_DIR, this.PdbName);
#region Amino Acid Pair
try
{
SharedFunctions.AminoAcidPairs(this.Strands, Global.OUTPUT_DIR, Global.DB_DIR, this.PdbName);
}
catch (Exception exception)
{
Console.WriteLine("Failed to make pairs");
string fileLocation3 = Global.OUTPUT_DIR + "AAPairErrorLog.txt";
using (StreamWriter file3 = new StreamWriter(fileLocation3, append: true))
{
string newLine3 = this.PdbName + "\t" + exception.InnerException + exception.Message + "\t" + exception.StackTrace + "\t" + exception.Source + "\t" + exception.Data + "\n";
file3.WriteLine(newLine3);
}
}
#endregion
if (PdbName == "2HLV")
{
SharedFunctions.setInOut(this.Strands, path, this.PdbName, this.Axis, this.Ccentroid, this.Ncentroid);
}
else
{
SharedFunctions.setInOutMin(this.Strands, Global.OUTPUT_DIR, this.PdbName, this.Ccentroid, this.Ncentroid);
}
SharedFunctions.WritePymolScriptForInOutStrands(this.Strands, Global.OUTPUT_DIR, Global.DB_DIR, PdbName, Ccentroid, Ncentroid);
this.AvgTilt = SharedFunctions.getTiltsByAA(this.Strands, path, this.PdbName, this.Axis, ref Global.AADict);
bool detail_variable_output = true;
if (detail_variable_output == true)
{
if (!System.IO.Directory.Exists(path + "detailCheck"))
{
System.IO.Directory.CreateDirectory(path + "detailCheck");
}
string fileLocation1 = path + "detailCheck/AllAtomVariables_" + this.PdbName + ".txt";
using (System.IO.StreamWriter file = new System.IO.StreamWriter(fileLocation1))
{
file.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}\t{9}\t{10}\t{11}\t{12}\t{13}\t{14}t{15}", "strand.ChainName", "strand.ChainNum", "strand.betaStrandNum", "strand.StrandNum", "res.ThreeLetCode", "res.OneLetCode", "res.SeqID", "res.ResNum", "res.Inward", "res.Atoms.Count", "atom.AtomName", "atom.AtomNum", "atom.AtomType", "atom.Coords.X", "atom.Coords.Y", "atom.Coords.Z");
foreach (Strand strand in this.Strands)
{
foreach (Res res in strand)
{
foreach (Atom atom in res)
{
if (atom.AtomName == "CA")
{
file.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}\t{9}\t{10}\t{11}\t{12}\t{13}\t{14}\t{15}", strand.ChainName, strand.ChainNum, strand.betaStrandNum, strand.StrandNum, res.ThreeLetCode, res.OneLetCode, res.SeqID, res.ResNum, res.Inward, res.Atoms.Count, atom.AtomName, atom.AtomNum, atom.AtomType, atom.Coords.X, atom.Coords.Y, atom.Coords.Z);
}
}
}
}
}
}
SharedFunctions.writePymolScriptForBarrelStrands(this.Strands, Global.OUTPUT_DIR, Global.DB_DIR, this.PdbName);
}
this.Success = true;
}