public SpreadsheetCell[] SpreadsheetDataRow()
{
var atomPoint1 = PointConversions.AtomPoint3D(InteractingAtomPair.Atom1);
var atomPoint2 = PointConversions.AtomPoint3D(InteractingAtomPair.Atom2);
var row = new[]
{
new SpreadsheetCell(ProteinId),
new SpreadsheetCell(InteractingAtomPair.Distance),
new SpreadsheetCell("-"),
new SpreadsheetCell(InteractingAtomPair.Atom1.chainID.FieldValue),
new SpreadsheetCell(ProteinInterfaceIdA),
new SpreadsheetCell(InteractingAtomPair.Atom1.resSeq.FieldValue),
new SpreadsheetCell(InteractingAtomPair.Atom1.name.FieldValue),
new SpreadsheetCell(AminoAcidConversions.AminoAcidNameToCode1L(InteractingAtomPair.Atom1.resName.FieldValue)),
new SpreadsheetCell(AminoAcidGroups.AminoAcidGroups.GetSubgroupColorNames(AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.Physicochemical)[AminoAcidGroups.AminoAcidGroups.ConvertAminoAcidNameCodeToSubgroupNumbers(AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.Physicochemical, InteractingAtomPair.Atom1.resName.FieldValue)[0]]),
new SpreadsheetCell(AminoAcidGroups.AminoAcidGroups.GetSubgroupColorNames(AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.Hydrophobicity)[AminoAcidGroups.AminoAcidGroups.ConvertAminoAcidNameCodeToSubgroupNumbers(AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.Hydrophobicity, InteractingAtomPair.Atom1.resName.FieldValue)[0]]),
new SpreadsheetCell(AminoAcidGroups.AminoAcidGroups.GetSubgroupColorNames(AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.PdbSum)[AminoAcidGroups.AminoAcidGroups.ConvertAminoAcidNameCodeToSubgroupNumbers(AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.PdbSum, InteractingAtomPair.Atom1.resName.FieldValue)[0]]),
new SpreadsheetCell(AminoAcidGroups.AminoAcidGroups.GetSubgroupColorNames(AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.UniProtKb)[AminoAcidGroups.AminoAcidGroups.ConvertAminoAcidNameCodeToSubgroupNumbers(AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.UniProtKb, InteractingAtomPair.Atom1.resName.FieldValue)[0]]),
new SpreadsheetCell(atomPoint1.X),
new SpreadsheetCell(atomPoint1.Y),
new SpreadsheetCell(atomPoint1.Z),
new SpreadsheetCell("<-->"),
new SpreadsheetCell(InteractingAtomPair.Atom2.chainID.FieldValue),
new SpreadsheetCell(ProteinInterfaceIdB),
new SpreadsheetCell(InteractingAtomPair.Atom2.resSeq.FieldValue),
new SpreadsheetCell(InteractingAtomPair.Atom2.name.FieldValue),
new SpreadsheetCell(AminoAcidConversions.AminoAcidNameToCode1L(InteractingAtomPair.Atom2.resName.FieldValue)),
new SpreadsheetCell(AminoAcidGroups.AminoAcidGroups.GetSubgroupColorNames(AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.Physicochemical)[AminoAcidGroups.AminoAcidGroups.ConvertAminoAcidNameCodeToSubgroupNumbers(AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.Physicochemical, InteractingAtomPair.Atom2.resName.FieldValue)[0]]),
new SpreadsheetCell(AminoAcidGroups.AminoAcidGroups.GetSubgroupColorNames(AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.Hydrophobicity)[AminoAcidGroups.AminoAcidGroups.ConvertAminoAcidNameCodeToSubgroupNumbers(AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.Hydrophobicity, InteractingAtomPair.Atom2.resName.FieldValue)[0]]),
new SpreadsheetCell(AminoAcidGroups.AminoAcidGroups.GetSubgroupColorNames(AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.PdbSum)[AminoAcidGroups.AminoAcidGroups.ConvertAminoAcidNameCodeToSubgroupNumbers(AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.PdbSum, InteractingAtomPair.Atom2.resName.FieldValue)[0]]),
new SpreadsheetCell(AminoAcidGroups.AminoAcidGroups.GetSubgroupColorNames(AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.UniProtKb)[AminoAcidGroups.AminoAcidGroups.ConvertAminoAcidNameCodeToSubgroupNumbers(AminoAcidGroups.AminoAcidGroups.EnumAminoAcidGroups.UniProtKb, InteractingAtomPair.Atom2.resName.FieldValue)[0]]),
new SpreadsheetCell(atomPoint2.X),
new SpreadsheetCell(atomPoint2.Y),
new SpreadsheetCell(atomPoint2.Z)
};
return(row);
}
public static List <Sequence> LoadStructureFile(ProteinBioClass.StructureChainListContainer pdb, string pdbId = "", char[] chainIdWhiteList = null, bool padMissingBool = true, int[] startResSeq = null, int[] endResSeq = null, char outsidePaddingChar = ' ', char insidePaddingChar = 'X')
{
var result = new List <Sequence>();
List <ProteinBioClass.AtomListContainer> x = pdb.ChainList;
var zeroBased = pdb.ChainList.Any(a => a.AtomList.Any(b => Int32.Parse(b.resSeq.FieldValue) == 0));
if ((chainIdWhiteList != null && chainIdWhiteList.Length > 0) && (startResSeq != null && startResSeq.Length > 0) && (endResSeq != null && endResSeq.Length > 0))
{
for (int chainIndex = 0; chainIndex < pdb.ChainList.Count; chainIndex++)
{
var chainId = pdb.ChainList[chainIndex].ChainId;
var chainStartResSeq = startResSeq[chainIdWhiteList.ToList().FindIndex(a => a == chainId)];
var chainEndResSeq = endResSeq[chainIdWhiteList.ToList().FindIndex(a => a == chainId)];
pdb.ChainList[chainIndex].AtomList = pdb.ChainList[chainIndex].AtomList.Where(a => Int32.Parse(a.resSeq.FieldValue) >= chainStartResSeq && Int32.Parse(a.resSeq.FieldValue) <= chainEndResSeq).ToList();
}
}
for (int index = 0; index < pdb.ChainList.Count; index++)
{
var suplAtoms = new List <ATOM_Record>();
foreach (var atom in pdb.ChainList[index].AtomList)
{
if (String.IsNullOrWhiteSpace(atom.iCode.FieldValue))
{
continue;
}
var resSeq = atom.resSeq.FieldValue;
var aa = atom.resName.FieldValue;
var atomName = atom.name.FieldValue;
var matches = pdb.ChainList[index].AtomList.Where(a => a.resSeq.FieldValue == atom.resSeq.FieldValue && a.resName.FieldValue == atom.resName.FieldValue && a.name.FieldValue == atom.name.FieldValue).ToList();
if (matches.Count <= 1)
{
continue;
}
var noIcode = matches.FindIndex(a => string.IsNullOrWhiteSpace(a.iCode.FieldValue));
if (noIcode > -1)
{
suplAtoms.AddRange(matches.Where((a, i) => i != noIcode).ToList());
}
else
{
suplAtoms.AddRange(matches.Skip(1).ToList());
}
}
//pdb.ChainList[index].AtomList = pdb.ChainList[index].AtomList.Where(a => String.IsNullOrWhiteSpace(a.iCode.FieldValue)).ToList();
pdb.ChainList[index].AtomList.RemoveAll(a => suplAtoms.Contains(a));
var chain = pdb.ChainList[index];
var first = chain.AtomList.Min(a => Int32.Parse(a.resSeq.FieldValue));
var last = chain.AtomList.Max(a => Int32.Parse(a.resSeq.FieldValue));
var resSeqOffset = first < 0 ? Math.Abs(first) + 1 : 0;
var chainAa = new char[last + (zeroBased ? 1 : 0) + resSeqOffset];
var chainAaMask = new bool[last + (zeroBased ? 1 : 0) + resSeqOffset];
for (var i = 0; i < chainAa.Length; i++)
{
chainAa[i] = outsidePaddingChar;
chainAaMask[i] = false;
}
foreach (var atom in chain.AtomList)
{
var aa = atom.resName.FieldValue;
if (String.IsNullOrWhiteSpace(aa))
{
aa = "" + insidePaddingChar;
}
var res = Int32.Parse(atom.resSeq.FieldValue);
if (!zeroBased)
{
res = res - 1;
}
res += resSeqOffset;
var aa1l = AminoAcidConversions.AminoAcidNameToCode1L(aa);
chainAa[res] = aa1l[0];
chainAaMask[res] = true;
}
for (var i = first; i <= last; i++)
{
var res = i;
res += resSeqOffset;
if (!zeroBased)
{
res = res - 1;
}
if (!chainAaMask[res])
{
chainAa[res] = insidePaddingChar;
}
}
var chainAaStr = String.Join("", chainAa);
if (!padMissingBool)
{
chainAaStr = chainAaStr.Trim(outsidePaddingChar);
}
result.Add(new Sequence(">" + pdbId + ":" + chain.ChainId, chainAaStr));
}
return(result);
}
static void Main(string[] args)
{
// the indexes of data, contacts1 and contacts2 all match
var data = MultiBindingInterface.LoadAuthorData(@"c:\multibinding\multibinding.csv", @"c:\multibinding\multibinding_homolog_clusters.csv");
var contactsPartner1 =
data.Select(
a =>
{
var x = ProteinBioClass.AtomPair.LoadAtomPairList(@"C:\multibinding\contacts\contacts_pdb" +
a.InteractionChainsPdb1.ToUpperInvariant() + ".pdb")
.Where(
b =>
(b.Atom1.chainID.FieldValue.ToUpperInvariant()[0] ==
a.InteractionChainsPdb1Chain1
&&
b.Atom2.chainID.FieldValue.ToUpperInvariant()[0] ==
a.InteractionChainsPdb1Chain2)
||
(b.Atom1.chainID.FieldValue.ToUpperInvariant()[0] ==
a.InteractionChainsPdb1Chain2
&&
b.Atom2.chainID.FieldValue.ToUpperInvariant()[0] ==
a.InteractionChainsPdb1Chain1)).ToList();
x = x.Select(c =>
{
if (c.Atom1.chainID.FieldValue.ToUpperInvariant()[0] == a.InteractionChainsPdb1Chain2)
{
c.SwapAtoms();
}
return(c);
}).ToList();
return(x);
}).ToList();
var contactsPartner2 =
data.Select(
a =>
{
var x = ProteinBioClass.AtomPair.LoadAtomPairList(@"C:\multibinding\contacts\contacts_pdb" +
a.InteractionChainsPdb2.ToUpperInvariant() + ".pdb")
.Where(
b =>
(b.Atom1.chainID.FieldValue.ToUpperInvariant()[0] ==
a.InteractionChainsPdb2Chain1
&&
b.Atom2.chainID.FieldValue.ToUpperInvariant()[0] ==
a.InteractionChainsPdb2Chain2)
||
(b.Atom1.chainID.FieldValue.ToUpperInvariant()[0] ==
a.InteractionChainsPdb2Chain2
&&
b.Atom2.chainID.FieldValue.ToUpperInvariant()[0] ==
a.InteractionChainsPdb2Chain1)).ToList();
x = x.Select(c =>
{
if (c.Atom1.chainID.FieldValue.ToUpperInvariant()[0] == a.InteractionChainsPdb2Chain2)
{
c.SwapAtoms();
}
return(c);
}).ToList();
return(x);
}).ToList();
var interfacePartner1 = contactsPartner1.Select(a =>
{
var resSeqChain1 = a.Select(b => int.Parse(b.Atom1.resSeq.FieldValue)).ToList();
var resSeqChain2 = a.Select(b => int.Parse(b.Atom2.resSeq.FieldValue)).ToList();
if (resSeqChain1.Count > 0 && resSeqChain2.Count > 0)
{
return(new Tuple <int, int, int, int>(resSeqChain1.Min(), resSeqChain1.Max(), resSeqChain2.Min(),
resSeqChain2.Max()));
}
else
{
return(null);
}
}).ToList();
var interfacePartner2 = contactsPartner2.Select(a =>
{
var resSeqChain1 = a.Select(b => int.Parse(b.Atom1.resSeq.FieldValue)).ToList();
var resSeqChain2 = a.Select(b => int.Parse(b.Atom2.resSeq.FieldValue)).ToList();
if (resSeqChain1.Count > 0 && resSeqChain2.Count > 0)
{
return(new Tuple <int, int, int, int>(resSeqChain1.Min(), resSeqChain1.Max(), resSeqChain2.Min(),
resSeqChain2.Max()));
}
else
{
return(null);
}
}).ToList();
// var resultData = new List<MultiBindingInterface>();
for (int index = 0; index < data.Count; index++)
{
var d = data[index];
var cp1 = contactsPartner1[index];
var cp2 = contactsPartner2[index];
var ip1 = interfacePartner1[index];
var ip2 = interfacePartner2[index];
if (d == null || cp1 == null || cp2 == null || ip1 == null || ip2 == null)
{
continue;
}
if (cp1.Count == 0 || cp2.Count == 0)
{
continue;
}
var p1c1_pdb = ProteinBioClass.PdbAtomicChains(@"c:\multibinding\pdb" + d.InteractionChainsPdb1 + ".pdb", new char[] { d.InteractionChainsPdb1Chain1 }, -1, -1, true);
var p1c2_pdb = ProteinBioClass.PdbAtomicChains(@"c:\multibinding\pdb" + d.InteractionChainsPdb1 + ".pdb", new char[] { d.InteractionChainsPdb1Chain2 }, -1, -1, true);
var p2c1_pdb = ProteinBioClass.PdbAtomicChains(@"c:\multibinding\pdb" + d.InteractionChainsPdb2 + ".pdb", new char[] { d.InteractionChainsPdb2Chain1 }, -1, -1, true);
var p2c2_pdb = ProteinBioClass.PdbAtomicChains(@"c:\multibinding\pdb" + d.InteractionChainsPdb2 + ".pdb", new char[] { d.InteractionChainsPdb2Chain2 }, -1, -1, true);
var p1c1_res_seq = p1c1_pdb.ChainList.First().AtomList.Select(a => int.Parse(a.resSeq.FieldValue)).ToList();
var p1c2_res_seq = p1c2_pdb.ChainList.First().AtomList.Select(a => int.Parse(a.resSeq.FieldValue)).ToList();
var p2c1_res_seq = p2c1_pdb.ChainList.First().AtomList.Select(a => int.Parse(a.resSeq.FieldValue)).ToList();
var p2c2_res_seq = p2c2_pdb.ChainList.First().AtomList.Select(a => int.Parse(a.resSeq.FieldValue)).ToList();
var cp1a1_res_seq = cp1.Select(a => int.Parse(a.Atom1.resSeq.FieldValue)).ToList();
var cp1a2_res_seq = cp1.Select(a => int.Parse(a.Atom2.resSeq.FieldValue)).ToList();
var cp2a1_res_seq = cp2.Select(a => int.Parse(a.Atom1.resSeq.FieldValue)).ToList();
var cp2a2_res_seq = cp2.Select(a => int.Parse(a.Atom2.resSeq.FieldValue)).ToList();
var cp1a1_min = cp1a1_res_seq.Min();
var cp1a1_max = cp1a1_res_seq.Max();
var cp1a2_min = cp1a2_res_seq.Min();
var cp1a2_max = cp1a2_res_seq.Max();
var cp2a1_min = cp2a1_res_seq.Min();
var cp2a1_max = cp2a1_res_seq.Max();
var cp2a2_min = cp2a2_res_seq.Min();
var cp2a2_max = cp2a2_res_seq.Max();
var cp1a1_best50_min = int.MinValue;
var cp1a1_best50_max = int.MinValue;
var cp1a1_best50_interactions = int.MinValue;
var cp1a1_best50_middle_finder = new List <Tuple <int, int, int> >();
var interface_target_length = 50;
for (var x = cp1a1_min - interface_target_length; x <= cp1a1_max; x++)
{
if (Math.Abs(cp1a1_max - cp1a1_min) <= interface_target_length)
{
cp1a1_best50_min = cp1a1_min;
cp1a1_best50_max = cp1a1_max;
cp1a1_best50_interactions = cp1a1_res_seq.Count;
break;
}
var min = x;
var max = x + interface_target_length > cp1a1_max ? cp1a1_max : x + interface_target_length;
var best50 = cp1a1_res_seq.Count(a => a >= cp1a1_best50_min && a <= cp1a1_best50_max);
if (best50 == cp1a1_best50_interactions)
{
cp1a1_best50_middle_finder.Add(new Tuple <int, int, int>(min, max, best50));
}
if (cp1a1_best50_interactions == int.MinValue || best50 > cp1a1_best50_interactions)
{
cp1a1_best50_middle_finder.Clear();
cp1a1_best50_middle_finder.Add(new Tuple <int, int, int>(min, max, best50));
cp1a1_best50_min = min;
cp1a1_best50_max = max;
cp1a1_best50_interactions = best50;
}
if (x + interface_target_length >= cp1a1_max)
{
break;
}
}
if (cp1a1_best50_middle_finder.Count > 2)
{
var middle = cp1a1_best50_middle_finder[cp1a1_best50_middle_finder.Count / 2];
cp1a1_best50_min = middle.Item1;
cp1a1_best50_max = middle.Item2;
cp1a1_best50_interactions = middle.Item3;
}
var cp1a2_best50_min = int.MinValue;
var cp1a2_best50_max = int.MinValue;
var cp1a2_best50_interactions = int.MinValue;
var cp1a2_best50_middle_finder = new List <Tuple <int, int, int> >();
for (var x = cp1a2_min - interface_target_length; x <= cp1a2_max; x++)
{
if (Math.Abs(cp1a2_max - cp1a2_min) <= interface_target_length)
{
cp1a2_best50_min = cp1a2_min;
cp1a2_best50_max = cp1a2_max;
cp1a2_best50_interactions = cp1a2_res_seq.Count;
break;
}
var min = x;
var max = x + interface_target_length > cp1a2_max ? cp1a2_max : x + interface_target_length;
var best50 = cp1a2_res_seq.Count(a => a >= cp1a2_best50_min && a <= cp1a2_best50_max);
if (best50 == cp1a2_best50_interactions)
{
cp1a2_best50_middle_finder.Add(new Tuple <int, int, int>(min, max, best50));
}
if (cp1a2_best50_interactions == int.MinValue || best50 > cp1a2_best50_interactions)
{
cp1a2_best50_middle_finder.Clear();
cp1a2_best50_middle_finder.Add(new Tuple <int, int, int>(min, max, best50));
cp1a2_best50_min = min;
cp1a2_best50_max = max;
cp1a2_best50_interactions = best50;
}
if (x + interface_target_length >= cp1a2_max)
{
break;
}
}
if (cp1a2_best50_middle_finder.Count > 2)
{
var middle = cp1a2_best50_middle_finder[cp1a2_best50_middle_finder.Count / 2];
cp1a2_best50_min = middle.Item1;
cp1a2_best50_max = middle.Item2;
cp1a2_best50_interactions = middle.Item3;
}
var cp2a1_best50_min = int.MinValue;
var cp2a1_best50_max = int.MinValue;
var cp2a1_best50_interactions = int.MinValue;
var cp2a1_best50_middle_finder = new List <Tuple <int, int, int> >();
for (var x = cp2a1_min - interface_target_length; x <= cp2a1_max; x++)
{
if (Math.Abs(cp2a1_max - cp2a1_min) <= interface_target_length)
{
cp2a1_best50_min = cp2a1_min;
cp2a1_best50_max = cp2a1_max;
cp2a1_best50_interactions = cp2a1_res_seq.Count;
break;
}
var min = x;
var max = x + interface_target_length > cp2a1_max ? cp2a1_max : x + interface_target_length;
var best50 = cp2a1_res_seq.Count(a => a >= cp2a1_best50_min && a <= cp2a1_best50_max);
if (best50 == cp2a1_best50_interactions)
{
cp2a1_best50_middle_finder.Add(new Tuple <int, int, int>(min, max, best50));
}
if (cp2a1_best50_interactions == int.MinValue || best50 > cp2a1_best50_interactions)
{
cp2a1_best50_middle_finder.Clear();
cp2a1_best50_middle_finder.Add(new Tuple <int, int, int>(min, max, best50));
cp2a1_best50_min = min;
cp2a1_best50_max = max;
cp2a1_best50_interactions = best50;
}
if (x + interface_target_length >= cp2a1_max)
{
break;
}
}
if (cp2a1_best50_middle_finder.Count > 2)
{
var middle = cp2a1_best50_middle_finder[cp2a1_best50_middle_finder.Count / 2];
cp2a1_best50_min = middle.Item1;
cp2a1_best50_max = middle.Item2;
cp2a1_best50_interactions = middle.Item3;
}
var cp2a2_best50_min = int.MinValue;
var cp2a2_best50_max = int.MinValue;
var cp2a2_best50_interactions = int.MinValue;
var cp2a2_best50_middle_finder = new List <Tuple <int, int, int> >();
for (var x = cp2a2_min - interface_target_length; x <= cp2a2_max; x++)
{
if (Math.Abs(cp2a2_max - cp2a2_min) <= interface_target_length)
{
cp2a2_best50_min = cp2a2_min;
cp2a2_best50_max = cp2a2_max;
cp2a2_best50_interactions = cp2a2_res_seq.Count;
break;
}
var min = x;
var max = x + interface_target_length > cp2a2_max ? cp2a2_max : x + interface_target_length;
var best50 = cp2a2_res_seq.Count(a => a >= cp2a2_best50_min && a <= cp2a2_best50_max);
if (best50 == cp2a2_best50_interactions)
{
cp2a2_best50_middle_finder.Add(new Tuple <int, int, int>(min, max, best50));
}
if (cp2a2_best50_interactions == int.MinValue || best50 > cp2a2_best50_interactions)
{
cp2a2_best50_middle_finder.Clear();
cp2a2_best50_middle_finder.Add(new Tuple <int, int, int>(min, max, best50));
cp2a2_best50_min = min;
cp2a2_best50_max = max;
cp2a2_best50_interactions = best50;
}
if (x + interface_target_length >= cp2a2_max)
{
break;
}
}
if (cp2a2_best50_middle_finder.Count > 2)
{
var middle = cp2a2_best50_middle_finder[cp2a2_best50_middle_finder.Count / 2];
cp2a2_best50_min = middle.Item1;
cp2a2_best50_max = middle.Item2;
cp2a2_best50_interactions = middle.Item3;
}
var cp1a1_interface = string.Join("", p1c1_pdb.ChainList.First().AtomList.Where(a =>
{
var l = int.Parse(a.resSeq.FieldValue);
return(l >= cp1a1_min && l <= cp1a1_max);
}).OrderBy(c => int.Parse(c.resSeq.FieldValue)).Select(b => AminoAcidConversions.AminoAcidNameToCode1L(b.resName.FieldValue)).ToList());
var cp1a2_interface = string.Join("", p1c2_pdb.ChainList.First().AtomList.Where(a =>
{
var l = int.Parse(a.resSeq.FieldValue);
return(l >= cp1a2_min && l <= cp1a2_max);
}).OrderBy(c => int.Parse(c.resSeq.FieldValue)).Select(b => AminoAcidConversions.AminoAcidNameToCode1L(b.resName.FieldValue)).ToList());
var cp2a1_interface = string.Join("", p2c1_pdb.ChainList.First().AtomList.Where(a =>
{
var l = int.Parse(a.resSeq.FieldValue);
return(l >= cp2a1_min && l <= cp2a1_max);
}).OrderBy(c => int.Parse(c.resSeq.FieldValue)).Select(b => AminoAcidConversions.AminoAcidNameToCode1L(b.resName.FieldValue)).ToList());
var cp2a2_interface = string.Join("", p2c2_pdb.ChainList.First().AtomList.Where(a =>
{
var l = int.Parse(a.resSeq.FieldValue);
return(l >= cp2a2_min && l <= cp2a2_max);
}).OrderBy(c => int.Parse(c.resSeq.FieldValue)).Select(b => AminoAcidConversions.AminoAcidNameToCode1L(b.resName.FieldValue)).ToList());
var cp1a1_interface_interactions = new string('_', cp1a1_interface.Length);
cp1a1_interface_interactions = string.Join("", cp1a1_interface_interactions.Select((a, i) => cp1a1_res_seq.Contains(i + cp1a1_min) ? "X" : "_").ToList());
var cp1a2_interface_interactions = new string('_', cp1a2_interface.Length);
cp1a2_interface_interactions = string.Join("", cp1a2_interface_interactions.Select((a, i) => cp1a2_res_seq.Contains(i + cp1a2_min) ? "X" : "_").ToList());
var cp2a1_interface_interactions = new string('_', cp2a1_interface.Length);
cp2a1_interface_interactions = string.Join("", cp2a1_interface_interactions.Select((a, i) => cp2a1_res_seq.Contains(i + cp2a1_min) ? "X" : "_").ToList());
var cp2a2_interface_interactions = new string('_', cp2a2_interface.Length);
cp2a2_interface_interactions = string.Join("", cp2a2_interface_interactions.Select((a, i) => cp2a2_res_seq.Contains(i + cp2a2_min) ? "X" : "_").ToList());
var cp1a1_interactions = cp1a1_interface_interactions.Count(a => a == 'X');
var cp1a2_interactions = cp1a2_interface_interactions.Count(a => a == 'X');
var cp2a1_interactions = cp2a1_interface_interactions.Count(a => a == 'X');
var cp2a2_interactions = cp2a2_interface_interactions.Count(a => a == 'X');
var cp1a1_best50_interface = string.Join("", p1c1_pdb.ChainList.First().AtomList.Where(a =>
{
var l = int.Parse(a.resSeq.FieldValue);
return(l >= cp1a1_best50_min && l <= cp1a1_best50_max);
}).OrderBy(c => int.Parse(c.resSeq.FieldValue)).Select(b => AminoAcidConversions.AminoAcidNameToCode1L(b.resName.FieldValue)).ToList());
var cp1a2_best50_interface = string.Join("", p1c2_pdb.ChainList.First().AtomList.Where(a =>
{
var l = int.Parse(a.resSeq.FieldValue);
return(l >= cp1a2_best50_min && l <= cp1a2_best50_max);
}).OrderBy(c => int.Parse(c.resSeq.FieldValue)).Select(b => AminoAcidConversions.AminoAcidNameToCode1L(b.resName.FieldValue)).ToList());
var cp2a1_best50_interface = string.Join("", p2c1_pdb.ChainList.First().AtomList.Where(a =>
{
var l = int.Parse(a.resSeq.FieldValue);
return(l >= cp2a1_best50_min && l <= cp2a1_best50_max);
}).OrderBy(c => int.Parse(c.resSeq.FieldValue)).Select(b => AminoAcidConversions.AminoAcidNameToCode1L(b.resName.FieldValue)).ToList());
var cp2a2_best50_interface = string.Join("", p2c2_pdb.ChainList.First().AtomList.Where(a =>
{
var l = int.Parse(a.resSeq.FieldValue);
return(l >= cp2a2_best50_min && l <= cp2a2_best50_max);
}).OrderBy(c => int.Parse(c.resSeq.FieldValue)).Select(b => AminoAcidConversions.AminoAcidNameToCode1L(b.resName.FieldValue)).ToList());
var cp1a1_best50_interface_interactions = new string('_', cp1a1_best50_interface.Length);
cp1a1_best50_interface_interactions = string.Join("", cp1a1_best50_interface_interactions.Select((a, i) => cp1a1_res_seq.Contains(i + cp1a1_best50_min) ? "X" : "_").ToList());
var cp1a2_best50_interface_interactions = new string('_', cp1a2_best50_interface.Length);
cp1a2_best50_interface_interactions = string.Join("", cp1a2_best50_interface_interactions.Select((a, i) => cp1a2_res_seq.Contains(i + cp1a2_best50_min) ? "X" : "_").ToList());
var cp2a1_best50_interface_interactions = new string('_', cp2a1_best50_interface.Length);
cp2a1_best50_interface_interactions = string.Join("", cp2a1_best50_interface_interactions.Select((a, i) => cp2a1_res_seq.Contains(i + cp2a1_best50_min) ? "X" : "_").ToList());
var cp2a2_best50_interface_interactions = new string('_', cp2a2_best50_interface.Length);
cp2a2_best50_interface_interactions = string.Join("", cp2a2_best50_interface_interactions.Select((a, i) => cp2a2_res_seq.Contains(i + cp2a2_best50_min) ? "X" : "_").ToList());
d.Pdb1Chain1InterfaceStart = ip1.Item1;
d.Pdb1Chain1InterfaceEnd = ip1.Item2;
d.Pdb1Chain1TotalInteractions = cp1a1_interactions;
d.Pdb1Chain1InterfaceSequence = cp1a1_interface;
d.Pdb1Chain1InterfaceMask = cp1a1_interface_interactions;
d.Pdb1Chain1Best50InterfaceStart = cp1a1_best50_min;
d.Pdb1Chain1Best50InterfaceEnd = cp1a1_best50_max;
d.Pdb1Chain1Best50TotalInteractions = cp1a1_best50_interactions;
d.Pdb1Chain1Best50InterfaceSequence = cp1a1_best50_interface;
d.Pdb1Chain1Best50InterfaceMask = cp1a1_best50_interface_interactions;
d.Pdb1Chain2InterfaceStart = ip1.Item3;
d.Pdb1Chain2InterfaceEnd = ip1.Item4;
d.Pdb1Chain2TotalInteractions = cp1a2_interactions;
d.Pdb1Chain2InterfaceSequence = cp1a2_interface;
d.Pdb1Chain2InterfaceMask = cp1a2_interface_interactions;
d.Pdb1Chain2Best50InterfaceStart = cp1a2_best50_min;
d.Pdb1Chain2Best50InterfaceEnd = cp1a2_best50_max;
d.Pdb1Chain2Best50TotalInteractions = cp1a2_best50_interactions;
d.Pdb1Chain2Best50InterfaceSequence = cp1a2_best50_interface;
d.Pdb1Chain2Best50InterfaceMask = cp1a2_best50_interface_interactions;
d.Pdb2Chain1InterfaceStart = ip2.Item1;
d.Pdb2Chain1InterfaceEnd = ip2.Item2;
d.Pdb2Chain1TotalInteractions = cp2a1_interactions;
d.Pdb2Chain1InterfaceSequence = cp2a1_interface;
d.Pdb2Chain1InterfaceMask = cp2a1_interface_interactions;
d.Pdb2Chain1Best50InterfaceStart = cp2a1_best50_min;
d.Pdb2Chain1Best50InterfaceEnd = cp2a1_best50_max;
d.Pdb2Chain1Best50TotalInteractions = cp2a1_best50_interactions;
d.Pdb2Chain1Best50InterfaceSequence = cp2a1_best50_interface;
d.Pdb2Chain1Best50InterfaceMask = cp2a1_best50_interface_interactions;
d.Pdb2Chain2InterfaceStart = ip2.Item3;
d.Pdb2Chain2InterfaceEnd = ip2.Item4;
d.Pdb2Chain2TotalInteractions = cp2a2_interactions;
d.Pdb2Chain2InterfaceSequence = cp2a2_interface;
d.Pdb2Chain2InterfaceMask = cp2a2_interface_interactions;
d.Pdb2Chain2Best50InterfaceStart = cp2a2_best50_min;
d.Pdb2Chain2Best50InterfaceEnd = cp2a2_best50_max;
d.Pdb2Chain2Best50TotalInteractions = cp2a2_best50_interactions;
d.Pdb2Chain2Best50InterfaceSequence = cp2a2_best50_interface;
d.Pdb2Chain2Best50InterfaceMask = cp2a2_best50_interface_interactions;
}
var output = data.Select(a => a.ToString()).ToList();
output.Insert(0, MultiBindingInterface.Header());
File.WriteAllLines(@"c:\multibinding\MultiBinding_parsed_results.csv", output);
return;
}
static void Main(string[] args)
{
// the indexes of data, contacts1 and contacts2 all match
var data = MultiBindingInterface.Load(@"c:\pdb\new_data_set.csv");
var contactsPartner1 =
data.Select(
a =>
{
var x = FindAtomicContacts.AtomPair.LoadAtomPairList(@"C:\pdb\new_data_set\contacts\contacts_" +
a.InteractionChainsPdb1.ToLowerInvariant() + ".pdb")
.Where(
b =>
(b.Atom1.chainID.FieldValue.ToUpperInvariant() ==
a.InteractionChainsPdb1Chain1.ToUpperInvariant()
&&
b.Atom2.chainID.FieldValue.ToUpperInvariant() ==
a.InteractionChainsPdb1Chain2.ToUpperInvariant())
||
(b.Atom1.chainID.FieldValue.ToUpperInvariant() ==
a.InteractionChainsPdb1Chain2.ToUpperInvariant()
&&
b.Atom2.chainID.FieldValue.ToUpperInvariant() ==
a.InteractionChainsPdb1Chain1.ToUpperInvariant())).ToList();
x = x.Select(c =>
{
if (c.Atom1.chainID.FieldValue.ToUpperInvariant() == a.InteractionChainsPdb1Chain2.ToUpperInvariant())
{
c.SwapAtoms();
}
return(c);
}).ToList();
return(x);
}).ToList();
var contactsPartner2 =
data.Select(
a =>
{
var x = FindAtomicContacts.AtomPair.LoadAtomPairList(@"C:\pdb\new_data_set\contacts\contacts_" +
a.InteractionChainsPdb2.ToLowerInvariant() + ".pdb")
.Where(
b =>
(b.Atom1.chainID.FieldValue.ToUpperInvariant() ==
a.InteractionChainsPdb2Chain1.ToUpperInvariant()
&&
b.Atom2.chainID.FieldValue.ToUpperInvariant() ==
a.InteractionChainsPdb2Chain2.ToUpperInvariant())
||
(b.Atom1.chainID.FieldValue.ToUpperInvariant() ==
a.InteractionChainsPdb2Chain2.ToUpperInvariant()
&&
b.Atom2.chainID.FieldValue.ToUpperInvariant() ==
a.InteractionChainsPdb2Chain1.ToUpperInvariant())).ToList();
x = x.Select(c =>
{
if (c.Atom1.chainID.FieldValue.ToUpperInvariant() == a.InteractionChainsPdb2Chain2.ToUpperInvariant())
{
c.SwapAtoms();
}
return(c);
}).ToList();
return(x);
}).ToList();
var interfacePartner1 = contactsPartner1.Select(a =>
{
var resSeqChain1 = a.Select(b => int.Parse(b.Atom1.resSeq.FieldValue)).ToList();
var resSeqChain2 = a.Select(b => int.Parse(b.Atom2.resSeq.FieldValue)).ToList();
if (resSeqChain1.Count > 0 && resSeqChain2.Count > 0)
{
return(new Tuple <int, int, int, int>(resSeqChain1.Min(), resSeqChain1.Max(), resSeqChain2.Min(),
resSeqChain2.Max()));
}
else
{
return(null);
}
}).ToList();
var interfacePartner2 = contactsPartner2.Select(a =>
{
var resSeqChain1 = a.Select(b => int.Parse(b.Atom1.resSeq.FieldValue)).ToList();
var resSeqChain2 = a.Select(b => int.Parse(b.Atom2.resSeq.FieldValue)).ToList();
if (resSeqChain1.Count > 0 && resSeqChain2.Count > 0)
{
return(new Tuple <int, int, int, int>(resSeqChain1.Min(), resSeqChain1.Max(), resSeqChain2.Min(),
resSeqChain2.Max()));
}
else
{
return(null);
}
}).ToList();
var resultData = new List <string>();
for (int index = 0; index < data.Count; index++)
{
var d = data[index];
var cp1 = contactsPartner1[index];
var cp2 = contactsPartner2[index];
var ip1 = interfacePartner1[index];
var ip2 = interfacePartner2[index];
if (d == null || cp1 == null || cp2 == null || ip1 == null || ip2 == null)
{
continue;
}
if (cp1.Count == 0 || cp2.Count == 0)
{
continue;
}
var p1c1_pdb = FindAtomicContacts.PdbAtomicChains(@"c:\pdb\new_data_set\" + d.InteractionChainsPdb1 + ".pdb", new string[] { d.InteractionChainsPdb1Chain1 }, -1, -1, true);
var p1c2_pdb = FindAtomicContacts.PdbAtomicChains(@"c:\pdb\new_data_set\" + d.InteractionChainsPdb1 + ".pdb", new string[] { d.InteractionChainsPdb1Chain2 }, -1, -1, true);
var p2c1_pdb = FindAtomicContacts.PdbAtomicChains(@"c:\pdb\new_data_set\" + d.InteractionChainsPdb2 + ".pdb", new string[] { d.InteractionChainsPdb2Chain1 }, -1, -1, true);
var p2c2_pdb = FindAtomicContacts.PdbAtomicChains(@"c:\pdb\new_data_set\" + d.InteractionChainsPdb2 + ".pdb", new string[] { d.InteractionChainsPdb2Chain2 }, -1, -1, true);
var p1c1_res_seq = p1c1_pdb.ChainList.First().AtomList.Select(a => int.Parse(a.resSeq.FieldValue)).ToList();
var p1c2_res_seq = p1c2_pdb.ChainList.First().AtomList.Select(a => int.Parse(a.resSeq.FieldValue)).ToList();
var p2c1_res_seq = p2c1_pdb.ChainList.First().AtomList.Select(a => int.Parse(a.resSeq.FieldValue)).ToList();
var p2c2_res_seq = p2c2_pdb.ChainList.First().AtomList.Select(a => int.Parse(a.resSeq.FieldValue)).ToList();
var cp1a1_res_seq = cp1.Select(a => int.Parse(a.Atom1.resSeq.FieldValue)).ToList();
var cp1a2_res_seq = cp1.Select(a => int.Parse(a.Atom2.resSeq.FieldValue)).ToList();
var cp2a1_res_seq = cp2.Select(a => int.Parse(a.Atom1.resSeq.FieldValue)).ToList();
var cp2a2_res_seq = cp2.Select(a => int.Parse(a.Atom2.resSeq.FieldValue)).ToList();
var cp1a1_min = cp1a1_res_seq.Min();
var cp1a1_max = cp1a1_res_seq.Max();
var cp1a2_min = cp1a2_res_seq.Min();
var cp1a2_max = cp1a2_res_seq.Max();
var cp2a1_min = cp2a1_res_seq.Min();
var cp2a1_max = cp2a1_res_seq.Max();
var cp2a2_min = cp2a2_res_seq.Min();
var cp2a2_max = cp2a2_res_seq.Max();
var cp1a1_best50_min = int.MinValue;
var cp1a1_best50_max = int.MinValue;
var cp1a1_best50_interactions = int.MinValue;
var cp1a1_best50_middle_finder = new List <Tuple <int, int, int> >();
var interface_target_length = 50;
for (var x = cp1a1_min - interface_target_length; x <= cp1a1_max; x++)
{
if (Math.Abs(cp1a1_max - cp1a1_min) <= interface_target_length)
{
cp1a1_best50_min = cp1a1_min;
cp1a1_best50_max = cp1a1_max;
cp1a1_best50_interactions = cp1a1_res_seq.Count;
break;
}
var min = x;
var max = x + interface_target_length > cp1a1_max ? cp1a1_max : x + interface_target_length;
var best50 = cp1a1_res_seq.Count(a => a >= cp1a1_best50_min && a <= cp1a1_best50_max);
if (best50 == cp1a1_best50_interactions)
{
cp1a1_best50_middle_finder.Add(new Tuple <int, int, int>(min, max, best50));
}
if (cp1a1_best50_interactions == int.MinValue || best50 > cp1a1_best50_interactions)
{
cp1a1_best50_middle_finder.Clear();
cp1a1_best50_middle_finder.Add(new Tuple <int, int, int>(min, max, best50));
cp1a1_best50_min = min;
cp1a1_best50_max = max;
cp1a1_best50_interactions = best50;
}
if (x + interface_target_length >= cp1a1_max)
{
break;
}
}
if (cp1a1_best50_middle_finder.Count > 2)
{
var middle = cp1a1_best50_middle_finder[cp1a1_best50_middle_finder.Count / 2];
cp1a1_best50_min = middle.Item1;
cp1a1_best50_max = middle.Item2;
cp1a1_best50_interactions = middle.Item3;
}
var cp1a2_best50_min = int.MinValue;
var cp1a2_best50_max = int.MinValue;
var cp1a2_best50_interactions = int.MinValue;
var cp1a2_best50_middle_finder = new List <Tuple <int, int, int> >();
for (var x = cp1a2_min - interface_target_length; x <= cp1a2_max; x++)
{
if (Math.Abs(cp1a2_max - cp1a2_min) <= interface_target_length)
{
cp1a2_best50_min = cp1a2_min;
cp1a2_best50_max = cp1a2_max;
cp1a2_best50_interactions = cp1a2_res_seq.Count;
break;
}
var min = x;
var max = x + interface_target_length > cp1a2_max ? cp1a2_max : x + interface_target_length;
var best50 = cp1a2_res_seq.Count(a => a >= cp1a2_best50_min && a <= cp1a2_best50_max);
if (best50 == cp1a2_best50_interactions)
{
cp1a2_best50_middle_finder.Add(new Tuple <int, int, int>(min, max, best50));
}
if (cp1a2_best50_interactions == int.MinValue || best50 > cp1a2_best50_interactions)
{
cp1a2_best50_middle_finder.Clear();
cp1a2_best50_middle_finder.Add(new Tuple <int, int, int>(min, max, best50));
cp1a2_best50_min = min;
cp1a2_best50_max = max;
cp1a2_best50_interactions = best50;
}
if (x + interface_target_length >= cp1a2_max)
{
break;
}
}
if (cp1a2_best50_middle_finder.Count > 2)
{
var middle = cp1a2_best50_middle_finder[cp1a2_best50_middle_finder.Count / 2];
cp1a2_best50_min = middle.Item1;
cp1a2_best50_max = middle.Item2;
cp1a2_best50_interactions = middle.Item3;
}
var cp2a1_best50_min = int.MinValue;
var cp2a1_best50_max = int.MinValue;
var cp2a1_best50_interactions = int.MinValue;
var cp2a1_best50_middle_finder = new List <Tuple <int, int, int> >();
for (var x = cp2a1_min - interface_target_length; x <= cp2a1_max; x++)
{
if (Math.Abs(cp2a1_max - cp2a1_min) <= interface_target_length)
{
cp2a1_best50_min = cp2a1_min;
cp2a1_best50_max = cp2a1_max;
cp2a1_best50_interactions = cp2a1_res_seq.Count;
break;
}
var min = x;
var max = x + interface_target_length > cp2a1_max ? cp2a1_max : x + interface_target_length;
var best50 = cp2a1_res_seq.Count(a => a >= cp2a1_best50_min && a <= cp2a1_best50_max);
if (best50 == cp2a1_best50_interactions)
{
cp2a1_best50_middle_finder.Add(new Tuple <int, int, int>(min, max, best50));
}
if (cp2a1_best50_interactions == int.MinValue || best50 > cp2a1_best50_interactions)
{
cp2a1_best50_middle_finder.Clear();
cp2a1_best50_middle_finder.Add(new Tuple <int, int, int>(min, max, best50));
cp2a1_best50_min = min;
cp2a1_best50_max = max;
cp2a1_best50_interactions = best50;
}
if (x + interface_target_length >= cp2a1_max)
{
break;
}
}
if (cp2a1_best50_middle_finder.Count > 2)
{
var middle = cp2a1_best50_middle_finder[cp2a1_best50_middle_finder.Count / 2];
cp2a1_best50_min = middle.Item1;
cp2a1_best50_max = middle.Item2;
cp2a1_best50_interactions = middle.Item3;
}
var cp2a2_best50_min = int.MinValue;
var cp2a2_best50_max = int.MinValue;
var cp2a2_best50_interactions = int.MinValue;
var cp2a2_best50_middle_finder = new List <Tuple <int, int, int> >();
for (var x = cp2a2_min - interface_target_length; x <= cp2a2_max; x++)
{
if (Math.Abs(cp2a2_max - cp2a2_min) <= interface_target_length)
{
cp2a2_best50_min = cp2a2_min;
cp2a2_best50_max = cp2a2_max;
cp2a2_best50_interactions = cp2a2_res_seq.Count;
break;
}
var min = x;
var max = x + interface_target_length > cp2a2_max ? cp2a2_max : x + interface_target_length;
var best50 = cp2a2_res_seq.Count(a => a >= cp2a2_best50_min && a <= cp2a2_best50_max);
if (best50 == cp2a2_best50_interactions)
{
cp2a2_best50_middle_finder.Add(new Tuple <int, int, int>(min, max, best50));
}
if (cp2a2_best50_interactions == int.MinValue || best50 > cp2a2_best50_interactions)
{
cp2a2_best50_middle_finder.Clear();
cp2a2_best50_middle_finder.Add(new Tuple <int, int, int>(min, max, best50));
cp2a2_best50_min = min;
cp2a2_best50_max = max;
cp2a2_best50_interactions = best50;
}
if (x + interface_target_length >= cp2a2_max)
{
break;
}
}
if (cp2a2_best50_middle_finder.Count > 2)
{
var middle = cp2a2_best50_middle_finder[cp2a2_best50_middle_finder.Count / 2];
cp2a2_best50_min = middle.Item1;
cp2a2_best50_max = middle.Item2;
cp2a2_best50_interactions = middle.Item3;
}
var cp1a1_interface = string.Join("", p1c1_pdb.ChainList.First().AtomList.Where(a =>
{
var l = int.Parse(a.resSeq.FieldValue);
return(l >= cp1a1_best50_min && l <= cp1a1_best50_max);
}).OrderBy(c => int.Parse(c.resSeq.FieldValue)).Select(b => AminoAcidConversions.AminoAcidNameToCode1L(b.resName.FieldValue)).ToList());
var cp1a2_interface = string.Join("", p1c2_pdb.ChainList.First().AtomList.Where(a =>
{
var l = int.Parse(a.resSeq.FieldValue);
return(l >= cp1a2_best50_min && l <= cp1a2_best50_max);
}).OrderBy(c => int.Parse(c.resSeq.FieldValue)).Select(b => AminoAcidConversions.AminoAcidNameToCode1L(b.resName.FieldValue)).ToList());
var cp2a1_interface = string.Join("", p2c1_pdb.ChainList.First().AtomList.Where(a =>
{
var l = int.Parse(a.resSeq.FieldValue);
return(l >= cp2a1_best50_min && l <= cp2a1_best50_max);
}).OrderBy(c => int.Parse(c.resSeq.FieldValue)).Select(b => AminoAcidConversions.AminoAcidNameToCode1L(b.resName.FieldValue)).ToList());
var cp2a2_interface = string.Join("", p2c2_pdb.ChainList.First().AtomList.Where(a =>
{
var l = int.Parse(a.resSeq.FieldValue);
return(l >= cp2a2_best50_min && l <= cp2a2_best50_max);
}).OrderBy(c => int.Parse(c.resSeq.FieldValue)).Select(b => AminoAcidConversions.AminoAcidNameToCode1L(b.resName.FieldValue)).ToList());
var cp1a1_interface_interactions = new string('_', cp1a1_interface.Length);
cp1a1_interface_interactions = string.Join("", cp1a1_interface_interactions.Select((a, i) => cp1a1_res_seq.Contains(i + cp1a1_best50_min) ? "X" : "_").ToList());
var cp1a2_interface_interactions = new string('_', cp1a2_interface.Length);
cp1a2_interface_interactions = string.Join("", cp1a2_interface_interactions.Select((a, i) => cp1a2_res_seq.Contains(i + cp1a2_best50_min) ? "X" : "_").ToList());
var cp2a1_interface_interactions = new string('_', cp2a1_interface.Length);
cp2a1_interface_interactions = string.Join("", cp2a1_interface_interactions.Select((a, i) => cp2a1_res_seq.Contains(i + cp2a1_best50_min) ? "X" : "_").ToList());
var cp2a2_interface_interactions = new string('_', cp2a2_interface.Length);
cp2a2_interface_interactions = string.Join("", cp2a2_interface_interactions.Select((a, i) => cp2a2_res_seq.Contains(i + cp2a2_best50_min) ? "X" : "_").ToList());
resultData.Add(string.Join(",", new string[] {
d.DomainSuperFamily,
d.InteractionChainsPdb1,
d.InteractionChainsPdb1Chain1, "" + ip1.Item1, "" + ip1.Item2, "" + cp1a1_best50_min, "" + cp1a1_best50_max, "" + cp1a1_best50_interactions, cp1a1_interface, cp1a1_interface_interactions,
d.InteractionChainsPdb1Chain2, "" + ip1.Item3, "" + ip1.Item4, "" + cp1a2_best50_min, "" + cp1a2_best50_max, "" + cp1a2_best50_interactions, cp1a2_interface, cp1a2_interface_interactions,
d.InteractionChainsPdb2,
d.InteractionChainsPdb2Chain1, "" + ip2.Item1, "" + ip2.Item2, "" + cp2a1_best50_min, "" + cp2a1_best50_max, "" + cp2a1_best50_interactions, cp2a1_interface, cp2a1_interface_interactions,
d.InteractionChainsPdb2Chain2, "" + ip2.Item3, "" + ip2.Item4, "" + cp2a2_best50_min, "" + cp2a2_best50_max, "" + cp2a2_best50_interactions, cp2a2_interface, cp2a2_interface_interactions,
}));
}
resultData.Insert(0, string.Join(",", new string[] {
"super family",
"partner 1 pdb id",
"partner 1 chain id 1", "p1c1 interface start", "p1c1 interface end", "p1c1 best 50 start", "p1c1 best 50 end", "p1c1 best 50 interactions", "p1c1 interface seq", "p1c1 interface mask",
"partner 1 chain id 2", "p1c2 interface start", "p1c1 interface end", "p1c2 best 50 start", "p1c2 best 50 end", "p1c2 best 50 interactions", "p1c2 interface seq", "p1c2 interface mask",
"partner 2 pdb id",
"partner 2 chain id 1", "p2c1 interface start", "p2c1 interface end", "p2c1 best 50 start", "p2c1 best 50 end", "p2c1 best 50 interactions", "p2c1 interface seq", "p2c1 interface mask",
"partner 2 chain id 2", "p2c2 interface start", "p2c2 interface end", "p2c2 best 50 start", "p2c2 best 50 end", "p2c2 best 50 interactions", "p2c2 interface seq", "p2c2 interface mask",
}));
File.WriteAllLines(@"c:\pdb\new_data_set_results.csv", resultData);
return;
}
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());
}
/// <summary>
/// Load proteinInterface data from the PDB file based on a list of already detected proteinInterfaces.
/// The detected proteinInterfaces may be missing data such as other atoms or residues which are also in the proteinInterface but were not
/// directly interacting.
/// The positions and lengths of the proteinInterfaces are also calculated.
/// </summary>
/// <param name="pdbFilename"></param>
/// <param name="pdbFileChains"></param>
/// <param name="singularAaToAaInteractions"></param>
/// <param name="proteinInterfacesClusteringResult"></param>
/// <param name="detectedBestStages"></param>
/// <param name="interactionBetweenProteinInterfacesContainer"></param>
/// <returns></returns>
public static List <ProteinInterfaceSequenceAndPositionData> AnalyseProteinInterfacesSequenceAndPositionData(
string pdbFilename,
Dictionary <string, List <string> > pdbIdChainIdList,
ProteinChainListContainer pdbFileChains,
ProteinChainListContainer singularAaToAaInteractions,
ClusteringFullResultListContainer proteinInterfacesClusteringResult,
int[] detectedBestStages,
InteractionBetweenProteinInterfacesListContainer interactionBetweenProteinInterfacesContainer)
{
if (string.IsNullOrWhiteSpace(pdbFilename))
{
throw new ArgumentOutOfRangeException(nameof(pdbFilename));
}
if (!File.Exists(pdbFilename))
{
throw new FileNotFoundException("File not found", pdbFilename);
}
if (ParameterValidation.IsProteinChainListContainerNullOrEmpty(singularAaToAaInteractions))
{
throw new ArgumentOutOfRangeException(nameof(singularAaToAaInteractions));
}
if (ParameterValidation.IsClusteringFullResultListContainerNullOrEmpty(proteinInterfacesClusteringResult))
{
throw new ArgumentOutOfRangeException(nameof(proteinInterfacesClusteringResult));
}
if (ParameterValidation.IsIntArrayNullOrEmpty(detectedBestStages))
{
throw new ArgumentOutOfRangeException(nameof(detectedBestStages));
}
// ProteinInterfaces are clusters with non-proteinInterfaces removed.
var result = new List <ProteinInterfaceSequenceAndPositionData>();
string proteinId = ProteinDataBankFileOperations.PdbIdFromPdbFilename(pdbFilename);
int totalChains = proteinInterfacesClusteringResult.ChainList.Count;
for (int chainIndex = 0; chainIndex < totalChains; chainIndex++)
{
int stageIndex = detectedBestStages[chainIndex];
string chainIdLetter = SpreadsheetFileHandler.AlphabetLetterRollOver(chainIndex);
List <ClusteringFullResultListContainer.Chain.Stage.Cluster> proteinInterfaceList = proteinInterfacesClusteringResult.ChainList[chainIndex].StageList[stageIndex].ClusterList;
List <ClusteringFullResultListContainer.Chain.Stage.Cluster> nonEmptyProteinInterfaceList = proteinInterfaceList.Where(a => a != null && a.AtomIndexList != null && a.AtomIndexList.Count > 0).ToList();
// loop through each proteinInterface
for (int proteinInterfaceIndex = 0; proteinInterfaceIndex < nonEmptyProteinInterfaceList.Count; proteinInterfaceIndex++)
{
ClusteringFullResultListContainer.Chain.Stage.Cluster proteinInterface = nonEmptyProteinInterfaceList[proteinInterfaceIndex];
// Find min and max residue sequence index value in the proteinInterface
MinMax proteinInterfaceResidueSequenceIndexes = MinMaxResidueSequenceIndex(proteinInterface, singularAaToAaInteractions, chainIndex);
int proteinInterfaceLength = CalculateProteinInterfaceLength(proteinInterfaceResidueSequenceIndexes.Min, proteinInterfaceResidueSequenceIndexes.Max);
string proteinInterfaceIdLetter = SpreadsheetFileHandler.AlphabetLetterRollOver(proteinInterfaceIndex);
var proteinInterfacePositionData = new ProteinInterfaceSequenceAndPositionData
{
FullProteinInterfaceId = new FullProteinInterfaceId(proteinId, chainIndex, proteinInterfaceIndex, proteinInterfaceResidueSequenceIndexes.Min, proteinInterfaceResidueSequenceIndexes.Max),
ChainIdLetter = chainIdLetter,
ProteinInterfaceIdLetter = proteinInterfaceIdLetter,
StartPosition = proteinInterfaceResidueSequenceIndexes.Min,
EndPosition = proteinInterfaceResidueSequenceIndexes.Max,
ProteinInterfaceLength = CalculateProteinInterfaceLength(proteinInterfaceResidueSequenceIndexes.Min, proteinInterfaceResidueSequenceIndexes.Max)
};
proteinInterfacePositionData.AminoAcidSequenceAllResidueSequenceIndexes = new ProteinInterfaceAminoAcidMetaData[proteinInterfacePositionData.ProteinInterfaceLength];
proteinInterfacePositionData.AminoAcidSequenceAll1L = "";
proteinInterfacePositionData.AminoAcidSequenceInteractionsAll1L = "";
proteinInterfacePositionData.AminoAcidSequenceInteractionsInsideProteinInterfacesOnly1L = "";
proteinInterfacePositionData.AminoAcidSequenceInteractionsNone1L = "";
proteinInterfacePositionData.AminoAcidSequenceInteractionsOutsideProteinInterfacesOnly1L = "";
proteinInterfacePositionData.AminoAcidSequenceAll3L = "";
proteinInterfacePositionData.AminoAcidSequenceInteractionsAll3L = "";
proteinInterfacePositionData.AminoAcidSequenceInteractionsInsideProteinInterfacesOnly3L = "";
proteinInterfacePositionData.AminoAcidSequenceInteractionsNone3L = "";
proteinInterfacePositionData.AminoAcidSequenceInteractionsOutsideProteinInterfacesOnly3L = "";
//int foundAtomCount = 0;
const string placeholder1L = "_";
const string placeholder3L = "___";
for (int residueSequenceIndex = proteinInterfaceResidueSequenceIndexes.Min; residueSequenceIndex <= proteinInterfaceResidueSequenceIndexes.Max; residueSequenceIndex++)
{
/* questions
* 1. does this reside interact with another reside which is also part of a proteinInterface?
* 2. if not, does this reside interact at all?
*/
var proteinInterfaceAminoAcidMetaData = new ProteinInterfaceAminoAcidMetaData();
proteinInterfacePositionData.AminoAcidSequenceAllResidueSequenceIndexes[proteinInterfacePositionData.AminoAcidSequenceAll1L.Length] = proteinInterfaceAminoAcidMetaData;
ATOM_Record foundAtomInsidePdbFile = AtomSearchMethods.FindAtomInsidePdbFileChain(pdbFileChains, chainIndex, residueSequenceIndex);
if (foundAtomInsidePdbFile == null)
{
// Non-CA atom is loaded here in case of missing CA atom to find the AA code for the resSeq index
var chainIdList = pdbIdChainIdList != null ? (pdbIdChainIdList.ContainsKey(proteinId) ? pdbIdChainIdList[proteinId].ToArray() : null) : null;
ProteinChainListContainer pdbFileChains2 = ProteinDataBankFileOperations.PdbAtomicChains(pdbFilename, chainIdList, -1, -1, false);
foundAtomInsidePdbFile = AtomSearchMethods.FindAtomInsidePdbFileChain(pdbFileChains2, chainIndex, residueSequenceIndex);
}
proteinInterfaceAminoAcidMetaData.PdbResidueSequenceIndex = residueSequenceIndex;
proteinInterfaceAminoAcidMetaData.ArrayMemberIndex = pdbFileChains.ChainList[chainIndex].AtomList.IndexOf(foundAtomInsidePdbFile);
proteinInterfaceAminoAcidMetaData.OppoproteinInterfaceInteractions = new bool[proteinInterfaceLength];
if (foundAtomInsidePdbFile != null)
{
proteinInterfacePositionData.AminoAcidSequenceAll1L += AminoAcidConversions.AminoAcidNameToCode1L(foundAtomInsidePdbFile.resName.FieldValue);
proteinInterfacePositionData.AminoAcidSequenceAll3L += foundAtomInsidePdbFile.resName.FieldValue.PadRight(3, '_');
}
else
{
proteinInterfacePositionData.AminoAcidSequenceAll1L += placeholder1L;
proteinInterfacePositionData.AminoAcidSequenceInteractionsAll1L += placeholder1L;
proteinInterfacePositionData.AminoAcidSequenceInteractionsInsideProteinInterfacesOnly1L += placeholder1L;
proteinInterfacePositionData.AminoAcidSequenceInteractionsOutsideProteinInterfacesOnly1L += placeholder1L;
proteinInterfacePositionData.AminoAcidSequenceInteractionsNone1L += placeholder1L;
proteinInterfacePositionData.AminoAcidSequenceAll3L += placeholder3L;
proteinInterfacePositionData.AminoAcidSequenceInteractionsAll3L += placeholder3L;
proteinInterfacePositionData.AminoAcidSequenceInteractionsInsideProteinInterfacesOnly3L += placeholder3L;
proteinInterfacePositionData.AminoAcidSequenceInteractionsOutsideProteinInterfacesOnly3L += placeholder3L;
proteinInterfacePositionData.AminoAcidSequenceInteractionsNone3L += placeholder3L;
proteinInterfaceAminoAcidMetaData.ProteinInterfaceInteractionType = ProteinInterfaceInteractionType.NoInteractionFound;
proteinInterfaceAminoAcidMetaData.NonProteinInterfaceInteractionResidueNames1L += placeholder1L;
proteinInterfaceAminoAcidMetaData.NonProteinInterfaceInteractionResidueNames3L += placeholder3L;
continue;
}
List <ATOM_Record> foundAtomInteractingWithAnotherProteinInterface = AtomSearchMethods.FindAtomInteractingWithOtherProteinInterfaces(foundAtomInsidePdbFile, interactionBetweenProteinInterfacesContainer, FindAtomInteractingWithAnotherProteinInterfaceOptions.FindAtomsInteractingWithOtherProteinInterfaces);
List <ATOM_Record> foundAtomInteractingWithNonProteinInterface = AtomSearchMethods.FindAtomInteractingWithOtherProteinInterfaces(foundAtomInsidePdbFile, interactionBetweenProteinInterfacesContainer, FindAtomInteractingWithAnotherProteinInterfaceOptions.FindAtomsInteractingWithNonProteinInterfaces);
proteinInterfaceAminoAcidMetaData.OppoproteinInterfaceInteractions = AminoAcidInteractionVector(singularAaToAaInteractions, proteinInterfacesClusteringResult, detectedBestStages, interactionBetweenProteinInterfacesContainer, chainIndex, proteinInterfaceIndex, residueSequenceIndex);
proteinInterfaceAminoAcidMetaData.ResidueName1L = AminoAcidConversions.AminoAcidNameToCode1L(foundAtomInsidePdbFile.resName.FieldValue);
proteinInterfaceAminoAcidMetaData.ResidueName3L = foundAtomInsidePdbFile.resName.FieldValue.PadRight(3, '_');
if (foundAtomInteractingWithAnotherProteinInterface != null)
{
foreach (ATOM_Record atom in foundAtomInteractingWithAnotherProteinInterface)
{
proteinInterfaceAminoAcidMetaData.ProteinInterfaceInteractionResidueNames1L += AminoAcidConversions.AminoAcidNameToCode1L(atom.resName.FieldValue);
proteinInterfaceAminoAcidMetaData.ProteinInterfaceInteractionResidueNames3L += atom.resName.FieldValue.PadRight(3, '_');
}
}
if (foundAtomInteractingWithNonProteinInterface != null)
{
foreach (ATOM_Record atom in foundAtomInteractingWithNonProteinInterface)
{
proteinInterfaceAminoAcidMetaData.NonProteinInterfaceInteractionResidueNames1L += AminoAcidConversions.AminoAcidNameToCode1L(atom.resName.FieldValue);
proteinInterfaceAminoAcidMetaData.NonProteinInterfaceInteractionResidueNames3L += atom.resName.FieldValue.PadRight(3, '_');
}
}
if (foundAtomInteractingWithAnotherProteinInterface != null && foundAtomInteractingWithAnotherProteinInterface.Count > 0)
{
proteinInterfacePositionData.AminoAcidSequenceInteractionsAll1L += AminoAcidConversions.AminoAcidNameToCode1L(foundAtomInsidePdbFile.resName.FieldValue);
proteinInterfacePositionData.AminoAcidSequenceInteractionsInsideProteinInterfacesOnly1L += AminoAcidConversions.AminoAcidNameToCode1L(foundAtomInsidePdbFile.resName.FieldValue);
proteinInterfacePositionData.AminoAcidSequenceInteractionsOutsideProteinInterfacesOnly1L += placeholder1L;
proteinInterfacePositionData.AminoAcidSequenceInteractionsNone1L += placeholder1L;
proteinInterfacePositionData.AminoAcidSequenceInteractionsAll3L += foundAtomInsidePdbFile.resName.FieldValue.PadRight(3, '_');
proteinInterfacePositionData.AminoAcidSequenceInteractionsInsideProteinInterfacesOnly3L += foundAtomInsidePdbFile.resName.FieldValue.PadRight(3, '_');
proteinInterfacePositionData.AminoAcidSequenceInteractionsOutsideProteinInterfacesOnly3L += placeholder3L;
proteinInterfacePositionData.AminoAcidSequenceInteractionsNone3L += placeholder3L;
proteinInterfaceAminoAcidMetaData.ProteinInterfaceInteractionType = ProteinInterfaceInteractionType.InteractionWithAnotherProteinInterface;
if (foundAtomInteractingWithNonProteinInterface != null && foundAtomInteractingWithNonProteinInterface.Count > 0)
{
proteinInterfaceAminoAcidMetaData.ProteinInterfaceInteractionType |= ProteinInterfaceInteractionType.InteractionWithNonProteinInterface;
}
}
else if (foundAtomInteractingWithNonProteinInterface != null && foundAtomInteractingWithNonProteinInterface.Count > 0)
{
proteinInterfacePositionData.AminoAcidSequenceInteractionsAll1L += AminoAcidConversions.AminoAcidNameToCode1L(foundAtomInsidePdbFile.resName.FieldValue);
proteinInterfacePositionData.AminoAcidSequenceInteractionsInsideProteinInterfacesOnly1L += placeholder1L;
proteinInterfacePositionData.AminoAcidSequenceInteractionsOutsideProteinInterfacesOnly1L += AminoAcidConversions.AminoAcidNameToCode1L(foundAtomInsidePdbFile.resName.FieldValue);
proteinInterfacePositionData.AminoAcidSequenceInteractionsNone1L += placeholder1L;
proteinInterfacePositionData.AminoAcidSequenceInteractionsAll3L += foundAtomInsidePdbFile.resName.FieldValue.PadRight(3, '_');
proteinInterfacePositionData.AminoAcidSequenceInteractionsInsideProteinInterfacesOnly3L += placeholder3L;
proteinInterfacePositionData.AminoAcidSequenceInteractionsOutsideProteinInterfacesOnly3L += foundAtomInsidePdbFile.resName.FieldValue.PadRight(3, '_');
proteinInterfacePositionData.AminoAcidSequenceInteractionsNone3L += placeholder3L;
proteinInterfaceAminoAcidMetaData.ProteinInterfaceInteractionType = ProteinInterfaceInteractionType.InteractionWithNonProteinInterface;
}
else
{
proteinInterfacePositionData.AminoAcidSequenceInteractionsAll1L += placeholder1L;
proteinInterfacePositionData.AminoAcidSequenceInteractionsInsideProteinInterfacesOnly1L += placeholder1L;
proteinInterfacePositionData.AminoAcidSequenceInteractionsOutsideProteinInterfacesOnly1L += placeholder1L;
proteinInterfacePositionData.AminoAcidSequenceInteractionsNone1L += AminoAcidConversions.AminoAcidNameToCode1L(foundAtomInsidePdbFile.resName.FieldValue);
proteinInterfacePositionData.AminoAcidSequenceInteractionsAll3L += placeholder3L;
proteinInterfacePositionData.AminoAcidSequenceInteractionsInsideProteinInterfacesOnly3L += placeholder3L;
proteinInterfacePositionData.AminoAcidSequenceInteractionsOutsideProteinInterfacesOnly3L += placeholder3L;
proteinInterfacePositionData.AminoAcidSequenceInteractionsNone3L += foundAtomInsidePdbFile.resName.FieldValue.PadRight(3, '_');
proteinInterfaceAminoAcidMetaData.ProteinInterfaceInteractionType = ProteinInterfaceInteractionType.NoInteractionFound;
}
}
result.Add(proteinInterfacePositionData);
}
}
return(result);
}