public static List <MultiBindingInterface> Load(string file)
{
var result = new List <MultiBindingInterface>();
var fileData = File.ReadAllLines(file);
var DomainSuperFamily = "";
for (int index = 0; index < fileData.Length; index++)
{
if (index == 0 || index == 1)
{
continue;
}
var line = fileData[index];
var lineSplit = line.Split(',');
var lineRecord = new MultiBindingInterface(
lineSplit[0],
lineSplit[1],
lineSplit[2],
lineSplit[3],
lineSplit[4],
lineSplit[5],
lineSplit[6],
lineSplit[7],
lineSplit[8],
lineSplit[9]);
if (!string.IsNullOrWhiteSpace(lineRecord.DomainSuperFamily))
{
DomainSuperFamily = lineRecord.DomainSuperFamily;
}
else
{
lineRecord.DomainSuperFamily = DomainSuperFamily;
}
result.Add(lineRecord);
}
result =
result.Where(
a =>
!string.IsNullOrWhiteSpace(a.InteractionChainsPdb1) &&
!string.IsNullOrWhiteSpace(a.InteractionChainsPdb2)).ToList();
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;
}
public static List <MultiBindingInterface> LoadAuthorData(string multibinding_filename, string pdb_clusters_filename)
{
var result = new List <MultiBindingInterface>();
var fileData = File.ReadAllLines(multibinding_filename);
var clusterData =
SequenceIdentityClustering.SequenceIdentityClustering.SequenceIdentityClusterMember.Load(pdb_clusters_filename);
//var DomainSuperFamily = "";
for (int index = 0; index < fileData.Length; index++)
{
if (index == 0 /* || index == 1*/)
{
continue;
}
var line = fileData[index];
var lineSplit = line.Split(',');
var lineRecord = new MultiBindingInterface(
int.Parse(lineSplit[0]),
lineSplit[1],
lineSplit[2],
lineSplit[3],
lineSplit[4],
-1,
lineSplit[5][0],
-1,
lineSplit[6][0],
lineSplit[7],
lineSplit[8][0],
-1,
lineSplit[9][0],
-1,
int.Parse(lineSplit[10]));
lineRecord.InteractionChainsPdb1Chain1ClusterIndex =
clusterData.FirstOrDefault(
a => a.PdbId.ToUpperInvariant() == lineRecord.InteractionChainsPdb1.ToUpperInvariant() &&
a.ChainId == lineRecord.InteractionChainsPdb1Chain1).ClusterIndex;
lineRecord.InteractionChainsPdb1Chain2ClusterIndex =
clusterData.FirstOrDefault(
a => a.PdbId.ToUpperInvariant() == lineRecord.InteractionChainsPdb1.ToUpperInvariant() &&
a.ChainId == lineRecord.InteractionChainsPdb1Chain2).ClusterIndex;
lineRecord.InteractionChainsPdb2Chain1ClusterIndex =
clusterData.FirstOrDefault(
a => a.PdbId.ToUpperInvariant() == lineRecord.InteractionChainsPdb2.ToUpperInvariant() &&
a.ChainId == lineRecord.InteractionChainsPdb2Chain1).ClusterIndex;
lineRecord.InteractionChainsPdb2Chain2ClusterIndex =
clusterData.FirstOrDefault(
a => a.PdbId.ToUpperInvariant() == lineRecord.InteractionChainsPdb2.ToUpperInvariant() &&
a.ChainId == lineRecord.InteractionChainsPdb2Chain2).ClusterIndex;
/*
* if (!string.IsNullOrWhiteSpace(lineRecord.DomainSuperFamily))
* DomainSuperFamily = lineRecord.DomainSuperFamily;
* else lineRecord.DomainSuperFamily = DomainSuperFamily;
*/
result.Add(lineRecord);
}
/*
* result =
* result.Where(
* a =>
* !string.IsNullOrWhiteSpace(a.InteractionChainsPdb1) &&
* !string.IsNullOrWhiteSpace(a.InteractionChainsPdb2)).ToList();
*/
return(result);
}
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;
}
