public static List <ATOM_Record> FindAtomInteractingWithOtherProteinInterfaces(ATOM_Record atom, InteractionBetweenProteinInterfacesListContainer interactionBetweenProteinInterfacesContainer, FindAtomInteractingWithAnotherProteinInterfaceOptions findAtomInteractingWithAnotherProteinInterfaceOptions)
{
if (ParameterValidation.IsAtomNullOrEmpty(atom))
{
throw new ArgumentNullException(nameof(atom));
}
if (ParameterValidation.IsInteractionBetweenProteinInterfacesListContainerNullOrEmpty(interactionBetweenProteinInterfacesContainer))
{
////////Console.WriteLine("empty");
return(null);
}
List <InteractionBetweenProteinInterfaces> searchList = null;
if (findAtomInteractingWithAnotherProteinInterfaceOptions == FindAtomInteractingWithAnotherProteinInterfaceOptions.FindAtomsInteractingWithOtherProteinInterfaces)
{
searchList = interactionBetweenProteinInterfacesContainer.InteractionBetweenProteinInterfacesList;
}
else if (findAtomInteractingWithAnotherProteinInterfaceOptions == FindAtomInteractingWithAnotherProteinInterfaceOptions.FindAtomsInteractingWithNonProteinInterfaces)
{
searchList = interactionBetweenProteinInterfacesContainer.InteractionBetweenNonProteinInterfacesList;
}
else
{
throw new NotImplementedException();
}
if (searchList == null)
{
////////Console.WriteLine("returning null");
return(null);
}
var result = new List <ATOM_Record>();
foreach (InteractionBetweenProteinInterfaces interaction in searchList)
{
if (interaction.Atom1.Atom == atom && interaction.Atom2.Atom != atom)
{
//return interaction.Atom1.Atom;
result.Add(interaction.Atom2.Atom);
}
if (interaction.Atom1.Atom != atom && interaction.Atom2.Atom == atom)
{
//return interaction.Atom2.Atom;
result.Add(interaction.Atom1.Atom);
}
}
//if (result.Count == 0)
//{
// //////Console.WriteLine("returning empty list");
//}
return(result);
}
public static ProteinInterfaceSymmetryModeValues CheckDimer2X2ProteinInterfaceSymmetry(InteractionBetweenProteinInterfacesListContainer interactionBetweenProteinInterfacesContainer)
{
if (ParameterValidation.IsInteractionBetweenProteinInterfacesListContainerNullOrEmpty(interactionBetweenProteinInterfacesContainer))
{
throw new ArgumentOutOfRangeException(nameof(interactionBetweenProteinInterfacesContainer));
}
//int? chainIdA = null;
//int? chainIdB = null;
//foreach (var interaction in interactionsBetweenProteinInterfaces.InteractionBetweenProteinInterfacesList)
//{
// if (chainIdA == null || interaction.Atom1.FullProteinInterfaceId.ChainId < chainIdA)
// {
// chainIdA = interaction.Atom1.FullProteinInterfaceId.ChainId;
// }
// if (chainIdA == null || interaction.Atom2.FullProteinInterfaceId.ChainId < chainIdA)
// {
// chainIdA = interaction.Atom2.FullProteinInterfaceId.ChainId;
// }
// if (chainIdB == null || interaction.Atom1.FullProteinInterfaceId.ChainId > chainIdB)
// {
// chainIdB = interaction.Atom1.FullProteinInterfaceId.ChainId;
// }
// if (chainIdB == null || interaction.Atom2.FullProteinInterfaceId.ChainId > chainIdB)
// {
// chainIdB = interaction.Atom2.FullProteinInterfaceId.ChainId;
// }
//}
int chainIdA = 0;
int chainIdB = 1;
//List<int> totalProteinInterfacesA = new List<int>();
//List<int> totalProteinInterfacesB = new List<int>();
int totalProteinInterfacesA = interactionBetweenProteinInterfacesContainer.InteractionBetweenProteinInterfacesList.Where(a => a.Atom1.FullProteinInterfaceId.ChainId == chainIdA).Select(a => a.Atom1.FullProteinInterfaceId.ProteinInterfaceId).Distinct().Count() +
interactionBetweenProteinInterfacesContainer.InteractionBetweenProteinInterfacesList.Where(a => a.Atom2.FullProteinInterfaceId.ChainId == chainIdA).Select(a => a.Atom2.FullProteinInterfaceId.ProteinInterfaceId).Distinct().Count();
int totalProteinInterfacesB = interactionBetweenProteinInterfacesContainer.InteractionBetweenProteinInterfacesList.Where(a => a.Atom1.FullProteinInterfaceId.ChainId == chainIdB).Select(a => a.Atom1.FullProteinInterfaceId.ProteinInterfaceId).Distinct().Count() +
interactionBetweenProteinInterfacesContainer.InteractionBetweenProteinInterfacesList.Where(a => a.Atom2.FullProteinInterfaceId.ChainId == chainIdB).Select(a => a.Atom2.FullProteinInterfaceId.ProteinInterfaceId).Distinct().Count();
//foreach (var interaction in interactionsBetweenProteinInterfaces.InteractionBetweenProteinInterfacesList)
//{
// if (interaction.Atom1.FullProteinInterfaceId.ChainId == chainIdA && (interaction.Atom1.FullProteinInterfaceId.ProteinInterfaceId != null && !totalProteinInterfacesA.Contains((int) interaction.Atom1.FullProteinInterfaceId.ProteinInterfaceId)))
// {
// totalProteinInterfacesA.Add((int) interaction.Atom1.FullProteinInterfaceId.ProteinInterfaceId);
// }
// if (interaction.Atom2.FullProteinInterfaceId.ChainId == chainIdA && (interaction.Atom2.FullProteinInterfaceId.ProteinInterfaceId != null && !totalProteinInterfacesA.Contains((int) interaction.Atom2.FullProteinInterfaceId.ProteinInterfaceId)))
// {
// totalProteinInterfacesA.Add((int) interaction.Atom2.FullProteinInterfaceId.ProteinInterfaceId);
// }
// //
// if (interaction.Atom1.FullProteinInterfaceId.ChainId == chainIdB && (interaction.Atom1.FullProteinInterfaceId.ProteinInterfaceId != null && !totalProteinInterfacesB.Contains((int) interaction.Atom1.FullProteinInterfaceId.ProteinInterfaceId)))
// {
// totalProteinInterfacesB.Add((int) interaction.Atom1.FullProteinInterfaceId.ProteinInterfaceId);
// }
// if (interaction.Atom2.FullProteinInterfaceId.ChainId == chainIdB && (interaction.Atom2.FullProteinInterfaceId.ProteinInterfaceId != null && !totalProteinInterfacesB.Contains((int) interaction.Atom2.FullProteinInterfaceId.ProteinInterfaceId)))
// {
// totalProteinInterfacesB.Add((int) interaction.Atom2.FullProteinInterfaceId.ProteinInterfaceId);
// }
//}
//var interactionsBetweenProteinInterfaces2 = new List<AtomPair>[totalProteinInterfacesA.Max() > totalProteinInterfacesA.Count ? totalProteinInterfacesA.Max() : totalProteinInterfacesA.Count, totalProteinInterfacesB.Max() > totalProteinInterfacesB.Count ? totalProteinInterfacesB.Max() : totalProteinInterfacesB.Count];
//var interactionsBetweenProteinInterfaces2 = new List<AtomPair>[totalProteinInterfacesA, totalProteinInterfacesB];
//foreach (var interaction in interactionsBetweenProteinInterfaces.InteractionBetweenProteinInterfacesList)
//{
// if (interaction.Atom1.FullProteinInterfaceId.ChainId == chainIdA && interaction.Atom2.FullProteinInterfaceId.ChainId == chainIdB)
// {
// AtomPair atomPair = new AtomPair(interaction.Atom1.Atom, interaction.Atom2.Atom, 0);
// interactionsBetweenProteinInterfaces2[(int)interaction.Atom1.FullProteinInterfaceId.ProteinInterfaceId, (int) interaction.Atom2 .ProteinInterfaceId].Add(atomPair);
// }
// else if (interaction.Atom1.FullProteinInterfaceId.ChainId == chainIdB && interaction.Atom2.FullProteinInterfaceId.ChainId == chainIdA)
// {
// AtomPair atomPair = new AtomPair(interaction.Atom2.Atom, interaction.Atom1.Atom, 0);
// interactionsBetweenProteinInterfaces2[(int)interaction.Atom2.FullProteinInterfaceId.ProteinInterfaceId, (int) interaction.Atom1.FullProteinInterfaceId.ProteinInterfaceId].Add(atomPair);
// }
//}
// C0S0 to C1S0 plus C0S1 to C1S1
//int Chain_A_ProteinInterface_A_to_Chain_B_ProteinInterface_A = interactionsBetweenProteinInterfaces2[0, 0].Count;
//int Chain_A_ProteinInterface_B_to_Chain_B_ProteinInterface_B = interactionsBetweenProteinInterfaces2[1, 1].Count;
const int proteinInterfaceIdA = StaticValues.ProteinInterfaceA;
const int proteinInterfaceIdB = StaticValues.ProteinInterfaceB;
int Chain_A_ProteinInterface_A_to_Chain_B_ProteinInterface_A = interactionBetweenProteinInterfacesContainer.InteractionBetweenProteinInterfacesList.Count(a => a.Atom1.FullProteinInterfaceId.ChainId == chainIdA && a.Atom2.FullProteinInterfaceId.ChainId == chainIdB && a.Atom1.FullProteinInterfaceId.ProteinInterfaceId == proteinInterfaceIdA && a.Atom2.FullProteinInterfaceId.ProteinInterfaceId == proteinInterfaceIdA) +
interactionBetweenProteinInterfacesContainer.InteractionBetweenProteinInterfacesList.Count(a => a.Atom1.FullProteinInterfaceId.ChainId == chainIdB && a.Atom2.FullProteinInterfaceId.ChainId == chainIdA && a.Atom1.FullProteinInterfaceId.ProteinInterfaceId == proteinInterfaceIdA && a.Atom2.FullProteinInterfaceId.ProteinInterfaceId == proteinInterfaceIdA);
int Chain_A_ProteinInterface_B_to_Chain_B_ProteinInterface_B = interactionBetweenProteinInterfacesContainer.InteractionBetweenProteinInterfacesList.Count(a => a.Atom1.FullProteinInterfaceId.ChainId == chainIdA && a.Atom2.FullProteinInterfaceId.ChainId == chainIdB && a.Atom1.FullProteinInterfaceId.ProteinInterfaceId == proteinInterfaceIdB && a.Atom2.FullProteinInterfaceId.ProteinInterfaceId == proteinInterfaceIdB) +
interactionBetweenProteinInterfacesContainer.InteractionBetweenProteinInterfacesList.Count(a => a.Atom1.FullProteinInterfaceId.ChainId == chainIdB && a.Atom2.FullProteinInterfaceId.ChainId == chainIdA && a.Atom1.FullProteinInterfaceId.ProteinInterfaceId == proteinInterfaceIdB && a.Atom2.FullProteinInterfaceId.ProteinInterfaceId == proteinInterfaceIdB);
int categoryStraight = Chain_A_ProteinInterface_A_to_Chain_B_ProteinInterface_A + Chain_A_ProteinInterface_B_to_Chain_B_ProteinInterface_B;
// C0S0 to C1S1 and C0S1 to C1S0
//int Chain_A_ProteinInterface_A_to_Chain_B_ProteinInterface_B = interactionsBetweenProteinInterfaces2[0, 1].Count;
//int Chain_A_ProteinInterface_B_to_Chain_B_ProteinInterface_A = interactionsBetweenProteinInterfaces2[1, 0].Count;
int Chain_A_ProteinInterface_A_to_Chain_B_ProteinInterface_B = interactionBetweenProteinInterfacesContainer.InteractionBetweenProteinInterfacesList.Count(a => a.Atom1.FullProteinInterfaceId.ChainId == chainIdA && a.Atom2.FullProteinInterfaceId.ChainId == chainIdB && a.Atom1.FullProteinInterfaceId.ProteinInterfaceId == proteinInterfaceIdA && a.Atom2.FullProteinInterfaceId.ProteinInterfaceId == proteinInterfaceIdB) +
interactionBetweenProteinInterfacesContainer.InteractionBetweenProteinInterfacesList.Count(a => a.Atom1.FullProteinInterfaceId.ChainId == chainIdB && a.Atom2.FullProteinInterfaceId.ChainId == chainIdA && a.Atom1.FullProteinInterfaceId.ProteinInterfaceId == proteinInterfaceIdB && a.Atom2.FullProteinInterfaceId.ProteinInterfaceId == proteinInterfaceIdA);
int Chain_A_ProteinInterface_B_to_Chain_B_ProteinInterface_A = interactionBetweenProteinInterfacesContainer.InteractionBetweenProteinInterfacesList.Count(a => a.Atom1.FullProteinInterfaceId.ChainId == chainIdA && a.Atom2.FullProteinInterfaceId.ChainId == chainIdB && a.Atom1.FullProteinInterfaceId.ProteinInterfaceId == proteinInterfaceIdB && a.Atom2.FullProteinInterfaceId.ProteinInterfaceId == proteinInterfaceIdA) +
interactionBetweenProteinInterfacesContainer.InteractionBetweenProteinInterfacesList.Count(a => a.Atom1.FullProteinInterfaceId.ChainId == chainIdB && a.Atom2.FullProteinInterfaceId.ChainId == chainIdA && a.Atom1.FullProteinInterfaceId.ProteinInterfaceId == proteinInterfaceIdA && a.Atom2.FullProteinInterfaceId.ProteinInterfaceId == proteinInterfaceIdB);
int categoryDiagonal = Chain_A_ProteinInterface_A_to_Chain_B_ProteinInterface_B + Chain_A_ProteinInterface_B_to_Chain_B_ProteinInterface_A;
var proteinInterfaceSymmetryModeEnum = ProteinInterfaceSymmetryModeEnum.Unknown;
// Top straight line ----------------------- Bottom straight line ------------------ Top to bottom diagonal line ----------- Bottom to top diagonal line
if (Chain_A_ProteinInterface_A_to_Chain_B_ProteinInterface_A == 0 && Chain_A_ProteinInterface_B_to_Chain_B_ProteinInterface_B == 0 &&
Chain_A_ProteinInterface_A_to_Chain_B_ProteinInterface_B == 0 && Chain_A_ProteinInterface_B_to_Chain_B_ProteinInterface_A == 0)
{
// Interaction Mode 0
proteinInterfaceSymmetryModeEnum = ProteinInterfaceSymmetryModeEnum.Unknown;
}
else if (Chain_A_ProteinInterface_A_to_Chain_B_ProteinInterface_A > 0 && Chain_A_ProteinInterface_B_to_Chain_B_ProteinInterface_B > 0 &&
Chain_A_ProteinInterface_A_to_Chain_B_ProteinInterface_B == 0 && Chain_A_ProteinInterface_B_to_Chain_B_ProteinInterface_A == 0)
{
// Interaction Mode 1
proteinInterfaceSymmetryModeEnum = ProteinInterfaceSymmetryModeEnum.Straight;
}
else if (Chain_A_ProteinInterface_A_to_Chain_B_ProteinInterface_A == 0 && Chain_A_ProteinInterface_B_to_Chain_B_ProteinInterface_B == 0 &&
Chain_A_ProteinInterface_A_to_Chain_B_ProteinInterface_B > 0 && Chain_A_ProteinInterface_B_to_Chain_B_ProteinInterface_A > 0)
{
// Interaction Mode 2
proteinInterfaceSymmetryModeEnum = ProteinInterfaceSymmetryModeEnum.Diagonal;
}
else if (Chain_A_ProteinInterface_A_to_Chain_B_ProteinInterface_A > 0 && Chain_A_ProteinInterface_B_to_Chain_B_ProteinInterface_B > 0 &&
Chain_A_ProteinInterface_A_to_Chain_B_ProteinInterface_B > 0 && Chain_A_ProteinInterface_B_to_Chain_B_ProteinInterface_A > 0)
{
// Interaction Mode 3
proteinInterfaceSymmetryModeEnum = ProteinInterfaceSymmetryModeEnum.StraightAndDiagonal;
}
else if (Chain_A_ProteinInterface_A_to_Chain_B_ProteinInterface_A > 0 && Chain_A_ProteinInterface_B_to_Chain_B_ProteinInterface_B == 0 &&
Chain_A_ProteinInterface_A_to_Chain_B_ProteinInterface_B > 0 && Chain_A_ProteinInterface_B_to_Chain_B_ProteinInterface_A > 0)
{
// Interaction Mode 4
proteinInterfaceSymmetryModeEnum = ProteinInterfaceSymmetryModeEnum.DiagonalAndTopStraight;
}
else if (Chain_A_ProteinInterface_A_to_Chain_B_ProteinInterface_A == 0 && Chain_A_ProteinInterface_B_to_Chain_B_ProteinInterface_B > 0 &&
Chain_A_ProteinInterface_A_to_Chain_B_ProteinInterface_B > 0 && Chain_A_ProteinInterface_B_to_Chain_B_ProteinInterface_A > 0)
{
// Interaction Mode 5
proteinInterfaceSymmetryModeEnum = ProteinInterfaceSymmetryModeEnum.DiagonalAndBottomStraight;
}
else if (Chain_A_ProteinInterface_A_to_Chain_B_ProteinInterface_A > 0 && Chain_A_ProteinInterface_B_to_Chain_B_ProteinInterface_B > 0 &&
Chain_A_ProteinInterface_A_to_Chain_B_ProteinInterface_B > 0 && Chain_A_ProteinInterface_B_to_Chain_B_ProteinInterface_A == 0)
{
// Interaction Mode 6
proteinInterfaceSymmetryModeEnum = ProteinInterfaceSymmetryModeEnum.StraightAndTopToBottomDiagonal;
}
else if (Chain_A_ProteinInterface_A_to_Chain_B_ProteinInterface_A > 0 && Chain_A_ProteinInterface_B_to_Chain_B_ProteinInterface_B > 0 &&
Chain_A_ProteinInterface_A_to_Chain_B_ProteinInterface_B == 0 &&
Chain_A_ProteinInterface_B_to_Chain_B_ProteinInterface_A > 0)
{
// Interaction Mode 7
proteinInterfaceSymmetryModeEnum = ProteinInterfaceSymmetryModeEnum.StraightAndBottomToTopDiagonal;
}
return(new ProteinInterfaceSymmetryModeValues(categoryDiagonal, categoryStraight, proteinInterfaceSymmetryModeEnum));
}