#include "MoleculeFunctionLibrary.h"
#include "Misc/Paths.h"
#include "Misc/FileHelper.h"

bool UMoleculeFunctionLibrary::ParsePDBFromString(const FString& PDBContent, TArray<FAtom>& OutAtoms, TArray<FBond>& OutBonds)
{
	OutAtoms.Empty();
	OutBonds.Empty();

	if (PDBContent.IsEmpty())
	{
		UE_LOG(LogTemp, Warning, TEXT("ParsePDBFromString: Input string is empty"));
		return false;
	}

	TArray<FString> Lines;
	PDBContent.ParseIntoArrayLines(Lines, true);

	for (const FString& Line : Lines)
	{
		if (!Line.StartsWith(TEXT("ATOM")) && !Line.StartsWith(TEXT("HETATM")))
			continue;

		if (Line.Len() < 54) // At least enough for X, Y, Z
			continue;

		FAtom Atom;

		// Coordinates (columns are 1-indexed in spec)
		Atom.Position.X = FCString::Atof(*Line.Mid(30, 8));
		Atom.Position.Y = FCString::Atof(*Line.Mid(38, 8));
		Atom.Position.Z = FCString::Atof(*Line.Mid(46, 8));

		// Element symbol (columns 77-78), fallback to atom name (columns 13-16)
		if (Line.Len() >= 78)
			Atom.Element = Line.Mid(76, 2).TrimStartAndEnd();
		if (Atom.Element.IsEmpty())
			Atom.Element = Line.Mid(12, 4).TrimStartAndEnd().Left(1); // fallback

		OutAtoms.Add(Atom);
	}

	// Bond inference: simple distance-based
	const float MaxBondDistance = 1.6f; // can tweak for different atom types
	for (int32 i = 0; i < OutAtoms.Num(); i++)
	{
		for (int32 j = i + 1; j < OutAtoms.Num(); j++)
		{
			if (FVector::Distance(OutAtoms[i].Position, OutAtoms[j].Position) <= MaxBondDistance)
			{
				FBond Bond;
				Bond.AtomIndex1 = i;
				Bond.AtomIndex2 = j;
				OutBonds.Add(Bond);
			}
		}
	}

	UE_LOG(LogTemp, Log, TEXT("Parsed %d atoms and %d bonds from string"), OutAtoms.Num(), OutBonds.Num());
	return true;
}