From e81d914017a424e5e15193ac84194ae4c62e6c12 Mon Sep 17 00:00:00 2001
From: sguionni <simon.guionniere@gmail.com>
Date: Thu, 6 Jun 2024 17:26:12 +0200
Subject: [PATCH] Unknown residue names

---
 .../src/app/component/chemistry/residue.cpp   | 37 +++++++++++++++++--
 lib/core/include/core/struct/molecule.hpp     |  1 +
 lib/core/src/core/chemdb/residue.cpp          |  2 +
 lib/core/src/core/struct/molecule.cpp         |  1 +
 lib/io/src/io/reader/molecule.cpp             |  7 +++-
 src/main.cpp                                  |  2 -
 6 files changed, 44 insertions(+), 6 deletions(-)

diff --git a/lib/app/src/app/component/chemistry/residue.cpp b/lib/app/src/app/component/chemistry/residue.cpp
index 6c36b7f3e..bb07f61e4 100644
--- a/lib/app/src/app/component/chemistry/residue.cpp
+++ b/lib/app/src/app/component/chemistry/residue.cpp
@@ -69,10 +69,41 @@ namespace VTX::App::Component::Chemistry
 
 	const std::string & Residue::getShortName() const
 	{
-		return ChemDB::Residue::SYMBOL_SHORT_STR[ int( getSymbol() ) ];
+		ChemDB::Residue::SYMBOL symbol = getSymbol();
+		if ( symbol == ChemDB::Residue::SYMBOL::UNKNOWN )
+		{
+			return _moleculePtr->_moleculeStruct.residueUnknownNames[ _index ];
+		}
+		else
+		{
+			return ChemDB::Residue::SYMBOL_SHORT_STR[ int( symbol ) ];
+		}
+	}
+	const std::string & Residue::getName() const
+	{
+		ChemDB::Residue::SYMBOL symbol = getSymbol();
+		if ( symbol == ChemDB::Residue::SYMBOL::UNKNOWN )
+		{
+			return _moleculePtr->_moleculeStruct.residueUnknownNames[ _index ];
+		}
+		else
+		{
+			return ChemDB::Residue::SYMBOL_STR[ int( symbol ) ];
+		}
+	}
+
+	const std::string & Residue::getLongName() const
+	{
+		ChemDB::Residue::SYMBOL symbol = getSymbol();
+		if ( symbol == ChemDB::Residue::SYMBOL::UNKNOWN )
+		{
+			return _moleculePtr->_moleculeStruct.residueUnknownNames[ _index ];
+		}
+		else
+		{
+			return ChemDB::Residue::SYMBOL_NAME[ int( symbol ) ];
+		}
 	}
-	const std::string & Residue::getName() const { return ChemDB::Residue::SYMBOL_STR[ int( getSymbol() ) ]; }
-	const std::string & Residue::getLongName() const { return ChemDB::Residue::SYMBOL_NAME[ int( getSymbol() ) ]; }
 
 	ChemDB::Atom::TYPE Residue::getAtomType() const
 	{
diff --git a/lib/core/include/core/struct/molecule.hpp b/lib/core/include/core/struct/molecule.hpp
index 75e2ece5e..d8dd25b47 100644
--- a/lib/core/include/core/struct/molecule.hpp
+++ b/lib/core/include/core/struct/molecule.hpp
@@ -53,6 +53,7 @@ namespace VTX::Core::Struct
 		std::vector<size_t>							  residueBondCounts;
 		std::vector<size_t>							  residueOriginalIds;
 		std::vector<ChemDB::SecondaryStructure::TYPE> residueSecondaryStructureTypes;
+		std::vector<std::string>					  residueUnknownNames;
 
 		void   initResidues( const size_t p_count );
 		size_t getResidueCount() const;
diff --git a/lib/core/src/core/chemdb/residue.cpp b/lib/core/src/core/chemdb/residue.cpp
index f6ddc53ff..ec9847155 100644
--- a/lib/core/src/core/chemdb/residue.cpp
+++ b/lib/core/src/core/chemdb/residue.cpp
@@ -30,6 +30,7 @@ namespace VTX::Core::ChemDB::Residue
 
 		return symbol.value_or( SYMBOL::UNKNOWN );
 	}
+
 	const SYMBOL getSymbolFromLongName( const std::string & p_residueName )
 	{
 		std::string formattedName = std::string( p_residueName.begin(), p_residueName.end() );
@@ -51,6 +52,7 @@ namespace VTX::Core::ChemDB::Residue
 
 		return SYMBOL::UNKNOWN;
 	}
+
 	const SYMBOL getSymbolFromAnyName( const std::string & p_residueName )
 	{
 		const size_t residueNameSize = p_residueName.size();
diff --git a/lib/core/src/core/struct/molecule.cpp b/lib/core/src/core/struct/molecule.cpp
index 3917ef05a..23f0bf360 100644
--- a/lib/core/src/core/struct/molecule.cpp
+++ b/lib/core/src/core/struct/molecule.cpp
@@ -47,6 +47,7 @@ namespace VTX::Core::Struct
 		residueBondCounts.resize( p_count, 0 );
 		residueOriginalIds.resize( p_count, 0 );
 		residueSecondaryStructureTypes.resize( p_count, ChemDB::SecondaryStructure::TYPE::UNKNOWN );
+		residueUnknownNames.resize( p_count );
 	}
 	size_t Molecule::getResidueCount() const { return residueSymbols.size(); }
 
diff --git a/lib/io/src/io/reader/molecule.cpp b/lib/io/src/io/reader/molecule.cpp
index 542469e29..4aff8fff1 100644
--- a/lib/io/src/io/reader/molecule.cpp
+++ b/lib/io/src/io/reader/molecule.cpp
@@ -3,10 +3,10 @@
 #include <core/chemdb/secondary_structure.hpp>
 #include <core/struct/molecule.hpp>
 #include <core/struct/trajectory.hpp>
-#include <util/enum.hpp>
 #include <map>
 #include <util/chrono.hpp>
 #include <util/constants.hpp>
+#include <util/enum.hpp>
 #include <util/logger.hpp>
 
 namespace VTX::IO::Reader
@@ -100,6 +100,7 @@ namespace VTX::IO::Reader
 
 			const ChemDB::Residue::SYMBOL residueSymbol = VTX::Core::ChemDB::Residue::getSymbolFromName( residueName );
 
+			// TODO: delete?
 			// int symbolValue;
 
 			// if ( residueSymbol == ChemDB::Residue::SYMBOL::UNKNOWN )
@@ -129,6 +130,10 @@ namespace VTX::IO::Reader
 			//}
 
 			p_molecule.residueSymbols[ residueIdx ] = residueSymbol;
+			if ( residueSymbol == ChemDB::Residue::SYMBOL::UNKNOWN )
+			{
+				p_molecule.residueUnknownNames[ residueIdx ] = residueName;
+			}
 
 			const std::string secondaryStructure
 				= p_chemfileStruct.getCurrentResidueStringProperty( "secondary_structure" );
diff --git a/src/main.cpp b/src/main.cpp
index 64c184fe2..9a8338f4a 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -10,8 +10,6 @@
 #include <vector>
 
 #ifdef _WIN32
-// #include <Windows.h>
-
 extern "C"
 {
 	__declspec( dllexport ) uint32_t NvOptimusEnablement			 = 0x00000001;