- Save residueIndexInOriginalChain and check it for residue search by…

… index
VTX-Molecular-Visualization · Nov 7, 2023 · ac8284e · ac8284e
1 parent 5ac1783
commit ac8284e
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Showing 6 changed files with 41 additions and 26 deletions.
diff --git a/lib/app/include/app/component/chemistry/residue.hpp b/lib/app/include/app/component/chemistry/residue.hpp
@@ -38,6 +38,8 @@ namespace VTX::App::Component::Chemistry
 		void					setBondCount( const size_t p_bondCount );
 		ChemDB::Residue::SYMBOL getSymbol() const;
 		void					setSymbol( const ChemDB::Residue::SYMBOL p_symbol );
+		size_t					getIndexInOriginalChain() const;
+		void					setIndexInOriginalChain( const size_t p_index );
 
 		const std::string & getShortName() const;
 		const std::string & getName() const;
@@ -52,12 +54,6 @@ namespace VTX::App::Component::Chemistry
 		ChemDB::Atom::TYPE getAtomType() const;
 		void			   setAtomType( const ChemDB::Atom::TYPE p_type );
 
-		size_t getIndexInOriginalChain() const { return _indexInOriginalChain; };
-		void   setIndexInOriginalChain( const size_t p_indexInOriginalChain )
-		{
-			_indexInOriginalChain = p_indexInOriginalChain;
-		};
-
 		const char getInsertionCode() const { return _insertionCode; }
 		void	   setInsertionCode( const char p_insertionCode ) { _insertionCode = p_insertionCode; }
 

diff --git a/lib/app/src/app/component/chemistry/residue.cpp b/lib/app/src/app/component/chemistry/residue.cpp
@@ -58,6 +58,15 @@ namespace VTX::App::Component::Chemistry
 		_moleculePtr->_moleculeStruct.residueSymbols[ _index ] = p_symbol;
 	}
 
+	size_t Residue::getIndexInOriginalChain() const
+	{
+		return _moleculePtr->_moleculeStruct.residueOriginalIds[ _index ];
+	}
+	void Residue::setIndexInOriginalChain( const size_t p_index )
+	{
+		_moleculePtr->_moleculeStruct.residueOriginalIds[ _index ] = p_index;
+	}
+
 	const std::string & Residue::getShortName() const
 	{
 		return ChemDB::Residue::SYMBOL_SHORT_STR[ int( getSymbol() ) ];

diff --git a/lib/core/include/core/struct/molecule.hpp b/lib/core/include/core/struct/molecule.hpp
@@ -49,6 +49,7 @@ namespace VTX::Core::Struct
 		std::vector<size_t>					 residueAtomCounts		 = std::vector<size_t>();
 		std::vector<size_t>					 residueFirstBondIndexes = std::vector<size_t>();
 		std::vector<size_t>					 residueBondCounts		 = std::vector<size_t>();
+		std::vector<size_t>					 residueOriginalIds		 = std::vector<size_t>();
 
 		void   initResidues( const size_t p_count );
 		size_t getResidueCount() const;

diff --git a/lib/core/src/core/struct/molecule.cpp b/lib/core/src/core/struct/molecule.cpp
@@ -40,6 +40,7 @@ namespace VTX::Core::Struct
 		residueAtomCounts.resize( p_count, 0 );
 		residueFirstBondIndexes.resize( p_count, INVALID_INDEX );
 		residueBondCounts.resize( p_count, 0 );
+		residueOriginalIds.resize( p_count, 0 );
 	}
 	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
@@ -15,9 +15,11 @@ namespace VTX::IO::Reader
 		_chemfilesReader = Reader::Chemfiles::readFile( p_path );
 		_fillStructure( *_chemfilesReader, p_molecule );
 	}
-	void Molecule::readBuffer( const std::string &			 p_buffer,
-							   const FilePath &				 p_path,
-							   VTX::Core::Struct::Molecule & p_molecule )
+	void Molecule::readBuffer(
+		const std::string &			  p_buffer,
+		const FilePath &			  p_path,
+		VTX::Core::Struct::Molecule & p_molecule
+	)
 	{
 		_chemfilesReader = Reader::Chemfiles::readBuffer( p_buffer, p_path );
 		_fillStructure( *_chemfilesReader, p_molecule );
@@ -49,7 +51,8 @@ namespace VTX::IO::Reader
 
 			const std::string chainName	  = p_chemfileStruct.getCurrentChainName();
 			const std::string chainId	  = p_chemfileStruct.getCurrentChainID();
-			std::string		  residueName = p_chemfileStruct.getCurrentResidueName();
+			const std::string residueName = p_chemfileStruct.getCurrentResidueName();
+			const size_t	  residueId	  = p_chemfileStruct.getCurrentResidueId();
 
 			const VTX::Core::ChemDB::Category::TYPE categoryEnum = _findCategoryType( fileExtension, residueName );
 
@@ -92,8 +95,9 @@ namespace VTX::IO::Reader
 			p_molecule.residueChainIndexes[ residueIdx ]	 = currentChainIndex;
 			p_molecule.residueFirstAtomIndexes[ residueIdx ] = ( p_chemfileStruct.getCurrentResidueFirstAtomIndex() );
 			p_molecule.residueAtomCounts[ residueIdx ]		 = atomCount;
+			p_molecule.residueOriginalIds[ residueIdx ]		 = residueId;
 
-			ChemDB::Residue::SYMBOL residueSymbol = VTX::Core::ChemDB::Residue::getSymbolFromName( residueName );
+			const ChemDB::Residue::SYMBOL residueSymbol = VTX::Core::ChemDB::Residue::getSymbolFromName( residueName );
 
 			// int symbolValue;
 
@@ -270,7 +274,8 @@ namespace VTX::IO::Reader
 	void Molecule::_readTrajectoryFrames(
 		IO::Reader::Chemfiles &												  p_chemfileStruct,
 		const std::vector<std::pair<VTX::Core::Struct::Molecule *, size_t>> & p_targets,
-		const size_t														  p_trajectoryFrameStart )
+		const size_t														  p_trajectoryFrameStart
+	)
 	{
 		// Fill other frames.
 		Util::Chrono timeReadingFrames;
@@ -303,7 +308,8 @@ namespace VTX::IO::Reader
 			if ( frameIdx > 1 && frameIdx % 100 == 0 )
 			{
 				VTX_DEBUG(
-					"Frames from {} to {} read in: {}s.", startingFrame, frameIdx, timeReadingFrames.intervalTime() );
+					"Frames from {} to {} read in: {}s.", startingFrame, frameIdx, timeReadingFrames.intervalTime()
+				);
 				startingFrame = frameIdx;
 			}
 #endif // DEBUG
@@ -328,8 +334,10 @@ namespace VTX::IO::Reader
 		}
 	}
 
-	VTX::Core::ChemDB::Category::TYPE Molecule::_findCategoryType( const std::string & p_fileExtension,
-																   const std::string & p_residueSymbol )
+	VTX::Core::ChemDB::Category::TYPE Molecule::_findCategoryType(
+		const std::string & p_fileExtension,
+		const std::string & p_residueSymbol
+	)
 	{
 		VTX::Core::ChemDB::Category::TYPE res;
 		if ( p_fileExtension == "pdb" || p_fileExtension == "mmcif" || p_fileExtension == "mmtf" )
@@ -372,9 +380,11 @@ namespace VTX::IO::Reader
 		const std::string residueSymbol = p_chemfileStruct.getCurrentResidueName();
 
 		// Check PSF.
-		if ( std::find( _configuration->solventResidueSymbols.begin(),
-						_configuration->solventResidueSymbols.end(),
-						residueSymbol )
+		if ( std::find(
+				 _configuration->solventResidueSymbols.begin(),
+				 _configuration->solventResidueSymbols.end(),
+				 residueSymbol
+			 )
 			 != _configuration->solventResidueSymbols.end() )
 		{
 			return ChemDB::Atom::TYPE::SOLVENT;

diff --git a/lib/python_binding/test/vtx_api_selection.cpp b/lib/python_binding/test/vtx_api_selection.cpp
@@ -122,11 +122,11 @@ TEST_CASE( "VTX_PYTHON_BINDING - VTX API Selection Tests", "[integration]" )
 		SelectionUtil::createSelection( allHistidineOn4HHB )
 	) );
 
-	// CHECK( SelectionUtil::checkSelection(
-	//	"test_mol_n_chain_res_1",
-	//	"select( mol_n='4HHB', chain_n='A', res_i=5 )",
-	//	SelectionUtil::createSelection( SelectionUtil::generateMoleculeData( "4HHB", {}, { 3 } ) )
-	//) ); // NO => Original index in scene not managed
+	CHECK( SelectionUtil::checkSelection(
+		"test_mol_n_chain_res_1",
+		"select( mol_n='4HHB', chain_n='B', res_i=4 )",
+		SelectionUtil::createSelection( SelectionUtil::generateMoleculeData( "4HHB", {}, { 144 } ) )
+	) );
 
 	// interpretor.runCommand( "select( mol_n='4HHB', atom_t='C')" ); // OK
 	// interpretor.runCommand( "select( mol_n='4HHB', res_n='HIS', atom_n='O')" ); // OK
@@ -148,9 +148,7 @@ TEST_CASE( "VTX_PYTHON_BINDING - VTX API Selection Tests", "[integration]" )
 	) );
 
 	CHECK( SelectionUtil::checkSelection(
-		"test_empty_2",
-		"select( mol_n='4HHB', res_n='his' )",
-		SelectionUtil::createSelection( allHistidineOn4HHB )
+		"test_empty_2", "select( mol_n='4HHB', res_n='his' )", SelectionUtil::createSelection( allHistidineOn4HHB )
 	) );
 
 	// CHECK( SelectionUtil::checkSelection(