fixed mtz-maker

git-svn-id: svn+ssh://gitlab/srv/svn-repos/pdb-redo/trunk@245 a1961a4f-ab94-4bcc-80e8-33b5a54de466

include/cif++/MapMaker.h

@@ -39,6 +39,18 @@ class Map
 	double mRMSDensity, mMeanDensity;
 	double mRMSDensity, mMeanDensity;
 };
 };
 
 
+using clipper::HKL_info;
+using clipper::HKL_data;
+using clipper::data32::F_phi;
+using clipper::data32::F_sigF;
+using clipper::data32::Phi_fom;
+using clipper::data32::Flag;
+
+using clipper::Spacegroup;
+using clipper::Cell;
+using clipper::Grid_sampling;
+
+	
 template<typename FTYPE>
 template<typename FTYPE>
 class MapMaker
 class MapMaker
 {
 {
@@ -46,15 +58,6 @@ class MapMaker
 	typedef Map<FTYPE> MapType;
 	typedef Map<FTYPE> MapType;
 	typedef typename MapType::Xmap Xmap;
 	typedef typename MapType::Xmap Xmap;
 
 
-	typedef clipper::HKL_data<clipper::data32::F_phi>	FPdata;
-	typedef clipper::HKL_data<clipper::data32::F_sigF>	FOdata;
-	typedef clipper::HKL_data<clipper::data32::Phi_fom>	WData;
-	
-	
-	typedef clipper::Spacegroup							Spacegroup;
-	typedef clipper::Cell								Cell;
-	typedef clipper::Grid_sampling						Grid_sampling;
-	
 	enum AnisoScalingFlag {
 	enum AnisoScalingFlag {
 		as_None, as_Observed, as_Calculated
 		as_None, as_Observed, as_Calculated
 	};
 	};
@@ -62,6 +65,9 @@ class MapMaker
 	MapMaker();
 	MapMaker();
 	~MapMaker();
 	~MapMaker();
 	
 	
+	MapMaker(const MapMaker&) = delete;
+	MapMaker& operator=(const MapMaker&) = delete;
+
 	void loadFromMTZ(const boost::filesystem::path& mtzFile,
 	void loadFromMTZ(const boost::filesystem::path& mtzFile,
 		float samplingRate = 4.5,
 		float samplingRate = 4.5,
 		std::initializer_list<std::string> fbLabels = { "FWT", "PHWT" },
 		std::initializer_list<std::string> fbLabels = { "FWT", "PHWT" },
@@ -69,6 +75,10 @@ class MapMaker
 		std::initializer_list<std::string> foLabels = { "FP", "SIGFP" },
 		std::initializer_list<std::string> foLabels = { "FP", "SIGFP" },
 		std::initializer_list<std::string> fcLabels = { "FC_ALL", "PHIC_ALL" });
 		std::initializer_list<std::string> fcLabels = { "FC_ALL", "PHIC_ALL" });
 
 
+	void loadFromReflections(const boost::filesystem::path& hklin,
+		const Structure& structure, bool noBulk, AnisoScalingFlag anisoScaling,
+		float samplingRate = 4.5, bool electronScattering = false);
+
 	void recalculateFromMTZ(const boost::filesystem::path& mtzFile,
 	void recalculateFromMTZ(const boost::filesystem::path& mtzFile,
 		const Structure& structure,
 		const Structure& structure,
 		bool noBulk, AnisoScalingFlag anisoScaling,
 		bool noBulk, AnisoScalingFlag anisoScaling,
@@ -81,6 +91,9 @@ class MapMaker
 		const boost::filesystem::path& fdMapFile,
 		const boost::filesystem::path& fdMapFile,
 		float reshi, float reslo);
 		float reshi, float reslo);
 
 
+	void writeMTZ(const boost::filesystem::path& file,
+		const std::string& project, const std::string& crystal);
+
 	MapType& fb()								{ return mFb; }
 	MapType& fb()								{ return mFb; }
 	MapType& fd()								{ return mFd; }
 	MapType& fd()								{ return mFd; }
 
 
@@ -90,26 +103,31 @@ class MapMaker
 	double resLow() const						{ return mResLow; }
 	double resLow() const						{ return mResLow; }
 	double resHigh() const						{ return mResHigh; }
 	double resHigh() const						{ return mResHigh; }
 
 
-	const Spacegroup& spacegroup() const		{ return mSpacegroup; }
-	const Cell& cell() const					{ return mCell; }
+	const Spacegroup& spacegroup() const		{ return mHKLInfo.spacegroup(); }
+	const Cell& cell() const					{ return mHKLInfo.cell(); }
 	const Grid_sampling& gridSampling() const	{ return mGrid; }
 	const Grid_sampling& gridSampling() const	{ return mGrid; }
 
 
   private:
   private:
 
 
-	void fixMTZ(FPdata& fb, FPdata& fd, FOdata& fo, FPdata& fc, WData& fom);
+	void fixMTZ();
+	void printStats();
 	
 	
-	void printStats(const clipper::HKL_info hklInfo,
-		const clipper::HKL_data<clipper::data32::F_sigF>& fo,
-		const clipper::HKL_data<clipper::data32::F_phi>& fc,
-		const clipper::HKL_data<clipper::data32::Flag>& free);
+	void recalc(const Structure& structure,
+		bool noBulk, AnisoScalingFlag anisoScaling,
+		float samplingRate = 4.5, bool electronScattering = false);
 
 
 	MapType				mFb, mFd;
 	MapType				mFb, mFd;
-	Spacegroup mSpacegroup;
-	Cell mCell;
 	Grid_sampling		mGrid;
 	Grid_sampling		mGrid;
 	float				mSamplingRate;
 	float				mSamplingRate;
 	double				mResLow, mResHigh;
 	double				mResLow, mResHigh;
 	int					mNumRefln = 1000, mNumParam = 20;
 	int					mNumRefln = 1000, mNumParam = 20;
+	
+	// Cached raw data
+	HKL_info			mHKLInfo;
+	HKL_data<F_sigF>	mFoData;
+	HKL_data<Flag>		mFreeData;
+	HKL_data<F_phi>		mFcData, mFbData, mFdData;
+	HKL_data<Phi_fom>	mPhiFomData;
 };
 };
 
 
 }
 }

src/PDB2Cif.cpp

@@ -4612,7 +4612,11 @@ void PDBFileParser::ParseConnectivtyAnnotation()
 				continue;
 				continue;
 			}
 			}
 			
 			
-			string distance = vS(74, 78);
+			string distance, details;
+			
+			if (mRec->is("LINK  "))
+			{
+				distance = vS(74, 78);
 				try
 				try
 				{
 				{
 					stod(distance);
 					stod(distance);
@@ -4623,11 +4627,18 @@ void PDBFileParser::ParseConnectivtyAnnotation()
 						cerr << "Distance value '" << distance << "' is not a valid float" << endl;
 						cerr << "Distance value '" << distance << "' is not a valid float" << endl;
 					distance.clear();
 					distance.clear();
 				}
 				}
+			}
+			else	// LINKR
+			{
+				details = vS(74, 78);	// the link ID 
+			}
 			
 			
 			getCategory("struct_conn")->emplace({
 			getCategory("struct_conn")->emplace({
 				{ "id", type + to_string(linkNr) },
 				{ "id", type + to_string(linkNr) },
 				{ "conn_type_id", type },
 				{ "conn_type_id", type },
 				
 				
+				{ "details", details },
+	
 				{ "ptnr1_label_asym_id", p1Asym },
 				{ "ptnr1_label_asym_id", p1Asym },
 				{ "ptnr1_label_comp_id", vS(18, 20) },
 				{ "ptnr1_label_comp_id", vS(18, 20) },
 				{ "ptnr1_label_seq_id", (isResseq1 and p1Seq) ? to_string(p1Seq) : "." },
 				{ "ptnr1_label_seq_id", (isResseq1 and p1Seq) ? to_string(p1Seq) : "." },