cif2map toegevoegd

git-svn-id: svn+ssh://gitlab/srv/svn-repos/pdb-redo/trunk@183 a1961a4f-ab94-4bcc-80e8-33b5a54de466

include/cif++/Cif++.h

@@ -978,6 +978,7 @@ class Category
 	// return index for known column, or the next available column index
 	size_t getColumnIndex(const string& name) const;
 	const string& getColumnName(size_t columnIndex) const;
+	vector<string> getColumnNames() const;
 
 	void reorderByIndex();
 

include/cif++/Structure.h

@@ -7,6 +7,8 @@
 
 #include <boost/any.hpp>
 
+#include <clipper/core/coords.h>
+
 #include "cif++/AtomType.h"
 #include "cif++/Point.h"
 #include "cif++/Compound.h"
@@ -114,6 +116,9 @@ class Atom
 
 	const File& getFile() const;
 	
+	// get clipper format Atom
+	clipper::Atom toClipper() const;
+
   private:
  	struct AtomImpl*			mImpl;
 };

src/Cif++.cpp

@@ -1078,6 +1078,14 @@ const string& Category::getColumnName(size_t columnIx) const
 	return mColumns.at(columnIx).mName;
 }
 
+vector<string> Category::getColumnNames() const
+{
+	vector<string> result;
+	for (auto& c: mColumns)
+		result.push_back(c.mName);
+	return result;
+}
+
 size_t Category::addColumn(const string& name)
 {
 	size_t result = getColumnIndex(name);

src/Structure.cpp

@@ -179,6 +179,53 @@ struct AtomImpl
 		catch (...) {}
 	}
 	
+	clipper::Atom toClipper() const
+	{
+		clipper::Atom result;
+		result.set_coord_orth(mLocation);
+		
+		if (mRow["occupancy"].empty())
+			result.set_occupancy(1.0);
+		else
+			result.set_occupancy(mRow["occupancy"].as<float>());
+		
+		string element = mRow["type_symbol"].as<string>();
+		if (not mRow["pdbx_formal_charge"].empty())
+		{
+			int charge = mRow["pdbx_formal_charge"].as<int>();
+			if (abs(charge > 1))
+				element += to_string(charge);
+			if (charge < 0)
+				element += '-';
+			else
+				element += '+';
+		}
+		result.set_element(element);
+		
+		if (not mRow["U_iso_or_equiv"].empty())
+			result.set_u_iso(mRow["U_iso_or_equiv"].as<float>());
+		else if (not mRow["B_iso_or_equiv"].empty())
+			result.set_u_iso(mRow["B_iso_or_equiv"].as<float>() / (8 * kPI * kPI));
+		else
+			throw runtime_error("Missing B_iso or U_iso");	
+		
+		auto& db = *mFile.impl().mDb;
+		auto& cat = db["atom_site_anisotrop"];
+		auto r = cat[cif::Key("id") == mId];
+		if (r.empty())
+			result.set_u_aniso_orth(clipper::U_aniso_orth(nan("0"), 0, 0, 0, 0, 0));
+		else
+		{
+			float u11, u12, u13, u22, u23, u33;
+			cif::tie(u11, u12, u13, u22, u23, u33) =
+				r.get("U[1][1]", "U[1][2]", "U[1][3]", "U[2][2]", "U[2][3]", "U[3][3]");
+			
+			result.set_u_aniso_orth(clipper::U_aniso_orth(u11, u12, u13, u22, u23, u33));
+		}
+		
+		return result;
+	}
+
 	void reference()
 	{
 		++mRefcount;
@@ -360,6 +407,11 @@ const File& Atom::getFile() const
 	return mImpl->mFile;
 }
 
+clipper::Atom Atom::toClipper() const
+{
+	return mImpl->toClipper();
+}
+
 // --------------------------------------------------------------------
 // residue