backup

git-svn-id: svn+ssh://gitlab/srv/svn-repos/pdb-redo/trunk@493 a1961a4f-ab94-4bcc-80e8-33b5a54de466

include/cif++/Symmetry.h

@@ -12,6 +12,7 @@ namespace mmcif
 
 
 clipper::Coord_orth CalculateOffsetForCell(const Structure& p, const clipper::Spacegroup& spacegroup, const clipper::Cell& cell);
 clipper::Coord_orth CalculateOffsetForCell(const Structure& p, const clipper::Spacegroup& spacegroup, const clipper::Cell& cell);
 std::vector<clipper::RTop_orth> AlternativeSites(const clipper::Spacegroup& spacegroup, const clipper::Cell& cell);
 std::vector<clipper::RTop_orth> AlternativeSites(const clipper::Spacegroup& spacegroup, const clipper::Cell& cell);
+int GetSpacegroupNumber(const std::string& spacegroup);	// alternative for clipper's parsing code
 
 
 // --------------------------------------------------------------------
 // --------------------------------------------------------------------
 // To iterate over all near symmetry copies of an atom
 // To iterate over all near symmetry copies of an atom

src/Symmetry.cpp

@@ -160,7 +160,7 @@ int32_t GetRotationalIndexNumber(int spacegroup, const clipper::RTop_frac& rt)
 
 
 	for (int i = 0; i < 3; ++i)
 	for (int i = 0; i < 3; ++i)
 	{
 	{
-		int n = (lrint(trn[i] * 24) + 24) % 24;
+		int n = lrint(trn[i] * 24);
 		int d = 24;
 		int d = 24;
 
 
 		if (n == 0 or abs(n) == 24)
 		if (n == 0 or abs(n) == 24)
@@ -172,6 +172,8 @@ int32_t GetRotationalIndexNumber(int spacegroup, const clipper::RTop_frac& rt)
 				n /= i;
 				n /= i;
 				d /= i;
 				d /= i;
 			}
 			}
+		
+		n = (n + d) % d;
 
 
 		switch (i)
 		switch (i)
 		{
 		{
@@ -201,6 +203,38 @@ int32_t GetRotationalIndexNumber(int spacegroup, const clipper::RTop_frac& rt)
 	throw runtime_error("Symmetry operation was not found in table, cannot find rotational number");
 	throw runtime_error("Symmetry operation was not found in table, cannot find rotational number");
 }
 }
 
 
+// --------------------------------------------------------------------
+// And unfortunately, clipper does not know all the spacegroup names mentioned in symop.lib
+
+int GetSpacegroupNumber(const std::string& spacegroup)
+{
+	int result = 0;
+
+	const size_t N = sizeof(kSpaceGroups) / sizeof(Spacegroup);
+	int32_t L = 0, R = static_cast<int32_t>(N - 1);
+	while (L <= R)
+	{
+		int32_t i = (L + R) / 2;
+
+		int d = spacegroup.compare(kSpaceGroups[i].name);
+
+		if (d > 0)
+			L = i + 1;
+		else if (d < 0)
+			R = i - 1;
+		else
+		{
+			result = kSpaceGroups[i].nr;
+			break;
+		}
+	}
+
+	if (result == 0)
+		throw runtime_error("Spacegroup name " + spacegroup + " was not found in table");
+	
+	return result;
+}
+
 // -----------------------------------------------------------------------
 // -----------------------------------------------------------------------
 
 
 string SymmetryAtomIteratorFactory::symop_mmcif(const Atom& a) const
 string SymmetryAtomIteratorFactory::symop_mmcif(const Atom& a) const

tools/symop-map-generator.cpp

@@ -121,8 +121,6 @@ class SymopParser
 
 
 	void parsepart(int row)
 	void parsepart(int row)
 	{
 	{
-		bool first = false;
-
 		do
 		do
 		{
 		{
 			int sign = m_lookahead == '-' ? -1 : 1;
 			int sign = m_lookahead == '-' ? -1 : 1;
@@ -149,7 +147,7 @@ class SymopParser
 	}
 	}
 
 
 	Token m_lookahead;
 	Token m_lookahead;
-	char m_nr;
+	int m_nr;
 
 
 	string m_s;
 	string m_s;
 	string::const_iterator m_p, m_e;
 	string::const_iterator m_p, m_e;
@@ -177,6 +175,8 @@ int main()
 
 
 		vector<tuple<int,int,string,array<int,15>>> data;
 		vector<tuple<int,int,string,array<int,15>>> data;
 
 
+		vector<tuple<string,int>> spacegroups;
+
 		// --------------------------------------------------------------------
 		// --------------------------------------------------------------------
 		
 		
 		string line;
 		string line;
@@ -228,6 +228,8 @@ int main()
 					spacegroupName = m[7];
 					spacegroupName = m[7];
 					symopnr = 1;
 					symopnr = 1;
 
 
+					spacegroups.emplace_back(spacegroupName, spacegroupNr);
+
 					state = State::InSpacegroup;
 					state = State::InSpacegroup;
 					break;
 					break;
 				}
 				}
@@ -237,11 +239,26 @@ int main()
 		// --------------------------------------------------------------------
 		// --------------------------------------------------------------------
 
 
 		sort(data.begin(), data.end());
 		sort(data.begin(), data.end());
+		sort(spacegroups.begin(), spacegroups.end());
 
 
 		// --------------------------------------------------------------------
 		// --------------------------------------------------------------------
 
 
 		cout << R"(// This file was generated from $CLIBD/symop.lib
 		cout << R"(// This file was generated from $CLIBD/symop.lib
 
 
+struct Spacegroup
+{
+	const char* name;
+	int nr;
+} kSpaceGroups[] =
+{
+)";
+
+		for (auto& [name, nr]: spacegroups)
+			cout << "\t{ \"" << name << "\", " << nr << " }," << endl;
+
+cout << R"(
+};
+
 union SymopData
 union SymopData
 {
 {
 	struct
 	struct