platonyzer work, adding a symop table generator

git-svn-id: svn+ssh://gitlab/srv/svn-repos/pdb-redo/trunk@483 a1961a4f-ab94-4bcc-80e8-33b5a54de466

include/cif++/DistanceMap.h

@@ -61,7 +61,9 @@ class SymmetryAtomIteratorFactory
 	// SymmetryAtomIteratorFactory(const Structure& p);
 	// SymmetryAtomIteratorFactory(const Structure& p);
 	SymmetryAtomIteratorFactory(const Structure& p, const clipper::Spacegroup& spacegroup, const clipper::Cell& cell)
 	SymmetryAtomIteratorFactory(const Structure& p, const clipper::Spacegroup& spacegroup, const clipper::Cell& cell)
 		: mD(DistanceMap::CalculateOffsetForCell(p, spacegroup, cell))
 		: mD(DistanceMap::CalculateOffsetForCell(p, spacegroup, cell))
-		, mRtOrth(DistanceMap::AlternativeSites(spacegroup, cell)) {}
+		, mRtOrth(DistanceMap::AlternativeSites(spacegroup, cell))
+		, mSpacegroup(spacegroup)
+		, mCell(cell) {}
 
 
 	SymmetryAtomIteratorFactory(const SymmetryAtomIteratorFactory&) = delete;
 	SymmetryAtomIteratorFactory(const SymmetryAtomIteratorFactory&) = delete;
 	SymmetryAtomIteratorFactory& operator=(const SymmetryAtomIteratorFactory&) = delete;
 	SymmetryAtomIteratorFactory& operator=(const SymmetryAtomIteratorFactory&) = delete;
@@ -156,9 +158,13 @@ class SymmetryAtomIteratorFactory
 		return SymmetryAtomIteratorRange(*this, a);
 		return SymmetryAtomIteratorRange(*this, a);
 	}
 	}
 
 
+	std::string symop_mmcif(const Atom& a) const;
+
   private:
   private:
 	Point									mD;			// needed to move atoms to center
 	Point									mD;			// needed to move atoms to center
 	std::vector<clipper::RTop_orth>			mRtOrth;
 	std::vector<clipper::RTop_orth>			mRtOrth;
+	clipper::Spacegroup						mSpacegroup;
+	clipper::Cell							mCell;
 };
 };
 
 
 }
 }

include/cif++/Structure.h

@@ -85,6 +85,7 @@ class Atom
 	Atom symmetryCopy(const Point& d, const clipper::RTop_orth& rt);
 	Atom symmetryCopy(const Point& d, const clipper::RTop_orth& rt);
 	bool isSymmetryCopy() const;
 	bool isSymmetryCopy() const;
 	std::string symmetry() const;
 	std::string symmetry() const;
+	const clipper::RTop_orth& symop() const;
 	
 	
 	const Compound& comp() const;
 	const Compound& comp() const;
 	bool isWater() const;
 	bool isWater() const;
@@ -112,7 +113,7 @@ class Atom
 	std::string authAsymId() const;
 	std::string authAsymId() const;
 	std::string authSeqId() const;
 	std::string authSeqId() const;
 	std::string pdbxAuthInsCode() const;
 	std::string pdbxAuthInsCode() const;
-	std::string authAltId() const;
+	std::string pdbxAuthAltId() const;
 	
 	
 	std::string labelID() const;// label_comp_id + '_' + label_asym_id + '_' + label_seq_id
 	std::string labelID() const;// label_comp_id + '_' + label_asym_id + '_' + label_seq_id
 	std::string pdbID() const;	// auth_comp_id + '_' + auth_asym_id + '_' + auth_seq_id + pdbx_PDB_ins_code
 	std::string pdbID() const;	// auth_comp_id + '_' + auth_asym_id + '_' + auth_seq_id + pdbx_PDB_ins_code

src/DistanceMap.cpp

@@ -450,4 +450,60 @@ vector<Atom> DistanceMap::near(const Atom& a, float maxDistance) const
 	return result;
 	return result;
 }
 }
 
 
+// -----------------------------------------------------------------------
+
+string SymmetryAtomIteratorFactory::symop_mmcif(const Atom& a) const
+{
+	string result;
+
+	if (not a.isSymmetryCopy())
+		result = "1_555";
+	else
+	{
+		auto rtop_o = a.symop();
+
+		for (int i = 0; i < mSpacegroup.num_symops(); ++i)
+		{
+			const auto& symop = mSpacegroup.symop(i);
+
+			for (int u: { -1, 0, 1})
+				for (int v: { -1, 0, 1})
+					for (int w: { -1, 0, 1})
+					{
+						// if (i == 0 and u == 0 and v == 0 and w == 0)
+						// 	continue;
+
+						auto rtop = clipper::RTop_frac(
+								symop.rot(), symop.trn() + clipper::Vec3<>(u, v, w)
+							).rtop_orth(mCell);
+						
+						if (rtop.rot().equals(rtop_o.rot(), 0.00001) and rtop.trn().equals(rtop_o.trn(), 0.000001))
+						{
+							// gotcha
+
+							auto rtop_f = rtop.rtop_frac(mCell);
+
+							uint32_t t[3] = {
+								static_cast<uint32_t>(5 + static_cast<int>(rint(rtop_f.trn()[0]))),
+								static_cast<uint32_t>(5 + static_cast<int>(rint(rtop_f.trn()[1]))),
+								static_cast<uint32_t>(5 + static_cast<int>(rint(rtop_f.trn()[2])))
+							};
+
+							if (t[0] > 9 or t[1] > 9 or t[2] > 9)
+								throw runtime_error("Symmetry operation has an out-of-range translation.");
+
+							result += to_string(1 + i) + "_"
+								   + to_string(t[0])
+								   + to_string(t[1])
+								   + to_string(t[2]);
+
+							return result;
+						}
+					}
+		}
+	}
+
+	return result;
+}
+
 }
 }

src/Structure.cpp

@@ -383,6 +383,7 @@ struct AtomImpl
 
 
 	clipper::RTop_orth	mRTop;
 	clipper::RTop_orth	mRTop;
 	Point				mD;
 	Point				mD;
+	int32_t				mRTix;
 };
 };
 
 
 //Atom::Atom(const File& f, const string& id)
 //Atom::Atom(const File& f, const string& id)
@@ -530,9 +531,9 @@ string Atom::authAtomId() const
 	return property<string>("auth_atom_id");
 	return property<string>("auth_atom_id");
 }
 }
 
 
-string Atom::authAltId() const
+string Atom::pdbxAuthAltId() const
 {
 {
-	return property<string>("auth_alt_id");
+	return property<string>("pdbx_auth_alt_id");
 }
 }
 
 
 string Atom::pdbxAuthInsCode() const
 string Atom::pdbxAuthInsCode() const
@@ -589,6 +590,11 @@ string Atom::symmetry() const
 	return clipper::Symop(mImpl->mRTop).format() + "\n" + mImpl->mRTop.format();
 	return clipper::Symop(mImpl->mRTop).format() + "\n" + mImpl->mRTop.format();
 }
 }
 
 
+const clipper::RTop_orth& Atom::symop() const
+{
+	return mImpl->mRTop;
+}
+
 const Compound& Atom::comp() const
 const Compound& Atom::comp() const
 {
 {
 	return mImpl->comp();
 	return mImpl->comp();

tools/symop-map-generator.cpp

+/*
+cd ~/projects/pdb-redo/libcif++/tools/
+clang++ -I ~/my-clipper/include -L ~/my-clipper/lib -o symop-map-generator symop-map-generator.cpp -lclipper-core
+./symop-map-generator
+
+*/
+
+#include <cassert>
+
+#include <iostream>
+#include <fstream>
+#include <regex>
+
+#include <cstdlib>
+
+#include <clipper/clipper.h>
+
+using namespace std;
+
+std::regex kNameRx(R"(^(\d+) +(\d+) +(\d+) +(\S+) +(\S+) +(\S+) +'([^']+)'( +'([^']+)')?(?: +!.+)?$)");
+
+class SymopParser
+{
+  public:
+	SymopParser(const std::string& s)
+		: m_s(s)
+		, m_p(s.begin())
+		, m_e(s.end())
+	{
+		m_lookahead = next_char();
+	}
+
+	void parse()
+	{
+		parsepart(0);
+		match(',');
+		parsepart(1);
+		match(',');
+		parsepart(2);
+		if (m_lookahead != 0)
+			throw runtime_error("symmetry expression contains more data than expected");
+	}
+
+  private:
+
+	char next_char()
+	{
+		char result = 0;
+		while (m_p != m_e)
+		{
+			char ch = *m_p++;
+			if (ch == ' ')
+				continue;
+
+			result = ch;
+			break;
+		}
+
+		return result;
+	}
+
+	void retract()
+	{
+		--m_p;
+	}
+
+	void match(char c)
+	{
+		if (m_lookahead != c)
+			throw runtime_error("Unexpected character " + m_lookahead + " expected " + c);
+		
+		m_lookahead = next_char();
+	}
+
+	void parsepart(int xyz)
+	{
+		if (isdigit(m_lookahead))
+		{
+			parserational(xyz);
+
+			switch (m_lookahead)
+			{
+				case '-':
+					match('-');
+					break;
+			}
+
+		}
+
+
+		}
+		if (m_lookahead == '+')
+		{
+			match('+');
+		}
+		else if (m_lookahead = '-')
+		{
+
+		}
+
+
+	}
+
+	tuple<int,int> parserational();
+
+	char m_lookahead;
+
+	string m_s;
+	string::iterator m_p, m_e;
+
+	int m_rot[3][3] = {};
+	int m_trn[3] = {};
+};
+
+int main()
+{
+	try
+	{
+		const char* CLIBD = getenv("CLIBD");
+		
+		if (CLIBD == nullptr)
+			throw runtime_error("CCP4 not sourced");
+
+		ifstream file(CLIBD + "/symop.lib"s);
+		if (not file.is_open())
+			throw runtime_error("Could not open symop.lib file");
+		
+		string line;
+		clipper::Spacegroup spacegroup;
+
+		enum class State { Initial, InSpacegroup, Error } state = State::Initial;
+
+		while (getline(file, line))
+		{
+			if (line.empty())
+				throw runtime_error("Invalid symop.lib file, contains empty line");
+			
+			switch (state)
+			{
+				case State::Error:
+				case State::InSpacegroup:
+					if (line[0] == ' ')
+					{
+						if (state == State::Error)
+							continue;
+						
+						
+
+
+						continue;
+					}
+					// fall through
+				
+				case State::Initial:
+				{
+					smatch m;
+					if (not regex_match(line, m, kNameRx))
+					{
+						cerr << line << endl;
+						throw runtime_error("Name line does not match regular expression");
+					}
+
+					int nr = stoi(m[1].str());
+					if (nr > 230)
+					{
+						state = State::Error;
+						continue;
+					}
+
+					try
+					{
+						spacegroup = clipper::Spacegroup(clipper::Spgr_descr(stoi(m[1].str())));
+						
+						if (spacegroup.num_symops() != stoi(m[2]))
+						{
+							cerr << line << endl
+								 << "Num of symops do not match: " << spacegroup.num_symops() << " <> " << m[2] << endl;
+							state = State::Error;
+							continue;
+						}
+
+						state = State::InSpacegroup;
+					}
+					catch (const clipper::Message_fatal& e)
+					{
+						cerr << line << endl
+							 << e.text() << endl;
+						state = State::Error;
+					}
+					break;
+				}
+			}
+		}
+		
+	}
+	catch (const exception& ex)
+	{
+		cerr << endl
+			 << "Program terminated due to error:" << endl
+			 << ex.what() << endl;
+	}
+	
+	
+	return 0;
+}