fixes in numeric conversions

include/cif++/model.hpp

@@ -608,7 +608,13 @@ class sugar : public residue
 	sugar(sugar &&rhs);
 	sugar(sugar &&rhs);
 	sugar &operator=(sugar &&rhs);
 	sugar &operator=(sugar &&rhs);
 
 
-	int num() const { return std::stoi(m_auth_seq_id); }
+	int num() const {
+		int result;
+		auto r = std::from_chars(m_auth_seq_id.data(), m_auth_seq_id.data() + m_auth_seq_id.length(), result);
+		if (r.ec != std::errc())
+			throw std::runtime_error("The auth_seq_id should be a number for a sugar");
+		return result;
+	}
 	std::string name() const;
 	std::string name() const;
 
 
 	/// \brief Return the atom the C1 is linked to
 	/// \brief Return the atom the C1 is linked to

src/file.cpp

@@ -115,8 +115,8 @@ void file::load_dictionary()
 		}
 		}
 	}
 	}
 
 
-	if (not m_validator)
-		load_dictionary("mmcif_pdbx.dic");	// TODO: maybe incorrect? Perhaps improve?
+	// if (not m_validator)
+	// 	load_dictionary("mmcif_pdbx.dic");	// TODO: maybe incorrect? Perhaps improve?
 }
 }
 
 
 void file::load_dictionary(std::string_view name)
 void file::load_dictionary(std::string_view name)

src/pdb/cif2pdb.cpp

@@ -704,16 +704,17 @@ class Ff : public FBase
 		else
 		else
 		{
 		{
 			std::string s{ text() };
 			std::string s{ text() };
-			try
-			{
-				os << std::stod(s);
-			}
-			catch (const std::exception &ex)
+
+			double d = 0;
+			auto r = cif::from_chars(s.data(), s.data() + s.length(), d);
+			if (r.ec != std::errc())
 			{
 			{
-				if (VERBOSE >= 0)
+				if (VERBOSE > 0)
 					std::cerr << "Failed to write '" << s << "' as a double, this indicates an error in the code for writing PDB files" << std::endl;
 					std::cerr << "Failed to write '" << s << "' as a double, this indicates an error in the code for writing PDB files" << std::endl;
 				os << s;
 				os << s;
 			}
 			}
+			else
+				os << d;
 		}
 		}
 	}
 	}
 };
 };

src/pdb/pdb2cif.cpp

@@ -1136,16 +1136,15 @@ void PDBFileParser::PreParseInput(std::istream &is)
 	{
 	{
 		std::string cs = lookahead.substr(offset, len);
 		std::string cs = lookahead.substr(offset, len);
 		cif::trim(cs);
 		cif::trim(cs);
-		int result;
+		int result = 0;
 
 
-		try
-		{
-			result = cs.empty() ? 0 : stoi(cs);
-		}
-		catch (...)
+		if (not cs.empty())
 		{
 		{
+			auto r = std::from_chars(cs.data(), cs.data() + cs.length(), result);
+			if (r.ec != std::errc())
 				throw std::runtime_error("Continuation std::string '" + cs + "' is not valid");
 				throw std::runtime_error("Continuation std::string '" + cs + "' is not valid");
 		}
 		}
+
 		return result;
 		return result;
 	};
 	};
 
 
@@ -1402,7 +1401,12 @@ void PDBFileParser::PreParseInput(std::istream &is)
 			link.symOpB = cur->vS(67, 72);    //	67 - 72         SymOP          sym2            Symmetry operator atom 2.
 			link.symOpB = cur->vS(67, 72);    //	67 - 72         SymOP          sym2            Symmetry operator atom 2.
 
 
 			if (type == "LINK") //	 1 -  6         Record name    "LINK  "
 			if (type == "LINK") //	 1 -  6         Record name    "LINK  "
-				link.distance = std::stof(cur->vF(74, 78));
+			{
+				auto f = cur->vF(74, 78);
+				auto r = cif::from_chars(f.data(), f.data() + f.length(), link.distance);
+				if (r.ec != std::errc() and cif::VERBOSE > 0)
+					std::cerr << "Error parsing link distance at line " << cur->mLineNr << std::endl;
+			}
 			//	74 – 78         Real(5.2)      Length          Link distance
 			//	74 – 78         Real(5.2)      Length          Link distance
 
 
 			mLinks.push_back(link);
 			mLinks.push_back(link);
@@ -5107,11 +5111,10 @@ void PDBFileParser::ParseConnectivtyAnnotation()
 			if (mRec->is("LINK  "))
 			if (mRec->is("LINK  "))
 			{
 			{
 				distance = vS(74, 78);
 				distance = vS(74, 78);
-				try
-				{
-					stod(distance);
-				}
-				catch (const std::invalid_argument &)
+
+				double d;
+				auto r = cif::from_chars(distance.data(), distance.data() + distance.length(), d);
+				if (r.ec != std::errc())
 				{
 				{
 					if (cif::VERBOSE > 0)
 					if (cif::VERBOSE > 0)
 						std::cerr << "Distance value '" << distance << "' is not a valid float in LINK record" << std::endl;
 						std::cerr << "Distance value '" << distance << "' is not a valid float in LINK record" << std::endl;
@@ -6211,6 +6214,10 @@ file read(std::istream &is)
 			result.load(is);
 			result.load(is);
 	}
 	}
 
 
+	// Must be a PDB like file, right?
+	if (result.get_validator() == nullptr)
+		result.load_dictionary("mmcif_pdbx.dic");
+
 	return result;
 	return result;
 }
 }
 
 

src/pdb/pdb2cif_remark_3.cpp

@@ -1207,13 +1207,15 @@ void Remark3Parser::storeCapture(const char *category, std::initializer_list<con
 			}
 			}
 			else if (iequals(category, "pdbx_refine_tls_group"))
 			else if (iequals(category, "pdbx_refine_tls_group"))
 			{
 			{
-				std::string tlsGroupID;
+				std::string tlsID;
 				if (not mDb["pdbx_refine_tls"].empty())
 				if (not mDb["pdbx_refine_tls"].empty())
-					tlsGroupID = mDb["pdbx_refine_tls"].back()["id"].as<std::string>();
+					tlsID = mDb["pdbx_refine_tls"].back()["id"].as<std::string>();
+				std::string tlsGroupID = cat.get_unique_id("");
 
 
-				cat.emplace({ { "pdbx_refine_id", mExpMethod },
+				cat.emplace({
+					{ "pdbx_refine_id", mExpMethod },
 					{ "id", tlsGroupID },
 					{ "id", tlsGroupID },
-					{ "refine_tls_id", tlsGroupID } });
+					{ "refine_tls_id", tlsID } });
 			}
 			}
 			else if (iequals(category, "pdbx_refine_tls"))
 			else if (iequals(category, "pdbx_refine_tls"))
 			{
 			{