Fix writing PDB CISPEP records

Better checking for open files
More verbose parser

include/cif++/parser.hpp

@@ -212,12 +212,16 @@ class sac_parser
 
 
 	void error(const std::string &msg)
 	void error(const std::string &msg)
 	{
 	{
+		if (cif::VERBOSE > 0)
+			std::cerr << "Error parsing mmCIF: " << msg << std::endl;
+
 		throw parse_error(m_line_nr, msg);
 		throw parse_error(m_line_nr, msg);
 	}
 	}
 
 
 	void warning(const std::string &msg)
 	void warning(const std::string &msg)
 	{
 	{
-		std::cerr << "parser warning at line" << m_line_nr << ": " << msg << std::endl;
+		if (cif::VERBOSE > 0)
+			std::cerr << "parser warning at line" << m_line_nr << ": " << msg << std::endl;
 	}
 	}
 
 
 	// production methods, these are pure virtual here
 	// production methods, these are pure virtual here

src/file.cpp

@@ -184,6 +184,8 @@ std::tuple<file::iterator, bool> file::emplace(std::string_view name)
 void file::load(const std::filesystem::path &p)
 void file::load(const std::filesystem::path &p)
 {
 {
 	gxrio::ifstream in(p);
 	gxrio::ifstream in(p);
+	if (not in.is_open())
+		throw std::runtime_error("Could not open file " + p.string());
 	load(in);
 	load(in);
 }
 }
 
 

src/parser.cpp

@@ -49,6 +49,9 @@ namespace cif
 sac_parser::sac_parser(std::istream &is, bool init)
 sac_parser::sac_parser(std::istream &is, bool init)
 	: m_source(*is.rdbuf())
 	: m_source(*is.rdbuf())
 {
 {
+	if (is.rdbuf() == nullptr)
+		throw std::runtime_error("Attempt to read from uninitialised stream");
+
 	m_validate = true;
 	m_validate = true;
 	m_line_nr = 1;
 	m_line_nr = 1;
 	m_bol = true;
 	m_bol = true;

src/pdb/cif2pdb.cpp

@@ -3226,7 +3226,8 @@ void WriteConnectivity(std::ostream &pdbFile, const datablock &db)
 				"pdbx_label_comp_id_2", "pdbx_auth_asym_id_2", "pdbx_auth_seq_id_2", "pdbx_PDB_ins_code_2",
 				"pdbx_label_comp_id_2", "pdbx_auth_asym_id_2", "pdbx_auth_seq_id_2", "pdbx_PDB_ins_code_2",
 				"pdbx_PDB_model_num", "pdbx_omega_angle");
 				"pdbx_PDB_model_num", "pdbx_omega_angle");
 
 
-		pdbFile << format("CISPEP %3d %3.3s %1.1s %4d%1.1s   %3.3s %1.1s %4d%1.1s       %3d       %6.2f", serNum, pep1, chainID1, seqNum1, icode1, pep2, chainID2, seqNum2, icode2, modNum, measure) << std::endl;
+		pdbFile << format("CISPEP %3.3s %3.3s %1.1s %4d%1.1s   %3.3s %1.1s %4d%1.1s       %3.3s       %6.2f",
+			serNum, pep1, chainID1, seqNum1, icode1, pep2, chainID2, seqNum2, icode2, modNum, measure) << std::endl;
 	}
 	}
 }
 }