refactored main using nested exceptions, fixed PDB parser a bit

git-svn-id: svn+ssh://gitlab/srv/svn-repos/pdb-redo/trunk@180 a1961a4f-ab94-4bcc-80e8-33b5a54de466

include/cif++/TlsParser.h

+/* 
+   Created by: Maarten L. Hekkelman
+   Date: dinsdag 07 november, 2017
+
+	Copyright 2017 NKI AVL
+	
+	Permission is hereby granted, free of charge, to any person obtaining 
+	a copy of this software and associated documentation files (the 
+	"Software"), to deal in the Software without restriction, including 
+	without limitation the rights to use, copy, modify, merge, publish, 
+	distribute, sublicense, and/or sell copies of the Software, and to 
+	permit persons to whom the Software is furnished to do so, subject to 
+	the following conditions:
+	
+	The above copyright notice and this permission notice shall be 
+	included in all copies or substantial portions of the Software.
+	
+	THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, 
+	EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF 
+	MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. 
+	IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY 
+	CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, 
+	TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE 
+	SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+#include <vector>
+#include <string>
+#include <tuple>
+
+#include "cif++/Cif++.h"
+
+namespace cif
+{
+	
+extern const int
+	kResidueNrWildcard,
+	kNoSeqNum;
+
+struct TLSSelection;
+typedef std::unique_ptr<TLSSelection> TLSSelectionPtr;
+
+struct TLSResidue;
+
+struct TLSSelection
+{
+	virtual ~TLSSelection() {}
+	virtual void CollectResidues(cif::Datablock& db, std::vector<TLSResidue>& residues, int indentLevel = 0) const = 0;
+	std::vector<std::tuple<std::string,int,int>> GetRanges(cif::Datablock& db, bool pdbNamespace) const;
+};
+
+// Low level: get the selections
+TLSSelectionPtr ParseSelectionDetails(const std::string& program, const std::string& selection);
+
+}

src/Cif++.cpp

@@ -1773,7 +1773,7 @@ Row& Row::operator=(const Row& rhs)
 void Row::assign(const string& name, const string& value, bool emplacing)
 void Row::assign(const string& name, const string& value, bool emplacing)
 {
 {
 	if (mData == nullptr)
 	if (mData == nullptr)
-		throw logic_error("invalid Row, no data");
+		throw logic_error("invalid Row, no data assigning value '" + value + "' to " + name);
 	
 	
 	auto cat = mData->mCategory;
 	auto cat = mData->mCategory;
 	auto cix = cat->addColumn(name);
 	auto cix = cat->addColumn(name);
@@ -1905,7 +1905,7 @@ bool Row::empty() const
 
 
 auto Row::begin() const -> const_iterator
 auto Row::begin() const -> const_iterator
 {
 {
-	return const_iterator(mData, mData->mValues);
+	return const_iterator(mData, mData ? mData->mValues : nullptr);
 }
 }
 
 
 auto Row::end() const -> const_iterator
 auto Row::end() const -> const_iterator

src/Compound.cpp

@@ -264,6 +264,7 @@ const Compound* CompoundFactory::create(std::string id)
 											value = 1.5;
 											value = 1.5;
 				else
 				else
 				{
 				{
+					if (VERBOSE)
 						cerr << "Unimplemented chem_comp_bond.type " << type << " in file " << resFile << endl;
 						cerr << "Unimplemented chem_comp_bond.type " << type << " in file " << resFile << endl;
 					value = 1.0;
 					value = 1.0;
 				}
 				}

src/PDB2CifRemark3.cpp

@@ -978,7 +978,10 @@ float Remark3Parser::parse()
 	}
 	}
 
 
 	if (not remarks.empty() and not iequals(remarks, "NULL"))
 	if (not remarks.empty() and not iequals(remarks, "NULL"))
+	{
+		if (not mDb["refine"].empty())
 			mDb["refine"].front()["details"] = remarks;
 			mDb["refine"].front()["details"] = remarks;
+	}
 
 
 	float score = float(lineCount - dropped) / lineCount;
 	float score = float(lineCount - dropped) / lineCount;