more quiet code

src/BondMap.cpp

@@ -180,7 +180,10 @@ bool CompoundBondMap::bonded(const std::string &compoundID, const std::string &a
 
 
 	auto compound = mmcif::CompoundFactory::instance().create(compoundID);
 	auto compound = mmcif::CompoundFactory::instance().create(compoundID);
 	if (not compound)
 	if (not compound)
-		std::cerr << "Missing compound bond info for " << compoundID << std::endl;
+	{
+		if (cif::VERBOSE >= 0)
+			std::cerr << "Missing compound bond info for " << compoundID << std::endl;
+	}
 	else
 	else
 	{
 	{
 		for (auto &atom : compound->bonds())
 		for (auto &atom : compound->bonds())
@@ -308,7 +311,7 @@ BondMap::BondMap(const Structure &p)
 	{
 	{
 		if (c == "HOH" or c == "H2O" or c == "WAT")
 		if (c == "HOH" or c == "H2O" or c == "WAT")
 		{
 		{
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "skipping water in bond map calculation" << std::endl;
 				std::cerr << "skipping water in bond map calculation" << std::endl;
 			continue;
 			continue;
 		}
 		}

src/Cif++.cpp

@@ -1497,7 +1497,7 @@ size_t Category::getColumnIndex(std::string_view name) const
 			break;
 			break;
 	}
 	}
 
 
-	if (VERBOSE and result == mColumns.size() and mCatValidator != nullptr) // validate the name, if it is known at all (since it was not found)
+	if (VERBOSE > 0 and result == mColumns.size() and mCatValidator != nullptr) // validate the name, if it is known at all (since it was not found)
 	{
 	{
 		auto iv = mCatValidator->getValidatorForItem(name);
 		auto iv = mCatValidator->getValidatorForItem(name);
 		if (iv == nullptr)
 		if (iv == nullptr)
@@ -2340,7 +2340,7 @@ void Category::validateLinks() const
 			if (not hasParent(r, *parentCat, *link))
 			if (not hasParent(r, *parentCat, *link))
 				++missing;
 				++missing;
 
 
-		if (missing)
+		if (missing and VERBOSE >= 0)
 		{
 		{
 			std::cerr << "Links for " << link->mLinkGroupLabel << " are incomplete" << std::endl
 			std::cerr << "Links for " << link->mLinkGroupLabel << " are incomplete" << std::endl
 					  << "  There are " << missing << " items in " << mName << " that don't have matching parent items in " << parentCat->mName << std::endl;
 					  << "  There are " << missing << " items in " << mName << " that don't have matching parent items in " << parentCat->mName << std::endl;
@@ -2900,7 +2900,7 @@ void Category::update_value(RowSet &&rows, const std::string &tag, const std::st
 				}
 				}
 
 
 				// cannot update this...
 				// cannot update this...
-				if (cif::VERBOSE)
+				if (cif::VERBOSE > 0)
 					std::cerr << "Cannot update child " << childCat->mName << "." << childTag << " with value " << value << std::endl;
 					std::cerr << "Cannot update child " << childCat->mName << "." << childTag << " with value " << value << std::endl;
 			}
 			}
 
 
@@ -3018,7 +3018,8 @@ void Row::assign(std::string_view name, const std::string &value, bool skipUpdat
 	}
 	}
 	catch (const std::exception &ex)
 	catch (const std::exception &ex)
 	{
 	{
-		std::cerr << "Could not assign value '" << value << "' to column _" << mData->mCategory->name() << '.' << name << std::endl;
+		if (cif::VERBOSE >= 0)
+			std::cerr << "Could not assign value '" << value << "' to column _" << mData->mCategory->name() << '.' << name << std::endl;
 		throw;
 		throw;
 	}
 	}
 }
 }
@@ -3181,7 +3182,7 @@ void Row::assign(size_t column, const std::string &value, bool skipUpdateLinked)
 			auto rows_n = childCat->find(std::move(cond_n));
 			auto rows_n = childCat->find(std::move(cond_n));
 			if (not rows_n.empty())
 			if (not rows_n.empty())
 			{
 			{
-				if (cif::VERBOSE)
+				if (cif::VERBOSE > 0)
 					std::cerr << "Will not rename in child category since there are already rows that link to the parent" << std::endl;
 					std::cerr << "Will not rename in child category since there are already rows that link to the parent" << std::endl;
 
 
 				continue;
 				continue;
@@ -3387,7 +3388,7 @@ void Row::swap(size_t cix, ItemRow *a, ItemRow *b)
 					}
 					}
 					else
 					else
 					{
 					{
-						if (VERBOSE)
+						if (VERBOSE > 0)
 							std::cerr << "In " << childCat->mName << " changing " << linkChildColName << ": " << r[linkChildColName].as<std::string>() << " => " << (i ? i->mText : "") << std::endl;
 							std::cerr << "In " << childCat->mName << " changing " << linkChildColName << ": " << r[linkChildColName].as<std::string>() << " => " << (i ? i->mText : "") << std::endl;
 						r[linkChildColName] = i ? i->mText : "";
 						r[linkChildColName] = i ? i->mText : "";
 					}
 					}
@@ -3496,7 +3497,8 @@ File::File(const std::filesystem::path &path, bool validate)
 	}
 	}
 	catch (const std::exception &ex)
 	catch (const std::exception &ex)
 	{
 	{
-		std::cerr << "Error while loading file " << path << std::endl;
+		if (cif::VERBOSE >= 0)
+			std::cerr << "Error while loading file " << path << std::endl;
 		throw;
 		throw;
 	}
 	}
 }
 }
@@ -3564,7 +3566,8 @@ void File::load(const std::filesystem::path &p)
 	}
 	}
 	catch (const std::exception &ex)
 	catch (const std::exception &ex)
 	{
 	{
-		std::cerr << "Error loading file " << path << std::endl;
+		if (cif::VERBOSE >= 0)
+			std::cerr << "Error loading file " << path << std::endl;
 		throw;
 		throw;
 	}
 	}
 }
 }
@@ -3660,7 +3663,7 @@ bool File::isValid()
 {
 {
 	if (mValidator == nullptr)
 	if (mValidator == nullptr)
 	{
 	{
-		if (VERBOSE)
+		if (VERBOSE > 0)
 			std::cerr << "No dictionary loaded explicitly, loading default" << std::endl;
 			std::cerr << "No dictionary loaded explicitly, loading default" << std::endl;
 
 
 		loadDictionary();
 		loadDictionary();

src/Cif2PDB.cpp

@@ -753,7 +753,8 @@ class Ff : public FBase
             }
             }
             catch (const std::exception& ex)
             catch (const std::exception& ex)
             {
             {
-                std::cerr << "Failed to write '" << s << "' as a double, this indicates an error in the code for writing PDB files" << std::endl;
+				if (cif::VERBOSE >= 0)
+	                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;
             }
             }
         }
         }
@@ -2329,7 +2330,8 @@ void WriteRemark200(std::ostream& pdbFile, Datablock& db)
 	}
 	}
 	catch (const std::exception& ex)
 	catch (const std::exception& ex)
 	{
 	{
-		std::cerr << ex.what() << std::endl;
+		if (cif::VERBOSE >= 0)
+			std::cerr << ex.what() << std::endl;
 	}
 	}
 }
 }
 
 
@@ -2390,7 +2392,8 @@ void WriteRemark280(std::ostream& pdbFile, Datablock& db)
 	}
 	}
 	catch (const std::exception& ex)
 	catch (const std::exception& ex)
 	{
 	{
-		std::cerr << ex.what() << std::endl;
+		if (cif::VERBOSE >= 0)
+			std::cerr << ex.what() << std::endl;
 	}
 	}
 }
 }
 
 

src/CifParser.cpp

@@ -288,7 +288,7 @@ SacParser::CIFToken SacParser::getNextToken()
 					mState = eStateTextField + 1;
 					mState = eStateTextField + 1;
 				else if (ch == kEOF)
 				else if (ch == kEOF)
 					error("unterminated textfield");
 					error("unterminated textfield");
-				else if (not isAnyPrint(ch))
+				else if (not isAnyPrint(ch) and cif::VERBOSE >= 0)
 					//					error("invalid character in text field '" + string({ static_cast<char>(ch) }) + "' (" + to_string((int)ch) + ")");
 					//					error("invalid character in text field '" + string({ static_cast<char>(ch) }) + "' (" + to_string((int)ch) + ")");
 					std::cerr << "invalid character in text field '" << std::string({static_cast<char>(ch)}) << "' (" << ch << ") line: " << mLineNr << std::endl;
 					std::cerr << "invalid character in text field '" << std::string({static_cast<char>(ch)}) << "' (" << ch << ") line: " << mLineNr << std::endl;
 				break;
 				break;
@@ -1220,7 +1220,7 @@ void DictParser::linkItems()
 	{
 	{
 		for (auto &iv : cv.mItemValidators)
 		for (auto &iv : cv.mItemValidators)
 		{
 		{
-			if (iv.mType == nullptr)
+			if (iv.mType == nullptr and cif::VERBOSE >= 0)
 				std::cerr << "Missing item_type for " << iv.mTag << std::endl;
 				std::cerr << "Missing item_type for " << iv.mTag << std::endl;
 		}
 		}
 	}
 	}
@@ -1255,7 +1255,8 @@ void DictParser::loadDictionary()
 	}
 	}
 	catch (const std::exception &)
 	catch (const std::exception &)
 	{
 	{
-		std::cerr << "Error parsing dictionary" << std::endl;
+		if (cif::VERBOSE >= 0)
+			std::cerr << "Error parsing dictionary" << std::endl;
 		throw;
 		throw;
 	}
 	}
 
 

src/CifUtils.cpp

@@ -1237,7 +1237,7 @@ std::filesystem::path gDataDir;
 
 
 void addDataDirectory(std::filesystem::path dataDir)
 void addDataDirectory(std::filesystem::path dataDir)
 {
 {
-	if (VERBOSE and not fs::exists(dataDir))
+	if (VERBOSE > 0 and not fs::exists(dataDir))
 		std::cerr << "The specified data directory " << dataDir << " does not exist" << std::endl;
 		std::cerr << "The specified data directory " << dataDir << " does not exist" << std::endl;
 	gDataDir = dataDir;
 	gDataDir = dataDir;
 }
 }

src/CifValidator.cpp

@@ -354,7 +354,7 @@ void Validator::reportError(const std::string &msg, bool fatal) const
 {
 {
 	if (mStrict or fatal)
 	if (mStrict or fatal)
 		throw ValidationError(msg);
 		throw ValidationError(msg);
-	else if (VERBOSE)
+	else if (VERBOSE > 0)
 		std::cerr << msg << std::endl;
 		std::cerr << msg << std::endl;
 }
 }
 
 

src/Compound.cpp

@@ -193,7 +193,7 @@ Compound::Compound(cif::Datablock &db, const std::string &id, const std::string
 			bond.type = BondType::delo;
 			bond.type = BondType::delo;
 		else
 		else
 		{
 		{
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "Unimplemented chem_comp_bond.type " << btype << " in " << id << std::endl;
 				std::cerr << "Unimplemented chem_comp_bond.type " << btype << " in " << id << std::endl;
 			bond.type = BondType::sing;
 			bond.type = BondType::sing;
 		}
 		}
@@ -520,7 +520,7 @@ Compound *CCDCompoundFactoryImpl::create(const std::string &id)
 		}
 		}
 	}
 	}
 
 
-	if (result == nullptr and cif::VERBOSE)
+	if (result == nullptr and cif::VERBOSE > 0)
 		std::cerr << "Could not locate compound " << id << " in the CCD components file" << std::endl;
 		std::cerr << "Could not locate compound " << id << " in the CCD components file" << std::endl;
 
 
 	return result;
 	return result;
@@ -645,13 +645,13 @@ CompoundFactory::CompoundFactory()
 	auto ccd = cif::loadResource("components.cif");
 	auto ccd = cif::loadResource("components.cif");
 	if (ccd)
 	if (ccd)
 		mImpl.reset(new CCDCompoundFactoryImpl(mImpl));
 		mImpl.reset(new CCDCompoundFactoryImpl(mImpl));
-	else if (cif::VERBOSE)
+	else if (cif::VERBOSE > 0)
 		std::cerr << "CCD components.cif file was not found" << std::endl;
 		std::cerr << "CCD components.cif file was not found" << std::endl;
 
 
 	const char *clibd_mon = getenv("CLIBD_MON");
 	const char *clibd_mon = getenv("CLIBD_MON");
 	if (clibd_mon != nullptr and fs::is_directory(clibd_mon))
 	if (clibd_mon != nullptr and fs::is_directory(clibd_mon))
 		mImpl.reset(new CCP4CompoundFactoryImpl(clibd_mon));
 		mImpl.reset(new CCP4CompoundFactoryImpl(clibd_mon));
-	else if (cif::VERBOSE)
+	else if (cif::VERBOSE > 0)
 		std::cerr << "CCP4 monomers library not found, CLIBD_MON is not defined" << std::endl;
 		std::cerr << "CCP4 monomers library not found, CLIBD_MON is not defined" << std::endl;
 
 
 }
 }
@@ -695,7 +695,8 @@ void CompoundFactory::setDefaultDictionary(const std::filesystem::path &inDictFi
 	}
 	}
 	catch (const std::exception &)
 	catch (const std::exception &)
 	{
 	{
-		std::cerr << "Error loading dictionary " << inDictFile << std::endl;
+		if (cif::VERBOSE >= 0)
+			std::cerr << "Error loading dictionary " << inDictFile << std::endl;
 		throw;
 		throw;
 	}
 	}
 }
 }
@@ -715,7 +716,8 @@ void CompoundFactory::pushDictionary(const std::filesystem::path &inDictFile)
 	}
 	}
 	catch (const std::exception &)
 	catch (const std::exception &)
 	{
 	{
-		std::cerr << "Error loading dictionary " << inDictFile << std::endl;
+		if (cif::VERBOSE >= 0)
+			std::cerr << "Error loading dictionary " << inDictFile << std::endl;
 		throw;
 		throw;
 	}
 	}
 }
 }

src/PDB2CifRemark3.cpp

@@ -1320,7 +1320,7 @@ bool Remark3Parser::parse(const std::string& expMethod, PDBRecord* r, cif::Datab
 
 
 	if (line != "REFINEMENT.")
 	if (line != "REFINEMENT.")
 	{
 	{
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 			std::cerr << "Unexpected data in REMARK 3" << std::endl;
 			std::cerr << "Unexpected data in REMARK 3" << std::endl;
 		return false;
 		return false;
 	}
 	}
@@ -1332,7 +1332,7 @@ bool Remark3Parser::parse(const std::string& expMethod, PDBRecord* r, cif::Datab
 
 
 	if (not std::regex_match(line, m, rxp))
 	if (not std::regex_match(line, m, rxp))
 	{
 	{
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 			std::cerr << "Expected valid PROGRAM line in REMARK 3" << std::endl;
 			std::cerr << "Expected valid PROGRAM line in REMARK 3" << std::endl;
 		return false;
 		return false;
 	}
 	}
@@ -1367,8 +1367,9 @@ bool Remark3Parser::parse(const std::string& expMethod, PDBRecord* r, cif::Datab
 		}
 		}
 		catch(const std::exception& e)
 		catch(const std::exception& e)
 		{
 		{
-			std::cerr << "Error parsing REMARK 3 with " << parser->program() << std::endl
-					  << e.what() << '\n';
+			if (cif::VERBOSE >= 0)
+				std::cerr << "Error parsing REMARK 3 with " << parser->program() << std::endl
+						  << e.what() << '\n';
 			score = 0;
 			score = 0;
 		}
 		}
 
 
@@ -1411,7 +1412,7 @@ bool Remark3Parser::parse(const std::string& expMethod, PDBRecord* r, cif::Datab
 			tryParser(new TNT_Remark3Parser(program, expMethod, r, db));
 			tryParser(new TNT_Remark3Parser(program, expMethod, r, db));
 		else if (ba::starts_with(program, "X-PLOR"))
 		else if (ba::starts_with(program, "X-PLOR"))
 			tryParser(new XPLOR_Remark3Parser(program, expMethod, r, db));
 			tryParser(new XPLOR_Remark3Parser(program, expMethod, r, db));
-		else if (cif::VERBOSE)
+		else if (cif::VERBOSE > 0)
 			std::cerr << "Skipping unknown program (" << program << ") in REMARK 3" << std::endl;
 			std::cerr << "Skipping unknown program (" << program << ") in REMARK 3" << std::endl;
 	}
 	}
 
 
@@ -1420,7 +1421,8 @@ bool Remark3Parser::parse(const std::string& expMethod, PDBRecord* r, cif::Datab
 	bool guessProgram = scores.empty() or scores.front().score < 0.9f;;
 	bool guessProgram = scores.empty() or scores.front().score < 0.9f;;
 	if (guessProgram)
 	if (guessProgram)
 	{
 	{
-		std::cerr << "Unknown or untrusted program in REMARK 3, trying all parsers to see if there is a match" << std::endl;
+		if (cif::VERBOSE >= 0)
+			std::cerr << "Unknown or untrusted program in REMARK 3, trying all parsers to see if there is a match" << std::endl;
 		
 		
 		tryParser(new BUSTER_TNT_Remark3Parser("BUSTER-TNT", expMethod, r, db));
 		tryParser(new BUSTER_TNT_Remark3Parser("BUSTER-TNT", expMethod, r, db));
 		tryParser(new CNS_Remark3Parser("CNS", expMethod, r, db));
 		tryParser(new CNS_Remark3Parser("CNS", expMethod, r, db));
@@ -1444,7 +1446,7 @@ bool Remark3Parser::parse(const std::string& expMethod, PDBRecord* r, cif::Datab
 
 
 		auto& best = scores.front();
 		auto& best = scores.front();
 
 
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 			std::cerr << "Choosing " << best.parser->program() << " version '" << best.parser->version() << "' as refinement program. Score = " << best.score << std::endl;
 			std::cerr << "Choosing " << best.parser->program() << " version '" << best.parser->version() << "' as refinement program. Score = " << best.score << std::endl;
 
 
 		auto& software = db["software"];
 		auto& software = db["software"];

src/Secondary.cpp

@@ -1240,7 +1240,7 @@ void DSSPImpl::calculateSecondaryStructure()
 		auto r1 = findRes(asym1, seq1);
 		auto r1 = findRes(asym1, seq1);
 		if (r1 == mResidues.end())
 		if (r1 == mResidues.end())
 		{
 		{
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "Missing (incomplete?) residue for SS bond when trying to find " << asym1 << '/' << seq1 << std::endl;
 				std::cerr << "Missing (incomplete?) residue for SS bond when trying to find " << asym1 << '/' << seq1 << std::endl;
 			continue;
 			continue;
 			// throw std::runtime_error("Invalid file, missing residue for SS bond");
 			// throw std::runtime_error("Invalid file, missing residue for SS bond");
@@ -1249,7 +1249,7 @@ void DSSPImpl::calculateSecondaryStructure()
 		auto r2 = findRes(asym2, seq2);
 		auto r2 = findRes(asym2, seq2);
 		if (r2 == mResidues.end())
 		if (r2 == mResidues.end())
 		{
 		{
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "Missing (incomplete?) residue for SS bond when trying to find " << asym2 << '/' << seq2 << std::endl;
 				std::cerr << "Missing (incomplete?) residue for SS bond when trying to find " << asym2 << '/' << seq2 << std::endl;
 			continue;
 			continue;
 			// throw std::runtime_error("Invalid file, missing residue for SS bond");
 			// throw std::runtime_error("Invalid file, missing residue for SS bond");
@@ -1300,7 +1300,7 @@ void DSSPImpl::calculateSecondaryStructure()
 	{
 	{
 		if (a == b)
 		if (a == b)
 		{
 		{
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "In the SS bonds list, the residue " << a->mM << " is bonded to itself" << std::endl;
 				std::cerr << "In the SS bonds list, the residue " << a->mM << " is bonded to itself" << std::endl;
 			continue;
 			continue;
 		}
 		}
@@ -1483,7 +1483,7 @@ SecondaryStructureType DSSP::operator()(const std::string &inAsymID, int inSeqID
 		{ return r.mM.asymID() == inAsymID and r.mM.seqID() == inSeqID; });
 		{ return r.mM.asymID() == inAsymID and r.mM.seqID() == inSeqID; });
 	if (i != mImpl->mResidues.end())
 	if (i != mImpl->mResidues.end())
 		result = i->mSecondaryStructure;
 		result = i->mSecondaryStructure;
-	else if (cif::VERBOSE)
+	else if (cif::VERBOSE > 0)
 		std::cerr << "Could not find secondary structure for " << inAsymID << ':' << inSeqID << std::endl;
 		std::cerr << "Could not find secondary structure for " << inAsymID << ':' << inSeqID << std::endl;
 	return result;
 	return result;
 }
 }
@@ -1501,7 +1501,7 @@ double DSSP::accessibility(const std::string &inAsymID, int inSeqID) const
 		{ return r.mM.asymID() == inAsymID and r.mM.seqID() == inSeqID; });
 		{ return r.mM.asymID() == inAsymID and r.mM.seqID() == inSeqID; });
 	if (i != mImpl->mResidues.end())
 	if (i != mImpl->mResidues.end())
 		result = i->mSecondaryStructure;
 		result = i->mSecondaryStructure;
-	else if (cif::VERBOSE)
+	else if (cif::VERBOSE > 0)
 		std::cerr << "Could not find secondary structure for " << inAsymID << ':' << inSeqID << std::endl;
 		std::cerr << "Could not find secondary structure for " << inAsymID << ':' << inSeqID << std::endl;
 	return result;
 	return result;
 }
 }
@@ -1526,7 +1526,7 @@ bool DSSP::isAlphaHelixEndBeforeStart(const std::string &inAsymID, int inSeqID)
 
 
 	if (i != mImpl->mResidues.end() and i + 1 != mImpl->mResidues.end())
 	if (i != mImpl->mResidues.end() and i + 1 != mImpl->mResidues.end())
 		result = i->GetHelixFlag(HelixType::rh_alpha) == Helix::End and (i + 1)->GetHelixFlag(HelixType::rh_alpha) == Helix::Start;
 		result = i->GetHelixFlag(HelixType::rh_alpha) == Helix::End and (i + 1)->GetHelixFlag(HelixType::rh_alpha) == Helix::Start;
-	else if (cif::VERBOSE)
+	else if (cif::VERBOSE > 0)
 		std::cerr << "Could not find secondary structure for " << inAsymID << ':' << inSeqID << std::endl;
 		std::cerr << "Could not find secondary structure for " << inAsymID << ':' << inSeqID << std::endl;
 
 
 	return result;
 	return result;

src/Structure.cpp

@@ -140,14 +140,14 @@ void FileImpl::load(const std::filesystem::path &path)
 		{
 		{
 			try
 			try
 			{
 			{
-				if (cif::VERBOSE)
+				if (cif::VERBOSE > 0)
 					std::cerr << "unrecognized file extension, trying cif" << std::endl;
 					std::cerr << "unrecognized file extension, trying cif" << std::endl;
 
 
 				mData.load(in);
 				mData.load(in);
 			}
 			}
 			catch (const cif::CifParserError &e)
 			catch (const cif::CifParserError &e)
 			{
 			{
-				if (cif::VERBOSE)
+				if (cif::VERBOSE > 0)
 					std::cerr << "Not cif, trying plain old PDB" << std::endl;
 					std::cerr << "Not cif, trying plain old PDB" << std::endl;
 
 
 				// pffft...
 				// pffft...
@@ -169,7 +169,8 @@ void FileImpl::load(const std::filesystem::path &path)
 	}
 	}
 	catch (const std::exception &ex)
 	catch (const std::exception &ex)
 	{
 	{
-		std::cerr << "Error trying to load file " << path << std::endl;
+		if (cif::VERBOSE >= 0)
+			std::cerr << "Error trying to load file " << path << std::endl;
 		throw;
 		throw;
 	}
 	}
 
 
@@ -317,7 +318,7 @@ const Compound &Atom::AtomImpl::comp() const
 
 
 		mCompound = CompoundFactory::instance().create(compID);
 		mCompound = CompoundFactory::instance().create(compID);
 
 
-		if (cif::VERBOSE and mCompound == nullptr)
+		if (cif::VERBOSE > 0 and mCompound == nullptr)
 			std::cerr << "Compound not found: '" << compID << '\'' << std::endl;
 			std::cerr << "Compound not found: '" << compID << '\'' << std::endl;
 	}
 	}
 
 
@@ -623,7 +624,7 @@ AtomView Residue::unique_atoms() const
 			firstAlt = alt;
 			firstAlt = alt;
 		else if (alt != firstAlt)
 		else if (alt != firstAlt)
 		{
 		{
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "skipping alternate atom " << atom << std::endl;
 				std::cerr << "skipping alternate atom " << atom << std::endl;
 			continue;
 			continue;
 		}
 		}
@@ -829,7 +830,7 @@ float Monomer::phi() const
 	}
 	}
 	catch (const std::exception &ex)
 	catch (const std::exception &ex)
 	{
 	{
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 			std::cerr << ex.what() << std::endl;
 			std::cerr << ex.what() << std::endl;
 	}
 	}
 
 
@@ -851,7 +852,7 @@ float Monomer::psi() const
 	}
 	}
 	catch (const std::exception &ex)
 	catch (const std::exception &ex)
 	{
 	{
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 			std::cerr << ex.what() << std::endl;
 			std::cerr << ex.what() << std::endl;
 	}
 	}
 
 
@@ -875,7 +876,7 @@ float Monomer::alpha() const
 	}
 	}
 	catch (const std::exception &ex)
 	catch (const std::exception &ex)
 	{
 	{
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 			std::cerr << ex.what() << std::endl;
 			std::cerr << ex.what() << std::endl;
 	}
 	}
 
 
@@ -903,7 +904,7 @@ float Monomer::kappa() const
 	}
 	}
 	catch (const std::exception &ex)
 	catch (const std::exception &ex)
 	{
 	{
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 			std::cerr << "When trying to calculate kappa for " << asymID() << ':' << seqID() << ": "
 			std::cerr << "When trying to calculate kappa for " << asymID() << ':' << seqID() << ": "
 					  << ex.what() << std::endl;
 					  << ex.what() << std::endl;
 	}
 	}
@@ -926,7 +927,7 @@ float Monomer::tco() const
 	}
 	}
 	catch (const std::exception &ex)
 	catch (const std::exception &ex)
 	{
 	{
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 			std::cerr << "When trying to calculate tco for " << asymID() << ':' << seqID() << ": "
 			std::cerr << "When trying to calculate tco for " << asymID() << ':' << seqID() << ": "
 					  << ex.what() << std::endl;
 					  << ex.what() << std::endl;
 	}
 	}
@@ -945,7 +946,7 @@ float Monomer::omega() const
 	}
 	}
 	catch (const std::exception &ex)
 	catch (const std::exception &ex)
 	{
 	{
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 			std::cerr << "When trying to calculate omega for " << asymID() << ':' << seqID() << ": "
 			std::cerr << "When trying to calculate omega for " << asymID() << ':' << seqID() << ": "
 					  << ex.what() << std::endl;
 					  << ex.what() << std::endl;
 	}
 	}
@@ -1016,7 +1017,7 @@ float Monomer::chi(size_t nr) const
 	}
 	}
 	catch (const std::exception &e)
 	catch (const std::exception &e)
 	{
 	{
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 			std::cerr << e.what() << std::endl;
 			std::cerr << e.what() << std::endl;
 		result = 0;
 		result = 0;
 	}
 	}
@@ -1182,7 +1183,7 @@ Polymer::Polymer(const Structure &s, const std::string &entityID, const std::str
 			ix[seqID] = index;
 			ix[seqID] = index;
 			emplace_back(*this, index, seqID, authSeqID, compoundID);
 			emplace_back(*this, index, seqID, authSeqID, compoundID);
 		}
 		}
-		else if (cif::VERBOSE)
+		else if (cif::VERBOSE > 0)
 		{
 		{
 			Monomer m{*this, index, seqID, authSeqID, compoundID};
 			Monomer m{*this, index, seqID, authSeqID, compoundID};
 			std::cerr << "Dropping alternate residue " << m << std::endl;
 			std::cerr << "Dropping alternate residue " << m << std::endl;
@@ -1327,7 +1328,7 @@ Structure::Structure(File &f, size_t modelNr, StructureOpenOptions options)
 		cif::tie(model_nr) = atomCat.front().get("pdbx_PDB_model_num");
 		cif::tie(model_nr) = atomCat.front().get("pdbx_PDB_model_num");
 		if (model_nr and *model_nr != mModelNr)
 		if (model_nr and *model_nr != mModelNr)
 		{
 		{
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "No atoms loaded for model 1, trying model " << *model_nr << std::endl;
 				std::cerr << "No atoms loaded for model 1, trying model " << *model_nr << std::endl;
 			mModelNr = *model_nr;
 			mModelNr = *model_nr;
 			loadAtomsForModel(options);
 			loadAtomsForModel(options);
@@ -1335,7 +1336,10 @@ Structure::Structure(File &f, size_t modelNr, StructureOpenOptions options)
 	}
 	}
 
 
 	if (mAtoms.empty())
 	if (mAtoms.empty())
-		std::cerr << "Warning: no atoms loaded" << std::endl;
+	{
+		if (cif::VERBOSE >= 0)
+			std::cerr << "Warning: no atoms loaded" << std::endl;
+	}
 	else
 	else
 		loadData();
 		loadData();
 }
 }
@@ -1443,7 +1447,7 @@ void Structure::loadData()
 
 
 		if (ri == resMap.end())
 		if (ri == resMap.end())
 		{
 		{
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "Missing residue for atom " << atom << std::endl;
 				std::cerr << "Missing residue for atom " << atom << std::endl;
 
 
 			assert(false);
 			assert(false);
@@ -2006,7 +2010,8 @@ void Structure::changeResidue(Residue &res, const std::string &newCompound,
 			{ return a.labelAtomID() == a1; });
 			{ return a.labelAtomID() == a1; });
 		if (i == atoms.end())
 		if (i == atoms.end())
 		{
 		{
-			std::cerr << "Missing atom for atom ID " << a1 << std::endl;
+			if (cif::VERBOSE >= 0)
+				std::cerr << "Missing atom for atom ID " << a1 << std::endl;
 			continue;
 			continue;
 		}
 		}
 
 

src/TlsParser.cpp

@@ -248,7 +248,7 @@ struct TLSSelectionNot : public TLSSelection
 		for (auto& r: residues)
 		for (auto& r: residues)
 			r.selected = not r.selected;
 			r.selected = not r.selected;
 
 
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 		{
 		{
 			std::cout << std::string(indentLevel * 2, ' ') << "NOT" << std::endl;
 			std::cout << std::string(indentLevel * 2, ' ') << "NOT" << std::endl;
 			DumpSelection(residues, indentLevel);
 			DumpSelection(residues, indentLevel);
@@ -267,7 +267,7 @@ struct TLSSelectionAll : public TLSSelection
 		for (auto& r: residues)
 		for (auto& r: residues)
 			r.selected = true;
 			r.selected = true;
 
 
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 		{
 		{
 			std::cout << std::string(indentLevel * 2, ' ') << "ALL" << std::endl;
 			std::cout << std::string(indentLevel * 2, ' ') << "ALL" << std::endl;
 			DumpSelection(residues, indentLevel);
 			DumpSelection(residues, indentLevel);
@@ -287,7 +287,7 @@ struct TLSSelectionChain : public TLSSelectionAll
 		for (auto& r: residues)
 		for (auto& r: residues)
 			r.selected = allChains or r.chainID == m_chain;
 			r.selected = allChains or r.chainID == m_chain;
 
 
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 		{
 		{
 			std::cout << std::string(indentLevel * 2, ' ') << "CHAIN " << m_chain << std::endl;
 			std::cout << std::string(indentLevel * 2, ' ') << "CHAIN " << m_chain << std::endl;
 			DumpSelection(residues, indentLevel);
 			DumpSelection(residues, indentLevel);
@@ -307,7 +307,7 @@ struct TLSSelectionResID : public TLSSelectionAll
 		for (auto& r: residues)
 		for (auto& r: residues)
 			r.selected = r.seqNr == m_seq_nr and r.iCode == m_icode;
 			r.selected = r.seqNr == m_seq_nr and r.iCode == m_icode;
 
 
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 		{
 		{
 			std::cout << std::string(indentLevel * 2, ' ') << "ResID " << m_seq_nr << (m_icode ? std::string { m_icode} : "") << std::endl;
 			std::cout << std::string(indentLevel * 2, ' ') << "ResID " << m_seq_nr << (m_icode ? std::string { m_icode} : "") << std::endl;
 			DumpSelection(residues, indentLevel);
 			DumpSelection(residues, indentLevel);
@@ -331,7 +331,7 @@ struct TLSSelectionRangeSeq : public TLSSelectionAll
 						  (r.seqNr <= m_last or m_last == kResidueNrWildcard));
 						  (r.seqNr <= m_last or m_last == kResidueNrWildcard));
 		}
 		}
 
 
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 		{
 		{
 			std::cout << std::string(indentLevel * 2, ' ') << "Range " << m_first << ':' << m_last << std::endl;
 			std::cout << std::string(indentLevel * 2, ' ') << "Range " << m_first << ':' << m_last << std::endl;
 			DumpSelection(residues, indentLevel);
 			DumpSelection(residues, indentLevel);
@@ -374,7 +374,7 @@ struct TLSSelectionRangeID : public TLSSelectionAll
 			}
 			}
 		}
 		}
 
 
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 		{
 		{
 			std::cout << std::string(indentLevel * 2, ' ') << "Through " << m_first << ':' << m_last << std::endl;
 			std::cout << std::string(indentLevel * 2, ' ') << "Through " << m_first << ':' << m_last << std::endl;
 			DumpSelection(residues, indentLevel);
 			DumpSelection(residues, indentLevel);
@@ -407,7 +407,7 @@ struct TLSSelectionUnion : public TLSSelection
 		for (auto ai = a.begin(), bi = b.begin(), ri = residues.begin(); ri != residues.end(); ++ai, ++bi, ++ri)
 		for (auto ai = a.begin(), bi = b.begin(), ri = residues.begin(); ri != residues.end(); ++ai, ++bi, ++ri)
 			ri->selected = ai->selected or bi->selected;
 			ri->selected = ai->selected or bi->selected;
 
 
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 		{
 		{
 			std::cout << std::string(indentLevel * 2, ' ') << "Union" << std::endl;
 			std::cout << std::string(indentLevel * 2, ' ') << "Union" << std::endl;
 			DumpSelection(residues, indentLevel);
 			DumpSelection(residues, indentLevel);
@@ -440,7 +440,7 @@ struct TLSSelectionIntersection : public TLSSelection
 		for (auto ai = a.begin(), bi = b.begin(), ri = residues.begin(); ri != residues.end(); ++ai, ++bi, ++ri)
 		for (auto ai = a.begin(), bi = b.begin(), ri = residues.begin(); ri != residues.end(); ++ai, ++bi, ++ri)
 			ri->selected = ai->selected and bi->selected;
 			ri->selected = ai->selected and bi->selected;
 
 
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 		{
 		{
 			std::cout << std::string(indentLevel * 2, ' ') << "Intersection" << std::endl;
 			std::cout << std::string(indentLevel * 2, ' ') << "Intersection" << std::endl;
 			DumpSelection(residues, indentLevel);
 			DumpSelection(residues, indentLevel);
@@ -462,7 +462,7 @@ struct TLSSelectionByName : public TLSSelectionAll
 		for (auto& r: residues)
 		for (auto& r: residues)
 			r.selected = r.name == m_name;
 			r.selected = r.name == m_name;
 
 
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 		{
 		{
 			std::cout << std::string(indentLevel * 2, ' ') << "Name " << m_name << std::endl;
 			std::cout << std::string(indentLevel * 2, ' ') << "Name " << m_name << std::endl;
 			DumpSelection(residues, indentLevel);
 			DumpSelection(residues, indentLevel);
@@ -488,7 +488,7 @@ struct TLSSelectionByElement : public TLSSelectionAll
 		for (auto& r: residues)
 		for (auto& r: residues)
 			r.selected = iequals(r.name, m_element);
 			r.selected = iequals(r.name, m_element);
 
 
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 		{
 		{
 			std::cout << std::string(indentLevel * 2, ' ') << "Element " << m_element << std::endl;
 			std::cout << std::string(indentLevel * 2, ' ') << "Element " << m_element << std::endl;
 			DumpSelection(residues, indentLevel);
 			DumpSelection(residues, indentLevel);
@@ -890,7 +890,7 @@ TLSSelectionPtr TLSSelectionParserImplPhenix::Parse()
 
 
 	Match(pt_EOLN);
 	Match(pt_EOLN);
 	
 	
-	if (extraParenthesis)
+	if (extraParenthesis and cif::VERBOSE > 0)
 		std::cerr << "WARNING: too many closing parenthesis in TLS selection statement" << std::endl;
 		std::cerr << "WARNING: too many closing parenthesis in TLS selection statement" << std::endl;
 	
 	
 	return result;
 	return result;
@@ -931,7 +931,7 @@ TLSSelectionPtr TLSSelectionParserImplPhenix::ParseFactor()
 		case '(':
 		case '(':
 			Match('(');
 			Match('(');
 			result = ParseAtomSelection();
 			result = ParseAtomSelection();
-			if (m_lookahead == pt_EOLN)
+			if (m_lookahead == pt_EOLN and cif::VERBOSE > 0)
 				std::cerr << "WARNING: missing closing parenthesis in TLS selection statement" << std::endl;
 				std::cerr << "WARNING: missing closing parenthesis in TLS selection statement" << std::endl;
 			else
 			else
 				Match(')');
 				Match(')');
@@ -1033,7 +1033,7 @@ TLSSelectionPtr TLSSelectionParserImplPhenix::ParseFactor()
 					result.reset(new TLSSelectionRangeID(from, to, icode_from, icode_to));
 					result.reset(new TLSSelectionRangeID(from, to, icode_from, icode_to));
 				else
 				else
 				{
 				{
-					if (cif::VERBOSE and (icode_from or icode_to))
+					if (cif::VERBOSE > 0 and (icode_from or icode_to))
 						std::cerr << "Warning, ignoring insertion codes" << std::endl;
 						std::cerr << "Warning, ignoring insertion codes" << std::endl;
 					
 					
 					result.reset(new TLSSelectionRangeSeq(from, to));
 					result.reset(new TLSSelectionRangeSeq(from, to));
@@ -1231,7 +1231,8 @@ TLSSelectionPtr TLSSelectionParserImplBuster::ParseGroup()
 				std::tie(chain2, seqNr2) = ParseAtom();
 				std::tie(chain2, seqNr2) = ParseAtom();
 				if (chain1 != chain2)
 				if (chain1 != chain2)
 				{
 				{
-					std::cerr << "Warning, ranges over multiple chains detected" << std::endl;
+					if (cif::VERBOSE > 0)
+						std::cerr << "Warning, ranges over multiple chains detected" << std::endl;
 					
 					
 					TLSSelectionPtr sc1(new TLSSelectionChain(chain1));
 					TLSSelectionPtr sc1(new TLSSelectionChain(chain1));
 					TLSSelectionPtr sr1(new TLSSelectionRangeSeq(seqNr1, kResidueNrWildcard));
 					TLSSelectionPtr sr1(new TLSSelectionRangeSeq(seqNr1, kResidueNrWildcard));
@@ -1289,7 +1290,7 @@ std::tuple<std::string,int> TLSSelectionParserImplBuster::ParseAtom()
 			Match(':');
 			Match(':');
 			std::string atom = m_value_s;
 			std::string atom = m_value_s;
 			
 			
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "Warning: ignoring atom ID '" << atom << "' in TLS selection" << std::endl;
 				std::cerr << "Warning: ignoring atom ID '" << atom << "' in TLS selection" << std::endl;
 			
 			
 			Match(bt_IDENT);
 			Match(bt_IDENT);
@@ -1810,7 +1811,8 @@ class TLSSelectionParser
 		}
 		}
 		catch (const std::exception& ex)
 		catch (const std::exception& ex)
 		{
 		{
-			std::cerr << "ParseError: " << ex.what() << std::endl;
+			if (cif::VERBOSE >= 0)
+				std::cerr << "ParseError: " << ex.what() << std::endl;
 		}
 		}
 		
 		
 		return result;
 		return result;
@@ -1834,14 +1836,14 @@ TLSSelectionPtr ParseSelectionDetails(const std::string& program, const std::str
 
 
 		if (not result)
 		if (not result)
 		{
 		{
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "Falling back to old BUSTER" << std::endl;
 				std::cerr << "Falling back to old BUSTER" << std::endl;
 			result = busterOld.Parse(selection);
 			result = busterOld.Parse(selection);
 		}
 		}
 		
 		
 		if (not result)
 		if (not result)
 		{
 		{
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "Falling back to PHENIX" << std::endl;
 				std::cerr << "Falling back to PHENIX" << std::endl;
 			result = phenix.Parse(selection);
 			result = phenix.Parse(selection);
 		}
 		}
@@ -1852,35 +1854,35 @@ TLSSelectionPtr ParseSelectionDetails(const std::string& program, const std::str
 
 
 		if (not result)
 		if (not result)
 		{
 		{
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "Falling back to BUSTER" << std::endl;
 				std::cerr << "Falling back to BUSTER" << std::endl;
 			result = buster.Parse(selection);
 			result = buster.Parse(selection);
 		}
 		}
 
 
 		if (not result)
 		if (not result)
 		{
 		{
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "Falling back to old BUSTER" << std::endl;
 				std::cerr << "Falling back to old BUSTER" << std::endl;
 			result = busterOld.Parse(selection);
 			result = busterOld.Parse(selection);
 		}
 		}
 	}
 	}
 	else
 	else
 	{
 	{
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 			std::cerr << "No known program specified, trying PHENIX" << std::endl;
 			std::cerr << "No known program specified, trying PHENIX" << std::endl;
 
 
 		result = phenix.Parse(selection);
 		result = phenix.Parse(selection);
 
 
 		if (not result)
 		if (not result)
 		{
 		{
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "Falling back to BUSTER" << std::endl;
 				std::cerr << "Falling back to BUSTER" << std::endl;
 			result = buster.Parse(selection);
 			result = buster.Parse(selection);
 		}
 		}
 
 
 		if (not result)
 		if (not result)
 		{
 		{
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "Falling back to old BUSTER" << std::endl;
 				std::cerr << "Falling back to old BUSTER" << std::endl;
 			result = busterOld.Parse(selection);
 			result = busterOld.Parse(selection);
 		}
 		}