removed using namespace std;

4b4757ee · Maarten L. Hekkelman · ac088dd0 · 4b4757ee · 4b4757ee · 4b4757ee
Commit 4b4757ee authored Sep 22, 2020 by Maarten L. Hekkelman
14 changed files
--- a/GNUmakefile.in
+++ b/GNUmakefile.in
@@ -97,7 +97,6 @@ LIBCIF_SRC		= AtomType.cpp \
 				  CifUtils.cpp \
 				  CifValidator.cpp \
 				  Compound.cpp \
-				  FixDMC.cpp \
 				  PDB2Cif.cpp \
 				  PDB2CifRemark3.cpp \
 				  Point.cpp \

--- a/src/AtomType.cpp
+++ b/src/AtomType.cpp
@@ -29,8 +29,6 @@
 #include "cif++/AtomType.hpp"
 #include "cif++/Cif++.hpp"
-using namespace std;
 namespace mmcif
 {
@@ -1237,7 +1235,7 @@ SFDataArrayElement kELSFData[] = {
 // --------------------------------------------------------------------
 // AtomTypeTraits
-AtomTypeTraits::AtomTypeTraits(const string& symbol)
+AtomTypeTraits::AtomTypeTraits(const std::string& symbol)
 	: mInfo(nullptr)
 {
 	for (auto& i: data::kKnownAtoms)
@@ -1250,20 +1248,20 @@ AtomTypeTraits::AtomTypeTraits(const string& symbol)
 	}
 	if (mInfo == nullptr)
-		throw invalid_argument("Not a known element: " + symbol);
+		throw std::invalid_argument("Not a known element: " + symbol);
 }
 AtomTypeTraits::AtomTypeTraits(AtomType t)
 {
 	if (t < H or t >= data::kKnownAtomsCount)
-		throw invalid_argument("atomType out of range");
+		throw std::invalid_argument("atomType out of range");
 	mInfo = &data::kKnownAtoms[t];
 	assert(mInfo->type == t);
 }
-bool AtomTypeTraits::isElement(const string& symbol)
+bool AtomTypeTraits::isElement(const std::string& symbol)
 {
 	bool result = false;
@@ -1279,7 +1277,7 @@ bool AtomTypeTraits::isElement(const string& symbol)
 	return result;
 }
-bool AtomTypeTraits::isMetal(const string& symbol)
+bool AtomTypeTraits::isMetal(const std::string& symbol)
 {
 	bool result = false;
@@ -1303,7 +1301,7 @@ auto AtomTypeTraits::wksf(int charge) const -> const SFData&
 			return sf.sf;
 	}
-	throw runtime_error("No scattering factor found for " + name() + to_string(charge));
+	throw std::runtime_error("No scattering factor found for " + name() + std::to_string(charge));
 }
 auto AtomTypeTraits::elsf() const -> const SFData&
@@ -1314,7 +1312,7 @@ auto AtomTypeTraits::elsf() const -> const SFData&
 			return sf.sf;
 	}
-	throw runtime_error("No scattering factor found for " + name());
+	throw std::runtime_error("No scattering factor found for " + name());
 }
 }
--- a/src/Cif++.cpp
+++ b/src/Cif++.cpp
--- a/src/CifParser.cpp
+++ b/src/CifParser.cpp
--- a/src/CifUtils.cpp
+++ b/src/CifUtils.cpp
@@ -47,7 +47,6 @@
 #include "cif++/CifUtils.hpp"
-using namespace std;
 namespace ba = boost::algorithm;
 namespace cif
@@ -80,7 +79,7 @@ const uint8_t kCharToLowerMap[256] =
 // --------------------------------------------------------------------
-bool iequals(const string& a, const string& b)
+bool iequals(const std::string& a, const std::string& b)
 {
 	bool result = a.length() == b.length();
 	for (auto ai = a.begin(), bi = b.begin(); result and ai != a.end() and bi != b.end(); ++ai, ++bi)
@@ -97,7 +96,7 @@ bool iequals(const char* a, const char* b)
 	return result and *a == *b;
 }
-int icompare(const string& a, const string& b)
+int icompare(const std::string& a, const std::string& b)
 {
 	int d = 0;
 	auto ai = a.begin(), bi = b.begin();
@@ -134,15 +133,15 @@ int icompare(const char* a, const char* b)
 	return d;
 }
-void toLower(string& s)
+void toLower(std::string& s)
 {
 	for (auto& c: s)
 		c = tolower(c);
 }
-string toLowerCopy(const string& s)
+std::string toLowerCopy(const std::string& s)
 {
-	string result(s);
+	std::string result(s);
 	for (auto& c: result)
 		c = tolower(c);
 	return result;
@@ -150,17 +149,17 @@ string toLowerCopy(const string& s)
 // --------------------------------------------------------------------
-tuple<string,string> splitTagName(const string& tag)
+std::tuple<std::string,std::string> splitTagName(const std::string& tag)
 {
 	if (tag.empty())
-		throw runtime_error("empty tag");
+		throw std::runtime_error("empty tag");
 	if (tag[0] != '_')
-		throw runtime_error("tag does not start with underscore");
+		throw std::runtime_error("tag does not start with underscore");
 	auto s = tag.find('.');
-	if (s == string::npos)
+	if (s == std::string::npos)
-		throw runtime_error("tag does not contain dot");
+		throw std::runtime_error("tag does not contain dot");
-	return tuple<string,string>{
+	return std::tuple<std::string,std::string>{
 		tag.substr(1, s - 1), tag.substr(s + 1)
 	};
 }	
@@ -236,7 +235,7 @@ const LineBreakClass kASCII_LBTable[128] =
 	kLBC_Alphabetic, kLBC_Alphabetic, kLBC_Alphabetic, kLBC_OpenPunctuation, kLBC_BreakAfter, kLBC_ClosePunctuation, kLBC_Alphabetic, kLBC_CombiningMark
 };
-string::const_iterator nextLineBreak(string::const_iterator text, string::const_iterator end)
+std::string::const_iterator nextLineBreak(std::string::const_iterator text, std::string::const_iterator end)
 {
 	if (text == end)
 		return text;
@@ -329,10 +328,10 @@ string::const_iterator nextLineBreak(string::const_iterator text, string::const_
 	return text;
 }
-vector<string> wrapLine(const string& text, unsigned int width)
+std::vector<std::string> wrapLine(const std::string& text, unsigned int width)
 {
-	vector<string> result;
+	std::vector<std::string> result;
-	vector<size_t> offsets = { 0 };
+	std::vector<size_t> offsets = { 0 };
 	auto b = text.begin();
 	while (b != text.end())
@@ -346,9 +345,9 @@ vector<string> wrapLine(const string& text, unsigned int width)
 	size_t count = offsets.size() - 1;
-	vector<size_t> minima(count + 1, 1000000);
+	std::vector<size_t> minima(count + 1, 1000000);
 	minima[0] = 0;
-	vector<size_t> breaks(count + 1, 0);
+	std::vector<size_t> breaks(count + 1, 0);
 	for (size_t i = 0; i < count; ++i)
 	{
@@ -390,12 +389,12 @@ vector<string> wrapLine(const string& text, unsigned int width)
 	return result;
 }
-vector<string> wordWrap(const string& text, unsigned int width)
+std::vector<std::string> wordWrap(const std::string& text, unsigned int width)
 {
-	vector<string> paragraphs;
+	std::vector<std::string> paragraphs;
 	ba::split(paragraphs, text, ba::is_any_of("\n"));
-	vector<string> result;
+	std::vector<std::string> result;
 	for (auto& p: paragraphs)
 	{
 		if (p.empty())
@@ -420,7 +419,7 @@ uint32_t get_terminal_width()
 }
 // I don't have a windows machine to test the following code, please accept my apologies in case it fails...
-string GetExecutablePath()
+std::string GetExecutablePath()
 {
 	WCHAR buffer[4096];
@@ -430,7 +429,7 @@ string GetExecutablePath()
 	wstring ws(buffer);
-	return string(ws.begin(), ws.end());
+	return std::string(ws.begin(), ws.end());
 }
 #else
@@ -447,11 +446,13 @@ uint32_t get_terminal_width()
    return result;
 }
-string get_executable_path()
+std::string get_executable_path()
 {
+	using namespace std::literals;
 	char path[PATH_MAX] = "";
 	if (readlink("/proc/self/exe", path, sizeof(path)) == -1)
-		throw runtime_error("could not get exe path "s + strerror(errno));
+		throw std::runtime_error("could not get exe path "s + strerror(errno));
 	return { path };
 }
@@ -461,7 +462,7 @@ string get_executable_path()
 struct ProgressImpl
 {
-					ProgressImpl(int64_t inMax, const string& inAction)
+					ProgressImpl(int64_t inMax, const std::string& inAction)
 						: mMax(inMax), mConsumed(0), mAction(inAction), mMessage(inAction)
 						, mThread(std::bind(&ProgressImpl::Run, this))
 						, mStart(boost::posix_time::second_clock::local_time()) {}
@@ -478,10 +479,10 @@ struct ProgressImpl
 	void			PrintDone();
 	int64_t			mMax;
-	atomic<int64_t>	mConsumed;
+	std::atomic<int64_t>	mConsumed;
 	int64_t			mLastConsumed = 0;
 	int				mSpinnerIndex = 0;
-	string			mAction, mMessage;
+	std::string			mAction, mMessage;
 	std::mutex		mMutex;
 	std::thread		mThread;
 	boost::timer::cpu_timer mTimer;
@@ -549,7 +550,7 @@ void ProgressImpl::PrintProgress()
 	uint32_t width = get_terminal_width();
-	string msg;
+	std::string msg;
 	msg.reserve(width + 1);
 	if (mMessage.length() <= 20)
 	{
@@ -604,23 +605,23 @@ void ProgressImpl::PrintProgress()
 //	msg += to_string(perc);
 //	msg += '%';
-	cout << '\r' << msg;
+	std::cout << '\r' << msg;
-	cout.flush();
+	std::cout.flush();
 }
 void ProgressImpl::PrintDone()
 {
-	string msg = mAction + " done in " + mTimer.format(0, "%ts cpu / %ws wall");
+	std::string msg = mAction + " done in " + mTimer.format(0, "%ts cpu / %ws wall");
 	uint32_t width = get_terminal_width();
 	if (msg.length() < width)
-		msg += string(width - msg.length(), ' ');
+		msg += std::string(width - msg.length(), ' ');
-	cout << '\r' << msg << endl;
+	std::cout << '\r' << msg << std::endl;
 }
-Progress::Progress(int64_t inMax, const string& inAction)
+Progress::Progress(int64_t inMax, const std::string& inAction)
 	: mImpl(nullptr)
 {
 	if (isatty(STDOUT_FILENO))

--- a/src/CifValidator.cpp
+++ b/src/CifValidator.cpp
@@ -34,7 +34,6 @@
 #include "cif++/CifParser.hpp"
 #include "cif++/CifValidator.hpp"
-using namespace std;
 namespace ba = boost::algorithm;
 extern int VERBOSE;
@@ -42,19 +41,19 @@ extern int VERBOSE;
 namespace cif
 {
-ValidationError::ValidationError(const string& msg)
+ValidationError::ValidationError(const std::string& msg)
 	: mMsg(msg)
 {
 }
-ValidationError::ValidationError(const string& cat, const string& item, const string& msg)
+ValidationError::ValidationError(const std::string& cat, const std::string& item, const std::string& msg)
 	: mMsg("When validating _" + cat + '.' + item + ": " + msg)
 {
 }
 // --------------------------------------------------------------------
-DDL_PrimitiveType mapToPrimitiveType(const string& s)
+DDL_PrimitiveType mapToPrimitiveType(const std::string& s)
 {
 	DDL_PrimitiveType result;
 	if (iequals(s, "char"))
@@ -90,7 +89,7 @@ int ValidateType::compare(const char* a, const char* b) const
 					double db = strtod(b, nullptr);
 					auto d = da - db;
-					if (abs(d) > numeric_limits<double>::epsilon())
+					if (std::abs(d) > std::numeric_limits<double>::epsilon())
 					{
 						if (d > 0)
 							result = 1;
@@ -177,12 +176,12 @@ int ValidateType::compare(const char* a, const char* b) const
 //
 //		parent->mChildren.insert(this);
 ////	
-////		if (mCategory->mKeys == vector<string>{mTag})
+////		if (mCategory->mKeys == std::vector<std::string>{mTag})
 ////			parent->mForeignKeys.insert(this);
 //	}
 //}
-void ValidateItem::operator()(string value) const
+void ValidateItem::operator()(std::string value) const
 {
 	if (not value.empty() and value != "?" and value != ".")
 	{
@@ -206,19 +205,19 @@ void ValidateCategory::addItemValidator(ValidateItem&& v)
 	v.mCategory = this;
-	auto r = mItemValidators.insert(move(v));
+	auto r = mItemValidators.insert(std::move(v));
 	if (not r.second and VERBOSE >= 4)
-		cout << "Could not add validator for item " << v.mTag << " to category " << mName << endl;
+		std::cout << "Could not add validator for item " << v.mTag << " to category " << mName << std::endl;
 }
-const ValidateItem* ValidateCategory::getValidatorForItem(string tag) const
+const ValidateItem* ValidateCategory::getValidatorForItem(std::string tag) const
 {
 	const ValidateItem* result = nullptr;
 	auto i = mItemValidators.find(ValidateItem{tag});
 	if (i != mItemValidators.end())
 		result = &*i;
 	else if (VERBOSE > 4)
-		cout << "No validator for tag " << tag << endl;
+		std::cout << "No validator for tag " << tag << std::endl;
 	return result;
 }
@@ -234,12 +233,12 @@ Validator::~Validator()
 void Validator::addTypeValidator(ValidateType&& v)
 {
-	auto r = mTypeValidators.insert(move(v));
+	auto r = mTypeValidators.insert(std::move(v));
 	if (not r.second and VERBOSE > 4)
-		cout << "Could not add validator for type " << v.mName << endl;
+		std::cout << "Could not add validator for type " << v.mName << std::endl;
 }
-const ValidateType* Validator::getValidatorForType(string typeCode) const
+const ValidateType* Validator::getValidatorForType(std::string typeCode) const
 {
 	const ValidateType* result = nullptr;
@@ -247,33 +246,33 @@ const ValidateType* Validator::getValidatorForType(string typeCode) const
 	if (i != mTypeValidators.end())
 		result = &*i;
 	else if (VERBOSE > 4)
-		cout << "No validator for type " << typeCode << endl;
+		std::cout << "No validator for type " << typeCode << std::endl;
 	return result;
 }
 void Validator::addCategoryValidator(ValidateCategory&& v)
 {
-	auto r = mCategoryValidators.insert(move(v));
+	auto r = mCategoryValidators.insert(std::move(v));
 	if (not r.second and VERBOSE > 4)
-		cout << "Could not add validator for category " << v.mName << endl;
+		std::cout << "Could not add validator for category " << v.mName << std::endl;
 }
-const ValidateCategory* Validator::getValidatorForCategory(string category) const
+const ValidateCategory* Validator::getValidatorForCategory(std::string category) const
 {
 	const ValidateCategory* result = nullptr;
 	auto i = mCategoryValidators.find(ValidateCategory{category});
 	if (i != mCategoryValidators.end())
 		result = &*i;
 	else if (VERBOSE > 4)
-		cout << "No validator for category " << category << endl;
+		std::cout << "No validator for category " << category << std::endl;
 	return result;
 }
-ValidateItem* Validator::getValidatorForItem(string tag) const
+ValidateItem* Validator::getValidatorForItem(std::string tag) const
 {
 	ValidateItem* result = nullptr;
-	string cat, item;
+	std::string cat, item;
 	std::tie(cat, item) = splitTagName(tag);
 	auto* cv = getValidatorForCategory(cat);
@@ -281,7 +280,7 @@ ValidateItem* Validator::getValidatorForItem(string tag) const
 		result = const_cast<ValidateItem*>(cv->getValidatorForItem(item));
 	if (result == nullptr and VERBOSE > 4)
-		cout << "No validator for item " << tag << endl;
+		std::cout << "No validator for item " << tag << std::endl;
 	return result;
 }
@@ -290,38 +289,38 @@ void Validator::addLinkValidator(ValidateLink&& v)
 {
 	assert(v.mParentKeys.size() == v.mChildKeys.size());
 	if (v.mParentKeys.size() != v.mChildKeys.size())
-		throw runtime_error("unequal number of keys for parent and child in link");
+		throw std::runtime_error("unequal number of keys for parent and child in link");
 	auto pcv = getValidatorForCategory(v.mParentCategory);
 	auto ccv = getValidatorForCategory(v.mChildCategory);
 	if (pcv == nullptr)
-		throw runtime_error("unknown parent category " + v.mParentCategory);
+		throw std::runtime_error("unknown parent category " + v.mParentCategory);
 	if (ccv == nullptr)
-		throw runtime_error("unknown child category " + v.mChildCategory);
+		throw std::runtime_error("unknown child category " + v.mChildCategory);
 	for (size_t i = 0; i < v.mParentKeys.size(); ++i)
 	{
 		auto piv = pcv->getValidatorForItem(v.mParentKeys[i]);
 		if (piv == nullptr)
-			throw runtime_error("unknown parent tag _" + v.mParentCategory + '.' + v.mParentKeys[i]);
+			throw std::runtime_error("unknown parent tag _" + v.mParentCategory + '.' + v.mParentKeys[i]);
 		auto civ = ccv->getValidatorForItem(v.mChildKeys[i]);
 		if (civ == nullptr)
-			throw runtime_error("unknown child tag _" + v.mChildCategory + '.' + v.mChildKeys[i]);
+			throw std::runtime_error("unknown child tag _" + v.mChildCategory + '.' + v.mChildKeys[i]);
 		if (civ->mType == nullptr and piv->mType != nullptr)
 			const_cast<ValidateItem*>(civ)->mType = piv->mType;
 	}		
-	mLinkValidators.emplace_back(move(v));
+	mLinkValidators.emplace_back(std::move(v));
 }
-vector<const ValidateLink*> Validator::getLinksForParent(const string& category) const
+std::vector<const ValidateLink*> Validator::getLinksForParent(const std::string& category) const
 {
-	vector<const ValidateLink*> result;
+	std::vector<const ValidateLink*> result;
 	for (auto& l: mLinkValidators)
 	{
@@ -332,9 +331,9 @@ vector<const ValidateLink*> Validator::getLinksForParent(const string& category)
 	return result;
 }
-vector<const ValidateLink*> Validator::getLinksForChild(const string& category) const
+std::vector<const ValidateLink*> Validator::getLinksForChild(const std::string& category) const
 {
-	vector<const ValidateLink*> result;
+	std::vector<const ValidateLink*> result;
 	for (auto& l: mLinkValidators)
 	{
@@ -345,12 +344,12 @@ vector<const ValidateLink*> Validator::getLinksForChild(const string& category) 
 	return result;
 }
-void Validator::reportError(const string& msg, bool fatal)
+void Validator::reportError(const std::string& msg, bool fatal)
 {
 	if (mStrict or fatal)
 		throw ValidationError(msg);
 	else if (VERBOSE)
-		cerr << msg << endl;
+		std::cerr << msg << std::endl;
 }
 }
--- a/src/Compound.cpp
+++ b/src/Compound.cpp
--- a/src/FixDMC.cpp
+++ b/src/FixDMC.cpp
-/*-
- * SPDX-License-Identifier: BSD-2-Clause
- * 
- * Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
- * 
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions are met:
- * 
- * 1. Redistributions of source code must retain the above copyright notice, this
- *    list of conditions and the following disclaimer
- * 2. Redistributions in binary form must reproduce the above copyright notice,
- *    this list of conditions and the following disclaimer in the documentation
- *    and/or other materials provided with the distribution.
- * 
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
- * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
- * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
- * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
- * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
- * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
- * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
- * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
- * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- */
-#include <set>
-#include <cif++/Structure.hpp>
-namespace mmcif
-{
-void addC(Monomer& mon)
-{
-}
-void addCA(Monomer& mon)
-{
-}
-void addN(Monomer& mon)
-{
-}
-void addO(Monomer& mon)
-{
-}
-void CreateMissingBackboneAtoms(Structure& structure, bool simplified)
-{
-	for (auto& poly: structure.polymers())
-	{
-		for (auto& mon: poly)
-		{
-			if (mon.isComplete() or mon.hasAlternateBackboneAtoms())
-				continue;
-			auto atomC = mon.atomByID("C");
-			auto atomCA = mon.atomByID("CA");
-			auto atomN = mon.atomByID("N");
-			auto atomO = mon.atomByID("O");
-			int missing = (atomC ? 0 : 1) + (atomCA ? 0 : 1) + (atomN ? 0 : 1) + (atomO ? 0 : 1);
-			switch (missing)
-			{
-				case 1:
-					if (not atomO)
-						addO(mon);
-					else if (not atomN)
-						addN(mon);
-					else if (not atomCA)
-						addCA(mon);
-					else if (not atomC)
-						addC(mon);
-					break;
-			}
-		}
-	}
-}
-}
\ No newline at end of file
--- a/src/PDB2Cif.cpp
+++ b/src/PDB2Cif.cpp
--- a/src/PDB2CifRemark3.cpp
+++ b/src/PDB2CifRemark3.cpp
--- a/src/Point.cpp
+++ b/src/Point.cpp
@@ -29,8 +29,6 @@
 #include "cif++/Point.hpp"
-using namespace std;
 namespace mmcif
 {
@@ -38,7 +36,7 @@ namespace mmcif
 quaternion Normalize(quaternion q)
 {
-	valarray<double> t(4);
+	std::valarray<double> t(4);
 	t[0] = q.R_component_1();
 	t[1] = q.R_component_2();
@@ -59,7 +57,7 @@ quaternion Normalize(quaternion q)
 // --------------------------------------------------------------------
-tuple<double,Point> QuaternionToAngleAxis(quaternion q)
+std::tuple<double,Point> QuaternionToAngleAxis(quaternion q)
 {
 	if (q.R_component_1() > 1)
 		q = Normalize(q);
@@ -75,10 +73,10 @@ tuple<double,Point> QuaternionToAngleAxis(quaternion q)
 	Point axis(q.R_component_2() / s, q.R_component_3() / s, q.R_component_4() / s);
-	return make_tuple(angle, axis);
+	return std::make_tuple(angle, axis);
 }
-Point CenterPoints(vector<Point>& Points)
+Point CenterPoints(std::vector<Point>& Points)
 {
 	Point t;
@@ -103,7 +101,7 @@ Point CenterPoints(vector<Point>& Points)
 	return t;
 }
-Point Centroid(vector<Point>& Points)
+Point Centroid(std::vector<Point>& Points)
 {
 	Point result;
@@ -115,12 +113,12 @@ Point Centroid(vector<Point>& Points)
 	return result;
 }
-double RMSd(const vector<Point>& a, const vector<Point>& b)
+double RMSd(const std::vector<Point>& a, const std::vector<Point>& b)
 {
 	double sum = 0;
 	for (uint32_t i = 0; i < a.size(); ++i)
 	{
-		valarray<double> d(3);
+		std::valarray<double> d(3);
 		d[0] = b[i].mX - a[i].mX;
 		d[1] = b[i].mY - a[i].mY;
@@ -131,7 +129,7 @@ double RMSd(const vector<Point>& a, const vector<Point>& b)
 		sum += d.sum();
 	}
-	return sqrt(sum / a.size());
+	return std::sqrt(sum / a.size());
 }
 // The next function returns the largest solution for a quartic equation
@@ -145,30 +143,30 @@ double RMSd(const vector<Point>& a, const vector<Point>& b)
 //  sqrt of a negative number)
 double LargestDepressedQuarticSolution(double a, double b, double c)
 {
-	complex<double> P = - (a * a) / 12 - c;
+	std::complex<double> P = - (a * a) / 12 - c;
-	complex<double> Q = - (a * a * a) / 108 + (a * c) / 3 - (b * b) / 8;
+	std::complex<double> Q = - (a * a * a) / 108 + (a * c) / 3 - (b * b) / 8;
-	complex<double> R = - Q / 2.0 + sqrt((Q * Q) / 4.0 + (P * P * P) / 27.0);
+	std::complex<double> R = - Q / 2.0 + std::sqrt((Q * Q) / 4.0 + (P * P * P) / 27.0);
-	complex<double> U = pow(R, 1 / 3.0);
+	std::complex<double> U = std::pow(R, 1 / 3.0);
-	complex<double> y;
+	std::complex<double> y;
 	if (U == 0.0)
-		y = -5.0 * a / 6.0 + U - pow(Q, 1.0 / 3.0);
+		y = -5.0 * a / 6.0 + U - std::pow(Q, 1.0 / 3.0);
 	else
 		y = -5.0 * a / 6.0 + U - P / (3.0 * U);
-	complex<double> W = sqrt(a + 2.0 * y);
+	std::complex<double> W = std::sqrt(a + 2.0 * y);
 	// And to get the final result:
 	// result = (±W + sqrt(-(3 * alpha + 2 * y ± 2 * beta / W))) / 2;
 	// We want the largest result, so:
-	valarray<double> t(4);
+	std::valarray<double> t(4);
-	t[0] = (( W + sqrt(-(3.0 * a + 2.0 * y + 2.0 * b / W))) / 2.0).real();
+	t[0] = (( W + std::sqrt(-(3.0 * a + 2.0 * y + 2.0 * b / W))) / 2.0).real();
-	t[1] = (( W + sqrt(-(3.0 * a + 2.0 * y - 2.0 * b / W))) / 2.0).real();
+	t[1] = (( W + std::sqrt(-(3.0 * a + 2.0 * y - 2.0 * b / W))) / 2.0).real();
-	t[2] = ((-W + sqrt(-(3.0 * a + 2.0 * y + 2.0 * b / W))) / 2.0).real();
+	t[2] = ((-W + std::sqrt(-(3.0 * a + 2.0 * y + 2.0 * b / W))) / 2.0).real();
-	t[3] = ((-W + sqrt(-(3.0 * a + 2.0 * y - 2.0 * b / W))) / 2.0).real();
+	t[3] = ((-W + std::sqrt(-(3.0 * a + 2.0 * y - 2.0 * b / W))) / 2.0).real();
 	return t.max();
 }
@@ -286,10 +284,10 @@ double LargestDepressedQuarticSolution(double a, double b, double c)
 Point Nudge(Point p, float offset)
 {
 	static std::random_device rd;
-	static mt19937_64 rng(rd());
+	static std::mt19937_64 rng(rd());
-	uniform_real_distribution<> randomAngle(0, 2 * kPI);
+	std::uniform_real_distribution<> randomAngle(0, 2 * kPI);
-	normal_distribution<> randomOffset(0, offset);
+	std::normal_distribution<> randomOffset(0, offset);
 	float theta = randomAngle(rng);
 	float phi1 = randomAngle(rng) - kPI;

--- a/src/Structure.cpp
+++ b/src/Structure.cpp
--- a/src/Symmetry.cpp
+++ b/src/Symmetry.cpp
@@ -32,8 +32,6 @@
 #include "cif++/Symmetry.hpp"
 #include "cif++/CifUtils.hpp"
-using namespace std;
 namespace mmcif
 {
@@ -51,7 +49,7 @@ int GetSpacegroupNumber(std::string spacegroup)
 	if (spacegroup == "P 21 21 2 A")
 		spacegroup = "P 21 21 2 (a)";
 	else if (spacegroup.empty())
-		throw runtime_error("No spacegroup, cannot continue");
+		throw std::runtime_error("No spacegroup, cannot continue");
 	int result = 0;
@@ -88,7 +86,7 @@ int GetSpacegroupNumber(std::string spacegroup)
 	}
 	if (result == 0)
-		throw runtime_error("Spacegroup name " + spacegroup + " was not found in table");
+		throw std::runtime_error("Spacegroup name " + spacegroup + " was not found in table");
 	return result;
 }

--- a/src/TlsParser.cpp
+++ b/src/TlsParser.cpp