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libcifpp
Commit 4b4757ee by Maarten L. Hekkelman
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removed using namespace std;

parent ac088dd0
Showing with 868 additions and 995 deletions
GNUmakefile.in
......@@ -97,7 +97,6 @@ LIBCIF_SRC = AtomType.cpp \
CifUtils.cpp \
CifValidator.cpp \
Compound.cpp \
FixDMC.cpp \
PDB2Cif.cpp \
PDB2CifRemark3.cpp \
Point.cpp \
......
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());
}
}
src/Cif++.cpp
......@@ -47,7 +47,6 @@
#include "cif++/CifValidator.hpp"
#include "cif++/CifUtils.hpp"
using namespace std;
namespace ba = boost::algorithm;
namespace io = boost::iostreams;
namespace fs = std::filesystem;
......@@ -115,7 +114,7 @@ void ItemValue::operator delete(void* p)
struct ItemColumn
{
string mName; // store lower-case, for optimization
std::string mName; // store lower-case, for optimization
const ValidateItem* mValidator;
};
......@@ -128,9 +127,9 @@ struct ItemRow
void drop(uint32_t columnIx);
const char* c_str(uint32_t columnIx) const;
string str() const
std::string str() const
{
stringstream s;
std::stringstream s;
s << '{';
for (auto v = mValues; v != nullptr; v = v->mNext)
......@@ -152,7 +151,7 @@ struct ItemRow
uint32_t mLineNr = 0;
};
ostream& operator<<(ostream& os, const ItemRow& r)
std::ostream& operator<<(std::ostream& os, const ItemRow& r)
{
os << r.mCategory->name() << '[';
for (auto iv = r.mValues; iv != nullptr; iv = iv->mNext)
......@@ -234,10 +233,10 @@ const char* ItemRow::c_str(uint32_t columnIx) const
namespace detail
{
ItemReference& ItemReference::operator=(const string& value)
ItemReference& ItemReference::operator=(const std::string& value)
{
if (mConst)
throw logic_error("Attempt to write to a constant row");
throw std::logic_error("Attempt to write to a constant row");
mRow.assign(mName, value, false);
return *this;
......@@ -342,7 +341,7 @@ std::ostream& operator<<(std::ostream& os, ItemReference& item)
// --------------------------------------------------------------------
// Datablock implementation
Datablock::Datablock(const string& name)
Datablock::Datablock(const std::string& name)
: mName(name), mValidator(nullptr), mNext(nullptr)
{
}
......@@ -352,11 +351,11 @@ Datablock::~Datablock()
delete mNext;
}
string Datablock::firstItem(const string& tag) const
std::string Datablock::firstItem(const std::string& tag) const
{
string result;
std::string result;
string catName, itemName;
std::string catName, itemName;
std::tie(catName, itemName) = splitTagName(tag);
for (auto& cat: mCategories)
......@@ -365,7 +364,7 @@ string Datablock::firstItem(const string& tag) const
{
for (auto row: cat)
{
result = row[itemName].as<string>();
result = row[itemName].as<std::string>();
break;
}
......@@ -376,7 +375,7 @@ string Datablock::firstItem(const string& tag) const
return result;
}
auto Datablock::emplace(const string& name) -> tuple<iterator,bool>
auto Datablock::emplace(const std::string& name) -> std::tuple<iterator,bool>
{
bool isNew = false;
iterator i = find_if(begin(), end(), [name](const Category& cat) -> bool
......@@ -388,17 +387,17 @@ auto Datablock::emplace(const string& name) -> tuple<iterator,bool>
i = mCategories.emplace(end(), *this, name, mValidator);
}
return make_tuple(i, isNew);
return std::make_tuple(i, isNew);
}
Category& Datablock::operator[](const string& name)
Category& Datablock::operator[](const std::string& name)
{
iterator i;
std::tie(i, ignore) = emplace(name);
std::tie(i, std::ignore) = emplace(name);
return *i;
}
Category* Datablock::get(const string& name)
Category* Datablock::get(const std::string& name)
{
auto i = find_if(begin(), end(), [name](const Category& cat) -> bool
{ return iequals(cat.name(), name); });
......@@ -409,7 +408,7 @@ Category* Datablock::get(const string& name)
bool Datablock::isValid()
{
if (mValidator == nullptr)
throw runtime_error("Validator not specified");
throw std::runtime_error("Validator not specified");
bool result = true;
for (auto& cat: *this)
......@@ -431,7 +430,7 @@ void Datablock::setValidator(Validator* v)
cat.setValidator(v);
}
void Datablock::add_software(const string& name, const string& classification, const string& versionNr, const string& versionDate)
void Datablock::add_software(const std::string& name, const std::string& classification, const std::string& versionNr, const std::string& versionDate)
{
Category& cat = operator[]("software");
int ordNr = cat.size() + 1;
......@@ -446,16 +445,16 @@ void Datablock::add_software(const string& name, const string& classification, c
});
}
void Datablock::getTagOrder(vector<string>& tags) const
void Datablock::getTagOrder(std::vector<std::string>& tags) const
{
for (auto& cat: *this)
cat.getTagOrder(tags);
}
void Datablock::write(ostream& os)
void Datablock::write(std::ostream& os)
{
os << "data_" << mName << endl
<< "# " << endl;
os << "data_" << mName << std::endl
<< "# " << std::endl;
// mmcif support, sort of. First write the 'entry' Category
// and if it exists, _AND_ we have a Validator, write out the
......@@ -488,17 +487,17 @@ void Datablock::write(ostream& os)
}
}
void Datablock::write(ostream& os, const vector<string>& order)
void Datablock::write(std::ostream& os, const std::vector<std::string>& order)
{
os << "data_" << mName << endl
<< "# " << endl;
os << "data_" << mName << std::endl
<< "# " << std::endl;
vector<string> catOrder;
std::vector<std::string> catOrder;
for (auto& o: order)
{
string cat, Item;
std::string cat, Item;
std::tie(cat, Item) = splitTagName(o);
if (find_if(catOrder.rbegin(), catOrder.rend(), [cat](const string& s) -> bool { return iequals(cat, s); }) == catOrder.rend())
if (find_if(catOrder.rbegin(), catOrder.rend(), [cat](const std::string& s) -> bool { return iequals(cat, s); }) == catOrder.rend())
catOrder.push_back(cat);
}
......@@ -508,10 +507,10 @@ void Datablock::write(ostream& os, const vector<string>& order)
if (cat == nullptr)
continue;
vector<string> items;
std::vector<std::string> items;
for (auto& o: order)
{
string catName, Item;
std::string catName, Item;
std::tie(catName, Item) = splitTagName(o);
if (catName == c)
......@@ -524,7 +523,7 @@ void Datablock::write(ostream& os, const vector<string>& order)
// for any Category we missed in the catOrder
for (auto& cat: mCategories)
{
if (find_if(catOrder.begin(), catOrder.end(), [&](const string& s) -> bool { return iequals(cat.name(), s); }) != catOrder.end())
if (find_if(catOrder.begin(), catOrder.end(), [&](const std::string& s) -> bool { return iequals(cat.name(), s); }) != catOrder.end())
continue;
cat.write(os);
......@@ -603,11 +602,11 @@ class RowComparator
}
private:
typedef function<int(const char*,const char*)> compareFunc;
typedef std::function<int(const char*,const char*)> compareFunc;
typedef tuple<size_t,compareFunc> keyComp;
typedef std::tuple<size_t,compareFunc> keyComp;
vector<keyComp> mComp;
std::vector<keyComp> mComp;
};
template<typename KeyIter>
......@@ -617,19 +616,19 @@ RowComparator::RowComparator(Category* cat, KeyIter b, KeyIter e)
for (auto ki = b; ki != e; ++ki)
{
string k = *ki;
std::string k = *ki;
size_t ix = cat->getColumnIndex(k);
auto iv = cv->getValidatorForItem(k);
if (iv == nullptr)
throw runtime_error("Incomplete dictionary, no Item Validator for Key " + k);
throw std::runtime_error("Incomplete dictionary, no Item Validator for Key " + k);
auto tv = iv->mType;
if (tv == nullptr)
throw runtime_error("Incomplete dictionary, no type Validator for Item " + k);
throw std::runtime_error("Incomplete dictionary, no type Validator for Item " + k);
using namespace placeholders;
using namespace std::placeholders;
mComp.emplace_back(ix, bind(&ValidateType::compare, tv, _1, _2));
}
......@@ -680,9 +679,9 @@ class CatIndex
void reconstruct();
// reorder the ItemRow's and returns new head and tail
tuple<ItemRow*,ItemRow*> reorder()
std::tuple<ItemRow*,ItemRow*> reorder()
{
tuple<ItemRow*,ItemRow*> result = make_tuple(nullptr, nullptr);
std::tuple<ItemRow*,ItemRow*> result = std::make_tuple(nullptr, nullptr);
if (mRoot != nullptr)
{
......@@ -691,7 +690,7 @@ class CatIndex
tail->mRow->mNext = nullptr;
result = make_tuple(head->mRow, tail->mRow);
result = std::make_tuple(head->mRow, tail->mRow);
}
return result;
......@@ -898,7 +897,7 @@ CatIndex::entry* CatIndex::insert(entry* h, ItemRow* v)
if (d < 0) h->mLeft = insert(h->mLeft, v);
else if (d > 0) h->mRight = insert(h->mRight, v);
else
throw runtime_error("Duplicate Key violation, cat: " + mCat.name() + " values: " + v->str());
throw std::runtime_error("Duplicate Key violation, cat: " + mCat.name() + " values: " + v->str());
if (isRed(h->mRight) and not isRed(h->mLeft))
h = rotateLeft(h);
......@@ -969,9 +968,9 @@ void CatIndex::reconstruct()
insert(r.mData);
// maybe reconstruction can be done quicker by using the following commented code.
// however, I've not had the time to think of a way to set the red/black flag correctly in that case.
// however, I've not had the time to think of a way to std::set the red/black flag correctly in that case.
// vector<ItemRow*> rows;
// std::vector<ItemRow*> rows;
// transform(mCat.begin(), mCat.end(), backInserter(rows),
// [](Row r) -> ItemRow* { assert(r.mData); return r.mData; });
//
......@@ -1039,7 +1038,7 @@ void CatIndex::reconstruct()
size_t CatIndex::size() const
{
stack<entry*> s;
std::stack<entry*> s;
s.push(mRoot);
size_t result = 0;
......@@ -1189,7 +1188,7 @@ RowSet& RowSet::operator=(RowSet&& rhs)
return *this;
}
RowSet& RowSet::orderBy(initializer_list<string> items)
RowSet& RowSet::orderBy(std::initializer_list<std::string> items)
{
RowComparator c(mCat, items.begin(), items.end());
......@@ -1200,7 +1199,7 @@ RowSet& RowSet::orderBy(initializer_list<string> items)
// --------------------------------------------------------------------
Category::Category(Datablock& db, const string& name, Validator* Validator)
Category::Category(Datablock& db, const std::string& name, Validator* Validator)
: mDb(db), mName(name), mValidator(Validator)
, mHead(nullptr), mTail(nullptr), mIndex(nullptr)
{
......@@ -1258,12 +1257,12 @@ void Category::setValidator(Validator* v)
mCatValidator = nullptr;
}
bool Category::hasColumn(const string& name) const
bool Category::hasColumn(const std::string& name) const
{
return getColumnIndex(name) < mColumns.size();
}
size_t Category::getColumnIndex(const string& name) const
size_t Category::getColumnIndex(const std::string& name) const
{
size_t result;
......@@ -1277,26 +1276,26 @@ size_t Category::getColumnIndex(const string& name) const
{
auto iv = mCatValidator->getValidatorForItem(name);
if (iv == nullptr)
cerr << "Invalid name used '" + name + "' is not a known column in " + mName << endl;
std::cerr << "Invalid name used '" + name + "' is not a known column in " + mName << std::endl;
}
return result;
}
const string& Category::getColumnName(size_t columnIx) const
const std::string& Category::getColumnName(size_t columnIx) const
{
return mColumns.at(columnIx).mName;
}
vector<string> Category::getColumnNames() const
std::vector<std::string> Category::getColumnNames() const
{
vector<string> result;
std::vector<std::string> result;
for (auto& c: mColumns)
result.push_back(c.mName);
return result;
}
size_t Category::addColumn(const string& name)
size_t Category::addColumn(const std::string& name)
{
size_t result = getColumnIndex(name);
......@@ -1343,7 +1342,7 @@ void Category::sort(std::function<int(const Row&, const Row&)> comparator)
if (mHead == nullptr)
return;
vector<ItemRow*> rows;
std::vector<ItemRow*> rows;
for (auto itemRow = mHead; itemRow != nullptr; itemRow = itemRow->mNext)
rows.push_back(itemRow);
......@@ -1382,9 +1381,9 @@ bool Category::empty() const
return mHead == nullptr or mHead->mValues == nullptr;
}
void Category::drop(const string& field)
void Category::drop(const std::string& field)
{
using namespace placeholders;
using namespace std::placeholders;
auto ci = find_if(mColumns.begin(), mColumns.end(),
[field](ItemColumn& c) -> bool { return iequals(c.mName, field); });
......@@ -1450,7 +1449,7 @@ bool Category::exists(Condition&& cond) const
return result;
}
RowSet Category::orderBy(std::initializer_list<string> items)
RowSet Category::orderBy(std::initializer_list<std::string> items)
{
RowSet result(*this);
result.insert(result.begin(), begin(), end());
......@@ -1471,10 +1470,10 @@ void Category::clear()
}
template<class Iter>
tuple<Row,bool> Category::emplace(Iter b, Iter e)
std::tuple<Row,bool> Category::emplace(Iter b, Iter e)
{
// First, make sure all mandatory fields are supplied
tuple<Row,bool> result = make_tuple(Row(), true);
std::tuple<Row,bool> result = std::make_tuple(Row(), true);
if (mCatValidator != nullptr and b != e)
{
......@@ -1497,12 +1496,12 @@ tuple<Row,bool> Category::emplace(Iter b, Iter e)
}
if (not seen and iv->mMandatory)
throw runtime_error("missing mandatory field " + col.mName + " for Category " + mName);
throw std::runtime_error("missing mandatory field " + col.mName + " for Category " + mName);
}
if (mIndex != nullptr)
{
unique_ptr<ItemRow> nr(new ItemRow{nullptr, this, nullptr});
std::unique_ptr<ItemRow> nr(new ItemRow{nullptr, this, nullptr});
Row r(nr.get());
auto keys = keyFields();
......@@ -1516,13 +1515,13 @@ tuple<Row,bool> Category::emplace(Iter b, Iter e)
if (test != nullptr)
{
if (VERBOSE > 1)
cerr << "Not inserting new record in " << mName << " (duplicate Key)" << endl;
result = make_tuple(Row(test), false);
std::cerr << "Not inserting new record in " << mName << " (duplicate Key)" << std::endl;
result = std::make_tuple(Row(test), false);
}
}
}
if (get<1>(result))
if (std::get<1>(result))
{
auto nr = new ItemRow{nullptr, this, nullptr};
......@@ -1544,7 +1543,7 @@ tuple<Row,bool> Category::emplace(Iter b, Iter e)
for (auto v = b; v != e; ++v)
r.assign(*v, true);
get<0>(result) = r;
std::get<0>(result) = r;
if (mIndex != nullptr)
mIndex->insert(nr);
......@@ -1553,7 +1552,7 @@ tuple<Row,bool> Category::emplace(Iter b, Iter e)
return result;
}
tuple<Row,bool> Category::emplace(Row r)
std::tuple<Row,bool> Category::emplace(Row r)
{
return emplace(r.begin(), r.end());
}
......@@ -1603,7 +1602,7 @@ size_t Category::erase(Condition&& cond, std::function<void(const Row&)>&& verbo
void Category::eraseOrphans(Condition&& cond)
{
vector<ItemRow*> remove;
std::vector<ItemRow*> remove;
cond.prepare(*this);
......@@ -1612,9 +1611,9 @@ void Category::eraseOrphans(Condition&& cond)
if (cond(*this, r) and isOrphan(r))
{
if (VERBOSE > 1)
cerr << "Removing orphaned record: " << endl
<< r << endl
<< endl;
std::cerr << "Removing orphaned record: " << std::endl
<< r << std::endl
<< std::endl;
remove.push_back(r.mData);
}
......@@ -1639,7 +1638,7 @@ auto Category::erase(iterator pos) -> iterator
keys = iset(mCatValidator->mKeys.begin(), mCatValidator->mKeys.end());
if (mHead == nullptr)
throw runtime_error("erase");
throw std::runtime_error("erase");
if (mIndex != nullptr)
mIndex->erase(r.mData);
......@@ -1666,7 +1665,7 @@ auto Category::erase(iterator pos) -> iterator
// in mmcif_pdbx.dic dictionary.
//
// For each link group in _pdbx_item_linked_group_list
// a set of keys from one category is mapped to another.
// a std::set of keys from one category is mapped to another.
// If all values in a child are the same as the specified parent ones
// the child is removed as well, recursively of course.
......@@ -1684,10 +1683,10 @@ auto Category::erase(iterator pos) -> iterator
{
const char* value = r[link->mParentKeys[ix]].c_str();
cond = move(cond) && (Key(link->mChildKeys[ix]) == value);
cond = std::move(cond) && (Key(link->mChildKeys[ix]) == value);
}
childCat->eraseOrphans(move(cond));
childCat->eraseOrphans(std::move(cond));
}
}
......@@ -1705,7 +1704,7 @@ auto Category::erase(iterator pos) -> iterator
return result;
}
void Category::getTagOrder(vector<string>& tags) const
void Category::getTagOrder(std::vector<std::string>& tags) const
{
for (auto& c: mColumns)
tags.push_back("_" + mName + "." + c.mName);
......@@ -1746,12 +1745,12 @@ bool Category::hasParent(Row r, const Category& parentCat, const ValidateLink& l
if (field.empty())
{
if (mCatValidator->mMandatoryFields.count(name) and field.is_null())
cond = move(cond) and (Key(link.mParentKeys[ix]) == Empty());
cond = std::move(cond) and (Key(link.mParentKeys[ix]) == Empty());
}
else
{
const char* value = field.c_str();
cond = move(cond) and (Key(link.mParentKeys[ix]) == value);
cond = std::move(cond) and (Key(link.mParentKeys[ix]) == value);
}
}
......@@ -1760,10 +1759,10 @@ bool Category::hasParent(Row r, const Category& parentCat, const ValidateLink& l
result = parentCat.exists(std::move(cond));
if (VERBOSE > 3 or (result == false and VERBOSE > 2))
cerr << "result = " << boolalpha << result << " for: '" << cond << "' in parent category " << link.mParentCategory << " for child cat " << mName << endl;
std::cerr << "result = " << std::boolalpha << result << " for: '" << cond << "' in parent category " << link.mParentCategory << " for child cat " << mName << std::endl;
}
else if (VERBOSE > 3 and cond.empty())
cerr << "Condition is empty due to missing data in parent category " << link.mParentCategory << " for child cat " << mName << endl;
std::cerr << "Condition is empty due to missing data in parent category " << link.mParentCategory << " for child cat " << mName << std::endl;
return result;
}
......@@ -1785,16 +1784,16 @@ bool Category::isOrphan(Row r)
for (size_t ix = 0; ix < link->mChildKeys.size(); ++ix)
{
const char* value = r[link->mChildKeys[ix]].c_str();
cond = move(cond) && (Key(link->mParentKeys[ix]) == value);
cond = std::move(cond) && (Key(link->mParentKeys[ix]) == value);
}
if (VERBOSE > 2)
cerr << "Check condition '" << cond << "' in parent category " << link->mParentCategory << " for child cat " << mName << endl;
std::cerr << "Check condition '" << cond << "' in parent category " << link->mParentCategory << " for child cat " << mName << std::endl;
if (parentCat->exists(std::move(cond)))
{
if (VERBOSE > 2)
cerr << "Not removing because row has a parent in category " << link->mParentCategory << endl;
std::cerr << "Not removing because row has a parent in category " << link->mParentCategory << std::endl;
isOrphan = false;
break;
......@@ -1823,7 +1822,7 @@ bool Category::hasChildren(Row r) const
{
const char* value = r[link->mParentKeys[ix]].c_str();
cond = move(cond) && (Key(link->mChildKeys[ix]) == value);
cond = std::move(cond) && (Key(link->mChildKeys[ix]) == value);
}
result = not childCat->find(std::move(cond)).empty();
......@@ -1840,12 +1839,12 @@ bool Category::isValid()
bool result = true;
if (mValidator == nullptr)
throw runtime_error("no Validator specified");
throw std::runtime_error("no Validator specified");
if (empty())
{
if (VERBOSE > 2)
cerr << "Skipping validation of empty Category " << mName << endl;
std::cerr << "Skipping validation of empty Category " << mName << std::endl;
return true;
}
......@@ -1947,8 +1946,8 @@ void Category::validateLinks() const
if (missing)
{
cerr << "Links for " << linkValidator->mLinkGroupLabel << " are incomplete" << endl
<< " There are " << missing << " items in " << mName << " that don't have matching parent items in " << parent->mName << endl;
std::cerr << "Links for " << linkValidator->mLinkGroupLabel << " are incomplete" << std::endl
<< " There are " << missing << " items in " << mName << " that don't have matching parent items in " << parent->mName << std::endl;
}
}
}
......@@ -1956,14 +1955,14 @@ void Category::validateLinks() const
const Validator& Category::getValidator() const
{
if (mValidator == nullptr)
throw runtime_error("no Validator defined yet");
throw std::runtime_error("no Validator defined yet");
return *mValidator;
}
iset Category::fields() const
{
if (mValidator == nullptr)
throw runtime_error("No Validator specified");
throw std::runtime_error("No Validator specified");
if (mCatValidator == nullptr)
mValidator->reportError("undefined Category", true);
......@@ -1977,7 +1976,7 @@ iset Category::fields() const
iset Category::mandatoryFields() const
{
if (mValidator == nullptr)
throw runtime_error("No Validator specified");
throw std::runtime_error("No Validator specified");
if (mCatValidator == nullptr)
mValidator->reportError("undefined Category", true);
......@@ -1988,7 +1987,7 @@ iset Category::mandatoryFields() const
iset Category::keyFields() const
{
if (mValidator == nullptr)
throw runtime_error("No Validator specified");
throw std::runtime_error("No Validator specified");
if (mCatValidator == nullptr)
mValidator->reportError("undefined Category", true);
......@@ -1996,15 +1995,15 @@ iset Category::keyFields() const
return iset{ mCatValidator->mKeys.begin(), mCatValidator->mKeys.end() };
}
set<size_t> Category::keyFieldsByIndex() const
std::set<size_t> Category::keyFieldsByIndex() const
{
if (mValidator == nullptr)
throw runtime_error("No Validator specified");
throw std::runtime_error("No Validator specified");
if (mCatValidator == nullptr)
mValidator->reportError("undefined Category", true);
set<size_t> result;
std::set<size_t> result;
for (auto& k: mCatValidator->mKeys)
result.insert(getColumnIndex(k));
......@@ -2026,18 +2025,18 @@ set<size_t> Category::keyFieldsByIndex() const
namespace detail
{
size_t writeValue(ostream& os, string value, size_t offset, size_t width)
size_t writeValue(std::ostream& os, std::string value, size_t offset, size_t width)
{
if (value.find('\n') != string::npos or width == 0 or value.length() >= 132) // write as text field
if (value.find('\n') != std::string::npos or width == 0 or value.length() >= 132) // write as text field
{
ba::replace_all(value, "\n;", "\n\\;");
if (offset > 0)
os << endl;
os << std::endl;
os << ';' << value;
if (not ba::ends_with(value, "\n"))
os << endl;
os << ';' << endl;
os << std::endl;
os << ';' << std::endl;
offset = 0;
}
else if (isUnquotedString(value.c_str()))
......@@ -2046,7 +2045,7 @@ size_t writeValue(ostream& os, string value, size_t offset, size_t width)
if (value.length() < width)
{
os << string(width - value.length(), ' ');
os << std::string(width - value.length(), ' ');
offset += width;
}
else
......@@ -2061,17 +2060,17 @@ size_t writeValue(ostream& os, string value, size_t offset, size_t width)
for (char q: { '\'', '"'})
{
auto p = value.find(q); // see if we can use the quote character
while (p != string::npos and isNonBlank(value[p + 1]) and value[p + 1] != q)
while (p != std::string::npos and isNonBlank(value[p + 1]) and value[p + 1] != q)
p = value.find(q, p + 1);
if (p != string::npos)
if (p != std::string::npos)
continue;
os << q << value << q;
if (value.length() + 2 < width)
{
os << string(width - value.length() - 2, ' ');
os << std::string(width - value.length() - 2, ' ');
offset += width;
}
else
......@@ -2087,9 +2086,9 @@ size_t writeValue(ostream& os, string value, size_t offset, size_t width)
if (not done)
{
if (offset > 0)
os << endl;
os << ';' << value << endl
<< ';' << endl;
os << std::endl;
os << ';' << value << std::endl
<< ';' << std::endl;
offset = 0;
}
}
......@@ -2099,7 +2098,7 @@ size_t writeValue(ostream& os, string value, size_t offset, size_t width)
}
void Category::write(ostream& os, const vector<int>& order, bool includeEmptyColumns)
void Category::write(std::ostream& os, const std::vector<int>& order, bool includeEmptyColumns)
{
if (empty())
return;
......@@ -2109,14 +2108,14 @@ void Category::write(ostream& os, const vector<int>& order, bool includeEmptyCol
if (needLoop)
{
os << "loop_" << endl;
os << "loop_" << std::endl;
vector<size_t> columnWidths;
std::vector<size_t> columnWidths;
for (auto cix: order)
{
auto& col = mColumns[cix];
os << '_' << mName << '.' << col.mName << ' ' << endl;
os << '_' << mName << '.' << col.mName << ' ' << std::endl;
columnWidths.push_back(2);
}
......@@ -2148,7 +2147,7 @@ void Category::write(ostream& os, const vector<int>& order, bool includeEmptyCol
{
size_t w = columnWidths[cix];
string s;
std::string s;
for (auto iv = Row->mValues; iv != nullptr; iv = iv->mNext)
{
if (iv->mColumnIndex == cix)
......@@ -2169,7 +2168,7 @@ void Category::write(ostream& os, const vector<int>& order, bool includeEmptyCol
if (offset + l >= 132 and offset > 0)
{
os << endl;
os << std::endl;
offset = 0;
}
......@@ -2177,13 +2176,13 @@ void Category::write(ostream& os, const vector<int>& order, bool includeEmptyCol
if (offset >= 132)
{
os << endl;
os << std::endl;
offset = 0;
}
}
if (offset > 0)
os << endl;
os << std::endl;
}
}
else
......@@ -2193,7 +2192,7 @@ void Category::write(ostream& os, const vector<int>& order, bool includeEmptyCol
for (auto& col: mColumns)
{
string tag = '_' + mName + '.' + col.mName;
std::string tag = '_' + mName + '.' + col.mName;
if (l < tag.length())
l = tag.length();
......@@ -2205,9 +2204,9 @@ void Category::write(ostream& os, const vector<int>& order, bool includeEmptyCol
{
auto& col = mColumns[cix];
os << '_' << mName << '.' << col.mName << string(l - col.mName.length() - mName.length() - 2, ' ');
os << '_' << mName << '.' << col.mName << std::string(l - col.mName.length() - mName.length() - 2, ' ');
string s;
std::string s;
for (auto iv = mHead->mValues; iv != nullptr; iv = iv->mNext)
{
if (iv->mColumnIndex == cix)
......@@ -2223,32 +2222,32 @@ void Category::write(ostream& os, const vector<int>& order, bool includeEmptyCol
size_t offset = l;
if (s.length() + l >= kMaxLineLength)
{
os << endl;
os << std::endl;
offset = 0;
}
if (detail::writeValue(os, s, offset, 1) != 0)
os << endl;
os << std::endl;
}
}
os << "# " << endl;
os << "# " << std::endl;
}
void Category::write(ostream& os)
void Category::write(std::ostream& os)
{
vector<int> order(mColumns.size());
std::vector<int> order(mColumns.size());
iota(order.begin(), order.end(), 0);
write(os, order, false);
}
void Category::write(ostream& os, const vector<string>& columns)
void Category::write(std::ostream& os, const std::vector<std::string>& columns)
{
// make sure all columns are present
for (auto& c: columns)
addColumn(c);
vector<int> order;
std::vector<int> order;
order.reserve(mColumns.size());
for (auto& c: columns)
......@@ -2307,15 +2306,15 @@ void Row::assign(const std::vector<Item>& values)
{
auto cat = mData->mCategory;
map<string,tuple<int,string,string>> changed;
std::map<std::string,std::tuple<int,std::string,std::string>> changed;
for (auto& value: values)
{
auto columnIx = cat->addColumn(value.name());
auto& col = cat->mColumns[columnIx];
string tag = col.mValidator ? col.mValidator->mTag : to_string(columnIx);
std::string tag = col.mValidator ? col.mValidator->mTag : std::to_string(columnIx);
changed[tag] = make_tuple(columnIx, operator[](columnIx).c_str(), value.value());
changed[tag] = std::make_tuple(columnIx, operator[](columnIx).c_str(), value.value());
assign(columnIx, value.value(), true);
}
......@@ -2337,29 +2336,29 @@ void Row::assign(const std::vector<Item>& values)
// continue;
Condition cond;
string childTag;
std::string childTag;
vector<Item> newValues;
std::vector<Item> newValues;
for (size_t ix = 0; ix < linked->mParentKeys.size(); ++ix)
{
string pk = linked->mParentKeys[ix];
string ck = linked->mChildKeys[ix];
std::string pk = linked->mParentKeys[ix];
std::string ck = linked->mChildKeys[ix];
if (changed.count(pk) > 0)
{
childTag = ck;
cond = move(cond) && (Key(ck) == std::get<1>(changed[pk]));
cond = std::move(cond) && (Key(ck) == std::get<1>(changed[pk]));
newValues.emplace_back(ck, std::get<2>(changed[pk]));
}
else
{
const char* value = (*this)[pk].c_str();
cond = move(cond) && (Key(ck) == value);
cond = std::move(cond) && (Key(ck) == value);
}
}
auto rows = childCat->find(move(cond));
auto rows = childCat->find(std::move(cond));
for (auto& cr: rows)
cr.assign(newValues);
}
......@@ -2371,24 +2370,24 @@ void Row::assign(const Item& value, bool skipUpdateLinked)
assign(value.name(), value.value(), skipUpdateLinked);
}
void Row::assign(const string& name, const string& value, bool skipUpdateLinked)
void Row::assign(const std::string& name, const std::string& value, bool skipUpdateLinked)
{
try
{
auto cat = mData->mCategory;
assign(cat->addColumn(name), value, skipUpdateLinked);
}
catch (const exception& ex)
catch (const std::exception& ex)
{
cerr << "Could not assign value '" << value << "' to column _" << mData->mCategory->name() << '.' << name << endl;
std::cerr << "Could not assign value '" << value << "' to column _" << mData->mCategory->name() << '.' << name << std::endl;
throw;
}
}
void Row::assign(size_t column, const string& value, bool skipUpdateLinked)
void Row::assign(size_t column, const std::string& value, bool skipUpdateLinked)
{
if (mData == nullptr)
throw logic_error("invalid Row, no data assigning value '" + value + "' to column with index " + to_string(column));
throw std::logic_error("invalid Row, no data assigning value '" + value + "' to column with index " + std::to_string(column));
auto cat = mData->mCategory;
auto& col = cat->mColumns[column];
......@@ -2408,7 +2407,7 @@ void Row::assign(size_t column, const string& value, bool skipUpdateLinked)
if (oldValue != nullptr and value == oldValue) // no need to update
return;
string oldStrValue = oldValue ? oldValue : "";
std::string oldStrValue = oldValue ? oldValue : "";
// check the value
if (col.mValidator)
......@@ -2489,35 +2488,35 @@ void Row::assign(size_t column, const string& value, bool skipUpdateLinked)
continue;
Condition cond;
string childTag;
std::string childTag;
for (size_t ix = 0; ix < linked->mParentKeys.size(); ++ix)
{
string pk = linked->mParentKeys[ix];
string ck = linked->mChildKeys[ix];
std::string pk = linked->mParentKeys[ix];
std::string ck = linked->mChildKeys[ix];
// TODO add code to *NOT* test mandatory fiels for Empty
if (pk == iv->mTag)
{
childTag = ck;
cond = move(cond) && ((Key(ck) == oldStrValue) or Key(ck) == Empty());
cond = std::move(cond) && ((Key(ck) == oldStrValue) or Key(ck) == Empty());
}
else
{
const char* value = (*this)[pk].c_str();
cond = move(cond) && ((Key(ck) == value) or Key(ck) == Empty());
cond = std::move(cond) && ((Key(ck) == value) or Key(ck) == Empty());
}
}
// if (cif::VERBOSE > 2)
// {
// std::cerr << "Parent: " << linked->mParentCategory << " Child: " << linked->mChildCategory << std::endl
// << cond << std::endl;
// std::std::cerr << "Parent: " << linked->mParentCategory << " Child: " << linked->mChildCategory << std::std::endl
// << cond << std::std::endl;
// }
auto rows = childCat->find(move(cond));
auto rows = childCat->find(std::move(cond));
for (auto& cr: rows)
cr.assign(childTag, value, false);
}
......@@ -2527,11 +2526,11 @@ void Row::assign(size_t column, const string& value, bool skipUpdateLinked)
void Row::swap(size_t cix, ItemRow* a, ItemRow* b)
{
if (a == nullptr or b == nullptr)
throw logic_error("invalid Rows in swap");
throw std::logic_error("invalid Rows in swap");
assert(a->mCategory == b->mCategory);
if (a->mCategory != b->mCategory)
throw logic_error("Categories not same in swap");
throw std::logic_error("Categories not same in swap");
auto cat = a->mCategory;
......@@ -2642,7 +2641,7 @@ void Row::swap(size_t cix, ItemRow* a, ItemRow* b)
if (childCatValidator == nullptr)
continue;
string linkChildColName;
std::string linkChildColName;
Condition cond[2];
for (size_t ab = 0; ab < 2; ++ab)
......@@ -2660,7 +2659,7 @@ void Row::swap(size_t cix, ItemRow* a, ItemRow* b)
find(childCatValidator->mMandatoryFields.begin(), childCatValidator->mMandatoryFields.end(), childColName) != childCatValidator->mMandatoryFields.end() or
find(parentCatValidator->mMandatoryFields.begin(), parentCatValidator->mMandatoryFields.end(), link->mParentKeys[ix]) != parentCatValidator->mMandatoryFields.end();
string childValue;
std::string childValue;
if (pcix == cix)
{
......@@ -2670,7 +2669,7 @@ void Row::swap(size_t cix, ItemRow* a, ItemRow* b)
}
else
{
string ps = r->c_str(pcix);
std::string ps = r->c_str(pcix);
if (not (ps.empty() or ps == "." or ps == "?"))
childValue = ps;
}
......@@ -2678,12 +2677,12 @@ void Row::swap(size_t cix, ItemRow* a, ItemRow* b)
if (not childValue.empty())
{
if (mandatory or pcix == cix)
cond[ab] = move(cond[ab]) and Key(childColName) == childValue;
cond[ab] = std::move(cond[ab]) and Key(childColName) == childValue;
else
cond[ab] = move(cond[ab]) and (Key(childColName) == childValue or Key(childColName) == Empty());
cond[ab] = std::move(cond[ab]) and (Key(childColName) == childValue or Key(childColName) == Empty());
}
else
cond[ab] = move(cond[ab]) and Key(childColName) == Empty();
cond[ab] = std::move(cond[ab]) and Key(childColName) == Empty();
}
}
......@@ -2696,10 +2695,10 @@ void Row::swap(size_t cix, ItemRow* a, ItemRow* b)
continue;
if (VERBOSE > 1)
cerr << "Fixing link from " << cat->mName << " to " << childCat->mName << " with " << endl
<< cond[ab] << endl;
std::cerr << "Fixing link from " << cat->mName << " to " << childCat->mName << " with " << std::endl
<< cond[ab] << std::endl;
rs.push_back(childCat->find(move(cond[ab])));
rs.push_back(childCat->find(std::move(cond[ab])));
}
for (size_t ab = 0; ab < 2; ++ab)
......@@ -2720,12 +2719,12 @@ void Row::swap(size_t cix, ItemRow* a, ItemRow* b)
if (n == link->mChildKeys.size())
{
if (VERBOSE > 1)
cerr << "All empty columns, skipping" << endl;
std::cerr << "All empty columns, skipping" << std::endl;
}
else
{
if (VERBOSE)
cerr << "In " << childCat->mName << " changing " << linkChildColName << ": " << r[linkChildColName] << " => " << (i ? i->mText : "") << endl;
std::cerr << "In " << childCat->mName << " changing " << linkChildColName << ": " << r[linkChildColName] << " => " << (i ? i->mText : "") << std::endl;
r[linkChildColName] = i ? i->mText : "";
}
}
......@@ -2800,11 +2799,11 @@ void Row::const_iterator::fetch()
std::ostream& operator<<(std::ostream& os, const Row& row)
{
auto category = row.mData->mCategory;
string catName = category->name();
std::string catName = category->name();
for (auto item = row.mData->mValues; item != nullptr; item = item->mNext)
{
string tagName = category->getColumnName(item->mColumnIndex);
os << '_' << catName << '.' << tagName << ' ' << item->mText << endl;
std::string tagName = category->getColumnName(item->mColumnIndex);
os << '_' << catName << '.' << tagName << ' ' << item->mText << std::endl;
}
return os;
......@@ -2818,7 +2817,7 @@ File::File()
{
}
File::File(istream& is, bool validate)
File::File(std::istream& is, bool validate)
: File()
{
load(is);
......@@ -2831,9 +2830,9 @@ File::File(const std::string& path, bool validate)
{
load(path);
}
catch (const exception& ex)
catch (const std::exception& ex)
{
cerr << "Error while loading file " << path << endl;
std::cerr << "Error while loading file " << path << std::endl;
throw;
}
}
......@@ -2880,9 +2879,9 @@ void File::load(const std::string& p)
{
fs::path path(p);
std::ifstream inFile(p, ios_base::in | ios_base::binary);
std::ifstream inFile(p, std::ios_base::in | std::ios_base::binary);
if (not inFile.is_open())
throw runtime_error("Could not open file: " + path.string());
throw std::runtime_error("Could not open file: " + path.string());
io::filtering_stream<io::input> in;
std::string ext;
......@@ -2904,9 +2903,9 @@ void File::load(const std::string& p)
{
load(in);
}
catch (const exception& ex)
catch (const std::exception& ex)
{
cerr << "Error loading file " << path << endl;
std::cerr << "Error loading file " << path << std::endl;
throw;
}
}
......@@ -2915,7 +2914,7 @@ void File::save(const std::string& p)
{
fs::path path(p);
std::ofstream outFile(p, ios_base::out | ios_base::binary);
std::ofstream outFile(p, std::ios_base::out | std::ios_base::binary);
io::filtering_stream<io::output> out;
if (path.extension() == ".gz")
......@@ -2933,7 +2932,7 @@ void File::save(const std::string& p)
save(out);
}
void File::load(istream& is)
void File::load(std::istream& is)
{
Validator* saved = mValidator;
setValidator(nullptr);
......@@ -2948,7 +2947,7 @@ void File::load(istream& is)
}
}
void File::save(ostream& os)
void File::save(std::ostream& os)
{
Datablock* e = mHead;
while (e != nullptr)
......@@ -2958,7 +2957,7 @@ void File::save(ostream& os)
}
}
void File::write(ostream& os, const vector<string>& order)
void File::write(std::ostream& os, const std::vector<std::string>& order)
{
Datablock* e = mHead;
while (e != nullptr)
......@@ -2968,7 +2967,7 @@ void File::write(ostream& os, const vector<string>& order)
}
}
Datablock* File::get(const string& name) const
Datablock* File::get(const std::string& name) const
{
const Datablock* result = mHead;
while (result != nullptr and not iequals(result->mName, name))
......@@ -2976,13 +2975,13 @@ Datablock* File::get(const string& name) const
return const_cast<Datablock*>(result);
}
Datablock& File::operator[](const string& name)
Datablock& File::operator[](const std::string& name)
{
Datablock* result = mHead;
while (result != nullptr and not iequals(result->mName, name))
result = result->mNext;
if (result == nullptr)
throw runtime_error("Datablock " + name + " does not exist");
throw std::runtime_error("Datablock " + name + " does not exist");
return *result;
}
......@@ -2991,7 +2990,7 @@ bool File::isValid()
if (mValidator == nullptr)
{
if (VERBOSE)
cerr << "No dictionary loaded explicitly, loading default" << endl;
std::cerr << "No dictionary loaded explicitly, loading default" << std::endl;
loadDictionary();
}
......@@ -3011,7 +3010,7 @@ void File::validateLinks() const
const Validator& File::getValidator() const
{
if (mValidator == nullptr)
throw runtime_error("no Validator defined yet");
throw std::runtime_error("no Validator defined yet");
return *mValidator;
}
......@@ -3037,7 +3036,7 @@ void File::loadDictionary(const char* dict)
}
catch (...) {}
fs::path dictFile = string("dictionaries/") + dict + ".dic";
fs::path dictFile = std::string("dictionaries/") + dict + ".dic";
try
{
......@@ -3054,7 +3053,7 @@ void File::loadDictionary(const char* dict)
if (dictData)
{
struct membuf : public streambuf
struct membuf : public std::streambuf
{
membuf(char* dict, size_t length)
{
......@@ -3062,19 +3061,19 @@ void File::loadDictionary(const char* dict)
}
} buffer(const_cast<char*>(dictData.data()), dictData.size());
istream is(&buffer);
std::istream is(&buffer);
loadDictionary(is);
break;
}
throw runtime_error("Dictionary not found or defined (" + name.string() + ")");
throw std::runtime_error("Dictionary not found or defined (" + name.string() + ")");
}
}
void File::loadDictionary(istream& is)
void File::loadDictionary(std::istream& is)
{
unique_ptr<Validator> v(new Validator());
std::unique_ptr<Validator> v(new Validator());
DictParser p(*v, is);
p.loadDictionary();
......@@ -3090,7 +3089,7 @@ void File::setValidator(Validator* v)
d->setValidator(mValidator);
}
void File::getTagOrder(vector<string>& tags) const
void File::getTagOrder(std::vector<std::string>& tags) const
{
for (auto d = mHead; d != nullptr; d = d->mNext)
d->getTagOrder(tags);
......
src/CifParser.cpp
......@@ -32,7 +32,6 @@
#include "cif++/CifParser.hpp"
#include "cif++/CifValidator.hpp"
using namespace std;
namespace ba = boost::algorithm;
extern int VERBOSE;
......@@ -54,8 +53,8 @@ const uint8_t kCharTraitsTable[128] = {
// --------------------------------------------------------------------
CifParserError::CifParserError(uint32_t lineNr, const string& message)
: runtime_error("parse error at line " + to_string(lineNr) + ": " + message)
CifParserError::CifParserError(uint32_t lineNr, const std::string& message)
: std::runtime_error("parse error at line " + std::to_string(lineNr) + ": " + message)
{
}
......@@ -94,7 +93,7 @@ SacParser::SacParser(std::istream& is)
mLookahead = getNextToken();
}
void SacParser::error(const string& msg)
void SacParser::error(const std::string& msg)
{
throw CifParserError(mLineNr, msg);
}
......@@ -130,11 +129,11 @@ int SacParser::getNextChar()
if (VERBOSE >= 6)
{
cerr << "getNextChar => ";
std::cerr << "getNextChar => ";
if (iscntrl(result) or not isprint(result))
cerr << int(result) << endl;
std::cerr << int(result) << std::endl;
else
cerr << char(result) << endl;
std::cerr << char(result) << std::endl;
}
return result;
......@@ -181,14 +180,14 @@ void SacParser::restart()
void SacParser::match(SacParser::CIFToken t)
{
if (mLookahead != t)
error(string("Unexpected token, expected ") + kTokenName[t] + " but found " + kTokenName[mLookahead]);
error(std::string("Unexpected token, expected ") + kTokenName[t] + " but found " + kTokenName[mLookahead]);
mLookahead = getNextToken();
}
SacParser::CIFToken SacParser::getNextToken()
{
const auto kEOF = char_traits<char>::eof();
const auto kEOF = std::char_traits<char>::eof();
CIFToken result = eCIFTokenUnknown;
int quoteChar = 0;
......@@ -291,7 +290,7 @@ SacParser::CIFToken SacParser::getNextToken()
error("unterminated textfield");
else if (not isAnyPrint(ch))
// error("invalid character in text field '" + string({ static_cast<char>(ch) }) + "' (" + to_string((int)ch) + ")");
cerr << "invalid character in text field '" << string({ static_cast<char>(ch) }) << "' (" << ch << ") line: " << mLineNr << endl;
std::cerr << "invalid character in text field '" << std::string({ static_cast<char>(ch) }) << "' (" << ch << ") line: " << mLineNr << std::endl;
break;
case eStateTextField + 1:
......@@ -469,7 +468,7 @@ SacParser::CIFToken SacParser::getNextToken()
case eStateValue + 1:
if (ch == '_') // first _, check for keywords
{
string s = toLowerCopy(mTokenValue);
std::string s = toLowerCopy(mTokenValue);
if (s == "global_")
result = eCIFTokenGLOBAL;
......@@ -511,12 +510,12 @@ SacParser::CIFToken SacParser::getNextToken()
if (VERBOSE >= 5)
{
cerr << kTokenName[result];
std::cerr << kTokenName[result];
if (mTokenType != eCIFValueUnknown)
cerr << ' ' << kValueName[mTokenType];
std::cerr << ' ' << kValueName[mTokenType];
if (result != eCIFTokenEOF)
cerr << " '" << mTokenValue << '\'';
cerr << endl;
std::cerr << " '" << mTokenValue << '\'';
std::cerr << std::endl;
}
return result;
......@@ -558,7 +557,7 @@ void SacParser::parseGlobal()
void SacParser::parseDataBlock()
{
string cat;
std::string cat;
while (mLookahead == eCIFTokenLOOP or mLookahead == eCIFTokenTag or mLookahead == eCIFTokenSAVE)
{
......@@ -570,11 +569,11 @@ void SacParser::parseDataBlock()
match(eCIFTokenLOOP);
vector<string> tags;
std::vector<std::string> tags;
while (mLookahead == eCIFTokenTag)
{
string catName, itemName;
std::string catName, itemName;
std::tie(catName, itemName) = splitTagName(mTokenValue);
if (cat.empty())
......@@ -607,7 +606,7 @@ void SacParser::parseDataBlock()
case eCIFTokenTag:
{
string catName, itemName;
std::string catName, itemName;
std::tie(catName, itemName) = splitTagName(mTokenValue);
if (not iequals(cat, catName))
......@@ -648,34 +647,34 @@ Parser::Parser(std::istream& is, File& f)
{
}
void Parser::produceDatablock(const string& name)
void Parser::produceDatablock(const std::string& name)
{
mDataBlock = new Datablock(name);
mFile.append(mDataBlock);
}
void Parser::produceCategory(const string& name)
void Parser::produceCategory(const std::string& name)
{
if (VERBOSE >= 4)
cerr << "producing category " << name << endl;
std::cerr << "producing category " << name << std::endl;
std::tie(mCat, ignore) = mDataBlock->emplace(name);
std::tie(mCat, std::ignore) = mDataBlock->emplace(name);
}
void Parser::produceRow()
{
if (VERBOSE >= 4)
cerr << "producing row for category " << mCat->name() << endl;
std::cerr << "producing row for category " << mCat->name() << std::endl;
mCat->emplace({});
mRow = mCat->back();
mRow.lineNr(mLineNr);
}
void Parser::produceItem(const string& category, const string& item, const string& value)
void Parser::produceItem(const std::string& category, const std::string& item, const std::string& value)
{
if (VERBOSE >= 4)
cerr << "producing _" << category << '.' << item << " -> " << value << endl;
std::cerr << "producing _" << category << '.' << item << " -> " << value << std::endl;
if (not iequals(category, mCat->name()))
error("inconsistent categories in loop_");
......@@ -688,9 +687,9 @@ void Parser::produceItem(const string& category, const string& item, const strin
struct DictParserDataImpl
{
// temporary values for constructing dictionaries
vector<ValidateCategory> mCategoryValidators;
map<string,vector<ValidateItem>> mItemValidators;
set<tuple<string,string>> mLinkedItems;
std::vector<ValidateCategory> mCategoryValidators;
std::map<std::string,std::vector<ValidateItem>> mItemValidators;
std::set<std::tuple<std::string,std::string>> mLinkedItems;
};
DictParser::DictParser(Validator& validator, std::istream& is)
......@@ -708,7 +707,7 @@ void DictParser::parseSaveFrame()
if (not mCollectedItemTypes)
mCollectedItemTypes = collectItemTypes();
string saveFrameName = mTokenValue;
std::string saveFrameName = mTokenValue;
if (saveFrameName.empty())
error("Invalid save frame, should contain more than just 'save_' here");
......@@ -727,14 +726,14 @@ void DictParser::parseSaveFrame()
match(eCIFTokenLOOP);
vector<string> tags;
std::vector<std::string> tags;
while (mLookahead == eCIFTokenTag)
{
string catName, itemName;
std::string catName, itemName;
std::tie(catName, itemName) = splitTagName(mTokenValue);
if (cat == dict.end())
std::tie(cat, ignore) = dict.emplace(catName);
std::tie(cat, std::ignore) = dict.emplace(catName);
else if (not iequals(cat->name(), catName))
error("inconsistent categories in loop_");
......@@ -758,11 +757,11 @@ void DictParser::parseSaveFrame()
}
else
{
string catName, itemName;
std::string catName, itemName;
std::tie(catName, itemName) = splitTagName(mTokenValue);
if (cat == dict.end() or not iequals(cat->name(), catName))
std::tie(cat, ignore) = dict.emplace(catName);
std::tie(cat, std::ignore) = dict.emplace(catName);
match(eCIFTokenTag);
......@@ -778,22 +777,22 @@ void DictParser::parseSaveFrame()
if (isCategorySaveFrame)
{
string category = dict.firstItem("_category.id");
std::string category = dict.firstItem("_category.id");
vector<string> keys;
std::vector<std::string> keys;
for (auto k: dict["category_key"])
keys.push_back(get<1>(splitTagName(k["name"].as<string>())));
keys.push_back(std::get<1>(splitTagName(k["name"].as<std::string>())));
iset groups;
for (auto g: dict["category_group"])
groups.insert(g["id"].as<string>());
groups.insert(g["id"].as<std::string>());
mImpl->mCategoryValidators.push_back(ValidateCategory{category, keys, groups});
}
else
{
// if the type code is missing, this must be a pointer, just skip it
string typeCode = dict.firstItem("_item_type.code");
std::string typeCode = dict.firstItem("_item_type.code");
const ValidateType* tv = nullptr;
if (not (typeCode.empty() or typeCode == "?"))
......@@ -801,9 +800,9 @@ void DictParser::parseSaveFrame()
iset ess;
for (auto e: dict["item_enumeration"])
ess.insert(e["value"].as<string>());
ess.insert(e["value"].as<std::string>());
string defaultValue = dict.firstItem("_item_default.value");
std::string defaultValue = dict.firstItem("_item_default.value");
bool defaultIsNull = false;
if (defaultValue.empty())
{
......@@ -817,11 +816,11 @@ void DictParser::parseSaveFrame()
// collect the dict from our dataBlock and construct validators
for (auto i: dict["item"])
{
string tagName, category, mandatory;
std::string tagName, category, mandatory;
cif::tie(tagName, category, mandatory) = i.get("name", "category_id", "mandatory_code");
string catName, itemName;
std::string catName, itemName;
std::tie(catName, itemName) = splitTagName(tagName);
if (catName.empty() or itemName.empty())
......@@ -844,12 +843,12 @@ void DictParser::parseSaveFrame()
{
if (VERBOSE > 2)
{
cerr << "inconsistent mandatory value for " << tagName << " in dictionary" << endl;
std::cerr << "inconsistent mandatory value for " << tagName << " in dictionary" << std::endl;
if (iequals(tagName, saveFrameName))
cerr << "choosing " << mandatory << endl;
std::cerr << "choosing " << mandatory << std::endl;
else
cerr << "choosing " << (vi->mMandatory ? "Y" : "N") << endl;
std::cerr << "choosing " << (vi->mMandatory ? "Y" : "N") << std::endl;
}
if (iequals(tagName, saveFrameName))
......@@ -859,7 +858,7 @@ void DictParser::parseSaveFrame()
if (vi->mType != nullptr and tv != nullptr and vi->mType != tv)
{
if (VERBOSE > 1)
cerr << "inconsistent type for " << tagName << " in dictionary" << endl;
std::cerr << "inconsistent type for " << tagName << " in dictionary" << std::endl;
}
// vi->mMandatory = (iequals(mandatory, "yes"));
......@@ -876,7 +875,7 @@ void DictParser::parseSaveFrame()
// collect the dict from our dataBlock and construct validators
for (auto i: dict["item_linked"])
{
string childTagName, parentTagName;
std::string childTagName, parentTagName;
cif::tie(childTagName, parentTagName) = i.get("child_name", "parent_name");
......@@ -892,12 +891,12 @@ void DictParser::linkItems()
auto& dict = *mDataBlock;
map<tuple<string,string,int>,size_t> linkIndex;
vector<tuple<vector<string>,vector<string>>> linkKeys;
std::map<std::tuple<std::string,std::string,int>,size_t> linkIndex;
std::vector<std::tuple<std::vector<std::string>,std::vector<std::string>>> linkKeys;
for (auto gl: dict["pdbx_item_linked_group_list"])
{
string child, parent;
std::string child, parent;
int link_group_id;
cif::tie(child, parent, link_group_id) = gl.get("child_name", "parent_name", "link_group_id");
......@@ -918,13 +917,13 @@ void DictParser::linkItems()
size_t ix = linkIndex.at(key);
get<0>(linkKeys.at(ix)).push_back(piv->mTag);
get<1>(linkKeys.at(ix)).push_back(civ->mTag);
std::get<0>(linkKeys.at(ix)).push_back(piv->mTag);
std::get<1>(linkKeys.at(ix)).push_back(civ->mTag);
}
// for (auto li: mImpl->mLinkedItems)
// {
// string child, parent;
// std::string child, parent;
// std::tie(child, parent) = li;
//
// auto civ = mValidator.getValidatorForItem(child);
......@@ -961,11 +960,11 @@ void DictParser::linkItems()
// look up the label
for (auto r: linkedGroup.find(cif::Key("category_id") == link.mChildCategory and cif::Key("link_group_id") == link.mLinkGroupID))
{
link.mLinkGroupLabel = r["label"].as<string>();
link.mLinkGroupLabel = r["label"].as<std::string>();
break;
}
mValidator.addLinkValidator(move(link));
mValidator.addLinkValidator(std::move(link));
}
// now make sure the itemType is specified for all itemValidators
......@@ -975,14 +974,14 @@ void DictParser::linkItems()
for (auto& iv: cv.mItemValidators)
{
if (iv.mType == nullptr)
cerr << "Missing item_type for " << iv.mTag << endl;
std::cerr << "Missing item_type for " << iv.mTag << std::endl;
}
}
}
void DictParser::loadDictionary()
{
unique_ptr<Datablock> dict;
std::unique_ptr<Datablock> dict;
Datablock* savedDatablock = mDataBlock;
try
......@@ -1007,15 +1006,15 @@ void DictParser::loadDictionary()
}
}
}
catch (const exception& ex)
catch (const std::exception& ex)
{
cerr << "Error parsing dictionary" << endl;
std::cerr << "Error parsing dictionary" << std::endl;
throw;
}
// store all validators
for (auto& ic: mImpl->mCategoryValidators)
mValidator.addCategoryValidator(move(ic));
mValidator.addCategoryValidator(std::move(ic));
mImpl->mCategoryValidators.clear();
for (auto& iv: mImpl->mItemValidators)
......@@ -1025,7 +1024,7 @@ void DictParser::loadDictionary()
error("Undefined category '" + iv.first);
for (auto& v: iv.second)
const_cast<ValidateCategory*>(cv)->addItemValidator(move(v));
const_cast<ValidateCategory*>(cv)->addItemValidator(std::move(v));
}
// check all item validators for having a typeValidator
......@@ -1040,8 +1039,8 @@ void DictParser::loadDictionary()
if (n)
{
auto r = info->front();
mValidator.dictName(r["title"].as<string>());
mValidator.dictVersion(r["version"].as<string>());
mValidator.dictName(r["title"].as<std::string>());
mValidator.dictVersion(r["version"].as<std::string>());
}
mDataBlock = savedDatablock;
......@@ -1060,7 +1059,7 @@ bool DictParser::collectItemTypes()
for (auto& t: dict["item_type_list"])
{
string code, primitiveCode, construct;
std::string code, primitiveCode, construct;
cif::tie(code, primitiveCode, construct) = t.get("code", "primitive_code", "construct");
ba::replace_all(construct, "\\n", "\n");
......@@ -1073,9 +1072,9 @@ bool DictParser::collectItemTypes()
code, mapToPrimitiveType(primitiveCode), std::regex(construct, std::regex::extended | std::regex::optimize)
};
mValidator.addTypeValidator(move(v));
mValidator.addTypeValidator(std::move(v));
}
catch (const exception& ex)
catch (const std::exception& ex)
{
throw_with_nested(CifParserError(t.lineNr(), "error in regular expression"));
}
......@@ -1086,7 +1085,7 @@ bool DictParser::collectItemTypes()
// mFileImpl.mTypeValidators.erase(v);
if (VERBOSE >= 5)
cerr << "Added type " << code << " (" << primitiveCode << ") => " << construct << endl;
std::cerr << "Added type " << code << " (" << primitiveCode << ") => " << construct << std::endl;
result = true;
}
......
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)
throw runtime_error("tag does not contain dot");
return tuple<string,string>{
if (s == std::string::npos)
throw std::runtime_error("tag does not contain dot");
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;
vector<size_t> offsets = { 0 };
std::vector<std::string> result;
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;
cout.flush();
std::cout << '\r' << msg;
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))
......
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;
}
}
src/Compound.cpp
......@@ -32,21 +32,15 @@
#include <boost/algorithm/string.hpp>
#if __has_include(<filesystem>)
#include <filesystem>
namespace fs = std::filesystem;
#elif __has_include(<boost/filesystem.hpp>)
#include <boost/filesystem.hpp>
namespace fs = boost::filesystem;
#endif
#include "cif++/Cif++.hpp"
#include "cif++/Point.hpp"
#include "cif++/Compound.hpp"
#include "cif++/CifUtils.hpp"
using namespace std;
namespace ba = boost::algorithm;
namespace fs = std::filesystem;
namespace mmcif
{
......@@ -83,12 +77,12 @@ struct CompoundBondLess
struct IsomerSet
{
vector<string> compounds;
std::vector<std::string> compounds;
};
struct IsomerSets
{
vector<IsomerSet> isomers;
std::vector<IsomerSet> isomers;
};
class IsomerDB
......@@ -97,8 +91,8 @@ class IsomerDB
static IsomerDB& instance();
size_t count(const string& compound) const;
const vector<string>& operator[](const string& compound) const;
size_t count(const std::string& compound) const;
const std::vector<std::string>& operator[](const std::string& compound) const;
private:
......@@ -111,14 +105,14 @@ IsomerDB::IsomerDB()
{
auto isomers = cif::rsrc_loader::load("isomers.txt");
if (not isomers)
throw runtime_error("Missing isomers.txt resource");
throw std::runtime_error("Missing isomers.txt resource");
struct membuf : public streambuf
struct membuf : public std::streambuf
{
membuf(char* data, size_t length) { this->setg(data, data, data + length); }
} buffer(const_cast<char*>(isomers.data()), isomers.size());
istream is(&buffer);
std::istream is(&buffer);
// #else
// cerr << "resource support was not compiled in, falling back to a local file" << endl;
// fs::path isomersFile = "isomers.txt";
......@@ -127,12 +121,12 @@ IsomerDB::IsomerDB()
// fs::ifstream is(isomersFile);
// if (not is.is_open())
// throw runtime_error("Could not open the file isomers.txt");
// throw std::runtime_error("Could not open the file isomers.txt");
// #endif
string line;
std::string line;
while (getline(is, line))
while (std::getline(is, line))
{
IsomerSet compounds;
ba::split(compounds.compounds, line, ba::is_any_of(":"));
......@@ -148,7 +142,7 @@ IsomerDB& IsomerDB::instance()
return sInstance;
}
size_t IsomerDB::count(const string& compound) const
size_t IsomerDB::count(const std::string& compound) const
{
size_t n = 0;
for (auto& d: mData.isomers)
......@@ -159,7 +153,7 @@ size_t IsomerDB::count(const string& compound) const
return n;
}
const vector<string>& IsomerDB::operator[](const string& compound) const
const std::vector<std::string>& IsomerDB::operator[](const std::string& compound) const
{
for (auto& d: mData.isomers)
{
......@@ -167,7 +161,7 @@ const vector<string>& IsomerDB::operator[](const string& compound) const
return d.compounds;
}
throw runtime_error("No isomer set found containing " + compound);
throw std::runtime_error("No isomer set found containing " + compound);
}
// --------------------------------------------------------------------
......@@ -177,16 +171,16 @@ const vector<string>& IsomerDB::operator[](const string& compound) const
struct Node
{
string id;
std::string id;
AtomType symbol;
vector<tuple<size_t,BondType>> links;
std::vector<std::tuple<size_t,BondType>> links;
size_t hydrogens = 0;
};
// Check to see if the nodes a[iA] and b[iB] are the start of a similar sub structure
bool SubStructuresAreIsomeric(
const vector<Node>& a, const vector<Node>& b, size_t iA, size_t iB,
vector<bool> visitedA, vector<bool> visitedB, vector<tuple<string,string>>& outMapping)
const std::vector<Node>& a, const std::vector<Node>& b, size_t iA, size_t iB,
std::vector<bool> visitedA, std::vector<bool> visitedB, std::vector<std::tuple<std::string,std::string>>& outMapping)
{
auto& na = a[iA];
auto& nb = b[iB];
......@@ -204,21 +198,21 @@ bool SubStructuresAreIsomeric(
// we now have two sets of links to compare.
// Compare each permutation of the second set of indices with the first
vector<size_t> ilb(N);
std::vector<size_t> ilb(N);
iota(ilb.begin(), ilb.end(), 0);
for (;;)
{
result = true;
vector<tuple<string,string>> m;
std::vector<std::tuple<std::string,std::string>> m;
for (size_t i = 0; result and i < N; ++i)
{
size_t lA, lB;
BondType typeA, typeB;
tie(lA, typeA) = na.links[i]; assert(lA < a.size());
tie(lB, typeB) = nb.links[ilb[i]]; assert(lB < b.size());
std::tie(lA, typeA) = na.links[i]; assert(lA < a.size());
std::tie(lB, typeB) = nb.links[ilb[i]]; assert(lB < b.size());
if (typeA != typeB or visitedA[lA] != visitedB[lB])
{
......@@ -255,15 +249,15 @@ bool SubStructuresAreIsomeric(
return result;
}
bool StructuresAreIsomeric(vector<CompoundAtom> atomsA, const vector<CompoundBond>& bondsA,
vector<CompoundAtom> atomsB, const vector<CompoundBond>& bondsB,
vector<tuple<string,string>>& outMapping)
bool StructuresAreIsomeric(std::vector<CompoundAtom> atomsA, const std::vector<CompoundBond>& bondsA,
std::vector<CompoundAtom> atomsB, const std::vector<CompoundBond>& bondsB,
std::vector<std::tuple<std::string,std::string>>& outMapping)
{
assert(atomsA.size() == atomsB.size());
assert(bondsA.size() == bondsB.size());
vector<Node> a, b;
map<string,size_t> ma, mb;
std::vector<Node> a, b;
std::map<std::string,size_t> ma, mb;
for (auto& atomA: atomsA)
{
......@@ -320,7 +314,7 @@ bool StructuresAreIsomeric(vector<CompoundAtom> atomsA, const vector<CompoundBon
if (b[ib].symbol != a[ia].symbol or a[ia].hydrogens != b[ib].hydrogens or a[ia].links.size() != b[ib].links.size())
continue;
vector<bool> va(N, false), vb(N, false);
std::vector<bool> va(N, false), vb(N, false);
if (SubStructuresAreIsomeric(a, b, ia, ib, va, vb, outMapping))
{
......@@ -350,7 +344,7 @@ Compound::Compound(const std::string& file, const std::string& id,
for (auto row: compoundAtoms)
{
string id, symbol, energy;
std::string id, symbol, energy;
float charge;
cif::tie(id, symbol, energy, charge) = row.get("atom_id", "type_symbol", "type_energy", "partial_charge");
......@@ -366,7 +360,7 @@ Compound::Compound(const std::string& file, const std::string& id,
for (auto row: compBonds)
{
CompoundBond b;
string type, aromatic;
std::string type, aromatic;
cif::tie(b.atomID[0], b.atomID[1], type, b.distance, b.esd) =
row.get("atom_id_1", "atom_id_2", "type", "value_dist", "value_dist_esd");
......@@ -381,7 +375,7 @@ Compound::Compound(const std::string& file, const std::string& id,
else
{
if (cif::VERBOSE)
cerr << "Unimplemented chem_comp_bond.type " << type << " in " << id << endl;
std::cerr << "Unimplemented chem_comp_bond.type " << type << " in " << id << std::endl;
b.type = singleBond;
}
......@@ -415,7 +409,7 @@ Compound::Compound(const std::string& file, const std::string& id,
for (auto row: db["chem_comp_chir"])
{
CompoundChiralCentre cc;
string volumeSign;
std::string volumeSign;
cif::tie(cc.id, cc.atomIDCentre, cc.atomID[0],
cc.atomID[1], cc.atomID[2], volumeSign) =
......@@ -431,7 +425,7 @@ Compound::Compound(const std::string& file, const std::string& id,
else
{
if (cif::VERBOSE)
cerr << "Unimplemented chem_comp_chir.volume_sign " << volumeSign << " in " << id << endl;
std::cerr << "Unimplemented chem_comp_chir.volume_sign " << volumeSign << " in " << id << std::endl;
continue;
}
......@@ -442,7 +436,7 @@ Compound::Compound(const std::string& file, const std::string& id,
for (auto row: compPlanes)
{
string atom_id, plane_id;
std::string atom_id, plane_id;
float esd;
cif::tie(atom_id, plane_id, esd) = row.get("atom_id", "plane_id", "dist_esd");
......@@ -454,18 +448,18 @@ Compound::Compound(const std::string& file, const std::string& id,
i->atomID.push_back(atom_id);
}
}
catch (const exception& ex)
catch (const std::exception& ex)
{
cerr << "Error loading ccp4 file for " << id << " from file " << file << endl;
std::cerr << "Error loading ccp4 file for " << id << " from file " << file << std::endl;
throw;
}
}
string Compound::formula() const
std::string Compound::formula() const
{
string result;
std::string result;
map<string,uint32_t> atoms;
std::map<std::string,uint32_t> atoms;
float chargeSum = 0;
for (auto r: mAtoms)
......@@ -480,7 +474,7 @@ string Compound::formula() const
result = "C";
if (c->second > 1)
result += to_string(c->second);
result += std::to_string(c->second);
atoms.erase(c);
......@@ -489,7 +483,7 @@ string Compound::formula() const
{
result += " H";
if (h->second > 1)
result += to_string(h->second);
result += std::to_string(h->second);
atoms.erase(h);
}
......@@ -502,12 +496,12 @@ string Compound::formula() const
result += a.first;
if (a.second > 1)
result += to_string(a.second);
result += std::to_string(a.second);
}
int charge = lrint(chargeSum);
if (charge != 0)
result += ' ' + to_string(charge);
result += ' ' + std::to_string(charge);
return result;
}
......@@ -532,9 +526,9 @@ int Compound::charge() const
return lrint(result);
}
string Compound::type() const
std::string Compound::type() const
{
string result;
std::string result;
// known groups are (counted from ccp4 monomer dictionary)
......@@ -579,7 +573,7 @@ bool Compound::isSugar() const
return cif::iequals(mGroup, "furanose") or cif::iequals(mGroup, "pyranose");
}
CompoundAtom Compound::getAtomByID(const string& atomID) const
CompoundAtom Compound::getAtomByID(const std::string& atomID) const
{
CompoundAtom result = {};
for (auto& a: mAtoms)
......@@ -592,12 +586,12 @@ CompoundAtom Compound::getAtomByID(const string& atomID) const
}
if (result.id != atomID)
throw out_of_range("No atom " + atomID + " in Compound " + mID);
throw std::out_of_range("No atom " + atomID + " in Compound " + mID);
return result;
}
const Compound* Compound::create(const string& id)
const Compound* Compound::create(const std::string& id)
{
auto result = CompoundFactory::instance().get(id);
if (result == nullptr)
......@@ -605,7 +599,7 @@ const Compound* Compound::create(const string& id)
return result;
}
bool Compound::atomsBonded(const string& atomId_1, const string& atomId_2) const
bool Compound::atomsBonded(const std::string& atomId_1, const std::string& atomId_2) const
{
auto i = find_if(mBonds.begin(), mBonds.end(),
[&](const CompoundBond& b)
......@@ -617,7 +611,7 @@ bool Compound::atomsBonded(const string& atomId_1, const string& atomId_2) const
return i != mBonds.end();
}
float Compound::atomBondValue(const string& atomId_1, const string& atomId_2) const
float Compound::atomBondValue(const std::string& atomId_1, const std::string& atomId_2) const
{
auto i = find_if(mBonds.begin(), mBonds.end(),
[&](const CompoundBond& b)
......@@ -652,7 +646,7 @@ bool Compound::isIsomerOf(const Compound& c) const
break;
// same number of atoms of each type?
map<AtomType,int> aTypeCount, bTypeCount;
std::map<AtomType,int> aTypeCount, bTypeCount;
bool sameAtomNames = true;
for (size_t i = 0; i < mAtoms.size(); ++i)
......@@ -687,13 +681,13 @@ bool Compound::isIsomerOf(const Compound& c) const
// implement rest of tests
vector<tuple<string,string>> mapping;
std::vector<std::tuple<std::string,std::string>> mapping;
result = StructuresAreIsomeric(mAtoms, mBonds, c.mAtoms, c.mBonds, mapping);
if (cif::VERBOSE and result)
{
for (auto& m: mapping)
cerr << " " << get<0>(m) << " => " << get<1>(m) << endl;
std::cerr << " " << std::get<0>(m) << " => " << std::get<1>(m) << std::endl;
}
break;
......@@ -702,20 +696,20 @@ bool Compound::isIsomerOf(const Compound& c) const
return result;
}
vector<tuple<string,string>> Compound::mapToIsomer(const Compound& c) const
std::vector<std::tuple<std::string,std::string>> Compound::mapToIsomer(const Compound& c) const
{
vector<tuple<string,string>> result;
std::vector<std::tuple<std::string,std::string>> result;
bool check = StructuresAreIsomeric(mAtoms, mBonds, c.mAtoms, c.mBonds, result);
if (not check)
throw runtime_error("Compounds " + id() + " and " + c.id() + " are not isomers in call to mapToIsomer");
throw std::runtime_error("Compounds " + id() + " and " + c.id() + " are not isomers in call to mapToIsomer");
return result;
}
vector<string> Compound::isomers() const
std::vector<std::string> Compound::isomers() const
{
vector<string> result;
std::vector<std::string> result;
auto& db = IsomerDB::instance();
if (db.count(mID))
......@@ -731,7 +725,7 @@ vector<string> Compound::isomers() const
return result;
}
float Compound::bondAngle(const string& atomId_1, const string& atomId_2, const string& atomId_3) const
float Compound::bondAngle(const std::string& atomId_1, const std::string& atomId_2, const std::string& atomId_3) const
{
float result = nanf("1");
......@@ -759,7 +753,7 @@ float Compound::bondAngle(const string& atomId_1, const string& atomId_2, const
// return c;
//}
float Compound::chiralVolume(const string& centreID) const
float Compound::chiralVolume(const std::string& centreID) const
{
float result = 0;
......@@ -808,7 +802,7 @@ Link::Link(cif::Datablock& db)
for (auto row: linkBonds)
{
LinkBond b;
string type, aromatic;
std::string type, aromatic;
cif::tie(b.atom[0].compID, b.atom[0].atomID,
b.atom[1].compID, b.atom[1].atomID, type, b.distance, b.esd) =
......@@ -825,7 +819,7 @@ Link::Link(cif::Datablock& db)
else
{
if (cif::VERBOSE)
cerr << "Unimplemented chem_link_bond.type " << type << " in " << mID << endl;
std::cerr << "Unimplemented chem_link_bond.type " << type << " in " << mID << std::endl;
b.type = singleBond;
}
......@@ -867,7 +861,7 @@ Link::Link(cif::Datablock& db)
for (auto row: linkChir)
{
LinkChiralCentre cc;
string volumeSign;
std::string volumeSign;
cif::tie(cc.id, cc.atomCentre.compID, cc.atomCentre.atomID,
cc.atom[0].compID, cc.atom[0].atomID,
......@@ -887,7 +881,7 @@ Link::Link(cif::Datablock& db)
else
{
if (cif::VERBOSE)
cerr << "Unimplemented chem_link_chir.volume_sign " << volumeSign << " in " << mID << endl;
std::cerr << "Unimplemented chem_link_chir.volume_sign " << volumeSign << " in " << mID << std::endl;
continue;
}
......@@ -898,7 +892,7 @@ Link::Link(cif::Datablock& db)
for (auto row: linkPlanes)
{
int compID;
string atomID, planeID;
std::string atomID, planeID;
float esd;
cif::tie(planeID, compID, atomID, esd) = row.get("plane_id", "atom_comp_id", "atom_id", "dist_esd");
......@@ -906,7 +900,7 @@ Link::Link(cif::Datablock& db)
auto i = find_if(mPlanes.begin(), mPlanes.end(), [&](auto& p) { return p.id == planeID;});
if (i == mPlanes.end())
{
vector<LinkAtom> atoms{LinkAtom{ compID, atomID }};
std::vector<LinkAtom> atoms{LinkAtom{ compID, atomID }};
mPlanes.emplace_back(LinkPlane{ planeID, move(atoms), esd });
}
else
......@@ -921,7 +915,7 @@ const Link& Link::create(const std::string& id)
result = CompoundFactory::instance().createLink(id);
if (result == nullptr)
throw runtime_error("Link with id " + id + " not found");
throw std::runtime_error("Link with id " + id + " not found");
return *result;
}
......@@ -960,7 +954,7 @@ float Link::bondAngle(const LinkAtom& atom1, const LinkAtom& atom2, const LinkAt
return result;
}
float Link::chiralVolume(const string& centreID) const
float Link::chiralVolume(const std::string& centreID) const
{
float result = 0;
......@@ -1001,7 +995,7 @@ float Link::chiralVolume(const string& centreID) const
// --------------------------------------------------------------------
// a factory class to generate compounds
const map<string,char> kAAMap{
const std::map<std::string,char> kAAMap{
{ "ALA", 'A' },
{ "ARG", 'R' },
{ "ASN", 'N' },
......@@ -1026,7 +1020,7 @@ const map<string,char> kAAMap{
{ "ASX", 'B' }
};
const map<string,char> kBaseMap{
const std::map<std::string,char> kBaseMap{
{ "A", 'A' },
{ "C", 'C' },
{ "G", 'G' },
......@@ -1050,8 +1044,8 @@ class CompoundFactoryImpl
delete mNext;
}
Compound* get(string id);
Compound* create(string id);
Compound* get(std::string id);
Compound* create(std::string id);
const Link* getLink(std::string id);
const Link* createLink(std::string id);
......@@ -1064,18 +1058,18 @@ class CompoundFactoryImpl
return result;
}
string unalias(const string& resName) const
std::string unalias(const std::string& resName) const
{
string result = resName;
std::string result = resName;
auto& e = const_cast<cif::File&>(mFile)["comp_synonym_list"];
for (auto& synonym: e["chem_comp_synonyms"])
{
if (ba::iequals(synonym["comp_alternative_id"].as<string>(), resName) == false)
if (ba::iequals(synonym["comp_alternative_id"].as<std::string>(), resName) == false)
continue;
result = synonym["comp_id"].as<string>();
result = synonym["comp_id"].as<std::string>();
ba::trim(result);
break;
}
......@@ -1086,13 +1080,13 @@ class CompoundFactoryImpl
return result;
}
bool isKnownPeptide(const string& resName)
bool isKnownPeptide(const std::string& resName)
{
return mKnownPeptides.count(resName) or
(mNext != nullptr and mNext->isKnownPeptide(resName));
}
bool isKnownBase(const string& resName)
bool isKnownBase(const std::string& resName)
{
return mKnownBases.count(resName) or
(mNext != nullptr and mNext->isKnownBase(resName));
......@@ -1102,11 +1096,11 @@ class CompoundFactoryImpl
std::shared_timed_mutex mMutex;
std::string mPath;
vector<Compound*> mCompounds;
vector<const Link*> mLinks;
/*unordered_*/set<string> mKnownPeptides;
set<string> mKnownBases;
set<string> mMissing;
std::vector<Compound*> mCompounds;
std::vector<const Link*> mLinks;
/*unordered_*/std::set<std::string> mKnownPeptides;
std::set<std::string> mKnownBases;
std::set<std::string> mMissing;
cif::File mFile;
cif::Category& mChemComp;
CompoundFactoryImpl* mNext;
......@@ -1121,7 +1115,7 @@ CompoundFactoryImpl::CompoundFactoryImpl(const std::string& file, CompoundFactor
for (auto& chemComp: mChemComp)
{
string group, threeLetterCode;
std::string group, threeLetterCode;
cif::tie(group, threeLetterCode) = chemComp.get("group", "three_letter_code");
......@@ -1136,17 +1130,17 @@ CompoundFactoryImpl::CompoundFactoryImpl(const std::string& file, CompoundFactor
//{
// CompoundFactoryImpl();
//
// Compound* get(string id);
// Compound* create(string id);
// Compound* get(std::string id);
// Compound* create(std::string id);
//
// void pushDictionary(const boost::filesystem::path& dictFile);
//
// // cif::File cf acts as owner of datablock
// cif::Datablock& getDatablock(const string& name, cif::File& cf);
// cif::Datablock& getDatablock(const std::string& name, cif::File& cf);
//
// deque<cif::File> mDictionaries;
// fs::path mClibdMon;
// vector<Compound*> mCompounds;
// std::vector<Compound*> mCompounds;
// boost::shared_mutex mMutex;
//};
//
......@@ -1154,7 +1148,7 @@ CompoundFactoryImpl::CompoundFactoryImpl(const std::string& file, CompoundFactor
//{
// const char* clibdMon = getenv("CLIBD_MON");
// if (clibdMon == nullptr)
// throw runtime_error("Cannot locate peptide list, please source the CCP4 environment");
// throw std::runtime_error("Cannot locate peptide list, please source the CCP4 environment");
// mClibdMon = clibdMon;
//}
//
......@@ -1165,7 +1159,7 @@ CompoundFactoryImpl::CompoundFactoryImpl(const std::string& file, CompoundFactor
// mDictionaries.emplace_back(dictFile);
//}
//
//cif::Datablock& CompoundFactoryImpl::getDatablock(const string& name, cif::File& cf)
//cif::Datablock& CompoundFactoryImpl::getDatablock(const std::string& name, cif::File& cf)
//{
// cif::Datablock* result = nullptr;
//
......@@ -1195,7 +1189,7 @@ CompoundFactoryImpl::CompoundFactoryImpl(const std::string& file, CompoundFactor
// }
// catch (...)
// {
// throw_with_nested(runtime_error("Error while loading " + resFile));
// throw_with_nested(std::runtime_error("Error while loading " + resFile));
// }
//
// result = cf.get(name);
......@@ -1203,12 +1197,12 @@ CompoundFactoryImpl::CompoundFactoryImpl(const std::string& file, CompoundFactor
// }
//
// if (result == nullptr)
// throw runtime_error("Failed to load datablock " + name);
// throw std::runtime_error("Failed to load datablock " + name);
//
// return *result;
//}
Compound* CompoundFactoryImpl::get(string id)
Compound* CompoundFactoryImpl::get(std::string id)
{
std::shared_lock lock(mMutex);
......@@ -1246,7 +1240,7 @@ Compound* CompoundFactoryImpl::create(std::string id)
{
auto row = rs.front();
string name, group;
std::string name, group;
uint32_t numberAtomsAll, numberAtomsNh;
cif::tie(name, group, numberAtomsAll, numberAtomsNh) =
row.get("name", "group", "number_atoms_all", "number_atoms_nh");
......@@ -1285,7 +1279,7 @@ Compound* CompoundFactoryImpl::create(std::string id)
return result;
}
const Link* CompoundFactoryImpl::getLink(string id)
const Link* CompoundFactoryImpl::getLink(std::string id)
{
std::shared_lock lock(mMutex);
......@@ -1341,7 +1335,7 @@ CompoundFactory::CompoundFactory()
{
const char* clibdMon = getenv("CLIBD_MON");
if (clibdMon == nullptr)
throw runtime_error("Cannot locate peptide list, please source the CCP4 environment");
throw std::runtime_error("Cannot locate peptide list, please source the CCP4 environment");
fs::path db = fs::path(clibdMon) / "list" / "mon_lib_list.cif";
......@@ -1360,22 +1354,22 @@ CompoundFactory& CompoundFactory::instance()
return *sInstance;
}
void CompoundFactory::pushDictionary(const string& inDictFile)
void CompoundFactory::pushDictionary(const std::string& inDictFile)
{
if (not fs::exists(inDictFile))
throw runtime_error("file not found: " + inDictFile);
throw std::runtime_error("file not found: " + inDictFile);
// ifstream file(inDictFile);
// if (not file.is_open())
// throw runtime_error("Could not open peptide list " + inDictFile);
// throw std::runtime_error("Could not open peptide list " + inDictFile);
try
{
mImpl = new CompoundFactoryImpl(inDictFile, mImpl);
}
catch (const exception& ex)
catch (const std::exception& ex)
{
cerr << "Error loading dictionary " << inDictFile << endl;
std::cerr << "Error loading dictionary " << inDictFile << std::endl;
throw;
}
}
......@@ -1407,17 +1401,17 @@ const Link* CompoundFactory::createLink(std::string id)
return mImpl->createLink(id);
}
bool CompoundFactory::isKnownPeptide(const string& resName) const
bool CompoundFactory::isKnownPeptide(const std::string& resName) const
{
return mImpl->isKnownPeptide(resName);
}
bool CompoundFactory::isKnownBase(const string& resName) const
bool CompoundFactory::isKnownBase(const std::string& resName) const
{
return mImpl->isKnownBase(resName);
}
string CompoundFactory::unalias(const string& resName) const
std::string CompoundFactory::unalias(const std::string& resName) const
{
return mImpl->unalias(resName);
}
......
src/FixDMC.cpp deleted 100644 → 0
/*-
* 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
src/PDB2Cif.cpp
This source diff could not be displayed because it is too large. You can view the blob instead.
src/PDB2CifRemark3.cpp
......@@ -33,14 +33,12 @@
#include <boost/date_time/gregorian/gregorian.hpp>
#include <boost/algorithm/string.hpp>
#include <boost/format.hpp>
// #include <boost/numeric/ublas/matrix.hpp>
#include "cif++/AtomType.hpp"
#include "cif++/Compound.hpp"
#include "cif++/PDB2CifRemark3.hpp"
#include "cif++/CifUtils.hpp"
using namespace std;
namespace ba = boost::algorithm;
using cif::Datablock;
......@@ -53,12 +51,12 @@ using cif::iequals;
struct TemplateLine
{
const char* rx;
int nextStateOffset;
const char* category;
initializer_list<const char*> items;
const char* lsRestrType = nullptr;
bool createNew;
const char* rx;
int nextStateOffset;
const char* category;
std::initializer_list<const char*> items;
const char* lsRestrType = nullptr;
bool createNew;
};
// --------------------------------------------------------------------
......@@ -168,10 +166,10 @@ const TemplateLine kBusterTNT_Template[] = {
class BUSTER_TNT_Remark3Parser : public Remark3Parser
{
public:
BUSTER_TNT_Remark3Parser(const string& name, const string& expMethod, PDBRecord* r, cif::Datablock& db)
BUSTER_TNT_Remark3Parser(const std::string& name, const std::string& expMethod, PDBRecord* r, cif::Datablock& db)
: Remark3Parser(name, expMethod, r, db,
kBusterTNT_Template, sizeof(kBusterTNT_Template) / sizeof(TemplateLine),
regex(R"((BUSTER(?:-TNT)?)(?: (\d+(?:\..+)?))?)")) {}
std::regex(R"((BUSTER(?:-TNT)?)(?: (\d+(?:\..+)?))?)")) {}
};
const TemplateLine kCNS_Template[] = {
......@@ -261,9 +259,9 @@ const TemplateLine kCNS_Template[] = {
class CNS_Remark3Parser : public Remark3Parser
{
public:
CNS_Remark3Parser(const string& name, const string& expMethod, PDBRecord* r, cif::Datablock& db)
CNS_Remark3Parser(const std::string& name, const std::string& expMethod, PDBRecord* r, cif::Datablock& db)
: Remark3Parser(name, expMethod, r, db, kCNS_Template,
sizeof(kCNS_Template) / sizeof(TemplateLine), regex(R"((CN[SX])(?: (\d+(?:\.\d+)?))?)")) {}
sizeof(kCNS_Template) / sizeof(TemplateLine), std::regex(R"((CN[SX])(?: (\d+(?:\.\d+)?))?)")) {}
};
const TemplateLine kPHENIX_Template[] = {
......@@ -339,9 +337,9 @@ const TemplateLine kPHENIX_Template[] = {
class PHENIX_Remark3Parser : public Remark3Parser
{
public:
PHENIX_Remark3Parser(const string& name, const string& expMethod, PDBRecord* r, cif::Datablock& db)
PHENIX_Remark3Parser(const std::string& name, const std::string& expMethod, PDBRecord* r, cif::Datablock& db)
: Remark3Parser(name, expMethod, r, db, kPHENIX_Template, sizeof(kPHENIX_Template) / sizeof(TemplateLine),
regex(R"((PHENIX)(?: \(PHENIX\.REFINE:) (\d+(?:\.[^)]+)?)\)?)")) {}
std::regex(R"((PHENIX)(?: \(PHENIX\.REFINE:) (\d+(?:\.[^)]+)?)\)?)")) {}
virtual void fixup();
};
......@@ -423,9 +421,9 @@ const TemplateLine kNUCLSQ_Template[] = {
class NUCLSQ_Remark3Parser : public Remark3Parser
{
public:
NUCLSQ_Remark3Parser(const string& name, const string& expMethod, PDBRecord* r, cif::Datablock& db)
NUCLSQ_Remark3Parser(const std::string& name, const std::string& expMethod, PDBRecord* r, cif::Datablock& db)
: Remark3Parser(name, expMethod, r, db, kNUCLSQ_Template, sizeof(kNUCLSQ_Template) / sizeof(TemplateLine),
regex(R"((NUCLSQ)(?: (\d+(?:\.\d+)?))?)")) {}
std::regex(R"((NUCLSQ)(?: (\d+(?:\.\d+)?))?)")) {}
virtual void fixup()
{
......@@ -512,9 +510,9 @@ const TemplateLine kPROLSQ_Template[] = {
class PROLSQ_Remark3Parser : public Remark3Parser
{
public:
PROLSQ_Remark3Parser(const string& name, const string& expMethod, PDBRecord* r, cif::Datablock& db)
PROLSQ_Remark3Parser(const std::string& name, const std::string& expMethod, PDBRecord* r, cif::Datablock& db)
: Remark3Parser(name, expMethod, r, db, kPROLSQ_Template, sizeof(kPROLSQ_Template) / sizeof(TemplateLine),
regex(R"((PROLSQ)(?: (\d+(?:\.\d+)?))?)")) {}
std::regex(R"((PROLSQ)(?: (\d+(?:\.\d+)?))?)")) {}
virtual void fixup()
{
......@@ -597,12 +595,12 @@ const TemplateLine kREFMAC_Template[] = {
class REFMAC_Remark3Parser : public Remark3Parser
{
public:
REFMAC_Remark3Parser(const string& name, const string& expMethod, PDBRecord* r, cif::Datablock& db)
REFMAC_Remark3Parser(const std::string& name, const std::string& expMethod, PDBRecord* r, cif::Datablock& db)
: Remark3Parser(name, expMethod, r, db, kREFMAC_Template, sizeof(kREFMAC_Template) / sizeof(TemplateLine),
regex(".+")) {}
std::regex(".+")) {}
virtual string program() { return "REFMAC"; }
virtual string version() { return ""; }
virtual std::string program() { return "REFMAC"; }
virtual std::string version() { return ""; }
};
const TemplateLine kREFMAC5_Template[] = {
......@@ -749,9 +747,9 @@ const TemplateLine kREFMAC5_Template[] = {
class REFMAC5_Remark3Parser : public Remark3Parser
{
public:
REFMAC5_Remark3Parser(const string& name, const string& expMethod, PDBRecord* r, cif::Datablock& db)
REFMAC5_Remark3Parser(const std::string& name, const std::string& expMethod, PDBRecord* r, cif::Datablock& db)
: Remark3Parser(name, expMethod, r, db, kREFMAC5_Template, sizeof(kREFMAC5_Template) / sizeof(TemplateLine),
regex(R"((REFMAC)(?: (\d+(?:\..+)?))?)")) {}
std::regex(R"((REFMAC)(?: (\d+(?:\..+)?))?)")) {}
};
const TemplateLine kSHELXL_Template[] = {
......@@ -807,9 +805,9 @@ const TemplateLine kSHELXL_Template[] = {
class SHELXL_Remark3Parser : public Remark3Parser
{
public:
SHELXL_Remark3Parser(const string& name, const string& expMethod, PDBRecord* r, cif::Datablock& db)
SHELXL_Remark3Parser(const std::string& name, const std::string& expMethod, PDBRecord* r, cif::Datablock& db)
: Remark3Parser(name, expMethod, r, db, kSHELXL_Template, sizeof(kSHELXL_Template) / sizeof(TemplateLine),
regex(R"((SHELXL)(?:-(\d+(?:\..+)?)))")) {}
std::regex(R"((SHELXL)(?:-(\d+(?:\..+)?)))")) {}
};
const TemplateLine kTNT_Template[] = {
......@@ -862,9 +860,9 @@ const TemplateLine kTNT_Template[] = {
class TNT_Remark3Parser : public Remark3Parser
{
public:
TNT_Remark3Parser(const string& name, const string& expMethod, PDBRecord* r, cif::Datablock& db)
TNT_Remark3Parser(const std::string& name, const std::string& expMethod, PDBRecord* r, cif::Datablock& db)
: Remark3Parser(name, expMethod, r, db, kTNT_Template, sizeof(kTNT_Template) / sizeof(TemplateLine),
regex(R"((TNT)(?: V. (\d+.+)?)?)")) {}
std::regex(R"((TNT)(?: V. (\d+.+)?)?)")) {}
};
const TemplateLine kXPLOR_Template[] = {
......@@ -940,9 +938,9 @@ const TemplateLine kXPLOR_Template[] = {
class XPLOR_Remark3Parser : public Remark3Parser
{
public:
XPLOR_Remark3Parser(const string& name, const string& expMethod, PDBRecord* r, cif::Datablock& db)
XPLOR_Remark3Parser(const std::string& name, const std::string& expMethod, PDBRecord* r, cif::Datablock& db)
: Remark3Parser(name, expMethod, r, db, kXPLOR_Template, sizeof(kXPLOR_Template) / sizeof(TemplateLine),
regex(R"((X-PLOR)(?: (\d+(?:\.\d+)?))?)")) {}
std::regex(R"((X-PLOR)(?: (\d+(?:\.\d+)?))?)")) {}
};
// --------------------------------------------------------------------
......@@ -954,7 +952,7 @@ Remark3Parser::Remark3Parser(const std::string& name, const std::string& expMeth
{
}
string Remark3Parser::nextLine()
std::string Remark3Parser::nextLine()
{
mLine.clear();
......@@ -985,11 +983,11 @@ string Remark3Parser::nextLine()
if (valueIndent > 4)
{
string indent(valueIndent - 4, ' ');
std::string indent(valueIndent - 4, ' ');
while (mRec->is("REMARK 3") and mRec->mVlen > valueIndent)
{
string v(mRec->mValue + 4, mRec->mValue + mRec->mVlen);
std::string v(mRec->mValue + 4, mRec->mValue + mRec->mVlen);
if (not ba::starts_with(v, indent))
break;
......@@ -1024,21 +1022,21 @@ string Remark3Parser::nextLine()
}
if (cif::VERBOSE >= 2)
cerr << "RM3: " << mLine << endl;
std::cerr << "RM3: " << mLine << std::endl;
return mLine;
}
bool Remark3Parser::match(const char* expr, int nextState)
{
regex rx(expr);
std::regex rx(expr);
bool result = regex_match(mLine, mM, rx);
if (result)
mState = nextState;
else if (cif::VERBOSE >= 3)
cerr << cif::coloured("No match:", cif::scWHITE, cif::scRED) << " '" << expr << '\'' << endl;
std::cerr << cif::coloured("No match:", cif::scWHITE, cif::scRED) << " '" << expr << '\'' << std::endl;
return result;
}
......@@ -1046,7 +1044,7 @@ bool Remark3Parser::match(const char* expr, int nextState)
float Remark3Parser::parse()
{
int lineCount = 0, dropped = 0;
string remarks;
std::string remarks;
mState = 0;
while (mRec != nullptr)
......@@ -1098,7 +1096,7 @@ float Remark3Parser::parse()
}
if (cif::VERBOSE >= 2)
cerr << cif::coloured("Dropping line:", cif::scWHITE, cif::scRED) << " '" << mLine << '\'' << endl;
std::cerr << cif::coloured("Dropping line:", cif::scWHITE, cif::scRED) << " '" << mLine << '\'' << std::endl;
++dropped;
}
......@@ -1114,43 +1112,43 @@ float Remark3Parser::parse()
return score;
}
string Remark3Parser::program()
std::string Remark3Parser::program()
{
string result = mName;
std::string result = mName;
smatch m;
std::smatch m;
if (regex_match(mName, m, mProgramVersion))
result = m[1].str();
return result;
}
string Remark3Parser::version()
std::string Remark3Parser::version()
{
string result;
std::string result;
smatch m;
std::smatch m;
if (regex_match(mName, m, mProgramVersion))
result = m[2].str();
return result;
}
void Remark3Parser::storeCapture(const char* category, initializer_list<const char*> items, bool createNew)
void Remark3Parser::storeCapture(const char* category, std::initializer_list<const char*> items, bool createNew)
{
int capture = 0;
for (auto item: items)
{
++capture;
string value = mM[capture].str();
std::string value = mM[capture].str();
ba::trim(value);
if (iequals(value, "NULL") or iequals(value, "NONE") or iequals(value, "Inf") or iequals(value, "+Inf") or iequals(value, string(value.length(), '*')))
if (iequals(value, "NULL") or iequals(value, "NONE") or iequals(value, "Inf") or iequals(value, "+Inf") or iequals(value, std::string(value.length(), '*')))
continue;
if (cif::VERBOSE >= 3)
cerr << "storing: '" << value << "' in _" << category << '.' << item << endl;
std::cerr << "storing: '" << value << "' in _" << category << '.' << item << std::endl;
auto& cat = mDb[category];
if (cat.empty() or createNew)
......@@ -1170,7 +1168,7 @@ void Remark3Parser::storeCapture(const char* category, initializer_list<const ch
});
else if (iequals(category, "refine_hist"))
{
string dResHigh, dResLow;
std::string dResHigh, dResLow;
for (auto r: mDb["refine"])
{
cif::tie(dResHigh, dResLow) = r.get("ls_d_res_high", "ls_d_res_low");
......@@ -1192,9 +1190,9 @@ void Remark3Parser::storeCapture(const char* category, initializer_list<const ch
}
else if (iequals(category, "pdbx_refine_tls_group"))
{
string tlsGroupID;
std::string tlsGroupID;
if (not mDb["pdbx_refine_tls"].empty())
tlsGroupID = mDb["pdbx_refine_tls"].back()["id"].as<string>();
tlsGroupID = mDb["pdbx_refine_tls"].back()["id"].as<std::string>();
cat.emplace({
{ "pdbx_refine_id", mExpMethod },
......@@ -1241,7 +1239,7 @@ void Remark3Parser::storeCapture(const char* category, initializer_list<const ch
}
}
void Remark3Parser::storeRefineLsRestr(const char* type, initializer_list<const char*> items)
void Remark3Parser::storeRefineLsRestr(const char* type, std::initializer_list<const char*> items)
{
Row r;
int capture = 0;
......@@ -1250,9 +1248,9 @@ void Remark3Parser::storeRefineLsRestr(const char* type, initializer_list<const
{
++capture;
string value = mM[capture].str();
std::string value = mM[capture].str();
ba::trim(value);
if (value.empty() or iequals(value, "NULL") or iequals(value, "Inf") or iequals(value, "+Inf") or iequals(value, string(value.length(), '*')))
if (value.empty() or iequals(value, "NULL") or iequals(value, "Inf") or iequals(value, "+Inf") or iequals(value, std::string(value.length(), '*')))
continue;
if (not r)
......@@ -1267,7 +1265,7 @@ void Remark3Parser::storeRefineLsRestr(const char* type, initializer_list<const
}
}
void Remark3Parser::updateRefineLsRestr(const char* type, initializer_list<const char*> items)
void Remark3Parser::updateRefineLsRestr(const char* type, std::initializer_list<const char*> items)
{
auto rows = mDb["refine_ls_restr"].find(cif::Key("type") == type and cif::Key("pdbx_refine_id") == mExpMethod);
if (rows.empty())
......@@ -1281,9 +1279,9 @@ void Remark3Parser::updateRefineLsRestr(const char* type, initializer_list<const
{
++capture;
string value = mM[capture].str();
std::string value = mM[capture].str();
ba::trim(value);
if (iequals(value, "NULL") or iequals(value, string(value.length(), '*')))
if (iequals(value, "NULL") or iequals(value, std::string(value.length(), '*')))
value.clear();
r[item] = value;
......@@ -1296,12 +1294,12 @@ void Remark3Parser::updateRefineLsRestr(const char* type, initializer_list<const
// --------------------------------------------------------------------
bool Remark3Parser::parse(const string& expMethod, PDBRecord* r, cif::Datablock& db)
bool Remark3Parser::parse(const std::string& expMethod, PDBRecord* r, cif::Datablock& db)
{
// simple version, only for the first few lines
auto getNextLine = [&]()
{
string result;
std::string result;
while (result.empty() and r != nullptr and r->is("REMARK 3"))
{
......@@ -1314,24 +1312,24 @@ bool Remark3Parser::parse(const string& expMethod, PDBRecord* r, cif::Datablock&
// All remark 3 records should start with the same data.
string line = getNextLine();
std::string line = getNextLine();
if (line != "REFINEMENT.")
{
if (cif::VERBOSE)
cerr << "Unexpected data in REMARK 3" << endl;
std::cerr << "Unexpected data in REMARK 3" << std::endl;
return false;
}
line = getNextLine();
regex rxp(R"(^PROGRAM\s*:\s*(.+))");
smatch m;
std::regex rxp(R"(^PROGRAM\s*:\s*(.+))");
std::smatch m;
if (not regex_match(line, m, rxp))
if (not std::regex_match(line, m, rxp))
{
if (cif::VERBOSE)
cerr << "Expected valid PROGRAM line in REMARK 3" << endl;
std::cerr << "Expected valid PROGRAM line in REMARK 3" << std::endl;
return false;
}
......@@ -1339,11 +1337,11 @@ bool Remark3Parser::parse(const string& expMethod, PDBRecord* r, cif::Datablock&
struct programScore
{
programScore(const string& program, Remark3Parser* parser, float score)
programScore(const std::string& program, Remark3Parser* parser, float score)
: program(program), parser(parser), score(score) {}
string program;
unique_ptr<Remark3Parser> parser;
std::string program;
std::unique_ptr<Remark3Parser> parser;
float score;
bool operator<(const programScore& rhs) const
......@@ -1352,11 +1350,11 @@ bool Remark3Parser::parse(const string& expMethod, PDBRecord* r, cif::Datablock&
}
};
vector<programScore> scores;
std::vector<programScore> scores;
auto tryParser = [&](Remark3Parser* p)
{
unique_ptr<Remark3Parser> parser(p);
std::unique_ptr<Remark3Parser> parser(p);
float score;
try
......@@ -1365,18 +1363,18 @@ bool Remark3Parser::parse(const string& expMethod, PDBRecord* r, cif::Datablock&
}
catch(const std::exception& e)
{
std::cerr << "Error parsing REMARK 3 with " << parser->program() << endl
std::cerr << "Error parsing REMARK 3 with " << parser->program() << std::endl
<< e.what() << '\n';
score = 0;
}
if (cif::VERBOSE >= 2)
cerr << "Score for " << parser->program() << ": " << score << endl;
std::cerr << "Score for " << parser->program() << ": " << score << std::endl;
if (score > 0)
{
string program = parser->program();
string version = parser->version();
std::string program = parser->program();
std::string version = parser->version();
scores.emplace_back(program, parser.release(), score);
}
......@@ -1385,7 +1383,7 @@ bool Remark3Parser::parse(const string& expMethod, PDBRecord* r, cif::Datablock&
for (auto p = make_split_iterator(line, ba::first_finder(", "));
not p.eof(); ++p)
{
string program(p->begin(), p->end());
std::string program(p->begin(), p->end());
if (ba::starts_with(program, "BUSTER"))
tryParser(new BUSTER_TNT_Remark3Parser(program, expMethod, r, db));
......@@ -1410,7 +1408,7 @@ bool Remark3Parser::parse(const string& expMethod, PDBRecord* r, cif::Datablock&
else if (ba::starts_with(program, "X-PLOR"))
tryParser(new XPLOR_Remark3Parser(program, expMethod, r, db));
else if (cif::VERBOSE)
cerr << "Skipping unknown program (" << program << ") in REMARK 3" << endl;
std::cerr << "Skipping unknown program (" << program << ") in REMARK 3" << std::endl;
}
sort(scores.begin(), scores.end());
......@@ -1418,7 +1416,7 @@ bool Remark3Parser::parse(const string& expMethod, PDBRecord* r, cif::Datablock&
bool guessProgram = scores.empty() or scores.front().score < 0.9f;;
if (guessProgram)
{
cerr << "Unknown or untrusted program in REMARK 3, trying all parsers to see if there is a match" << endl;
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 CNS_Remark3Parser("CNS", expMethod, r, db));
......@@ -1443,11 +1441,11 @@ bool Remark3Parser::parse(const string& expMethod, PDBRecord* r, cif::Datablock&
auto& best = scores.front();
if (cif::VERBOSE)
cerr << "Choosing " << best.parser->program() << " version '" << best.parser->version() << "' as refinement program. Score = " << best.score << endl;
std::cerr << "Choosing " << best.parser->program() << " version '" << best.parser->version() << "' as refinement program. Score = " << best.score << std::endl;
auto& software = db["software"];
string program = best.parser->program();
string version = best.parser->version();
std::string program = best.parser->program();
std::string version = best.parser->version();
software.emplace({
{ "name", program },
......
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;
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> P = - (a * a) / 12 - c;
std::complex<double> Q = - (a * a * a) / 108 + (a * c) / 3 - (b * b) / 8;
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[1] = (( W + 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[3] = ((-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 + std::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 + 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);
normal_distribution<> randomOffset(0, offset);
std::uniform_real_distribution<> randomAngle(0, 2 * kPI);
std::normal_distribution<> randomOffset(0, offset);
float theta = randomAngle(rng);
float phi1 = randomAngle(rng) - kPI;
......
src/Structure.cpp
......@@ -28,14 +28,7 @@
#include <numeric>
#include <fstream>
#if __has_include(<filesystem>)
#include <filesystem>
namespace fs = std::filesystem;
#elif __has_include(<boost/filesystem.hpp>)
#include <boost/filesystem.hpp>
namespace fs = boost::filesystem;
#endif
#include <boost/algorithm/string.hpp>
#include <boost/iostreams/filtering_stream.hpp>
......@@ -49,8 +42,7 @@ namespace fs = boost::filesystem;
#include "cif++/Cif2PDB.hpp"
// #include "cif++/AtomShape.hpp"
using namespace std;
namespace fs = std::filesystem;
namespace ba = boost::algorithm;
namespace io = boost::iostreams;
......@@ -75,12 +67,12 @@ void FileImpl::load(const std::string& p)
{
fs::path path(p);
std::ifstream inFile(path, ios_base::in | ios_base::binary);
std::ifstream inFile(path, std::ios_base::in | std::ios_base::binary);
if (not inFile.is_open())
throw runtime_error("No such file: " + path.string());
throw std::runtime_error("No such file: " + path.string());
io::filtering_stream<io::input> in;
string ext = path.extension().string();
std::string ext = path.extension().string();
if (path.extension() == ".bz2")
{
......@@ -107,14 +99,14 @@ void FileImpl::load(const std::string& p)
try
{
if (cif::VERBOSE)
cerr << "unrecognized file extension, trying cif" << endl;
std::cerr << "unrecognized file extension, trying cif" << std::endl;
mData.load(in);
}
catch (const cif::CifParserError& e)
{
if (cif::VERBOSE)
cerr << "Not cif, trying plain old PDB" << endl;
std::cerr << "Not cif, trying plain old PDB" << std::endl;
// pffft...
in.reset();
......@@ -122,7 +114,7 @@ void FileImpl::load(const std::string& p)
if (inFile.is_open())
inFile.seekg(0);
else
inFile.open(path, ios_base::in | ios::binary);
inFile.open(path, std::ios_base::in | std::ios::binary);
if (path.extension() == ".bz2")
in.push(io::bzip2_decompressor());
......@@ -135,9 +127,9 @@ void FileImpl::load(const std::string& p)
}
}
}
catch (const exception& ex)
catch (const std::exception& ex)
{
cerr << "Error trying to load file " << path << endl;
std::cerr << "Error trying to load file " << path << std::endl;
throw;
}
......@@ -148,14 +140,14 @@ void FileImpl::load(const std::string& p)
// if (mData.getValidator() == nullptr)
mData.loadDictionary("mmcif_pdbx");
if (not mData.isValid())
cerr << "Invalid mmCIF file" << (cif::VERBOSE ? "." : " use --verbose option to see errors") << endl;
std::cerr << "Invalid mmCIF file" << (cif::VERBOSE ? "." : " use --verbose option to see errors") << std::endl;
}
void FileImpl::save(const std::string& p)
{
fs::path path(p);
std::ofstream outFile(p, ios_base::out | ios_base::binary);
std::ofstream outFile(p, std::ios_base::out | std::ios_base::binary);
io::filtering_stream<io::output> out;
if (path.extension() == ".gz")
......@@ -194,7 +186,7 @@ struct AtomImpl
{
}
AtomImpl(const File& f, const string& id)
AtomImpl(const File& f, const std::string& id)
: mFile(f), mID(id), mRefcount(1), mCompound(nullptr)
{
auto& db = *mFile.impl().mDb;
......@@ -205,7 +197,7 @@ struct AtomImpl
prefetch();
}
AtomImpl(const File& f, const string& id, cif::Row row)
AtomImpl(const File& f, const std::string& id, cif::Row row)
: mFile(f), mID(id), mRefcount(1), mRow(row), mCompound(nullptr)
{
prefetch();
......@@ -227,7 +219,7 @@ struct AtomImpl
void prefetch()
{
// Prefetch some data
string symbol;
std::string symbol;
cif::tie(symbol, mAtomID, mCompID, mAsymID, mSeqID, mAltID) =
mRow.get("type_symbol", "label_atom_id", "label_comp_id", "label_asym_id", "label_seq_id", "label_alt_id");
......@@ -239,7 +231,7 @@ struct AtomImpl
mLocation = Point(x, y, z);
string compID;
std::string compID;
cif::tie(compID) = mRow.get("label_comp_id");
mCompound = Compound::create(compID);
......@@ -255,12 +247,12 @@ struct AtomImpl
// else
// result.set_occupancy(mRow["occupancy"].as<float>());
// string element = mRow["type_symbol"].as<string>();
// std::string element = mRow["type_symbol"].as<std::string>();
// if (not mRow["pdbx_formal_charge"].empty())
// {
// int charge = mRow["pdbx_formal_charge"].as<int>();
// if (abs(charge) > 1)
// element += to_string(charge);
// element += std::to_string(charge);
// if (charge < 0)
// element += '-';
// else
......@@ -273,7 +265,7 @@ struct AtomImpl
// else if (not mRow["B_iso_or_equiv"].empty())
// result.set_u_iso(mRow["B_iso_or_equiv"].as<float>() / (8 * kPI * kPI));
// else
// throw runtime_error("Missing B_iso or U_iso");
// throw std::runtime_error("Missing B_iso or U_iso");
// auto& db = *mFile.impl().mDb;
// auto& cat = db["atom_site_anisotrop"];
......@@ -324,7 +316,7 @@ struct AtomImpl
{
assert(not mSymmetryCopy);
if (mSymmetryCopy)
throw runtime_error("Moving symmetry copy");
throw std::runtime_error("Moving symmetry copy");
if (not mClone)
{
......@@ -346,17 +338,17 @@ struct AtomImpl
{
if (mCompound == nullptr)
{
string compID;
std::string compID;
cif::tie(compID) = mRow.get("label_comp_id");
mCompound = Compound::create(compID);
if (cif::VERBOSE and mCompound == nullptr)
cerr << "Compound not found: '" << compID << '\'' << endl;
std::cerr << "Compound not found: '" << compID << '\'' << std::endl;
}
if (mCompound == nullptr)
throw runtime_error("no compound");
throw std::runtime_error("no compound");
return *mCompound;
}
......@@ -371,9 +363,9 @@ struct AtomImpl
return mRadius;
}
const string& property(const string& name) const
const std::string& property(const std::string& name) const
{
static string kEmptyString;
static std::string kEmptyString;
auto i = mCachedProperties.find(name);
if (i == mCachedProperties.end())
......@@ -382,7 +374,7 @@ struct AtomImpl
if (v.empty())
return kEmptyString;
return mCachedProperties[name] = v.as<string>();
return mCachedProperties[name] = v.as<std::string>();
}
else
return i->second;
......@@ -404,21 +396,21 @@ struct AtomImpl
}
const File& mFile;
string mID;
std::string mID;
AtomType mType;
string mAtomID;
string mCompID;
string mAsymID;
std::string mAtomID;
std::string mCompID;
std::string mAsymID;
int mSeqID;
string mAltID;
std::string mAltID;
Point mLocation;
int mRefcount;
cif::Row mRow;
mutable const Compound* mCompound;
float mRadius = nan("4");
mutable map<string,string> mCachedProperties;
mutable std::map<std::string,std::string> mCachedProperties;
bool mSymmetryCopy = false;
bool mClone = false;
......@@ -428,7 +420,7 @@ struct AtomImpl
// int32_t mRTix;
};
//Atom::Atom(const File& f, const string& id)
//Atom::Atom(const File& f, const std::string& id)
// : mImpl(new AtomImpl(f, id))
//{
//}
......@@ -491,25 +483,25 @@ Atom& Atom::operator=(const Atom& rhs)
}
template<>
string Atom::property<string>(const string& name) const
std::string Atom::property<std::string>(const std::string& name) const
{
return impl()->property(name);
}
template<>
int Atom::property<int>(const string& name) const
int Atom::property<int>(const std::string& name) const
{
auto v = impl()->property(name);
return v.empty() ? 0 : stoi(v);
}
template<>
float Atom::property<float>(const string& name) const
float Atom::property<float>(const std::string& name) const
{
return stof(impl()->property(name));
}
const string& Atom::id() const
const std::string& Atom::id() const
{
return impl()->mID;
}
......@@ -524,9 +516,9 @@ int Atom::charge() const
return property<int>("pdbx_formal_charge");
}
string Atom::energyType() const
std::string Atom::energyType() const
{
string result;
std::string result;
if (impl() and impl()->mCompound)
result = impl()->mCompound->getAtomByID(impl()->mAtomID).typeEnergy;
......@@ -538,12 +530,12 @@ float Atom::uIso() const
{
float result;
if (not property<string>("U_iso_or_equiv").empty())
if (not property<std::string>("U_iso_or_equiv").empty())
result = property<float>("U_iso_or_equiv");
else if (not property<string>("B_iso_or_equiv").empty())
else if (not property<std::string>("B_iso_or_equiv").empty())
result = property<float>("B_iso_or_equiv") / (8 * kPI * kPI);
else
throw runtime_error("Missing B_iso or U_iso");
throw std::runtime_error("Missing B_iso or U_iso");
return result;
}
......@@ -558,22 +550,22 @@ float Atom::occupancy() const
return property<float>("occupancy");
}
string Atom::labelAtomID() const
std::string Atom::labelAtomID() const
{
return impl()->mAtomID;
}
string Atom::labelCompID() const
std::string Atom::labelCompID() const
{
return impl()->mCompID;
}
string Atom::labelAsymID() const
std::string Atom::labelAsymID() const
{
return impl()->mAsymID;
}
string Atom::labelAltID() const
std::string Atom::labelAltID() const
{
return impl()->mAltID;
}
......@@ -588,48 +580,48 @@ int Atom::labelSeqID() const
return impl()->mSeqID;
}
string Atom::authAsymID() const
std::string Atom::authAsymID() const
{
return property<string>("auth_asym_id");
return property<std::string>("auth_asym_id");
}
string Atom::authAtomID() const
std::string Atom::authAtomID() const
{
return property<string>("auth_atom_id");
return property<std::string>("auth_atom_id");
}
string Atom::pdbxAuthAltID() const
std::string Atom::pdbxAuthAltID() const
{
return property<string>("pdbx_auth_alt_id");
return property<std::string>("pdbx_auth_alt_id");
}
string Atom::pdbxAuthInsCode() const
std::string Atom::pdbxAuthInsCode() const
{
return property<string>("pdbx_PDB_ins_code");
return property<std::string>("pdbx_PDB_ins_code");
}
string Atom::authCompID() const
std::string Atom::authCompID() const
{
return property<string>("auth_comp_id");
return property<std::string>("auth_comp_id");
}
string Atom::authSeqID() const
std::string Atom::authSeqID() const
{
return property<string>("auth_seq_id");
return property<std::string>("auth_seq_id");
}
string Atom::labelID() const
std::string Atom::labelID() const
{
return property<string>("label_comp_id") + '_' + impl()->mAsymID + '_' + to_string(impl()->mSeqID) + ':' + impl()->mAtomID;
return property<std::string>("label_comp_id") + '_' + impl()->mAsymID + '_' + std::to_string(impl()->mSeqID) + ':' + impl()->mAtomID;
}
string Atom::pdbID() const
std::string Atom::pdbID() const
{
return
property<string>("auth_comp_id") + '_' +
property<string>("auth_asym_id") + '_' +
property<string>("auth_seq_id") +
property<string>("pdbx_PDB_ins_code");
property<std::string>("auth_comp_id") + '_' +
property<std::string>("auth_asym_id") + '_' +
property<std::string>("auth_seq_id") +
property<std::string>("pdbx_PDB_ins_code");
}
Point Atom::location() const
......@@ -652,7 +644,7 @@ void Atom::location(Point p)
// return impl()->mSymmetryCopy;
// }
// string Atom::symmetry() const
// std::string Atom::symmetry() const
// {
// return clipper::Symop(impl()->mRTop).format() + "\n" + impl()->mRTop.format();
// }
......@@ -690,7 +682,7 @@ bool Atom::operator==(const Atom& rhs) const
// // verbose
// if (cif::VERBOSE > 1)
// cout << "Calculated radius for " << AtomTypeTraits(impl()->mType).name() << " with charge " << charge() << " is " << impl()->mRadius << endl;
// cout << "Calculated radius for " << AtomTypeTraits(impl()->mType).name() << " with charge " << charge() << " is " << impl()->mRadius << std::endl;
// }
float Atom::radius() const
......@@ -705,7 +697,7 @@ int Atom::compare(const Atom& b) const
void Atom::setID(int id)
{
impl()->mID = to_string(id);
impl()->mID = std::to_string(id);
}
std::ostream& operator<<(std::ostream& os, const Atom& atom)
......@@ -723,8 +715,8 @@ std::ostream& operator<<(std::ostream& os, const Atom& atom)
// --------------------------------------------------------------------
// residue
Residue::Residue(const Structure& structure, const string& compoundID,
const string& asymID, const string& authSeqID)
Residue::Residue(const Structure& structure, const std::string& compoundID,
const std::string& asymID, const std::string& authSeqID)
: mStructure(&structure), mCompoundID(compoundID)
, mAsymID(asymID), mAuthSeqID(authSeqID)
{
......@@ -745,8 +737,8 @@ Residue::Residue(const Structure& structure, const string& compoundID,
assert(not mAtoms.empty());
}
Residue::Residue(const Structure& structure, const string& compoundID,
const string& asymID, int seqID)
Residue::Residue(const Structure& structure, const std::string& compoundID,
const std::string& asymID, int seqID)
: mStructure(&structure), mCompoundID(compoundID)
, mAsymID(asymID), mSeqID(seqID)
{
......@@ -766,43 +758,43 @@ Residue::Residue(const Structure& structure, const string& compoundID,
}
Residue::Residue(Residue&& rhs)
: mStructure(rhs.mStructure), mCompoundID(move(rhs.mCompoundID)), mAsymID(move(rhs.mAsymID))
, mSeqID(rhs.mSeqID), mAuthSeqID(rhs.mAuthSeqID), mAtoms(move(rhs.mAtoms))
: mStructure(rhs.mStructure), mCompoundID(std::move(rhs.mCompoundID)), mAsymID(std::move(rhs.mAsymID))
, mSeqID(rhs.mSeqID), mAuthSeqID(rhs.mAuthSeqID), mAtoms(std::move(rhs.mAtoms))
{
//cerr << "move constructor residue" << endl;
//std::cerr << "move constructor residue" << std::endl;
rhs.mStructure = nullptr;
}
Residue& Residue::operator=(Residue&& rhs)
{
//cerr << "move assignment residue" << endl;
//std::cerr << "move assignment residue" << std::endl;
mStructure = rhs.mStructure; rhs.mStructure = nullptr;
mCompoundID = move(rhs.mCompoundID);
mAsymID = move(rhs.mAsymID);
mCompoundID = std::move(rhs.mCompoundID);
mAsymID = std::move(rhs.mAsymID);
mSeqID = rhs.mSeqID;
mAuthSeqID = rhs.mAuthSeqID;
mAtoms = move(rhs.mAtoms);
mAtoms = std::move(rhs.mAtoms);
return *this;
}
Residue::~Residue()
{
//cerr << "~Residue" << endl;
//std::cerr << "~Residue" << std::endl;
}
string Residue::authInsCode() const
std::string Residue::authInsCode() const
{
assert(mStructure);
string result;
std::string result;
try
{
char iCode;
tie(ignore, ignore, iCode) = mStructure->MapLabelToAuth(mAsymID, mSeqID);
tie(std::ignore, std::ignore, iCode) = mStructure->MapLabelToAuth(mAsymID, mSeqID);
result = string{ iCode };
result = std::string{ iCode };
ba::trim(result);
}
catch (...)
......@@ -812,15 +804,15 @@ string Residue::authInsCode() const
return result;
}
string Residue::authAsymID() const
std::string Residue::authAsymID() const
{
assert(mStructure);
string result;
std::string result;
try
{
tie(result, ignore, ignore) = mStructure->MapLabelToAuth(mAsymID, mSeqID);
tie(result, std::ignore, std::ignore) = mStructure->MapLabelToAuth(mAsymID, mSeqID);
}
catch (...)
{
......@@ -830,17 +822,17 @@ string Residue::authAsymID() const
return result;
}
string Residue::authSeqID() const
std::string Residue::authSeqID() const
{
assert(mStructure);
string result;
std::string result;
try
{
int seqID;
tie(ignore, seqID, ignore) = mStructure->MapLabelToAuth(mAsymID, mSeqID);
result = to_string(seqID);
tie(std::ignore, seqID, std::ignore) = mStructure->MapLabelToAuth(mAsymID, mSeqID);
result = std::to_string(seqID);
}
catch (...)
{
......@@ -853,14 +845,14 @@ const Compound& Residue::compound() const
{
auto result = Compound::create(mCompoundID);
if (result == nullptr)
throw runtime_error("Failed to create compound " + mCompoundID);
throw std::runtime_error("Failed to create compound " + mCompoundID);
return *result;
}
const AtomView& Residue::atoms() const
{
if (mStructure == nullptr)
throw runtime_error("Invalid Residue object");
throw std::runtime_error("Invalid Residue object");
return mAtoms;
}
......@@ -868,7 +860,7 @@ const AtomView& Residue::atoms() const
std::string Residue::unique_alt_id() const
{
if (mStructure == nullptr)
throw runtime_error("Invalid Residue object");
throw std::runtime_error("Invalid Residue object");
auto firstAlt = std::find_if(mAtoms.begin(), mAtoms.end(), [](auto& a) { return not a.labelAltID().empty(); });
......@@ -878,7 +870,7 @@ std::string Residue::unique_alt_id() const
AtomView Residue::unique_atoms() const
{
if (mStructure == nullptr)
throw runtime_error("Invalid Residue object");
throw std::runtime_error("Invalid Residue object");
AtomView result;
std::string firstAlt;
......@@ -907,7 +899,7 @@ AtomView Residue::unique_atoms() const
return result;
}
Atom Residue::atomByID(const string& atomID) const
Atom Residue::atomByID(const std::string& atomID) const
{
Atom result;
......@@ -939,40 +931,40 @@ bool Residue::isEntity() const
return a1.size() == a2.size();
}
string Residue::authID() const
std::string Residue::authID() const
{
string result;
std::string result;
try
{
char chainID, iCode;
int seqNum;
tie(chainID, seqNum, iCode) = mStructure->MapLabelToAuth(mAsymID, mSeqID);
std::tie(chainID, seqNum, iCode) = mStructure->MapLabelToAuth(mAsymID, mSeqID);
result = chainID + to_string(seqNum);
result = chainID + std::to_string(seqNum);
if (iCode != ' ' and iCode != 0)
result += iCode;
}
catch (...)
{
result = mAsymID + to_string(mSeqID);
result = mAsymID + std::to_string(mSeqID);
}
return result;
}
string Residue::labelID() const
std::string Residue::labelID() const
{
if (mCompoundID == "HOH")
return mAsymID + mAuthSeqID;
else
return mAsymID + to_string(mSeqID);
return mAsymID + std::to_string(mSeqID);
}
tuple<Point,float> Residue::centerAndRadius() const
std::tuple<Point,float> Residue::centerAndRadius() const
{
vector<Point> pts;
std::vector<Point> pts;
for (auto& a: mAtoms)
pts.push_back(a.location());
......@@ -986,7 +978,7 @@ tuple<Point,float> Residue::centerAndRadius() const
radius = d;
}
return make_tuple(center, radius);
return std::make_tuple(center, radius);
}
bool Residue::hasAlternateAtoms() const
......@@ -1008,11 +1000,11 @@ std::ostream& operator<<(std::ostream& os, const Residue& res)
// monomer
//Monomer::Monomer(Monomer&& rhs)
// : Residue(move(rhs)), mPolymer(rhs.mPolymer), mIndex(rhs.mIndex)
// : Residue(std::move(rhs)), mPolymer(rhs.mPolymer), mIndex(rhs.mIndex)
//{
//}
Monomer::Monomer(const Polymer& polymer, uint32_t index, int seqID, const string& compoundID)
Monomer::Monomer(const Polymer& polymer, uint32_t index, int seqID, const std::string& compoundID)
: Residue(*polymer.structure(), compoundID, polymer.asymID(), seqID)
, mPolymer(&polymer)
, mIndex(index)
......@@ -1020,15 +1012,15 @@ Monomer::Monomer(const Polymer& polymer, uint32_t index, int seqID, const string
}
Monomer::Monomer(Monomer&& rhs)
: Residue(move(rhs)), mPolymer(rhs.mPolymer), mIndex(rhs.mIndex)
: Residue(std::move(rhs)), mPolymer(rhs.mPolymer), mIndex(rhs.mIndex)
{
cerr << "move constructor monomer" << endl;
std::cerr << "move constructor monomer" << std::endl;
// mStructure = rhs.mStructure; rhs.mStructure = nullptr;
// mCompoundID = move(rhs.mCompoundID);
// mAsymID = move(rhs.mAsymID);
// mCompoundID = std::move(rhs.mCompoundID);
// mAsymID = std::move(rhs.mAsymID);
// mSeqID = rhs.mSeqID;
// mAtoms = move(rhs.mAtoms);
// mAtoms = std::move(rhs.mAtoms);
//
// mPolymer = rhs.mPolymer; rhs.mPolymer = nullptr;
// mIndex = rhs.mIndex;
......@@ -1037,9 +1029,9 @@ cerr << "move constructor monomer" << endl;
Monomer& Monomer::operator=(Monomer&& rhs)
{
cerr << "move assignment monomer" << endl;
std::cerr << "move assignment monomer" << std::endl;
Residue::operator=(move(rhs));
Residue::operator=(std::move(rhs));
mPolymer = rhs.mPolymer; rhs.mPolymer = nullptr;
mIndex = rhs.mIndex;
......@@ -1080,10 +1072,10 @@ float Monomer::phi() const
result = DihedralAngle(prev.C().location(), N().location(), CAlpha().location(), C().location());
}
}
catch (const exception& ex)
catch (const std::exception& ex)
{
if (cif::VERBOSE)
cerr << ex.what() << endl;
std::cerr << ex.what() << std::endl;
}
return result;
......@@ -1102,10 +1094,10 @@ float Monomer::psi() const
result = DihedralAngle(N().location(), CAlpha().location(), C().location(), next.N().location());
}
}
catch (const exception& ex)
catch (const std::exception& ex)
{
if (cif::VERBOSE)
cerr << ex.what() << endl;
std::cerr << ex.what() << std::endl;
}
return result;
......@@ -1126,10 +1118,10 @@ float Monomer::alpha() const
result = DihedralAngle(prev.CAlpha().location(), CAlpha().location(), next.CAlpha().location(), nextNext.CAlpha().location());
}
}
catch (const exception& ex)
catch (const std::exception& ex)
{
if (cif::VERBOSE)
cerr << ex.what() << endl;
std::cerr << ex.what() << std::endl;
}
return result;
......@@ -1154,11 +1146,11 @@ float Monomer::kappa() const
}
}
}
catch (const exception& ex)
catch (const std::exception& ex)
{
if (cif::VERBOSE)
cerr << "When trying to calculate kappa for " << asymID() << ':' << seqID() << ": "
<< ex.what() << endl;
std::cerr << "When trying to calculate kappa for " << asymID() << ':' << seqID() << ": "
<< ex.what() << std::endl;
}
return result;
......@@ -1177,11 +1169,11 @@ float Monomer::tco() const
result = CosinusAngle(C().location(), O().location(), prev.C().location(), prev.O().location());
}
}
catch (const exception& ex)
catch (const std::exception& ex)
{
if (cif::VERBOSE)
cerr << "When trying to calculate tco for " << asymID() << ':' << seqID() << ": "
<< ex.what() << endl;
std::cerr << "When trying to calculate tco for " << asymID() << ':' << seqID() << ": "
<< ex.what() << std::endl;
}
return result;
......@@ -1196,17 +1188,17 @@ float Monomer::omega() const
if (not is_last_in_chain())
result = omega(*this, mPolymer->operator[](mIndex + 1));
}
catch (const exception& ex)
catch (const std::exception& ex)
{
if (cif::VERBOSE)
cerr << "When trying to calculate omega for " << asymID() << ':' << seqID() << ": "
<< ex.what() << endl;
std::cerr << "When trying to calculate omega for " << asymID() << ':' << seqID() << ": "
<< ex.what() << std::endl;
}
return result;
}
const map<string,vector<string>> kChiAtomsMap = {
const std::map<std::string,std::vector<std::string>> kChiAtomsMap = {
{ "ASP", {"CG", "OD1"} },
{ "ASN", {"CG", "OD1"} },
{ "ARG", {"CG", "CD", "NE", "CZ"} },
......@@ -1248,7 +1240,7 @@ float Monomer::chi(size_t nr) const
auto i = kChiAtomsMap.find(mCompoundID);
if (i != kChiAtomsMap.end() and nr < i->second.size())
{
vector<string> atoms{ "N", "CA", "CB" };
std::vector<std::string> atoms{ "N", "CA", "CB" };
atoms.insert(atoms.end(), i->second.begin(), i->second.end());
......@@ -1410,7 +1402,7 @@ bool Monomer::isCis(const mmcif::Monomer& a, const mmcif::Monomer& b)
// if (index < polySeq.size())
// {
// int seqID;
// string asymID, monID;
// std::string asymID, monID;
// cif::tie(asymID, seqID, monID) =
// polySeq[mIndex].get("asym_id", "seq_id", "mon_id");
//
......@@ -1423,7 +1415,7 @@ bool Monomer::isCis(const mmcif::Monomer& a, const mmcif::Monomer& b)
// if (index >= mPolySeq.size())
// throw out_of_range("Invalid index for residue in polymer");
//
// string compoundID;
// std::string compoundID;
// int seqID;
//
// auto r = mPolySeq[index];
......@@ -1449,7 +1441,7 @@ bool Monomer::isCis(const mmcif::Monomer& a, const mmcif::Monomer& b)
// if (mIndex < polySeq.size())
// {
// int seqID;
// string asymID, monID;
// std::string asymID, monID;
// cif::tie(asymID, seqID, monID) =
// polySeq[mIndex].get("asym_id", "seq_id", "mon_id");
//
......@@ -1459,11 +1451,11 @@ bool Monomer::isCis(const mmcif::Monomer& a, const mmcif::Monomer& b)
// return *this;
//}
//Polymer::Polymer(const Structure& s, const string& asymID)
//Polymer::Polymer(const Structure& s, const std::string& asymID)
// : mStructure(const_cast<Structure*>(&s)), mAsymID(asymID)
// , mPolySeq(s.category("pdbx_poly_seq_scheme").find(cif::Key("asym_id") == mAsymID))
//{
// mEntityID = mPolySeq.front()["entity_id"].as<string>();
// mEntityID = mPolySeq.front()["entity_id"].as<std::string>();
//
//#if DEBUG
// for (auto r: mPolySeq)
......@@ -1473,35 +1465,35 @@ bool Monomer::isCis(const mmcif::Monomer& a, const mmcif::Monomer& b)
//}
//Polymer::Polymer(Polymer&& rhs)
// : vector<Monomer>(move(rhs))
// : std::vector<Monomer>(std::move(rhs))
// , mStructure(rhs.mStructure)
// , mEntityID(move(rhs.mEntityID)), mAsymID(move(rhs.mAsymID)), mPolySeq(move(rhs.mPolySeq))
// , mEntityID(std::move(rhs.mEntityID)), mAsymID(std::move(rhs.mAsymID)), mPolySeq(std::move(rhs.mPolySeq))
//{
// rhs.mStructure = nullptr;
//}
//
//Polymer& Polymer::operator=(Polymer&& rhs)
//{
// vector<Monomer>::operator=(move(rhs));
// std::vector<Monomer>::operator=(std::move(rhs));
// mStructure = rhs.mStructure; rhs.mStructure = nullptr;
// mEntityID = move(rhs.mEntityID);
// mAsymID = move(rhs.mAsymID);
// mPolySeq = move(rhs.mPolySeq);
// mEntityID = std::move(rhs.mEntityID);
// mAsymID = std::move(rhs.mAsymID);
// mPolySeq = std::move(rhs.mPolySeq);
// return *this;
//}
Polymer::Polymer(const Structure& s, const string& entityID, const string& asymID)
Polymer::Polymer(const Structure& s, const std::string& entityID, const std::string& asymID)
: mStructure(const_cast<Structure*>(&s)), mEntityID(entityID), mAsymID(asymID)
, mPolySeq(s.category("pdbx_poly_seq_scheme"), cif::Key("asym_id") == mAsymID and cif::Key("entity_id") == mEntityID)
{
map<uint32_t,uint32_t> ix;
std::map<uint32_t,uint32_t> ix;
reserve(mPolySeq.size());
for (auto r: mPolySeq)
{
int seqID;
string compoundID;
std::string compoundID;
cif::tie(seqID, compoundID) = r.get("seq_id", "mon_id");
uint32_t index = size();
......@@ -1520,9 +1512,9 @@ Polymer::Polymer(const Structure& s, const string& entityID, const string& asymI
}
}
string Polymer::chainID() const
std::string Polymer::chainID() const
{
return mPolySeq.front()["pdb_strand_id"].as<string>();
return mPolySeq.front()["pdb_strand_id"].as<std::string>();
}
Monomer& Polymer::getBySeqID(int seqID)
......@@ -1531,7 +1523,7 @@ Monomer& Polymer::getBySeqID(int seqID)
if (m.seqID() == seqID)
return m;
throw runtime_error("Monomer with seqID " + to_string(seqID) + " not found in polymer " + mAsymID);
throw std::runtime_error("Monomer with seqID " + std::to_string(seqID) + " not found in polymer " + mAsymID);
}
const Monomer& Polymer::getBySeqID(int seqID) const
......@@ -1540,16 +1532,16 @@ const Monomer& Polymer::getBySeqID(int seqID) const
if (m.seqID() == seqID)
return m;
throw runtime_error("Monomer with seqID " + to_string(seqID) + " not found in polymer " + mAsymID);
throw std::runtime_error("Monomer with seqID " + std::to_string(seqID) + " not found in polymer " + mAsymID);
}
int Polymer::Distance(const Monomer& a, const Monomer& b) const
{
int result = numeric_limits<int>::max();
int result = std::numeric_limits<int>::max();
if (a.asymID() == b.asymID())
{
int ixa = numeric_limits<int>::max(), ixb = numeric_limits<int>::max();
int ixa = std::numeric_limits<int>::max(), ixb = std::numeric_limits<int>::max();
int ix = 0, f = 0;
for (auto& m: *this)
......@@ -1600,14 +1592,14 @@ void File::load(const std::string& p)
//
// struct entity
// {
// string id;
// string type;
// std::string id;
// std::string type;
// };
// vector<entity> entities;
// std::vector<entity> entities;
//
// for (auto& _e: db["entity"])
// {
// string type = _e["type"];
// std::string type = _e["type"];
// ba::to_lower(type);
// entities.push_back({ _e["id"], type });
// }
......@@ -1617,13 +1609,13 @@ void File::load(const std::string& p)
// {
// AtomPtr ap(new Atom(this, atom_site));
//
// string entity_id = atom_site["entity_id"];
// std::string entity_id = atom_site["entity_id"];
//
// auto e = find_if(entities.begin(), entities.end(), [=](entity& e) -> bool { return e.id == entity_id; });
// if (e == entities.end())
// throw runtime_error("Entity " + entity_id + " is not defined");
// throw std::runtime_error("Entity " + entity_id + " is not defined");
//
// string comp_id, asym_id, seq_id;
// std::string comp_id, asym_id, seq_id;
// cif::tie(comp_id, seq_id) = atom_site.get("label_comp_id", "label_asym_id", "label_seq_id");
//
// auto r = find_if(m_residues.begin(), m_residues.end(), [=](residue_ptr& res) -> bool
......@@ -1655,7 +1647,7 @@ cif::Datablock& File::data()
assert(mImpl->mDb);
if (mImpl == nullptr or mImpl->mDb == nullptr)
throw runtime_error("No data loaded");
throw std::runtime_error("No data loaded");
return *mImpl->mDb;
}
......@@ -1665,7 +1657,7 @@ cif::File& File::file()
assert(mImpl);
if (mImpl == nullptr)
throw runtime_error("No data loaded");
throw std::runtime_error("No data loaded");
return mImpl->mData;
}
......@@ -1720,7 +1712,7 @@ void Structure::loadData()
for (auto& r: polySeqScheme)
{
string asymID, entityID, seqID, monID;
std::string asymID, entityID, seqID, monID;
cif::tie(asymID, entityID, seqID, monID) =
r.get("asym_id", "entity_id", "seq_id", "mon_id");
......@@ -1732,7 +1724,7 @@ void Structure::loadData()
for (auto& r: nonPolyScheme)
{
string asymID, monID, pdbSeqNum;
std::string asymID, monID, pdbSeqNum;
cif::tie(asymID, monID, pdbSeqNum) =
r.get("asym_id", "mon_id", "pdb_seq_num");
......@@ -1745,7 +1737,7 @@ void Structure::loadData()
void Structure::updateAtomIndex()
{
mAtomIndex = vector<size_t>(mAtoms.size());
mAtomIndex = std::vector<size_t>(mAtoms.size());
iota(mAtomIndex.begin(), mAtomIndex.end(), 0);
......@@ -1774,10 +1766,10 @@ AtomView Structure::waters() const
// Get the entity id for water
auto& entityCat = db["entity"];
string waterEntityID;
std::string waterEntityID;
for (auto& e: entityCat)
{
string id, type;
std::string id, type;
cif::tie(id, type) = e.get("id", "type");
if (ba::iequals(type, "water"))
{
......@@ -1788,28 +1780,28 @@ AtomView Structure::waters() const
for (auto& a: mAtoms)
{
if (a.property<string>("label_entity_id") == waterEntityID)
if (a.property<std::string>("label_entity_id") == waterEntityID)
result.push_back(a);
}
return result;
}
Atom Structure::getAtomByID(string id) const
Atom Structure::getAtomByID(std::string id) const
{
auto i = lower_bound(mAtomIndex.begin(), mAtomIndex.end(),
auto i = std::lower_bound(mAtomIndex.begin(), mAtomIndex.end(),
id, [this](auto& a, auto& b) { return mAtoms[a].id() < b; });
// auto i = find_if(mAtoms.begin(), mAtoms.end(),
// [&id](auto& a) { return a.id() == id; });
if (i == mAtomIndex.end() or mAtoms[*i].id() != id)
throw out_of_range("Could not find atom with id " + id);
throw std::out_of_range("Could not find atom with id " + id);
return mAtoms[*i];
}
Atom Structure::getAtomByLabel(const string& atomID, const string& asymID, const string& compID, int seqID, const string& altID)
Atom Structure::getAtomByLabel(const std::string& atomID, const std::string& asymID, const std::string& compID, int seqID, const std::string& altID)
{
for (auto& a: mAtoms)
{
......@@ -1823,7 +1815,7 @@ Atom Structure::getAtomByLabel(const string& atomID, const string& asymID, const
}
}
throw out_of_range("Could not find atom with specified label");
throw std::out_of_range("Could not find atom with specified label");
}
File& Structure::getFile() const
......@@ -1837,25 +1829,25 @@ cif::Category& Structure::category(const char* name) const
return db[name];
}
tuple<char,int,char> Structure::MapLabelToAuth(
const string& asymID, int seqID) const
std::tuple<char,int,char> Structure::MapLabelToAuth(
const std::string& asymID, int seqID) const
{
auto& db = *getFile().impl().mDb;
tuple<char,int,char> result;
std::tuple<char,int,char> result;
bool found = false;
for (auto r: db["pdbx_poly_seq_scheme"].find(
cif::Key("asym_id") == asymID and
cif::Key("seq_id") == seqID))
{
string auth_asym_id, pdb_ins_code;
std::string auth_asym_id, pdb_ins_code;
int pdb_seq_num;
cif::tie(auth_asym_id, pdb_seq_num, pdb_ins_code) =
r.get("pdb_strand_id", "pdb_seq_num", "pdb_ins_code");
result = make_tuple(auth_asym_id.front(), pdb_seq_num,
result = std::make_tuple(auth_asym_id.front(), pdb_seq_num,
pdb_ins_code.empty() ? ' ' : pdb_ins_code.front());
found = true;
......@@ -1868,13 +1860,13 @@ tuple<char,int,char> Structure::MapLabelToAuth(
cif::Key("asym_id") == asymID and
cif::Key("seq_id") == seqID))
{
string pdb_strand_id, pdb_ins_code;
std::string pdb_strand_id, pdb_ins_code;
int pdb_seq_num;
cif::tie(pdb_strand_id, pdb_seq_num, pdb_ins_code) =
r.get("pdb_strand_id", "pdb_seq_num", "pdb_ins_code");
result = make_tuple(pdb_strand_id.front(), pdb_seq_num,
result = std::make_tuple(pdb_strand_id.front(), pdb_seq_num,
pdb_ins_code.empty() ? ' ' : pdb_ins_code.front());
found = true;
......@@ -1885,13 +1877,13 @@ tuple<char,int,char> Structure::MapLabelToAuth(
return result;
}
tuple<string,int,string,string> Structure::MapLabelToPDB(
const string& asymID, int seqID, const string& monID,
const string& authSeqID) const
std::tuple<std::string,int,std::string,std::string> Structure::MapLabelToPDB(
const std::string& asymID, int seqID, const std::string& monID,
const std::string& authSeqID) const
{
auto& db = datablock();
tuple<string,int,string,string> result;
std::tuple<std::string,int,std::string,std::string> result;
if (monID == "HOH")
{
......@@ -1927,12 +1919,12 @@ tuple<string,int,string,string> Structure::MapLabelToPDB(
return result;
}
tuple<string,int,string> Structure::MapPDBToLabel(const string& asymID, int seqID,
const string& compID, const string& iCode) const
std::tuple<std::string,int,std::string> Structure::MapPDBToLabel(const std::string& asymID, int seqID,
const std::string& compID, const std::string& iCode) const
{
auto& db = datablock();
tuple<string,int,string> result;
std::tuple<std::string,int,std::string> result;
if (iCode.empty())
{
......@@ -1988,11 +1980,11 @@ cif::Datablock& Structure::datablock() const
return *mFile.impl().mDb;
}
void Structure::insertCompound(const string& compoundID, bool isEntity)
void Structure::insertCompound(const std::string& compoundID, bool isEntity)
{
auto compound = Compound::create(compoundID);
if (compound == nullptr)
throw runtime_error("Trying to insert unknown compound " + compoundID + " (not found in CCP4 monomers lib)");
throw std::runtime_error("Trying to insert unknown compound " + compoundID + " (not found in CCP4 monomers lib)");
cif::Datablock& db = *mFile.impl().mDb;
......@@ -2014,7 +2006,7 @@ void Structure::insertCompound(const string& compoundID, bool isEntity)
if (pdbxEntityNonpoly.find(cif::Key("comp_id") == compoundID).empty())
{
auto& entity = db["entity"];
string entityID = to_string(entity.size() + 1);
std::string entityID = std::to_string(entity.size() + 1);
entity.emplace({
{ "id", entityID },
......@@ -2101,7 +2093,7 @@ void Structure::removeAtom(Atom& a)
for (auto i = atomSites.begin(); i != atomSites.end(); ++i)
{
string id;
std::string id;
cif::tie(id) = i->get("id");
if (id == a.id())
......@@ -2125,10 +2117,10 @@ void Structure::swapAtoms(Atom& a1, Atom& a2)
auto rs2 = atomSites.find(cif::Key("id") == a2.id());
if (rs1.size() != 1)
throw runtime_error("Cannot swap atoms since the number of atoms with id " + a1.id() + " is " + to_string(rs1.size()));
throw std::runtime_error("Cannot swap atoms since the number of atoms with id " + a1.id() + " is " + std::to_string(rs1.size()));
if (rs2.size() != 1)
throw runtime_error("Cannot swap atoms since the number of atoms with id " + a2.id() + " is " + to_string(rs2.size()));
throw std::runtime_error("Cannot swap atoms since the number of atoms with id " + a2.id() + " is " + std::to_string(rs2.size()));
auto r1 = rs1.front();
auto r2 = rs2.front();
......@@ -2149,12 +2141,12 @@ void Structure::moveAtom(Atom& a, Point p)
a.location(p);
}
void Structure::changeResidue(const Residue& res, const string& newCompound,
const vector<tuple<string,string>>& remappedAtoms)
void Structure::changeResidue(const Residue& res, const std::string& newCompound,
const std::vector<std::tuple<std::string,std::string>>& remappedAtoms)
{
cif::Datablock& db = *mFile.impl().mDb;
string entityID;
std::string entityID;
// First make sure the compound is already known or insert it.
// And if the residue is an entity, we must make sure it exists
......@@ -2165,13 +2157,13 @@ void Structure::changeResidue(const Residue& res, const string& newCompound,
for (auto& a: remappedAtoms)
{
string a1, a2;
std::string a1, a2;
tie(a1, a2) = a;
auto i = find_if(atoms.begin(), atoms.end(), [&](const Atom& a) { return a.labelAtomID() == a1; });
if (i == atoms.end())
{
cerr << "Missing atom for atom ID " << a1 << endl;
std::cerr << "Missing atom for atom ID " << a1 << std::endl;
continue;
}
......
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;
}
......
src/TlsParser.cpp
......@@ -26,32 +26,18 @@
#include "cif++/Config.hpp"
#include <termios.h>
#include <sys/ioctl.h>
#include <iostream>
#include <iomanip>
#include <boost/program_options.hpp>
#include <boost/algorithm/string.hpp>
#include "cif++/CifUtils.hpp"
#include "cif++/Structure.hpp"
#include "cif++/TlsParser.hpp"
using namespace std;
namespace po = boost::program_options;
namespace ba = boost::algorithm;
namespace c = mmcif;
namespace cif
{
const int
kResidueNrWildcard = numeric_limits<int>::min(),
kNoSeqNum = numeric_limits<int>::max() - 1;
using namespace std;
kResidueNrWildcard = std::numeric_limits<int>::min(),
kNoSeqNum = std::numeric_limits<int>::max() - 1;
// --------------------------------------------------------------------
// We parse selection statements and create a selection expression tree
......@@ -60,14 +46,14 @@ using namespace std;
struct TLSResidue
{
string chainID;
int seqNr;
char iCode;
string name;
bool selected;
std::string chainID;
int seqNr;
char iCode;
std::string name;
bool selected;
string asymID;
int seqID;
std::string asymID;
int seqID;
bool operator==(const TLSResidue& rhs) const
{
......@@ -79,9 +65,9 @@ struct TLSResidue
}
};
void DumpSelection(const vector<TLSResidue>& selected, int indentLevel)
void DumpSelection(const std::vector<TLSResidue>& selected, int indentLevel)
{
string indent(indentLevel * 2, ' ');
std::string indent(indentLevel * 2, ' ');
auto i = selected.begin();
bool first = true;
......@@ -89,35 +75,35 @@ void DumpSelection(const vector<TLSResidue>& selected, int indentLevel)
// First print in PDB space
while (i != selected.end())
{
auto b = find_if(i, selected.end(), [](auto s) -> bool { return s.selected; });
auto b = std::find_if(i, selected.end(), [](auto s) -> bool { return s.selected; });
if (b == selected.end())
break;
if (first)
cout << indent << "PDB:" << endl;
std::cout << indent << "PDB:" << std::endl;
first = false;
auto e = find_if(b, selected.end(), [b](auto s) -> bool { return s.chainID != b->chainID or not s.selected; });
auto e = std::find_if(b, selected.end(), [b](auto s) -> bool { return s.chainID != b->chainID or not s.selected; });
cout << indent << " >> " << b->chainID << ' ' << b->seqNr << ':' << (e - 1)->seqNr << endl;
std::cout << indent << " >> " << b->chainID << ' ' << b->seqNr << ':' << (e - 1)->seqNr << std::endl;
i = e;
}
// Then in mmCIF space
if (not first)
cout << indent << "mmCIF:" << endl;
std::cout << indent << "mmCIF:" << std::endl;
i = selected.begin();
while (i != selected.end())
{
auto b = find_if(i, selected.end(), [](auto s) -> bool { return s.selected; });
auto b = std::find_if(i, selected.end(), [](auto s) -> bool { return s.selected; });
if (b == selected.end())
break;
auto e = find_if(b, selected.end(), [b](auto s) -> bool { return s.asymID != b->asymID or not s.selected; });
auto e = std::find_if(b, selected.end(), [b](auto s) -> bool { return s.asymID != b->asymID or not s.selected; });
string asymID = b->asymID;
std::string asymID = b->asymID;
int from = b->seqID, to = from;
for (auto j = b + 1; j != e; ++j)
......@@ -127,18 +113,18 @@ void DumpSelection(const vector<TLSResidue>& selected, int indentLevel)
else if (j->seqID != to) // probably an insertion code
{
if (from == kNoSeqNum or to == kNoSeqNum)
cout << indent << " >> " << asymID << endl;
std::cout << indent << " >> " << asymID << std::endl;
else
cout << indent << " >> " << asymID << ' ' << from << ':' << to << endl;
std::cout << indent << " >> " << asymID << ' ' << from << ':' << to << std::endl;
asymID = b->asymID;
from = to = b->seqID;
}
}
if (from == kNoSeqNum or to == kNoSeqNum)
cout << indent << " >> " << asymID << endl;
std::cout << indent << " >> " << asymID << std::endl;
else
cout << indent << " >> " << asymID << ' ' << from << ':' << to << endl;
std::cout << indent << " >> " << asymID << ' ' << from << ':' << to << std::endl;
i = e;
}
......@@ -146,22 +132,22 @@ void DumpSelection(const vector<TLSResidue>& selected, int indentLevel)
if (first)
{
if (isatty(STDOUT_FILENO))
cout << indent << cif::coloured("Empty selection") << endl;
std::cout << indent << cif::coloured("Empty selection") << std::endl;
else
cout << indent << cif::coloured("Empty selection") << endl;
std::cout << indent << cif::coloured("Empty selection") << std::endl;
}
}
vector<tuple<string,int,int>> TLSSelection::GetRanges(Datablock& db, bool pdbNamespace) const
std::vector<std::tuple<std::string,int,int>> TLSSelection::GetRanges(Datablock& db, bool pdbNamespace) const
{
vector<TLSResidue> selected;
std::vector<TLSResidue> selected;
// Collect the residues from poly seq scheme...
for (auto r: db["pdbx_poly_seq_scheme"])
{
string chain, seqNr, iCode, name;
std::string chain, seqNr, iCode, name;
string asymID;
std::string asymID;
int seqID;
if (pdbNamespace)
......@@ -177,7 +163,7 @@ vector<tuple<string,int,int>> TLSSelection::GetRanges(Datablock& db, bool pdbNam
continue;
if (iCode.length() > 1)
throw runtime_error("invalid iCode");
throw std::runtime_error("invalid iCode");
selected.push_back({chain, stoi(seqNr), iCode[0], name, false, asymID, seqID});
}
......@@ -185,7 +171,7 @@ vector<tuple<string,int,int>> TLSSelection::GetRanges(Datablock& db, bool pdbNam
// ... those from the nonpoly scheme
for (auto r: db["pdbx_nonpoly_scheme"])
{
string chain, seqNr, iCode, name, asymID;
std::string chain, seqNr, iCode, name, asymID;
if (pdbNamespace)
{
......@@ -204,7 +190,7 @@ vector<tuple<string,int,int>> TLSSelection::GetRanges(Datablock& db, bool pdbNam
continue;
if (iCode.length() > 1)
throw runtime_error("invalid iCode");
throw std::runtime_error("invalid iCode");
selected.push_back({chain, stoi(seqNr), iCode[0], name, false, asymID, kNoSeqNum});
}
......@@ -222,17 +208,17 @@ vector<tuple<string,int,int>> TLSSelection::GetRanges(Datablock& db, bool pdbNam
CollectResidues(db, selected);
vector<tuple<string,int,int>> result;
std::vector<std::tuple<std::string,int,int>> result;
auto i = selected.begin();
while (i != selected.end())
{
auto b = find_if(i, selected.end(), [](auto s) -> bool { return s.selected; });
auto b = std::find_if(i, selected.end(), [](auto s) -> bool { return s.selected; });
if (b == selected.end())
break;
auto e = find_if(b, selected.end(), [b](auto s) -> bool { return s.asymID != b->asymID or not s.selected; });
auto e = std::find_if(b, selected.end(), [b](auto s) -> bool { return s.asymID != b->asymID or not s.selected; });
// return ranges with strict increasing sequence numbers.
// So when there's a gap in the sequence we split the range.
......@@ -240,9 +226,9 @@ vector<tuple<string,int,int>> TLSSelection::GetRanges(Datablock& db, bool pdbNam
result.push_back(make_tuple(b->asymID, b->seqID, b->seqID));
for (auto j = b + 1; j != e; ++j)
{
if (j->seqID == get<2>(result.back()) + 1)
get<2>(result.back()) = j->seqID;
else if (j->seqID != get<2>(result.back())) // probably an insertion code
if (j->seqID == std::get<2>(result.back()) + 1)
std::get<2>(result.back()) = j->seqID;
else if (j->seqID != std::get<2>(result.back())) // probably an insertion code
result.push_back(make_tuple(b->asymID, j->seqID, j->seqID));
}
......@@ -257,7 +243,7 @@ struct TLSSelectionNot : public TLSSelection
TLSSelectionNot(TLSSelectionPtr selection)
: selection(selection.release()) {}
virtual void CollectResidues(Datablock& db, vector<TLSResidue>& residues, int indentLevel) const
virtual void CollectResidues(Datablock& db, std::vector<TLSResidue>& residues, int indentLevel) const
{
selection->CollectResidues(db, residues, indentLevel + 1);
......@@ -266,7 +252,7 @@ struct TLSSelectionNot : public TLSSelection
if (cif::VERBOSE)
{
cout << string(indentLevel * 2, ' ') << "NOT" << endl;
std::cout << std::string(indentLevel * 2, ' ') << "NOT" << std::endl;
DumpSelection(residues, indentLevel);
}
}
......@@ -278,14 +264,14 @@ struct TLSSelectionAll : public TLSSelection
{
TLSSelectionAll() {}
virtual void CollectResidues(Datablock& db, vector<TLSResidue>& residues, int indentLevel) const
virtual void CollectResidues(Datablock& db, std::vector<TLSResidue>& residues, int indentLevel) const
{
for (auto& r: residues)
r.selected = true;
if (cif::VERBOSE)
{
cout << string(indentLevel * 2, ' ') << "ALL" << endl;
std::cout << std::string(indentLevel * 2, ' ') << "ALL" << std::endl;
DumpSelection(residues, indentLevel);
}
}
......@@ -293,10 +279,10 @@ struct TLSSelectionAll : public TLSSelection
struct TLSSelectionChain : public TLSSelectionAll
{
TLSSelectionChain(const string& chainID)
TLSSelectionChain(const std::string& chainID)
: m_chain(chainID) {}
virtual void CollectResidues(Datablock& db, vector<TLSResidue>& residues, int indentLevel) const
virtual void CollectResidues(Datablock& db, std::vector<TLSResidue>& residues, int indentLevel) const
{
bool allChains = m_chain == "*";
......@@ -305,12 +291,12 @@ struct TLSSelectionChain : public TLSSelectionAll
if (cif::VERBOSE)
{
cout << string(indentLevel * 2, ' ') << "CHAIN " << m_chain << endl;
std::cout << std::string(indentLevel * 2, ' ') << "CHAIN " << m_chain << std::endl;
DumpSelection(residues, indentLevel);
}
}
string m_chain;
std::string m_chain;
};
struct TLSSelectionResID : public TLSSelectionAll
......@@ -318,14 +304,14 @@ struct TLSSelectionResID : public TLSSelectionAll
TLSSelectionResID(int seqNr, char iCode)
: m_seq_nr(seqNr), m_icode(iCode) {}
virtual void CollectResidues(Datablock& db, vector<TLSResidue>& residues, int indentLevel) const
virtual void CollectResidues(Datablock& db, std::vector<TLSResidue>& residues, int indentLevel) const
{
for (auto& r: residues)
r.selected = r.seqNr == m_seq_nr and r.iCode == m_icode;
if (cif::VERBOSE)
{
cout << string(indentLevel * 2, ' ') << "ResID " << m_seq_nr << (m_icode ? string { m_icode} : "") << endl;
std::cout << std::string(indentLevel * 2, ' ') << "ResID " << m_seq_nr << (m_icode ? std::string { m_icode} : "") << std::endl;
DumpSelection(residues, indentLevel);
}
}
......@@ -339,7 +325,7 @@ struct TLSSelectionRangeSeq : public TLSSelectionAll
TLSSelectionRangeSeq(int first, int last)
: m_first(first), m_last(last) {}
virtual void CollectResidues(Datablock& db, vector<TLSResidue>& residues, int indentLevel) const
virtual void CollectResidues(Datablock& db, std::vector<TLSResidue>& residues, int indentLevel) const
{
for (auto& r: residues)
{
......@@ -349,7 +335,7 @@ struct TLSSelectionRangeSeq : public TLSSelectionAll
if (cif::VERBOSE)
{
cout << string(indentLevel * 2, ' ') << "Range " << m_first << ':' << m_last << endl;
std::cout << std::string(indentLevel * 2, ' ') << "Range " << m_first << ':' << m_last << std::endl;
DumpSelection(residues, indentLevel);
}
}
......@@ -362,21 +348,21 @@ struct TLSSelectionRangeID : public TLSSelectionAll
TLSSelectionRangeID(int first, int last, char icodeFirst = 0, char icodeLast = 0)
: m_first(first), m_last(last), m_icode_first(icodeFirst), m_icode_last(icodeLast) {}
virtual void CollectResidues(Datablock& db, vector<TLSResidue>& residues, int indentLevel) const
virtual void CollectResidues(Datablock& db, std::vector<TLSResidue>& residues, int indentLevel) const
{
// need to do this per chain
set<string> chains;
std::set<std::string> chains;
for (auto& r: residues)
chains.insert(r.chainID);
for (string chain: chains)
for (std::string chain: chains)
{
auto f = find_if(residues.begin(), residues.end(),
auto f = std::find_if(residues.begin(), residues.end(),
[=](auto r) -> bool {
return r.chainID == chain and r.seqNr == m_first and r.iCode == m_icode_first;
});
auto l = find_if(residues.begin(), residues.end(),
auto l = std::find_if(residues.begin(), residues.end(),
[=](auto r) -> bool {
return r.chainID == chain and r.seqNr == m_last and r.iCode == m_icode_last;
});
......@@ -392,7 +378,7 @@ struct TLSSelectionRangeID : public TLSSelectionAll
if (cif::VERBOSE)
{
cout << string(indentLevel * 2, ' ') << "Through " << m_first << ':' << m_last << endl;
std::cout << std::string(indentLevel * 2, ' ') << "Through " << m_first << ':' << m_last << std::endl;
DumpSelection(residues, indentLevel);
}
}
......@@ -409,7 +395,7 @@ struct TLSSelectionUnion : public TLSSelection
TLSSelectionUnion(TLSSelectionPtr& lhs, TLSSelectionPtr&& rhs)
: lhs(lhs.release()), rhs(rhs.release()) {}
virtual void CollectResidues(Datablock& db, vector<TLSResidue>& residues, int indentLevel) const
virtual void CollectResidues(Datablock& db, std::vector<TLSResidue>& residues, int indentLevel) const
{
auto a = residues;
for_each(a.begin(), a.end(), [](auto& r) { r.selected = false; });
......@@ -425,7 +411,7 @@ struct TLSSelectionUnion : public TLSSelection
if (cif::VERBOSE)
{
cout << string(indentLevel * 2, ' ') << "Union" << endl;
std::cout << std::string(indentLevel * 2, ' ') << "Union" << std::endl;
DumpSelection(residues, indentLevel);
}
}
......@@ -442,7 +428,7 @@ struct TLSSelectionIntersection : public TLSSelection
TLSSelectionIntersection(TLSSelectionPtr& lhs, TLSSelectionPtr&& rhs)
: lhs(lhs.release()), rhs(rhs.release()) {}
virtual void CollectResidues(Datablock& db, vector<TLSResidue>& residues, int indentLevel) const
virtual void CollectResidues(Datablock& db, std::vector<TLSResidue>& residues, int indentLevel) const
{
auto a = residues;
for_each(a.begin(), a.end(), [](auto& r) { r.selected = false; });
......@@ -458,7 +444,7 @@ struct TLSSelectionIntersection : public TLSSelection
if (cif::VERBOSE)
{
cout << string(indentLevel * 2, ' ') << "Intersection" << endl;
std::cout << std::string(indentLevel * 2, ' ') << "Intersection" << std::endl;
DumpSelection(residues, indentLevel);
}
}
......@@ -470,31 +456,31 @@ struct TLSSelectionIntersection : public TLSSelection
struct TLSSelectionByName : public TLSSelectionAll
{
public:
TLSSelectionByName(const string& resname)
TLSSelectionByName(const std::string& resname)
: m_name(resname) {}
virtual void CollectResidues(Datablock& db, vector<TLSResidue>& residues, int indentLevel) const
virtual void CollectResidues(Datablock& db, std::vector<TLSResidue>& residues, int indentLevel) const
{
for (auto& r: residues)
r.selected = r.name == m_name;
if (cif::VERBOSE)
{
cout << string(indentLevel * 2, ' ') << "Name " << m_name << endl;
std::cout << std::string(indentLevel * 2, ' ') << "Name " << m_name << std::endl;
DumpSelection(residues, indentLevel);
}
}
string m_name;
std::string m_name;
};
struct TLSSelectionByElement : public TLSSelectionAll
{
public:
TLSSelectionByElement(const string& element)
TLSSelectionByElement(const std::string& element)
: m_element(element) {}
virtual void CollectResidues(Datablock& db, vector<TLSResidue>& residues, int indentLevel) const
virtual void CollectResidues(Datablock& db, std::vector<TLSResidue>& residues, int indentLevel) const
{
// rationale... We want to select residues only. So we select
// residues that have just a single atom of type m_element.
......@@ -506,12 +492,12 @@ struct TLSSelectionByElement : public TLSSelectionAll
if (cif::VERBOSE)
{
cout << string(indentLevel * 2, ' ') << "Element " << m_element << endl;
std::cout << std::string(indentLevel * 2, ' ') << "Element " << m_element << std::endl;
DumpSelection(residues, indentLevel);
}
}
string m_element;
std::string m_element;
};
// --------------------------------------------------------------------
......@@ -519,7 +505,7 @@ struct TLSSelectionByElement : public TLSSelectionAll
class TLSSelectionParserImpl
{
public:
TLSSelectionParserImpl(const string& selection)
TLSSelectionParserImpl(const std::string& selection)
: m_selection(selection), m_p(m_selection.begin()), m_end(m_selection.end()) {}
virtual TLSSelectionPtr Parse() = 0;
......@@ -528,12 +514,12 @@ class TLSSelectionParserImpl
virtual int GetNextToken() = 0;
virtual void Match(int token);
virtual string ToString(int token) = 0;
virtual std::string ToString(int token) = 0;
string m_selection;
string::iterator m_p, m_end;
std::string m_selection;
std::string::iterator m_p, m_end;
int m_lookahead;
string m_token;
std::string m_token;
};
......@@ -543,19 +529,19 @@ void TLSSelectionParserImpl::Match(int token)
m_lookahead = GetNextToken();
else
{
string expected;
std::string expected;
if (token >= 256)
expected = ToString(token);
else
expected = { char(token) };
string found;
std::string found;
if (m_lookahead >= 256)
found = ToString(m_lookahead) + " (" + m_token + ')';
else
found = { char(m_lookahead) };
throw runtime_error("Expected " + expected + " but found " + found);
throw std::runtime_error("Expected " + expected + " but found " + found);
}
}
......@@ -564,7 +550,7 @@ void TLSSelectionParserImpl::Match(int token)
class TLSSelectionParserImplPhenix : public TLSSelectionParserImpl
{
public:
TLSSelectionParserImplPhenix(const string& selection)
TLSSelectionParserImplPhenix(const std::string& selection)
: TLSSelectionParserImpl(selection)
{
m_lookahead = GetNextToken();
......@@ -601,10 +587,10 @@ class TLSSelectionParserImplPhenix : public TLSSelectionParserImpl
};
virtual int GetNextToken();
virtual string ToString(int token);
virtual std::string ToString(int token);
int m_value_i;
string m_value_s;
std::string m_value_s;
char m_icode;
};
......@@ -793,7 +779,7 @@ int TLSSelectionParserImplPhenix::GetNextToken()
if (ch == '\'')
result = pt_STRING;
else if (ch == 0)
throw runtime_error("Unexpected end of selection, missing quote character?");
throw std::runtime_error("Unexpected end of selection, missing quote character?");
else
m_value_s += ch;
break;
......@@ -814,7 +800,7 @@ int TLSSelectionParserImplPhenix::GetNextToken()
if (ch == '\"')
result = pt_STRING;
else if (ch == 0)
throw runtime_error("Unexpected end of selection, missing quote character?");
throw std::runtime_error("Unexpected end of selection, missing quote character?");
else
m_value_s += ch;
break;
......@@ -857,7 +843,7 @@ int TLSSelectionParserImplPhenix::GetNextToken()
return result;
}
string TLSSelectionParserImplPhenix::ToString(int token)
std::string TLSSelectionParserImplPhenix::ToString(int token)
{
switch (token)
{
......@@ -891,7 +877,7 @@ TLSSelectionPtr TLSSelectionParserImplPhenix::Parse()
Match(pt_KW_PDB);
// Match(pt_KW_ENTRY);
throw runtime_error("Unimplemented PDB ENTRY specification");
throw std::runtime_error("Unimplemented PDB ENTRY specification");
}
TLSSelectionPtr result = ParseAtomSelection();
......@@ -907,7 +893,7 @@ TLSSelectionPtr TLSSelectionParserImplPhenix::Parse()
Match(pt_EOLN);
if (extraParenthesis)
cerr << "WARNING: too many closing parenthesis in TLS selection statement" << endl;
std::cerr << "WARNING: too many closing parenthesis in TLS selection statement" << std::endl;
return result;
}
......@@ -948,7 +934,7 @@ TLSSelectionPtr TLSSelectionParserImplPhenix::ParseFactor()
Match('(');
result = ParseAtomSelection();
if (m_lookahead == pt_EOLN)
cerr << "WARNING: missing closing parenthesis in TLS selection statement" << endl;
std::cerr << "WARNING: missing closing parenthesis in TLS selection statement" << std::endl;
else
Match(')');
break;
......@@ -962,10 +948,10 @@ TLSSelectionPtr TLSSelectionParserImplPhenix::ParseFactor()
{
Match(pt_KW_CHAIN);
string chainID = m_value_s;
std::string chainID = m_value_s;
if (m_lookahead == pt_NUMBER) // sigh
{
chainID = to_string(m_value_i);
chainID = std::to_string(m_value_i);
Match(pt_NUMBER);
}
else
......@@ -978,7 +964,7 @@ TLSSelectionPtr TLSSelectionParserImplPhenix::ParseFactor()
case pt_KW_RESNAME:
{
Match(pt_KW_RESNAME);
string name = m_value_s;
std::string name = m_value_s;
Match(pt_IDENT);
result.reset(new TLSSelectionByName(name));
break;
......@@ -987,7 +973,7 @@ TLSSelectionPtr TLSSelectionParserImplPhenix::ParseFactor()
case pt_KW_ELEMENT:
{
Match(pt_KW_ELEMENT);
string element = m_value_s;
std::string element = m_value_s;
Match(pt_IDENT);
result.reset(new TLSSelectionByElement(element));
break;
......@@ -1050,7 +1036,7 @@ TLSSelectionPtr TLSSelectionParserImplPhenix::ParseFactor()
else
{
if (cif::VERBOSE and (icode_from or icode_to))
cerr << "Warning, ignoring insertion codes" << endl;
std::cerr << "Warning, ignoring insertion codes" << std::endl;
result.reset(new TLSSelectionRangeSeq(from, to));
}
......@@ -1067,7 +1053,7 @@ TLSSelectionPtr TLSSelectionParserImplPhenix::ParseFactor()
break;
default:
throw runtime_error("Unexpected token " + ToString(m_lookahead) + " (" + m_token + ')');
throw std::runtime_error("Unexpected token " + ToString(m_lookahead) + " (" + m_token + ')');
}
return result;
......@@ -1078,7 +1064,7 @@ TLSSelectionPtr TLSSelectionParserImplPhenix::ParseFactor()
class TLSSelectionParserImplBuster : public TLSSelectionParserImpl
{
public:
TLSSelectionParserImplBuster(const string& selection);
TLSSelectionParserImplBuster(const std::string& selection);
virtual TLSSelectionPtr Parse();
......@@ -1092,19 +1078,19 @@ class TLSSelectionParserImplBuster : public TLSSelectionParserImpl
};
virtual int GetNextToken();
virtual string ToString(int token);
virtual std::string ToString(int token);
TLSSelectionPtr ParseGroup();
tuple<string,int> ParseAtom();
std::tuple<std::string,int> ParseAtom();
TLSSelectionPtr ParseOldGroup();
int m_value_i;
string m_value_s;
std::string m_value_s;
bool m_parsing_old_style = false;
};
TLSSelectionParserImplBuster::TLSSelectionParserImplBuster(const string& selection)
TLSSelectionParserImplBuster::TLSSelectionParserImplBuster(const std::string& selection)
: TLSSelectionParserImpl(selection)
{
m_lookahead = GetNextToken();
......@@ -1192,12 +1178,12 @@ int TLSSelectionParserImplBuster::GetNextToken()
return result;
}
string TLSSelectionParserImplBuster::ToString(int token)
std::string TLSSelectionParserImplBuster::ToString(int token)
{
switch (token)
{
case bt_IDENT: return "identifier (" + m_value_s + ')';
case bt_NUMBER: return "number (" + to_string(m_value_i) + ')';
case bt_NUMBER: return "number (" + std::to_string(m_value_i) + ')';
case bt_EOLN: return "end of line";
default:
......@@ -1210,7 +1196,7 @@ TLSSelectionPtr TLSSelectionParserImplBuster::ParseGroup()
{
TLSSelectionPtr result;
auto add = [&result](const string& chainID, int from, int to)
auto add = [&result](const std::string& chainID, int from, int to)
{
TLSSelectionPtr sc(new TLSSelectionChain(chainID));
TLSSelectionPtr sr(new TLSSelectionRangeSeq(from, to));
......@@ -1226,13 +1212,13 @@ TLSSelectionPtr TLSSelectionParserImplBuster::ParseGroup()
do
{
string chain1;
std::string chain1;
int seqNr1;
std::tie(chain1, seqNr1) = ParseAtom();
if (m_lookahead == '-')
{
string chain2;
std::string chain2;
int seqNr2 = seqNr1;
Match('-');
......@@ -1247,7 +1233,7 @@ TLSSelectionPtr TLSSelectionParserImplBuster::ParseGroup()
std::tie(chain2, seqNr2) = ParseAtom();
if (chain1 != chain2)
{
cerr << "Warning, ranges over multiple chains detected" << endl;
std::cerr << "Warning, ranges over multiple chains detected" << std::endl;
TLSSelectionPtr sc1(new TLSSelectionChain(chain1));
TLSSelectionPtr sr1(new TLSSelectionRangeSeq(seqNr1, kResidueNrWildcard));
......@@ -1281,9 +1267,9 @@ TLSSelectionPtr TLSSelectionParserImplBuster::ParseGroup()
return result;
}
tuple<string,int> TLSSelectionParserImplBuster::ParseAtom()
std::tuple<std::string,int> TLSSelectionParserImplBuster::ParseAtom()
{
string chain = m_value_s;
std::string chain = m_value_s;
int seqNr = kResidueNrWildcard;
if (m_lookahead == '*')
......@@ -1303,10 +1289,10 @@ tuple<string,int> TLSSelectionParserImplBuster::ParseAtom()
if (m_lookahead == ':')
{
Match(':');
string atom = m_value_s;
std::string atom = m_value_s;
if (cif::VERBOSE)
cerr << "Warning: ignoring atom ID '" << atom << "' in TLS selection" << endl;
std::cerr << "Warning: ignoring atom ID '" << atom << "' in TLS selection" << std::endl;
Match(bt_IDENT);
}
......@@ -1327,7 +1313,7 @@ TLSSelectionPtr TLSSelectionParserImplBuster::Parse()
class TLSSelectionParserImplBusterOld : public TLSSelectionParserImpl
{
public:
TLSSelectionParserImplBusterOld(const string& selection)
TLSSelectionParserImplBusterOld(const std::string& selection)
: TLSSelectionParserImpl(selection)
{
m_lookahead = GetNextToken();
......@@ -1368,10 +1354,10 @@ class TLSSelectionParserImplBusterOld : public TLSSelectionParserImpl
};
virtual int GetNextToken();
virtual string ToString(int token);
virtual std::string ToString(int token);
int m_value_i;
string m_value_s;
std::string m_value_s;
int m_value_r[2];
};
......@@ -1493,7 +1479,7 @@ int TLSSelectionParserImplBusterOld::GetNextToken()
case st_CHAINRESID:
if (isalpha(ch))
{
m_value_s += to_string(m_value_i);
m_value_s += std::to_string(m_value_i);
m_value_s += ch;
state = st_IDENT;
}
......@@ -1533,7 +1519,7 @@ int TLSSelectionParserImplBusterOld::GetNextToken()
if (ch == '\'')
result = pt_STRING;
else if (ch == 0)
throw runtime_error("Unexpected end of selection, missing quote character?");
throw std::runtime_error("Unexpected end of selection, missing quote character?");
else
m_value_s += ch;
break;
......@@ -1570,14 +1556,14 @@ int TLSSelectionParserImplBusterOld::GetNextToken()
return result;
}
string TLSSelectionParserImplBusterOld::ToString(int token)
std::string TLSSelectionParserImplBusterOld::ToString(int token)
{
switch (token)
{
case pt_IDENT: return "identifier (" + m_value_s + ')';
case pt_STRING: return "string (" + m_value_s + ')';
case pt_NUMBER: return "number (" + to_string(m_value_i) + ')';
case pt_RANGE: return "range (" + to_string(m_value_r[0]) + ':' + to_string(m_value_r[1]) + ')';
case pt_NUMBER: return "number (" + std::to_string(m_value_i) + ')';
case pt_RANGE: return "range (" + std::to_string(m_value_r[0]) + ':' + std::to_string(m_value_r[1]) + ')';
case pt_EOLN: return "end of line";
case pt_KW_ALL: return "ALL";
......@@ -1605,7 +1591,7 @@ TLSSelectionPtr TLSSelectionParserImplBusterOld::Parse()
Match(pt_KW_PDB);
// Match(pt_KW_ENTRY);
throw runtime_error("Unimplemented PDB ENTRY specification");
throw std::runtime_error("Unimplemented PDB ENTRY specification");
}
TLSSelectionPtr result = ParseAtomSelection();
......@@ -1662,10 +1648,10 @@ TLSSelectionPtr TLSSelectionParserImplBusterOld::ParseFactor()
{
Match(pt_KW_CHAIN);
string chainID = m_value_s;
std::string chainID = m_value_s;
if (m_lookahead == pt_NUMBER) // sigh
{
chainID = to_string(m_value_i);
chainID = std::to_string(m_value_i);
Match(pt_NUMBER);
}
else
......@@ -1678,7 +1664,7 @@ TLSSelectionPtr TLSSelectionParserImplBusterOld::ParseFactor()
case pt_KW_RESNAME:
{
Match(pt_KW_RESNAME);
string name = m_value_s;
std::string name = m_value_s;
Match(pt_IDENT);
result.reset(new TLSSelectionByName(name));
break;
......@@ -1704,7 +1690,7 @@ TLSSelectionPtr TLSSelectionParserImplBusterOld::ParseFactor()
break;
default:
throw runtime_error("Unexpected token " + ToString(m_lookahead));
throw std::runtime_error("Unexpected token " + ToString(m_lookahead));
}
return result;
......@@ -1766,7 +1752,7 @@ TLSSelectionPtr TLSSelectionParserImplBusterOld::ParseChainResid()
int from, to;
from = to = m_value_i;
string chainID = m_value_s;
std::string chainID = m_value_s;
Match(pt_CHAINRESID);
......@@ -1776,7 +1762,7 @@ TLSSelectionPtr TLSSelectionParserImplBusterOld::ParseChainResid()
to = m_value_i;
if (m_value_s != chainID)
throw runtime_error("Cannot have two different chainIDs in a range selection");
throw std::runtime_error("Cannot have two different chainIDs in a range selection");
Match(pt_CHAINRESID);
}
......@@ -1807,7 +1793,7 @@ TLSSelectionPtr TLSSelectionParserImplBusterOld::ParseChainResid()
class TLSSelectionParserBase
{
public:
virtual TLSSelectionPtr Parse(const string& selection) const = 0;
virtual TLSSelectionPtr Parse(const std::string& selection) const = 0;
virtual ~TLSSelectionParserBase() {}
};
......@@ -1815,7 +1801,7 @@ template<typename IMPL>
class TLSSelectionParser
{
public:
virtual TLSSelectionPtr Parse(const string& selection) const
virtual TLSSelectionPtr Parse(const std::string& selection) const
{
TLSSelectionPtr result;
......@@ -1824,9 +1810,9 @@ class TLSSelectionParser
IMPL p(selection);
result = p.Parse();
}
catch (const exception& ex)
catch (const std::exception& ex)
{
cerr << "ParseError: " << ex.what() << endl;
std::cerr << "ParseError: " << ex.what() << std::endl;
}
return result;
......@@ -1836,7 +1822,7 @@ class TLSSelectionParser
// --------------------------------------------------------------------
TLSSelectionPtr ParseSelectionDetails(const string& program, const string& selection)
TLSSelectionPtr ParseSelectionDetails(const std::string& program, const std::string& selection)
{
TLSSelectionParser<TLSSelectionParserImplPhenix> phenix;
TLSSelectionParser<TLSSelectionParserImplBuster> buster;
......@@ -1851,14 +1837,14 @@ TLSSelectionPtr ParseSelectionDetails(const string& program, const string& selec
if (not result)
{
if (cif::VERBOSE)
cerr << "Falling back to old BUSTER" << endl;
std::cerr << "Falling back to old BUSTER" << std::endl;
result = busterOld.Parse(selection);
}
if (not result)
{
if (cif::VERBOSE)
cerr << "Falling back to PHENIX" << endl;
std::cerr << "Falling back to PHENIX" << std::endl;
result = phenix.Parse(selection);
}
}
......@@ -1869,35 +1855,35 @@ TLSSelectionPtr ParseSelectionDetails(const string& program, const string& selec
if (not result)
{
if (cif::VERBOSE)
cerr << "Falling back to BUSTER" << endl;
std::cerr << "Falling back to BUSTER" << std::endl;
result = buster.Parse(selection);
}
if (not result)
{
if (cif::VERBOSE)
cerr << "Falling back to old BUSTER" << endl;
std::cerr << "Falling back to old BUSTER" << std::endl;
result = busterOld.Parse(selection);
}
}
else
{
if (cif::VERBOSE)
cerr << "No known program specified, trying PHENIX" << endl;
std::cerr << "No known program specified, trying PHENIX" << std::endl;
result = phenix.Parse(selection);
if (not result)
{
if (cif::VERBOSE)
cerr << "Falling back to BUSTER" << endl;
std::cerr << "Falling back to BUSTER" << std::endl;
result = buster.Parse(selection);
}
if (not result)
{
if (cif::VERBOSE)
cerr << "Falling back to old BUSTER" << endl;
std::cerr << "Falling back to old BUSTER" << std::endl;
result = busterOld.Parse(selection);
}
}
......
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