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Commit 4206f266 by maarten
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Remove orphans 

git-svn-id: svn+ssh://gitlab/srv/svn-repos/pdb-redo/trunk@409 a1961a4f-ab94-4bcc-80e8-33b5a54de466
parent dd7a4f11
Showing with 301 additions and 66 deletions
include/cif++/Cif++.h
...@@ -237,11 +237,9 @@ class Datablock ...@@ -237,11 +237,9 @@ class Datablock
namespace detail namespace detail
{ {
// ItemReference is a helper class // ItemReference is a helper class
struct ItemReference class ItemReference
{ {
const char* mName; public:
size_t mColumn;
ItemRow* mRow;
template<typename T> template<typename T>
ItemReference& operator=(const T& value) ItemReference& operator=(const T& value)
...@@ -293,6 +291,20 @@ namespace detail ...@@ -293,6 +291,20 @@ namespace detail
bool operator!=(const string& s) const { return s != c_str(); } bool operator!=(const string& s) const { return s != c_str(); }
bool operator==(const string& s) const { return s == c_str(); } bool operator==(const string& s) const { return s == c_str(); }
private:
friend class ::cif::Row;
ItemReference(const char* name, size_t column, Row& row)
: mName(name), mColumn(column), mRow(row) {}
ItemReference(const char* name, size_t column, const Row& row)
: mName(name), mColumn(column), mRow(const_cast<Row&>(row)), mConst(true) {}
const char* mName;
size_t mColumn;
Row& mRow;
bool mConst = false;
}; };
template<> template<>
...@@ -514,10 +526,28 @@ class Row ...@@ -514,10 +526,28 @@ class Row
friend class RowComparator; friend class RowComparator;
friend struct detail::ItemReference; friend struct detail::ItemReference;
Row(ItemRow* data = nullptr) : mData(data) {} Row(ItemRow* data = nullptr, bool cascadeUpdate = true)
: mData(data), mCascadeUpdate(cascadeUpdate) {}
Row(const ItemRow* data)
: Row(const_cast<ItemRow*>(data), false)
{}
Row(const Row& rhs); Row(const Row& rhs);
Row& operator=(const Row& rhs); Row& operator=(const Row& rhs);
/// When updating a value, you might want to change linked records as well
/// But not always.
void setCascadeUpdate(bool cascadeUpdate)
{
mCascadeUpdate = cascadeUpdate;
}
void setCascadeDelet(bool cascadeDelete)
{
mCascadeDelete = cascadeDelete;
}
struct const_iterator : public std::iterator<std::forward_iterator_tag, const Item> struct const_iterator : public std::iterator<std::forward_iterator_tag, const Item>
{ {
typedef std::iterator<std::forward_iterator_tag, Item> baseType; typedef std::iterator<std::forward_iterator_tag, Item> baseType;
...@@ -557,33 +587,35 @@ class Row ...@@ -557,33 +587,35 @@ class Row
// TODO: implement real const version? // TODO: implement real const version?
friend class detail::ItemReference;
const detail::ItemReference operator[](size_t column) const const detail::ItemReference operator[](size_t column) const
{ {
return detail::ItemReference{"<anonymous column>", column, mData}; return detail::ItemReference("<anonymous column>", column, *this);
} }
const detail::ItemReference operator[](const char* itemTag) const const detail::ItemReference operator[](const char* itemTag) const
{ {
size_t column = ColumnForItemTag(itemTag); size_t column = ColumnForItemTag(itemTag);
return detail::ItemReference{itemTag, column, mData}; return detail::ItemReference(itemTag, column, *this);
} }
detail::ItemReference operator[](const char* itemTag) detail::ItemReference operator[](const char* itemTag)
{ {
size_t column = ColumnForItemTag(itemTag); size_t column = ColumnForItemTag(itemTag);
return detail::ItemReference{itemTag, column, mData}; return detail::ItemReference(itemTag, column, *this);
} }
const detail::ItemReference operator[](const string& itemTag) const const detail::ItemReference operator[](const string& itemTag) const
{ {
size_t column = ColumnForItemTag(itemTag.c_str()); size_t column = ColumnForItemTag(itemTag.c_str());
return detail::ItemReference{itemTag.c_str(), column, mData}; return detail::ItemReference(itemTag.c_str(), column, *this);
} }
detail::ItemReference operator[](const string& itemTag) detail::ItemReference operator[](const string& itemTag)
{ {
size_t column = ColumnForItemTag(itemTag.c_str()); size_t column = ColumnForItemTag(itemTag.c_str());
return detail::ItemReference{itemTag.c_str(), column, mData}; return detail::ItemReference(itemTag.c_str(), column, *this);
} }
template<typename... C> template<typename... C>
...@@ -612,6 +644,8 @@ class Row ...@@ -612,6 +644,8 @@ class Row
private: private:
friend std::ostream& operator<<(std::ostream& os, const Row& row);
void assign(const string& name, const string& value, bool emplacing); void assign(const string& name, const string& value, bool emplacing);
void assign(size_t column, const string& value, bool emplacing); void assign(size_t column, const string& value, bool emplacing);
void assign(const Item& i, bool emplacing); void assign(const Item& i, bool emplacing);
...@@ -622,10 +656,14 @@ class Row ...@@ -622,10 +656,14 @@ class Row
ItemRow* mData; ItemRow* mData;
uint32 mLineNr = 0; uint32 mLineNr = 0;
bool mCascadeUpdate = true;
bool mCascadeDelete = true;
}; };
// swap for Rows is defined below // swap for Rows is defined below
std::ostream& operator<<(std::ostream& os, const Row& row);
// -------------------------------------------------------------------- // --------------------------------------------------------------------
// some more templates to be able to do querying // some more templates to be able to do querying
...@@ -651,7 +689,7 @@ struct AllConditionImpl : public ConditionImpl ...@@ -651,7 +689,7 @@ struct AllConditionImpl : public ConditionImpl
struct Condition struct Condition
{ {
Condition() : mImpl(new detail::AllConditionImpl()) {} Condition() : mImpl(nullptr) {}
Condition(detail::ConditionImpl* impl) : mImpl(impl) {} Condition(detail::ConditionImpl* impl) : mImpl(impl) {}
Condition(Condition&& rhs) Condition(Condition&& rhs)
...@@ -673,6 +711,7 @@ struct Condition ...@@ -673,6 +711,7 @@ struct Condition
void prepare(const Category& c) void prepare(const Category& c)
{ {
if (mImpl)
mImpl->prepare(c); mImpl->prepare(c);
mPrepared = true; mPrepared = true;
} }
...@@ -681,12 +720,12 @@ struct Condition ...@@ -681,12 +720,12 @@ struct Condition
{ {
assert(mImpl); assert(mImpl);
assert(mPrepared); assert(mPrepared);
return mImpl->test(c, r); return mImpl ? mImpl->test(c, r) : false;
} }
std::string str() const std::string str() const
{ {
return mImpl->str(); return mImpl ? mImpl->str() : "";
} }
detail::ConditionImpl* mImpl; detail::ConditionImpl* mImpl;
...@@ -919,12 +958,20 @@ struct orConditionImpl : public ConditionImpl ...@@ -919,12 +958,20 @@ struct orConditionImpl : public ConditionImpl
inline Condition operator&&(Condition&& a, Condition&& b) inline Condition operator&&(Condition&& a, Condition&& b)
{ {
if (a.mImpl and b.mImpl)
return Condition(new detail::andConditionImpl(std::move(a), std::move(b))); return Condition(new detail::andConditionImpl(std::move(a), std::move(b)));
if (a.mImpl)
return Condition(std::move(a));
return Condition(std::move(b));
} }
inline Condition operator||(Condition&& a, Condition&& b) inline Condition operator||(Condition&& a, Condition&& b)
{ {
if (a.mImpl and b.mImpl)
return Condition(new detail::orConditionImpl(std::move(a), std::move(b))); return Condition(new detail::orConditionImpl(std::move(a), std::move(b)));
if (a.mImpl)
return Condition(std::move(a));
return Condition(std::move(b));
} }
inline inline
...@@ -1073,8 +1120,6 @@ class Category ...@@ -1073,8 +1120,6 @@ class Category
const string name() const { return mName; } const string name() const { return mName; }
const detail::ItemReference getFirstItem(const char* ItemName) const;
struct iterator : public std::iterator<std::forward_iterator_tag, Row> struct iterator : public std::iterator<std::forward_iterator_tag, Row>
{ {
friend class Category; friend class Category;
...@@ -1101,6 +1146,32 @@ class Category ...@@ -1101,6 +1146,32 @@ class Category
iterator begin(); iterator begin();
iterator end(); iterator end();
struct const_iterator : public std::iterator<std::forward_iterator_tag, const Row>
{
friend class Category;
typedef std::iterator<std::forward_iterator_tag, const Row> baseType;
typedef typename baseType::pointer pointer;
typedef typename baseType::reference reference;
const_iterator(const ItemRow* data) : mCurrent(data) {}
reference operator*() { return mCurrent; }
pointer operator->() { return &mCurrent; }
const_iterator& operator++();
const_iterator operator++(int) { const_iterator result(*this); this->operator++(); return result; }
bool operator==(const const_iterator& rhs) const { return mCurrent == rhs.mCurrent; }
bool operator!=(const const_iterator& rhs) const { return not (mCurrent == rhs.mCurrent); }
private:
const Row mCurrent;
};
const_iterator begin() const;
const_iterator end() const;
bool empty() const; bool empty() const;
size_t size() const; size_t size() const;
...@@ -1132,6 +1203,12 @@ class Category ...@@ -1132,6 +1203,12 @@ class Category
void erase(Row r); void erase(Row r);
void erase(iterator ri); void erase(iterator ri);
void eraseOrphans(Condition&& cond);
/// an orphan is a row that is the child side of one or more
/// links and for which there is no single parent left.
bool isOrphan(Row r);
bool isValid(); bool isValid();
const Validator& getValidator() const; const Validator& getValidator() const;
...@@ -1157,6 +1234,7 @@ class Category ...@@ -1157,6 +1234,7 @@ class Category
vector<string> getColumnNames() const; vector<string> getColumnNames() const;
void reorderByIndex(); void reorderByIndex();
void sort(std::function<int(const Row&, const Row&)> comparator);
private: private:
......
include/cif++/Structure.h
...@@ -141,7 +141,12 @@ class Atom ...@@ -141,7 +141,12 @@ class Atom
std::swap(mImpl, b.mImpl); std::swap(mImpl, b.mImpl);
} }
int compare(const Atom& b) const;
private: private:
friend class Structure;
void setID(int id);
struct AtomImpl* mImpl; struct AtomImpl* mImpl;
}; };
...@@ -392,6 +397,10 @@ class Structure ...@@ -392,6 +397,10 @@ class Structure
void changeResidue(const Residue& res, const std::string& newCompound, void changeResidue(const Residue& res, const std::string& newCompound,
const std::vector<std::tuple<std::string,std::string>>& remappedAtoms); const std::vector<std::tuple<std::string,std::string>>& remappedAtoms);
/// To sort the atoms in order of model > asym-id > res-id > atom-id
/// Will asssign new atom_id's to all atoms. Be carefull
void sortAtoms();
// iterator for all residues // iterator for all residues
class residue_iterator : public std::iterator<std::forward_iterator_tag, const Residue> class residue_iterator : public std::iterator<std::forward_iterator_tag, const Residue>
......
src/Cif++.cpp
...@@ -212,7 +212,10 @@ namespace detail ...@@ -212,7 +212,10 @@ namespace detail
template<> template<>
ItemReference& ItemReference::operator=(const string& value) ItemReference& ItemReference::operator=(const string& value)
{ {
Row(mRow).assign(mName, value, false); if (mConst)
throw logic_error("Attempt to write to a constant row");
mRow.assign(mName, value, false);
return *this; return *this;
} }
...@@ -220,11 +223,11 @@ const char* ItemReference::c_str() const ...@@ -220,11 +223,11 @@ const char* ItemReference::c_str() const
{ {
const char* result = kEmptyResult; const char* result = kEmptyResult;
if (mRow != nullptr /* and mRow->mCategory != nullptr*/) if (mRow.mData != nullptr /* and mRow.mData->mCategory != nullptr*/)
{ {
// assert(mRow->mCategory); // assert(mRow.mData->mCategory);
for (auto iv = mRow->mValues; iv != nullptr; iv = iv->mNext) for (auto iv = mRow.mData->mValues; iv != nullptr; iv = iv->mNext)
{ {
if (iv->mColumnIndex == mColumn) if (iv->mColumnIndex == mColumn)
{ {
...@@ -243,9 +246,9 @@ const char* ItemReference::c_str(const char* defaultValue) const ...@@ -243,9 +246,9 @@ const char* ItemReference::c_str(const char* defaultValue) const
{ {
const char* result = defaultValue; const char* result = defaultValue;
if (mRow != nullptr and mRow->mCategory != nullptr) if (mRow.mData != nullptr and mRow.mData->mCategory != nullptr)
{ {
for (auto iv = mRow->mValues; iv != nullptr; iv = iv->mNext) for (auto iv = mRow.mData->mValues; iv != nullptr; iv = iv->mNext)
{ {
if (iv->mColumnIndex == mColumn) if (iv->mColumnIndex == mColumn)
{ {
...@@ -257,9 +260,9 @@ const char* ItemReference::c_str(const char* defaultValue) const ...@@ -257,9 +260,9 @@ const char* ItemReference::c_str(const char* defaultValue) const
} }
} }
if (result == defaultValue and mColumn < mRow->mCategory->mColumns.size()) // not found, perhaps the category has a default defined? if (result == defaultValue and mColumn < mRow.mData->mCategory->mColumns.size()) // not found, perhaps the category has a default defined?
{ {
auto iv = mRow->mCategory->mColumns[mColumn].mValidator; auto iv = mRow.mData->mCategory->mColumns[mColumn].mValidator;
if (iv != nullptr and not iv->mDefault.empty()) if (iv != nullptr and not iv->mDefault.empty())
result = iv->mDefault.c_str(); result = iv->mDefault.c_str();
} }
...@@ -275,7 +278,7 @@ bool ItemReference::empty() const ...@@ -275,7 +278,7 @@ bool ItemReference::empty() const
void ItemReference::swap(ItemReference& b) void ItemReference::swap(ItemReference& b)
{ {
Row::swap(mColumn, mRow, b.mRow); Row::swap(mColumn, mRow.mData, b.mRow.mData);
} }
} }
...@@ -304,7 +307,12 @@ string Datablock::firstItem(const string& tag) const ...@@ -304,7 +307,12 @@ string Datablock::firstItem(const string& tag) const
{ {
if (iequals(cat.name(), catName)) if (iequals(cat.name(), catName))
{ {
result = cat.getFirstItem(itemName.c_str()).as<string>(); for (auto row: cat)
{
result = row[itemName].as<string>();
break;
}
break; break;
} }
} }
...@@ -1227,6 +1235,35 @@ void Category::reorderByIndex() ...@@ -1227,6 +1235,35 @@ void Category::reorderByIndex()
std::tie(mHead, mTail) = mIndex->reorder(); std::tie(mHead, mTail) = mIndex->reorder();
} }
void Category::sort(std::function<int(const Row&, const Row&)> comparator)
{
if (mHead == nullptr)
return;
vector<ItemRow*> rows;
for (auto itemRow = mHead; itemRow != nullptr; itemRow = itemRow->mNext)
rows.push_back(itemRow);
std::stable_sort(rows.begin(), rows.end(),
[&rows,&comparator](ItemRow* ia, ItemRow* ib)
{
Row ra(ia);
Row rb(ib);
return comparator(ra, rb) < 0;
});
mHead = rows.front();
mTail = rows.back();
auto r = mHead;
for (size_t i = 1; i < rows.size(); ++i)
r = r->mNext = rows[i];
r->mNext = nullptr;
assert(r == mTail);
assert(size() == rows.size());
}
size_t Category::size() const size_t Category::size() const
{ {
size_t result = 0; size_t result = 0;
...@@ -1433,6 +1470,29 @@ void Category::erase(Condition&& cond) ...@@ -1433,6 +1470,29 @@ void Category::erase(Condition&& cond)
erase(r); erase(r);
} }
void Category::eraseOrphans(Condition&& cond)
{
RowSet remove(*this);
cond.prepare(*this);
for (auto r: *this)
{
if (cond(*this, r) and isOrphan(r))
{
if (VERBOSE > 1)
cerr << "Removing orphaned record: " << endl
<< r << endl
<< endl;
remove.push_back(r);
}
}
for (auto r: remove)
erase(r);
}
void Category::erase(iterator p) void Category::erase(iterator p)
{ {
erase(*p); erase(*p);
...@@ -1444,6 +1504,30 @@ void Category::erase(Row r) ...@@ -1444,6 +1504,30 @@ void Category::erase(Row r)
if (mCatValidator) if (mCatValidator)
keys = iset(mCatValidator->mKeys.begin(), mCatValidator->mKeys.end()); keys = iset(mCatValidator->mKeys.begin(), mCatValidator->mKeys.end());
if (mHead == nullptr)
throw runtime_error("erase");
if (mIndex != nullptr)
mIndex->erase(r.mData);
if (r == mHead)
{
mHead = mHead->mNext;
r.mData->mNext = nullptr;
}
else
{
for (auto pi = mHead; pi != nullptr; pi = pi->mNext)
{
if (pi->mNext == r.mData)
{
pi->mNext = r.mData->mNext;
r.mData->mNext = nullptr;
break;
}
}
}
// links are created based on the _pdbx_item_linked_group_list entries // links are created based on the _pdbx_item_linked_group_list entries
// in mmcif_pdbx.dic dictionary. // in mmcif_pdbx.dic dictionary.
// //
...@@ -1467,34 +1551,10 @@ void Category::erase(Row r) ...@@ -1467,34 +1551,10 @@ void Category::erase(Row r)
cond = move(cond) && (Key(link->mChildKeys[ix]) == value); cond = move(cond) && (Key(link->mChildKeys[ix]) == value);
} }
childCat->erase(move(cond)); childCat->eraseOrphans(move(cond));
} }
if (mHead == nullptr)
throw runtime_error("erase");
if (mIndex != nullptr)
mIndex->erase(r.mData);
if (r == mHead)
{
mHead = mHead->mNext;
r.mData->mNext = nullptr;
delete r.mData; delete r.mData;
}
else
{
for (auto pi = mHead; pi != nullptr; pi = pi->mNext)
{
if (pi->mNext == r.mData)
{
pi->mNext = r.mData->mNext;
r.mData->mNext = nullptr;
delete r.mData;
break;
}
}
}
// reset mTail, if needed // reset mTail, if needed
if (r == mTail) if (r == mTail)
...@@ -1512,12 +1572,6 @@ void Category::getTagOrder(vector<string>& tags) const ...@@ -1512,12 +1572,6 @@ void Category::getTagOrder(vector<string>& tags) const
tags.push_back("_" + mName + "." + c.mName); tags.push_back("_" + mName + "." + c.mName);
} }
const detail::ItemReference Category::getFirstItem(const char* itemName) const
{
size_t column = getColumnIndex(itemName);
return detail::ItemReference{itemName, column, mHead};
}
Category::iterator Category::begin() Category::iterator Category::begin()
{ {
return iterator(mHead); return iterator(mHead);
...@@ -1528,6 +1582,46 @@ Category::iterator Category::end() ...@@ -1528,6 +1582,46 @@ Category::iterator Category::end()
return iterator(nullptr); return iterator(nullptr);
} }
Category::const_iterator Category::begin() const
{
return const_iterator(mHead);
}
Category::const_iterator Category::end() const
{
return const_iterator(nullptr);
}
bool Category::isOrphan(Row r)
{
// be safe
if (mCatValidator == nullptr)
return false;
bool isOrphan = true;
for (auto& link: mValidator->getLinksForChild(mName))
{
auto parentCat = mDb.get(link->mParentCategory);
if (parentCat == nullptr)
continue;
Condition cond;
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);
}
if (parentCat->exists(std::move(cond)))
{
isOrphan = false;
break;
}
}
return isOrphan;
}
bool Category::isValid() bool Category::isValid()
{ {
bool result = true; bool result = true;
...@@ -1931,12 +2025,14 @@ void Category::write(ostream& os, const vector<string>& columns) ...@@ -1931,12 +2025,14 @@ void Category::write(ostream& os, const vector<string>& columns)
Row::Row(const Row& rhs) Row::Row(const Row& rhs)
: mData(rhs.mData) : mData(rhs.mData)
, mCascadeUpdate(rhs.mCascadeUpdate)
{ {
} }
Row& Row::operator=(const Row& rhs) Row& Row::operator=(const Row& rhs)
{ {
mData = rhs.mData; mData = rhs.mData;
mCascadeUpdate = rhs.mCascadeUpdate;
return *this; return *this;
} }
...@@ -2043,7 +2139,7 @@ void Row::assign(size_t column, const string& value, bool emplacing) ...@@ -2043,7 +2139,7 @@ void Row::assign(size_t column, const string& value, bool emplacing)
// see if we need to update any child categories that depend on this value // see if we need to update any child categories that depend on this value
auto iv = col.mValidator; auto iv = col.mValidator;
if (not emplacing and iv != nullptr) if (not emplacing and iv != nullptr and mCascadeUpdate)
{ {
auto& validator = cat->getValidator(); auto& validator = cat->getValidator();
auto& db = cat->db(); auto& db = cat->db();
...@@ -2284,6 +2380,19 @@ void Row::const_iterator::fetch() ...@@ -2284,6 +2380,19 @@ void Row::const_iterator::fetch()
mPtr->mText); mPtr->mText);
} }
std::ostream& operator<<(std::ostream& os, const Row& row)
{
auto category = row.mData->mCategory;
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;
}
return os;
}
// -------------------------------------------------------------------- // --------------------------------------------------------------------
File::File() File::File()
......
src/CifValidator.cpp
...@@ -308,13 +308,18 @@ vector<const ValidateLink*> Validator::getLinksForParent(const string& category) ...@@ -308,13 +308,18 @@ vector<const ValidateLink*> Validator::getLinksForParent(const string& category)
return result; return result;
} }
//const ValidateLink* Validator::getLinksForChild(const string& category) const vector<const ValidateLink*> Validator::getLinksForChild(const string& category) const
//{ {
// auto i = find_if(mLinkValidators.begin(), mLinkValidators.end(), vector<const ValidateLink*> result;
// [&](auto& l) { return l.mChildCategory == category; });
// for (auto& l: mLinkValidators)
// return i == mLinkValidators.end() ? nullptr : &(*i); {
//} if (l.mChildCategory == category)
result.push_back(&l);
}
return result;
}
void Validator::reportError(const string& msg, bool fatal) void Validator::reportError(const string& msg, bool fatal)
{ {
......
src/Structure.cpp
...@@ -350,6 +350,16 @@ struct AtomImpl ...@@ -350,6 +350,16 @@ struct AtomImpl
return i->second; return i->second;
} }
int compare(const AtomImpl& b) const
{
int d = mAsymID.compare(b.mAsymID);
if (d == 0)
d = mSeqID - b.mSeqID;
if (d == 0)
d = mAtomID.compare(b.mAtomID);
return d;
}
const File& mFile; const File& mFile;
string mId; string mId;
AtomType mType; AtomType mType;
...@@ -586,6 +596,16 @@ float Atom::radius() const ...@@ -586,6 +596,16 @@ float Atom::radius() const
return mImpl->mRadius; return mImpl->mRadius;
} }
int Atom::compare(const Atom& b) const
{
return mImpl == b.mImpl ? 0 : mImpl->compare(*b.mImpl);
}
void Atom::setID(int id)
{
mImpl->mId = to_string(id);
}
// -------------------------------------------------------------------- // --------------------------------------------------------------------
// residue // residue
...@@ -1321,6 +1341,20 @@ void Structure::updateAtomIndex() ...@@ -1321,6 +1341,20 @@ void Structure::updateAtomIndex()
sort(mAtomIndex.begin(), mAtomIndex.end(), [this](size_t a, size_t b) { return mAtoms[a].id() < mAtoms[b].id(); }); sort(mAtomIndex.begin(), mAtomIndex.end(), [this](size_t a, size_t b) { return mAtoms[a].id() < mAtoms[b].id(); });
} }
void Structure::sortAtoms()
{
sort(mAtoms.begin(), mAtoms.end(), [](auto& a, auto& b) { return a.compare(b) < 0; });
int id = 1;
for (auto& atom: mAtoms)
{
atom.setID(id);
++id;
}
updateAtomIndex();
}
AtomView Structure::waters() const AtomView Structure::waters() const
{ {
AtomView result; AtomView result;
...@@ -1670,11 +1704,11 @@ void Structure::swapAtoms(Atom& a1, Atom& a2) ...@@ -1670,11 +1704,11 @@ void Structure::swapAtoms(Atom& a1, Atom& a2)
auto l1 = r1.front()["label_atom_id"]; auto l1 = r1.front()["label_atom_id"];
auto l2 = r2.front()["label_atom_id"]; auto l2 = r2.front()["label_atom_id"];
std::swap(l1, l2); l1.swap(l2);
auto l3 = r1.front()["auth_atom_id"]; auto l3 = r1.front()["auth_atom_id"];
auto l4 = r2.front()["auth_atom_id"]; auto l4 = r2.front()["auth_atom_id"];
std::swap(l3, l4); l3.swap(l4);
} }
void Structure::moveAtom(Atom& a, Point p) void Structure::moveAtom(Atom& a, Point p)
......
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