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libcifpp
Commit 3eb7e4c5 by Maarten L. Hekkelman
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Potential fix

parent fd08678f
Showing with 468 additions and 82 deletions
include/cif++/Cif++.hpp
...@@ -1115,6 +1115,20 @@ Condition operator==(const Key& key, const T& v) ...@@ -1115,6 +1115,20 @@ Condition operator==(const Key& key, const T& v)
{ return r[tag].template compare<T>(v, icase) == 0; }, s.str())); { return r[tag].template compare<T>(v, icase) == 0; }, s.str()));
} }
inline Condition operator==(const Key& key, const char *value)
{
if (value != nullptr and *value != 0)
{
std::ostringstream s;
s << " == " << value;
return Condition(new detail::KeyCompareConditionImpl(key.mItemTag, [tag = key.mItemTag, value](const Category& c, const Row& r, bool icase)
{ return r[tag].compare(value, icase) == 0; }, s.str()));
}
else
return Condition(new detail::KeyIsEmptyConditionImpl(key.mItemTag));
}
// inline Condition operator==(const Key& key, const detail::ItemReference& v) // inline Condition operator==(const Key& key, const detail::ItemReference& v)
// { // {
// if (v.empty()) // if (v.empty())
...@@ -1537,23 +1551,24 @@ class RowSet ...@@ -1537,23 +1551,24 @@ class RowSet
typedef std::vector<Row> base_type; typedef std::vector<Row> base_type;
public: public:
using size_type = std::size_t; using size_type = std::size_t;
using difference_type = std::ptrdiff_t; using difference_type = std::ptrdiff_t;
RowSet(Category& cat); RowSet(Category &cat);
RowSet(Category& cat, Condition&& cond); RowSet(Category &cat, Condition &&cond);
RowSet(const RowSet& rhs); RowSet(const RowSet &rhs);
RowSet(RowSet&& rhs); RowSet(RowSet &&rhs);
virtual ~RowSet(); virtual ~RowSet();
RowSet& operator=(const RowSet& rhs); RowSet &operator=(const RowSet &rhs);
RowSet& operator=(RowSet&& rhs); RowSet &operator=(RowSet &&rhs);
RowSet& orderBy(const std::string& Item) RowSet &orderBy(const std::string &Item)
{ return orderBy({ Item }); } {
return orderBy({Item});
}
RowSet& orderBy(std::initializer_list<std::string> Items); RowSet &orderBy(std::initializer_list<std::string> Items);
class iterator class iterator
{ {
...@@ -1561,22 +1576,26 @@ class RowSet ...@@ -1561,22 +1576,26 @@ class RowSet
using iterator_category = std::forward_iterator_tag; using iterator_category = std::forward_iterator_tag;
using value_type = Row; using value_type = Row;
using difference_type = std::ptrdiff_t; using difference_type = std::ptrdiff_t;
using pointer = value_type*; using pointer = value_type *;
using reference = value_type&; using reference = value_type &;
iterator() {} iterator() {}
iterator(const iterator& i) iterator(const iterator &i)
: mPos(i.mPos) : mPos(i.mPos)
, mEnd(i.mEnd) , mEnd(i.mEnd)
, mCurrentRow(i.mCurrentRow) {} , mCurrentRow(i.mCurrentRow)
{
}
iterator(const std::vector<ItemRow*>::iterator& p, const std::vector<ItemRow*>::iterator& e) iterator(const std::vector<ItemRow *>::iterator &p, const std::vector<ItemRow *>::iterator &e)
: mPos(p) : mPos(p)
, mEnd(e) , mEnd(e)
, mCurrentRow(p == e ? nullptr : *p) {} , mCurrentRow(p == e ? nullptr : *p)
{
}
iterator& operator=(const iterator& i) iterator &operator=(const iterator &i)
{ {
mPos = i.mPos; mPos = i.mPos;
mEnd = i.mEnd; mEnd = i.mEnd;
...@@ -1587,7 +1606,7 @@ class RowSet ...@@ -1587,7 +1606,7 @@ class RowSet
reference operator*() { return mCurrentRow; } reference operator*() { return mCurrentRow; }
pointer operator->() { return &mCurrentRow; } pointer operator->() { return &mCurrentRow; }
iterator& operator++() iterator &operator++()
{ {
++mPos; ++mPos;
if (mPos != mEnd) if (mPos != mEnd)
...@@ -1604,9 +1623,10 @@ class RowSet ...@@ -1604,9 +1623,10 @@ class RowSet
return t; return t;
} }
iterator& operator+=(difference_type i) iterator &operator+=(difference_type i)
{ {
while (i-- > 0) operator++(); while (i-- > 0)
operator++();
return *this; return *this;
} }
...@@ -1617,28 +1637,27 @@ class RowSet ...@@ -1617,28 +1637,27 @@ class RowSet
return result; return result;
} }
friend iterator operator+(difference_type i, const iterator& iter) friend iterator operator+(difference_type i, const iterator &iter)
{ {
auto result = iter; auto result = iter;
result += i; result += i;
return result; return result;
} }
friend difference_type operator-(const iterator& a, const iterator& b) friend difference_type operator-(const iterator &a, const iterator &b)
{ {
return std::distance(a.mPos, b.mPos); return std::distance(a.mPos, b.mPos);
} }
bool operator==(const iterator& i) const { return mPos == i.mPos; } bool operator==(const iterator &i) const { return mPos == i.mPos; }
bool operator!=(const iterator& i) const { return mPos != i.mPos; } bool operator!=(const iterator &i) const { return mPos != i.mPos; }
private: private:
friend class RowSet; friend class RowSet;
std::vector<ItemRow*>::iterator current() const { return mPos; } std::vector<ItemRow *>::iterator current() const { return mPos; }
std::vector<ItemRow*>::iterator mPos, mEnd; std::vector<ItemRow *>::iterator mPos, mEnd;
Row mCurrentRow; Row mCurrentRow;
}; };
...@@ -1649,7 +1668,7 @@ class RowSet ...@@ -1649,7 +1668,7 @@ class RowSet
size_t size() const { return mItems.size(); } size_t size() const { return mItems.size(); }
bool empty() const { return mItems.empty(); } bool empty() const { return mItems.empty(); }
template<typename InputIterator> template <typename InputIterator>
iterator insert(iterator pos, InputIterator b, InputIterator e) iterator insert(iterator pos, InputIterator b, InputIterator e)
{ {
difference_type offset = pos - begin(); difference_type offset = pos - begin();
...@@ -1658,17 +1677,27 @@ class RowSet ...@@ -1658,17 +1677,27 @@ class RowSet
return begin() + offset; return begin() + offset;
} }
iterator insert(iterator pos, Row& row) iterator insert(iterator pos, Row &row)
{ {
return insert(pos, row.mData); return insert(pos, row.mData);
} }
iterator insert(iterator pos, ItemRow* item) iterator insert(iterator pos, ItemRow *item)
{ {
auto p = mItems.insert(pos.current(), item); auto p = mItems.insert(pos.current(), item);
return iterator(p, mItems.end()); return iterator(p, mItems.end());
} }
iterator push_back(ItemRow *item)
{
return insert(end(), item);
}
iterator push_back(Row &row)
{
return insert(end(), row.mData);
}
void make_unique() void make_unique()
{ {
std::sort(mItems.begin(), mItems.end()); std::sort(mItems.begin(), mItems.end());
...@@ -1676,8 +1705,8 @@ class RowSet ...@@ -1676,8 +1705,8 @@ class RowSet
} }
private: private:
Category* mCat; Category *mCat;
std::vector<ItemRow*> mItems; std::vector<ItemRow *> mItems;
// Condition* mCond; // Condition* mCond;
}; };
...@@ -1819,6 +1848,10 @@ class Category ...@@ -1819,6 +1848,10 @@ class Category
void erase(Row r); void erase(Row r);
iterator erase(iterator ri); iterator erase(iterator ri);
/// \brief Create a copy of Row \a r and return the copy. If this row has
/// a single key field, this will be updated with a new unique value.
Row copyRow(const Row &r);
// erase without cascade, should only be used when speed is needed // erase without cascade, should only be used when speed is needed
size_t erase_nocascade(Condition&& cond) size_t erase_nocascade(Condition&& cond)
...@@ -1900,6 +1933,10 @@ class Category ...@@ -1900,6 +1933,10 @@ class Category
// a sequence number. This function will be called until the result is // a sequence number. This function will be called until the result is
// unique in the context of this category // unique in the context of this category
std::string getUniqueID(std::function<std::string(int)> generator = cif::cifIdForNumber); std::string getUniqueID(std::function<std::string(int)> generator = cif::cifIdForNumber);
std::string getUniqueID(const std::string &prefix)
{
return getUniqueID([prefix](int nr) { return prefix + std::to_string(nr); });
}
private: private:
......
src/Cif++.cpp
...@@ -1745,6 +1745,36 @@ auto Category::erase(iterator pos) -> iterator ...@@ -1745,6 +1745,36 @@ auto Category::erase(iterator pos) -> iterator
return result; return result;
} }
Row Category::copyRow(const Row &row)
{
// copy the values
std::vector<Item> items;
std::copy(row.begin(), row.end(), std::back_inserter(items));
if (mCatValidator and mCatValidator->mKeys.size() == 1)
{
auto key = mCatValidator->mKeys.front();
auto kv = mCatValidator->getValidatorForItem(key);
for (auto &item : items)
{
if (item.name() != key)
continue;
if (kv->mType->mPrimitiveType == DDL_PrimitiveType::Numb)
item.value(getUniqueID(""));
else
item.value(getUniqueID(mName + "_id_"));
break;
}
}
auto &&[ result, inserted ] = emplace(items.begin(), items.end());
// assert(inserted);
return result;
}
void Category::getTagOrder(std::vector<std::string>& tags) const void Category::getTagOrder(std::vector<std::string>& tags) const
{ {
for (auto& c: mColumns) for (auto& c: mColumns)
...@@ -2400,6 +2430,127 @@ void Category::write(std::ostream& os, const std::vector<std::string>& columns) ...@@ -2400,6 +2430,127 @@ void Category::write(std::ostream& os, const std::vector<std::string>& columns)
// -------------------------------------------------------------------- // --------------------------------------------------------------------
void Category::update_value(RowSet &&rows, const std::string &tag, const std::string &value)
{
if (rows.empty())
return;
auto colIx = getColumnIndex(tag);
if (colIx >= mColumns.size())
throw std::runtime_error("Invalid column " + value + " for " + mName);
auto& col = mColumns[colIx];
// check the value
if (col.mValidator)
(*col.mValidator)(value);
// first some sanity checks, what was the old value and is it the same for all rows?
std::string oldValue = rows.front()[tag].c_str();
for (auto &row: rows)
{
if (oldValue != row[tag].c_str())
throw std::runtime_error("Inconsistent old values in update_value");
}
if (oldValue == value) // no need to do anything
return;
// update rows, but do not cascade
for (auto &row: rows)
row.assign(colIx, value, true);
// see if we need to update any child categories that depend on this value
auto& validator = getValidator();
auto& db = mDb;
for (auto parent: rows)
{
for (auto linked: validator.getLinksForParent(mName))
{
auto childCat = db.get(linked->mChildCategory);
if (childCat == nullptr)
continue;
if (std::find(linked->mParentKeys.begin(), linked->mParentKeys.end(), tag) == linked->mParentKeys.end())
continue;
Condition cond;
std::string childTag;
for (size_t ix = 0; ix < linked->mParentKeys.size(); ++ix)
{
std::string pk = linked->mParentKeys[ix];
std::string ck = linked->mChildKeys[ix];
// TODO add code to *NOT* test mandatory fields for Empty
if (pk == tag)
{
childTag = ck;
cond = std::move(cond) && Key(ck) == oldValue;
}
else
cond = std::move(cond) && Key(ck) == parent[pk].c_str();
}
auto children = RowSet{ *childCat, std::move(cond) };
if (children.empty())
continue;
// now be careful. If we search back from child to parent and still find a valid parent row
// we cannot simply rename the child but will have to create a new child. Unless that new
// child already exists of course.
for (auto child: children)
{
Condition cond;
for (size_t ix = 0; ix < linked->mParentKeys.size(); ++ix)
{
std::string pk = linked->mParentKeys[ix];
std::string ck = linked->mChildKeys[ix];
// TODO add code to *NOT* test mandatory fields for Empty
cond = std::move(cond) && Key(pk) == child[ck].c_str();
}
auto parents = find(std::move(cond));
if (parents.empty())
continue;
// oops, we need to split this child, unless a row already exists for the new value
Condition check;
for (size_t ix = 0; ix < linked->mParentKeys.size(); ++ix)
{
std::string pk = linked->mParentKeys[ix];
std::string ck = linked->mChildKeys[ix];
// TODO add code to *NOT* test mandatory fields for Empty
if (pk == tag)
check = std::move(check) && Key(ck) == value;
else
check = std::move(check) && Key(ck) == parent[pk].c_str();
}
if (childCat->exists(std::move(check))) // phew..., narrow escape
continue;
// create the actual copy
childCat->copyRow(child);
}
// finally, update the children
childCat->update_value(std::move(children), childTag, value);
}
}
}
// --------------------------------------------------------------------
Row::Row(const Row& rhs) Row::Row(const Row& rhs)
: mData(rhs.mData) : mData(rhs.mData)
, mCascade(rhs.mCascade) , mCascade(rhs.mCascade)
......
test/RXA.cif 0 → 100644
data_RXA
#
_chem_comp.id RXA
_chem_comp.name "RENAMED RETINOIC ACID"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C20 H28 O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2016-10-18
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces 3KV
_chem_comp.formula_weight 300.435
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code RXA
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1CBS
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
RXA C1 C1 C 0 1 N N N 21.972 29.831 16.739 -4.684 0.932 -0.497 C1 RXA 1
RXA C2 C2 C 0 1 N N N 20.921 30.524 15.841 -5.837 0.190 -1.176 C2 RXA 2
RXA C3 C3 C 0 1 N N N 20.245 29.635 14.848 -6.441 -0.798 -0.171 C3 RXA 3
RXA C4 C4 C 0 1 N N N 19.555 28.479 15.488 -5.418 -1.903 0.100 C4 RXA 4
RXA C5 C5 C 0 1 N N N 20.389 27.812 16.587 -4.082 -1.301 0.429 C5 RXA 5
RXA C6 C6 C 0 1 N N N 21.425 28.446 17.218 -3.756 -0.048 0.161 C6 RXA 6
RXA C7 C7 C 0 1 N N N 22.242 27.851 18.297 -2.457 0.396 0.516 C7 RXA 7
RXA C8 C8 C 0 1 N N N 21.868 26.977 19.240 -1.363 -0.229 0.007 C8 RXA 8
RXA C9 C9 C 0 1 N N N 22.705 26.434 20.286 -0.076 0.257 0.298 C9 RXA 9
RXA C10 C10 C 0 1 N N N 22.159 25.536 21.131 1.022 -0.370 -0.213 C10 RXA 10
RXA C11 C11 C 0 1 N N N 22.875 24.924 22.234 2.306 0.115 0.077 C11 RXA 11
RXA C12 C12 C 0 1 N N N 22.237 24.026 22.990 3.405 -0.513 -0.435 C12 RXA 12
RXA C13 C13 C 0 1 N N N 22.856 23.377 24.125 4.689 -0.028 -0.144 C13 RXA 13
RXA C14 C14 C 0 1 N N N 22.135 22.473 24.834 5.787 -0.655 -0.656 C14 RXA 14
RXA C15 C15 C 0 1 N N N 22.563 21.710 26.016 7.077 -0.265 -0.244 C15 RXA 15
RXA C16 C16 C 0 1 N N N 22.238 30.737 17.948 -5.246 1.886 0.559 C16 RXA 16
RXA C17 C17 C 0 1 N N N 23.292 29.620 15.948 -3.911 1.737 -1.544 C17 RXA 17
RXA C18 C18 C 0 1 N N N 19.791 26.449 16.947 -3.056 -2.175 1.103 C18 RXA 18
RXA C19 C19 C 0 1 N N N 24.181 26.841 20.385 0.090 1.471 1.175 C19 RXA 19
RXA C20 C20 C 0 1 N N N 24.303 23.747 24.489 4.855 1.186 0.733 C20 RXA 20
RXA O1 O1 O 0 1 N N N 23.640 21.075 25.978 7.210 0.553 0.648 O1 RXA 21
RXA O2 O2 O 0 1 N N N 21.840 21.712 27.037 8.166 -0.798 -0.840 O2 RXA 22
RXA H21 H21 H 0 1 N N N 20.147 30.955 16.494 -6.598 0.905 -1.490 H21 RXA 23
RXA H22 H22 H 0 1 N N N 21.425 31.330 15.288 -5.462 -0.353 -2.044 H22 RXA 24
RXA H31 H31 H 0 1 N N N 19.501 30.227 14.295 -6.673 -0.278 0.759 H31 RXA 25
RXA H32 H32 H 0 1 N N N 21.001 29.250 14.148 -7.349 -1.234 -0.586 H32 RXA 26
RXA H41 H41 H 0 1 N N N 18.613 28.835 15.931 -5.756 -2.511 0.938 H41 RXA 27
RXA H42 H42 H 0 1 N N N 19.335 27.730 14.713 -5.322 -2.531 -0.786 H42 RXA 28
RXA H7 H7 H 0 1 N N N 23.276 28.162 18.329 -2.337 1.230 1.191 H7 RXA 29
RXA H8 H8 H 0 1 N N N 20.840 26.645 19.217 -1.482 -1.100 -0.622 H8 RXA 30
RXA H10 H10 H 0 1 N N N 21.127 25.256 20.977 0.903 -1.241 -0.842 H10 RXA 31
RXA H11 H11 H 0 1 N N N 23.902 25.189 22.440 2.425 0.985 0.706 H11 RXA 32
RXA H12 H12 H 0 1 N N N 21.216 23.774 22.743 3.286 -1.383 -1.063 H12 RXA 33
RXA H14 H14 H 0 1 N N N 21.127 22.292 24.490 5.667 -1.451 -1.376 H14 RXA 34
RXA H161 H161 H 0 0 N N N 22.984 30.265 18.604 -5.802 1.316 1.303 H161 RXA 35
RXA H162 H162 H 0 0 N N N 22.618 31.709 17.601 -4.426 2.415 1.044 H162 RXA 36
RXA H163 H163 H 0 0 N N N 21.302 30.887 18.506 -5.911 2.605 0.081 H163 RXA 37
RXA H171 H171 H 0 0 N N N 24.033 29.127 16.595 -4.598 2.394 -2.077 H171 RXA 38
RXA H172 H172 H 0 0 N N N 23.095 28.989 15.069 -3.146 2.335 -1.050 H172 RXA 39
RXA H173 H173 H 0 0 N N N 23.683 30.595 15.620 -3.439 1.054 -2.251 H173 RXA 40
RXA H181 H181 H 0 0 N N N 20.397 25.979 17.736 -3.448 -3.187 1.201 H181 RXA 41
RXA H182 H182 H 0 0 N N N 18.761 26.584 17.308 -2.145 -2.194 0.503 H182 RXA 42
RXA H183 H183 H 0 0 N N N 19.786 25.804 16.056 -2.831 -1.775 2.092 H183 RXA 43
RXA H191 H191 H 0 0 N N N 24.647 26.327 21.238 0.171 1.159 2.216 H191 RXA 44
RXA H192 H192 H 0 0 N N N 24.702 26.559 19.458 0.993 2.008 0.885 H192 RXA 45
RXA H193 H193 H 0 0 N N N 24.252 27.929 20.529 -0.774 2.125 1.058 H193 RXA 46
RXA H201 H201 H 0 0 N N N 24.620 23.168 25.369 5.026 0.871 1.762 H201 RXA 47
RXA H202 H202 H 0 0 N N N 24.965 23.516 23.641 5.707 1.771 0.386 H202 RXA 48
RXA H203 H203 H 0 0 N N N 24.360 24.822 24.717 3.952 1.795 0.685 H203 RXA 49
RXA HO2 HO2 H 0 1 N N N 22.244 21.180 27.713 9.006 -0.469 -0.490 HO2 RXA 50
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
RXA C1 C2 SING N N 1
RXA C1 C6 SING N N 2
RXA C1 C16 SING N N 3
RXA C1 C17 SING N N 4
RXA C2 C3 SING N N 5
RXA C2 H21 SING N N 6
RXA C2 H22 SING N N 7
RXA C3 C4 SING N N 8
RXA C3 H31 SING N N 9
RXA C3 H32 SING N N 10
RXA C4 C5 SING N N 11
RXA C4 H41 SING N N 12
RXA C4 H42 SING N N 13
RXA C5 C6 DOUB N N 14
RXA C5 C18 SING N N 15
RXA C6 C7 SING N N 16
RXA C7 C8 DOUB N E 17
RXA C7 H7 SING N N 18
RXA C8 C9 SING N N 19
RXA C8 H8 SING N N 20
RXA C9 C10 DOUB N E 21
RXA C9 C19 SING N N 22
RXA C10 C11 SING N N 23
RXA C10 H10 SING N N 24
RXA C11 C12 DOUB N E 25
RXA C11 H11 SING N N 26
RXA C12 C13 SING N N 27
RXA C12 H12 SING N N 28
RXA C13 C14 DOUB N E 29
RXA C13 C20 SING N N 30
RXA C14 C15 SING N N 31
RXA C14 H14 SING N N 32
RXA C15 O1 DOUB N N 33
RXA C15 O2 SING N N 34
RXA C16 H161 SING N N 35
RXA C16 H162 SING N N 36
RXA C16 H163 SING N N 37
RXA C17 H171 SING N N 38
RXA C17 H172 SING N N 39
RXA C17 H173 SING N N 40
RXA C18 H181 SING N N 41
RXA C18 H182 SING N N 42
RXA C18 H183 SING N N 43
RXA C19 H191 SING N N 44
RXA C19 H192 SING N N 45
RXA C19 H193 SING N N 46
RXA C20 H201 SING N N 47
RXA C20 H202 SING N N 48
RXA C20 H203 SING N N 49
RXA O2 HO2 SING N N 50
#
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
RXA SMILES ACDLabs 12.01 "C1(CCCC(=C1\C=C\C(=C\C=C\C(=C\C(=O)O)C)C)C)(C)C"
RXA InChI InChI 1.03 "InChI=1S/C20H28O2/c1-15(8-6-9-16(2)14-19(21)22)11-12-18-17(3)10-7-13-20(18,4)5/h6,8-9,11-12,14H,7,10,13H2,1-5H3,(H,21,22)/b9-6+,12-11+,15-8+,16-14+"
RXA InChIKey InChI 1.03 SHGAZHPCJJPHSC-YCNIQYBTSA-N
RXA SMILES_CANONICAL CACTVS 3.385 "CC1=C(\C=C\C(C)=C\C=C\C(C)=C\C(O)=O)C(C)(C)CCC1"
RXA SMILES CACTVS 3.385 "CC1=C(C=CC(C)=CC=CC(C)=CC(O)=O)C(C)(C)CCC1"
RXA SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CC1=C(C(CCC1)(C)C)/C=C/C(=C/C=C/C(=C/C(=O)O)/C)/C"
RXA SMILES "OpenEye OEToolkits" 1.7.6 "CC1=C(C(CCC1)(C)C)C=CC(=CC=CC(=CC(=O)O)C)C"
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
RXA "SYSTEMATIC NAME" ACDLabs 12.01 "retinoic acid"
RXA "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohexen-1-yl)nona-2,4,6,8-tetraenoic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
RXA "Create component" 1999-07-08 RCSB
RXA "Modify descriptor" 2011-06-04 RCSB
RXA "Other modification" 2016-10-18 RCSB
#
test/unit-test.cpp
...@@ -1271,7 +1271,7 @@ save__cat_1.id ...@@ -1271,7 +1271,7 @@ save__cat_1.id
_item.mandatory_code yes _item.mandatory_code yes
_item_linked.child_name '_cat_2.parent_id' _item_linked.child_name '_cat_2.parent_id'
_item_linked.parent_name '_cat_1.id' _item_linked.parent_name '_cat_1.id'
_item_type.code code _item_type.code int
save_ save_
save__cat_1.name save__cat_1.name
...@@ -1396,7 +1396,6 @@ _cat_2.desc ...@@ -1396,7 +1396,6 @@ _cat_2.desc
1 aap 1 'Een dier' 1 aap 1 'Een dier'
2 aap 2 'Een andere aap' 2 aap 2 'Een andere aap'
3 noot 1 'walnoot bijvoorbeeld' 3 noot 1 'walnoot bijvoorbeeld'
4 n2 1 hazelnoot
loop_ loop_
_cat_3.id _cat_3.id
...@@ -1439,63 +1438,73 @@ _cat_3.num ...@@ -1439,63 +1438,73 @@ _cat_3.num
BOOST_CHECK(num == 2); BOOST_CHECK(num == 2);
BOOST_CHECK(name == "aap"); BOOST_CHECK(name == "aap");
int i = 0;
for (const auto &[id, name, num, desc]: cat2.rows<int,std::string,int,std::string>({"id", "name", "num", "desc"}))
{
switch (++i)
{
case 1:
BOOST_CHECK(id == 1);
BOOST_CHECK(num == 1);
BOOST_CHECK(name == "aapje");
BOOST_CHECK(desc == "Een dier");
break;
case 2:
BOOST_CHECK(id == 2);
BOOST_CHECK(num == 2);
BOOST_CHECK(name == "aap");
BOOST_CHECK(desc == "Een andere aap");
break;
// // check a rename in parent and child case 3:
BOOST_CHECK(id == 3);
// for (auto r: cat1.find(cif::Key("id") == 1)) BOOST_CHECK(num == 1);
// { BOOST_CHECK(name == "noot");
// r["id"] = 10; BOOST_CHECK(desc == "walnoot bijvoorbeeld");
// break; break;
// }
// BOOST_CHECK(cat1.size() == 3);
// BOOST_CHECK(cat2.size() == 4);
// BOOST_CHECK(cat1.find(cif::Key("id") == 1).size() == 0);
// BOOST_CHECK(cat1.find(cif::Key("id") == 10).size() == 1);
// BOOST_CHECK(cat2.find(cif::Key("parent_id") == 1).size() == 0);
// BOOST_CHECK(cat2.find(cif::Key("parent_id") == 10).size() == 2);
// // check a rename in parent and child, this time only one child should be renamed
// for (auto r: cat1.find(cif::Key("id") == 2))
// {
// r["id"] = 20;
// break;
// }
// BOOST_CHECK(cat1.size() == 3);
// BOOST_CHECK(cat2.size() == 4);
// BOOST_CHECK(cat1.find(cif::Key("id") == 2).size() == 0);
// BOOST_CHECK(cat1.find(cif::Key("id") == 20).size() == 1);
// BOOST_CHECK(cat2.find(cif::Key("parent_id") == 2).size() == 1);
// BOOST_CHECK(cat2.find(cif::Key("parent_id") == 20).size() == 1);
// BOOST_CHECK(cat2.find(cif::Key("parent_id") == 2 and cif::Key("name2") == "noot").size() == 0);
// BOOST_CHECK(cat2.find(cif::Key("parent_id") == 2 and cif::Key("name2") == "n2").size() == 1);
// BOOST_CHECK(cat2.find(cif::Key("parent_id") == 20 and cif::Key("name2") == "noot").size() == 1);
// BOOST_CHECK(cat2.find(cif::Key("parent_id") == 20 and cif::Key("name2") == "n2").size() == 0);
// // // --------------------------------------------------------------------
// // cat1.erase(cif::Key("id") == 10); default:
BOOST_FAIL("Unexpected record");
}
}
// // BOOST_CHECK(cat1.size() == 2); BOOST_CHECK(cat1.size() == 4);
// // BOOST_CHECK(cat2.size() == 2); i = 0;
for (const auto &[id, name, desc]: cat1.rows<int,std::string,std::string>({"id", "name", "desc"}))
{
switch (++i)
{
case 1:
BOOST_CHECK(id == 1);
BOOST_CHECK(name == "aapje");
BOOST_CHECK(desc == "Aap");
break;
// // cat1.erase(cif::Key("id") == 20); case 2:
BOOST_CHECK(id == 2);
BOOST_CHECK(name == "noot");
BOOST_CHECK(desc == "Noot");
break;
// // BOOST_CHECK(cat1.size() == 1); case 3:
// // BOOST_CHECK(cat2.size() == 1); BOOST_CHECK(id == 3);
BOOST_CHECK(name == "mies");
BOOST_CHECK(desc == "Mies");
break;
case 4:
BOOST_CHECK(id == 4);
BOOST_CHECK(name == "aap");
BOOST_CHECK(desc == "Aap");
break;
default:
BOOST_FAIL("Unexpected record");
}
}
f.save(std::cout);
} }
// -------------------------------------------------------------------- // --------------------------------------------------------------------
......
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