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libcifpp
Commit 2f249048 by Maarten L. Hekkelman
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Merge branch 'develop' of github.com:PDB-REDO/libcifpp into develop

parents 974cb40a c01c16ea
Showing with 1673 additions and 309 deletions
.gitignore
......@@ -12,3 +12,5 @@ CMakeSettings.json
msvc/
Testing/
rsrc/feature-request.txt
test/test-create_sugar_?.cif
test/oprofile_data/
CMakeLists.txt
......@@ -192,6 +192,10 @@ set(project_sources
${PROJECT_SOURCE_DIR}/src/symmetry.cpp
${PROJECT_SOURCE_DIR}/src/model.cpp
${PROJECT_SOURCE_DIR}/src/pdb/cif2pdb.cpp
${PROJECT_SOURCE_DIR}/src/pdb/pdb2cif.cpp
${PROJECT_SOURCE_DIR}/src/pdb/pdb2cif_remark_3.cpp
)
set(project_headers
......@@ -216,7 +220,12 @@ set(project_headers
${PROJECT_SOURCE_DIR}/include/cif++/symmetry.hpp
${PROJECT_SOURCE_DIR}/include/cif++/model.hpp
)
${PROJECT_SOURCE_DIR}/include/cif++/pdb/cif2pdb.hpp
${PROJECT_SOURCE_DIR}/include/cif++/pdb/io.hpp
${PROJECT_SOURCE_DIR}/include/cif++/pdb/pdb2cif.hpp
${PROJECT_SOURCE_DIR}/include/cif++/pdb/pdb2cif_remark_3.hpp
)
add_library(cifpp ${project_sources} ${project_headers} ${PROJECT_SOURCE_DIR}/src/symop_table_data.hpp)
add_library(cifpp::cifpp ALIAS cifpp)
......@@ -370,8 +379,7 @@ if(ENABLE_TESTING)
find_package(Boost REQUIRED headers)
list(APPEND CIFPP_tests unit-v2 unit-3d format model
# rename-compound sugar
list(APPEND CIFPP_tests unit-v2 unit-3d format model rename-compound sugar
)
foreach(CIFPP_TEST IN LISTS CIFPP_tests)
......
include/cif++.hpp
......@@ -35,4 +35,6 @@
#include <cif++/point.hpp>
#include <cif++/symmetry.hpp>
#include <cif++/model.hpp>
\ No newline at end of file
#include <cif++/model.hpp>
#include <cif++/pdb/io.hpp>
include/cif++/category.hpp
......@@ -88,7 +88,7 @@ class category
const category_validator *get_cat_validator() const { return m_cat_validator; }
bool is_valid() const;
void validate_links() const;
bool validate_links() const;
bool operator==(const category &rhs) const;
bool operator!=(const category &rhs) const
......@@ -159,6 +159,22 @@ class category
}
// --------------------------------------------------------------------
// A category can have a key, as defined by the validator/dictionary
/// @brief The key type
using key_type = row_initializer;
/// @brief Return a row_handle for the row specified by \a key
/// @param key The value for the key, fields specified in the dictionary should have a value
/// @return The row found in the index, or an undefined row_handle
row_handle operator[](const key_type &key);
const row_handle operator[](const key_type &key) const
{
return const_cast<category *>(this)->operator[](key);
}
// --------------------------------------------------------------------
template <typename... Ts, typename... Ns>
iterator_proxy<const category, Ts...> rows(Ns... names) const
......@@ -290,12 +306,19 @@ class category
{
cond.prepare(*this);
for (auto r : *this)
auto sh = cond.single();
if (sh.has_value() and *sh)
result = true;
else
{
if (cond(r))
for (auto r : *this)
{
result = true;
break;
if (cond(r))
{
result = true;
break;
}
}
}
}
......@@ -335,7 +358,7 @@ class category
iterator emplace(row_initializer &&ri)
{
return this->emplace(ri.m_items.begin(), ri.m_items.end());
return this->emplace(ri.begin(), ri.end());
}
template <typename ItemIter>
......@@ -527,6 +550,14 @@ class category
return create_item(ix, i.value());
}
item_value *create_item(const std::tuple<std::string_view,std::string> &i)
{
const auto &[name, value] = i;
uint16_t ix = add_column(name);
return create_item(ix, value);
}
void delete_item(item_value *iv)
{
if (iv->m_length >= item_value::kBufferSize)
......
include/cif++/condition.hpp
......@@ -30,6 +30,7 @@
#include <functional>
#include <iostream>
#include <regex>
#include <utility>
#include <cif++/row.hpp>
......@@ -52,9 +53,10 @@ namespace detail
{
virtual ~condition_impl() {}
virtual void prepare(const category &c) {}
virtual condition_impl *prepare(const category &c) { return this; }
virtual bool test(row_handle r) const = 0;
virtual void str(std::ostream &os) const = 0;
virtual std::optional<row_handle> single() const { return {}; };
};
struct all_condition_impl : public condition_impl
......@@ -105,12 +107,7 @@ class condition
m_impl = nullptr;
}
void prepare(const category &c)
{
if (m_impl)
m_impl->prepare(c);
m_prepared = true;
}
void prepare(const category &c);
bool operator()(row_handle r) const
{
......@@ -122,6 +119,11 @@ class condition
explicit operator bool() { return not empty(); }
bool empty() const { return m_impl == nullptr; }
std::optional<row_handle> single() const
{
return m_impl ? m_impl->single() : std::optional<row_handle>();
}
friend condition operator||(condition &&a, condition &&b);
friend condition operator&&(condition &&a, condition &&b);
......@@ -143,6 +145,9 @@ class condition
}
private:
void optimise(condition_impl *&impl);
condition_impl *m_impl;
bool m_prepared = false;
};
......@@ -156,9 +161,10 @@ namespace detail
{
}
void prepare(const category &c) override
condition_impl *prepare(const category &c) override
{
m_item_ix = get_column_ix(c, m_item_tag);
return this;
}
bool test(row_handle r) const override
......@@ -175,6 +181,85 @@ namespace detail
size_t m_item_ix = 0;
};
struct key_equals_condition_impl : public condition_impl
{
key_equals_condition_impl(item &&i)
: m_item_tag(i.name())
, m_value(i.value())
{
}
condition_impl *prepare(const category &c) override;
bool test(row_handle r) const override
{
return m_single_hit.has_value() ?
*m_single_hit == r :
r[m_item_ix].compare(m_value, m_icase) == 0;
}
void str(std::ostream &os) const override
{
os << m_item_tag << (m_icase ? "^ " : " ") << " == " << m_value;
}
virtual std::optional<row_handle> single() const override
{
return m_single_hit;
}
std::string m_item_tag;
size_t m_item_ix = 0;
bool m_icase = false;
std::string m_value;
std::optional<row_handle> m_single_hit;
};
struct key_equals_or_empty_condition_impl : public condition_impl
{
key_equals_or_empty_condition_impl(key_equals_condition_impl *equals, key_is_empty_condition_impl *empty)
: m_item_tag(equals->m_item_tag)
, m_value(equals->m_value)
, m_icase(equals->m_icase)
, m_single_hit(equals->m_single_hit)
{
assert(empty->m_item_ix == equals->m_item_ix);
}
condition_impl *prepare(const category &c) override
{
m_item_ix = get_column_ix(c, m_item_tag);
m_icase = is_column_type_uchar(c, m_item_tag);
return this;
}
bool test(row_handle r) const override
{
bool result = false;
if (m_single_hit.has_value())
result = *m_single_hit == r;
else
result = r[m_item_ix].empty() or r[m_item_ix].compare(m_value, m_icase) == 0;
return result;
}
void str(std::ostream &os) const override
{
os << m_item_tag << (m_icase ? "^ " : " ") << " == " << m_value << " OR " << m_item_tag << " IS NULL";
}
virtual std::optional<row_handle> single() const override
{
return m_single_hit;
}
std::string m_item_tag;
size_t m_item_ix = 0;
bool m_icase = false;
std::string m_value;
std::optional<row_handle> m_single_hit;
};
struct key_compare_condition_impl : public condition_impl
{
template <typename COMP>
......@@ -185,10 +270,11 @@ namespace detail
{
}
void prepare(const category &c) override
condition_impl *prepare(const category &c) override
{
m_item_ix = get_column_ix(c, m_item_tag);
m_icase = is_column_type_uchar(c, m_item_tag);
return this;
}
bool test(row_handle r) const override
......@@ -217,9 +303,10 @@ namespace detail
{
}
void prepare(const category &c) override
condition_impl *prepare(const category &c) override
{
m_item_ix = get_column_ix(c, m_item_tag);
return this;
}
bool test(row_handle r) const override
......@@ -318,44 +405,84 @@ namespace detail
std::regex mRx;
};
// TODO: Optimize and_condition by having a list of sub items.
// That way you can also collapse multiple _is_ conditions in
// case they make up an indexed tuple.
struct and_condition_impl : public condition_impl
{
and_condition_impl(condition &&a, condition &&b)
: mA(nullptr)
, mB(nullptr)
{
std::swap(mA, a.m_impl);
std::swap(mB, b.m_impl);
mSub.emplace_back(std::exchange(a.m_impl, nullptr));
mSub.emplace_back(std::exchange(b.m_impl, nullptr));
}
~and_condition_impl()
{
delete mA;
delete mB;
for (auto sub : mSub)
delete sub;
}
void prepare(const category &c) override
{
mA->prepare(c);
mB->prepare(c);
}
condition_impl *prepare(const category &c) override;
bool test(row_handle r) const override
{
return mA->test(r) and mB->test(r);
bool result = true;
for (auto sub : mSub)
{
if (sub->test(r))
continue;
result = false;
break;
}
return result;
}
void str(std::ostream &os) const override
{
os << '(';
mA->str(os);
os << ") AND (";
mB->str(os);
bool first = true;
for (auto sub : mSub)
{
if (first)
first = false;
else
os << " AND ";
sub->str(os);
}
os << ')';
}
condition_impl *mA;
condition_impl *mB;
virtual std::optional<row_handle> single() const override
{
std::optional<row_handle> result;
for (auto sub : mSub)
{
auto s = sub->single();
if (not result.has_value())
{
result = s;
continue;
}
if (s == result)
continue;
result.reset();
break;
}
return result;
}
std::vector<condition_impl *> mSub;
};
struct or_condition_impl : public condition_impl
......@@ -374,11 +501,7 @@ namespace detail
delete mB;
}
void prepare(const category &c) override
{
mA->prepare(c);
mB->prepare(c);
}
condition_impl *prepare(const category &c) override;
bool test(row_handle r) const override
{
......@@ -394,6 +517,19 @@ namespace detail
os << ')';
}
virtual std::optional<row_handle> single() const override
{
auto sa = mA->single();
auto sb = mB->single();
if (sa.has_value() and sb.has_value() and sa != sb)
sa.reset();
else if (not sa.has_value())
sa = sb;
return sa;
}
condition_impl *mA;
condition_impl *mB;
};
......@@ -411,9 +547,10 @@ namespace detail
delete mA;
}
void prepare(const category &c) override
condition_impl *prepare(const category &c) override
{
mA->prepare(c);
mA = mA->prepare(c);
return this;
}
bool test(row_handle r) const override
......@@ -480,27 +617,13 @@ struct key
template <typename T>
condition operator==(const key &key, const T &v)
{
std::ostringstream s;
s << " == " << v;
return condition(new detail::key_compare_condition_impl(
key.m_item_tag, [tag = key.m_item_tag, v](row_handle r, bool icase)
{ return r[tag].template compare<T>(v, icase) == 0; },
s.str()));
return condition(new detail::key_equals_condition_impl({ key.m_item_tag, v }));
}
inline condition operator==(const key &key, const char *value)
{
if (value != nullptr and *value != 0)
{
std::ostringstream s;
s << " == " << value;
return condition(new detail::key_compare_condition_impl(
key.m_item_tag, [tag = key.m_item_tag, value](row_handle r, bool icase)
{ return r[tag].compare(value, icase) == 0; },
s.str()));
}
return condition(new detail::key_equals_condition_impl({ key.m_item_tag, value }));
else
return condition(new detail::key_is_empty_condition_impl(key.m_item_tag));
}
......
include/cif++/datablock.hpp
......@@ -66,7 +66,7 @@ class datablock : public std::list<category>
const validator *get_validator() const;
bool is_valid() const;
void validate_links() const;
bool validate_links() const;
// --------------------------------------------------------------------
......
include/cif++/file.hpp
......@@ -79,13 +79,25 @@ class file : public std::list<datablock>
bool is_valid() const;
bool is_valid();
void validate_links() const;
bool validate_links() const;
void load_dictionary();
void load_dictionary(std::string_view name);
bool contains(std::string_view name) const;
datablock &front()
{
assert(not empty());
return std::list<datablock>::front();
}
const datablock &front() const
{
assert(not empty());
return std::list<datablock>::front();
}
datablock &operator[](std::string_view name);
const datablock &operator[](std::string_view name) const;
......
include/cif++/item.hpp
......@@ -59,10 +59,8 @@ class item
/// content a single character string with content \a value
item(std::string_view name, char value)
: m_name(name)
, m_value(m_buffer, 1)
, m_value({ value })
{
m_buffer[0] = value;
m_buffer[1] = 0;
}
/// \brief constructor for an item with name \a name and as
......@@ -75,13 +73,15 @@ class item
using namespace std;
using namespace cif;
auto r = to_chars(m_buffer, m_buffer + sizeof(m_buffer) - 1, value, chars_format::fixed, precision);
char buffer[32];
auto r = to_chars(buffer, buffer + sizeof(buffer) - 1, value, chars_format::fixed, precision);
if (r.ec != std::errc())
throw std::runtime_error("Could not format number");
assert(r.ptr >= m_buffer and r.ptr < m_buffer + sizeof(m_buffer));
assert(r.ptr >= buffer and r.ptr < buffer + sizeof(buffer));
*r.ptr = 0;
m_value = std::string_view(m_buffer, r.ptr - m_buffer);
m_value.assign(buffer, r.ptr - buffer);
}
/// \brief constructor for an item with name \a name and as
......@@ -94,13 +94,15 @@ class item
using namespace std;
using namespace cif;
auto r = to_chars(m_buffer, m_buffer + sizeof(m_buffer) - 1, value, chars_format::general);
char buffer[32];
auto r = to_chars(buffer, buffer + sizeof(buffer) - 1, value, chars_format::general);
if (r.ec != std::errc())
throw std::runtime_error("Could not format number");
assert(r.ptr >= m_buffer and r.ptr < m_buffer + sizeof(m_buffer));
assert(r.ptr >= buffer and r.ptr < buffer + sizeof(buffer));
*r.ptr = 0;
m_value = std::string_view(m_buffer, r.ptr - m_buffer);
m_value.assign(buffer, r.ptr - buffer);
}
/// \brief constructor for an item with name \a name and as
......@@ -109,13 +111,15 @@ class item
item(const std::string_view name, const T &value)
: m_name(name)
{
auto r = std::to_chars(m_buffer, m_buffer + sizeof(m_buffer) - 1, value);
char buffer[32];
auto r = std::to_chars(buffer, buffer + sizeof(buffer) - 1, value);
if (r.ec != std::errc())
throw std::runtime_error("Could not format number");
assert(r.ptr >= m_buffer and r.ptr < m_buffer + sizeof(m_buffer));
assert(r.ptr >= buffer and r.ptr < buffer + sizeof(buffer));
*r.ptr = 0;
m_value = std::string_view(m_buffer, r.ptr - m_buffer);
m_value.assign(buffer, r.ptr - buffer);
}
/// \brief constructor for an item with name \a name and as
......@@ -152,10 +156,17 @@ class item
/// \brief the length of the value string
size_t length() const { return m_value.length(); }
/// \brief support for structured binding
template<size_t N>
decltype(auto) get() const
{
if constexpr (N == 0) return name();
else if constexpr (N == 1) return value();
}
private:
std::string_view m_name;
std::string_view m_value;
char m_buffer[64]; // TODO: optimize this magic number, might be too large
std::string m_value;
};
// --------------------------------------------------------------------
......@@ -193,7 +204,7 @@ struct item_value
// By using std::string_view instead of c_str we obain a
// nice performance gain since we avoid many calls to strlen.
std::string_view text() const
constexpr inline std::string_view text() const
{
return { m_length >= kBufferSize ? m_data : m_local_data, m_length };
}
......@@ -289,9 +300,6 @@ struct item_handle
std::string_view text() const;
// bool operator!=(const std::string &s) const { return s != c_str(); }
// bool operator==(const std::string &s) const { return s == c_str(); }
item_handle(uint16_t column, row_handle &row)
: m_column(column)
, m_row_handle(row)
......@@ -491,3 +499,21 @@ struct item_handle::item_value_as<T, std::enable_if_t<std::is_same_v<T, std::str
};
} // namespace cif
namespace std
{
template<> struct tuple_size<::cif::item>
: public std::integral_constant<std::size_t, 2> {};
template<> struct tuple_element<0, ::cif::item>
{
using type = decltype(std::declval<::cif::item>().name());
};
template<> struct tuple_element<1, ::cif::item>
{
using type = decltype(std::declval<::cif::item>().value());
};
}
\ No newline at end of file
include/cif++/model.hpp
......@@ -34,19 +34,6 @@
#include <format>
#endif
/*
To modify a structure, you will have to use actions.
The currently supported actions are:
// - Move atom to new location
- Remove atom
// - Add new atom that was formerly missing
// - Add alternate residue
-
*/
namespace cif::mm
{
......@@ -63,16 +50,23 @@ class atom
private:
struct atom_impl : public std::enable_shared_from_this<atom_impl>
{
atom_impl(datablock &db, std::string_view id, row_handle row)
atom_impl(datablock &db, std::string_view id)
: m_db(db)
, m_cat(db["atom_site"])
, m_id(id)
, m_row(row)
{
prefetch();
auto r = row();
if (r)
tie(m_location.m_x, m_location.m_y, m_location.m_z) = r.get("Cartn_x", "Cartn_y", "Cartn_z");
}
// constructor for a symmetry copy of an atom
atom_impl(const atom_impl &impl, const point &loc, const std::string &sym_op);
atom_impl(const atom_impl &impl, const point &loc, const std::string &sym_op)
: atom_impl(impl)
{
m_location = loc;
m_symop = sym_op;
}
atom_impl(const atom_impl &i) = default;
......@@ -84,95 +78,41 @@ class atom
int get_charge() const;
void moveTo(const point &p)
{
if (m_symop != "1_555")
throw std::runtime_error("Moving symmetry copy");
#if __cpp_lib_format
m_row.assign("Cartn_x", std::format("{:.3f}", p.getX()), false, false);
m_row.assign("Cartn_y", std::format("{:.3f}", p.getY()), false, false);
m_row.assign("Cartn_z", std::format("{:.3f}", p.getZ()), false, false);
#else
m_row.assign("Cartn_x", format("%.3f", p.m_x).str(), false, false);
m_row.assign("Cartn_y", format("%.3f", p.m_y).str(), false, false);
m_row.assign("Cartn_z", format("%.3f", p.m_z).str(), false, false);
#endif
m_location = p;
}
void moveTo(const point &p);
// const compound *compound() const;
std::string get_property(std::string_view name) const
std::string get_property(std::string_view name) const;
int get_property_int(std::string_view name) const;
float get_property_float(std::string_view name) const;
void set_property(const std::string_view name, const std::string &value);
row_handle row()
{
return m_row[name].as<std::string>();
// for (auto &&[tag, ref] : mCachedRefs)
// {
// if (tag == name)
// return ref.as<std::string>();
// }
// mCachedRefs.emplace_back(name, const_cast<Row &>(mRow)[name]);
// return std::get<1>(mCachedRefs.back()).as<std::string>();
return m_cat[{{"id", m_id}}];
}
int get_property_int(std::string_view name) const
const row_handle row() const
{
int result = 0;
if (not m_row[name].empty())
{
auto s = get_property(name);
std::from_chars_result r = std::from_chars(s.data(), s.data() + s.length(), result);
if (r.ec != std::errc() and VERBOSE > 0)
std::cerr << "Error converting " << s << " to number for property " << name << std::endl;
}
return result;
return m_cat[{{"id", m_id}}];
}
float get_property_float(std::string_view name) const
row_handle row_aniso()
{
float result = 0;
if (not m_row[name].empty())
{
auto s = get_property(name);
std::from_chars_result r = cif::from_chars(s.data(), s.data() + s.length(), result);
if (r.ec != std::errc() and VERBOSE > 0)
std::cerr << "Error converting " << s << " to number for property " << name << std::endl;
}
return result;
auto cat = m_db.get("atom_site_anisotrop");
return cat ? cat->find1(key("id") == m_id) : row_handle{};
}
void set_property(const std::string_view name, const std::string &value)
const row_handle row_aniso() const
{
m_row.assign(name, value, true, true);
auto cat = m_db.get("atom_site_anisotrop");
return cat ? cat->find1(key("id") == m_id) : row_handle{};
}
// const datablock &m_db;
// std::string mID;
// atom_type mType;
// std::string mAtomID;
// std::string mCompID;
// std::string m_asym_id;
// int m_seq_id;
// std::string mAltID;
// std::string m_auth_seq_id;
// point mLocation;
// row_handle mRow;
// // mutable std::vector<std::tuple<std::string, detail::ItemReference>> mCachedRefs;
// mutable const compound *mcompound = nullptr;
// bool mSymmetryCopy = false;
// bool mClone = false;
const datablock &m_db;
category &m_cat;
std::string m_id;
row_handle m_row;
point m_location;
std::string m_symop = "1_555";
};
......@@ -191,7 +131,7 @@ class atom
}
atom(datablock &db, row_handle &row)
: atom(std::make_shared<atom_impl>(db, row["id"].as<std::string>(), row))
: atom(std::make_shared<atom_impl>(db, row["id"].as<std::string>()))
{
}
......@@ -295,20 +235,27 @@ class atom
set_location(loc);
}
// // for direct access to underlying data, be careful!
// const row_handle getRow() const { return impl().mRow; }
// const row_handle getRowAniso() const;
// for direct access to underlying data, be careful!
const row_handle get_row() const { return impl().row(); }
const row_handle get_row_aniso() const { return impl().row_aniso(); }
// bool isSymmetryCopy() const { return impl().mSymmetryCopy; }
// std::string symmetry() const { return impl().mSymmetryOperator; }
// const compound &compound() const;
// bool is_water() const { return impl().mCompID == "HOH" or impl().mCompID == "H2O" or impl().mCompID == "WAT"; }
bool is_water() const
{
auto comp_id = get_label_comp_id();
return comp_id == "HOH" or comp_id == "H2O" or comp_id == "WAT";
}
int get_charge() const { return impl().get_charge(); }
// float uIso() const;
// bool getAnisoU(float anisou[6]) const { return impl().getAnisoU(anisou); }
// float occupancy() const;
float get_occupancy() const { return get_property_float("occupancy"); }
// specifications
......@@ -681,7 +628,10 @@ class sugar : public residue
size_t get_link_nr() const
{
return m_link ? std::stoi(m_link.get_auth_seq_id()) : 0;
size_t result = 0;
if (m_link)
result = m_link.get_property_int("auth_seq_id");
return result;
}
private:
......@@ -778,6 +728,8 @@ class structure
~structure() = default;
size_t get_model_nr() const { return m_model_nr; }
const std::vector<atom> &atoms() const { return m_atoms; }
// std::vector<atom> &atoms() { return m_atoms; }
......@@ -897,10 +849,10 @@ class structure
/// \param entity_id The entity ID of the new nonpoly
/// \param atoms The array of sets of item data containing the data for the atoms.
/// \return The newly create asym ID
std::string create_non_poly(const std::string &entity_id, std::vector<std::vector<item>> &atom_info);
std::string create_non_poly(const std::string &entity_id, std::vector<row_initializer> atoms);
/// \brief Create a new (sugar) branch with one first NAG containing atoms constructed from \a nag_atom_info
branch &create_branch(std::vector<std::vector<item>> &nag_atom_info);
/// \brief Create a new (sugar) branch with one first NAG containing atoms constructed from \a atoms
branch &create_branch(std::vector<row_initializer> atoms);
/// \brief Extend an existing (sugar) branch identified by \a asymID with one sugar containing atoms constructed from \a atom_info
///
......@@ -908,7 +860,7 @@ class structure
/// \param atom_info Array containing the info for the atoms to construct for the new sugar
/// \param link_sugar The sugar to link to, note: this is the sugar number (1 based)
/// \param link_atom The atom id of the atom linked in the sugar
branch &extend_branch(const std::string &asym_id, std::vector<std::vector<item>> &atom_info,
branch &extend_branch(const std::string &asym_id, std::vector<row_initializer> atom_info,
int link_sugar, const std::string &link_atom);
/// \brief Remove \a branch
......
include/cif++/pdb/TlsParser.hpp 0 → 100644
/*-
* 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.
*/
#pragma once
#include <vector>
#include <string>
#include <tuple>
#include <cif++.hpp>
namespace cif
{
extern const int
kResidueNrWildcard,
kNoSeqNum;
struct TLSSelection;
typedef std::unique_ptr<TLSSelection> TLSSelectionPtr;
struct TLSResidue;
struct TLSSelection
{
virtual ~TLSSelection() {}
virtual void CollectResidues(cif::datablock& db, std::vector<TLSResidue>& residues, std::size_t indentLevel = 0) const = 0;
std::vector<std::tuple<std::string,int,int>> GetRanges(cif::datablock& db, bool pdbNamespace) const;
};
// Low level: get the selections
TLSSelectionPtr ParseSelectionDetails(const std::string& program, const std::string& selection);
}
include/cif++/pdb/cif2pdb.hpp 0 → 100644
/*-
* 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.
*/
#pragma once
#include <cif++.hpp>
namespace cif::pdb
{
/// \brief Just the HEADER, COMPND, SOURCE and AUTHOR lines
void write_header_lines(std::ostream &os, const datablock &data);
std::string get_HEADER_line(const datablock &data, std::string::size_type truncate_at = 127);
std::string get_COMPND_line(const datablock &data, std::string::size_type truncate_at = 127);
std::string get_SOURCE_line(const datablock &data, std::string::size_type truncate_at = 127);
std::string get_AUTHOR_line(const datablock &data, std::string::size_type truncate_at = 127);
} // namespace pdbx
include/cif++/pdb/io.hpp 0 → 100644
/*-
* SPDX-License-Identifier: BSD-2-Clause
*
* Copyright (c) 2022 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.
*/
#pragma once
#include <cif++.hpp>
namespace cif::pdb
{
file read(std::istream &is);
void write(std::ostream &os, const datablock &db);
inline void write(std::ostream &os, const file &f)
{
write(os, f.front());
}
}
\ No newline at end of file
include/cif++/pdb/pdb2cif.hpp 0 → 100644
/*-
* 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.
*/
#pragma once
#include <cif++.hpp>
namespace cif::pdb
{
// --------------------------------------------------------------------
struct PDBRecord
{
PDBRecord *mNext;
uint32_t mLineNr;
char mName[11];
size_t mVlen;
char mValue[1];
PDBRecord(uint32_t lineNr, const std::string &name, const std::string &value);
~PDBRecord();
void *operator new(size_t);
void *operator new(size_t size, size_t vLen);
void operator delete(void *p);
void operator delete(void *p, size_t vLen);
bool is(const char *name) const;
char vC(size_t column);
std::string vS(size_t columnFirst, size_t columnLast = std::numeric_limits<size_t>::max());
int vI(int columnFirst, int columnLast);
std::string vF(size_t columnFirst, size_t columnLast);
};
// --------------------------------------------------------------------
void ReadPDBFile(std::istream &pdbFile, file &cifFile);
} // namespace pdbx
\ No newline at end of file
include/cif++/pdb/pdb2cif_remark_3.hpp 0 → 100644
/*-
* 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.
*/
#pragma once
#include <cif++/pdb/pdb2cif.hpp>
// --------------------------------------------------------------------
namespace cif::pdb
{
struct TemplateLine;
class Remark3Parser
{
public:
virtual ~Remark3Parser() {}
static bool parse(const std::string &expMethod, PDBRecord *r, cif::datablock &db);
virtual std::string program();
virtual std::string version();
protected:
Remark3Parser(const std::string &name, const std::string &expMethod, PDBRecord *r, cif::datablock &db,
const TemplateLine templatelines[], uint32_t templateLineCount, std::regex programVersion);
virtual float parse();
std::string nextLine();
bool match(const char *expr, int nextState);
void storeCapture(const char *category, std::initializer_list<const char *> items, bool createNew = false);
void storeRefineLsRestr(const char *type, std::initializer_list<const char *> values);
void updateRefineLsRestr(const char *type, std::initializer_list<const char *> values);
virtual void fixup() {}
std::string mName;
std::string mExpMethod;
PDBRecord *mRec;
cif::datablock mDb;
std::string mLine;
std::smatch mM;
uint32_t mState;
const TemplateLine *mTemplate;
uint32_t mTemplateCount;
std::regex mProgramVersion;
};
} // namespace pdbx
include/cif++/point.hpp
......@@ -484,7 +484,7 @@ struct point_type
}
#if HAVE_LIBCLIPPER
constexpr operator clipper::Coord_orth() const
operator clipper::Coord_orth() const
{
return clipper::Coord_orth(m_x, m_y, m_z);
}
......
include/cif++/row.hpp
......@@ -196,7 +196,7 @@ class row_handle
explicit operator bool() const
{
return m_category != nullptr and m_row != nullptr;
return not empty();
}
item_handle operator[](uint32_t column_ix)
......@@ -259,7 +259,12 @@ class row_handle
uint16_t add_column(std::string_view name);
operator row *()
row *get_row()
{
return m_row;
}
const row *get_row() const
{
return m_row;
}
......@@ -277,7 +282,7 @@ class row_handle
// --------------------------------------------------------------------
class row_initializer
class row_initializer : public std::vector<item>
{
public:
friend class category;
......@@ -289,20 +294,29 @@ class row_initializer
row_initializer &operator=(row_initializer &&) = default;
row_initializer(std::initializer_list<item> items)
: m_items(items)
: std::vector<item>(items)
{
}
template <typename ItemIter, std::enable_if_t<std::is_same_v<typename ItemIter::value_type, item>, int> = 0>
row_initializer(ItemIter b, ItemIter e)
: m_items(b, e)
: std::vector<item>(b, e)
{
}
row_initializer(row_handle rh);
private:
std::vector<item> m_items;
void set_value(std::string_view name, std::string_view value);
void set_value(const item &i)
{
set_value(i.name(), i.value());
}
void set_value_if_empty(std::string_view name, std::string_view value);
void set_value_if_empty(const item &i)
{
set_value_if_empty(i.name(), i.value());
}
};
} // namespace cif
\ No newline at end of file
src/category.cpp
......@@ -52,7 +52,7 @@ class row_comparator
for (auto k : cv->m_keys)
{
size_t ix = cat.get_column_ix(k);
size_t ix = cat.add_column(k);
auto iv = cv->get_validator_for_item(k);
if (iv == nullptr)
......@@ -96,6 +96,32 @@ class row_comparator
return d;
}
int operator()(const row_initializer &a, const row *b) const
{
assert(b);
row_handle rhb(m_category, *b);
int d = 0, i = 0;
for (auto &c : m_comparator)
{
size_t k;
compareFunc f;
std::tie(k, f) = c;
std::string_view ka = a[i++].value();
std::string_view kb = rhb[k].text();
d = f(ka, kb);
if (d != 0)
break;
}
return d;
}
private:
typedef std::function<int(std::string_view, std::string_view)> compareFunc;
typedef std::tuple<size_t, compareFunc> key_comparator;
......@@ -126,6 +152,7 @@ class category_index
}
row *find(row *k) const;
row *find_by_value(row_initializer k) const;
void insert(row *r);
void erase(row *r);
......@@ -331,6 +358,37 @@ row *category_index::find(row *k) const
return r ? r->m_row : nullptr;
}
row *category_index::find_by_value(row_initializer k) const
{
// sort the values in k first
row_initializer k2;
for (auto &f : m_category.key_field_indices())
{
auto fld = m_category.get_column_name(f);
auto ki = find_if(k.begin(), k.end(), [&fld](auto &i) { return i.name() == fld; });
if (ki == k.end())
k2.emplace_back(fld, "");
else
k2.emplace_back(*ki);
}
const entry *r = m_root;
while (r != nullptr)
{
int d = m_row_comparator(k2, r->m_row);
if (d < 0)
r = r->m_left;
else if (d > 0)
r = r->m_right;
else
break;
}
return r ? r->m_row : nullptr;
}
void category_index::insert(row *k)
{
m_root = insert(m_root, k);
......@@ -353,7 +411,10 @@ category_index::entry *category_index::insert(entry *h, row *v)
std::ostringstream os;
for (auto col : m_category.fields())
os << col << ": " << std::quoted(rh[col].text()) << "; ";
{
if (rh[col])
os << col << ": " << std::quoted(rh[col].text()) << "; ";
}
throw std::runtime_error("Duplicate Key violation, cat: " + m_category.name() + " values: " + os.str());
}
......@@ -426,7 +487,7 @@ void category_index::reconstruct()
m_root = nullptr;
for (auto r : m_category)
insert(r);
insert(r.get_row());
// 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.
......@@ -756,10 +817,14 @@ bool category::is_valid() const
// check index?
if (m_index)
{
if (m_index->size() != size())
m_validator->report_error("size of index is not equal to size of category " + m_name, true);
// m_index->validate();
for (auto r : *this)
{
if (m_index->find(r) != r)
auto p = r.get_row();
if (m_index->find(p) != p)
m_validator->report_error("Key not found in index for category " + m_name, true);
}
}
......@@ -813,10 +878,12 @@ bool category::is_valid() const
return result;
}
void category::validate_links() const
bool category::validate_links() const
{
if (not m_validator)
return;
return false;
bool result = true;
for (auto &link : m_parent_links)
{
......@@ -825,6 +892,12 @@ void category::validate_links() const
if (parent == nullptr)
continue;
// this particular case should be skipped, that's because it is wrong:
// there are atoms that are not part of a polymer, and thus will have no
// parent in that category.
if (name() == "atom_site" and (parent->name() == "pdbx_poly_seq_scheme" or parent->name() == "entity_poly_seq"))
continue;
size_t missing = 0;
category first_missing_rows(name());
......@@ -843,13 +916,15 @@ void category::validate_links() const
if (missing)
{
result = false;
std::cerr << "Links for " << link.v->m_link_group_label << " are incomplete" << std::endl
<< " There are " << missing << " items in " << m_name << " that don't have matching parent items in " << parent->m_name << std::endl;
<< " There are " << missing << " items in " << m_name << " that don't have matching parent items in " << parent->m_name << std::endl;
if (VERBOSE)
{
std::cerr << "showing first " << first_missing_rows.size() << " rows" << std::endl
<< std::endl;
<< std::endl;
first_missing_rows.write(std::cerr, link.v->m_child_keys, false);
......@@ -857,6 +932,19 @@ void category::validate_links() const
}
}
}
return result;
}
// --------------------------------------------------------------------
row_handle category::operator[](const key_type &key)
{
if (m_index == nullptr)
throw std::logic_error("Category " + m_name + " does not have an index");
auto row = m_index->find_by_value(key);
return row != nullptr ? row_handle{ *this, *row } : row_handle{};
}
// --------------------------------------------------------------------
......@@ -898,6 +986,11 @@ condition category::get_children_condition(row_handle rh, const category &childC
condition result;
iset mandatoryChildFields;
auto childCatValidator = m_validator->get_validator_for_category(childCat.name());
if (childCatValidator != nullptr)
mandatoryChildFields = childCatValidator->m_mandatory_fields;
for (auto &link : m_validator->get_links_for_parent(m_name))
{
if (link->m_child_category != childCat.m_name)
......@@ -914,14 +1007,13 @@ condition category::get_children_condition(row_handle rh, const category &childC
if (parentValue.empty())
cond = std::move(cond) and key(childKey) == null;
else if (link->m_parent_keys.size() > 1 and not mandatoryChildFields.contains(childKey))
cond = std::move(cond) and (key(childKey) == parentValue.text() or key(childKey) == null);
else
cond = std::move(cond) and key(childKey) == parentValue.text();
}
if (result)
result = std::move(result) or std::move(cond);
else
result = std::move(cond);
result = std::move(result) or std::move(cond);
}
return result;
......@@ -1004,7 +1096,7 @@ std::vector<row_handle> category::get_linked(row_handle r, const category &cat)
category::iterator category::erase(iterator pos)
{
row_handle rh = *pos;
row *r = rh;
row *r = rh.get_row();
iterator result = ++pos;
iset keys;
......@@ -1137,9 +1229,14 @@ void category::erase_orphans(condition &&cond, category &parent)
continue;
if (VERBOSE > 1)
{
category c(m_name);
c.emplace(r);
std::cerr << "Removing orphaned record: " << std::endl
<< r << std::endl
<< c << std::endl
<< std::endl;
}
remove.emplace_back(r.m_row);
}
......@@ -1526,6 +1623,11 @@ category::iterator category::insert_impl(const_iterator pos, row *n)
if (n == nullptr)
throw std::runtime_error("Invalid pointer passed to insert");
// #ifndef NDEBUG
// if (m_validator)
// is_valid();
// #endif
try
{
// First, make sure all mandatory fields are supplied
......@@ -1606,57 +1708,62 @@ category::iterator category::insert_impl(const_iterator pos, row *n)
delete_row(n);
throw;
}
}
category::iterator category::erase_impl(const_iterator pos)
{
if (pos == cend())
return end();
assert(false);
// TODO: implement
// row *n = const_cast<row *>(pos.row());
// row *cur;
// if (m_head == n)
// {
// m_head = static_cast<row *>(m_head->m_next);
// if (m_head == nullptr)
// m_tail = nullptr;
// n->m_next = nullptr;
// delete_row(n);
// cur = m_head;
// }
// else
// {
// cur = static_cast<row *>(n->m_next);
// if (m_tail == n)
// m_tail = static_cast<row *>(n->m_prev);
// row *p = m_head;
// while (p != nullptr and p->m_next != n)
// p = p->m_next;
// if (p != nullptr and p->m_next == n)
// {
// p->m_next = n->m_next;
// if (p->m_next != nullptr)
// p->m_next->m_prev = p;
// n->m_next = nullptr;
// }
// else
// throw std::runtime_error("remove for a row not found in the list");
// delete_row(n);
// }
// return iterator(*this, cur);
// #ifndef NDEBUG
// if (m_validator)
// is_valid();
// #endif
}
// category::iterator category::erase_impl(const_iterator pos)
// {
// if (pos == cend())
// return end();
// assert(false);
// // TODO: implement
// // row *n = const_cast<row *>(pos.row());
// // row *cur;
// // if (m_head == n)
// // {
// // m_head = static_cast<row *>(m_head->m_next);
// // if (m_head == nullptr)
// // m_tail = nullptr;
// // n->m_next = nullptr;
// // delete_row(n);
// // cur = m_head;
// // }
// // else
// // {
// // cur = static_cast<row *>(n->m_next);
// // if (m_tail == n)
// // m_tail = static_cast<row *>(n->m_prev);
// // row *p = m_head;
// // while (p != nullptr and p->m_next != n)
// // p = p->m_next;
// // if (p != nullptr and p->m_next == n)
// // {
// // p->m_next = n->m_next;
// // if (p->m_next != nullptr)
// // p->m_next->m_prev = p;
// // n->m_next = nullptr;
// // }
// // else
// // throw std::runtime_error("remove for a row not found in the list");
// // delete_row(n);
// // }
// // return iterator(*this, cur);
// }
void category::swap_item(size_t column_ix, row_handle &a, row_handle &b)
{
assert(this == a.m_category);
......@@ -1714,7 +1821,7 @@ void category::swap_item(size_t column_ix, row_handle &a, row_handle &b)
v->m_next = vb->m_next;
vb->m_next = nullptr;
if (rb->m_tail = vb)
if (rb->m_tail == vb)
rb->m_tail = v;
break;
......
src/condition.cpp
......@@ -58,4 +58,81 @@ bool is_column_type_uchar(const category &cat, std::string_view col)
return result;
}
namespace detail
{
condition_impl *key_equals_condition_impl::prepare(const category &c)
{
m_item_ix = get_column_ix(c, m_item_tag);
m_icase = is_column_type_uchar(c, m_item_tag);
if (c.get_cat_validator() != nullptr and
c.key_field_indices().contains(m_item_ix) and
c.key_field_indices().size() == 1)
{
m_single_hit = c[{ { m_item_tag, m_value } }];
}
return this;
}
condition_impl *and_condition_impl::prepare(const category &c)
{
for (auto &sub : mSub)
sub = sub->prepare(c);
for (;;)
{
auto si = find_if(mSub.begin(), mSub.end(), [](condition_impl *sub) { return dynamic_cast<and_condition_impl *>(sub) != nullptr; });
if (si == mSub.end())
break;
and_condition_impl *sub_and = static_cast<and_condition_impl *>(*si);
mSub.erase(si);
mSub.insert(mSub.end(), sub_and->mSub.begin(), sub_and->mSub.end());
sub_and->mSub.clear();
delete sub_and;
}
return this;
}
condition_impl *or_condition_impl::prepare(const category &c)
{
condition_impl *result = this;
mA = mA->prepare(c);
mB = mB->prepare(c);
key_equals_condition_impl *equals = dynamic_cast<key_equals_condition_impl*>(mA);
key_is_empty_condition_impl *empty = dynamic_cast<key_is_empty_condition_impl*>(mB);
if (equals == nullptr and empty == nullptr)
{
equals = dynamic_cast<key_equals_condition_impl*>(mB);
empty = dynamic_cast<key_is_empty_condition_impl*>(mA);
}
if (equals != nullptr and empty != nullptr)
{
result = new detail::key_equals_or_empty_condition_impl(equals, empty);
result = result->prepare(c);
delete this;
}
return result;
}
} // namespace detail
void condition::prepare(const category &c)
{
if (m_impl)
m_impl = m_impl->prepare(c);
m_prepared = true;
}
} // namespace cif
src/datablock.cpp
......@@ -54,10 +54,14 @@ bool datablock::is_valid() const
return result;
}
void datablock::validate_links() const
bool datablock::validate_links() const
{
bool result = true;
for (auto &cat : *this)
cat.validate_links();
result = cat.validate_links() and result;
return result;
}
// --------------------------------------------------------------------
......@@ -70,7 +74,11 @@ category &datablock::operator[](std::string_view name)
if (i != end())
return *i;
emplace_back(name);
auto &cat = emplace_back(name);
if (m_validator)
cat.set_validator(m_validator, *this);
return back();
}
......
src/file.cpp
......@@ -48,6 +48,9 @@ bool file::is_valid() const
for (auto &d : *this)
result = d.is_valid() and result;
if (result)
result = validate_links();
return result;
}
......@@ -66,16 +69,23 @@ bool file::is_valid()
for (auto &d : *this)
result = d.is_valid() and result;
if (result)
result = validate_links();
return result;
}
void file::validate_links() const
bool file::validate_links() const
{
if (m_validator == nullptr)
std::runtime_error("No validator loaded explicitly, cannot continue");
bool result = true;
for (auto &db : *this)
db.validate_links();
result = db.validate_links() and result;
return result;
}
void file::load_dictionary()
......@@ -196,6 +206,9 @@ void file::save(const std::filesystem::path &p) const
void file::save(std::ostream &os) const
{
// if (not is_valid())
// std::cout << "File is not valid!" << std::endl;
for (auto &db : *this)
db.write(os);
}
......
src/pdb/cif2pdb.cpp 0 → 100644
This source diff could not be displayed because it is too large. You can view the blob instead.
src/pdb/pdb2cif.cpp 0 → 100644
This source diff could not be displayed because it is too large. You can view the blob instead.
src/point.cpp
......@@ -327,7 +327,7 @@ std::tuple<double, point> quaternion_to_angle_axis(quaternion q)
point axis(q.get_b() / s, q.get_c() / s, q.get_d() / s);
return std::make_tuple(angle, axis);
return { angle, axis };
}
point center_points(std::vector<point> &Points)
......
src/row.cpp
......@@ -65,11 +65,31 @@ row_initializer::row_initializer(row_handle rh)
assert(rh.m_category);
assert(rh.m_row);
row *r = rh;
row *r = rh.get_row();
auto &cat = *rh.m_category;
for (auto i = r->m_head; i != nullptr; i = i->m_next)
m_items.emplace_back(cat.get_column_name(i->m_column_ix), i->text());
emplace_back(cat.get_column_name(i->m_column_ix), i->text());
}
void row_initializer::set_value(std::string_view name, std::string_view value)
{
for (auto &i : *this)
{
if (i.name() == name)
{
i.value(value);
return;
}
}
emplace_back(name, value);
}
void row_initializer::set_value_if_empty(std::string_view name, std::string_view value)
{
if (find_if(begin(), end(), [name](auto &i) { return i.name() == name; }) == end())
emplace_back(name, value);
}
} // namespace cif
\ No newline at end of file
test/REA.cif 0 → 100644
data_REA
#
_chem_comp.id REA
_chem_comp.name "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 REA
_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
REA C1 C1 C 0 1 N N N 21.972 29.831 16.739 -4.684 0.932 -0.497 C1 REA 1
REA C2 C2 C 0 1 N N N 20.921 30.524 15.841 -5.837 0.190 -1.176 C2 REA 2
REA C3 C3 C 0 1 N N N 20.245 29.635 14.848 -6.441 -0.798 -0.171 C3 REA 3
REA C4 C4 C 0 1 N N N 19.555 28.479 15.488 -5.418 -1.903 0.100 C4 REA 4
REA C5 C5 C 0 1 N N N 20.389 27.812 16.587 -4.082 -1.301 0.429 C5 REA 5
REA C6 C6 C 0 1 N N N 21.425 28.446 17.218 -3.756 -0.048 0.161 C6 REA 6
REA C7 C7 C 0 1 N N N 22.242 27.851 18.297 -2.457 0.396 0.516 C7 REA 7
REA C8 C8 C 0 1 N N N 21.868 26.977 19.240 -1.363 -0.229 0.007 C8 REA 8
REA C9 C9 C 0 1 N N N 22.705 26.434 20.286 -0.076 0.257 0.298 C9 REA 9
REA C10 C10 C 0 1 N N N 22.159 25.536 21.131 1.022 -0.370 -0.213 C10 REA 10
REA C11 C11 C 0 1 N N N 22.875 24.924 22.234 2.306 0.115 0.077 C11 REA 11
REA C12 C12 C 0 1 N N N 22.237 24.026 22.990 3.405 -0.513 -0.435 C12 REA 12
REA C13 C13 C 0 1 N N N 22.856 23.377 24.125 4.689 -0.028 -0.144 C13 REA 13
REA C14 C14 C 0 1 N N N 22.135 22.473 24.834 5.787 -0.655 -0.656 C14 REA 14
REA C15 C15 C 0 1 N N N 22.563 21.710 26.016 7.077 -0.265 -0.244 C15 REA 15
REA C16 C16 C 0 1 N N N 22.238 30.737 17.948 -5.246 1.886 0.559 C16 REA 16
REA C17 C17 C 0 1 N N N 23.292 29.620 15.948 -3.911 1.737 -1.544 C17 REA 17
REA C18 C18 C 0 1 N N N 19.791 26.449 16.947 -3.056 -2.175 1.103 C18 REA 18
REA C19 C19 C 0 1 N N N 24.181 26.841 20.385 0.090 1.471 1.175 C19 REA 19
REA C20 C20 C 0 1 N N N 24.303 23.747 24.489 4.855 1.186 0.733 C20 REA 20
REA O1 O1 O 0 1 N N N 23.640 21.075 25.978 7.210 0.553 0.648 O1 REA 21
REA O2 O2 O 0 1 N N N 21.840 21.712 27.037 8.166 -0.798 -0.840 O2 REA 22
REA H21 H21 H 0 1 N N N 20.147 30.955 16.494 -6.598 0.905 -1.490 H21 REA 23
REA H22 H22 H 0 1 N N N 21.425 31.330 15.288 -5.462 -0.353 -2.044 H22 REA 24
REA H31 H31 H 0 1 N N N 19.501 30.227 14.295 -6.673 -0.278 0.759 H31 REA 25
REA H32 H32 H 0 1 N N N 21.001 29.250 14.148 -7.349 -1.234 -0.586 H32 REA 26
REA H41 H41 H 0 1 N N N 18.613 28.835 15.931 -5.756 -2.511 0.938 H41 REA 27
REA H42 H42 H 0 1 N N N 19.335 27.730 14.713 -5.322 -2.531 -0.786 H42 REA 28
REA H7 H7 H 0 1 N N N 23.276 28.162 18.329 -2.337 1.230 1.191 H7 REA 29
REA H8 H8 H 0 1 N N N 20.840 26.645 19.217 -1.482 -1.100 -0.622 H8 REA 30
REA H10 H10 H 0 1 N N N 21.127 25.256 20.977 0.903 -1.241 -0.842 H10 REA 31
REA H11 H11 H 0 1 N N N 23.902 25.189 22.440 2.425 0.985 0.706 H11 REA 32
REA H12 H12 H 0 1 N N N 21.216 23.774 22.743 3.286 -1.383 -1.063 H12 REA 33
REA H14 H14 H 0 1 N N N 21.127 22.292 24.490 5.667 -1.451 -1.376 H14 REA 34
REA H161 H161 H 0 0 N N N 22.984 30.265 18.604 -5.802 1.316 1.303 H161 REA 35
REA H162 H162 H 0 0 N N N 22.618 31.709 17.601 -4.426 2.415 1.044 H162 REA 36
REA H163 H163 H 0 0 N N N 21.302 30.887 18.506 -5.911 2.605 0.081 H163 REA 37
REA H171 H171 H 0 0 N N N 24.033 29.127 16.595 -4.598 2.394 -2.077 H171 REA 38
REA H172 H172 H 0 0 N N N 23.095 28.989 15.069 -3.146 2.335 -1.050 H172 REA 39
REA H173 H173 H 0 0 N N N 23.683 30.595 15.620 -3.439 1.054 -2.251 H173 REA 40
REA H181 H181 H 0 0 N N N 20.397 25.979 17.736 -3.448 -3.187 1.201 H181 REA 41
REA H182 H182 H 0 0 N N N 18.761 26.584 17.308 -2.145 -2.194 0.503 H182 REA 42
REA H183 H183 H 0 0 N N N 19.786 25.804 16.056 -2.831 -1.775 2.092 H183 REA 43
REA H191 H191 H 0 0 N N N 24.647 26.327 21.238 0.171 1.159 2.216 H191 REA 44
REA H192 H192 H 0 0 N N N 24.702 26.559 19.458 0.993 2.008 0.885 H192 REA 45
REA H193 H193 H 0 0 N N N 24.252 27.929 20.529 -0.774 2.125 1.058 H193 REA 46
REA H201 H201 H 0 0 N N N 24.620 23.168 25.369 5.026 0.871 1.762 H201 REA 47
REA H202 H202 H 0 0 N N N 24.965 23.516 23.641 5.707 1.771 0.386 H202 REA 48
REA H203 H203 H 0 0 N N N 24.360 24.822 24.717 3.952 1.795 0.685 H203 REA 49
REA HO2 HO2 H 0 1 N N N 22.244 21.180 27.713 9.006 -0.469 -0.490 HO2 REA 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
REA C1 C2 SING N N 1
REA C1 C6 SING N N 2
REA C1 C16 SING N N 3
REA C1 C17 SING N N 4
REA C2 C3 SING N N 5
REA C2 H21 SING N N 6
REA C2 H22 SING N N 7
REA C3 C4 SING N N 8
REA C3 H31 SING N N 9
REA C3 H32 SING N N 10
REA C4 C5 SING N N 11
REA C4 H41 SING N N 12
REA C4 H42 SING N N 13
REA C5 C6 DOUB N N 14
REA C5 C18 SING N N 15
REA C6 C7 SING N N 16
REA C7 C8 DOUB N E 17
REA C7 H7 SING N N 18
REA C8 C9 SING N N 19
REA C8 H8 SING N N 20
REA C9 C10 DOUB N E 21
REA C9 C19 SING N N 22
REA C10 C11 SING N N 23
REA C10 H10 SING N N 24
REA C11 C12 DOUB N E 25
REA C11 H11 SING N N 26
REA C12 C13 SING N N 27
REA C12 H12 SING N N 28
REA C13 C14 DOUB N E 29
REA C13 C20 SING N N 30
REA C14 C15 SING N N 31
REA C14 H14 SING N N 32
REA C15 O1 DOUB N N 33
REA C15 O2 SING N N 34
REA C16 H161 SING N N 35
REA C16 H162 SING N N 36
REA C16 H163 SING N N 37
REA C17 H171 SING N N 38
REA C17 H172 SING N N 39
REA C17 H173 SING N N 40
REA C18 H181 SING N N 41
REA C18 H182 SING N N 42
REA C18 H183 SING N N 43
REA C19 H191 SING N N 44
REA C19 H192 SING N N 45
REA C19 H193 SING N N 46
REA C20 H201 SING N N 47
REA C20 H202 SING N N 48
REA C20 H203 SING N N 49
REA 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
REA SMILES ACDLabs 12.01 "C1(CCCC(=C1\C=C\C(=C\C=C\C(=C\C(=O)O)C)C)C)(C)C"
REA 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+"
REA InChIKey InChI 1.03 SHGAZHPCJJPHSC-YCNIQYBTSA-N
REA SMILES_CANONICAL CACTVS 3.385 "CC1=C(\C=C\C(C)=C\C=C\C(C)=C\C(O)=O)C(C)(C)CCC1"
REA SMILES CACTVS 3.385 "CC1=C(C=CC(C)=CC=CC(C)=CC(O)=O)C(C)(C)CCC1"
REA 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"
REA 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
REA "SYSTEMATIC NAME" ACDLabs 12.01 "retinoic acid"
REA "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
REA "Create component" 1999-07-08 RCSB
REA "Modify descriptor" 2011-06-04 RCSB
REA "Other modification" 2016-10-18 RCSB
#
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/UN_.cif 0 → 100644
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
UN_ UN_ UN_NINE L-peptide 13 6 .
#
data_comp_UN_
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
UN_ N N NT3 1 0.227 -1.259 0.452
UN_ H H H 0 0.069 -1.019 1.421
UN_ H2 H H 0 1.104 -1.640 0.356
UN_ H3 H H 0 -0.424 -1.909 0.174
UN_ CA C CH1 0 0.103 -0.030 -0.392
UN_ HA H H 0 0.160 -0.299 -1.339
UN_ CB C CH3 0 -1.244 0.625 -0.159
UN_ HB3 H H 0 -1.857 -0.018 0.234
UN_ HB2 H H 0 -1.605 0.932 -1.008
UN_ HB1 H H 0 -1.150 1.385 0.442
UN_ C C C 0 1.270 0.922 -0.094
UN_ O O O 0 2.008 1.323 -0.994
UN_ OXT O OC -1 1.498 1.305 1.054
loop_
_chem_comp_tree.comp_id
_chem_comp_tree.atom_id
_chem_comp_tree.atom_back
_chem_comp_tree.atom_forward
_chem_comp_tree.connect_type
UN_ N n/a CA START
UN_ H N . .
UN_ H2 N . .
UN_ H3 N . .
UN_ CA N C .
UN_ HA CA . .
UN_ CB CA HB3 .
UN_ HB1 CB . .
UN_ HB2 CB . .
UN_ HB3 CB . .
UN_ C CA . END
UN_ O C . .
UN_ OXT C . .
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.aromatic
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
UN_ CB CA SINGLE n 1.509 0.014
UN_ CA C SINGLE n 1.533 0.011
UN_ C O DOUBLE n 1.247 0.019
UN_ C OXT SINGLE n 1.247 0.019
UN_ CA N SINGLE n 1.482 0.010
UN_ CB HB3 SINGLE n 0.972 0.015
UN_ CB HB2 SINGLE n 0.972 0.015
UN_ CB HB1 SINGLE n 0.972 0.015
UN_ CA HA SINGLE n 0.986 0.020
UN_ N H SINGLE n 0.911 0.020
UN_ N H2 SINGLE n 0.911 0.020
UN_ N H3 SINGLE n 0.911 0.020
loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
UN_ CA CB HB3 109.546 1.50
UN_ CA CB HB2 109.546 1.50
UN_ CA CB HB1 109.546 1.50
UN_ HB3 CB HB2 109.386 1.50
UN_ HB3 CB HB1 109.386 1.50
UN_ HB2 CB HB1 109.386 1.50
UN_ CB CA C 111.490 1.50
UN_ CB CA N 109.912 1.50
UN_ CB CA HA 108.878 1.50
UN_ C CA N 109.627 1.50
UN_ C CA HA 108.541 1.50
UN_ N CA HA 108.529 1.50
UN_ CA C O 117.159 1.57
UN_ CA C OXT 117.159 1.57
UN_ O C OXT 125.683 1.50
UN_ CA N H 109.643 1.50
UN_ CA N H2 109.643 1.50
UN_ CA N H3 109.643 1.50
UN_ H N H2 109.028 2.41
UN_ H N H3 109.028 2.41
UN_ H2 N H3 109.028 2.41
loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
UN_ hh1 N CA CB HB3 60.000 15.000 3
UN_ sp2_sp3_1 O C CA CB 0.000 10.00 6
UN_ sp3_sp3_10 CB CA N H 180.000 10.00 3
loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
UN_ chir_1 CA N C CB positive
loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
UN_ plan-1 C 0.020
UN_ plan-1 CA 0.020
UN_ plan-1 O 0.020
UN_ plan-1 OXT 0.020
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
UN_ SMILES ACDLabs 10.04 "O=C(O)C(N)C"
UN_ SMILES_CANONICAL CACTVS 3.341 "C[C@H](N)C(O)=O"
UN_ SMILES CACTVS 3.341 "C[CH](N)C(O)=O"
UN_ SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C[C@@H](C(=O)O)N"
UN_ SMILES "OpenEye OEToolkits" 1.5.0 "CC(C(=O)O)N"
UN_ InChI InChI 1.03 "InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m0/s1"
UN_ InChIKey InChI 1.03 QNAYBMKLOCPYGJ-REOHCLBHSA-N
UN_ ? acedrg 195 "dictionary generator"
UN_ ? acedrg_database 11 "data source"
UN_ ? rdkit 2017.03.2 "Chemoinformatics tool"
UN_ ? refmac5 5.8.0189 "optimization tool"
test/model-test.cpp
......@@ -87,6 +87,7 @@ BOOST_AUTO_TEST_CASE(create_nonpoly_1)
auto atoms = R"(
data_HEM
loop_
_atom_site.id
_atom_site.group_PDB
_atom_site.type_symbol
_atom_site.label_atom_id
......@@ -98,13 +99,15 @@ _atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
HETATM C CHA . ? -5.248 39.769 -0.250 1.00 7.67 ?
HETATM C CHB . ? -3.774 36.790 3.280 1.00 7.05 ?
HETATM C CHC . ? -2.879 33.328 0.013 1.00 7.69 ?
HETATM C CHD . ? -4.342 36.262 -3.536 1.00 8.00 ?
1 HETATM C CHA . ? -5.248 39.769 -0.250 1.00 7.67 ?
2 HETATM C CHB . ? -3.774 36.790 3.280 1.00 7.05 ?
3 HETATM C CHC . ? -2.879 33.328 0.013 1.00 7.69 ?
4 HETATM C CHD . ? -4.342 36.262 -3.536 1.00 8.00 ?
# that's enough to test with
)"_cf;
atoms.load_dictionary("mmcif_pdbx");
auto &hem_data = atoms["HEM"];
auto &atom_site = hem_data["atom_site"];
......@@ -177,6 +180,7 @@ _struct_asym.pdbx_blank_PDB_chainid_flag N
_struct_asym.pdbx_modified N
_struct_asym.details ?
#
_atom_type.symbol C
)"_cf;
expected.load_dictionary("mmcif_pdbx.dic");
......
test/rename-compound-test.cpp
#include "../include/cif++/Cif++.hpp"
#include "../include/cif++/PDB2Cif.hpp"
#include "../include/cif++/Structure.hpp"
/*-
* SPDX-License-Identifier: BSD-2-Clause
*
* Copyright (c) 2021 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 <cif++.hpp>
#include <iostream>
#include <fstream>
......@@ -22,16 +46,21 @@ int main(int argc, char* argv[])
if (std::filesystem::exists(testdir / ".." / "rsrc" / "mmcif_pdbx.dic"))
cif::add_file_resource("mmcif_pdbx.dic", testdir / ".." / "rsrc" / "mmcif_pdbx.dic");
mmcif::CompoundFactory::instance().pushDictionary(testdir / "REA.cif");
mmcif::CompoundFactory::instance().pushDictionary(testdir / "RXA.cif");
cif::compound_factory::instance().push_dictionary(testdir / "REA.cif");
cif::compound_factory::instance().push_dictionary(testdir / "RXA.cif");
mmcif::file f(testdir / ".."/"examples"/"1cbs.cif.gz");
mmcif::Structure structure(f);
cif::file f(testdir / ".."/"examples"/"1cbs.cif.gz");
cif::mm::structure structure(f);
auto &res = structure.getResidue("B");
auto &res = structure.get_residue("B");
structure.change_residue(res, "RXA", {});
structure.cleanupEmptyCategories();
structure.cleanup_empty_categories();
f.save(std::cout);
if (not f.is_valid())
throw std::runtime_error("Invalid");
f.save(std::cout);
}
......
test/sugar-test.cpp
......@@ -29,8 +29,7 @@
#include <stdexcept>
#include <cif++/cif.hpp>
#include <cif++/structure/Structure.hpp>
#include <cif++.hpp>
// --------------------------------------------------------------------
......@@ -66,7 +65,7 @@ bool init_unit_test()
// initialize CCD location
cif::add_file_resource("components.cif", gTestDir / ".." / "data" / "ccd-subset.cif");
mmcif::CompoundFactory::instance().pushDictionary(gTestDir / "HEM.cif");
cif::compound_factory::instance().push_dictionary(gTestDir / "HEM.cif");
return true;
}
......@@ -78,10 +77,10 @@ BOOST_AUTO_TEST_CASE(sugar_name_1)
using namespace cif::literals;
const std::filesystem::path example(gTestDir / "1juh.cif.gz");
mmcif::file file(example.string());
mmcif::Structure s(file);
cif::file file(example.string());
cif::mm::structure s(file);
auto &db = s.datablock();
auto &db = s.get_datablock();
auto &entity = db["entity"];
auto &branches = s.branches();
......@@ -90,7 +89,7 @@ BOOST_AUTO_TEST_CASE(sugar_name_1)
for (auto &branch : branches)
{
auto entityID = branch.front().entityID();
auto entityID = branch.front().get_entity_id();
auto name = entity.find1<std::string>("id"_key == entityID, "pdbx_description");
BOOST_CHECK_EQUAL(branch.name(), name);
......@@ -104,20 +103,23 @@ BOOST_AUTO_TEST_CASE(create_sugar_1)
using namespace cif::literals;
const std::filesystem::path example(gTestDir / "1juh.cif.gz");
mmcif::file file(example.string());
mmcif::Structure s(file);
cif::file file(example.string());
cif::mm::structure s(file);
// collect atoms from asym L first
auto &NAG = s.getResidue("L");
auto &NAG = s.get_residue("L");
auto nagAtoms = NAG.atoms();
std::vector<std::vector<cif::Item>> ai;
std::vector<cif::row_initializer> ai;
auto &db = s.datablock();
auto &db = s.get_datablock();
auto &as = db["atom_site"];
// NOTE, row_initializer does not actually hold the data, so copy it first
// before it gets destroyed by remove_residue
for (auto r : as.find("label_asym_id"_key == "L"))
ai.emplace_back(r.begin(), r.end());
auto &ri = ai.emplace_back(r);
s.remove_residue(NAG);
......@@ -127,6 +129,10 @@ BOOST_AUTO_TEST_CASE(create_sugar_1)
BOOST_CHECK_EQUAL(branch.size(), 1);
BOOST_CHECK_EQUAL(branch[0].atoms().size(), nagAtoms.size());
BOOST_CHECK(file.is_valid());
file.save(gTestDir / "test-create_sugar_1.cif");
}
// --------------------------------------------------------------------
......@@ -136,36 +142,40 @@ BOOST_AUTO_TEST_CASE(create_sugar_2)
using namespace cif::literals;
const std::filesystem::path example(gTestDir / "1juh.cif.gz");
mmcif::file file(example.string());
mmcif::Structure s(file);
cif::file file(example.string());
cif::mm::structure s(file);
// Get branch for H
auto &bH = s.getBranchByAsymID("H");
auto &bH = s.get_branch_by_asym_id("H");
BOOST_CHECK_EQUAL(bH.size(), 2);
std::vector<std::vector<cif::Item>> ai[2];
std::vector<cif::row_initializer> ai[2];
auto &db = s.datablock();
auto &db = s.get_datablock();
auto &as = db["atom_site"];
for (size_t i = 0; i < 2; ++i)
{
for (auto r : as.find("label_asym_id"_key == "H" and "auth_seq_id"_key == i + 1))
ai[i].emplace_back(r.begin(), r.end());
auto &ri = ai[i].emplace_back(r);
}
s.remove_branch(bH);
BOOST_CHECK(file.is_valid());
auto &bN = s.create_branch(ai[0]);
s.extend_branch(bN.asymID(), ai[1], 1, "O4");
s.extend_branch(bN.get_asym_id(), ai[1], 1, "O4");
BOOST_CHECK_EQUAL(bN.name(), "2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose");
BOOST_CHECK_EQUAL(bN.size(), 2);
BOOST_CHECK(file.is_valid());
file.save(gTestDir / "test-create_sugar_2.cif");
BOOST_CHECK_NO_THROW(mmcif::Structure s2(file));
BOOST_CHECK_NO_THROW(cif::mm::structure s2(file));
}
// --------------------------------------------------------------------
......@@ -175,11 +185,11 @@ BOOST_AUTO_TEST_CASE(delete_sugar_1)
using namespace cif::literals;
const std::filesystem::path example(gTestDir / "1juh.cif.gz");
mmcif::file file(example.string());
mmcif::Structure s(file);
cif::file file(example.string());
cif::mm::structure s(file);
// Get branch for H
auto &bG = s.getBranchByAsymID("G");
auto &bG = s.get_branch_by_asym_id("G");
BOOST_CHECK_EQUAL(bG.size(), 4);
......@@ -187,12 +197,14 @@ BOOST_AUTO_TEST_CASE(delete_sugar_1)
BOOST_CHECK_EQUAL(bG.size(), 1);
auto &bN = s.getBranchByAsymID("G");
auto &bN = s.get_branch_by_asym_id("G");
BOOST_CHECK_EQUAL(bN.name(), "2-acetamido-2-deoxy-beta-D-glucopyranose");
BOOST_CHECK_EQUAL(bN.size(), 1);
file.save(gTestDir / "test-create_sugar_3.cif");
BOOST_CHECK(file.is_valid());
// file.save(gTestDir / "test-create_sugar_3.cif");
BOOST_CHECK_NO_THROW(mmcif::Structure s2(file));
BOOST_CHECK_NO_THROW(cif::mm::structure s2(file));
}
test/unit-v2-test.cpp
......@@ -142,13 +142,17 @@ BOOST_AUTO_TEST_CASE(item_1)
BOOST_CHECK_EQUAL(i2.value(), ci2.value());
BOOST_CHECK_EQUAL(i3.value(), ci3.value());
item mi1(std::move(i1));
item mi2(std::move(i2));
item mi3(std::move(i3));
item mi1(std::move(ci1));
item mi2(std::move(ci2));
item mi3(std::move(ci3));
BOOST_CHECK_EQUAL(i1.value(), mi1.value());
BOOST_CHECK_EQUAL(i2.value(), mi2.value());
BOOST_CHECK_EQUAL(i3.value(), mi3.value());
BOOST_CHECK(ci1.empty());
BOOST_CHECK(ci2.empty());
BOOST_CHECK(ci3.empty());
}
// --------------------------------------------------------------------
......@@ -1037,12 +1041,12 @@ _cat_2.desc
cat1.erase(cif::key("id") == 10);
BOOST_CHECK_EQUAL(cat1.size(), 2);
BOOST_CHECK_EQUAL(cat2.size(), 3); // TODO: Is this really what we want?
BOOST_CHECK_EQUAL(cat2.size(), 2); // TODO: Is this really what we want?
cat1.erase(cif::key("id") == 20);
BOOST_CHECK_EQUAL(cat1.size(), 1);
BOOST_CHECK_EQUAL(cat2.size(), 2); // TODO: Is this really what we want?
BOOST_CHECK_EQUAL(cat2.size(), 1); // TODO: Is this really what we want?
}
// --------------------------------------------------------------------
......@@ -1514,8 +1518,6 @@ _cat_2.parent_id3
// --------------------------------------------------------------------
// --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(d6)
{
const char dict[] = R"(
......@@ -2859,4 +2861,112 @@ _cat_1.name
auto &audit_conform = f2.front()["audit_conform"];
BOOST_CHECK_EQUAL(audit_conform.front()["dict_name"].as<std::string>(), "test_dict.dic");
BOOST_CHECK_EQUAL(audit_conform.front()["dict_version"].as<float>(), 1.0);
}
\ No newline at end of file
}
// --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(ix_op_1)
{
const char dict[] = R"(
data_test_dict.dic
_datablock.id test_dict.dic
_datablock.description
;
A test dictionary
;
_dictionary.title test_dict.dic
_dictionary.datablock_id test_dict.dic
_dictionary.version 1.0
loop_
_item_type_list.code
_item_type_list.primitive_code
_item_type_list.construct
code char
'[][_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]*'
text char
'[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
int numb
'[+-]?[0-9]+'
save_cat_1
_category.description 'A simple test category'
_category.id cat_1
_category.mandatory_code yes
loop_
_category_key.name '_cat_1.id'
'_cat_1.id_2'
save_
save__cat_1.id
_item.name '_cat_1.id'
_item.category_id cat_1
_item.mandatory_code yes
_item_type.code int
save_
save__cat_1.id_2
_item.name '_cat_1.id_2'
_item.category_id cat_1
_item.mandatory_code no
_item_type.code int
save_
)";
struct membuf : public std::streambuf
{
membuf(char *text, size_t length)
{
this->setg(text, text, text + length);
}
} buffer(const_cast<char *>(dict), sizeof(dict) - 1);
std::istream is_dict(&buffer);
auto validator = cif::parse_dictionary("test", is_dict);
cif::file f;
f.set_validator(&validator);
// --------------------------------------------------------------------
const char data[] = R"(
data_test
loop_
_cat_1.id
_cat_1.id_2
1 10
2 20
3 ?
)";
// --------------------------------------------------------------------
struct data_membuf : public std::streambuf
{
data_membuf(char *text, size_t length)
{
this->setg(text, text, text + length);
}
} data_buffer(const_cast<char *>(data), sizeof(data) - 1);
std::istream is_data(&data_buffer);
f.load(is_data);
auto &cat1 = f.front()["cat_1"];
using key_type = cif::category::key_type;
using test_tuple_type = std::tuple<key_type,bool>;
test_tuple_type TESTS[] = {
{ {{"id", 1}, {"id_2", 10}}, true },
{ {{"id_2", 10}, {"id", 1}}, true },
{ {{"id", 1}, {"id_2", 20}}, false },
{ {{"id", 3} }, true },
};
for (const auto &[key, test] : TESTS)
BOOST_CHECK_EQUAL((bool)cat1[key], test);
}
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