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libcifpp
Commit adc316d6 by Maarten L. Hekkelman
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Use index in lookup, when available 

start branch code in model::structure (not done yet)
parent 6a0b6b99
Showing with 965 additions and 171 deletions
.gitignore
......@@ -12,3 +12,4 @@ CMakeSettings.json
msvc/
Testing/
rsrc/feature-request.txt
test/test-create_sugar_2.cif
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
......@@ -306,6 +306,12 @@ class category
{
cond.prepare(*this);
auto sh = cond.single();
if (sh.has_value() and *sh)
result = true;
else
{
for (auto r : *this)
{
if (cond(r))
......@@ -315,6 +321,7 @@ class category
}
}
}
}
return result;
}
......
include/cif++/condition.hpp
......@@ -55,6 +55,7 @@ namespace detail
virtual void prepare(const category &c) {}
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
......@@ -122,6 +123,11 @@ 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);
......@@ -175,6 +181,40 @@ namespace detail
size_t m_item_ix = 0;
};
struct key_is_condition_impl : public condition_impl
{
key_is_condition_impl(item &&i)
: m_item_tag(i.name())
, m_value(i.value())
{
}
void 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_compare_condition_impl : public condition_impl
{
template <typename COMP>
......@@ -354,6 +394,13 @@ namespace detail
os << ')';
}
virtual std::optional<row_handle> single() const override
{
auto sa = mA->single();
auto sb = mB->single();
return sa == sb ? sa : std::optional<row_handle>();
}
condition_impl *mA;
condition_impl *mB;
};
......@@ -394,6 +441,19 @@ 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;
};
......@@ -480,27 +540,13 @@ 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_is_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_is_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
......@@ -79,7 +79,7 @@ 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);
......
include/cif++/model.hpp
......@@ -52,13 +52,21 @@ class atom
{
atom_impl(datablock &db, std::string_view id)
: m_db(db)
, m_cat(db["atom_site"])
, m_id(id)
{
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;
......@@ -80,7 +88,18 @@ class atom
void set_property(const std::string_view name, const std::string &value);
row_handle row()
{
return m_cat[{{"id", m_id}}];
}
const row_handle row() const
{
return m_cat[{{"id", m_id}}];
}
const datablock &m_db;
category &m_cat;
std::string m_id;
point m_location;
std::string m_symop = "1_555";
......@@ -99,10 +118,10 @@ class atom
{
}
// atom(datablock &db, row_handle &row)
// : atom(std::make_shared<atom_impl>(db, row["id"].as<std::string>(), row))
// {
// }
atom(datablock &db, row_handle &row)
: atom(std::make_shared<atom_impl>(db, row["id"].as<std::string>()))
{
}
// a special constructor to create symmetry copies
atom(const atom &rhs, const point &symmmetry_location, const std::string &symmetry_operation)
......
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;
}
......@@ -300,6 +305,13 @@ class row_initializer : public std::vector<item>
}
row_initializer(row_handle rh);
void set_value(std::string_view name, std::string_view value);
void set_value_if_empty(std::string_view name, std::string_view value);
void set_value_if_empty(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)
......@@ -365,7 +365,7 @@ row *category_index::find_by_value(row_initializer k) const
row_initializer k2;
for (auto &f : m_category.key_field_indices())
{
std::string fld = fld=m_category.get_column_name(f);
auto fld = m_category.get_column_name(f);
auto ki = find_if(k.begin(), k.end(), [&fld](item &i) { return i.name() == fld; });
if (ki == k.end())
......@@ -411,7 +411,10 @@ category_index::entry *category_index::insert(entry *h, row *v)
std::ostringstream os;
for (auto col : m_category.fields())
{
if (rh[col])
os << col << ": " << std::quoted(rh[col].text()) << "; ";
}
throw std::runtime_error("Duplicate Key violation, cat: " + m_category.name() + " values: " + os.str());
}
......@@ -484,7 +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.
......@@ -814,10 +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);
}
}
......@@ -871,10 +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)
{
......@@ -883,6 +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());
......@@ -901,6 +916,8 @@ 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;
......@@ -915,6 +932,8 @@ void category::validate_links() const
}
}
}
return result;
}
// --------------------------------------------------------------------
......@@ -1073,7 +1092,7 @@ 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;
......@@ -1206,10 +1225,15 @@ 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);
}
......@@ -1595,6 +1619,11 @@ 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
......@@ -1675,6 +1704,11 @@ category::iterator category::insert_impl(const_iterator pos, row *n)
delete_row(n);
throw;
}
// #ifndef NDEBUG
// if (m_validator)
// is_valid();
// #endif
}
category::iterator category::erase_impl(const_iterator pos)
......
src/condition.cpp
......@@ -58,4 +58,22 @@ bool is_column_type_uchar(const category &cat, std::string_view col)
return result;
}
namespace detail
{
void key_is_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 } }];
}
}
} // namespace detail
} // 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
......@@ -66,16 +66,23 @@ 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()
......
src/model.cpp
......@@ -43,77 +43,63 @@ namespace cif::mm
// --------------------------------------------------------------------
// atom
// constructor for a symmetry copy of an atom
atom::atom_impl::atom_impl(const atom_impl &impl, const point &loc, const std::string &sym_op)
: m_db(impl.m_db)
, m_id(impl.m_id)
// , m_row(impl.m_row)
, m_location(loc)
, m_symop(sym_op)
{
}
void atom::atom_impl::prefetch()
{
// tie(m_location.m_x, m_location.m_y, m_location.m_z) = m_row.get("Cartn_x", "Cartn_y", "Cartn_z");
}
void atom::atom_impl::moveTo(const point &p)
{
// if (m_symop != "1_555")
// throw std::runtime_error("Moving symmetry copy");
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;
auto r = row();
#if __cpp_lib_format
r.assign("Cartn_x", std::format("{:.3f}", p.getX()), false, false);
r.assign("Cartn_y", std::format("{:.3f}", p.getY()), false, false);
r.assign("Cartn_z", std::format("{:.3f}", p.getZ()), false, false);
#else
r.assign("Cartn_x", format("%.3f", p.m_x).str(), false, false);
r.assign("Cartn_y", format("%.3f", p.m_y).str(), false, false);
r.assign("Cartn_z", format("%.3f", p.m_z).str(), false, false);
#endif
m_location = p;
}
// const compound *compound() const;
std::string atom::atom_impl::get_property(std::string_view name) const
{
// return m_row[name].as<std::string>();
return row()[name].as<std::string>();
}
int atom::atom_impl::get_property_int(std::string_view name) 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;
// }
if (not 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;
}
float atom::atom_impl::get_property_float(std::string_view name) const
{
float 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;
// }
if (not 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;
}
void atom::atom_impl::set_property(const std::string_view name, const std::string &value)
{
// m_row.assign(name, value, true, true);
row().assign(name, value, true, true);
}
// int atom::atom_impl::compare(const atom_impl &b) const
......@@ -150,17 +136,17 @@ void atom::atom_impl::set_property(const std::string_view name, const std::strin
int atom::atom_impl::get_charge() const
{
// auto formalCharge = m_row["pdbx_formal_charge"].as<std::optional<int>>();
auto formalCharge = row()["pdbx_formal_charge"].as<std::optional<int>>();
// if (not formalCharge.has_value())
// {
// auto c = cif::compound_factory::instance().create(get_property("label_comp_id"));
if (not formalCharge.has_value())
{
auto c = cif::compound_factory::instance().create(get_property("label_comp_id"));
// if (c != nullptr and c->atoms().size() == 1)
// formalCharge = c->atoms().front().charge;
// }
if (c != nullptr and c->atoms().size() == 1)
formalCharge = c->atoms().front().charge;
}
// return formalCharge.value_or(0);
return formalCharge.value_or(0);
}
// const Compound *atom::atom_impl::compound() const
......@@ -1765,7 +1751,6 @@ void structure::remove_atom(atom &a, bool removeFromResidue)
using namespace literals;
auto &atomSites = m_db["atom_site"];
atomSites.erase("id"_key == a.id());
if (removeFromResidue)
{
......@@ -1781,6 +1766,8 @@ void structure::remove_atom(atom &a, bool removeFromResidue)
}
}
atomSites.erase("id"_key == a.id());
assert(m_atom_index.size() == m_atoms.size());
#ifndef NDEBUG
......@@ -2034,14 +2021,14 @@ void structure::remove_sugar(sugar &s)
dix.insert(tix);
for (auto atom : branch[tix - 1].atoms())
remove_atom(atom, false);
for (auto &s : branch)
{
if (s.get_link_nr() == tix)
test.push(s.num());
}
for (auto atom : branch[tix - 1].atoms())
remove_atom(atom, false);
}
branch.erase(remove_if(branch.begin(), branch.end(), [dix](const sugar &s) { return dix.count(s.num()); }), branch.end());
......@@ -2089,9 +2076,6 @@ void structure::remove_branch(branch &branch)
{
using namespace literals;
m_db["pdbx_branch_scheme"].erase("asym_id"_key == branch.get_asym_id());
m_db["struct_asym"].erase("id"_key == branch.get_asym_id());
for (auto &sugar : branch)
{
auto atoms = sugar.atoms();
......@@ -2099,6 +2083,9 @@ void structure::remove_branch(branch &branch)
remove_atom(atom);
}
m_db["pdbx_branch_scheme"].erase("asym_id"_key == branch.get_asym_id());
m_db["struct_asym"].erase("id"_key == branch.get_asym_id());
m_branches.erase(remove(m_branches.begin(), m_branches.end(), branch), m_branches.end());
}
......@@ -2199,28 +2186,22 @@ std::string structure::create_non_poly(const std::string &entity_id, std::vector
auto &res = m_non_polymers.emplace_back(*this, comp_id, asym_id, 0, "1");
auto appendUnlessSet = [](row_initializer &ai, item &&i)
{
if (find_if(ai.begin(), ai.end(), [name = i.name()](item &ci)
{ return ci.name() == name; }) == ai.end())
ai.emplace_back(std::move(i));
};
for (auto &atom : atoms)
{
auto atom_id = atom_site.get_unique_id("");
appendUnlessSet(atom, {"group_PDB", "HETATM"});
appendUnlessSet(atom, {"id", atom_id});
appendUnlessSet(atom, {"label_comp_id", comp_id});
appendUnlessSet(atom, {"label_asym_id", asym_id});
appendUnlessSet(atom, {"label_seq_id", ""});
appendUnlessSet(atom, {"label_entity_id", entity_id});
appendUnlessSet(atom, {"auth_comp_id", comp_id});
appendUnlessSet(atom, {"auth_asym_id", asym_id});
appendUnlessSet(atom, {"auth_seq_id", 1});
appendUnlessSet(atom, {"pdbx_PDB_model_num", 1});
appendUnlessSet(atom, {"label_alt_id", ""});
atom.set_value("name", atom_id);
atom.set_value("label_asym_id", asym_id);
atom.set_value_if_empty({"group_PDB", "HETATM"});
atom.set_value_if_empty({"label_comp_id", comp_id});
atom.set_value_if_empty({"label_seq_id", ""});
atom.set_value_if_empty({"label_entity_id", entity_id});
atom.set_value_if_empty({"auth_comp_id", comp_id});
atom.set_value_if_empty({"auth_asym_id", asym_id});
atom.set_value_if_empty({"auth_seq_id", 1});
atom.set_value_if_empty({"pdbx_PDB_model_num", 1});
atom.set_value_if_empty({"label_alt_id", ""});
auto row = atom_site.emplace(atom.begin(), atom.end());
......@@ -2269,28 +2250,22 @@ branch &structure::create_branch(std::vector<row_initializer> atoms)
auto &atom_site = m_db["atom_site"];
auto appendUnlessSet = [](row_initializer &ai, item &&i)
{
if (find_if(ai.begin(), ai.end(), [name = i.name()](item &ci)
{ return ci.name() == name; }) == ai.end())
ai.emplace_back(std::move(i));
};
for (auto &atom : atoms)
{
auto atom_id = atom_site.get_unique_id("");
appendUnlessSet(atom, {"group_PDB", "HETATM"});
appendUnlessSet(atom, {"id", atom_id});
appendUnlessSet(atom, {"label_comp_id", "NAG"});
appendUnlessSet(atom, {"label_asym_id", asym_id});
appendUnlessSet(atom, {"label_seq_id", "."});
appendUnlessSet(atom, {"label_entity_id", tmp_entity_id});
appendUnlessSet(atom, {"auth_comp_id", "NAG"});
appendUnlessSet(atom, {"auth_asym_id", asym_id});
appendUnlessSet(atom, {"auth_seq_id", 1});
appendUnlessSet(atom, {"pdbx_PDB_model_num", 1});
appendUnlessSet(atom, {"label_alt_id", ""});
atom.set_value("id", atom_id);
atom.set_value("label_asym_id", asym_id);
atom.set_value_if_empty({"group_PDB", "HETATM"});
atom.set_value_if_empty({"label_comp_id", "NAG"});
atom.set_value_if_empty({"label_seq_id", "."});
atom.set_value_if_empty({"label_entity_id", tmp_entity_id});
atom.set_value_if_empty({"auth_comp_id", "NAG"});
atom.set_value_if_empty({"auth_asym_id", asym_id});
atom.set_value_if_empty({"auth_seq_id", 1});
atom.set_value_if_empty({"pdbx_PDB_model_num", 1});
atom.set_value_if_empty({"label_alt_id", ""});
auto row = atom_site.emplace(atom.begin(), atom.end());
......@@ -2300,6 +2275,7 @@ branch &structure::create_branch(std::vector<row_initializer> atoms)
// now we can create the entity and get the real ID
auto entity_id = create_entity_for_branch(branch);
assert(not entity_id.empty());
struct_asym.emplace({
{"id", asym_id},
......@@ -2360,13 +2336,6 @@ branch &structure::extend_branch(const std::string &asym_id, std::vector<row_ini
auto &atom_site = m_db["atom_site"];
auto appendUnlessSet = [](std::vector<item> &ai, item &&i)
{
if (find_if(ai.begin(), ai.end(), [name = i.name()](item &ci)
{ return ci.name() == name; }) == ai.end())
ai.emplace_back(std::move(i));
};
auto bi = std::find_if(m_branches.begin(), m_branches.end(), [asym_id](branch &b)
{ return b.get_asym_id() == asym_id; });
if (bi == m_branches.end())
......@@ -2382,19 +2351,20 @@ branch &structure::extend_branch(const std::string &asym_id, std::vector<row_ini
{
auto atom_id = atom_site.get_unique_id("");
appendUnlessSet(atom, {"group_PDB", "HETATM"});
appendUnlessSet(atom, {"id", atom_id});
appendUnlessSet(atom, {"label_asym_id", asym_id});
appendUnlessSet(atom, {"label_comp_id", compoundID});
appendUnlessSet(atom, {"label_entity_id", tmp_entity_id});
appendUnlessSet(atom, {"auth_comp_id", compoundID});
appendUnlessSet(atom, {"auth_asym_id", asym_id});
appendUnlessSet(atom, {"pdbx_PDB_model_num", 1});
appendUnlessSet(atom, {"label_alt_id", ""});
atom.set_value("id", atom_id);
atom.set_value("label_asym_id", asym_id);
atom.set_value_if_empty({"group_PDB", "HETATM"});
atom.set_value_if_empty({"label_comp_id", compoundID});
atom.set_value_if_empty({"label_entity_id", tmp_entity_id});
atom.set_value_if_empty({"auth_comp_id", compoundID});
atom.set_value_if_empty({"auth_asym_id", asym_id});
atom.set_value_if_empty({"pdbx_PDB_model_num", 1});
atom.set_value_if_empty({"label_alt_id", ""});
auto row = atom_site.emplace(atom.begin(), atom.end());
auto &newAtom = emplace_atom(std::make_shared<atom::atom_impl>(m_db, atom_id, row));
auto &newAtom = emplace_atom(std::make_shared<atom::atom_impl>(m_db, atom_id));
sugar.add_atom(newAtom);
}
......@@ -2444,15 +2414,13 @@ std::string structure::create_entity_for_branch(branch &branch)
{
using namespace literals;
std::string entityName = branch.name(), entityID;
std::string entityName = branch.name();
auto &entity = m_db["entity"];
try
{
entityID = entity.find1<std::string>("type"_key == "branched" and "pdbx_description"_key == entityName, "id");
}
catch (const std::exception &e)
std::string entityID = entity.find1<std::string>("type"_key == "branched" and "pdbx_description"_key == entityName, "id");
if (entityID.empty())
{
entityID = entity.get_unique_id("");
......
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)
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](item &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"];
......
test/sugar-test.cpp
......@@ -115,8 +115,17 @@ BOOST_AUTO_TEST_CASE(create_sugar_1)
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
std::list<std::string> storage;
for (auto r : as.find("label_asym_id"_key == "L"))
ai.emplace_back(r);
{
auto &ri = ai.emplace_back(r);
for (auto &rii : ri)
rii.value(storage.emplace_back(rii.value()));
}
s.remove_residue(NAG);
......@@ -143,6 +152,7 @@ BOOST_AUTO_TEST_CASE(create_sugar_2)
BOOST_CHECK_EQUAL(bH.size(), 2);
std::list<std::string> storage;
std::vector<cif::row_initializer> ai[2];
auto &db = s.get_datablock();
......@@ -151,7 +161,11 @@ BOOST_AUTO_TEST_CASE(create_sugar_2)
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);
{
auto &ri = ai[i].emplace_back(r);
for (auto &rii : ri)
rii.value(storage.emplace_back(rii.value()));
}
}
s.remove_branch(bH);
......
test/unit-v2-test.cpp
......@@ -1514,8 +1514,6 @@ _cat_2.parent_id3
// --------------------------------------------------------------------
// --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(d6)
{
const char dict[] = R"(
......@@ -2860,3 +2858,111 @@ _cat_1.name
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);
}
// --------------------------------------------------------------------
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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