Skip to content

Commit

Permalink
Load inline compound info as restraints, not CCD info
Browse files Browse the repository at this point in the history
  • Loading branch information
@mhekkel
mhekkel committed Dec 20, 2023
1 parent 05d78c9 commit 5169834
Show file tree
Hide file tree
Showing 2 changed files with 172 additions and 26 deletions.
53 changes: 51 additions & 2 deletions include/cif++/compound.hpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -168,14 +168,18 @@ class compound

private:
friend class compound_factory_impl;
friend class local_compound_factory_impl;

compound(cif::datablock &db);
compound(cif::datablock &db, const std::string &id, const std::string &name, const std::string &type, const std::string &group);
compound(cif::datablock &db, int);

std::string m_id;
std::string m_name;
std::string m_type;
std::string m_group;
/// @cond
// m_group is no longer used
std::string __m_group;
/// @endcond
std::string m_formula;
float m_formula_weight = 0;
int m_formal_charge = 0;
Expand Down Expand Up @@ -214,6 +218,20 @@ class compound_factory
/// Override any previously loaded dictionary with @a inDictFile
void push_dictionary(const std::filesystem::path &inDictFile);

/** @brief Override any previously loaded dictionary with the data in @a file
*
* @note experimental feature
*
* Load the file @a file as a source for compound information. This may
* be e.g. a regular mmCIF file with extra files containing compound
* information.
*
* Be carefull to remove the block again, best use @ref cif::compound_source
* as a stack based object.
*/

void push_dictionary(const file &file);

/// Remove the last pushed dictionary
void pop_dictionary();

Expand Down Expand Up @@ -251,4 +269,35 @@ class compound_factory
std::shared_ptr<compound_factory_impl> m_impl;
};

// --------------------------------------------------------------------

/**
* @brief Stack based source for compound info.
*
* Use this class to temporarily add a compound source to the
* compound_factory.
*
* @code{.cpp}
* cif::file f("1cbs-with-custom-rea.cif");
* cif::compound_source cs(f);
*
* auto &cf = cif::compound_factory::instance();
* auto rea_compound = cf.create("REA");
* @endcode
*/

class compound_source
{
public:
compound_source(const cif::file &file)
{
cif::compound_factory::instance().push_dictionary(file);
}

~compound_source()
{
cif::compound_factory::instance().pop_dictionary();
}
};

} // namespace cif
145 changes: 121 additions & 24 deletions src/compound.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -142,8 +142,6 @@ compound::compound(cif::datablock &db)
// The name should not contain newline characters since that triggers validation errors later on
cif::replace_all(m_name, "\n", "");

m_group = "non-polymer";

auto &chemCompAtom = db["chem_comp_atom"];
for (auto row : chemCompAtom)
{
Expand All @@ -153,6 +151,9 @@ compound::compound(cif::datablock &db)
row.get("atom_id", "type_symbol", "charge", "pdbx_aromatic_flag", "pdbx_leaving_atom_flag", "pdbx_stereo_config",
"model_Cartn_x", "model_Cartn_y", "model_Cartn_z");
atom.type_symbol = atom_type_traits(type_symbol).type();
if (stereo_config.empty())
atom.stereo_config = stereo_config_type::N;
else
atom.stereo_config = parse_stereo_config_from_string(stereo_config);
m_atoms.push_back(std::move(atom));
}
Expand All @@ -163,17 +164,28 @@ compound::compound(cif::datablock &db)
compound_bond bond;
std::string valueOrder;
cif::tie(bond.atom_id[0], bond.atom_id[1], valueOrder, bond.aromatic, bond.stereo_config) = row.get("atom_id_1", "atom_id_2", "value_order", "pdbx_aromatic_flag", "pdbx_stereo_config");
if (valueOrder.empty())
bond.type = bond_type::sing;
else
bond.type = parse_bond_type_from_string(valueOrder);
m_bonds.push_back(std::move(bond));
}
}

compound::compound(cif::datablock &db, const std::string &id, const std::string &name, const std::string &type, const std::string &group)
: m_id(id)
, m_name(name)
, m_type(type)
, m_group(group)
compound::compound(cif::datablock &db, int)
{
auto &chemComp = db["chem_comp"];

if (chemComp.size() != 1)
throw std::runtime_error("Invalid compound file, chem_comp should contain a single row");

cif::tie(m_id, m_name) =
chemComp.front().get("id", "name");

cif::trim(m_name);

m_type = "NON-POLYMER";

auto &chemCompAtom = db["chem_comp_atom"];
for (auto row : chemCompAtom)
{
Expand All @@ -184,7 +196,6 @@ compound::compound(cif::datablock &db, const std::string &id, const std::string
atom.type_symbol = atom_type_traits(type_symbol).type();

m_formal_charge += atom.charge;
m_formula_weight += atom_type_traits(atom.type_symbol).weight();

m_atoms.push_back(std::move(atom));
}
Expand All @@ -209,11 +220,39 @@ compound::compound(cif::datablock &db, const std::string &id, const std::string
else
{
if (cif::VERBOSE > 0)
std::cerr << "Unimplemented chem_comp_bond.type " << btype << " in " << id << '\n';
std::cerr << "Unimplemented chem_comp_bond.type " << btype << " in " << db.name() << '\n';
bond.type = bond_type::sing;
}
m_bonds.push_back(std::move(bond));
}

// reconstruct a formula and weight

m_formula_weight = 0;

std::map<atom_type, int> f;
for (auto &atom : m_atoms)
f[atom.type_symbol] += 1;

if (f.count(atom_type::C))
{
atom_type_traits att(atom_type::C);
m_formula += att.symbol() + std::to_string(f[atom_type::C]) + ' ';
m_formula_weight += att.weight() * f[atom_type::C];
}

for (const auto &[type, count] : f)
{
if (type == atom_type::C)
continue;

atom_type_traits att(type);
m_formula += att.symbol() + std::to_string(count) + ' ';
m_formula_weight += att.weight() * count;
}

if (not m_formula.empty())
m_formula.pop_back();
}

compound_atom compound::get_atom_by_atom_id(const std::string &atom_id) const
Expand Down Expand Up @@ -260,13 +299,12 @@ float compound::bond_length(const std::string &atomId_1, const std::string &atom
auto a = get_atom_by_atom_id(atomId_1);
auto b = get_atom_by_atom_id(atomId_2);

result = distance(point{a.x, a.y, a.z}, point{b.x, b.y, b.z});
result = distance(point{ a.x, a.y, a.z }, point{ b.x, b.y, b.z });
}

return result;
}


// --------------------------------------------------------------------
// known amino acids and bases

Expand Down Expand Up @@ -316,7 +354,7 @@ class compound_factory_impl : public std::enable_shared_from_this<compound_facto
compound_factory_impl();
compound_factory_impl(const fs::path &file, std::shared_ptr<compound_factory_impl> next);

~compound_factory_impl()
virtual ~compound_factory_impl()
{
for (auto c : m_compounds)
delete c;
Expand Down Expand Up @@ -373,13 +411,15 @@ class compound_factory_impl : public std::enable_shared_from_this<compound_facto
os << "CCD components.cif resource\n";
else
os << "CCD components file: " << std::quoted(m_file.string()) << '\n';

if (m_next)
m_next->describe(os);
}

private:
compound *create(const std::string &id);
protected:
compound_factory_impl(std::shared_ptr<compound_factory_impl> next);

virtual compound *create(const std::string &id);

std::shared_timed_mutex mMutex;

Expand All @@ -395,10 +435,15 @@ compound_factory_impl::compound_factory_impl()
{
}

compound_factory_impl::compound_factory_impl(std::shared_ptr<compound_factory_impl> next)
: m_next(next)
{
}

compound_factory_impl::compound_factory_impl(const fs::path &file, std::shared_ptr<compound_factory_impl> next)
: m_file(file)
, m_next(next)
: compound_factory_impl(next)
{
m_file = file;
}

compound *compound_factory_impl::create(const std::string &id)
Expand Down Expand Up @@ -476,6 +521,45 @@ compound *compound_factory_impl::create(const std::string &id)

// --------------------------------------------------------------------

class local_compound_factory_impl : public compound_factory_impl
{
public:
local_compound_factory_impl(const cif::file &file, std::shared_ptr<compound_factory_impl> next)
: compound_factory_impl(next)
, m_local_file(file)
{
}

compound *create(const std::string &id) override;

private:
const cif::file &m_local_file;
};

compound *local_compound_factory_impl::create(const std::string &id)
{
compound *result = nullptr;

for (auto &db : m_local_file)
{
if (db.name() == "comp_" + id)
{
cif::datablock db_copy(db);

result = new compound(db_copy, 1);

std::shared_lock lock(mMutex);
m_compounds.push_back(result);

break;
}
}

return result;
}

// --------------------------------------------------------------------

std::unique_ptr<compound_factory> compound_factory::s_instance;
thread_local std::unique_ptr<compound_factory> compound_factory::tl_instance;
bool compound_factory::s_use_thread_local_instance;
Expand Down Expand Up @@ -553,6 +637,18 @@ void compound_factory::push_dictionary(const fs::path &inDictFile)
}
}

void compound_factory::push_dictionary(const cif::file &inDictFile)
{
try
{
m_impl.reset(new local_compound_factory_impl(inDictFile, m_impl));
}
catch (const std::exception &)
{
std::throw_with_nested(std::runtime_error("Error loading dictionary from local mmCIF file"));
}
}

void compound_factory::pop_dictionary()
{
if (m_impl)
Expand Down Expand Up @@ -584,25 +680,26 @@ void compound_factory::report_missing_compound(const std::string &compound_id)
{
using namespace cif::colour;

std::clog << "\n" << cif::coloured("Configuration error:", white, red) << "\n\n"
std::clog << "\n"
<< cif::coloured("Configuration error:", white, red) << "\n\n"
<< "The attempt to retrieve compound information for " << std::quoted(compound_id) << " failed.\n\n"
<< "This information is searched for in a CCD file called components.cif or\n"
<< "components.cif.gz which should be located in one of the following directories:\n\n";

cif::list_data_directories(std::clog);

std::clog << "\n(Note that you can add a directory to the search paths by setting the \n"
<< "LIBCIFPP_DATA_DIR environmental variable)\n\n";

#if defined(CACHE_DIR)
#if defined(CACHE_DIR)
std::clog << "On Linux an optional cron script might have been installed that automatically updates\n"
<< "components.cif and mmCIF dictionary files. This script only works when the file\n"
<< "libcifpp.conf contains an uncommented line with the text:\n\n"
<< "update=true\n\n"
<< "If you do not have a working cron script, you can manually update the files\n"
<< "in /var/cache/libcifpp using the following commands:\n\n"
<< "curl -o " << CACHE_DIR << "/components.cif https://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz\n"
<< "curl -o " << CACHE_DIR << "/mmcif_pdbx.dic https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic.gz\n"
<< "curl -o " << CACHE_DIR << "/components.cif https://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz\n"
<< "curl -o " << CACHE_DIR << "/mmcif_pdbx.dic https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic.gz\n"
<< "curl -o " << CACHE_DIR << "/mmcif_ma.dic https://github.com/ihmwg/ModelCIF/raw/master/dist/mmcif_ma.dic\n\n";
#endif

Expand All @@ -613,9 +710,9 @@ void compound_factory::report_missing_compound(const std::string &compound_id)
}
else
std::clog << "No compound factory objects are created since none of the data sources is found.\n";

cif::list_file_resources(std::clog);

std::clog.flush();
}
}
Expand Down

0 comments on commit 5169834

Please sign in to comment.