mirror of
https://github.com/PDB-REDO/dssp.git
synced 2026-06-04 13:44:21 +08:00
First working version
This commit is contained in:
Maarten L. Hekkelman
324
python-module/dssp-python-plugin.cpp
Normal file
324
python-module/dssp-python-plugin.cpp
Normal file
@@ -0,0 +1,324 @@
|
||||
#include <boost/python.hpp>
|
||||
#include <python3.11/Python.h>
|
||||
|
||||
#include <dssp.hpp>
|
||||
|
||||
struct statistics_wrapper
|
||||
{
|
||||
int get_residues() { return m_stats.count.residues; }
|
||||
int get_chains() { return m_stats.count.chains; }
|
||||
int get_SS_bridges() { return m_stats.count.SS_bridges; }
|
||||
int get_intra_chain_SS_bridges() { return m_stats.count.intra_chain_SS_bridges; }
|
||||
int get_H_bonds() { return m_stats.count.H_bonds; }
|
||||
int get_H_bonds_in_antiparallel_bridges() { return m_stats.count.H_bonds_in_antiparallel_bridges; }
|
||||
int get_H_bonds_in_parallel_bridges() { return m_stats.count.H_bonds_in_parallel_bridges; }
|
||||
|
||||
dssp::statistics m_stats;
|
||||
};
|
||||
|
||||
struct residue_info_wrapper
|
||||
{
|
||||
};
|
||||
|
||||
class dssp_wrapper
|
||||
{
|
||||
public:
|
||||
dssp_wrapper(std::string data, int model_nr = 1, int min_poly_proline_stretch_length = 3, bool calculateSurfaceAccessibility = false)
|
||||
{
|
||||
struct membuf : public std::streambuf
|
||||
{
|
||||
membuf(char *text, size_t length)
|
||||
{
|
||||
this->setg(text, text, text + length);
|
||||
}
|
||||
} buffer(const_cast<char *>(data.data()), data.length());
|
||||
|
||||
std::istream is(&buffer);
|
||||
|
||||
auto f = cif::pdb::read(is);
|
||||
m_dssp.reset(new dssp(f.front(), model_nr, min_poly_proline_stretch_length, calculateSurfaceAccessibility));
|
||||
}
|
||||
|
||||
dssp_wrapper(const dssp_wrapper &) = default;
|
||||
dssp_wrapper &operator=(const dssp_wrapper &) = default;
|
||||
|
||||
statistics_wrapper get_statistics()
|
||||
{
|
||||
statistics_wrapper result{ .m_stats = m_dssp->get_statistics() };
|
||||
return result;
|
||||
}
|
||||
|
||||
struct residue_info_handle
|
||||
{
|
||||
residue_info_handle(dssp::residue_info info)
|
||||
: m_info(info)
|
||||
{
|
||||
}
|
||||
|
||||
operator dssp::residue_info &() { return m_info; }
|
||||
|
||||
dssp::residue_info m_info;
|
||||
};
|
||||
|
||||
class iterator
|
||||
{
|
||||
public:
|
||||
using iterator_category = std::forward_iterator_tag;
|
||||
using value_type = dssp::residue_info;
|
||||
using difference_type = std::ptrdiff_t;
|
||||
using pointer = value_type *;
|
||||
using reference = residue_info_handle;
|
||||
|
||||
iterator(dssp::residue_info info)
|
||||
: m_current(info)
|
||||
{
|
||||
}
|
||||
|
||||
iterator(const iterator &i) = default;
|
||||
iterator &operator=(const iterator &i) = default;
|
||||
|
||||
reference operator*() { return residue_info_handle(m_current); }
|
||||
pointer operator->() { return &m_current; }
|
||||
|
||||
iterator &operator++()
|
||||
{
|
||||
m_current = m_current.next();
|
||||
return *this;
|
||||
}
|
||||
|
||||
iterator operator++(int)
|
||||
{
|
||||
auto tmp(*this);
|
||||
this->operator++();
|
||||
return tmp;
|
||||
}
|
||||
|
||||
bool operator==(const iterator &rhs) const
|
||||
{
|
||||
return m_current == rhs.m_current;
|
||||
}
|
||||
|
||||
private:
|
||||
dssp::residue_info m_current;
|
||||
};
|
||||
|
||||
auto begin() { return iterator(*m_dssp->begin()); }
|
||||
auto end() { return iterator({}); }
|
||||
|
||||
auto get(std::string asym_id, int nr)
|
||||
{
|
||||
return m_dssp->operator[]({ asym_id, nr });
|
||||
}
|
||||
|
||||
private:
|
||||
std::shared_ptr<dssp> m_dssp;
|
||||
};
|
||||
|
||||
// shamelessly copied from a stack overflow comment
|
||||
// https://stackoverflow.com/questions/36485840/wrap-boostoptional-using-boostpython
|
||||
|
||||
// Custom exceptions
|
||||
struct AttributeError : std::exception
|
||||
{
|
||||
const char *what() const throw() { return "AttributeError exception"; }
|
||||
};
|
||||
|
||||
struct TypeError : std::exception
|
||||
{
|
||||
const char *what() const throw() { return "TypeError exception"; }
|
||||
};
|
||||
|
||||
// Set python exceptions
|
||||
void translate(const std::exception &e)
|
||||
{
|
||||
if (dynamic_cast<const AttributeError *>(&e))
|
||||
PyErr_SetString(PyExc_AttributeError, e.what());
|
||||
if (dynamic_cast<const TypeError *>(&e))
|
||||
PyErr_SetString(PyExc_TypeError, e.what());
|
||||
}
|
||||
|
||||
struct to_python_optional
|
||||
{
|
||||
static PyObject *convert(const std::optional<float> &obj)
|
||||
{
|
||||
if (obj)
|
||||
return boost::python::incref(boost::python::object(*obj).ptr());
|
||||
else
|
||||
return boost::python::incref(boost::python::object().ptr());
|
||||
}
|
||||
};
|
||||
|
||||
struct to_python_list_of_floats
|
||||
{
|
||||
static PyObject *convert(const std::vector<float> &v)
|
||||
{
|
||||
boost::python::list list;
|
||||
for (auto value : v)
|
||||
list.append(value);
|
||||
return boost::python::incref(boost::python::object(list).ptr());
|
||||
}
|
||||
};
|
||||
|
||||
struct to_python_point
|
||||
{
|
||||
static PyObject *convert(const std::tuple<float, float, float> &v)
|
||||
{
|
||||
boost::python::dict p;
|
||||
p["x"] = std::get<0>(v);
|
||||
p["y"] = std::get<1>(v);
|
||||
p["z"] = std::get<2>(v);
|
||||
return boost::python::incref(boost::python::object(p).ptr());
|
||||
}
|
||||
};
|
||||
|
||||
struct to_python_partner
|
||||
{
|
||||
static PyObject *convert(const std::tuple<dssp::residue_info, double> &v)
|
||||
{
|
||||
boost::python::type_info iv = boost::python::type_id<dssp::residue_info>();
|
||||
const boost::python::converter::registration* cv = boost::python::converter::registry::query(iv);
|
||||
assert(cv != nullptr);
|
||||
if (cv == nullptr)
|
||||
throw std::runtime_error("Missing registration");
|
||||
|
||||
if (auto &[ri, e] = v; ri)
|
||||
{
|
||||
auto c = cv->to_python(&ri);
|
||||
return boost::python::incref(boost::python::make_tuple(boost::python::handle<>(c), e).ptr());
|
||||
}
|
||||
else
|
||||
return boost::python::incref(boost::python::make_tuple(boost::python::object(), 0).ptr());
|
||||
}
|
||||
};
|
||||
|
||||
struct to_python_bridge_partner
|
||||
{
|
||||
static PyObject *convert(const std::tuple<dssp::residue_info, int, dssp::ladder_direction_type> &v)
|
||||
{
|
||||
if (auto &[ri, nr, direction] = v; ri)
|
||||
{
|
||||
boost::python::type_info iv = boost::python::type_id<dssp::residue_info>();
|
||||
const boost::python::converter::registration* cv = boost::python::converter::registry::query(iv);
|
||||
assert(cv != nullptr);
|
||||
|
||||
boost::python::type_info dv = boost::python::type_id<dssp::ladder_direction_type>();
|
||||
const boost::python::converter::registration* ev = boost::python::converter::registry::query(dv);
|
||||
assert(ev != nullptr);
|
||||
|
||||
auto c = cv->to_python(&ri);
|
||||
auto e = ev->to_python(&direction);
|
||||
|
||||
return boost::python::incref(boost::python::make_tuple(
|
||||
boost::python::handle<>(c), nr, boost::python::handle<>(e)).ptr());
|
||||
}
|
||||
else
|
||||
return boost::python::incref(boost::python::make_tuple(boost::python::object(), 0, boost::python::object()).ptr());
|
||||
}
|
||||
};
|
||||
|
||||
bool test_bond_between_residues(PyObject *a, PyObject *b)
|
||||
{
|
||||
const auto &a_ri = boost::python::extract<dssp::residue_info&>(a);
|
||||
const auto &b_ri = boost::python::extract<dssp::residue_info&>(b);
|
||||
|
||||
return test_bond(a_ri, b_ri);
|
||||
}
|
||||
|
||||
BOOST_PYTHON_MODULE(mkdssp)
|
||||
{
|
||||
using namespace boost::python;
|
||||
|
||||
register_exception_translator<AttributeError>(&translate);
|
||||
register_exception_translator<TypeError>(&translate);
|
||||
|
||||
to_python_converter<std::optional<float>, to_python_optional>();
|
||||
to_python_converter<std::vector<float>, to_python_list_of_floats>();
|
||||
to_python_converter<std::tuple<float, float, float>, to_python_point>();
|
||||
to_python_converter<std::tuple<dssp::residue_info, double>, to_python_partner>();
|
||||
to_python_converter<std::tuple<dssp::residue_info, int, dssp::ladder_direction_type>, to_python_bridge_partner>();
|
||||
|
||||
enum_<dssp::structure_type>("structure_type")
|
||||
.value("Loop", dssp::structure_type::Loop)
|
||||
.value("Alphahelix", dssp::structure_type::Alphahelix)
|
||||
.value("Betabridge", dssp::structure_type::Betabridge)
|
||||
.value("Strand", dssp::structure_type::Strand)
|
||||
.value("Helix_3", dssp::structure_type::Helix_3)
|
||||
.value("Helix_5", dssp::structure_type::Helix_5)
|
||||
.value("Helix_PPII", dssp::structure_type::Helix_PPII)
|
||||
.value("Turn", dssp::structure_type::Turn)
|
||||
.value("Bend", dssp::structure_type::Bend);
|
||||
|
||||
enum_<dssp::helix_type>("helix_type")
|
||||
.value("_3_10", dssp::helix_type::_3_10)
|
||||
.value("alpha", dssp::helix_type::alpha)
|
||||
.value("pi", dssp::helix_type::pi)
|
||||
.value("pp", dssp::helix_type::pp);
|
||||
|
||||
enum_<dssp::helix_position_type>("helix_position_type")
|
||||
.value("None", dssp::helix_position_type::None)
|
||||
.value("Start", dssp::helix_position_type::Start)
|
||||
.value("End", dssp::helix_position_type::End)
|
||||
.value("StartAndEnd", dssp::helix_position_type::StartAndEnd)
|
||||
.value("Middle", dssp::helix_position_type::Middle);
|
||||
|
||||
enum_<dssp::ladder_direction_type>("ladder_direction_type")
|
||||
.value("parallel", dssp::ladder_direction_type::parallel)
|
||||
.value("anti_parallel", dssp::ladder_direction_type::antiparallel);
|
||||
|
||||
enum_<dssp::chain_break_type>("chain_break_type")
|
||||
.value("None", dssp::chain_break_type::None)
|
||||
.value("NewChain", dssp::chain_break_type::NewChain)
|
||||
.value("Gap", dssp::chain_break_type::Gap);
|
||||
|
||||
class_<statistics_wrapper>("statistic_counts")
|
||||
.add_property("residues", &statistics_wrapper::get_residues)
|
||||
.add_property("chains", &statistics_wrapper::get_chains)
|
||||
.add_property("SS_bridges", &statistics_wrapper::get_SS_bridges)
|
||||
.add_property("intra_chain_SS_bridges", &statistics_wrapper::get_intra_chain_SS_bridges)
|
||||
.add_property("H_bonds", &statistics_wrapper::get_H_bonds)
|
||||
.add_property("H_bonds_in_antiparallel_bridges", &statistics_wrapper::get_H_bonds_in_antiparallel_bridges)
|
||||
.add_property("H_bonds_in_parallel_bridges", &statistics_wrapper::get_H_bonds_in_parallel_bridges);
|
||||
|
||||
class_<dssp::residue_info>("residue_info")
|
||||
.add_property("asym_id", &dssp::residue_info::asym_id)
|
||||
.add_property("seq_id", &dssp::residue_info::seq_id)
|
||||
.add_property("alt_id", &dssp::residue_info::alt_id)
|
||||
.add_property("compound_id", &dssp::residue_info::compound_id)
|
||||
.add_property("compound_letter", &dssp::residue_info::compound_letter)
|
||||
.add_property("auth_asym_id", &dssp::residue_info::auth_asym_id)
|
||||
.add_property("auth_seq_id", &dssp::residue_info::auth_seq_id)
|
||||
.add_property("pdb_strand_id", &dssp::residue_info::pdb_strand_id)
|
||||
.add_property("pdb_seq_num", &dssp::residue_info::pdb_seq_num)
|
||||
.add_property("pdb_ins_code", &dssp::residue_info::pdb_ins_code)
|
||||
.add_property("alpha", &dssp::residue_info::alpha)
|
||||
.add_property("kappa", &dssp::residue_info::kappa)
|
||||
.add_property("phi", &dssp::residue_info::phi)
|
||||
.add_property("psi", &dssp::residue_info::psi)
|
||||
.add_property("tco", &dssp::residue_info::tco)
|
||||
.add_property("omega", &dssp::residue_info::omega)
|
||||
.add_property("is_pre_pro", &dssp::residue_info::is_pre_pro)
|
||||
.add_property("is_cis", &dssp::residue_info::is_cis)
|
||||
.add_property("chiral_volume", &dssp::residue_info::chiral_volume)
|
||||
.add_property("chi", &dssp::residue_info::chi)
|
||||
.add_property("ca_location", &dssp::residue_info::ca_location)
|
||||
.add_property("chain_break", &dssp::residue_info::chain_break)
|
||||
.add_property("nr", &dssp::residue_info::nr)
|
||||
.add_property("type", &dssp::residue_info::type)
|
||||
.add_property("ssBridgeNr", &dssp::residue_info::ssBridgeNr)
|
||||
.def("helix", &dssp::residue_info::helix)
|
||||
.add_property("is_alpha_helix_end_before_start", &dssp::residue_info::is_alpha_helix_end_before_start)
|
||||
.add_property("bend", &dssp::residue_info::bend)
|
||||
.add_property("accessibility", &dssp::residue_info::accessibility)
|
||||
.def("bridge_partner", &dssp::residue_info::bridge_partner)
|
||||
.add_property("sheet", &dssp::residue_info::sheet)
|
||||
.add_property("strand", &dssp::residue_info::strand)
|
||||
.def("acceptor", &dssp::residue_info::acceptor)
|
||||
.def("donor", &dssp::residue_info::donor);
|
||||
|
||||
class_<dssp_wrapper, boost::noncopyable>("dssp", init<std::string, optional<int, int, bool>>())
|
||||
.add_property("statistics", &dssp_wrapper::get_statistics)
|
||||
.def("__iter__", iterator<dssp_wrapper>())
|
||||
.def("get", &dssp_wrapper::get);
|
||||
|
||||
def("TestBond", test_bond_between_residues);
|
||||
}
|
||||
Reference in New Issue
Block a user