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#include <boost/python.hpp>
#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
#include <ost/mol/alg/contact_overlap.hh>
#include <ost/mol/alg/domain_find.hh>
using namespace boost::python;
using namespace ost;
using namespace ost::mol::alg;
SimilarityMatrix (*com_a)(const ost::seq::AlignmentHandle&,
Real, int, int)=&ContactOverlapMap;
SimilarityMatrix (*com_b)(const ost::seq::AlignmentHandle&,
Real, OverlapMode, Real)=&ContactOverlapMap;
SimilarityMatrix (*com_c)(const DistanceMatrix&, const DistanceMatrix&,
Real, OverlapMode, Real)=&ContactOverlapMap;
void export_contact_overlap()
{
class_<SimilarityMatrix>("SimilarityMatrix", init<int, Real>())
.def("Get", &SimilarityMatrix::Get,
return_value_policy<copy_const_reference>())
.def("Set", &SimilarityMatrix::Set)
.def("GetSize", &SimilarityMatrix::GetSize)
.add_property("size", &SimilarityMatrix::GetSize)
.def("AsImage", &SimilarityMatrix::AsImage)
.def("Save", &SimilarityMatrix::Save)
.def("Load", &SimilarityMatrix::Load).staticmethod("Load")
;
class_<DistanceMatrix, DistanceMatrixPtr>("DistanceMatrix", no_init)
.def("Create", &DistanceMatrix::Create).staticmethod("Create")
.def("FromAln", &DistanceMatrix::FromAln,
(arg("aln"), arg("index")=1)).staticmethod("FromAln")
.def("Get", &DistanceMatrix::Get,
return_value_policy<copy_const_reference>())
.def("Set", &DistanceMatrix::Set)
.def("GetSize", &DistanceMatrix::GetSize)
.add_property("size", &DistanceMatrix::GetSize)
;
enum_<OverlapMode>("OverlapMode")
.value("OM_RELATIVE", OM_RELATIVE)
.value("OM_ABSOLUTE", OM_ABSOLUTE)
.export_values()
;
def("DomainsFromCOM", &DomainsFromCOM, (arg("idx_a")=-1, arg("idx_b")=-1));
def("ContactOverlap", &ContactOverlap, (arg("dist_mat_a"), arg("dist_mat_b"),
arg("tolerance")=0.1,
arg("mode")=OM_RELATIVE,
arg("max_dist")=1e6));
class_<ContactList>("ContactList", init<>())
.def(vector_indexing_suite<ContactList>())
;
def("Contacts", &Contacts);
def("CalcContactNodeDegree", &CalcContactNodeDegree);
def("LocalDistanceTest", &LocalDistanceTest);
def("ContactOverlapMap", com_a);
def("ContactOverlapMap", com_b, (arg("mode")=OM_RELATIVE,
arg("max_dist")=1e6));
def("ContactOverlapMap", com_c, (arg("mode")=OM_RELATIVE,
arg("max_dist")=1e6));
class_<Domain>("Domain", no_init)
.def_readwrite("views", &Domain::views)
.def_readwrite("views", &Domain::views)
.def_readwrite("inter_s", &Domain::inter_s)
.def_readwrite("inter_d", &Domain::inter_d)
.def_readwrite("intra_s", &Domain::intra_s)
.def_readwrite("intra_d", &Domain::intra_d)
;
class_<std::vector<Domain> >("DomainList", init<>())
.def(vector_indexing_suite<std::vector<Domain> >())
;
class_<Domains, DomainsPtr>("Domains", no_init)
.def("FromCOM", Domains::FromCOM,
(arg("sim"), arg("aln"), arg("idx_a")=-1,
arg("idx_b")=-1)).staticmethod("FromCOM")
.def("FromAln", Domains::FromAln,
(arg("aln"), arg("tolerance")=1.5,
arg("radius")=1e6, arg("threshold")=0.5, arg("idx_a")=0, arg("idx_b")=1)).staticmethod("FromAln")
.def("FromDistMats", Domains::FromDistMats,
(arg("dmat_a"), arg("dmat_b"), arg("tolerance")=1.5,
arg("radius")=1e6, arg("threshold")=0.5,
arg("num_threads")=1,
arg("defined_only")=true,
arg("adj_map")=false)).staticmethod("FromDistMats")
.add_property("domains", make_function(&Domains::GetDomains,
return_value_policy<copy_const_reference>()))
.add_property("components", make_function(&Domains::GetComponents,
return_value_policy<copy_const_reference>()))
.add_property("adj_map", &Domains::GetAdjMap)
.add_property("num_free", &Domains::GetNumFreeResidues)
.add_property("free_d", &Domains::GetFreeD)
.add_property("free_s", &Domains::GetFreeS)
;
}
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