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// Copyright 2018 Global Phasing Ltd.
#include "gemmi/monlib.hpp"
#include "common.h"
#include <nanobind/stl/bind_map.h>
#include <nanobind/stl/map.h>
#include <nanobind/stl/string.h>
#include <nanobind/stl/tuple.h> // for MonLib::match_link
#include <nanobind/stl/vector.h>
using namespace gemmi;
using monomers_type = std::map<std::string, ChemComp>;
using links_type = std::map<std::string, ChemLink>;
using modifications_type = std::map<std::string, ChemMod>;
NB_MAKE_OPAQUE(monomers_type)
NB_MAKE_OPAQUE(links_type)
NB_MAKE_OPAQUE(modifications_type)
void add_monlib(nb::module_& m) {
nb::class_<ChemMod> chemmod(m, "ChemMod");
nb::class_<ChemLink> chemlink(m, "ChemLink");
nb::class_<EnerLib> enerlib(m, "EnerLib");
nb::bind_map<monomers_type, rv_ri>(m, "ChemCompMap");
nb::bind_map<links_type, rv_ri>(m, "ChemLinkMap");
nb::bind_map<modifications_type, rv_ri>(m, "ChemModMap");
nb::class_<ChemLink::Side>(chemlink, "Side")
.def(nb::init<>())
.def_rw("comp", &ChemLink::Side::comp)
.def_rw("mod", &ChemLink::Side::mod)
.def_rw("group", &ChemLink::Side::group)
.def("__repr__", [](const ChemLink::Side& self) {
return "<gemmi.ChemLink.Side " + self.comp + "/" +
ChemComp::group_str(self.group) + ">";
});
nb::class_<ChemMod::AtomMod>(chemmod, "AtomMod")
.def_rw("func", &ChemMod::AtomMod::func)
.def_rw("old_id", &ChemMod::AtomMod::old_id)
.def_rw("new_id", &ChemMod::AtomMod::new_id)
.def_rw("el", &ChemMod::AtomMod::el)
.def_rw("charge", &ChemMod::AtomMod::charge)
.def_rw("chem_type", &ChemMod::AtomMod::chem_type)
;
chemlink
.def(nb::init<>())
.def_rw("id", &ChemLink::id)
.def_rw("name", &ChemLink::name)
.def_rw("side1", &ChemLink::side1)
.def_rw("side2", &ChemLink::side2)
.def_rw("rt", &ChemLink::rt)
.def("__repr__", [](const ChemLink& self) {
return "<gemmi.ChemLink " + self.id + ">";
});
chemmod
.def(nb::init<>())
.def_rw("id", &ChemMod::id)
.def_rw("name", &ChemMod::name)
.def_rw("comp_id", &ChemMod::comp_id)
.def_rw("group_id", &ChemMod::group_id)
.def_rw("atom_mods", &ChemMod::atom_mods)
.def_rw("rt", &ChemMod::rt)
.def("__repr__", [](const ChemMod& self) {
return "<gemmi.ChemMod " + self.id + ">";
});
nb::class_<EnerLib::Atom>(enerlib, "Atom")
.def_ro("element", &EnerLib::Atom::element)
.def_ro("hb_type", &EnerLib::Atom::hb_type)
.def_ro("vdw_radius", &EnerLib::Atom::vdw_radius)
.def_ro("vdwh_radius", &EnerLib::Atom::vdwh_radius)
.def_ro("ion_radius", &EnerLib::Atom::ion_radius)
.def_ro("valency", &EnerLib::Atom::valency)
.def_ro("sp", &EnerLib::Atom::sp)
;
enerlib
.def_ro("atoms", &EnerLib::atoms)
;
nb::class_<MonLib>(m, "MonLib")
.def(nb::init<>())
.def_prop_rw("monomer_dir",
[](const MonLib& self) { return self.monomer_dir; },
&MonLib::set_monomer_dir)
.def_ro("ener_lib", &MonLib::ener_lib)
.def_ro("monomers", &MonLib::monomers)
.def_ro("links", &MonLib::links)
.def_ro("modifications", &MonLib::modifications)
.def("get_link", &MonLib::get_link, nb::arg("link_id"),
nb::rv_policy::reference_internal)
.def("get_mod", &MonLib::get_mod, nb::arg("name"),
nb::rv_policy::reference_internal)
.def("match_link", &MonLib::match_link,
nb::arg("res1"), nb::arg("atom1"), nb::arg("alt1"),
nb::arg("res2"), nb::arg("atom2"), nb::arg("alt2"),
nb::arg("min_bond_sq")=0.,
nb::rv_policy::reference_internal)
.def("test_link", [](const MonLib& self, const ChemLink& link,
const std::string& res1, const std::string& atom1,
const std::string& res2, const std::string& atom2) {
const ChemComp::Aliasing* aliasing1 = nullptr;
const ChemComp::Aliasing* aliasing2 = nullptr;
bool match = (!link.rt.bonds.empty() &&
self.link_side_matches_residue(link.side1, res1, &aliasing1) &&
self.link_side_matches_residue(link.side2, res2, &aliasing2) &&
atom_match_with_alias(link.rt.bonds[0].id1.atom, atom1, aliasing1) &&
atom_match_with_alias(link.rt.bonds[0].id2.atom, atom2, aliasing2));
return std::make_tuple(match, aliasing1, aliasing2);
}, nb::arg("link"), nb::arg("res1"), nb::arg("atom1"), nb::arg("res2"), nb::arg("atom2"),
nb::rv_policy::reference_internal)
.def("add_monomer_if_present", &MonLib::add_monomer_if_present)
.def("read_monomer_doc", &MonLib::read_monomer_doc)
.def("read_monomer_cif", &MonLib::read_monomer_cif)
.def("read_monomer_lib", &MonLib::read_monomer_lib,
nb::arg("monomer_dir"), nb::arg("resnames"), nb::arg("logging")=nb::none())
.def("find_ideal_distance", [](const MonLib& self, CRA &cra1, CRA cra2) {
return self.find_ideal_distance(cra1, cra2);
})
.def("update_old_atom_names", &MonLib::update_old_atom_names,
nb::arg("st"), nb::arg("logging")=nb::none())
.def("path", &MonLib::path, nb::arg("code")=std::string())
.def("__repr__", [](const MonLib& self) {
return "<gemmi.MonLib with " +
std::to_string(self.monomers.size()) + " monomers, " +
std::to_string(self.links.size()) + " links, " +
std::to_string(self.modifications.size()) + " modifications>";
})
.def("clone", [](const MonLib& self) { return new MonLib(self); });
m.def("read_monomer_lib", &read_monomer_lib,
nb::arg("monomer_dir"), nb::arg("resnames"),
nb::arg("libin")=std::string(), nb::arg("ignore_missing")=false);
}
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