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More pybind methods and properties #1342

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Sep 13, 2023
Merged

More pybind methods and properties #1342

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80c0921
Include stl / eigen support for Pybind11
ghutchis May 18, 2021
021703d
Add more methods and properties
ghutchis Sep 13, 2023
e90da0d
Fix some compile errors
ghutchis Sep 13, 2023
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48 changes: 48 additions & 0 deletions python/core.cpp
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Original file line number Diff line number Diff line change
@@ -1,8 +1,11 @@
#include <pybind11/eigen.h>
#include <pybind11/pybind11.h>
#include <pybind11/stl.h>

#include <avogadro/core/cube.h>
#include <avogadro/core/gaussiansettools.h>
#include <avogadro/core/molecule.h>
#include <avogadro/core/unitcell.h>

namespace py = pybind11;

Expand All @@ -19,6 +22,12 @@ PYBIND11_MODULE(core, m)
.def_property_readonly("index", &Atom::index, "Index in the molecule")
.def_property("atomic_number", &Atom::atomicNumber, &Atom::setAtomicNumber,
"The atomic number")
.def_property("position", &Atom::position3d, &Atom::setPosition3d,
"The 3D position of the atom")
.def_property("formal_charge", &Atom::formalCharge, &Atom::setFormalCharge,
"The formal charge of the atom")
.def_property("is_selected", &Atom::selected, &Atom::setSelected,
"Whether the atom is selected")
.def("is_valid", &Atom::isValid, "Check if the object is valid");

using bondBase = BondTemplate<Molecule>;
Expand All @@ -40,6 +49,32 @@ PYBIND11_MODULE(core, m)
Bond (Molecule::*addBond1)(Index, Index, unsigned char) = &Molecule::addBond;
Bond (Molecule::*addBond2)(const Atom&, const Atom&, unsigned char) =
&Molecule::addBond;
Bond (Molecule::*bond0)(Index) const = &Molecule::bond;
Bond (Molecule::*bond1)(const Atom&, const Atom&) const = &Molecule::bond;
Bond (Molecule::*bond2)(Index, Index) const = &Molecule::bond;
Cube* (Molecule::*cube0)(Index) = &Molecule::cube;

py::class_<UnitCell>(m, "UnitCell")
.def(py::init<>())
.def_property_readonly("a", &UnitCell::a, "The a lattice parameter")
.def_property_readonly("b", &UnitCell::b, "The b lattice parameter")
.def_property_readonly("c", &UnitCell::c, "The c lattice parameter")
.def_property_readonly("alpha", &UnitCell::alpha,
"The alpha lattice parameter")
.def_property_readonly("beta", &UnitCell::beta,
"The beta lattice parameter")
.def_property_readonly("gamma", &UnitCell::gamma,
"The gamma lattice parameter")
.def_property_readonly("volume", &UnitCell::volume,
"The volume of the unit cell")
.def("set_cell_parameters", &UnitCell::setCellParameters,
"Set the unit cell parameters a b c alpha beta gamma")
.def_property("cell_matrix", &UnitCell::cellMatrix,
&UnitCell::setCellMatrix, "The unit cell vector matrix")
.def("distance", &UnitCell::distance,
"Calculate the distance between two points in the unit cell");

UnitCell* (Molecule::*unitCell0)() = &Molecule::unitCell;

py::class_<Molecule>(m, "Molecule")
.def(py::init<>())
Expand All @@ -49,14 +84,27 @@ PYBIND11_MODULE(core, m)
.def("atom_count", atomCount0, "The number of atoms")
.def("atom_count", atomCount1,
"The number of atoms with the supplied atomic number")
.def("atom", &Molecule::atom, "The atom at the specified index")
.def("add_bond", addBond1, "Add a new bond", py::arg("a1"), py::arg("a2"),
py::arg("order") = 1)
.def("add_bond", addBond2, "Add a new bond", py::arg("a1"), py::arg("a2"),
py::arg("order") = 1)
.def("bond_count", &Molecule::bondCount, "The number of bonds")
.def("bond", bond0, "The bond at the specified index")
.def("bond", bond1, "The bond between the specified atoms")
.def("bond", bond2, "The bond between the specified atoms")
.def("add_cube", &Molecule::addCube, py::return_value_policy::reference,
"Add a new cube")
.def("cube_count", &Molecule::cubeCount, "The number of cubes")
.def("cube", cube0, "The cube at the specified index")
.def_property_readonly("radius", &Molecule::radius,
"The radius of the molecule")
.def_property_readonly("center", &Molecule::centerOfGeometry,
"The center of geometry of the molecule")
.def_property_readonly("mass_center", &Molecule::centerOfMass,
"The center of mass of the molecule")
.def_property_readonly("unit_cell", unitCell0,
"The unit cell of the molecule, if defined")
.def("has_custom_elements", &Molecule::hasCustomElements,
"Returns true if the molecule contains any custom elements")
.def("formula", &Molecule::formula, "The chemical formula of the molecule",
Expand Down
1 change: 1 addition & 0 deletions python/io.cpp
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
#include <pybind11/pybind11.h>
#include <pybind11/stl.h>

#include <avogadro/core/molecule.h>
#include <avogadro/io/fileformatmanager.h>
Expand Down
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