From 731213bebadf4be577d83dce360f3b5eac9d1360 Mon Sep 17 00:00:00 2001 From: Oskar Weser Date: Wed, 15 Jan 2025 16:03:28 -0500 Subject: [PATCH 1/3] don't unnecessarily divide by r thanks for spotting this nwhel --- src/chemcoord/_cartesian_coordinates/_cart_transformation.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/chemcoord/_cartesian_coordinates/_cart_transformation.py b/src/chemcoord/_cartesian_coordinates/_cart_transformation.py index 6cfcd7b..dc1ffea 100644 --- a/src/chemcoord/_cartesian_coordinates/_cart_transformation.py +++ b/src/chemcoord/_cartesian_coordinates/_cart_transformation.py @@ -1095,7 +1095,7 @@ def get_S_inv(v): if r == 0: return np.array([0.0, 0.0, 0.0]) alpha = arccos(-z / r) - delta = arctan2(-y / r, x / r) + delta = arctan2(-y, x) return np.array([r, alpha, delta]) From 5d4c5f777e1e54ab150ca545e545e9ebbe09cfa5 Mon Sep 17 00:00:00 2001 From: Oskar Weser Date: Wed, 15 Jan 2025 16:05:06 -0500 Subject: [PATCH 2/3] renamed from_pyscf_molecule -> from_pyscf --- src/chemcoord/_cartesian_coordinates/_cartesian_class_io.py | 2 +- tests/cartesian_coordinates/Cartesian/test_io.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/chemcoord/_cartesian_coordinates/_cartesian_class_io.py b/src/chemcoord/_cartesian_coordinates/_cartesian_class_io.py index 285bb32..02c604d 100644 --- a/src/chemcoord/_cartesian_coordinates/_cartesian_class_io.py +++ b/src/chemcoord/_cartesian_coordinates/_cartesian_class_io.py @@ -268,7 +268,7 @@ def read_xyz(cls, buf, start_index=0, get_bonds=True, nrows=None, engine=None): return molecule @classmethod - def from_pyscf_molecule(cls, mol): + def from_pyscf(cls, mol): """Create an instance of the own class from a PySCF molecule Args: diff --git a/tests/cartesian_coordinates/Cartesian/test_io.py b/tests/cartesian_coordinates/Cartesian/test_io.py index dde0428..bc9d486 100644 --- a/tests/cartesian_coordinates/Cartesian/test_io.py +++ b/tests/cartesian_coordinates/Cartesian/test_io.py @@ -74,4 +74,4 @@ def test_xyz_cast(): def test_pyscf_conversion(): m = Cartesian.read_xyz(get_complete_path("water.xyz")) - assert allclose(Cartesian.from_pyscf_molecule(m.to_pyscf()), m) + assert allclose(Cartesian.from_pyscf(m.to_pyscf()), m) From b226b0224a8191a0e6bf8575cb65270ddd1be32f Mon Sep 17 00:00:00 2001 From: Oskar Weser Date: Wed, 15 Jan 2025 16:08:41 -0500 Subject: [PATCH 3/3] added missing rst files for pyscf --- .../chemcoord.AsymmetricUnitCartesian.rst | 2 ++ docs/source/src_Cartesian/chemcoord.Cartesian.rst | 2 ++ .../src_Cartesian/chemcoord.Cartesian.from_pyscf.rst | 8 ++++++++ .../src_Cartesian/chemcoord.Cartesian.to_pyscf.rst | 8 ++++++++ 4 files changed, 20 insertions(+) create mode 100644 docs/source/src_Cartesian/src_Cartesian/chemcoord.Cartesian.from_pyscf.rst create mode 100644 docs/source/src_Cartesian/src_Cartesian/chemcoord.Cartesian.to_pyscf.rst diff --git a/docs/source/src_AsymmetricUnitCartesian/chemcoord.AsymmetricUnitCartesian.rst b/docs/source/src_AsymmetricUnitCartesian/chemcoord.AsymmetricUnitCartesian.rst index 385af16..c488e5d 100644 --- a/docs/source/src_AsymmetricUnitCartesian/chemcoord.AsymmetricUnitCartesian.rst +++ b/docs/source/src_AsymmetricUnitCartesian/chemcoord.AsymmetricUnitCartesian.rst @@ -30,6 +30,7 @@ ~AsymmetricUnitCartesian.fragmentate ~AsymmetricUnitCartesian.from_ase_atoms ~AsymmetricUnitCartesian.from_pymatgen_molecule + ~AsymmetricUnitCartesian.from_pyscf ~AsymmetricUnitCartesian.get_align_transf ~AsymmetricUnitCartesian.get_angle_degrees ~AsymmetricUnitCartesian.get_ase_atoms @@ -70,6 +71,7 @@ ~AsymmetricUnitCartesian.symmetrize ~AsymmetricUnitCartesian.to_cjson ~AsymmetricUnitCartesian.to_latex + ~AsymmetricUnitCartesian.to_pyscf ~AsymmetricUnitCartesian.to_string ~AsymmetricUnitCartesian.to_xyz ~AsymmetricUnitCartesian.to_zmat diff --git a/docs/source/src_Cartesian/chemcoord.Cartesian.rst b/docs/source/src_Cartesian/chemcoord.Cartesian.rst index f5ff0d5..e3b7969 100644 --- a/docs/source/src_Cartesian/chemcoord.Cartesian.rst +++ b/docs/source/src_Cartesian/chemcoord.Cartesian.rst @@ -30,6 +30,7 @@ ~Cartesian.fragmentate ~Cartesian.from_ase_atoms ~Cartesian.from_pymatgen_molecule + ~Cartesian.from_pyscf ~Cartesian.get_align_transf ~Cartesian.get_angle_degrees ~Cartesian.get_ase_atoms @@ -69,6 +70,7 @@ ~Cartesian.symmetrize ~Cartesian.to_cjson ~Cartesian.to_latex + ~Cartesian.to_pyscf ~Cartesian.to_string ~Cartesian.to_xyz ~Cartesian.to_zmat diff --git a/docs/source/src_Cartesian/src_Cartesian/chemcoord.Cartesian.from_pyscf.rst b/docs/source/src_Cartesian/src_Cartesian/chemcoord.Cartesian.from_pyscf.rst new file mode 100644 index 0000000..3ec000a --- /dev/null +++ b/docs/source/src_Cartesian/src_Cartesian/chemcoord.Cartesian.from_pyscf.rst @@ -0,0 +1,8 @@ +:orphan: + +chemcoord.Cartesian.from\_pyscf +==================================== + +.. currentmodule:: chemcoord + +.. automethod:: Cartesian.from_pyscf diff --git a/docs/source/src_Cartesian/src_Cartesian/chemcoord.Cartesian.to_pyscf.rst b/docs/source/src_Cartesian/src_Cartesian/chemcoord.Cartesian.to_pyscf.rst new file mode 100644 index 0000000..70a7412 --- /dev/null +++ b/docs/source/src_Cartesian/src_Cartesian/chemcoord.Cartesian.to_pyscf.rst @@ -0,0 +1,8 @@ +:orphan: + +chemcoord.Cartesian.to\_pyscf +=========================== + +.. currentmodule:: chemcoord + +.. automethod:: Cartesian.to_pyscf \ No newline at end of file