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Add gdb format molecule reading #291

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Add gdb format molecule reading #291

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98e21e7
add gdb parsing
loriab Jun 11, 2022
03a1380
format and changelog
loriab Jun 11, 2022
a72c726
allow gdb to work through Molecule
loriab Jun 12, 2022
508817f
more gdb and error tests
loriab Jun 13, 2022
829dd44
format
loriab Jun 13, 2022
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format and changelog
  • Loading branch information
@loriab
loriab committed Jun 11, 2022
commit 03a13805074033a870f8788dea0a0e372104cd3f
11 changes: 8 additions & 3 deletions docs/source/changelog.rst
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Expand Up @@ -17,14 +17,18 @@ Changelog
.. +++++++++


0.25.0 / 2022-MM-DD
0.25.0 / 2022-06-DD
-------------------

Breaking Changes
++++++++++++++++

New Features
++++++++++++
- (:pr:`288`, :pr:`291`) The molecule ``from_string`` parser learned new format
``dtype="gdb"`` from https://www.nature.com/articles/sdata201422/tables/3 .
At present, dtype must be specified explicitly to trigger this parsing; it is
not in the customary fallback sequence of unspecified dtype.

Enhancements
++++++++++++
Expand All @@ -37,8 +41,9 @@ Enhancements

Bug Fixes
+++++++++
- (:pr:`286`) Sphinx autodocumentation with typing of ``qcelemental.testing.compare_recursive`` no longer
warns about circular import.
- (:pr:`286`) Sphinx autodocumentation with typing of
``qcelemental.testing.compare_recursive`` no longer warns about circular
import.


0.24.0 / 2021-11-18
Expand Down
37 changes: 25 additions & 12 deletions qcelemental/tests/test_molparse_from_string.py
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Original file line number Diff line number Diff line change
Expand Up @@ -920,10 +920,12 @@ def test_xyzp_qm_7e():
assert compare_recursive(ans7, intermed, tnm() + ": intermediate")
assert compare_molrecs(fullans, final["qm"], tnm() + ": full qm")


@pytest.mark.parametrize(
"string",
[
pytest.param("""5
pytest.param(
"""5
gdb 1 157.7118 157.70997 157.70699 0. 13.21 -0.3877 0.1171 0.5048 35.3641 0.044749 -40.47893 -40.476062 -40.475117 -40.498597 6.469
C -0.0126981359 1.0858041578 0.0080009958 -0.535689
H 0.002150416 -0.0060313176 0.0019761204 0.133921
Expand All @@ -932,8 +934,11 @@ def test_xyzp_qm_7e():
H -0.5238136345 1.4379326443 0.9063972942 0.133923
1341.307 1341.3284 1341.365 1562.6731 1562.7453 3038.3205 3151.6034 3151.6788 3151.7078
C C
InChI=1S/CH4/h1H4 InChI=1S/CH4/h1H4""", id="gdb missing atom charge"),
pytest.param("""5
InChI=1S/CH4/h1H4 InChI=1S/CH4/h1H4""",
id="gdb missing atom charge",
),
pytest.param(
"""5
catinhat 5 1.0 2.0 3.0
C -0.0126981359 1.0858041578 0.0080009958 -0.535689
H 0.002150416 -0.0060313176 0.0019761204 0.133921
Expand All @@ -942,8 +947,11 @@ def test_xyzp_qm_7e():
H -0.5238136345 1.4379326443 0.9063972942 0.133923
1341.307 1341.3284 1341.365 1562.6731 1562.7453 3038.3205 3151.6034 3151.6788 3151.7078
C C
InChI=1S/CH4/h1H4 InChI=1S/CH4/h1H4""", id="gdb bad properties line"),
pytest.param("""5
InChI=1S/CH4/h1H4 InChI=1S/CH4/h1H4""",
id="gdb bad properties line",
),
pytest.param(
"""5
gdb 1 157.7118 157.70997 157.70699 0. 13.21 -0.3877 0.1171 0.5048 35.3641 0.044749 -40.47893 -40.476062 -40.475117 -40.498597 6.469
C -0.0126981359 1.0858041578 0.0080009958 -0.535689
H 0.002150416 -0.0060313176 0.0019761204 0.133921
Expand All @@ -952,8 +960,11 @@ def test_xyzp_qm_7e():
H -0.5238136345 1.4379326443 0.9063972942 0.133923
1341.307 1341.3284 1341.365 1562.6731 1562.7453 3038.3205 3151.6034
C C
InChI=1S/CH4/h1H4 InChI=1S/CH4/h1H4""", id="gdb freq short"),
pytest.param("""5
InChI=1S/CH4/h1H4 InChI=1S/CH4/h1H4""",
id="gdb freq short",
),
pytest.param(
"""5
gdb 1 157.7118 157.70997 157.70699 0. 13.21 -0.3877 0.1171 0.5048 35.3641 0.044749 -40.47893 -40.476062 -40.475117 -40.498597 6.469
C -0.0126981359 1.0858041578 0.0080009958 -0.535689
H 0.002150416 -0.0060313176 0.0019761204 0.133921
Expand All @@ -962,8 +973,10 @@ def test_xyzp_qm_7e():
H -0.5238136345 1.4379326443 0.9063972942 0.133923
1341.307 1341.3284 1341.365 1562.6731 1562.7453 3038.3205 3151.6034 3151.6788 3151.7078 12.0 12.0
C C
InChI=1S/CH4/h1H4 InChI=1S/CH4/h1H4""", id="gdb freq long"),
]
InChI=1S/CH4/h1H4 InChI=1S/CH4/h1H4""",
id="gdb freq long",
),
],
)
def test_xyz_gdb_error(string):

Expand Down Expand Up @@ -1003,7 +1016,7 @@ def test_xyz_gdb_error(string):
1.4379326443,
0.9063972942,
],
id="methane"
id="methane",
),
pytest.param(
"""20
Expand Down Expand Up @@ -1095,7 +1108,7 @@ def test_xyz_gdb_error(string):
-4.5389119798,
2.3916335805,
],
id="mol2"
id="mol2",
),
pytest.param(
"""17
Expand Down Expand Up @@ -1175,7 +1188,7 @@ def test_xyz_gdb_error(string):
-2.687136563,
0.4367361986,
],
id="mol3"
id="mol3",
),
],
)
Expand Down