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ENH: support tpx 133 (GMX 2024.1) #4523

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Mar 25, 2024
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ENH: support tpx 133 (GMX 2024.1) #4523

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ENH: support tpx 133 (GMX 2024.1)
tylerjereddy Mar 21, 2024
26098bb
DOC: PR 4523 revisions
tylerjereddy Mar 25, 2024
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2 changes: 1 addition & 1 deletion package/MDAnalysis/topology/tpr/setting.py
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Expand Up @@ -38,7 +38,7 @@
"""

#: Gromacs TPR file format versions that can be read by the TPRParser.
SUPPORTED_VERSIONS = (58, 73, 83, 100, 103, 110, 112, 116, 119, 122, 127, 129)
SUPPORTED_VERSIONS = (58, 73, 83, 100, 103, 110, 112, 116, 119, 122, 127, 129, 133)

# Some constants
STRLEN = 4096
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Binary file added testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2024.tpr
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Binary file added testsuite/MDAnalysisTests/data/tprs/all_bonded/dummy_2024.tpr
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Binary file added testsuite/MDAnalysisTests/data/tprs/virtual_sites/extra-interactions-2024.tpr
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9 changes: 6 additions & 3 deletions testsuite/MDAnalysisTests/datafiles.py
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Expand Up @@ -82,14 +82,14 @@
"TPR450", "TPR451", "TPR452", "TPR453", "TPR454", "TPR455", "TPR455Double",
"TPR460", "TPR461", "TPR502", "TPR504", "TPR505", "TPR510", "TPR2016",
"TPR2018", "TPR2019B3", "TPR2020B2", "TPR2020", "TPR2020Double",
"TPR2021", "TPR2021Double", "TPR2022RC1", "TPR2023",
"TPR2021", "TPR2021Double", "TPR2022RC1", "TPR2023", "TPR2024",
"TPR510_bonded", "TPR2016_bonded", "TPR2018_bonded", "TPR2019B3_bonded",
"TPR2020B2_bonded", "TPR2020_bonded", "TPR2020_double_bonded",
"TPR2021_bonded", "TPR2021_double_bonded", "TPR2022RC1_bonded",
"TPR334_bonded", "TPR2023_bonded",
"TPR334_bonded", "TPR2023_bonded", "TPR2024_bonded",
"TPR_EXTRA_2021", "TPR_EXTRA_2020", "TPR_EXTRA_2018",
"TPR_EXTRA_2016", "TPR_EXTRA_407", "TPR_EXTRA_2022RC1",
"TPR_EXTRA_2023",
"TPR_EXTRA_2023", "TPR_EXTRA_2024",
"PDB_sub_sol", "PDB_sub_dry", # TRRReader sub selection
"TRR_sub_sol",
"XTC_sub_sol",
Expand Down Expand Up @@ -398,6 +398,7 @@
TPR2021 = (_data_ref / 'tprs/2lyz_gmx_2021.tpr').as_posix()
TPR2022RC1 = (_data_ref / 'tprs/2lyz_gmx_2022-rc1.tpr').as_posix()
TPR2023 = (_data_ref / 'tprs/2lyz_gmx_2023.tpr').as_posix()
TPR2024 = (_data_ref / 'tprs/2lyz_gmx_2024.tpr').as_posix()
# double precision
TPR455Double = (_data_ref / 'tprs/drew_gmx_4.5.5.double.tpr').as_posix()
TPR460 = (_data_ref / 'tprs/ab42_gmx_4.6.tpr').as_posix()
Expand All @@ -417,7 +418,9 @@
TPR2021_double_bonded = (_data_ref / 'tprs/all_bonded/dummy_2021_double.tpr').as_posix()
TPR2022RC1_bonded = (_data_ref / 'tprs/all_bonded/dummy_2022-rc1.tpr').as_posix()
TPR2023_bonded = (_data_ref / 'tprs/all_bonded/dummy_2023.tpr').as_posix()
TPR2024_bonded = (_data_ref / 'tprs/all_bonded/dummy_2024.tpr').as_posix()
# all interactions
TPR_EXTRA_2024 = (_data_ref / 'tprs/virtual_sites/extra-interactions-2024.tpr').as_posix()
TPR_EXTRA_2023 = (_data_ref / 'tprs/virtual_sites/extra-interactions-2023.tpr').as_posix()
TPR_EXTRA_2022RC1 = (_data_ref / 'tprs/virtual_sites/extra-interactions-2022-rc1.tpr').as_posix()
TPR_EXTRA_2021 = (_data_ref / 'tprs/virtual_sites/extra-interactions-2021.tpr').as_posix()
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13 changes: 8 additions & 5 deletions testsuite/MDAnalysisTests/topology/test_tprparser.py
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Expand Up @@ -32,14 +32,14 @@
TPR450, TPR451, TPR452, TPR453, TPR454, TPR455, TPR455Double,
TPR460, TPR461, TPR502, TPR504, TPR505, TPR510, TPR510_bonded,
TPR2016, TPR2018, TPR2019B3, TPR2020B2, TPR2020, TPR2020Double,
TPR2021, TPR2021Double, TPR2022RC1, TPR2023,
TPR2021, TPR2021Double, TPR2022RC1, TPR2023, TPR2024,
TPR2016_bonded, TPR2018_bonded, TPR2019B3_bonded,
TPR2020B2_bonded, TPR2020_bonded, TPR2020_double_bonded,
TPR2021_bonded, TPR2021_double_bonded, TPR334_bonded,
TPR2022RC1_bonded, TPR2023_bonded,
TPR2022RC1_bonded, TPR2023_bonded, TPR2024_bonded,
TPR_EXTRA_2021, TPR_EXTRA_2020, TPR_EXTRA_2018,
TPR_EXTRA_2016, TPR_EXTRA_407, TPR_EXTRA_2022RC1,
TPR_EXTRA_2023,
TPR_EXTRA_2023, TPR_EXTRA_2024,
XTC,
)
from MDAnalysisTests.topology.base import ParserBase
Expand All @@ -57,6 +57,8 @@
TPR2020_double_bonded,
TPR2022RC1_bonded,
TPR2023_bonded,
TPR2024_bonded,
TPR_EXTRA_2024,
TPR_EXTRA_2023,
TPR_EXTRA_2022RC1,
TPR_EXTRA_2021,
Expand Down Expand Up @@ -130,7 +132,8 @@ class TestTPRGromacsVersions(TPRAttrs):
TPR407, TPR450, TPR451, TPR452, TPR453, TPR454,
TPR455, TPR502, TPR504, TPR505, TPR510, TPR2016,
TPR2018, TPR2019B3, TPR2020, TPR2020Double,
TPR2021, TPR2021Double, TPR2022RC1, TPR2023,])
TPR2021, TPR2021Double, TPR2022RC1, TPR2023,
TPR2024])
def filename(self, request):
return request.param

Expand Down Expand Up @@ -257,7 +260,7 @@ def test_all_impropers(topology, impr):
@pytest.fixture(params=(
TPR400, TPR402, TPR403, TPR404, TPR405, TPR406, TPR407, TPR450, TPR451,
TPR452, TPR453, TPR454, TPR502, TPR504, TPR505, TPR510, TPR2016, TPR2018,
TPR2023,
TPR2023, TPR2024,
))
def bonds_water(request):
parser = MDAnalysis.topology.TPRParser.TPRParser(request.param).parse()
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