ENH: support tpx 134 (GMX 2024.4) (#4866)

* ENH: support tpx 134 (GMX 2024.4)

* Fixes gh-4855.

* Add support for reading topology data from `.tpr` files
produced by GROMACS 2024.4, corresponding to tpx version
`134`.

* My approach was similar to the one I used in gh-4523, except
for two things: 1) I retrieved the current generation (`28`) from
a `print` in our own binary parser rather than rebuilding
GMX from source with added `printf`, and more importantly 2) I
had to add some shims because the `.tpr` format has changed.

* With regard to the additional field data now stored in the
`.tpr` format, I was involved in reviewing it upstream at:
https://gitlab.com/gromacs/gromacs/-/merge_requests/4544.
You can see that the changes related to the MARTINI functional
form made it into the `v2024.4` tag i.e., here:
https://gitlab.com/gromacs/gromacs/-/blob/v2024.4/src/gromacs/gmxpreprocess/convparm.cpp?ref_type=tags#L372

* DOC: PR 4866 revisions

* Remove the periods (`.`) from Tyler's identifier
in the `CHANGELOG` to satisfy reviewer comments.

package/CHANGELOG

@@ -14,11 +14,13 @@ The rules for this file:
 
 
 -------------------------------------------------------------------------------
-??/??/?? IAlibay, ChiahsinChu, RMeli, tanishy7777, talagayev
+??/??/?? IAlibay, ChiahsinChu, RMeli, tanishy7777, talagayev,
+         tylerjereddy
 
  * 2.9.0
 
 Fixes
+ * Add support for TPR files produced by GROMACS 2024.4
  * Fixes invalid default unit from Angstrom to Angstrom^{-3} for convert_density() function. (Issue #4829)
  * Fixes deprecation warning Array to scalar convertion. Replaced atan2() with np.arctan2() (Issue #4339)
  * Replaced mutable defaults with None and initialized them within

package/MDAnalysis/topology/TPRParser.py

@@ -67,6 +67,7 @@
    127        28             2022                 yes
    129        28             2023                 yes
    133        28             2024.1               yes
+   134        28             2024.4               yes
    ========== ============== ==================== =====
 
 .. [*] Files generated by the beta versions of Gromacs 2020 are NOT supported.

package/MDAnalysis/topology/tpr/setting.py

@@ -38,7 +38,8 @@
 """
 
 #: 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, 133)
+SUPPORTED_VERSIONS = (58, 73, 83, 100, 103, 110, 112,
+                      116, 119, 122, 127, 129, 133, 134)
 
 # Some constants
 STRLEN = 4096

package/MDAnalysis/topology/tpr/utils.py

@@ -481,6 +481,10 @@ def do_iparams(data, functypes, fver):
         elif i in [setting.F_RESTRANGLES]:
             data.unpack_real()  # harmonic.rA
             data.unpack_real()  # harmonic.krA
+            if fver >= 134:
+                data.unpack_real()  # harmonic.rB
+                data.unpack_real()  # harmonic.krB
+
         elif i in [setting.F_LINEAR_ANGLES]:
             data.unpack_real()  # linangle.klinA
             data.unpack_real()  # linangle.aA
@@ -598,6 +602,9 @@ def do_iparams(data, functypes, fver):
         elif i in [setting.F_RESTRDIHS]:
             data.unpack_real()  # pdihs.phiA
             data.unpack_real()  # pdihs.cpA
+            if fver >= 134:
+                data.unpack_real()  # pdihs.phiB
+                data.unpack_real()  # pdihs.cpB
         elif i in [setting.F_DISRES]:
             data.unpack_int()  # disres.label
             data.unpack_int()  # disres.type
@@ -640,6 +647,8 @@ def do_iparams(data, functypes, fver):
 
         elif i in [setting.F_CBTDIHS]:
             ndo_real(data, setting.NR_CBTDIHS)  # cbtdihs.cbtcA
+            if fver >= 134:
+                ndo_real(data, setting.NR_CBTDIHS)  # cbtdihs.cbtcB
 
         elif i in [setting.F_RBDIHS]:
             ndo_real(data, setting.NR_RBDIHS)  # iparams_rbdihs_rbcA

testsuite/MDAnalysisTests/datafiles.py

@@ -86,13 +86,15 @@
     "TPR460", "TPR461", "TPR502", "TPR504", "TPR505", "TPR510", "TPR2016",
     "TPR2018", "TPR2019B3", "TPR2020B2", "TPR2020", "TPR2020Double",
     "TPR2021", "TPR2021Double", "TPR2022RC1", "TPR2023", "TPR2024",
+    "TPR2024_4",
     "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", "TPR2024_bonded",
+    "TPR2024_4_bonded",
     "TPR_EXTRA_2021", "TPR_EXTRA_2020", "TPR_EXTRA_2018",
     "TPR_EXTRA_2016", "TPR_EXTRA_407", "TPR_EXTRA_2022RC1",
-    "TPR_EXTRA_2023", "TPR_EXTRA_2024",
+    "TPR_EXTRA_2023", "TPR_EXTRA_2024", "TPR_EXTRA_2024_4",
     "PDB_sub_sol", "PDB_sub_dry",  # TRRReader sub selection
     "TRR_sub_sol",
     "XTC_sub_sol",
@@ -407,6 +409,7 @@
 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()
+TPR2024_4 = (_data_ref / 'tprs/2lyz_gmx_2024_4.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()
@@ -427,7 +430,9 @@
 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()
+TPR2024_4_bonded = (_data_ref / 'tprs/all_bonded/dummy_2024_4.tpr').as_posix()
 # all interactions
+TPR_EXTRA_2024_4 = (_data_ref / 'tprs/virtual_sites/extra-interactions-2024_4.tpr').as_posix()
 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()

testsuite/MDAnalysisTests/topology/test_tprparser.py

@@ -32,14 +32,15 @@
     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, TPR2024,
+    TPR2021, TPR2021Double, TPR2022RC1, TPR2023, TPR2024, TPR2024_4,
     TPR2016_bonded, TPR2018_bonded, TPR2019B3_bonded,
     TPR2020B2_bonded, TPR2020_bonded, TPR2020_double_bonded,
     TPR2021_bonded, TPR2021_double_bonded, TPR334_bonded,
     TPR2022RC1_bonded, TPR2023_bonded, TPR2024_bonded,
+    TPR2024_4_bonded,
     TPR_EXTRA_2021, TPR_EXTRA_2020, TPR_EXTRA_2018,
     TPR_EXTRA_2016, TPR_EXTRA_407, TPR_EXTRA_2022RC1,
-    TPR_EXTRA_2023, TPR_EXTRA_2024,
+    TPR_EXTRA_2023, TPR_EXTRA_2024, TPR_EXTRA_2024_4,
     XTC,
 )
 from MDAnalysisTests.topology.base import ParserBase
@@ -58,6 +59,8 @@
     TPR2022RC1_bonded,
     TPR2023_bonded,
     TPR2024_bonded,
+    TPR2024_4_bonded,
+    TPR_EXTRA_2024_4,
     TPR_EXTRA_2024,
     TPR_EXTRA_2023,
     TPR_EXTRA_2022RC1,
@@ -135,7 +138,7 @@ class TestTPRGromacsVersions(TPRAttrs):
                             TPR455, TPR502, TPR504, TPR505, TPR510, TPR2016,
                             TPR2018, TPR2019B3, TPR2020, TPR2020Double,
                             TPR2021, TPR2021Double, TPR2022RC1, TPR2023,
-                            TPR2024])
+                            TPR2024, TPR2024_4])
     def filename(self, request):
         return request.param
 
@@ -262,7 +265,7 @@ 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, TPR2024,
+    TPR2023, TPR2024, TPR2024_4,
 ))
 def bonds_water(request):
     parser = MDAnalysis.topology.TPRParser.TPRParser(request.param).parse()