Add kwarg to index TPRParser from 0 or 1 (#3152)

* add kwarg

* change default to True for 2.0

* fix tests to index resids from 0 again

* Update package/CHANGELOG

Co-authored-by: Oliver Beckstein <orbeckst@gmail.com>

* change default arg for TPR utilities and remove warnings

* updated to 1.1.0

Co-authored-by: Oliver Beckstein <orbeckst@gmail.com>

package/CHANGELOG

@@ -133,6 +133,8 @@ Enhancements
     explicit in the topology (Issue #2468, PR #2775)
 
 Changes
+  * TPRParser now loads TPR files with `tpr_resid_from_one=True` by default, 
+    which starts TPR resid indexing from 1 (instead of 0 as in 1.x) (Issue #2364, PR #3152)
   * Introduces encore specific C compiler arguments to allow for lowering of
     optimisations on non-x86 platforms (Issue #1389, PR #3149)
   * Continuous integration uses mamba rather than conda to install the

package/MDAnalysis/topology/TPRParser.py

@@ -176,12 +176,27 @@ class TPRParser(TopologyReaderBase):
     """
     format = 'TPR'
 
-    def parse(self, **kwargs):
+    def parse(self, tpr_resid_from_one=True, **kwargs):
         """Parse a Gromacs TPR file into a MDAnalysis internal topology structure.
 
+        Parameters
+        ----------
+        tpr_resid_from_one: bool (optional)
+            Toggle whether to index resids from 1 or 0 from TPR files.
+            TPR files index resids from 0 by default, even though GRO and ITP
+            files index from 1.
+
         Returns
         -------
         structure : dict
+
+
+        .. versionchanged:: 1.1.0
+            Added the ``tpr_resid_from_one`` keyword to control if
+            resids are indexed from 0 or 1. Default ``False``.
+
+        .. versionchanged:: 2.0.0
+            Changed to ``tpr_resid_from_one=True`` by default.
         """
         with openany(self.filename, mode='rb') as infile:
             tprf = infile.read()
@@ -219,7 +234,8 @@ def parse(self, **kwargs):
             tpr_utils.ndo_real(data, state_ngtc)        # relevant to Berendsen tcoupl_lambda
 
         if th.bTop:
-            tpr_top = tpr_utils.do_mtop(data, th.fver)
+            tpr_top = tpr_utils.do_mtop(data, th.fver,
+                                        tpr_resid_from_one=tpr_resid_from_one)
         else:
             msg = f"{self.filename}: No topology found in tpr file"
             logger.critical(msg)

package/MDAnalysis/topology/tpr/utils.py

@@ -46,6 +46,7 @@
 
 The module also contains the :func:`do_inputrec` to read the TPR header with.
 """
+
 import numpy as np
 import xdrlib
 import struct
@@ -284,7 +285,7 @@ def extract_box_info(data, fver):
     return obj.Box(box, box_rel, box_v)
 
 
-def do_mtop(data, fver):
+def do_mtop(data, fver, tpr_resid_from_one=False):
     # mtop: the topology of the whole system
     symtab = do_symtab(data)
     do_symstr(data, symtab)  # system_name
@@ -371,6 +372,9 @@ def do_mtop(data, fver):
     molnums = np.array(molnums, dtype=np.int32)
     segids = np.array(segids, dtype=object)
     resids = np.array(resids, dtype=np.int32)
+    if tpr_resid_from_one:
+        resids += 1
+
     resnames = np.array(resnames, dtype=object)
     (residx, new_resids,
      (new_resnames,

testsuite/MDAnalysisTests/analysis/test_density.py

@@ -148,7 +148,7 @@ class DensityParameters(object):
 
     @pytest.fixture()
     def universe(self):
-        return mda.Universe(self.topology, self.trajectory)
+        return mda.Universe(self.topology, self.trajectory, tpr_resid_from_one=False)
 
 class TestDensityAnalysis(DensityParameters):
     def check_DensityAnalysis(self, ag, ref_meandensity,

testsuite/MDAnalysisTests/core/test_atomselections.py

@@ -485,7 +485,7 @@ class TestSelectionsTPR(object):
     @staticmethod
     @pytest.fixture(scope='class')
     def universe():
-        return MDAnalysis.Universe(TPR,XTC)
+        return MDAnalysis.Universe(TPR, XTC, tpr_resid_from_one=False)
 
     @pytest.mark.parametrize('selstr', [
         'same fragment as bynum 1',
@@ -1299,7 +1299,7 @@ def test_mass_sel_warning(u_fake_masses):
 
 
 @pytest.mark.parametrize("selstr,n_res", [
-    ("resnum -10 to 3", 14),
+    ("resnum -10 to 3", 13),
     ("resnum -5--3", 3),  # select -5 to -3
     ("resnum -3 : -5", 0),  # wrong way around
 ])

testsuite/MDAnalysisTests/topology/test_tprparser.py

@@ -39,6 +39,7 @@
 )
 from MDAnalysisTests.topology.base import ParserBase
 import MDAnalysis.topology.TPRParser
+import MDAnalysis as mda
 
 BONDED_TPRS = (
     TPR510_bonded,
@@ -287,3 +288,14 @@ def test_elements():
         'H', '', 'Na', 'Na', 'Na', 'Na',
     ], dtype=object)
     assert_equal(topology.elements.values[-20:], reference)
+
+
+@pytest.mark.parametrize("resid_from_one,resid_addition", [
+    (False, 0),
+    (True, 1),  # status quo for 2.x
+    ])
+def test_resids(resid_from_one, resid_addition):
+    u = mda.Universe(TPR, tpr_resid_from_one=resid_from_one)
+    resids = np.arange(len(u.residues)) + resid_addition
+    assert_equal(u.residues.resids, resids,
+                 err_msg="tpr_resid_from_one kwarg not switching resids")