Add no selection option to RMSD analysis class

package/AUTHORS

@@ -276,6 +276,7 @@ Chronological list of authors
   - Kunj Sinha
   - Ayush Agarwal
   - Parth Uppal
+  - Olivier Languin--Cattoën
 
 External code
 -------------

package/CHANGELOG

@@ -16,7 +16,8 @@ The rules for this file:
 -------------------------------------------------------------------------------
 ??/??/?? IAlibay, orbeckst, marinegor, tylerjereddy, ljwoods2, marinegor,
          spyke7, talagayev, tanii1125, BradyAJohnston, hejamu, jeremyleung521,
-         harshitgajjela-droid, kunjsinha, aygarwal, jauy123, Dreamstick9
+         harshitgajjela-droid, kunjsinha, aygarwal, jauy123, Dreamstick9,
+         ollyfutur
 
  * 2.11.0
 
@@ -42,6 +43,8 @@ Fixes
    DSSP by porting upstream PyDSSP 0.9.1 fix (Issue #4913)
 
 Enhancements
+ * Added `select=None` in `analysis.rms.RMSD` to perform no selection on
+   the input `atomgroup` and `reference` (Issue #5300, PR #5296)
  * MOL2Parser now reads unit cell dimensions from @<TRIPOS>CRYSIN records (Issue #3341)
  * Reduces duplication of code in _apply() function (Issue #5247, PR #5294)
  * Added new top-level `MDAnalysis.fetch` module (PR #4943)

package/MDAnalysis/analysis/rms.py

@@ -287,17 +287,19 @@ def process_selection(select):
 
     Parameters
     ----------
-    select : str or tuple or dict
+    select : str or tuple or dict or None
 
         - `str` -> Any valid string selection
         - `dict` -> ``{'mobile':sel1, 'reference':sel2}``
         - `tuple` -> ``(sel1, sel2)``
+        - ``None``
 
     Returns
     -------
     dict
         selections for 'reference' and 'mobile'. Values are guarenteed to be
-        iterable (so that one can provide selections to retain order)
+        iterable (so that one can provide selections to retain order) or
+        ``None`` if no selection is to be performed.
 
     Notes
     -----
@@ -325,10 +327,16 @@ def process_selection(select):
                 "select dictionary must contain entries for keys "
                 "'mobile' and 'reference'."
             ) from None
+    elif select is None:
+        select = {"reference": None, "mobile": None}
     else:
-        raise TypeError("'select' must be either a string, 2-tuple, or dict")
-    select["mobile"] = asiterable(select["mobile"])
-    select["reference"] = asiterable(select["reference"])
+        raise TypeError(
+            "'select' must be either a string, 2-tuple, dict or None"
+        )
+    if select["mobile"] is not None:
+        select["mobile"] = asiterable(select["mobile"])
+    if select["reference"] is not None:
+        select["reference"] = asiterable(select["reference"])
     return select
 
 
@@ -394,7 +402,7 @@ def __init__(
         reference : AtomGroup or Universe (optional)
             Group of reference atoms; if ``None`` then the current frame of
             `atomgroup` is used.
-        select : str or dict or tuple (optional)
+        select : str or dict or tuple or None (optional)
             The selection to operate on; can be one of:
 
             1. any valid selection string for
@@ -405,16 +413,21 @@ def __init__(
                and *sel2* are valid selection strings that are applied to
                `atomgroup` and `reference` respectively (the
                :func:`MDAnalysis.analysis.align.fasta2select` function returns such
-               a dictionary based on a ClustalW_ or STAMP_ sequence alignment); or
+               a dictionary based on a ClustalW_ or STAMP_ sequence alignment) or
+               ``None`` if no selection is to be performed; or
 
             3. a tuple ``(sel1, sel2)``
 
+            4. ``None``
+
             When using 2. or 3. with *sel1* and *sel2* then these selection strings
             are applied to `atomgroup` and `reference` respectively and should
             generate *groups of equivalent atoms*.  *sel1* and *sel2* can each also
             be a *list of selection strings* to generate a
             :class:`~MDAnalysis.core.groups.AtomGroup` with defined atom order as
-            described under :ref:`ordered-selections-label`).
+            described under :ref:`ordered-selections-label`). When using ``None``
+            no selection is performed and all atoms from `atomgroup` or `reference`
+            are used in their original order.
 
         groupselections : list (optional)
             A list of selections as described for `select`, with the difference
@@ -539,8 +552,16 @@ def __init__(
         self.tol_mass = tol_mass
         self.ref_frame = ref_frame
         self.weights_groupselections = weights_groupselections
-        self.ref_atoms = self.reference.select_atoms(*select["reference"])
-        self.mobile_atoms = self.atomgroup.select_atoms(*select["mobile"])
+        self.ref_atoms = (
+            self.reference.select_atoms(*select["reference"])
+            if select["reference"] is not None
+            else self.reference
+        )
+        self.mobile_atoms = (
+            self.atomgroup.select_atoms(*select["mobile"])
+            if select["mobile"] is not None
+            else self.atomgroup
+        )
 
         if len(self.ref_atoms) != len(self.mobile_atoms):
             err = (

testsuite/MDAnalysisTests/analysis/test_rms.py

@@ -475,6 +475,40 @@ def test_rmsd_attr_warning(self, universe, client_RMSD):
         with pytest.warns(DeprecationWarning, match=wmsg):
             assert_equal(RMSD.rmsd, RMSD.results.rmsd)
 
+    def test_rmsd_no_selection(self, universe, correct_values, client_RMSD):
+        reference = MDAnalysis.Universe(PSF, DCD)
+        ref = reference.select_atoms("name CA")
+        ag = universe.select_atoms("name CA")
+        order = np.arange(len(ag))
+        order[0] = 2
+        order[2] = 0
+
+        # select=None will not sort the atomgroups
+        RMSD = MDAnalysis.analysis.rms.RMSD(
+            ag[order], reference=ref, select=None
+        )
+        RMSD.run(step=49, **client_RMSD)
+        assert not np.allclose(RMSD.results.rmsd, correct_values)
+
+        RMSD = MDAnalysis.analysis.rms.RMSD(
+            ag[order], reference=ref[order], select=None
+        )
+        RMSD.run(step=49, **client_RMSD)
+        assert_almost_equal(
+            RMSD.results.rmsd,
+            correct_values,
+            4,
+            err_msg="error: rmsd profile should match "
+            "between true values and calculated values",
+        )
+
+    def test_rmsd_misuse_selec_raises_TypeError(self, universe):
+        with pytest.raises(TypeError):
+            RMSD = MDAnalysis.analysis.rms.RMSD(
+                universe,
+                select=42,
+            )
+
 
 class TestRMSF(object):
     @pytest.fixture()