From 630beea35997e1ad63cdcab6a4644a0b5a034251 Mon Sep 17 00:00:00 2001
From: Cloudac7 <812556867@qq.com>
Date: Fri, 13 Oct 2023 23:15:32 +0800
Subject: [PATCH 01/13] feat: add box selection

doc: add doc about box selection

fix: reformat with darker and flake8
---
 package/AUTHORS                               |  1 +
 package/CHANGELOG                             |  1 +
 package/MDAnalysis/core/selection.py          | 83 +++++++++++++++++++
 .../source/documentation_pages/selections.rst | 17 ++++
 .../core/test_atomselections.py               | 59 ++++++++++---
 5 files changed, 151 insertions(+), 10 deletions(-)

diff --git a/package/AUTHORS b/package/AUTHORS
index c413c90462d..a5929bc129a 100644
--- a/package/AUTHORS
+++ b/package/AUTHORS
@@ -222,6 +222,7 @@ Chronological list of authors
   - Shubham Kumar
   - Zaheer Timol
   - Geongi Moon
+  - Yunpei Liu
 
 External code
 -------------
diff --git a/package/CHANGELOG b/package/CHANGELOG
index 1cc96ddea05..a51e172a5c4 100644
--- a/package/CHANGELOG
+++ b/package/CHANGELOG
@@ -42,6 +42,7 @@ Enhancements
     (Issue #3994, PR #4281)  
   * Add support for reading chainID info from Autodock PDBQT files (Issue #4207,
     PR #4284)
+  * Add a new geometric selection: box
 
 Changes
   * Biopython is now an optional dependency (Issue #3820, PR #4332)
diff --git a/package/MDAnalysis/core/selection.py b/package/MDAnalysis/core/selection.py
index 2edbf79e01b..f85a45a43b8 100644
--- a/package/MDAnalysis/core/selection.py
+++ b/package/MDAnalysis/core/selection.py
@@ -537,6 +537,89 @@ def _apply(self, group):
         return group[np.asarray(indices, dtype=np.int64)]
 
 
+class BoxSelection(Selection):
+    token = "box"
+    precedence = 1
+    index_map = {"x": 0, "y": 1, "z": 2}
+
+    def __init__(self, parser, tokens):
+        super().__init__(parser, tokens)
+        self.periodic = parser.periodic
+        self.direction = tokens.popleft()
+        if len(self.direction) > 3:
+            raise ValueError(
+                "The direction '{}' is not valid. Must be combination of {}"
+                "".format(self.direction, list(self.index_map.keys()))
+            )
+        else:
+            for d in self.direction:
+                if d not in self.index_map:
+                    raise ValueError(
+                        "The direction '{}' is not valid."
+                        "Must be combination "
+                        "of {}".format(self.direction, list(self.index_map.keys()))
+                    )
+                setattr(self, "{}max".format(d), float(tokens.popleft()))
+                setattr(self, "{}min".format(d), float(tokens.popleft()))
+        self.sel = parser.parse_expression(self.precedence)
+
+    @return_empty_on_apply
+    def _apply(self, group):
+        sel = self.sel.apply(group)
+        if len(sel) == 0:
+            return group[[]]
+        # Calculate vectors between point of interest and our group
+        vecs = group.positions - sel.center_of_geometry()
+        range_map = {}
+
+        for d in self.direction:
+            axis_index = self.index_map.get(d)
+            axis_max = self.__getattribute__("{}max".format(d))
+            axis_min = self.__getattribute__("{}min".format(d))
+            range_map[axis_index] = (axis_min, axis_max)
+
+        if self.periodic and group.dimensions is not None:
+            box = group.dimensions[:3]
+
+            for k, v in range_map.items():
+                axis_index = k
+                axis_min, axis_max = v[0], v[1]
+
+                axis_height = axis_max - axis_min
+                if axis_height > box[axis_index]:
+                    raise NotImplementedError(
+                        "The total length of the box selection in {} ({:.3f}) "
+                        "is larger than the unit cell's {} dimension ({:.3f}). Can "
+                        "only do selections where it is smaller or equal."
+                        "".format(
+                            self.direction[axis_index],
+                            axis_height,
+                            self.direction[axis_index],
+                            box[axis_index],
+                        )
+                    )
+
+            if np.all(group.dimensions[3:] == 90.0):
+                # Orthogonal version
+                vecs -= box[:3] * np.rint(vecs / box[:3])
+            else:
+                # Triclinic version
+                tribox = group.universe.trajectory.ts.triclinic_dimensions
+                vecs -= tribox[2] * np.rint(vecs[:, 2] / tribox[2][2])[:, None]
+                vecs -= tribox[1] * np.rint(vecs[:, 1] / tribox[1][1])[:, None]
+                vecs -= tribox[0] * np.rint(vecs[:, 0] / tribox[0][0])[:, None]
+
+        # Deal with each dimension criteria
+        mask = None
+        for k, v in range_map.items():
+            if mask is None:
+                mask = (vecs[:, k] > v[0]) & (vecs[:, k] < v[1])
+            else:
+                mask &= (vecs[:, k] > v[0]) & (vecs[:, k] < v[1])
+
+        return group[mask]
+
+
 class AtomSelection(Selection):
     token = 'atom'
 
diff --git a/package/doc/sphinx/source/documentation_pages/selections.rst b/package/doc/sphinx/source/documentation_pages/selections.rst
index 6ee7f26bc2d..605d21bcd6a 100644
--- a/package/doc/sphinx/source/documentation_pages/selections.rst
+++ b/package/doc/sphinx/source/documentation_pages/selections.rst
@@ -277,6 +277,23 @@ cyzone *externalRadius* *zMax* *zMin* *selection*
        relative to the COG of *selection*, instead of absolute z-values
        in the box.
 
+box *dimension(s)* *d1_Max* *d1_Min* (*d2_Max* *d2_Min*) (*d3_Max* *d3_Min*) *selection*
+    select all atoms around a box centered in the center of geometry (COG)
+    of a given selection, e.g. ``box x 10 -5 protein`` selects the center
+    of geometry of protein, and creates a zone of 15 Angstroms in x axis, 
+    extending from 10 above the COG to 5 below. ``box yz 10 -8 6 -10 protein`` 
+    selects COG of protein, and creates an orthogonal zone extending from 
+    10 above the COG to 8 below in y, and from 6 above the COG to 10 below in z. 
+    ``box xyz 10 -5 6 -8 9 -7 protein`` selects COG of protein, and creates
+    an orthogonal box of extending from 10 above the COG to 5 below in x, 
+    from 6 above the COG to 8 below in y, and from 9 above the COG to 
+    7 below in z. *dimension(s)* can be any or any combination of **x**, 
+    **y**, and **z**, but should not be longer than 3 characters, 
+    e.g. ``x``, ``yz``, ``zx``, ``xyz``. Positive values for *d\*_Min*, 
+    or negative ones for *d\*_Max* are allowed. Number of groups of 
+    *d\*_Max* and *d\*_Min* should be equal to the number of characters in 
+    *dimension(s)*.
+
 point *x* *y* *z*  *distance*
     selects all atoms within a cutoff of a point in space, make sure
     coordinate is separated by spaces, e.g. ``point 5.0 5.0 5.0 3.5``
diff --git a/testsuite/MDAnalysisTests/core/test_atomselections.py b/testsuite/MDAnalysisTests/core/test_atomselections.py
index 6915e6a95d1..72c67d84c8b 100644
--- a/testsuite/MDAnalysisTests/core/test_atomselections.py
+++ b/testsuite/MDAnalysisTests/core/test_atomselections.py
@@ -246,6 +246,22 @@ def test_point(self, universe):
 
         assert_equal(set(ag.indices), set(idx))
 
+    @pytest.mark.parametrize(
+        "selstr, expected_value",
+        [
+            ("box x 2.0 -2.0 index 1281", 418),
+            ("box yz 2.0 -2.0 2.0 -2.0 index 1280", 58),
+            ("box xyz 2.0 -2.0 2.0 -2.0 2.0 -2.0 index 1279", 10),
+        ],
+    )
+    def test_box(self, universe, selstr, expected_value):
+        sel = universe.select_atoms(selstr)
+        assert_equal(len(sel), expected_value)
+
+    def test_empty_box(self, universe):
+        empty = universe.select_atoms("box y 10 -10 name NOT_A_NAME")
+        assert_equal(len(empty), 0)
+
     def test_prop(self, universe):
         sel = universe.select_atoms('prop y <= 16')
         sel2 = universe.select_atoms('prop abs z < 8')
@@ -1270,16 +1286,39 @@ def test_similarity_selection_icodes(u_pdb_icodes, selection, n_atoms):
 
     assert len(sel.atoms) == n_atoms
 
-@pytest.mark.parametrize('selection', [
-    'all', 'protein', 'backbone', 'nucleic', 'nucleicbackbone',
-    'name O', 'name N*', 'resname stuff', 'resname ALA', 'type O',
-    'index 0', 'index 1', 'bynum 1-10',
-    'segid SYSTEM', 'resid 163', 'resid 1-10', 'resnum 2',
-    'around 10 resid 1', 'point 0 0 0 10', 'sphzone 10 resid 1',
-    'sphlayer 0 10 index 1', 'cyzone 15 4 -8 index 0',
-    'cylayer 5 10 10 -8 index 1', 'prop abs z <= 100',
-    'byres index 0', 'same resid as index 0',
-])
+
+@pytest.mark.parametrize(
+    "selection",
+    [
+        "all",
+        "protein",
+        "backbone",
+        "nucleic",
+        "nucleicbackbone",
+        "name O",
+        "name N*",
+        "resname stuff",
+        "resname ALA",
+        "type O",
+        "index 0",
+        "index 1",
+        "bynum 1-10",
+        "segid SYSTEM",
+        "resid 163",
+        "resid 1-10",
+        "resnum 2",
+        "around 10 resid 1",
+        "point 0 0 0 10",
+        "sphzone 10 resid 1",
+        "sphlayer 0 10 index 1",
+        "cyzone 15 4 -8 index 0",
+        "cylayer 5 10 10 -8 index 1",
+        "prop abs z <= 100",
+        "byres index 0",
+        "same resid as index 0",
+        "box xz 3 2 4 -5 index 0",
+    ],
+)
 def test_selections_on_empty_group(u_pdb_icodes, selection):
     ag = u_pdb_icodes.atoms[[]].select_atoms(selection)
     assert len(ag) == 0

From 2f94545a8f5cfc325aa2c63571b039e47b0dc5a2 Mon Sep 17 00:00:00 2001
From: Cloudac7 <812556867@qq.com>
Date: Wed, 25 Oct 2023 22:43:36 +0800
Subject: [PATCH 02/13] test: add test for orthogonal distance style: reformat
 as pep8

---
 package/CHANGELOG                                  |  2 +-
 package/MDAnalysis/core/selection.py               | 14 ++++++++------
 package/doc/sphinx/source/conf.py                  |  2 ++
 .../MDAnalysisTests/core/test_atomselections.py    |  6 ++++++
 4 files changed, 17 insertions(+), 7 deletions(-)

diff --git a/package/CHANGELOG b/package/CHANGELOG
index a51e172a5c4..ae67b27b38a 100644
--- a/package/CHANGELOG
+++ b/package/CHANGELOG
@@ -42,7 +42,7 @@ Enhancements
     (Issue #3994, PR #4281)  
   * Add support for reading chainID info from Autodock PDBQT files (Issue #4207,
     PR #4284)
-  * Add a new geometric selection: box
+  * Add a new geometric selection: box (Issue #4323, PR #4324)
 
 Changes
   * Biopython is now an optional dependency (Issue #3820, PR #4332)
diff --git a/package/MDAnalysis/core/selection.py b/package/MDAnalysis/core/selection.py
index f85a45a43b8..a8ddf23c01e 100644
--- a/package/MDAnalysis/core/selection.py
+++ b/package/MDAnalysis/core/selection.py
@@ -541,6 +541,7 @@ class BoxSelection(Selection):
     token = "box"
     precedence = 1
     index_map = {"x": 0, "y": 1, "z": 2}
+    axis_map = ["x", "y", "z"]
 
     def __init__(self, parser, tokens):
         super().__init__(parser, tokens)
@@ -556,8 +557,9 @@ def __init__(self, parser, tokens):
                 if d not in self.index_map:
                     raise ValueError(
                         "The direction '{}' is not valid."
-                        "Must be combination "
-                        "of {}".format(self.direction, list(self.index_map.keys()))
+                        "Must be combination of {}".format(
+                            self.direction, list(self.index_map.keys())
+                        )
                     )
                 setattr(self, "{}max".format(d), float(tokens.popleft()))
                 setattr(self, "{}min".format(d), float(tokens.popleft()))
@@ -589,12 +591,12 @@ def _apply(self, group):
                 if axis_height > box[axis_index]:
                     raise NotImplementedError(
                         "The total length of the box selection in {} ({:.3f}) "
-                        "is larger than the unit cell's {} dimension ({:.3f}). Can "
-                        "only do selections where it is smaller or equal."
+                        "is larger than the unit cell's {} dimension ({:.3f}). "
+                        "Can only do selections where it is smaller or equal."
                         "".format(
-                            self.direction[axis_index],
+                            self.axis_map[axis_index],
                             axis_height,
-                            self.direction[axis_index],
+                            self.axis_map[axis_index],
                             box[axis_index],
                         )
                     )
diff --git a/package/doc/sphinx/source/conf.py b/package/doc/sphinx/source/conf.py
index a1a461ed14b..1ad76dfb9aa 100644
--- a/package/doc/sphinx/source/conf.py
+++ b/package/doc/sphinx/source/conf.py
@@ -14,6 +14,8 @@
 import sys
 import os
 import datetime
+sys.path.insert(0, os.path.abspath('../../..'))
+
 import MDAnalysis as mda
 # Custom MDA Formating
 from pybtex.style.formatting.unsrt import Style as UnsrtStyle
diff --git a/testsuite/MDAnalysisTests/core/test_atomselections.py b/testsuite/MDAnalysisTests/core/test_atomselections.py
index 72c67d84c8b..c340d823133 100644
--- a/testsuite/MDAnalysisTests/core/test_atomselections.py
+++ b/testsuite/MDAnalysisTests/core/test_atomselections.py
@@ -814,6 +814,12 @@ def test_sphzone(self, u, periodic, expected):
 
         assert len(sel) == expected
 
+    @pytest.mark.parametrize("periodic,expected", ([True, 29], [False, 17]))
+    def test_box(self, u, periodic, expected):
+        sel = u.select_atoms("box xyz 5 2 10 -5 6 -2 resid 1", periodic=periodic)
+
+        assert len(sel) == expected
+
 
 class TestTriclinicDistanceSelections(BaseDistanceSelection):
     @pytest.fixture()

From 01758fce9badf27d179b16719106483c3b9fa6a0 Mon Sep 17 00:00:00 2001
From: Cloudac7 <812556867@qq.com>
Date: Thu, 26 Oct 2023 13:18:21 +0800
Subject: [PATCH 03/13] test: add test in triclinic cell for box selection
 test: add error catching for box selection fix: prevent abnormal input in
 direction

---
 package/MDAnalysis/core/selection.py          | 26 +++++++++++-----
 .../core/test_atomselections.py               | 30 +++++++++++++++++++
 2 files changed, 48 insertions(+), 8 deletions(-)

diff --git a/package/MDAnalysis/core/selection.py b/package/MDAnalysis/core/selection.py
index a8ddf23c01e..5fd710d6555 100644
--- a/package/MDAnalysis/core/selection.py
+++ b/package/MDAnalysis/core/selection.py
@@ -541,26 +541,36 @@ class BoxSelection(Selection):
     token = "box"
     precedence = 1
     index_map = {"x": 0, "y": 1, "z": 2}
+    combination = [
+        "x",
+        "y",
+        "z",
+        "xy",
+        "xz",
+        "yz",
+        "yx",
+        "zx",
+        "zy",
+        "xyz",
+        "xzy",
+        "yxz",
+        "yzx",
+        "zxy",
+        "zyx",
+    ]
     axis_map = ["x", "y", "z"]
 
     def __init__(self, parser, tokens):
         super().__init__(parser, tokens)
         self.periodic = parser.periodic
         self.direction = tokens.popleft()
-        if len(self.direction) > 3:
+        if self.direction not in self.combination:
             raise ValueError(
                 "The direction '{}' is not valid. Must be combination of {}"
                 "".format(self.direction, list(self.index_map.keys()))
             )
         else:
             for d in self.direction:
-                if d not in self.index_map:
-                    raise ValueError(
-                        "The direction '{}' is not valid."
-                        "Must be combination of {}".format(
-                            self.direction, list(self.index_map.keys())
-                        )
-                    )
                 setattr(self, "{}max".format(d), float(tokens.popleft()))
                 setattr(self, "{}min".format(d), float(tokens.popleft()))
         self.sel = parser.parse_expression(self.precedence)
diff --git a/testsuite/MDAnalysisTests/core/test_atomselections.py b/testsuite/MDAnalysisTests/core/test_atomselections.py
index c340d823133..499170ba4e1 100644
--- a/testsuite/MDAnalysisTests/core/test_atomselections.py
+++ b/testsuite/MDAnalysisTests/core/test_atomselections.py
@@ -820,6 +820,28 @@ def test_box(self, u, periodic, expected):
 
         assert len(sel) == expected
 
+    @pytest.mark.parametrize(
+        "selection,error,expected",
+        (
+            [
+                "box xyz 10 -5 90 -90 6 -2 resid 1",
+                NotImplementedError,
+                "The total length of the box selection in y",
+            ],
+            [
+                "box yyy 10 -5 7 -7 6 -2 resid 1",
+                SelectionError,
+                "Must be combination of",
+            ],
+            ["box a 10 -5 resid 1", SelectionError, "Must be combination of"],
+        ),
+    )
+    def test_box_error(self, u, selection, error, expected):
+        with pytest.raises(error) as excinfo:
+            u.select_atoms(selection)
+        exec_msg = str(excinfo.value)
+        assert expected in exec_msg
+
 
 class TestTriclinicDistanceSelections(BaseDistanceSelection):
     @pytest.fixture()
@@ -883,6 +905,14 @@ def test_empty_sphzone(self, u):
         empty = u.select_atoms('sphzone 5.0 name NOT_A_NAME')
         assert len(empty) == 0
 
+    def test_box(self, u):
+        ag = u.select_atoms("box z 2.5 -2.5 resid 1")
+        assert len(ag) == 4241
+
+    def test_empty_box(self, u):
+        ag = u.select_atoms("box z 2.5 -2.5 name NOT_A_NAME")
+        assert len(ag) == 0
+
     def test_point_1(self, u):
         # The example selection
         ag = u.select_atoms('point 5.0 5.0 5.0 3.5')

From 953b33a3d512fdc347ad8951585ab0b827685e6f Mon Sep 17 00:00:00 2001
From: Cloudac7 <812556867@qq.com>
Date: Mon, 6 Nov 2023 10:31:35 +0800
Subject: [PATCH 04/13] fix: remove extra line in sphinx conf.py style:
 reformat CHANGELOG

---
 package/CHANGELOG                 | 4 ++--
 package/doc/sphinx/source/conf.py | 1 -
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/package/CHANGELOG b/package/CHANGELOG
index ae67b27b38a..052fb6f8b00 100644
--- a/package/CHANGELOG
+++ b/package/CHANGELOG
@@ -15,7 +15,7 @@ The rules for this file:
 
 -------------------------------------------------------------------------------
 ??/??/?? IAlibay, ianmkenney, PicoCentauri, pgbarletta, p-j-smith, 
-         richardjgowers, lilyminium, ALescoulie, hmacdope
+         richardjgowers, lilyminium, ALescoulie, hmacdope, Cloudac7
 
  * 2.7.0
 
@@ -30,6 +30,7 @@ Fixes
   * Fix atom charge reading in PDBQT parser (Issue #4282, PR #4283)
 
 Enhancements
+  * Add a new geometric selection: box (Issue #4323, PR #4324)
   * Add faster nucleic acid Major and Minor pair distance calculators using
     AnalysisBase for updated nucleicacids module (Issue #3720, PR #3735)
   * Adds external sidebar links (Issue #4296)
@@ -42,7 +43,6 @@ Enhancements
     (Issue #3994, PR #4281)  
   * Add support for reading chainID info from Autodock PDBQT files (Issue #4207,
     PR #4284)
-  * Add a new geometric selection: box (Issue #4323, PR #4324)
 
 Changes
   * Biopython is now an optional dependency (Issue #3820, PR #4332)
diff --git a/package/doc/sphinx/source/conf.py b/package/doc/sphinx/source/conf.py
index 1ad76dfb9aa..083e0a39244 100644
--- a/package/doc/sphinx/source/conf.py
+++ b/package/doc/sphinx/source/conf.py
@@ -14,7 +14,6 @@
 import sys
 import os
 import datetime
-sys.path.insert(0, os.path.abspath('../../..'))
 
 import MDAnalysis as mda
 # Custom MDA Formating

From 79e307fb15afdc7640afeb0106a02e326edf9427 Mon Sep 17 00:00:00 2001
From: Cloudac7 <812556867@qq.com>
Date: Wed, 8 Nov 2023 10:15:28 +0800
Subject: [PATCH 05/13] fix: use `minimize_vectors` to calculate min vec

---
 package/MDAnalysis/core/selection.py                  | 10 +---------
 testsuite/MDAnalysisTests/core/test_atomselections.py |  2 +-
 2 files changed, 2 insertions(+), 10 deletions(-)

diff --git a/package/MDAnalysis/core/selection.py b/package/MDAnalysis/core/selection.py
index 5fd710d6555..f523590c22b 100644
--- a/package/MDAnalysis/core/selection.py
+++ b/package/MDAnalysis/core/selection.py
@@ -611,15 +611,7 @@ def _apply(self, group):
                         )
                     )
 
-            if np.all(group.dimensions[3:] == 90.0):
-                # Orthogonal version
-                vecs -= box[:3] * np.rint(vecs / box[:3])
-            else:
-                # Triclinic version
-                tribox = group.universe.trajectory.ts.triclinic_dimensions
-                vecs -= tribox[2] * np.rint(vecs[:, 2] / tribox[2][2])[:, None]
-                vecs -= tribox[1] * np.rint(vecs[:, 1] / tribox[1][1])[:, None]
-                vecs -= tribox[0] * np.rint(vecs[:, 0] / tribox[0][0])[:, None]
+            vecs = distances.minimize_vectors(vecs, group.dimensions)
 
         # Deal with each dimension criteria
         mask = None
diff --git a/testsuite/MDAnalysisTests/core/test_atomselections.py b/testsuite/MDAnalysisTests/core/test_atomselections.py
index 499170ba4e1..18c1329b4bb 100644
--- a/testsuite/MDAnalysisTests/core/test_atomselections.py
+++ b/testsuite/MDAnalysisTests/core/test_atomselections.py
@@ -907,7 +907,7 @@ def test_empty_sphzone(self, u):
 
     def test_box(self, u):
         ag = u.select_atoms("box z 2.5 -2.5 resid 1")
-        assert len(ag) == 4241
+        assert len(ag) == 4237
 
     def test_empty_box(self, u):
         ag = u.select_atoms("box z 2.5 -2.5 name NOT_A_NAME")

From 7b3fb0dd388c9b508a40834f4ea59f2b98ec3b6c Mon Sep 17 00:00:00 2001
From: Cloudac7 <812556867@qq.com>
Date: Wed, 8 Nov 2023 11:08:19 +0800
Subject: [PATCH 06/13] fix: set default dmin and dmax for box selection

---
 package/MDAnalysis/core/groups.py             | 20 ++++++++
 package/MDAnalysis/core/selection.py          | 46 +++++++++++--------
 .../source/documentation_pages/selections.rst | 36 ++++++++-------
 .../core/test_atomselections.py               | 16 +++----
 4 files changed, 76 insertions(+), 42 deletions(-)

diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py
index a73aef445dd..6d588f3d33d 100644
--- a/package/MDAnalysis/core/groups.py
+++ b/package/MDAnalysis/core/groups.py
@@ -3111,6 +3111,26 @@ def select_atoms(self, sel, *othersel, periodic=True, rtol=1e-05,
                 radius 5, external radius 10 centered on the COG. In z, the
                 cylinder extends from 10 above the COG to 8 below. Positive
                 values for *zMin*, or negative ones for *zMax*, are allowed.
+            box *dimensions* *d1_min* *d1_max* (*d2_min* *d2_max*) (*d3_min* *d3_max*) *selection*
+                Select all atoms within a box region centered 
+                on the center of geometry (COG) of a given selection.
+                *dimensions* Specifies which dimension(s) to apply 
+                the box selection on. Can be ``x``, ``y``, ``z``, 
+                or any combination like ``xy``, ``yz``, ``zx``, ``xyz`` 
+                (up to 3 characters). *d\*_min*, *d\*_max* are the minimum and 
+                maximum bounds along the first specified dimension. 
+                Positive values are above/right/front of the COG, 
+                negatives are below/left/behind. Should be specified 
+                for each dimension. *selection* specifies the selection 
+                to center the box on. e.g. ``box x -5 10 protein`` 
+                selects a 15 Angstrom box along x centered 
+                on the COG of protein, extending 5 Angstroms 
+                below to 10 Angstroms above. ``box yz -8 10 -10 6 protein`` 
+                selects a box with y extending 8 below to 10 above the COG, 
+                and z extending 10 below to 6 above. 
+                ``box xyz -5 10 -8 6 -7 9 protein`` selects 
+                a 3D box with x -5 to 10, y -8 to 6, and z -7 to 9 relative
+                to the protein COG.
 
         **Connectivity**
 
diff --git a/package/MDAnalysis/core/selection.py b/package/MDAnalysis/core/selection.py
index f523590c22b..6813a2216fd 100644
--- a/package/MDAnalysis/core/selection.py
+++ b/package/MDAnalysis/core/selection.py
@@ -540,7 +540,6 @@ def _apply(self, group):
 class BoxSelection(Selection):
     token = "box"
     precedence = 1
-    index_map = {"x": 0, "y": 1, "z": 2}
     combination = [
         "x",
         "y",
@@ -564,15 +563,25 @@ def __init__(self, parser, tokens):
         super().__init__(parser, tokens)
         self.periodic = parser.periodic
         self.direction = tokens.popleft()
+        self.xmin, self.xmax = None, None
+        self.ymin, self.ymax = None, None
+        self.zmin, self.zmax = None, None
         if self.direction not in self.combination:
             raise ValueError(
                 "The direction '{}' is not valid. Must be combination of {}"
-                "".format(self.direction, list(self.index_map.keys()))
+                "".format(self.direction, ["x", "y", "z"])
             )
         else:
             for d in self.direction:
-                setattr(self, "{}max".format(d), float(tokens.popleft()))
-                setattr(self, "{}min".format(d), float(tokens.popleft()))
+                if d == "x":
+                    self.xmin = float(tokens.popleft())
+                    self.xmax = float(tokens.popleft())
+                elif d == "y":
+                    self.ymin = float(tokens.popleft())
+                    self.ymax = float(tokens.popleft())
+                elif d == "z":
+                    self.zmin = float(tokens.popleft())
+                    self.zmax = float(tokens.popleft())
         self.sel = parser.parse_expression(self.precedence)
 
     @return_empty_on_apply
@@ -582,21 +591,20 @@ def _apply(self, group):
             return group[[]]
         # Calculate vectors between point of interest and our group
         vecs = group.positions - sel.center_of_geometry()
-        range_map = {}
-
-        for d in self.direction:
-            axis_index = self.index_map.get(d)
-            axis_max = self.__getattribute__("{}max".format(d))
-            axis_min = self.__getattribute__("{}min".format(d))
-            range_map[axis_index] = (axis_min, axis_max)
+        range_map = {
+            0: (self.xmin, self.xmax),
+            1: (self.ymin, self.ymax),
+            2: (self.zmin, self.zmax),
+        }
 
         if self.periodic and group.dimensions is not None:
             box = group.dimensions[:3]
 
-            for k, v in range_map.items():
-                axis_index = k
-                axis_min, axis_max = v[0], v[1]
-
+            for idx, limits in range_map.items():
+                axis_index = idx
+                axis_min, axis_max = limits[0], limits[1]
+                if axis_min is None or axis_max is None:
+                    continue
                 axis_height = axis_max - axis_min
                 if axis_height > box[axis_index]:
                     raise NotImplementedError(
@@ -615,11 +623,13 @@ def _apply(self, group):
 
         # Deal with each dimension criteria
         mask = None
-        for k, v in range_map.items():
+        for idx, limits in range_map.items():
+            if limits[0] is None or limits[1] is None:
+                continue
             if mask is None:
-                mask = (vecs[:, k] > v[0]) & (vecs[:, k] < v[1])
+                mask = (vecs[:, idx] > limits[0]) & (vecs[:, idx] < limits[1])
             else:
-                mask &= (vecs[:, k] > v[0]) & (vecs[:, k] < v[1])
+                mask &= (vecs[:, idx] > limits[0]) & (vecs[:, idx] < limits[1])
 
         return group[mask]
 
diff --git a/package/doc/sphinx/source/documentation_pages/selections.rst b/package/doc/sphinx/source/documentation_pages/selections.rst
index 605d21bcd6a..400d612640a 100644
--- a/package/doc/sphinx/source/documentation_pages/selections.rst
+++ b/package/doc/sphinx/source/documentation_pages/selections.rst
@@ -277,22 +277,26 @@ cyzone *externalRadius* *zMax* *zMin* *selection*
        relative to the COG of *selection*, instead of absolute z-values
        in the box.
 
-box *dimension(s)* *d1_Max* *d1_Min* (*d2_Max* *d2_Min*) (*d3_Max* *d3_Min*) *selection*
-    select all atoms around a box centered in the center of geometry (COG)
-    of a given selection, e.g. ``box x 10 -5 protein`` selects the center
-    of geometry of protein, and creates a zone of 15 Angstroms in x axis, 
-    extending from 10 above the COG to 5 below. ``box yz 10 -8 6 -10 protein`` 
-    selects COG of protein, and creates an orthogonal zone extending from 
-    10 above the COG to 8 below in y, and from 6 above the COG to 10 below in z. 
-    ``box xyz 10 -5 6 -8 9 -7 protein`` selects COG of protein, and creates
-    an orthogonal box of extending from 10 above the COG to 5 below in x, 
-    from 6 above the COG to 8 below in y, and from 9 above the COG to 
-    7 below in z. *dimension(s)* can be any or any combination of **x**, 
-    **y**, and **z**, but should not be longer than 3 characters, 
-    e.g. ``x``, ``yz``, ``zx``, ``xyz``. Positive values for *d\*_Min*, 
-    or negative ones for *d\*_Max* are allowed. Number of groups of 
-    *d\*_Max* and *d\*_Min* should be equal to the number of characters in 
-    *dimension(s)*.
+box *dimensions* *d1_min* *d1_max* (*d2_min* *d2_max*) (*d3_min* *d3_max*) *selection*
+    Select all atoms within a box region centered 
+    on the center of geometry (COG) of a given selection.
+    *dimensions* Specifies which dimension(s) to apply 
+    the box selection on. Can be ``x``, ``y``, ``z``, 
+    or any combination like ``xy``, ``yz``, ``zx``, ``xyz`` 
+    (up to 3 characters). *d\*_min*, *d\*_max* are the minimum and 
+    maximum bounds along the first specified dimension. 
+    Positive values are above/right/front of the COG, 
+    negatives are below/left/behind. Should be specified 
+    for each dimension. *selection* specifies the selection 
+    to center the box on. e.g. ``box x -5 10 protein`` 
+    selects a 15 Angstrom box along x centered 
+    on the COG of protein, extending 5 Angstroms 
+    below to 10 Angstroms above. ``box yz -8 10 -10 6 protein`` 
+    selects a box with y extending 8 below to 10 above the COG, 
+    and z extending 10 below to 6 above. 
+    ``box xyz -5 10 -8 6 -7 9 protein`` selects 
+    a 3D box with x -5 to 10, y -8 to 6, and z -7 to 9 relative
+    to the protein COG.
 
 point *x* *y* *z*  *distance*
     selects all atoms within a cutoff of a point in space, make sure
diff --git a/testsuite/MDAnalysisTests/core/test_atomselections.py b/testsuite/MDAnalysisTests/core/test_atomselections.py
index 18c1329b4bb..bfd720ef042 100644
--- a/testsuite/MDAnalysisTests/core/test_atomselections.py
+++ b/testsuite/MDAnalysisTests/core/test_atomselections.py
@@ -249,9 +249,9 @@ def test_point(self, universe):
     @pytest.mark.parametrize(
         "selstr, expected_value",
         [
-            ("box x 2.0 -2.0 index 1281", 418),
-            ("box yz 2.0 -2.0 2.0 -2.0 index 1280", 58),
-            ("box xyz 2.0 -2.0 2.0 -2.0 2.0 -2.0 index 1279", 10),
+            ("box x -2.0 2.0 index 1281", 418),
+            ("box yz -2.0 2.0 -2.0 2.0 index 1280", 58),
+            ("box xyz -2.0 2.0 -2.0 2.0 -2.0 2.0 index 1279", 10),
         ],
     )
     def test_box(self, universe, selstr, expected_value):
@@ -816,7 +816,7 @@ def test_sphzone(self, u, periodic, expected):
 
     @pytest.mark.parametrize("periodic,expected", ([True, 29], [False, 17]))
     def test_box(self, u, periodic, expected):
-        sel = u.select_atoms("box xyz 5 2 10 -5 6 -2 resid 1", periodic=periodic)
+        sel = u.select_atoms("box xyz 2 5 -5 10 -2 6 resid 1", periodic=periodic)
 
         assert len(sel) == expected
 
@@ -824,12 +824,12 @@ def test_box(self, u, periodic, expected):
         "selection,error,expected",
         (
             [
-                "box xyz 10 -5 90 -90 6 -2 resid 1",
+                "box xyz -5 10 -90 90 -2 6 resid 1",
                 NotImplementedError,
                 "The total length of the box selection in y",
             ],
             [
-                "box yyy 10 -5 7 -7 6 -2 resid 1",
+                "box yyy -5 10 -7 7 -2 6 resid 1",
                 SelectionError,
                 "Must be combination of",
             ],
@@ -906,11 +906,11 @@ def test_empty_sphzone(self, u):
         assert len(empty) == 0
 
     def test_box(self, u):
-        ag = u.select_atoms("box z 2.5 -2.5 resid 1")
+        ag = u.select_atoms("box z -2.5 2.5 resid 1")
         assert len(ag) == 4237
 
     def test_empty_box(self, u):
-        ag = u.select_atoms("box z 2.5 -2.5 name NOT_A_NAME")
+        ag = u.select_atoms("box z -2.5 2.5 name NOT_A_NAME")
         assert len(ag) == 0
 
     def test_point_1(self, u):

From 827397ccb5c8b781e6d73a09d40765e0eb4ac266 Mon Sep 17 00:00:00 2001
From: Cloudac7 <812556867@qq.com>
Date: Wed, 8 Nov 2023 11:13:20 +0800
Subject: [PATCH 07/13] doc: format docstring as well as doc for selections

---
 package/MDAnalysis/core/groups.py             | 34 +++++++++---------
 .../source/documentation_pages/selections.rst | 35 ++++++++-----------
 2 files changed, 32 insertions(+), 37 deletions(-)

diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py
index 6d588f3d33d..70d826d7675 100644
--- a/package/MDAnalysis/core/groups.py
+++ b/package/MDAnalysis/core/groups.py
@@ -3111,24 +3111,24 @@ def select_atoms(self, sel, *othersel, periodic=True, rtol=1e-05,
                 radius 5, external radius 10 centered on the COG. In z, the
                 cylinder extends from 10 above the COG to 8 below. Positive
                 values for *zMin*, or negative ones for *zMax*, are allowed.
-            box *dimensions* *d1_min* *d1_max* (*d2_min* *d2_max*) (*d3_min* *d3_max*) *selection*
-                Select all atoms within a box region centered 
+            box *dimensions* *dN_min* *dN_max* *selection*
+                Select all atoms within a box region centered
                 on the center of geometry (COG) of a given selection.
-                *dimensions* Specifies which dimension(s) to apply 
-                the box selection on. Can be ``x``, ``y``, ``z``, 
-                or any combination like ``xy``, ``yz``, ``zx``, ``xyz`` 
-                (up to 3 characters). *d\*_min*, *d\*_max* are the minimum and 
-                maximum bounds along the first specified dimension. 
-                Positive values are above/right/front of the COG, 
-                negatives are below/left/behind. Should be specified 
-                for each dimension. *selection* specifies the selection 
-                to center the box on. e.g. ``box x -5 10 protein`` 
-                selects a 15 Angstrom box along x centered 
-                on the COG of protein, extending 5 Angstroms 
-                below to 10 Angstroms above. ``box yz -8 10 -10 6 protein`` 
-                selects a box with y extending 8 below to 10 above the COG, 
-                and z extending 10 below to 6 above. 
-                ``box xyz -5 10 -8 6 -7 9 protein`` selects 
+                *dimensions* Specifies which dimension(s) to apply
+                the box selection on. Can be ``x``, ``y``, ``z``,
+                or any combination like ``xy``, ``yz``, ``zx``, ``xyz``
+                (up to 3 characters). *dN_min*, *dN_max* are the minimum and
+                maximum bounds along the first specified dimension.
+                Positive values are above/right/front of the COG,
+                negatives are below/left/behind, and should be specified
+                for each dimension. *selection* specifies the selection
+                to center the box on. e.g. ``box x -5 10 protein``
+                selects a 15 Angstrom box along x centered
+                on the COG of protein, extending 5 Angstroms
+                below to 10 Angstroms above. ``box yz -8 10 -10 6 protein``
+                selects a box with y extending 8 below to 10 above the COG,
+                and z extending 10 below to 6 above.
+                ``box xyz -5 10 -8 6 -7 9 protein`` selects
                 a 3D box with x -5 to 10, y -8 to 6, and z -7 to 9 relative
                 to the protein COG.
 
diff --git a/package/doc/sphinx/source/documentation_pages/selections.rst b/package/doc/sphinx/source/documentation_pages/selections.rst
index 400d612640a..196446bc9df 100644
--- a/package/doc/sphinx/source/documentation_pages/selections.rst
+++ b/package/doc/sphinx/source/documentation_pages/selections.rst
@@ -277,26 +277,21 @@ cyzone *externalRadius* *zMax* *zMin* *selection*
        relative to the COG of *selection*, instead of absolute z-values
        in the box.
 
-box *dimensions* *d1_min* *d1_max* (*d2_min* *d2_max*) (*d3_min* *d3_max*) *selection*
-    Select all atoms within a box region centered 
-    on the center of geometry (COG) of a given selection.
-    *dimensions* Specifies which dimension(s) to apply 
-    the box selection on. Can be ``x``, ``y``, ``z``, 
-    or any combination like ``xy``, ``yz``, ``zx``, ``xyz`` 
-    (up to 3 characters). *d\*_min*, *d\*_max* are the minimum and 
-    maximum bounds along the first specified dimension. 
-    Positive values are above/right/front of the COG, 
-    negatives are below/left/behind. Should be specified 
-    for each dimension. *selection* specifies the selection 
-    to center the box on. e.g. ``box x -5 10 protein`` 
-    selects a 15 Angstrom box along x centered 
-    on the COG of protein, extending 5 Angstroms 
-    below to 10 Angstroms above. ``box yz -8 10 -10 6 protein`` 
-    selects a box with y extending 8 below to 10 above the COG, 
-    and z extending 10 below to 6 above. 
-    ``box xyz -5 10 -8 6 -7 9 protein`` selects 
-    a 3D box with x -5 to 10, y -8 to 6, and z -7 to 9 relative
-    to the protein COG.
+box *dimensions* *dN_min* *dN_max* *selection*
+    Select all atoms within a box region centered on the center of 
+    geometry (COG) of a given selection. *dimensions* Specifies 
+    which dimension(s) to apply the box selection on. Can be ``x``, 
+    ``y``, ``z``, or any combination like ``xy``, ``yz``, ``zx``, ``xyz`` 
+    (up to 3 characters). *dN_min*, *dN_max* are the minimum and maximum 
+    bounds along the first specified dimension. Positive values are 
+    above/right/front of the COG, negatives are below/left/behind. 
+    Should be specified for each dimension. *selection* specifies the selection 
+    to center the box on. e.g. ``box x -5 10 protein`` selects a 15 Angstrom 
+    box along x centered on the COG of protein, extending 5 Angstroms below to 
+    10 Angstroms above. ``box yz -8 10 -10 6 protein`` selects a box with 
+    y extending 8 below to 10 above the COG, and z extending 10 below to 6 above. 
+    ``box xyz -5 10 -8 6 -7 9 protein`` selects a 3D box with x -5 to 10, 
+    y -8 to 6, and z -7 to 9 relative to the protein COG.
 
 point *x* *y* *z*  *distance*
     selects all atoms within a cutoff of a point in space, make sure

From 773ef5a729be34c94cc19f6b5736acfd991613d8 Mon Sep 17 00:00:00 2001
From: Cloudac7 <812556867@qq.com>
Date: Fri, 10 Nov 2023 11:04:40 +0800
Subject: [PATCH 08/13] Squashed commit of the following:

commit 8d7f2ce009499430e97dacd6a4e765c2dc6cbd56
Author: Futaki Haduki <812556867@qq.com>
Date:   Thu Nov 9 17:23:57 2023 +0800

    Update package/MDAnalysis/core/groups.py

    Co-authored-by: Rocco Meli <r.meli@bluemail.ch>

commit cfdec5b44f911216ed30fae32fe472debe790afe
Author: Futaki Haduki <812556867@qq.com>
Date:   Thu Nov 9 17:23:44 2023 +0800

    Update package/MDAnalysis/core/groups.py

    Co-authored-by: Rocco Meli <r.meli@bluemail.ch>
---
 package/MDAnalysis/core/groups.py             |  9 ++---
 package/MDAnalysis/core/selection.py          | 39 ++++++++-----------
 .../source/documentation_pages/selections.rst |  6 +--
 3 files changed, 23 insertions(+), 31 deletions(-)

diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py
index 70d826d7675..f50aeca1e18 100644
--- a/package/MDAnalysis/core/groups.py
+++ b/package/MDAnalysis/core/groups.py
@@ -3111,14 +3111,13 @@ def select_atoms(self, sel, *othersel, periodic=True, rtol=1e-05,
                 radius 5, external radius 10 centered on the COG. In z, the
                 cylinder extends from 10 above the COG to 8 below. Positive
                 values for *zMin*, or negative ones for *zMax*, are allowed.
-            box *dimensions* *dN_min* *dN_max* *selection*
+            box *dimensions* *dN_min* *dN_max* [*dN_min* *dN_max*] [*dN_min* *dN_max*] *selection*
                 Select all atoms within a box region centered
                 on the center of geometry (COG) of a given selection.
                 *dimensions* Specifies which dimension(s) to apply
-                the box selection on. Can be ``x``, ``y``, ``z``,
-                or any combination like ``xy``, ``yz``, ``zx``, ``xyz``
-                (up to 3 characters). *dN_min*, *dN_max* are the minimum and
-                maximum bounds along the first specified dimension.
+                the box selection on. Can be ``x``, ``y``, ``z``, ``xy``, 
+                ``yz``, ``xz``, or ``xyz`. *dN_min*, *dN_max* are the minimum 
+                and maximum bounds along each specified dimension.
                 Positive values are above/right/front of the COG,
                 negatives are below/left/behind, and should be specified
                 for each dimension. *selection* specifies the selection
diff --git a/package/MDAnalysis/core/selection.py b/package/MDAnalysis/core/selection.py
index 6813a2216fd..d66a304b246 100644
--- a/package/MDAnalysis/core/selection.py
+++ b/package/MDAnalysis/core/selection.py
@@ -540,24 +540,8 @@ def _apply(self, group):
 class BoxSelection(Selection):
     token = "box"
     precedence = 1
-    combination = [
-        "x",
-        "y",
-        "z",
-        "xy",
-        "xz",
-        "yz",
-        "yx",
-        "zx",
-        "zy",
-        "xyz",
-        "xzy",
-        "yxz",
-        "yzx",
-        "zxy",
-        "zyx",
-    ]
     axis_map = ["x", "y", "z"]
+    axis_set = {"x", "y", "z", "xy", "xz", "yz", "xyz"}
 
     def __init__(self, parser, tokens):
         super().__init__(parser, tokens)
@@ -566,22 +550,31 @@ def __init__(self, parser, tokens):
         self.xmin, self.xmax = None, None
         self.ymin, self.ymax = None, None
         self.zmin, self.zmax = None, None
-        if self.direction not in self.combination:
-            raise ValueError(
-                "The direction '{}' is not valid. Must be combination of {}"
-                "".format(self.direction, ["x", "y", "z"])
-            )
-        else:
+
+        if self.direction in self.axis_set:
             for d in self.direction:
                 if d == "x":
                     self.xmin = float(tokens.popleft())
                     self.xmax = float(tokens.popleft())
+                    if self.xmin > self.xmax:
+                        raise ValueError("xmin must be less than or equal to xmax")
                 elif d == "y":
                     self.ymin = float(tokens.popleft())
                     self.ymax = float(tokens.popleft())
+                    if self.ymin > self.ymax:
+                        raise ValueError("ymin must be less than or equal to ymax")
                 elif d == "z":
                     self.zmin = float(tokens.popleft())
                     self.zmax = float(tokens.popleft())
+                    if self.zmin > self.zmax:
+                        raise ValueError("zmin must be less than or equal to zmax")
+        else:
+            raise ValueError(
+                "The direction '{}' is not valid. "
+                "Must be one of {}"
+                "".format(self.direction, ", ".join(self.axis_set))
+            )
+
         self.sel = parser.parse_expression(self.precedence)
 
     @return_empty_on_apply
diff --git a/package/doc/sphinx/source/documentation_pages/selections.rst b/package/doc/sphinx/source/documentation_pages/selections.rst
index 196446bc9df..9d500e08a27 100644
--- a/package/doc/sphinx/source/documentation_pages/selections.rst
+++ b/package/doc/sphinx/source/documentation_pages/selections.rst
@@ -280,9 +280,9 @@ cyzone *externalRadius* *zMax* *zMin* *selection*
 box *dimensions* *dN_min* *dN_max* *selection*
     Select all atoms within a box region centered on the center of 
     geometry (COG) of a given selection. *dimensions* Specifies 
-    which dimension(s) to apply the box selection on. Can be ``x``, 
-    ``y``, ``z``, or any combination like ``xy``, ``yz``, ``zx``, ``xyz`` 
-    (up to 3 characters). *dN_min*, *dN_max* are the minimum and maximum 
+    which dimension(s) to apply the box selection on. 
+    Can be ``x``, ``y``, ``z``, ``xy``, ``yz``, ``xz``, or ``xyz`. 
+    *dN_min*, *dN_max* are the minimum and maximum 
     bounds along the first specified dimension. Positive values are 
     above/right/front of the COG, negatives are below/left/behind. 
     Should be specified for each dimension. *selection* specifies the selection 

From 04307264c719f8070322a32054008c73f91762fd Mon Sep 17 00:00:00 2001
From: Cloudac7 <812556867@qq.com>
Date: Fri, 10 Nov 2023 11:09:57 +0800
Subject: [PATCH 09/13] fix: rollback unexpected change in unittest

---
 .../core/test_atomselections.py               | 43 +++++--------------
 1 file changed, 11 insertions(+), 32 deletions(-)

diff --git a/testsuite/MDAnalysisTests/core/test_atomselections.py b/testsuite/MDAnalysisTests/core/test_atomselections.py
index bfd720ef042..52e839ace3f 100644
--- a/testsuite/MDAnalysisTests/core/test_atomselections.py
+++ b/testsuite/MDAnalysisTests/core/test_atomselections.py
@@ -1323,38 +1323,17 @@ def test_similarity_selection_icodes(u_pdb_icodes, selection, n_atoms):
     assert len(sel.atoms) == n_atoms
 
 
-@pytest.mark.parametrize(
-    "selection",
-    [
-        "all",
-        "protein",
-        "backbone",
-        "nucleic",
-        "nucleicbackbone",
-        "name O",
-        "name N*",
-        "resname stuff",
-        "resname ALA",
-        "type O",
-        "index 0",
-        "index 1",
-        "bynum 1-10",
-        "segid SYSTEM",
-        "resid 163",
-        "resid 1-10",
-        "resnum 2",
-        "around 10 resid 1",
-        "point 0 0 0 10",
-        "sphzone 10 resid 1",
-        "sphlayer 0 10 index 1",
-        "cyzone 15 4 -8 index 0",
-        "cylayer 5 10 10 -8 index 1",
-        "prop abs z <= 100",
-        "byres index 0",
-        "same resid as index 0",
-        "box xz 3 2 4 -5 index 0",
-    ],
-)
+@pytest.mark.parametrize('selection', [
+    'all', 'protein', 'backbone', 'nucleic', 'nucleicbackbone',
+    'name O', 'name N*', 'resname stuff', 'resname ALA', 'type O',
+    'index 0', 'index 1', 'bynum 1-10',
+    'segid SYSTEM', 'resid 163', 'resid 1-10', 'resnum 2',
+    'around 10 resid 1', 'point 0 0 0 10', 'sphzone 10 resid 1',
+    'sphlayer 0 10 index 1', 'cyzone 15 4 -8 index 0',
+    'cylayer 5 10 10 -8 index 1', 'prop abs z <= 100',
+    'byres index 0', 'same resid as index 0',
+    'box xz 3 2 4 -5 index 0',
+])
 def test_selections_on_empty_group(u_pdb_icodes, selection):
     ag = u_pdb_icodes.atoms[[]].select_atoms(selection)
     assert len(ag) == 0

From 75928d48a5577dec726046fef0b0caf15e5043d7 Mon Sep 17 00:00:00 2001
From: Cloudac7 <812556867@qq.com>
Date: Tue, 23 Jul 2024 16:06:34 +0800
Subject: [PATCH 10/13] test: fix wrong error message

---
 testsuite/MDAnalysisTests/core/test_atomselections.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/testsuite/MDAnalysisTests/core/test_atomselections.py b/testsuite/MDAnalysisTests/core/test_atomselections.py
index 233e7f02794..f68cd0e2553 100644
--- a/testsuite/MDAnalysisTests/core/test_atomselections.py
+++ b/testsuite/MDAnalysisTests/core/test_atomselections.py
@@ -835,9 +835,9 @@ def test_box(self, u, periodic, expected):
             [
                 "box yyy -5 10 -7 7 -2 6 resid 1",
                 SelectionError,
-                "Must be combination of",
+                "Must be one of",
             ],
-            ["box a 10 -5 resid 1", SelectionError, "Must be combination of"],
+            ["box a 10 -5 resid 1", SelectionError, "Must be one of"],
         ),
     )
     def test_box_error(self, u, selection, error, expected):

From 37b3bf4e90ed4ee354449d6b89c258f8a93fc4c8 Mon Sep 17 00:00:00 2001
From: Cloudac7 <812556867@qq.com>
Date: Thu, 25 Jul 2024 11:08:21 +0800
Subject: [PATCH 11/13] refactor: rename the selection as `zone`; feat: remove
 check on unit cell for `zone`

---
 package/MDAnalysis/core/groups.py             | 18 +++++-----
 package/MDAnalysis/core/selection.py          | 28 +++-------------
 .../source/documentation_pages/selections.rst | 16 ++++-----
 .../core/test_atomselections.py               | 33 +++++++++----------
 4 files changed, 38 insertions(+), 57 deletions(-)

diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py
index ec9b66b373f..ebcab33fc93 100644
--- a/package/MDAnalysis/core/groups.py
+++ b/package/MDAnalysis/core/groups.py
@@ -3271,24 +3271,24 @@ def select_atoms(self, sel, *othersel, periodic=True, rtol=1e-05,
                 radius 5, external radius 10 centered on the COG. In z, the
                 cylinder extends from 10 above the COG to 8 below. Positive
                 values for *zMin*, or negative ones for *zMax*, are allowed.
-            box *dimensions* *dN_min* *dN_max* [*dN_min* *dN_max*] [*dN_min* *dN_max*] *selection*
-                Select all atoms within a box region centered
+            zone *dimensions* *dN_min* *dN_max* [*dN_min* *dN_max*] [*dN_min* *dN_max*] *selection*
+                Select all atoms within a zone in shape of an orthognol box centered
                 on the center of geometry (COG) of a given selection.
                 *dimensions* Specifies which dimension(s) to apply
-                the box selection on. Can be ``x``, ``y``, ``z``, ``xy``, 
+                the zone selection on. Can be ``x``, ``y``, ``z``, ``xy``, 
                 ``yz``, ``xz``, or ``xyz`. *dN_min*, *dN_max* are the minimum 
                 and maximum bounds along each specified dimension.
                 Positive values are above/right/front of the COG,
                 negatives are below/left/behind, and should be specified
                 for each dimension. *selection* specifies the selection
-                to center the box on. e.g. ``box x -5 10 protein``
-                selects a 15 Angstrom box along x centered
+                to center the zone on. e.g. ``zone x -5 10 protein``
+                selects a 15 Angstrom zone along x centered
                 on the COG of protein, extending 5 Angstroms
-                below to 10 Angstroms above. ``box yz -8 10 -10 6 protein``
-                selects a box with y extending 8 below to 10 above the COG,
+                below to 10 Angstroms above. ``zone yz -8 10 -10 6 protein``
+                selects a zone with y extending 8 below to 10 above the COG,
                 and z extending 10 below to 6 above.
-                ``box xyz -5 10 -8 6 -7 9 protein`` selects
-                a 3D box with x -5 to 10, y -8 to 6, and z -7 to 9 relative
+                ``zone xyz -5 10 -8 6 -7 9 protein`` selects
+                a 3D zone with x -5 to 10, y -8 to 6, and z -7 to 9 relative
                 to the protein COG.
 
         **Connectivity**
diff --git a/package/MDAnalysis/core/selection.py b/package/MDAnalysis/core/selection.py
index d66a304b246..5dc110cd463 100644
--- a/package/MDAnalysis/core/selection.py
+++ b/package/MDAnalysis/core/selection.py
@@ -537,8 +537,10 @@ def _apply(self, group):
         return group[np.asarray(indices, dtype=np.int64)]
 
 
-class BoxSelection(Selection):
-    token = "box"
+class ZoneSelection(Selection):
+    from MDAnalysis.lib.mdamath import triclinic_vectors
+
+    token = 'zone'
     precedence = 1
     axis_map = ["x", "y", "z"]
     axis_set = {"x", "y", "z", "xy", "xz", "yz", "xyz"}
@@ -591,27 +593,7 @@ def _apply(self, group):
         }
 
         if self.periodic and group.dimensions is not None:
-            box = group.dimensions[:3]
-
-            for idx, limits in range_map.items():
-                axis_index = idx
-                axis_min, axis_max = limits[0], limits[1]
-                if axis_min is None or axis_max is None:
-                    continue
-                axis_height = axis_max - axis_min
-                if axis_height > box[axis_index]:
-                    raise NotImplementedError(
-                        "The total length of the box selection in {} ({:.3f}) "
-                        "is larger than the unit cell's {} dimension ({:.3f}). "
-                        "Can only do selections where it is smaller or equal."
-                        "".format(
-                            self.axis_map[axis_index],
-                            axis_height,
-                            self.axis_map[axis_index],
-                            box[axis_index],
-                        )
-                    )
-
+            # TODO: a more general judgement
             vecs = distances.minimize_vectors(vecs, group.dimensions)
 
         # Deal with each dimension criteria
diff --git a/package/doc/sphinx/source/documentation_pages/selections.rst b/package/doc/sphinx/source/documentation_pages/selections.rst
index 9d500e08a27..cfaa71b3596 100644
--- a/package/doc/sphinx/source/documentation_pages/selections.rst
+++ b/package/doc/sphinx/source/documentation_pages/selections.rst
@@ -277,20 +277,20 @@ cyzone *externalRadius* *zMax* *zMin* *selection*
        relative to the COG of *selection*, instead of absolute z-values
        in the box.
 
-box *dimensions* *dN_min* *dN_max* *selection*
-    Select all atoms within a box region centered on the center of 
-    geometry (COG) of a given selection. *dimensions* Specifies 
-    which dimension(s) to apply the box selection on. 
+zone *dimensions* *dN_min* *dN_max* *selection*
+    Select all atoms within a zone in shape of an orthognol box 
+    centered on the center of geometry (COG) of a given selection. 
+    *dimensions* Specifies which dimension(s) to apply the zone selection on. 
     Can be ``x``, ``y``, ``z``, ``xy``, ``yz``, ``xz``, or ``xyz`. 
     *dN_min*, *dN_max* are the minimum and maximum 
     bounds along the first specified dimension. Positive values are 
     above/right/front of the COG, negatives are below/left/behind. 
     Should be specified for each dimension. *selection* specifies the selection 
-    to center the box on. e.g. ``box x -5 10 protein`` selects a 15 Angstrom 
-    box along x centered on the COG of protein, extending 5 Angstroms below to 
-    10 Angstroms above. ``box yz -8 10 -10 6 protein`` selects a box with 
+    to center the zone on. e.g. ``zone x -5 10 protein`` selects a 15 Angstrom 
+    zone along x centered on the COG of protein, extending 5 Angstroms below to 
+    10 Angstroms above. ``zone yz -8 10 -10 6 protein`` selects a zone with 
     y extending 8 below to 10 above the COG, and z extending 10 below to 6 above. 
-    ``box xyz -5 10 -8 6 -7 9 protein`` selects a 3D box with x -5 to 10, 
+    ``zone xyz -5 10 -8 6 -7 9 protein`` selects a 3D zone with x -5 to 10, 
     y -8 to 6, and z -7 to 9 relative to the protein COG.
 
 point *x* *y* *z*  *distance*
diff --git a/testsuite/MDAnalysisTests/core/test_atomselections.py b/testsuite/MDAnalysisTests/core/test_atomselections.py
index f68cd0e2553..2018f901aa4 100644
--- a/testsuite/MDAnalysisTests/core/test_atomselections.py
+++ b/testsuite/MDAnalysisTests/core/test_atomselections.py
@@ -250,17 +250,17 @@ def test_point(self, universe):
     @pytest.mark.parametrize(
         "selstr, expected_value",
         [
-            ("box x -2.0 2.0 index 1281", 418),
-            ("box yz -2.0 2.0 -2.0 2.0 index 1280", 58),
-            ("box xyz -2.0 2.0 -2.0 2.0 -2.0 2.0 index 1279", 10),
+            ("zone x -2.0 2.0 index 1281", 418),
+            ("zone yz -2.0 2.0 -2.0 2.0 index 1280", 58),
+            ("zone xyz -2.0 2.0 -2.0 2.0 -2.0 2.0 index 1279", 10),
         ],
     )
-    def test_box(self, universe, selstr, expected_value):
+    def test_zone(self, universe, selstr, expected_value):
         sel = universe.select_atoms(selstr)
         assert_equal(len(sel), expected_value)
 
-    def test_empty_box(self, universe):
-        empty = universe.select_atoms("box y 10 -10 name NOT_A_NAME")
+    def test_empty_zone(self, universe):
+        empty = universe.select_atoms("zone y -10 10 name NOT_A_NAME")
         assert_equal(len(empty), 0)
 
     def test_prop(self, universe):
@@ -819,8 +819,8 @@ def test_sphzone(self, u, periodic, expected):
         assert len(sel) == expected
 
     @pytest.mark.parametrize("periodic,expected", ([True, 29], [False, 17]))
-    def test_box(self, u, periodic, expected):
-        sel = u.select_atoms("box xyz 2 5 -5 10 -2 6 resid 1", periodic=periodic)
+    def test_zone(self, u, periodic, expected):
+        sel = u.select_atoms("zone xyz 2 5 -5 10 -2 6 resid 1", periodic=periodic)
 
         assert len(sel) == expected
 
@@ -828,19 +828,18 @@ def test_box(self, u, periodic, expected):
         "selection,error,expected",
         (
             [
-                "box xyz -5 10 -90 90 -2 6 resid 1",
-                NotImplementedError,
-                "The total length of the box selection in y",
-            ],
-            [
-                "box yyy -5 10 -7 7 -2 6 resid 1",
+                "zone yyy -5 10 -7 7 -2 6 resid 1",
                 SelectionError,
                 "Must be one of",
             ],
-            ["box a 10 -5 resid 1", SelectionError, "Must be one of"],
+            [
+                "zone a -10 5 resid 1", 
+                SelectionError, 
+                "Must be one of"
+            ],
         ),
     )
-    def test_box_error(self, u, selection, error, expected):
+    def test_zone_error(self, u, selection, error, expected):
         with pytest.raises(error) as excinfo:
             u.select_atoms(selection)
         exec_msg = str(excinfo.value)
@@ -1336,7 +1335,7 @@ def test_similarity_selection_icodes(u_pdb_icodes, selection, n_atoms):
     'sphlayer 0 10 index 1', 'cyzone 15 4 -8 index 0',
     'cylayer 5 10 10 -8 index 1', 'prop abs z <= 100',
     'byres index 0', 'same resid as index 0',
-    'box xz 3 2 4 -5 index 0',
+    'zone xz 2 3 -5 4 index 0',
 ])
 def test_selections_on_empty_group(u_pdb_icodes, selection):
     ag = u_pdb_icodes.atoms[[]].select_atoms(selection)

From 3fa7de3f33c4667b2b49cd10958c68e83a3f292c Mon Sep 17 00:00:00 2001
From: Cloudac7 <812556867@qq.com>
Date: Thu, 25 Jul 2024 11:36:10 +0800
Subject: [PATCH 12/13] test: fix typo

---
 testsuite/MDAnalysisTests/core/test_atomselections.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/testsuite/MDAnalysisTests/core/test_atomselections.py b/testsuite/MDAnalysisTests/core/test_atomselections.py
index 2018f901aa4..b8ceda18719 100644
--- a/testsuite/MDAnalysisTests/core/test_atomselections.py
+++ b/testsuite/MDAnalysisTests/core/test_atomselections.py
@@ -908,12 +908,12 @@ def test_empty_sphzone(self, u):
         empty = u.select_atoms('sphzone 5.0 name NOT_A_NAME')
         assert len(empty) == 0
 
-    def test_box(self, u):
-        ag = u.select_atoms("box z -2.5 2.5 resid 1")
+    def test_zone(self, u):
+        ag = u.select_atoms("zone z -2.5 2.5 resid 1")
         assert len(ag) == 4237
 
-    def test_empty_box(self, u):
-        ag = u.select_atoms("box z -2.5 2.5 name NOT_A_NAME")
+    def test_empty_zone(self, u):
+        ag = u.select_atoms("zone z -2.5 2.5 name NOT_A_NAME")
         assert len(ag) == 0
 
     def test_point_1(self, u):

From 3f4f6199ce96c2ba7c0dc06974bbf43a139b0501 Mon Sep 17 00:00:00 2001
From: Cloudac7 <812556867@qq.com>
Date: Thu, 25 Jul 2024 12:03:25 +0800
Subject: [PATCH 13/13] test: add tests of limits for `zone`

---
 .../MDAnalysisTests/core/test_atomselections.py   | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/testsuite/MDAnalysisTests/core/test_atomselections.py b/testsuite/MDAnalysisTests/core/test_atomselections.py
index b8ceda18719..80906b43ab0 100644
--- a/testsuite/MDAnalysisTests/core/test_atomselections.py
+++ b/testsuite/MDAnalysisTests/core/test_atomselections.py
@@ -837,6 +837,21 @@ def test_zone(self, u, periodic, expected):
                 SelectionError, 
                 "Must be one of"
             ],
+            [
+                "zone x 10 -5 resid 1", 
+                SelectionError, 
+                "xmin must be less than or equal to xmax"
+            ],
+            [
+                "zone y 7 -7 resid 1", 
+                SelectionError, 
+                "ymin must be less than or equal to ymax"
+            ],
+            [
+                "zone z 6 -2 resid 1", 
+                SelectionError, 
+                "zmin must be less than or equal to zmax"
+            ],
         ),
     )
     def test_zone_error(self, u, selection, error, expected):