adding element attribute to txyz parser (#3826)

* adding element attribute to txyz parser

* adding elements when names is valid only

* update docstring and change log

* Update TXYZParser.py

* Update TXYZParser.py

* Update TXYZParser.py

* Update TXYZParser.py

* Update TXYZParser.py

* Update TXYZParser.py

* Update TXYZParser.py

* Update CHANGELOG

* Apply suggestions from code review

Co-authored-by: Jonathan Barnoud <[email protected]>

* Apply suggestions from code review

Co-authored-by: Jonathan Barnoud <[email protected]>

Co-authored-by: Jonathan Barnoud <[email protected]>

package/CHANGELOG

@@ -13,7 +13,6 @@ The rules for this file:
   * release numbers follow "Semantic Versioning" http://semver.org
 
 ------------------------------------------------------------------------------
-
 ??/??/?? IAlibay, Luthaf, hmacdope, rafaelpap, jbarnoud, BFedder, aya9aladdin
 
  * 2.4.0
@@ -53,6 +52,7 @@ Changes
   * The "AMBER" entry in setup.py's extra_requires has now been removed. Please
     use `pip install ./package[extra_formats]` instead (PR #3810)
   * `Universe.empty` emmits less warnings (PR #3814)
+  * adding element attribute to TXYZParser if all atom names are valid element symbols (PR #3826)
 
 Deprecations
 

package/MDAnalysis/topology/TXYZParser.py

@@ -45,8 +45,10 @@
 
 import itertools
 import numpy as np
+import warnings
 
 from . import guessers
+from .tables import SYMB2Z
 from ..lib.util import openany
 from .base import TopologyReaderBase
 from ..core.topology import Topology
@@ -59,6 +61,7 @@
     Resids,
     Resnums,
     Segids,
+    Elements,
 )
 
 
@@ -69,8 +72,11 @@ class TXYZParser(TopologyReaderBase):
 
     - Atomnames
     - Atomtypes
+    - Elements (if all atom names are element symbols)
 
     .. versionadded:: 0.17.0
+    .. versionchanged:: 2.4.0
+       Adding the `Element` attribute if all names are valid element symbols.
     """
     format = ['TXYZ', 'ARC']
 
@@ -126,7 +132,14 @@ def parse(self, **kwargs):
                  Resnums(np.array([1])),
                  Segids(np.array(['SYSTEM'], dtype=object)),
                  ]
-
+        if all(n.capitalize() in SYMB2Z for n in names):
+            attrs.append(Elements(np.array(names, dtype=object)))
+
+        else:
+            warnings.warn("Element information is missing, elements attribute "
+                          "will not be populated. If needed these can be "
+                          "guessed using MDAnalysis.topology.guessers.")
+
         top = Topology(natoms, 1, 1,
                        attrs=attrs)
 

testsuite/MDAnalysisTests/topology/test_txyz.py

@@ -22,15 +22,16 @@
 #
 import MDAnalysis as mda
 import pytest
+import numpy as np
 
 from MDAnalysisTests.topology.base import ParserBase
-from MDAnalysisTests.datafiles import TXYZ, ARC
-
+from MDAnalysisTests.datafiles import TXYZ, ARC, ARC_PBC
+from numpy.testing import assert_equal
 
 class TestTXYZParser(ParserBase):
     parser = mda.topology.TXYZParser.TXYZParser
     guessed_attrs = ['masses']
-    expected_attrs = ['ids', 'names', 'bonds', 'types']
+    expected_attrs = ['ids', 'names', 'bonds', 'types', 'elements']
     expected_n_residues = 1
     expected_n_atoms = 9
     expected_n_segments = 1
@@ -51,3 +52,26 @@ def test_atom_type_type(self, top):
         types = top.types.values
         type_is_str = [isinstance(atom_type, str) for atom_type in types]
         assert all(type_is_str)
+
+def test_TXYZ_elements():
+    """The test checks whether elements attribute are assigned
+    properly given a TXYZ file with valid elements record.
+    """
+    u = mda.Universe(TXYZ, format='TXYZ')
+    element_list = np.array(['C', 'H', 'H', 'O', 'H', 'C', 'H', 'H', 'H'], dtype=object)
+    assert_equal(u.atoms.elements, element_list)
+
+
+def test_missing_elements_noattribute():
+    """Check that:
+
+    1) a warning is raised if elements are missing
+    2) the elements attribute is not set
+    """
+    wmsg = ("Element information is missing, elements attribute will not be "
+            "populated")
+    with pytest.warns(UserWarning, match=wmsg):
+        u = mda.Universe(ARC_PBC)
+    with pytest.raises(AttributeError):
+        _ = u.atoms.elements
+