taking a swing at #3825

package/CHANGELOG

@@ -13,7 +13,6 @@ The rules for this file:
   * release numbers follow "Semantic Versioning" http://semver.org
 
 ------------------------------------------------------------------------------
-
 ??/??/?? IAlibay, pgbarletta, mglagolev, hmacdope, manuel.nuno.melo, chrispfae, 
          ooprathamm, MeetB7, BFedder
  * 2.5.0
@@ -31,6 +30,9 @@ Enhancements
   * AuxReaders are now pickle-able and copy-able (Issue #1785, PR #3887)
   * Add pickling support for Atom, Residue, Segment, ResidueGroup 
     and SegmentGroup. (PR #3953)
+* PDBReader now populates ts.data['tempfactor'] with the tempfactor for
+  each atom *for each frame*.  Note, this does not affect the topology (i.e.
+  `AtomGroup.tempfactors` is not dynamically updated. (Issue #3825)
 
 Changes
   * As per NEP29 the minimum supported NumPy version has been raised to 1.21

package/MDAnalysis/coordinates/PDB.py

@@ -242,6 +242,9 @@ class PDBReader(base.ReaderBase):
     .. versionchanged:: 1.0.0
        Raise user warning for CRYST1_ record with unitary valuse
        (cubic box with sides of 1 Å) and do not set cell dimensions.
+    .. versionchanged:: 2.5.0
+       Tempfactors (aka bfactors) are now read into the ts.data dictionary each
+       frame.  Occupancies are also read into this dictionary.
     """
     format = ['PDB', 'ENT']
     units = {'time': None, 'length': 'Angstrom'}
@@ -397,6 +400,7 @@ def _read_frame(self, frame):
 
         pos = 0
         occupancy = np.ones(self.n_atoms)
+        tempfactor = np.zeros(self.n_atoms)
 
         # Seek to start and read until start of next frame
         self._pdbfile.seek(start)
@@ -414,6 +418,10 @@ def _read_frame(self, frame):
                 except ValueError:
                     # Be tolerant for ill-formated or empty occupancies
                     pass
+                try:
+                    tempfactor[pos] = line[60:66]
+                except ValueError:
+                    pass
                 pos += 1
             elif line[:6] == 'CRYST1':
                 # does an implicit str -> float conversion
@@ -455,6 +463,8 @@ def _read_frame(self, frame):
                 self.convert_pos_from_native(self.ts.dimensions[:3])
         self.ts.frame = frame
         self.ts.data['occupancy'] = occupancy
+        self.ts.data['tempfactor'] = tempfactor
+
         return self.ts
 
     def close(self):

testsuite/MDAnalysisTests/coordinates/test_pdb.py

@@ -31,7 +31,7 @@
 from MDAnalysisTests.coordinates.reference import (RefAdKSmall,
                                                    RefAdK)
 from MDAnalysisTests.datafiles import (PDB, PDB_small, PDB_multiframe,
-                                       PDB_full,
+                                       PDB_full, PDB_varying,
                                        XPDB_small, PSF, DCD, CONECT, CRD,
                                        INC_PDB, PDB_xlserial, ALIGN, ENT,
                                        PDB_cm, PDB_cm_gz, PDB_cm_bz2,
@@ -965,6 +965,31 @@ def test_first_residue(self, universe):
         assert len(universe.residues[0].atoms) == 19
 
 
+class TestPDBVaryingOccTmp:
+    @staticmethod
+    @pytest.fixture(scope='class')
+    def u():
+        return mda.Universe(PDB_varying)
+
+    def test_ts_data_keys(self, u):
+        ts = u.trajectory.ts
+
+        assert 'occupancy' in ts.data
+        assert 'tempfactor' in ts.data
+
+    def test_varying_occupancy(self, u):
+        u.trajectory[0]
+        assert u.trajectory.ts.data['occupancy'][0] == pytest.approx(1.0)
+        u.trajectory[1]
+        assert u.trajectory.ts.data['occupancy'][0] == pytest.approx(0.9)
+
+    def test_varying_tempfactor(self, u):
+        u.trajectory[0]
+        assert u.trajectory.ts.data['tempfactor'][0] == pytest.approx(23.44)
+        u.trajectory[1]
+        assert u.trajectory.ts.data['tempfactor'][0] == pytest.approx(24.44)
+
+
 class TestIncompletePDB(object):
     """Tests for Issue #396
 

testsuite/MDAnalysisTests/data/varying_occ_tmp.pdb

@@ -0,0 +1,10 @@
+HEADER    This is maybe what a protein looks like from space
+REMARK    Contains varying occupancies and tempfactors for a single atom
+MODEL 1
+CRYST1  216.489  216.489  216.489  90.00  90.00  90.00 P 1           1
+ATOM      1  N   PRO A   1       0.401  40.138  17.790  1.00 23.44           N
+ENDMDL
+MODEL 2
+ATOM      1  N   PRO A   1       1.401  41.138  18.790  0.90 24.44           N
+ENDMDL
+END

testsuite/MDAnalysisTests/datafiles.py

@@ -55,6 +55,7 @@
     "PDB_conect2TER",  # Conect record to a TER entry (Issue 936)
     "PDB_singleconect",  # Conect record with one entry (Issue 937)
     "PDB_icodes",  # stripped down version of 1osm, has icodes!
+    "PDB_varying",  # varying occupancies and tempfactors
     "XPDB_small",
     "PDB_full",   # PDB 4E43 (full HEADER, TITLE, COMPND, REMARK, altloc)
     "ALIGN",  # Various way to align atom names in PDB files
@@ -317,6 +318,7 @@
 PDB_conect2TER = resource_filename(__name__, 'data/CONECT2TER.pdb')
 PDB_singleconect = resource_filename(__name__, 'data/SINGLECONECT.pdb')
 PDB_icodes = resource_filename(__name__, 'data/1osm.pdb.gz')
+PDB_varying = resource_filename(__name__, 'data/varying_occ_tmp.pdb')
 PDB_CRYOEM_BOX = resource_filename(__name__, 'data/5a7u.pdb')
 PDB_CHECK_RIGHTHAND_PA = resource_filename(__name__, 'data/6msm.pdb.bz2')
 FHIAIMS = resource_filename(__name__, 'data/fhiaims.in')