chore: release v1.4.1

PQAnalysis/io/info_file_reader.py

@@ -117,26 +117,30 @@
 
             entry_counter = 0
 
-            for line in lines[3:-2]:
-                line = line.split()
+            for raw_line in lines[3:]:
+                if not raw_line.strip():
+                    continue
 
-                if len(line) == 8:
+                if raw_line.lstrip().startswith("-"):
+                    break
 
-                    info[line[1]] = entry_counter
-                    units[line[1]] = line[3]
-                    entry_counter += 1
-
-                    info[line[4]] = entry_counter
-                    units[line[4]] = line[6]
-                    entry_counter += 1
-
-                else:
+                line = raw_line.split()
 
+                if len(line) not in (5, 8):
                     self.logger.error(
                         f"Info file {self.filename} is not in PQ format.",
                         exception=MDEngineFormatError
                     )
 
+                info[line[1]] = entry_counter
+                units[line[1]] = line[3]
+                entry_counter += 1
+
+                if len(line) == 8:
+                    info[line[4]] = entry_counter
+                    units[line[4]] = line[6]
+                    entry_counter += 1
+
         return info, units
 
     def _read_qmcfc(self) -> Tuple[Dict, None]:

tests/data/readEnergyFile/qmmm.en

@@ -0,0 +1 @@
+         1	    330.958920766485	   1687.087653155208	 -38105.791953033971	 -20573.206966944799	     25.000000000000	   3946.119527788006	      0.000000000000	 -26084.300634669558	   4605.596120792379	                   0	         1.75899e-14	     0.71956

tests/data/readEnergyFile/qmmm.info

@@ -0,0 +1,11 @@
+-----------------------------------------------------------------------------------------
+|                                     PQ info file                                      |
+-----------------------------------------------------------------------------------------
+|   SIMULATION-TIME         0.00200 ps       TEMPERATURE           330.95892 K          |
+|   PRESSURE             1687.08765 bar      E(TOT)             -38105.79195 kcal/mol   |
+|   E(QM)              -20573.20697 kcal/mol N(QM-ATOMS)            25.00000 -          |
+|   E(KIN)               3946.11953 kcal/mol E(INTRA)                0.00000 kcal/mol   |
+|   E(COUL)            -26084.30063 kcal/mol E(NON-COUL)          4605.59612 kcal/mol   |
+|   N(SM-MOL)                     0 -                                                   |
+|   MOMENTUM                1.8e-14 amuA/fs  LOOPTIME                0.71956 s          |
+-----------------------------------------------------------------------------------------

tests/io/test_energyFileReader.py

@@ -153,6 +153,16 @@ def test_read(self, test_with_data_dir):
         assert energy.info_given == True
         assert energy.units_given == True
 
+        reader = EnergyFileReader("qmmm.en")
+        energy = reader.read()
+        assert energy.data.shape == (13, 1)
+        assert len(energy.info) == 13
+        assert energy.info["N(SM-MOL)"] == 10
+        assert energy.units["N(SM-MOL)"] == "-"
+        assert energy.data[energy.info["N(SM-MOL)"], 0] == 0
+        assert energy.info["MOMENTUM"] == 11
+        assert energy.info["LOOPTIME"] == 12
+
         reader = EnergyFileReader("md-01_noinfo.en")
         energy = reader.read()
         assert np.allclose(energy.data, data_ref)

tests/io/test_infoFileReader.py

@@ -117,3 +117,18 @@ def test_read(test_with_data_dir):
     assert str(
         exception.value
     ) == "Info file md-01.info is not in qmcfc format."
+
+
+@pytest.mark.parametrize("example_dir", ["readEnergyFile"], indirect=False)
+def test_read_pq_info_with_single_entry_row(test_with_data_dir):
+    reader = InfoFileReader("qmmm.info")
+
+    info, units = reader.read()
+
+    assert len(info) == 13
+    assert info["N(SM-MOL)"] == 10
+    assert units["N(SM-MOL)"] == "-"
+    assert info["MOMENTUM"] == 11
+    assert units["MOMENTUM"] == "amuA/fs"
+    assert info["LOOPTIME"] == 12
+    assert units["LOOPTIME"] == "s"