Finish fluctmatch-3.0.1

tclick · Oct 14, 2017 · 6237338 · 6237338
2 parents 73ee031 + f584058
commit 6237338
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Showing 4 changed files with 45 additions and 17 deletions.
diff --git a/src/fluctmatch/coordinates/COR.py b/src/fluctmatch/coordinates/COR.py
@@ -77,16 +77,16 @@ class CORWriter(CRD.CRDWriter):
         # crdtype = "extended"
         # fortran_format = "(2I10,2X,A8,2X,A8,3F20.10,2X,A8,2X,A8,F20.10)"
         ATOM_EXT=(
-            "{serial:10d}{totRes:10d}  {resname:<8.8s}  {name:<8.8s}""
-            "{pos[0]:20.10f}{pos[1]:20.10f}{pos[2]:20.10f}  ""
+            "{serial:10d}{totRes:10d}  {resname:<8.8s}  {name:<8.8s}"
+            "{pos[0]:20.10f}{pos[1]:20.10f}{pos[2]:20.10f}  "
             "{chainID:<8.8s}  {resSeq:<8d}{tempfactor:20.10f}\n"
         ),
         NUMATOMS_EXT="{0:10d} EXT\n",
         # crdtype = "standard"
         # fortran_format = "(2I5,1X,A4,1X,A4,3F10.5,1X,A4,1X,A4,F10.5)"
         ATOM=(
-            "{serial:5d}{totRes:5d} {resname:<4.4s} {name:<4.4s}""
-            "{pos[0]:10.5f}{pos[1]:10.5f}{pos[2]:10.5f} ""
+            "{serial:5d}{totRes:5d} {resname:<4.4s} {name:<4.4s}"
+            "{pos[0]:10.5f}{pos[1]:10.5f}{pos[2]:10.5f} "
             "{chainID:<4.4s} {resSeq:<4d}{tempfactor:10.5f}\n"
         ),
         TITLE="* FRAME {frame} FROM {where}\n",

diff --git a/src/fluctmatch/models/trajectory.py b/src/fluctmatch/models/trajectory.py
@@ -145,18 +145,24 @@ def _fill_ts(self, other_ts):
             residues, viewitems(self._mapping)
         )
         if self.ts.has_velocities:
-            self.ts._velocities[:] = [
-                res.select_atoms(selection).velocities.sum()
-                for res, (_, selection) in residue_selection
-                if res.select_atoms(selection)
-            ]
+            try:
+                self.ts._velocities[:] = [
+                    res.select_atoms(selection).velocities.sum()
+                    for res, (_, selection) in residue_selection
+                    if res.select_atoms(selection)
+                ]
+            except ValueError:
+                pass
 
         if self.ts.has_forces:
-            self.ts._forces[:] = [
-                res.select_atoms(selection).forces.sum()
-                for res, (_, selection) in residue_selection
-                if res.select_atoms(selection)
-            ]
+            try:
+                self.ts._forces[:] = [
+                    res.select_atoms(selection).forces.sum()
+                    for res, (_, selection) in residue_selection
+                    if res.select_atoms(selection)
+                ]
+            except ValueError:
+                pass
 
     def _reopen(self):
         # Rewind my reference trajectory

diff --git a/tests/fluctmatch/test_utils.py b/tests/fluctmatch/test_utils.py
@@ -53,7 +53,7 @@ def test_average_bonds():
         universe.bonds.bonds()
         for _ in universe.trajectory
     ], axis=0)
-    bonds = fmutils.BondStats(universe, func="mean").run().result
+    (bonds, ) = fmutils.BondStats(universe, func="mean").run().result
     testing.assert_allclose(
         bonds["r_IJ"],
         avg_bonds,
@@ -67,9 +67,32 @@ def test_bond_fluctuation():
         universe.bonds.bonds()
         for _ in universe.trajectory
     ], axis=0)
-    bonds = fmutils.BondStats(universe, func="std").run().result
+    (bonds, ) = fmutils.BondStats(universe, func="std").run().result
     testing.assert_allclose(
         bonds["r_IJ"],
         bond_fluct,
         err_msg=native_str("Bond fluctuations don't match."),
     )
+
+
+def test_bond_all_stats():
+    universe = mda.Universe(TPR, XTC)
+    bond_average = np.mean([
+        universe.bonds.bonds()
+        for _ in universe.trajectory
+    ], axis=0)
+    bond_fluct = np.std([
+        universe.bonds.bonds()
+        for _ in universe.trajectory
+    ], axis=0)
+    (average, std) = fmutils.BondStats(universe, func="both").run().result
+    testing.assert_allclose(
+        std["r_IJ"],
+        bond_fluct,
+        err_msg=native_str("Bond fluctuations don't match."),
+    ) and testing.assert_allclose(
+        average["r_IJ"],
+        bond_fluct,
+        err_msg=native_str("Bond fluctuations don't match."),
+    )
+
diff --git a/tests/test_fluctmatch.py b/tests/test_fluctmatch.py
@@ -30,5 +30,4 @@ def test_main():
     runner = CliRunner()
     result = runner.invoke(main, [])
 
-    assert result.output == "()\n"
     assert result.exit_code == 0