Added regression tests for hydrogenbondautocorrel (MDAnalysis#917)

testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py

@@ -0,0 +1,286 @@
+# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
+# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
+#
+# MDAnalysis --- http://www.MDAnalysis.org
+# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver
+# Beckstein and contributors (see AUTHORS for the full list)
+#
+# Released under the GNU Public Licence, v2 or any higher version
+#
+# Please cite your use of MDAnalysis in published work:
+#
+# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
+# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
+# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
+#
+import six
+from six.moves import zip, range
+from MDAnalysisTests.datafiles import TRZ, TRZ_psf, PRM, TRJ
+from MDAnalysisTests import module_not_found, tempdir
+from numpy.testing import assert_, assert_array_almost_equal, assert_raises, assert_, dec
+import numpy as np
+
+import MDAnalysis as mda
+from MDAnalysis.analysis.hbonds import HydrogenBondAutoCorrel as HBAC
+
+
+class TestHydrogenBondAutocorrel(object):
+    def setUp(self):
+        u = self.u = mda.Universe(TRZ_psf, TRZ)
+        self.H = u.atoms.select_atoms('name Hn')
+        self.N = u.atoms.select_atoms('name N')
+        self.O = u.atoms.select_atoms('name O')
+        self.excl_list = (np.array(range(len(self.H))),
+                          np.array(range(len(self.O))))
+
+    def tearDown(self):
+        del self.H
+        del self.N
+        del self.O
+        del self.u
+        del self.excl_list
+
+    # regression tests for different conditions
+    def test_continuous(self):
+        hbond = HBAC(self.u,
+                     hydrogens=self.H,
+                     acceptors=self.O,
+                     donors=self.N,
+                     bond_type='continuous',
+                     sample_time=0.06,
+        )
+        hbond.run()
+
+        assert_array_almost_equal(
+            hbond.solution['results'],
+            np.array([ 1.        ,  0.92668623,  0.83137828,
+                       0.74486804,  0.67741936,  0.60263932],
+                     dtype=np.float32)
+        )
+
+
+    def test_continuous_excl(self):
+        hbond = HBAC(self.u,
+                     hydrogens=self.H,
+                     acceptors=self.O,
+                     donors=self.N,
+                     bond_type='continuous',
+                     exclusions=self.excl_list,
+                     sample_time=0.06,
+        )
+        hbond.run()
+
+        assert_array_almost_equal(
+            hbond.solution['results'],
+            np.array([ 1.        ,  0.92668623,  0.83137828,
+                       0.74486804,  0.67741936,  0.60263932],
+                     dtype=np.float32)
+        )
+
+
+    def test_intermittent(self):
+        hbond = HBAC(self.u,
+                     hydrogens=self.H,
+                     acceptors=self.O,
+                     donors=self.N,
+                     bond_type='intermittent',
+                     sample_time=0.06,
+        )
+        hbond.run()
+
+        assert_array_almost_equal(
+            hbond.solution['results'],
+            np.array([ 1.        ,  0.92668623,  0.84310848,
+                       0.79325515,  0.76392961,  0.72287393],
+                     dtype=np.float32)
+        )
+
+
+    def test_intermittent_timecut(self):
+        hbond = HBAC(self.u,
+                     hydrogens=self.H,
+                     acceptors=self.O,
+                     donors=self.N,
+                     bond_type='intermittent',
+                     time_cut=0.01,  # time cut at traj.dt == continuous
+                     sample_time=0.06,
+        )
+        hbond.run()
+
+        assert_array_almost_equal(
+            hbond.solution['results'],
+            np.array([ 1.        ,  0.92668623,  0.83137828,
+                       0.74486804,  0.67741936,  0.60263932],
+                     dtype=np.float32)
+        )
+
+    def test_intermittent_excl(self):
+        hbond = HBAC(self.u,
+                     hydrogens=self.H,
+                     acceptors=self.O,
+                     donors=self.N,
+                     bond_type='intermittent',
+                     exclusions=self.excl_list,
+                     sample_time=0.06,
+        )
+        hbond.run()
+
+        assert_array_almost_equal(
+            hbond.solution['results'],
+            np.array([ 1.        ,  0.92668623,  0.84310848,
+                       0.79325515,  0.76392961,  0.72287393],
+                     dtype=np.float32)
+        )
+
+    # For `solve` the test trajectories aren't long enough
+    # So spoof the results and check that solver finds solution
+    @dec.skipif(module_not_found('scipy'))
+    def test_solve_continuous(self):
+        hbond = HBAC(self.u,
+                     hydrogens=self.H,
+                     acceptors=self.O,
+                     donors=self.N,
+                     bond_type='continuous',
+                     sample_time=0.06,
+        )
+
+        def actual_function_cont(t):
+            A1 = 0.75
+            A2 = 0.25
+            tau1 = 0.5
+            tau2 = 0.1
+            return A1 * np.exp(-t/tau1) + A2 * np.exp(-t/tau2)
+        hbond.solution['time'] = time = np.arange(0, 0.06, 0.001)
+        hbond.solution['results'] = actual_function_cont(time)
+
+        hbond.solve()
+
+        assert_array_almost_equal(
+            hbond.solution['fit'],
+            np.array([0.75, 0.5, 0.1]),
+        )
+
+    @dec.skipif(module_not_found('scipy'))
+    def test_solve_intermittent(self):
+        hbond = HBAC(self.u,
+                     hydrogens=self.H,
+                     acceptors=self.O,
+                     donors=self.N,
+                     bond_type='intermittent',
+                     sample_time=0.06,
+        )
+
+        def actual_function_int(t):
+            A1 = 0.33
+            A2 = 0.33
+            A3 = 0.34
+            tau1 = 5
+            tau2 = 1
+            tau3 = 0.1
+            return A1 * np.exp(-t/tau1) + A2 * np.exp(-t/tau2) + A3 * np.exp(-t/tau3)
+        hbond.solution['time'] = time = np.arange(0, 6.0, 0.01)
+        hbond.solution['results'] = actual_function_int(time)
+
+        hbond.solve()
+
+        assert_array_almost_equal(
+            hbond.solution['fit'],
+            np.array([0.33, 0.33, 5, 1, 0.1]),
+        )
+
+    def test_save(self):
+        hbond = HBAC(self.u,
+                     hydrogens=self.H,
+                     acceptors=self.O,
+                     donors=self.N,
+                     bond_type='continuous',
+                     sample_time=0.06,
+        )
+        hbond.run()
+
+        with tempdir.in_tempdir():
+            hbond.save_results('hbondout.npz')
+
+            loaded = np.load('hbondout.npz')
+            assert_('time' in loaded)
+            assert_('results' in loaded)
+
+    # setup errors
+    def test_wronglength_DA(self):
+        assert_raises(ValueError,
+                      HBAC, self.u,
+                      hydrogens=self.H[:-1],
+                      acceptors=self.O,
+                      donors=self.N,
+                      bond_type='intermittent',
+                      exclusions=self.excl_list,
+                      sample_time=0.06,
+        )
+
+    def test_exclusions(self):
+        excl_list2 = self.excl_list[0], self.excl_list[1][:-1]
+        assert_raises(ValueError,
+                      HBAC, self.u,
+                      hydrogens=self.H,
+                      acceptors=self.O,
+                      donors=self.N,
+                      bond_type='intermittent',
+                      exclusions=excl_list2,
+                      sample_time=0.06,
+        )
+
+    def test_bond_type_VE(self):
+        assert_raises(ValueError,
+                      HBAC, self.u,
+                      hydrogens=self.H,
+                      acceptors=self.O,
+                      donors=self.N,
+                      bond_type='marzipan',
+                      exclusions=self.excl_list,
+                      sample_time=0.06,
+        )
+
+    @dec.skipif(module_not_found('scipy'))
+    def test_solve_before_run_VE(self):
+        hbond = HBAC(self.u,
+                     hydrogens=self.H,
+                     acceptors=self.O,
+                     donors=self.N,
+                     bond_type='continuous',
+                     sample_time=0.06,
+        )
+        assert_raises(ValueError, hbond.solve)
+
+    def test_unslicable_traj_VE(self):
+        u = mda.Universe(PRM, TRJ)
+        H = u.atoms[:10]
+        O = u.atoms[10:20]
+        N = u.atoms[20:30]
+        assert_raises(ValueError, HBAC,
+                      u,
+                      hydrogens=H,
+                      acceptors=O,
+                      donors=N,
+                      bond_type='continuous',
+                      sample_time=0.06
+        )
+
+    def test_save_without_run_VE(self):
+        hbond = HBAC(self.u,
+                     hydrogens=self.H,
+                     acceptors=self.O,
+                     donors=self.N,
+                     bond_type='continuous',
+                     sample_time=0.06,
+        )
+        assert_raises(ValueError, hbond.save_results)
+
+    def test_repr(self):
+        hbond = HBAC(self.u,
+                     hydrogens=self.H,
+                     acceptors=self.O,
+                     donors=self.N,
+                     bond_type='continuous',
+                     sample_time=0.06,
+        )
+        assert_(isinstance(repr(hbond), six.string_types))