def test_frame_mdtraj_read_xtc(self): logging.disable(logging.WARNING) frame = Frame(gro="test/data/water.gro", xtc="test/data/water.xtc", xtc_reader="mdtraj") logging.disable(logging.NOTSET) self.assertEqual(663, frame.natoms) # These are the coordinates from the gro file np.testing.assert_allclose(np.array([0.696, 1.33, 1.211]), frame.residues[0].atoms[0].coords) np.testing.assert_allclose(np.array([1.89868, 1.89868, 1.89868]), frame.box) frame.next_frame() # These coordinates are from the xtc file np.testing.assert_allclose(np.array([1.176, 1.152, 1.586]), frame.residues[0].atoms[0].coords) np.testing.assert_allclose(np.array([1.9052, 1.9052, 1.9052]), frame.box) frame.next_frame() np.testing.assert_allclose(np.array([1.122, 1.130, 1.534]), frame.residues[0].atoms[0].coords) np.testing.assert_allclose(np.array([1.90325272, 1.90325272, 1.90325272]), frame.box)
def test_bondset_boltzmann_invert(self): measure = BondSet("test/data/sugar.bnd", DummyOptions) frame = Frame("test/data/sugar.gro", xtc="test/data/sugar.xtc") mapping = Mapping("test/data/sugar.map", DummyOptions) cgframe = mapping.apply(frame) while frame.next_frame(): cgframe = mapping.apply(frame, cgframe=cgframe) measure.apply(cgframe) measure.boltzmann_invert() self.support_check_mean_fc(measure["ALLA"], 1)
def test_frame_write_xtc_mdtraj(self): try: os.remove("water_test2.xtc") except IOError: pass logging.disable(logging.WARNING) frame = Frame(gro="test/data/water.gro", xtc="test/data/water.xtc", xtc_reader="mdtraj") logging.disable(logging.NOTSET) while frame.next_frame(): frame.write_xtc("water_test2.xtc")
def test_bondset_boltzmann_invert_mdtraj(self): logging.disable(logging.WARNING) frame = Frame("test/data/sugar.gro", xtc="test/data/sugar.xtc", xtc_reader="mdtraj") logging.disable(logging.NOTSET) measure = BondSet("test/data/sugar.bnd", DummyOptions) mapping = Mapping("test/data/sugar.map", DummyOptions) cgframe = mapping.apply(frame) while frame.next_frame(): cgframe = mapping.apply(frame, cgframe=cgframe) measure.apply(cgframe) measure.boltzmann_invert() self.support_check_mean_fc(measure["ALLA"], 1)
def test_full_itp_sugar(self): measure = BondSet("test/data/sugar.bnd", DummyOptions) frame = Frame("test/data/sugar.gro", xtc="test/data/sugar.xtc") mapping = Mapping("test/data/sugar.map", DummyOptions) cgframe = mapping.apply(frame) while frame.next_frame(): cgframe = mapping.apply(frame, cgframe=cgframe) measure.apply(cgframe) measure.boltzmann_invert() logging.disable(logging.WARNING) measure.write_itp("sugar_out.itp", mapping) logging.disable(logging.NOTSET) self.assertTrue(cmp_whitespace_float("sugar_out.itp", "test/data/sugar_out.itp", float_rel_error=0.001))
def test_bondset_boltzmann_invert_func_forms(self): class FuncFormOptions(DummyOptions): length_form = "CosHarmonic" angle_form = "Harmonic" dihedral_form = "MartiniDefaultLength" measure = BondSet("test/data/sugar.bnd", FuncFormOptions) frame = Frame("test/data/sugar.gro", xtc="test/data/sugar.xtc") mapping = Mapping("test/data/sugar.map", DummyOptions) cgframe = mapping.apply(frame) while frame.next_frame(): cgframe = mapping.apply(frame, cgframe=cgframe) measure.apply(cgframe) measure.boltzmann_invert() self.support_check_mean_fc(measure["ALLA"], 3)
def test_bondset_boltzmann_invert_manual_default_fc(self): class FuncFormOptions(DummyOptions): length_form = "MartiniDefaultLength" angle_form = "MartiniDefaultAngle" dihedral_form = "MartiniDefaultDihedral" measure = BondSet("test/data/sugar.bnd", FuncFormOptions) frame = Frame("test/data/sugar.gro", xtc="test/data/sugar.xtc") mapping = Mapping("test/data/sugar.map", DummyOptions) cgframe = mapping.apply(frame) while frame.next_frame(): cgframe = mapping.apply(frame, cgframe=cgframe) measure.apply(cgframe) measure.boltzmann_invert() self.support_check_mean_fc(measure["ALLA"], 2)
def test_full_itp_sugar(self): measure = BondSet("test/data/sugar.bnd", DummyOptions) frame = Frame("test/data/sugar.gro", xtc="test/data/sugar.xtc") mapping = Mapping("test/data/sugar.map", DummyOptions) cgframe = mapping.apply(frame) while frame.next_frame(): cgframe = mapping.apply(frame, cgframe=cgframe) measure.apply(cgframe) measure.boltzmann_invert() logging.disable(logging.WARNING) measure.write_itp("sugar_out.itp", mapping) logging.disable(logging.NOTSET) self.assertTrue( cmp_whitespace_float("sugar_out.itp", "test/data/sugar_out.itp", float_rel_error=0.001))