Revert rotate default to before #1022

package/CHANGELOG

@@ -127,8 +127,7 @@ Changes
     (Issue #1010)
   * atoms.translate/rotateby don't accept AtomGroup tuples as
     parameters anymore (Issue #1025)
-  * atoms.rotate by default now uses the centroid as center of
-    rotation like rotateby (Issue #1022)
+  * atoms.rotate can be given center of rotation (Issue #1022)
   * XTCFile and TRRFile only raise IOError now on error.
   * Deprecate usage of MDAnalaysis.core.AtomGroup
   * get_writer_for() returns NullWriter when filename=None instead of

package/MDAnalysis/core/groups.py

@@ -672,34 +672,31 @@ def translate(self, t):
         atomgroup.universe.trajectory.ts.positions[atomgroup.indices] += vector
         return self
 
-    def rotate(self, R, point=None):
+    def rotate(self, R, point=(0, 0, 0)):
         r"""Apply a rotation matrix `R` to the selection's coordinates.
+        :math:`\mathsf{R}` is a 3x3 orthogonal matrix that transforms a vector
+        :math:`\mathbf{x} \rightarrow \mathbf{x}'`:
+
+        .. math::
+
+            \mathbf{x}' = \mathsf{R}\mathbf{x}
 
         Parameters
         ----------
         R : array_like
             3x3 rotation matrix to use for applying rotation.
         point : array_like, optional
-            Center of rotation. If ``None`` then the center of geometry of this
-            group is used.
+            Center of rotation
 
         Returns
         -------
         self : AtomGroup
 
         Notes
         -----
-        By default (``point=None``) the rotation is performed around
-        the centroid of the group (:meth:`center_of_geometry`). In
-        order to perform a rotation around, say, the origin, use
-        ``point=[0, 0, 0]``.
-
-        :math:`\mathsf{R}` is a 3x3 orthogonal matrix that transforms a vector
-        :math:`\mathbf{x} \rightarrow \mathbf{x}'`:
-
-        .. math::
-
-            \mathbf{x}' = \mathsf{R}\mathbf{x}
+        By default rotates around center of origin ``point=(0, 0, 0)``. To
+        rotate around center of geometry of the atomgroup use ``ag.rotate(R,
+        point=ag.centroid)``.
 
         See Also
         --------
@@ -708,10 +705,10 @@ def rotate(self, R, point=None):
 
         """
         R = np.asarray(R)
-        point = np.asarray(point) if point is not None else self.centroid()
+        point = np.asarray(point)
 
-        self.translate(-point)
         # changes the coordinates (in place)
+        self.translate(-point)
         x = self.atoms.unique.universe.trajectory.ts.positions
         idx = self.atoms.unique.indices
         x[idx] = np.dot(x[idx], R.T)

testsuite/MDAnalysisTests/analysis/test_align.py

@@ -23,7 +23,7 @@
 import warnings
 import os.path
 
-import MDAnalysis
+import MDAnalysis as mda
 import MDAnalysis.analysis.align as align
 import MDAnalysis.analysis.rms as rms
 from MDAnalysis import SelectionError
@@ -35,7 +35,7 @@
 import numpy as np
 from nose.plugins.attrib import attr
 
-from MDAnalysisTests.datafiles import PSF, DCD, FASTA
+from MDAnalysisTests.datafiles import PSF, DCD, FASTA, ALIGN_BOUND, ALIGN_UNBOUND
 from MDAnalysisTests import executable_not_found, parser_not_found, tempdir
 
 # I want to catch all warnings in the tests. If this is not set at the start it
@@ -94,8 +94,8 @@ class TestAlign(TestCase):
     @dec.skipif(parser_not_found('DCD'),
                 'DCD parser not available. Are you using python 3?')
     def setUp(self):
-        self.universe = MDAnalysis.Universe(PSF, DCD)
-        self.reference = MDAnalysis.Universe(PSF, DCD)
+        self.universe = mda.Universe(PSF, DCD)
+        self.reference = mda.Universe(PSF, DCD)
         # output is always same as input (=DCD)
         self.tempdir = tempdir.TempDir()
         self.outfile = os.path.join(self.tempdir.name, 'align_test.dcd')
@@ -170,7 +170,7 @@ def test_rms_fit_trj(self):
         self.reference.trajectory[-1]
         align.rms_fit_trj(self.universe, self.reference, select="all",
                           filename=self.outfile, verbose=False)
-        fitted = MDAnalysis.Universe(PSF, self.outfile)
+        fitted = mda.Universe(PSF, self.outfile)
         # RMSD against the reference frame
         # calculated on Mac OS X x86 with MDA 0.7.2 r689
         # VMD: 6.9378711
@@ -198,7 +198,7 @@ def test_AlignTraj(self):
         self.reference.trajectory[-1]
         x = align.AlignTraj(self.universe, self.reference,
                             filename=self.outfile).run()
-        fitted = MDAnalysis.Universe(PSF, self.outfile)
+        fitted = mda.Universe(PSF, self.outfile)
 
         rmsd_outfile = os.path.join(self.tempdir.name, 'rmsd')
         x.save(rmsd_outfile)
@@ -220,7 +220,7 @@ def test_AlignTraj(self):
     def test_AlignTraj_weighted(self):
         x = align.AlignTraj(self.universe, self.reference,
                             filename=self.outfile, weights='mass').run()
-        fitted = MDAnalysis.Universe(PSF, self.outfile)
+        fitted = mda.Universe(PSF, self.outfile)
         assert_almost_equal(x.rmsd[0], 0,  decimal=3)
         assert_almost_equal(x.rmsd[-1], 6.9033, decimal=3)
 
@@ -244,7 +244,7 @@ def test_AlignTraj_custom_weights(self):
     def test_AlignTraj_custom_mass_weights(self):
         x = align.AlignTraj(self.universe, self.reference,
                             filename=self.outfile, weights=self.reference.atoms.masses).run()
-        fitted = MDAnalysis.Universe(PSF, self.outfile)
+        fitted = mda.Universe(PSF, self.outfile)
         assert_almost_equal(x.rmsd[0], 0,  decimal=3)
         assert_almost_equal(x.rmsd[-1], 6.9033, decimal=3)
 
@@ -259,7 +259,7 @@ def test_AlignTraj_weights_deprecated(self):
             x = align.AlignTraj(self.universe, self.reference,
                                 filename=self.outfile, mass_weighted=True).run()
         assert_equal(len(warn), 1)
-        fitted = MDAnalysis.Universe(PSF, self.outfile)
+        fitted = mda.Universe(PSF, self.outfile)
         assert_almost_equal(x.rmsd[0], 0,  decimal=3)
         assert_almost_equal(x.rmsd[-1], 6.9033, decimal=3)
 
@@ -272,7 +272,7 @@ def test_AlignTraj_partial_fit(self):
         # fitting on a partial selection should still write the whole topology
         align.AlignTraj(self.universe, self.reference, select='resid 1-20',
                         filename=self.outfile, weights='mass').run()
-        MDAnalysis.Universe(PSF, self.outfile)
+        mda.Universe(PSF, self.outfile)
 
     def test_AlignTraj_in_memory(self):
         self.reference.trajectory[-1]
@@ -313,6 +313,20 @@ def different_atoms():
 
         assert_raises(SelectionError, different_atoms)
 
+    @staticmethod
+    def test_alignto_partial_universe():
+        u_bound = mda.Universe(ALIGN_BOUND)
+        u_free = mda.Universe(ALIGN_UNBOUND)
+        selection = 'segid B'
+
+        segB_bound = u_bound.select_atoms(selection)
+        segB_free = u_free.select_atoms(selection)
+        segB_free.translate(segB_bound.centroid() - segB_free.centroid())
+
+        align.alignto(u_free, u_bound, select=selection)
+        assert_array_almost_equal(segB_bound.positions, segB_free.positions, decimal=3)
+
+
 
 class TestAlignmentProcessing(object):
     def setUp(self):
@@ -351,7 +365,7 @@ def test_fasta2select_ClustalW(self):
                      err_msg="selection string has unexpected length")
 
 def test_sequence_alignment():
-    u = MDAnalysis.Universe(PSF)
+    u = mda.Universe(PSF)
     reference = u.atoms
     mobile = u.select_atoms("resid 122-159")
     aln = align.sequence_alignment(mobile, reference)

testsuite/MDAnalysisTests/core/test_atomgroup.py

@@ -328,16 +328,25 @@ def test_translate(self):
         assert_array_almost_equal(diff, disp, decimal=5)
 
     def test_rotate(self):
+        # ensure that selection isn't centered at 0, 0, 0
+        self.u.atoms.translate((1, 1, 1))
+        self.coords += 1
+
+        # check identify does nothing
         R = np.eye(3)
         self.u.atoms.rotate(R)
         assert_array_almost_equal(self.u.atoms.positions, self.coords)
 
-        vec = np.array([[1, 0, 0], [-1, 0, 0]])
-        axis = np.array([0, 0, 1])
-
+        # check default rotation center is at 0, 0, 0. Changing this center
+        # will break an unpredictable amount of old code.
         ag = self.u.atoms[:2]
-        ag.positions = vec
+        ag.positions = np.array([[1, 0, 0], [-1, 0, 0]])
+        ag.rotate(transformations.rotation_matrix(1, [0, 0, 1])[:3, :3])
+        assert_array_almost_equal(ag.positions[0], [np.cos(1), np.sin(1), 0])
 
+        # check general rotation cases
+        vec = np.array([[1, 0, 0], [-1, 0, 0]])
+        axis = np.array([0, 0, 1])
         for angle in np.linspace(0, np.pi):
             R = transformations.rotation_matrix(angle, axis)
             ag.positions = vec.copy()

testsuite/MDAnalysisTests/datafiles.py

@@ -133,6 +133,8 @@
     "AUX_XVG", "XVG_BAD_NCOL", #for testing .xvg auxiliary reader
     "AUX_XVG_LOWF", "AUX_XVG_HIGHF",
     "MMTF", "MMTF_gz",
+    "ALIGN_BOUND",  # two component bound system
+    "ALIGN_UNBOUND", # two component unbound system
 ]
 
 from pkg_resources import resource_filename
@@ -362,5 +364,8 @@
 MMTF = resource_filename(__name__, 'data/173D.mmtf')
 MMTF_gz = resource_filename(__name__, 'data/5KIH.mmtf.gz')
 
+ALIGN_BOUND = resource_filename(__name__, 'data/analysis/align_bound.pdb.gz')
+ALIGN_UNBOUND = resource_filename(__name__, 'data/analysis/align_unbound.pdb.gz')
+
 # This should be the last line: clean up namespace
 del resource_filename

testsuite/setup.py

@@ -206,7 +206,7 @@ def dynamic_author_list():
                          'data/*.xml',
                          'data/coordinates/*',
                          'data/*xvg',
-                         'data/*.mmtf', 'data/*.mmtf.gz',
+                         'data/*.mmtf', 'data/*.mmtf.gz', 'data/analysis/*'
                         ],
           },
           classifiers=CLASSIFIERS,