[coor/feat/util] _describe_atom returns chain index if two or more ch…

…ains are present (markovmodel#823)
gph82 · Jun 7, 2016 · a39eb67 · a39eb67
1 parent ecd07bc
commit a39eb67
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Showing 2 changed files with 41 additions and 6 deletions.
diff --git a/pyemma/coordinates/data/featurization/util.py b/pyemma/coordinates/data/featurization/util.py
@@ -36,7 +36,10 @@ def _describe_atom(topology, index):
     :return:
     """
     at = topology.atom(index)
-    return "%s %i %s %i" % (at.residue.name, at.residue.resSeq, at.name, at.index)
+    if topology.n_chains > 1:
+        return "%s %i %s %i %i" % (at.residue.name, at.residue.resSeq, at.name, at.index, at.residue.chain.index )
+    else:
+        return "%s %i %s %i"    % (at.residue.name, at.residue.resSeq, at.name, at.index)
 
 
 def _catch_unhashable(x):

diff --git a/pyemma/coordinates/tests/test_featurizer.py b/pyemma/coordinates/tests/test_featurizer.py
@@ -28,7 +28,7 @@
 
 # from pyemma.coordinates.data import featurizer as ft
 from pyemma.coordinates.data.featurization.featurizer import MDFeaturizer, CustomFeature
-from pyemma.coordinates.data.featurization.util import _parse_pairwise_input
+from pyemma.coordinates.data.featurization.util import _parse_pairwise_input, _describe_atom
 from six.moves import range
 import pkg_resources
 
@@ -63,10 +63,10 @@
 ATOM    001  CA  ASN A  01      1.0000   0.000  0.0000  1.00 0.000           C
 ATOM    002  MW  ACE A  02      2.0000   0.000  0.0000  1.00 0.000           X
 ATOM    003  CA  ASN A  03      3.0000   0.000  0.0000  1.00 0.000           C
-ATOM    004  MW  ACE A  04      4.0000   0.000  0.0000  1.00 0.000           X
-ATOM    005  CA  ASN A  05      5.0000   0.000  0.0000  1.00 0.000           C
-ATOM    006  MW  ACE A  06      6.0000   0.000  0.0000  1.00 0.000           X
-ATOM    007  CA  ASN A  07      7.0000   0.000  0.0000  1.00 0.000           C
+ATOM    004  MW  ACE B  04      4.0000   0.000  0.0000  1.00 0.000           X
+ATOM    005  CA  ASN B  05      5.0000   0.000  0.0000  1.00 0.000           C
+ATOM    006  MW  ACE B  06      6.0000   0.000  0.0000  1.00 0.000           X
+ATOM    007  CA  ASN B  07      7.0000   0.000  0.0000  1.00 0.000           C
 """
 
 def verbose_assertion_minrmsd(ref_Y, test_Y, test_obj):
@@ -744,6 +744,38 @@ def test_two_redundants_overlap(self):
                                             )))
         assert np.allclose(dist_list, _parse_pairwise_input(group1, group2, self.feat._logger))
 
+class TestUtils(unittest.TestCase):
+    @classmethod
+    def setUpClass(cls):
+        import tempfile
+        cls.bogus_geom_pdbfile = tempfile.mkstemp(suffix=".pdb")[1]
+        print(cls.bogus_geom_pdbfile)
+        with open(cls.bogus_geom_pdbfile, 'w') as fh:
+            fh.write(bogus_geom_pdbfile)
+        super(TestUtils, cls).setUpClass()
+
+
+    @classmethod
+    def tearDownClass(cls):
+        try:
+            os.unlink(cls.bogus_geom_pdbfile)
+        except EnvironmentError:
+            pass
+
+        super(TestUtils, cls).tearDownClass()
+
+    @classmethod
+    def setUp(self):
+        self.traj = mdtraj.load(self.bogus_geom_pdbfile)
+
+    def test_describe_atom(self):
+        str1 = _describe_atom(self.traj.topology, 0)
+        str2 = _describe_atom(self.traj.topology,self.traj.n_atoms-1)
+        assert len(str1.split()) >=4
+        assert len(str2.split()) >=4
+        assert str1.split()[-1] == '0'
+        assert str2.split()[-1] == '1'
+
 class TestStaticMethods(unittest.TestCase):
 
     def setUp(self):