Merge pull request #653 from MDAnalysis/issue-461-nucleicselections

Added extra resnames to 'nucleic' selection closes #461
MDAnalysis · Jan 25, 2016 · 5330a7c · 5330a7c
2 parents f13d8c8 + 8bb8d38
commit 5330a7c
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diff --git a/package/CHANGELOG b/package/CHANGELOG
@@ -38,6 +38,8 @@ Fixes
     (Issue #639)
   * The 'atom' selection keyword returns an empty selection rather than an
     error when no atoms are are found. (Issue #644)
+  * nucleic selection will now detect nucleic residue names suffixed with 3 or 5
+    (Issue #461)
 
 
 01/16/16 tyler.je.reddy, kain88-de, richardjgowers, manuel.nuno.melo,

diff --git a/package/MDAnalysis/core/Selection.py b/package/MDAnalysis/core/Selection.py
@@ -735,7 +735,11 @@ class NucleicSelection(Selection):
 
     nucl_res = np.array([
         'ADE', 'URA', 'CYT', 'GUA', 'THY', 'DA', 'DC', 'DG', 'DT', 'RA',
-        'RU', 'RG', 'RC', 'A', 'T', 'U', 'C', 'G'
+        'RU', 'RG', 'RC', 'A', 'T', 'U', 'C', 'G',
+        'DA5', 'DC5', 'DG5', 'DT5',
+        'DA3', 'DC3', 'DG3', 'DT3',
+        'RA5', 'RU5', 'RG5', 'RC5',
+        'RA3', 'RU3', 'RG3', 'RC3'
     ])
 
     def __init__(self, parser, tokens):

diff --git a/testsuite/MDAnalysisTests/data/nucl_res.pdb b/testsuite/MDAnalysisTests/data/nucl_res.pdb
@@ -0,0 +1,42 @@
+MODEL
+CRYST1 80.000   80.000   80.000  60.00  60.00  90.00
+ATOM      1 CA   ADE     1      00.000  00.000  00.000  1.00 84.71
+ATOM      2 CA   URA     2      01.000  01.000  01.000  1.00 68.59
+ATOM      3 CA   CYT     3      02.000  02.000  02.000  1.00 48.30
+ATOM      4 CA   GUA     4      03.000  03.000  03.000  1.00 49.38
+ATOM      5 CA   THY     5      04.000  04.000  04.000  1.00 42.10
+ATOM      6 CA   DA      6      04.000  04.000  04.000  1.00 42.10
+ATOM      7 CA   DC      7      04.000  04.000  04.000  1.00 42.10
+ATOM      8 CA   DG      8      04.000  04.000  04.000  1.00 42.10
+ATOM      9 CA   DT      9      04.000  04.000  04.000  1.00 42.10
+ATOM     10 CA   RA      10     04.000  04.000  04.000  1.00 42.10
+ATOM     11 CA   RU      11     04.000  04.000  04.000  1.00 42.10
+ATOM     12 CA   RG      12     04.000  04.000  04.000  1.00 42.10
+ATOM     13 CA   RC      13     04.000  04.000  04.000  1.00 42.10
+ATOM     14 CA   A       14     04.000  04.000  04.000  1.00 42.10
+ATOM     15 CA   T       15     04.000  04.000  04.000  1.00 42.10
+ATOM     16 CA   U       16     04.000  04.000  04.000  1.00 42.10
+ATOM     17 CA   C       17     04.000  04.000  04.000  1.00 42.10
+ATOM     18 CA   G       18     04.000  04.000  04.000  1.00 42.10
+ATOM     19 CA   DA5     19     04.000  04.000  04.000  1.00 42.10
+ATOM     20 CA   DC5     20     04.000  04.000  04.000  1.00 42.10
+ATOM     21 CA   DG5     21     04.000  04.000  04.000  1.00 42.10
+ATOM     22 CA   DT5     22     04.000  04.000  04.000  1.00 42.10
+ATOM     23 CA   DA3     23     04.000  04.000  04.000  1.00 42.10
+ATOM     24 CA   DC3     24     04.000  04.000  04.000  1.00 42.10
+ATOM     25 CA   DG3     25     04.000  04.000  04.000  1.00 42.10
+ATOM     26 CA   DT3     26     04.000  04.000  04.000  1.00 42.10
+ATOM     27 CA   RA5     27     04.000  04.000  04.000  1.00 42.10
+ATOM     28 CA   RU5     28     04.000  04.000  04.000  1.00 42.10
+ATOM     29 CA   RG5     29     04.000  04.000  04.000  1.00 42.10
+ATOM     30 CA   RC5     30     04.000  04.000  04.000  1.00 42.10
+ATOM     31 CA   RA3     31     04.000  04.000  04.000  1.00 42.10
+ATOM     32 CA   RU3     32     04.000  04.000  04.000  1.00 42.10
+ATOM     33 CA   RG3     33     04.000  04.000  04.000  1.00 42.10
+ATOM     34 CA   RC3     34     04.000  04.000  04.000  1.00 42.10
+ATOM     35 CA   TAF     35     04.000  04.000  04.000  1.00 42.10
+ATOM     36 CA   ERU     36     04.000  04.000  04.000  1.00 42.10
+ATOM     37 CA   SEN     37     04.000  04.000  04.000  1.00 42.10
+ATOM     38 CA   T__     38     04.000  04.000  04.000  1.00 42.10
+ATOM     39 CA   S__     39     04.000  04.000  04.000  1.00 42.10
+END
diff --git a/testsuite/MDAnalysisTests/datafiles.py b/testsuite/MDAnalysisTests/datafiles.py
@@ -105,6 +105,7 @@
     "COORDINATES_XTC",
     "COORDINATES_TRR",
     "COORDINATES_TOPOLOGY",
+    "NUCLsel",
 ]
 
 from pkg_resources import resource_filename
@@ -294,3 +295,6 @@
 
 Plength = resource_filename(__name__, 'data/plength.gro')
 Martini_membrane_gro = resource_filename(__name__, 'data/martini_dppc_chol_bilayer.gro')
+
+# Contains one of each residue in 'nucleic' selections
+NUCLsel = resource_filename(__name__, 'data/nucl_res.pdb')
diff --git a/testsuite/MDAnalysisTests/test_atomselections.py b/testsuite/MDAnalysisTests/test_atomselections.py
@@ -42,7 +42,7 @@
     PSF, DCD,
     PRMpbc, TRJpbc_bz2,
     PSF_NAMD, PDB_NAMD,
-    GRO, NUCL, TPR, XTC,
+    GRO, NUCL, NUCLsel, TPR, XTC,
     TRZ_psf, TRZ,
     PDB_full,
 )
@@ -464,6 +464,13 @@ def test_nucleic(self):
         assert_equal(rna.n_atoms, 739)
         assert_equal(rna.n_residues, 23)
 
+    def test_nucleic_all(self):
+        u = mda.Universe(NUCLsel)
+
+        sel = u.select_atoms('nucleic')
+
+        assert_(len(sel) == 34)
+
     def test_nucleicbackbone(self):
         rna = self.universe.select_atoms("nucleicbackbone")
         assert_equal(rna.n_residues, 23)