Updated chem_shifts_by_residue() and corresponding tutorial

MoseleyBioinformaticsLab · Jan 3, 2017 · 1dc6035 · 1dc6035
1 parent 3bc0444
commit 1dc6035
Showing 1 changed file with 60 additions and 38 deletions.
diff --git a/docs/tutorial.rst b/docs/tutorial.rst
@@ -326,48 +326,70 @@ using bracket accessors.
    sequence id and amino acid residue type; `values` - chemical shift data):
 
    >>> starfile.chem_shifts_by_residue()
-   [OrderedDict([(('1', 'MET'), OrderedDict([('H', '8.55'),
-                                             ('HA', '4.548'),
-                                             ('HB2', '1.994'),
-                                             ('HB3', '2.118'),
-                                             ('CA', '55.489'),
-                                             ('CB', '32.848'),
-                                             ('N', '122.221')])),
-                 (('2', 'SER'), OrderedDict([('H', '8.225'),
-                                             ('HA', '4.420'),
-                                             ('HB2', '3.805'),
-                                             ('HB3', '3.857'),
-                                             ('CA', '58.593'),
-                                             ('CB', '64.057'),
-                                             ('N', '117.197')])),
-                 (('3', 'GLU'), OrderedDict([('H', '8.002'),
-                                             ('HA', '4.848'),
-                                             ('HB2', '1.852'),
-                                             ('HB3', '1.963'),
-                                             ('HG2', '1.981'),
-                                             ('HG3', '2.191'),
-                                             ('CA', '55.651'),
-                                             ('CB', '32.952'),
-                                             ('CG', '37.425'),
-                                             ('N', '119.833')])), ...
+   [OrderedDict([
+       (1, OrderedDict([('AA3Code', 'MET'),
+                        ('Seq_ID', 1),
+                        ('H', '8.55'),
+                        ('HA', '4.548'),
+                        ('HB2', '1.994'),
+                        ('HB3', '2.118'),
+                        ('CA', '55.489'),
+                        ('CB', '32.848'),
+                        ('N', '122.221')])),
+       (2, OrderedDict([('AA3Code', 'SER'),
+                        ('Seq_ID', 2),
+                        ('H', '8.225'),
+                        ('HA', '4.420'),
+                        ('HB2', '3.805'),
+                        ('HB3', '3.857'),
+                        ('CA', '58.593'),
+                        ('CB', '64.057'),
+                        ('N', '117.197')])),
+       (3, OrderedDict([('AA3Code', 'GLU'),
+                        ('Seq_ID', 3),
+                        ('H', '8.002'),
+                        ('HA', '4.848'),
+                        ('HB2', '1.852'),
+                        ('HB3', '1.963'),
+                        ('HG2', '1.981'),
+                        ('HG3', '2.191'),
+                        ('CA', '55.651'),
+                        ('CB', '32.952'),
+                        ('CG', '37.425'),
+                        ('N', '119.833')])), ...
    ...
    ]
    >>>
    >>> starfile.chem_shifts_by_residue(aminoacids=["SER"], atoms=["CA", "CB"])
-   [OrderedDict([(('2', 'SER'), OrderedDict([('CA', '58.593'),
-                                             ('CB', '64.057')])),
-                 (('8', 'SER'), OrderedDict([('CA', '57.456'),
-                                             ('CB', '64.863')])),
-                 (('9', 'SER'), OrderedDict([('CA', '57.852'),
-                                             ('CB', '67.332')])),
-                 (('34', 'SER'), OrderedDict([('CA', '59.113'),
-                                              ('CB', '66.248')])),
-                 (('46', 'SER'), OrderedDict([('CA', '55.939'),
-                                              ('CB', '66.829')])),
-                 (('95', 'SER'), OrderedDict([('CA', '57.013'),
-                                              ('CB', '66.501')])),
-                 (('108', 'SER'), OrderedDict([('CA', '61.617'),
-                                               ('CB', '62.493')]))])
+   [OrderedDict([
+       (2, OrderedDict([('AA3Code', 'SER'),
+                        ('Seq_ID', 2),
+                        ('CA', '58.593'),
+                        ('CB', '64.057')])),
+       (8, OrderedDict([('AA3Code', 'SER'),
+                        ('Seq_ID', 8),
+                        ('CA', '57.456'),
+                        ('CB', '64.863')])),
+       (9, OrderedDict([('AA3Code', 'SER'),
+                        ('Seq_ID', 9),
+                        ('CA', '57.852'),
+                        ('CB', '67.332')])),
+       (34, OrderedDict([('AA3Code', 'SER'),
+                         ('Seq_ID', 34),
+                         ('CA', '59.113'),
+                         ('CB', '66.248')])),
+       (46, OrderedDict([('AA3Code', 'SER'),
+                         ('Seq_ID', 46),
+                         ('CA', '55.939'),
+                         ('CB', '66.829')])),
+       (95, OrderedDict([('AA3Code', 'SER'),
+                         ('Seq_ID', 95),
+                         ('CA', '57.013'),
+                         ('CB', '66.501')])),
+       (108, OrderedDict([('AA3Code', 'SER'),
+                         ('Seq_ID', 108),
+                         ('CA', '61.617'),
+                         ('CB', '62.493')]))])
    ]
    >>>