Add pyrrolysine to LPeptideAlphabet

Relates ihmwg/python-modelcif#55.

Author: benmwebb

ihm/__init__.py

@@ -1203,6 +1203,7 @@ class LPeptideAlphabet(Alphabet):
                   ('Y', 'TYR', 'TYROSINE', 'C9 H11 N O3'),
                   ('B', 'ASX', 'ASP/ASN AMBIGUOUS', 'C4 H6 N O2 X2'),
                   ('Z', 'GLX', 'GLU/GLN AMBIGUOUS', 'C5 H8 N O2 X2'),
+                  ('O', 'PYL', 'PYRROLYSINE', 'C12 H21 N3 O3'),
                   ('U', 'SEC', 'SELENOCYSTEINE', 'C3 H7 N O2 Se')])
     _comps['G'] = PeptideChemComp('GLY', 'G', 'G', name='GLYCINE',
                                   formula="C2 H5 N O2")

test/test_main.py

@@ -147,13 +147,19 @@ def test_l_peptide_alphabet(self):
         self.assertAlmostEqual(a._comps['Z'].formula_weight, 114.124,
                                delta=0.01)
 
+        self.assertEqual(a._comps['O'].id, 'PYL')
+        self.assertEqual(a._comps['O'].name, "PYRROLYSINE")
+        self.assertEqual(a._comps['O'].formula, 'C12 H21 N3 O3')
+        self.assertAlmostEqual(a._comps['O'].formula_weight, 255.318,
+                               delta=0.01)
+
         a = ihm.LPeptideAlphabet()
         self.assertIn('MSE', a)
         self.assertNotIn('DG', a)
-        self.assertEqual(len(a.keys), 25)
-        self.assertEqual(len(a.values), 25)
+        self.assertEqual(len(a.keys), 26)
+        self.assertEqual(len(a.values), 26)
         self.assertEqual(sorted(a.keys)[0], 'A')
-        self.assertEqual(len(a.items), 25)
+        self.assertEqual(len(a.items), 26)
         item0 = sorted(a.items)[0]
         self.assertEqual(item0[0], 'A')
         self.assertEqual(item0[1].id, 'ALA')