Documentation update

modules/io/tests/test_mmcif_writer.cc

@@ -372,7 +372,7 @@ BOOST_AUTO_TEST_CASE(mmcif_writer_small_sugars)
   writer.Write("test", out);
 
   String s=out.str();
-  // Check that the mmCIF output contains 2 non-polymer entities
+  // Check that the mmCIF output contains a branched entity
   BOOST_CHECK_NE(s.find("loop_\n_entity.id\n_entity.type\n1 branched"),
                  String::npos);
   // Check that atoms are HETATMs since non-poly

modules/seq/alg/doc/seqalg.rst

@@ -226,7 +226,7 @@ Algorithms for Alignments
     calculated as the number of matches divided by the length of the longer
     sequence. If set to `seq.alg.RefMode.ALIGNMENT` (the default), the sequence
     identity is calculated as the number of matches divided by the number of
-    aligned residues. 
+    aligned residues (not including the gaps).
   :type ref_mode: int
   :param seq_a: the index of the first sequence
   :type seq_a: int