Allow specifying a chain sequence offset

Add a per-chain offset, which defaults to
zero, which maps from the sequence index
(which always starts at 1) to the residue
index (which may not).

doc/DecoratorsAndAttributes.md

@@ -71,6 +71,7 @@ The category name is `sequence` and it includes information about the types and
 | `residue index`  | int       |  The index of a residue                          |
 | `chain id`       | string    |  The chain ID                                    |
 | `sequence`       | string    |  Primary sequence of a chain                     |
+| `sequence offset`| int       |  Offset from sequence index to residue index     |
 | `chain type`     | string    |  Type of chain sequence (e.g. Protein, DNA, RNA) |
 | `first residue index` | int  |  The index of the first residue (in a domain)    |
 | `last residue index` | int   |  The index of the last residue (in a domain)     |

test/test_chain.py

@@ -19,9 +19,11 @@ def test_chain(self):
         # Check defaults
         self.assertEqual(c.get_chain_type(), 'UnknownChainType')
         self.assertEqual(c.get_sequence(), '')
+        self.assertEqual(c.get_sequence_offset(), 0)
         # Check setters
         c.set_chain_type('LPolypeptide')
         c.set_sequence('CGY')
+        c.set_sequence_offset(10)
         c.set_chain_id('X')
 
         # Check both const and non-const getters
@@ -34,6 +36,7 @@ def check_rmf(self, cf, c0, c1):
         c = cf.get(c0)
         self.assertEqual(c.get_chain_type(), 'LPolypeptide')
         self.assertEqual(c.get_sequence(), 'CGY')
+        self.assertEqual(c.get_sequence_offset(), 10)
         self.assertEqual(c.get_chain_id(), 'X')
 
 if __name__ == '__main__':

tools/build/make_decorators.py

@@ -177,6 +177,7 @@
                   "Chain",
                   [Attribute("chain id", "String"),
                    Attribute("sequence", "String", default=""),
+                   Attribute("sequence offset", "Int", default=0),
                    Attribute("chain type", "String",
                              default='UnknownChainType')])