From 33489152dc832027953b33cd42a2ab96a303c3f0 Mon Sep 17 00:00:00 2001
From: Sam Ireland <sam.ireland.uk@gmail.com>
Date: Fri, 12 Jan 2018 16:28:58 +0000
Subject: [PATCH] Add full residue names (resolves #12)

---
 atomium/structures/molecules.py              | 16 ++++++++++++++--
 tests/integration/test_pdb.py                |  4 ++++
 tests/unit/structure_tests/test_molecules.py |  7 +++++++
 3 files changed, 25 insertions(+), 2 deletions(-)

diff --git a/atomium/structures/molecules.py b/atomium/structures/molecules.py
index 89e48285..d8560540 100644
--- a/atomium/structures/molecules.py
+++ b/atomium/structures/molecules.py
@@ -297,15 +297,16 @@ def molecule_id(self, molecule_id=None):
         return self._id
 
 
-    def name(self, name=None):
+    def name(self, name=None, full=False):
         """Returns the molecule's name. If a value is given, the name will be
         updated, provided it is a string.
 
         :param int name: If given, the name will be set to this.
+        :param bool full: If ``True`` the full English name will be returned.
         :raises TypeError: if the name given is not str."""
 
         if name is None:
-            return self._name
+            return RESIDUES.get(self._name, self._name) if full else self._name
         else:
             if not isinstance(name, str):
                 raise TypeError("Molecule name '{}' is not str".format(name))
@@ -489,3 +490,14 @@ def chain(self):
 
         for atom in self.atoms():
             return atom.chain()
+
+
+
+RESIDUES = {
+ "GLY": "glycine", "ALA": "alanine", "VAL": "valine", "LEU": "leucine",
+ "ILE": "isoleucine", "MET": "methionine", "PHE": "phenylalanine",
+ "TRP": "tryptophan", "PRO": "proline", "SER": "serine", "THR": "threonine",
+ "CYS": "cysteine", "TYR": "tyrosine", "ASN": "asparagine", "GLN": "glutamine",
+ "ASP": "aspartic acid", "GLU": "glutamic acid", "LYS": "lysine",
+ "ARG": "arginine", "HIS": "histidine", "HOH": "water"
+}
diff --git a/tests/integration/test_pdb.py b/tests/integration/test_pdb.py
index b31220b2..8aaf11e1 100644
--- a/tests/integration/test_pdb.py
+++ b/tests/integration/test_pdb.py
@@ -40,8 +40,11 @@ def test_can_read_pdb(self):
 
         # Residues are correct
         self.assertEqual(chaina[0].name(), "VAL")
+        self.assertEqual(chaina[0].name(full=True), "valine")
         self.assertEqual(chaina[0].next().name(), "MET")
+        self.assertEqual(chaina[0].next().name(full=True), "methionine")
         self.assertEqual(chaina[-1].name(), "ILE")
+        self.assertEqual(chaina[-1].name(full=True), "isoleucine")
         self.assertEqual(chaina[-1].previous().name(), "SER")
         self.assertEqual(len(chaina.residues(name="ASN")), 6)
         for residue in chaina:
@@ -77,6 +80,7 @@ def test_can_read_pdb(self):
         mol = model.molecule(molecule_id="A2001")
         self.assertIs(mol.model(), model)
         self.assertEqual(mol.name(), "XMP")
+        self.assertEqual(mol.name(full=True), "XMP")
         self.assertEqual(len(mol.atoms()), 24)
 
         # Bindsites are correct
diff --git a/tests/unit/structure_tests/test_molecules.py b/tests/unit/structure_tests/test_molecules.py
index 55c98caf..bdf66880 100644
--- a/tests/unit/structure_tests/test_molecules.py
+++ b/tests/unit/structure_tests/test_molecules.py
@@ -94,6 +94,13 @@ def test_molecule_name_property(self):
         self.assertIs(mol._name, mol.name())
 
 
+    def test_molecule_name_property_full(self):
+        mol = Molecule(self.atom1, self.atom2, self.atom3, name="VAL")
+        self.assertEqual(mol.name(full=True), "valine")
+        mol = Molecule(self.atom1, self.atom2, self.atom3, name="VL")
+        self.assertEqual(mol.name(full=True), "VL")
+
+
     def test_can_update_molecule_name(self):
         mol = Molecule(self.atom1, self.atom2, self.atom3, name="VAL")
         mol.name("HIS")