From f0bb2f388077e636554378b4308b5752e5dd545a Mon Sep 17 00:00:00 2001
From: Sam Ireland <sam.ireland.uk@gmail.com>
Date: Sat, 2 Dec 2017 17:29:53 +0000
Subject: [PATCH] Final 0.8 changes

---
 README.rst                         | 29 +++++++++++++++++++++++++----
 atomium/files/pdbstring2pdbdict.py | 22 ++++++++++++++--------
 atomium/structures/molecules.py    |  3 +++
 3 files changed, 42 insertions(+), 12 deletions(-)

diff --git a/README.rst b/README.rst
index fb063870..7df09aa3 100644
--- a/README.rst
+++ b/README.rst
@@ -1,10 +1,10 @@
-.. |travis| image:: https://api.travis-ci.org/samirelanduk/atomium.svg?branch=0.7
+.. |travis| image:: https://api.travis-ci.org/samirelanduk/atomium.svg?branch=0.8
 
-.. _travis: https://travis-ci.org/samirelanduk/atomium/
+.. _travis https://travis-ci.org/samirelanduk/atomium/
 
-.. |coveralls| image:: https://coveralls.io/repos/github/samirelanduk/atomium/badge.svg?branch=0.7
+.. |coveralls| image:: https://coveralls.io/repos/github/samirelanduk/atomium/badge.svg?branch=0.8
 
-.. _coveralls: https://coveralls.io/github/samirelanduk/atomium/
+.. _coveralls https://coveralls.io/github/samirelanduk/atomium/
 
 .. |pypi| image:: https://img.shields.io/pypi/pyversions/atomium.svg
 
@@ -102,6 +102,12 @@ from the RCSB over the internet using the PDB code:
   datetime.date(2002, 5, 6)
   >>> pdb.resolution()
   1.9
+  >>> pdb.rfactor()
+  0.193
+  >>> pdb.classification()
+  'LYASE'
+  >>> pdb.technique()
+  'X-RAY DIFFRACTION'
   >>> pdb2.model()
   <Model (2156 atoms)>
 
@@ -311,6 +317,21 @@ The ``Xyz`` or ``Pdb`` object itself can also be saved:
 Changelog
 ---------
 
+Release 0.8.0
+~~~~~~~~~~~~~
+
+`2 December 2017`
+
+* Added option to get water residues in binding sites.
+* Added extra PDB meta information parsing, such as:
+
+	* Classification
+	* Experimental Technique
+	* Source Organism
+	* Expression Organism
+	* R-factor
+
+
 Release 0.7.0
 ~~~~~~~~~~~~~
 
diff --git a/atomium/files/pdbstring2pdbdict.py b/atomium/files/pdbstring2pdbdict.py
index 835f4f24..26a412dd 100644
--- a/atomium/files/pdbstring2pdbdict.py
+++ b/atomium/files/pdbstring2pdbdict.py
@@ -123,6 +123,20 @@ def extract_source(pdb_dict, lines):
             pdb_dict["expression_system"] = matches[0]
 
 
+def extract_technique(pdb_dict, lines):
+    """Takes a ``dict`` and adds technique information to it by parsing file
+    lines.
+
+    :param dict pdb_dict: the ``dict`` to update.
+    :param list lines: the file lines to read from."""
+
+    line = get_line("EXPDTA", lines)
+    if line:
+        pdb_dict["technique"] = line[6:].strip()
+        if pdb_dict["technique"]: return
+    pdb_dict["technique"] = None
+
+
 def extract_structure(pdb_dict, lines):
     """Takes a ``dict`` and adds structure information to it by parsing file
     lines.
@@ -150,14 +164,6 @@ def extract_structure(pdb_dict, lines):
     extract_connections(pdb_dict, conect_lines)
 
 
-def extract_technique(pdb_dict, lines):
-    line = get_line("EXPDTA", lines)
-    if line:
-        pdb_dict["technique"] = line[6:].strip()
-        if pdb_dict["technique"]: return
-    pdb_dict["technique"] = None
-
-
 def lines_to_model(atom_lines, hetatm_lines):
     """Creates a model ``dict`` from ATOM lines and HETATM lines.
 
diff --git a/atomium/structures/molecules.py b/atomium/structures/molecules.py
index a7bbc99d..89e48285 100644
--- a/atomium/structures/molecules.py
+++ b/atomium/structures/molecules.py
@@ -345,6 +345,9 @@ def site(self, include_water=False):
         all the residues with a non-hydrogen atom within 4 Angstroms of a
         non-hydrogen atom in the molecule.
 
+        :param bool include_water: If ``True``, water molecules will be\
+        obtained as well as residues.
+
         :rtype: :py:class:`.Site`"""
 
         from .chains import Site