Final 0.5 changes

README.rst

@@ -48,7 +48,8 @@ Requirements
 ~~~~~~~~~~~~
 
 atomium requires the Python library
-`geometrica <https://geometrica.samireland.com/>`_ - pip will install this
+`points <https://points.samireland.com/>`_ and
+`requests <https://docs.python-requests.org/>`_ - pip will install these
 automatically when it installs atomium.
 
 
@@ -85,6 +86,9 @@ from the RCSB over the internet using the PDB code:
   >>> pdb2.model()
   <Model (2156 atoms)>
 
+If the PDB has multiple models, these can be accessed using the
+``Pdb.models`` method.
+
 The Model
 ~~~~~~~~~
 
@@ -239,7 +243,7 @@ Residues are also a kind of Molecule, and have other useful properties:
   <Residue A24 (ARG, 11 atoms)>
   >>> pdb.model().residue("A23").previous()
   <Residue A22 (MET, 8 atoms)>
-  
+
 
 Saving
 ~~~~~~
@@ -266,6 +270,21 @@ The ``Xyz`` or ``Pdb`` object itself can also be saved:
 Changelog
 ---------
 
+Release 0.5.0
+~~~~~~~~~~~~~
+
+`16 September 2017`
+
+* Added atom temperature factors.
+* Added bond vector production.
+* Added parse time tests and reduced parse time by over a half.
+* Changed way atoms are stored in structures to make ID lookup orders of \
+  magnitude faster.
+* Made IDs immutable.
+* Added multiple model parsing and saving.
+* Added option to fetch PDBs from PDBe rather than RCSB.
+
+
 Release 0.4.0
 ~~~~~~~~~~~~~
 

atomium/structures/molecules.py

@@ -74,10 +74,10 @@ def atom(self, *args, **kwargs):
         atom matches the criteria you give, it might not be the same atom that
         is returned each time you call this method.
 
-        :param str element: If given, only atoms whose element matches this\
-        will be searched.
         :param int atom_id: If given, only atoms whose atom ID matches this\
         will be searched.
+        :param str element: If given, only atoms whose element matches this\
+        will be searched.
         :param str name: If given, only atoms whose name matches this will be\
         searched.
         :rtype: ``Atom``"""

docs/source/api.rst

@@ -31,7 +31,7 @@ Converters
     api/structure2xyzstring
     api/string2pdbfile
     api/pdbfile2pdbdatafile
-    api/pdbdatafile2model
+    api/pdbdatafile2models
     api/pdbdatafile2pdb
     api/pdb2pdbdatafile
     api/structure2pdbdatafile

docs/source/api/pdbdatafile2models.rst

@@ -0,0 +1,6 @@
+``atomium.converters.pdbdatafile2models`` (Pdb datafile to models conversion)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. automodule:: atomium.converters.pdbdatafile2models
+    :members:
+    :inherited-members:

docs/source/changelog.rst

@@ -9,8 +9,8 @@ Release 0.5.0
 * Added atom temperature factors.
 * Added bond vector production.
 * Added parse time tests and reduced parse time by over a half.
-* Changed way atoms are stored in structures to make ID lookup orders of\
-magnitude faster.
+* Changed way atoms are stored in structures to make ID lookup orders of \
+  magnitude faster.
 * Made IDs immutable.
 * Added multiple model parsing and saving.
 * Added option to fetch PDBs from PDBe rather than RCSB.

docs/source/overview.rst

@@ -31,8 +31,8 @@ from the RCSB over the internet using the PDB code:
   >>> pdb2.model()
   <Model (2156 atoms)>
 
-If the PDB has multiple models, these can be accessed using the :py:meth:`
-~.Pdb.models` method.
+If the PDB has multiple models, these can be accessed using the
+:py:meth:`~.Pdb.models` method.
 
 The Model
 ~~~~~~~~~
@@ -188,7 +188,7 @@ Residues are also a kind of Molecule, and have other useful properties:
   <Residue A24 (ARG, 11 atoms)>
   >>> pdb.model().residue("A23").previous()
   <Residue A22 (MET, 8 atoms)>
-  
+
 
 Saving
 ~~~~~~

setup.py

@@ -24,5 +24,5 @@
  ],
  keywords="chemistry bioinformatics proteins biochemistry molecules PDB XYZ",
  packages=["atomium", "atomium.files", "atomium.converters", "atomium.structures"],
- install_requires=["geometrica"]
+ install_requires=["geometrica", "points", "requests"]
 )