1.0.0 docs

LICENSE

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2018 Sam Ireland
+Copyright (c) 2019 Sam Ireland
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.rst

@@ -74,6 +74,31 @@ fetching structures over SSH,
 and `valerius <https://valerius.samireland.com>`_ for dealing with sequences.
 
 
+Testing
+~~~~~~~
+
+To test a local version of atomium, cd to the atomium directory and run:
+
+``$ python -m unittest discover tests``
+
+You can opt to only run unit tests or integration tests:
+
+``$ python -m unittest discover tests.unit``
+``$ python -m unittest discover tests.integration``
+
+You can run the 'big test' to get a random 1000 structures, parse them all, and
+report any problems:
+
+``$ python tests/big.py``
+
+Finally, to perform speed profiles you can run:
+
+``$ python tests/time/time.py``
+
+...which creates various profiles that SnakeViz can visualise.
+
+
+
 Overview
 --------
 
@@ -112,7 +137,7 @@ Once you've got your ``File`` object, what can you do with it?
 Annotation
 ##########
 
-There is various meta information contained within the ``File`` object.
+There is meta information contained within the ``File`` object:
 
     >>> pdb1.title
     'CRYSTAL STRUCTURE OF OROTIDINE MONOPHOSPHATE DECARBOXYLASE COMPLEX WITH XMP'
@@ -177,8 +202,6 @@ the asymmetric unit with 1,842 atoms, and then generate two of its possible
 biological assemblies by passing in their IDs.
 
 
-
-
 Model Contents
 ##############
 
@@ -203,6 +226,8 @@ The basic structures within a model are chains, residues, ligands, and atoms.
     037)>, <Residue PRO (A.129)>, <Residue PRO (B.1161)>, <Residue TYR (A.206)>}
     >>> pdb1.model.chain('B').residue('B.1206')
     <Residue TYR (B.1206)>
+    >>> pdb1.model.chain('B').residue('B.1206').helix
+    True
     >>> pdb1.model.ligands()
     {<Ligand BU2 (A.5001)>, <Ligand XMP (A.2001)>, <Ligand BU2 (B.5002)>, <Ligan
     d XMP (B.2002)>}
@@ -346,6 +371,25 @@ results.
 Changelog
 ---------
 
+Release 1.0.0
+~~~~~~~~~~~~~
+
+`23 June 2019`
+
+* Saving now issues warning if the stucture has duplicate IDs.
+* Missing residues parsed for all three file types.
+* Crystallographic information now parsed.
+* Refactor of atomic structures.
+* Refactor of .mmtf parsing.
+* Structure copying now retains all properties.
+* Fixed bug in parsing .cif expression systems.
+* Full names of ligands and modified residues now parsed.
+* Secondary structure information parsed and available now.
+* Atoms now have covalent radius property for calculating bond cutoffs.
+* .pdb parsing can now handle heavy water (DOD).
+* General speed improvements.
+
+
 Release 0.12.2
 ~~~~~~~~~~~~~~
 

atomium/utilities.py

@@ -13,6 +13,7 @@ def open(path, *args, **kwargs):
     it accordingly.
 
     For example:
+
         >>> atomium.open('/path/to/file.pdb', data_dict=True)
 
     This will parse file.pdb as a .pdb file, but only go as far as converting it
@@ -39,6 +40,7 @@ def fetch(code, *args, **kwargs):
     look in that location.
 
     For example:
+    
         >>> atomium.fetch('1lol.mmtf', file_dict=True)
     
     This will get the .mmtf version of structure 1LOL, but only go as far as

docs/source/changelog.rst

@@ -1,6 +1,25 @@
 Changelog
 ---------
 
+Release 1.0.0
+~~~~~~~~~~~~~
+
+`23 June 2019`
+
+* Saving now issues warning if the stucture has duplicate IDs.
+* Missing residues parsed for all three file types.
+* Crystallographic information now parsed.
+* Refactor of atomic structures.
+* Refactor of .mmtf parsing.
+* Structure copying now retains all properties.
+* Fixed bug in parsing .cif expression systems.
+* Full names of ligands and modified residues now parsed.
+* Secondary structure information parsed and available now.
+* Atoms now have covalent radius property for calculating bond cutoffs.
+* .pdb parsing can now handle heavy water (DOD).
+* General speed improvements.
+
+
 Release 0.12.2
 ~~~~~~~~~~~~~~
 

docs/source/installing.rst

@@ -33,3 +33,28 @@ structures from the RCSB, `paramiko <http://www.paramiko.org//>`_ for
 fetching structures over SSH,
 `msgpack <https://github.com/msgpack/msgpack-python>`_ for parsing .mmtf files,
 and `valerius <https://valerius.samireland.com>`_ for dealing with sequences.
+
+
+Testing
+~~~~~~~
+
+To test a local version of atomium, cd to the atomium directory and run:
+
+``$ python -m unittest discover tests``
+
+You can opt to only run unit tests or integration tests:
+
+``$ python -m unittest discover tests.unit``
+``$ python -m unittest discover tests.integration``
+
+You can run the 'big test' to get a random 1000 structures, parse them all, and
+report any problems:
+
+``$ python tests/big.py``
+
+Finally, to perform speed profiles you can run:
+
+``$ python tests/time/time.py``
+
+...which creates various profiles that SnakeViz can visualise.
+

docs/source/overview.rst

@@ -36,7 +36,7 @@ Once you've got your :py:class:`.File` object, what can you do with it?
 Annotation
 ##########
 
-There is various meta information contained within the :py:class:`.File` object.
+There is meta information contained within the :py:class:`.File` object:
 
     >>> pdb1.title
     'CRYSTAL STRUCTURE OF OROTIDINE MONOPHOSPHATE DECARBOXYLASE COMPLEX WITH XMP'
@@ -101,8 +101,6 @@ the asymmetric unit with 1,842 atoms, and then generate two of its possible
 biological assemblies by passing in their IDs.
 
 
-
-
 Model Contents
 ##############
 
@@ -127,6 +125,8 @@ The basic structures within a model are chains, residues, ligands, and atoms.
     037)>, <Residue PRO (A.129)>, <Residue PRO (B.1161)>, <Residue TYR (A.206)>}
     >>> pdb1.model.chain('B').residue('B.1206')
     <Residue TYR (B.1206)>
+    >>> pdb1.model.chain('B').residue('B.1206').helix
+    True
     >>> pdb1.model.ligands()
     {<Ligand BU2 (A.5001)>, <Ligand XMP (A.2001)>, <Ligand BU2 (B.5002)>, <Ligan
     d XMP (B.2002)>}