Documentation update (#134)

*  Update the documentation for nlesc-nano/data-CAT#25.

CAT/__version__.py

@@ -1,3 +1,3 @@
 """The **CAT** version."""
 
-__version__ = '0.9.5'
+__version__ = '0.9.6'

CHANGELOG.rst

@@ -11,6 +11,11 @@ This project adheres to `Semantic Versioning <http://semver.org/>`_.
 * WiP: Added an option the import pre-built quantum dots.
 
 
+0.9.6
+*****
+* Updated the documentation for https://github.com/nlesc-nano/data-CAT/pull/25.
+
+
 0.9.5
 *****
 * Fixed a bug where rdkit molecules were not properly converted into numpy arrays.

README.rst

@@ -16,7 +16,7 @@
 
 
 ##############################
-Compound Attachment Tool 0.9.5
+Compound Attachment Tool 0.9.6
 ##############################
 
 **CAT** is a collection of tools designed for the construction of various chemical compounds.

docs/7_database.rst

@@ -77,18 +77,85 @@ Index
     OpenQD
     OpenYaml
 
+    PDBContainer
+    DTYPE_ATOM
+    DTYPE_BOND
+
 
 API
 ---
 .. autoclass:: Database
     :members:
+
 .. autoclass:: DFProxy
+
 .. autoclass:: OpenLig
     :members:
     :inherited-members:
+
 .. autoclass:: OpenQD
     :members:
     :inherited-members:
+
 .. autoclass:: OpenYaml
     :members:
     :inherited-members:
+
+.. autoclass:: PDBContainer
+    :members: atoms, bonds, atom_count, bond_count, __getitem__, __len__, from_molecules, to_molecules, from_hdf5, to_hdf5
+
+.. data:: DTYPE_ATOM
+    :type: Mapping[str, np.dtype]
+    :value: ...
+
+    A mapping representing the dtype of :attr:`PDBContainer.atoms`.
+
+    Most field names are based on to their, identically named, counterpart as produced by
+    :func:`readpdb()<scm.plams.interfaces.molecule.rdkit.readpdb>`,
+    the data in question being stored in the
+    :class:`Atom.properties.pdb_info<scm.plams.mol.atom.Atom>` block.
+
+    There are six exception to this general rule:
+
+    * ``x``, ``y`` & ``z``: Based on :class:`Atom.x<scm.plams.mol.atom.Atom>`,
+      :class:`Atom.y<scm.plams.mol.atom.Atom>` and :class:`Atom.z<scm.plams.mol.atom.Atom>`.
+    * ``symbol``: Based on :class:`Atom.symbol<scm.plams.mol.atom.Atom>`.
+    * ``charge``: Based on :class:`Atom.properties.charge<scm.plams.mol.atom.Atom>`.
+    * ``charge_float``: Based on :class:`Atom.properties.charge_float<scm.plams.mol.atom.Atom>`.
+
+    .. code:: python
+
+        mappingproxy({
+            'IsHeteroAtom':  dtype('bool'),
+            'SerialNumber':  dtype('int16'),
+            'Name':          dtype('S4'),
+            'ResidueName':   dtype('S3'),
+            'ChainId':       dtype('S1'),
+            'ResidueNumber': dtype('int16'),
+            'x':             dtype('float32'),
+            'y':             dtype('float32'),
+            'z':             dtype('float32'),
+            'Occupancy':     dtype('float32'),
+            'TempFactor':    dtype('float32'),
+            'symbol':        dtype('S4'),
+            'charge':        dtype('int8'),
+            'charge_float':  dtype('float64')
+        })
+
+
+.. data:: DTYPE_BOND
+    :type: Mapping[str, np.dtype]
+    :value: ...
+
+    A mapping representing the dtype of :attr:`PDBContainer.bonds`.
+
+    Field names are based on to their, identically named,
+    counterpart in :class:`~scm.plams.mol.bond.Bond`.
+
+    .. code:: python
+
+        mappingproxy({
+            'atom1': dtype('int32'),
+            'atom2': dtype('int32'),
+            'order': dtype('int8')
+        })

docs/conf.py

@@ -77,7 +77,7 @@
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the built documents.
-release = '0.9.5'  # The full version, including alpha/beta/rc tags.
+release = '0.9.6'  # The full version, including alpha/beta/rc tags.
 version = release.rsplit('.', maxsplit=1)[0]
 
 

setup.py

@@ -29,7 +29,7 @@
     'pydocstyle>=5.0.0',
     'pytest-pydocstyle>=2.1',
     'pytest-mock',
-    'data-CAT@git+https://github.com/nlesc-nano/data-CAT@master'
+    'data-CAT@git+https://github.com/nlesc-nano/data-CAT@devel'
 ]
 
 if sys.version_info[1] > 6: