Documentation update (duartegroup#31)

* Update citation and add additional documentation * Bump version to 1.0.0
ss0832 · Feb 22, 2021 · 32772f2 · 32772f2
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diff --git a/README.md b/README.md
@@ -11,7 +11,7 @@ reactant(s) and product(s).
 ### Dependencies
 * [Python](https://www.python.org/) > v. 3.5
 * One of:
-   * [ORCA](https://sites.google.com/site/orcainputlibrary/home/) > v. 4.2
+   * [ORCA](https://sites.google.com/site/orcainputlibrary/home/) > v. 4.1
    * [Gaussian09](https://gaussian.com/glossary/g09/)
    * [Gaussian16](https://gaussian.com/gaussian16/)
    * [NWChem](http://www.nwchem-sw.org/index.php/Main_Page)
@@ -35,9 +35,8 @@ see the [installation guide](https://duartegroup.github.io/autodE/install.html)
 ## Usage
 
 Reaction profiles in  **autodE** are generated by initialising _Reactant_ and _Product_ objects, 
-generating a _Reaction_ from those and invoking a method  e.g. _locate_transition_state()_ 
-or _calculate_reaction_profile()_. For example, to  calculate the reaction profile for 
-a 1,2 hydrogen shift in a propyl radical
+generating a _Reaction_ from those and invoking _calculate_reaction_profile()_. 
+For example, to  calculate the profile for a 1,2 hydrogen shift in a propyl radical
 
 ```python
 import autode as ade
@@ -66,12 +65,14 @@ Bugs and feature requests should be raised on the [issue page](https://github.co
 If **autodE** is used in a publication please consider citing the [paper](https://doi.org/10.1002/anie.202011941):
 
 ```
-@article{autodE2020,
+@article{autodE,
   doi = {10.1002/anie.202011941},
   url = {https://doi.org/10.1002/anie.202011941},
-  year = {2020},
-  month = oct,
+  year = {2021},
   publisher = {Wiley},
+  volume = {60},
+  number = {8},
+  pages = {4266--4274},
   author = {Tom A. Young and Joseph J. Silcock and Alistair J. Sterling and Fernanda Duarte},
   title = {{autodE}: Automated Calculation of Reaction Energy Profiles {\textendash} Application to Organic and Organometallic Reactions},
   journal = {Angewandte Chemie International Edition}

diff --git a/autode/__init__.py b/autode/__init__.py
@@ -16,7 +16,7 @@
 from autode import neb
 from autode import mol_graphs
 
-__version__ = '1.0.0b3'
+__version__ = '1.0.0'
 
 
 __all__ = [

diff --git a/autode/input_output.py b/autode/input_output.py
@@ -75,6 +75,6 @@ def atoms_to_xyz_file(atoms, filename, title_line='', append=False):
 
         for atom in atoms:
             x, y, z = atom.coord
-            print(f'{atom.label:<3}{x:^10.5f}{y:^10.5f}{z:^10.5f}',
+            print(f'{atom.label:<3}{x:10.5f}{y:10.5f}{z:10.5f}',
                   file=xyz_file)
     return None
diff --git a/doc/citation.rst b/doc/citation.rst
@@ -0,0 +1,12 @@
+Citation
+========
+
+If **autodE** is used in a published work please consider citing the `paper <https://doi.org/10.1002/anie.202011941>`_ alongside all the methods used.
+
+
+.. note::
+
+    T. A. Young, J. J. Silcock, A. J. Sterling, F. Duarte, *autodE:
+    Automated Calculation of Reaction Energy Profiles— Application to
+    Organic and Organometallic Reactions* Angew. Chem. Int. Ed. 2021, **60**, 4266.
+
diff --git a/doc/common/curtius.png b/doc/common/curtius.png
diff --git a/doc/common/curtius.py b/doc/common/curtius.py
@@ -0,0 +1,6 @@
+import autode as ade
+ade.Config.n_cores = 8
+
+rxn = ade.Reaction('CC(N=[N+]=[N-])=O>>CN=C=O.N#N')
+rxn.locate_transition_state()
+rxn.ts.print_xyz_file(filename='ts.xyz')
diff --git a/doc/common/curtius_ts.png b/doc/common/curtius_ts.png
diff --git a/doc/common/curtius_ts.xyz b/doc/common/curtius_ts.xyz
@@ -0,0 +1,11 @@
+9
+
+C   -1.39241  0.07121   0.43067  
+C   -0.04556  -0.33487  -0.30235 
+N   0.68638   0.45200   0.41896  
+N   2.38870   0.17768   -0.19102 
+N   3.46715   0.37885   -0.11094 
+O   0.02674   -1.13494  -1.20133 
+H   -1.32812  0.81952   1.22935  
+H   -2.03100  0.44587   -0.38050 
+H   -1.77188  -0.87532  0.83854  
diff --git a/doc/common/logo.png b/doc/common/logo.png
diff --git a/doc/common/vaskas_conformers.py b/doc/common/vaskas_conformers.py
@@ -1,10 +1,8 @@
-from autode import Molecule
-from autode.input_output import xyz_file_to_atoms
+import autode as ade
 from autode.conformers import conf_gen, Conformer
-from autode.methods import XTB
 
 # Initialise the complex from a .xyz file containing a square planar structure
-vaskas = Molecule(name='vaskas', atoms=xyz_file_to_atoms('vaskas.xyz'))
+vaskas = ade.Molecule('vaskas.xyz')
 
 # Set up some distance constraints where the keys are the atom indexes and
 # the value the distance in Å. Fixing the Cl-P, Cl-P and Cl-C(=O) distances
@@ -25,5 +23,5 @@
     # Generate a conformer from these atoms then optimise with XTB
     conformer = Conformer(name=f'vaskas_conf{n}', atoms=atoms)
 
-    conformer.optimise(method=XTB())
+    conformer.optimise(method=ade.methods.XTB())
     conformer.print_xyz_file()
diff --git a/doc/examples/tss.rst b/doc/examples/tss.rst
@@ -2,17 +2,52 @@
 Transition States
 *****************
 
+In addition to generating full reaction profiles directly **autodE** provides
+automated access to transition states (TSs). TSs are found either from a
+reaction, where bond rearrangements are found and TS located along each
+possible path, or from 3D structures of reactants & products, and a given bond
+rearrangement.
+
+------------
+
+Default: Reaction
+*****************
+
+
+.. image:: ../common/curtius.png
+
+For a simple Curtius rearrangement copied as a SMILES string directly from
+Chemdraw\ :sup:`TM`\  (selecting reactants and products with arrows and '+' then Edit->Copy As->SMILES)
+the TS can be located with
+
+
+.. literalinclude:: ../common/curtius.py
+
 
-Default
-*******
+Out (visualised)
+
+.. image:: ../common/curtius_ts.png
+   :width: 450
+   :align: center
+
+
+.. note::
+    :code:`locate_transition_state` only locates a single transtion state for
+    each possible bond rearrangment and does not attempt to search the conformational
+    space.
+
+
+------------
+
+
+Default: Reactants and products
+*******************************
 
 .. image:: ../common/cope.png
 
 
-In addition to generating full reaction profiles directly **autodE** provides
-automated access to transition states. Given a specific bond rearrangement
-generating a TS from known structures of reactants and products can be achieved
-for a simple Cope rearrangement with
+Given a specific bond rearrangement generating a TS from known structures of
+reactants and products can be achieved for a simple Cope rearrangement with
 
 
 .. literalinclude:: ../common/cope.py
@@ -30,6 +65,7 @@ where the xyz files used are:
 
 .. literalinclude:: ../common/cope_p.xyz
 
+------------
 
 CI-NEB
 ******

diff --git a/doc/index.rst b/doc/index.rst
@@ -1,18 +1,19 @@
 .. _contents:
 
-Overview of autodE_
-=====================
+.. image:: common/logo.png
+   :width: 450
+   :align: center
 
-.. _autodE: https://github.com/duartegroup/autodE
+Overview
+========
 
-**autodE** is a Python module designed for the automated calculation of reaction
-profiles from reactant(s) and product(s) given as 1D SMILES or 3D structures.
-Functionality for conformational sampling (RR algorithm) and transition state
-finding (NEB, CI-NEB, adapt.) is also available.
+.. _autodE: https://github.com/duartegroup/autodE
 
 
-.. warning::
-    **autodE** is still beta release. Please report any bugs `here <https://github.com/duartegroup/autodE/issues>`_
+`autodE <https://github.com/duartegroup/autodE/>`_ is a Python module designed for the automated generation of reaction
+profiles as fast as possible. Profiles are generated using a double-ended search form reactant(s) and product(s)
+given as 1D SMILES or 3D structures. Functionality for conformational sampling (RR algorithm) and transition state
+finding (NEB, CI-NEB, adapt.) is also available.
 
 
 Documentation
@@ -33,10 +34,10 @@ Documentation
    troubleshooting
    examples/index
    changelog
+   citation
 
 Indices and tables
 ==================
 
 * :ref:`genindex`
 * :ref:`modindex`
-* :ref:`search`
diff --git a/doc/install.rst b/doc/install.rst
@@ -32,7 +32,7 @@ First clone the repository and ``cd`` there::
 
 then, install the appropriate dependencies (you may want to create a new virtual environment)::
 
-    $ conda config --append channels conda-forge --append channels omnia
+    $ conda config --append channels conda-forge
     $ conda install --file requirements.txt
 
 finally::

diff --git a/doc/quickstart.rst b/doc/quickstart.rst
@@ -75,6 +75,9 @@ From reactants and products form a reaction in water and calculate the reaction
 This function call will return a plot something like:
 
 .. image:: common/sn2_reaction_profile.png
+   :width: 550
+   :align: center
+
 
 as *sn2_reaction_profile.png* in the current working directory, where conformers
 of the reactant and products have been searched and the profile calculated at

diff --git a/setup.py b/setup.py
@@ -1,13 +1,12 @@
 from setuptools import setup
 from Cython.Build import cythonize
 from setuptools.extension import Extension
-import autode
 
 
 extensions = [Extension('cconf_gen', ['autode/conformers/cconf_gen.pyx'])]
 
 setup(name='autode',
-      version=autode.__version__,
+      version='1.0.0',
       packages=['autode',
                 'autode.conformers',
                 'autode.pes',