Examples
========
.. highlight:: bash
cockatoo command line
----------------------
cockatoo comes with a command line utility for computing distances. To get a
list of commands run::
$ cockatoo --help
Usage: cockatoo [OPTIONS] COMMAND [ARGS]...
Options:
-v, --verbose Turn on verbose logging
--help Show this message and exit.
Commands:
cdist Compute the distance between 2 cocktails
convert Convert CSV screen to JSON format
hclust Perform hierarchical clustering on a screen
isim Compute the internal similarity score for a...
sdist Compute the distance between 2 screens
version Print cockatoo version
To get help for a specific command run::
$ cockatoo sdist --help
Usage: cockatoo sdist [OPTIONS]
Compute the distance between 2 screens
Options:
-1, --screen1 PATH Path to screen1 in JSON format [required]
-2, --screen2 PATH Path to screen2 in JSON format [required]
-w, --weights WEIGHTS weights=1,1
--help Show this message and exit.
Compute distance between cocktails
+++++++++++++++++++++++++++++++++++
Create two JSON files (ck1.json, ck1.json) describing your cocktails. See
:doc:`../tutorial` for file format specification. Then run::
$ cockatoo cdist -1 ck1.json -2 ck1.json
Compute distance between screens
+++++++++++++++++++++++++++++++++++
Create two JSON files (s1.json, s2.json) describing your screens. See
:doc:`../tutorial` for file format specification. Then run::
$ cockatoo sdist -1 s1.json -2 s2.json
Convert CSV screen to JSON
+++++++++++++++++++++++++++
Converting a screen stored in CSV format to JSON requires your CSV file to be in
a specific format, see the :doc:`../tutorial` for more info. You will also need
a compound summary file which includes data on each compound found in your
cocktails. See the data/hwi-compounds.csv file for an example. To convert the
screen run::
$ cockatoo convert -i screen.csv -o screen.json -n screen_name -s hwi-compounds.csv
Compute interal similarity
+++++++++++++++++++++++++++
This command will compute the interal similarity score for a given screen.
Create a JSON file (s1.json) describing your screen. See :doc:`../tutorial` for
file format specification. Then run::
$ cockatoo isim -s s1.json
Hierarchical clustering
+++++++++++++++++++++++++++
This command will perform hierarchical clustering on a given screen. This
command requires python modules: `numpy `_, `scipy
`_, and `matplotlib `_ to be
installed. Create a JSON file (s1.json) describing your screen. See
:doc:`../tutorial` for file format specification. Then run::
$ cockatoo -v hclust -s s1.json -p -d -n
cockatoo API
----------------------
An example of using cockatoo python API:
.. code-block:: python
import cockatoo
ck1 = cockatoo.screen.parse_cocktail('ck1.json')
ck2 = cockatoo.screen.parse_cocktail('ck2.json')
dist = cockatoo.metric.distance(ck1, ck2)
print "Distance: {}".format(dist)