This directory contains examples of defining atoms, bonds, molecules and reactions in Atomese using several different execution environments: 1) Scheme, 2) Python, 3) Python within Jupyter notebooks. Recall that Atomese can be freely mixed between scheme and python: under the covers, the data is always in Atomese, and not in the programming language environment itself. (See the examples in the core AtomSpace git repo for demos.)
Changedir to the python directory and use the Python 3 interpreter
to run scripts there:
$ python3 intro_example.py
This is the most basic demo: it shows how to create a single atom, a single chemical bond, and a methane molecule.
If you run python virtualenv, and are experiencing issues with undefined
symbols, then try adding /usr/local/lib/python3.11/dist-packages/
to your PYTHON_PATH and adding /usr/local/lib/opencog/ to your
LD_LIBRARY_PATH.
The scheme directory contains a much more complex example. It uses the AtomSpace query engine to define a rewrite rule that performs an esterification reaction. Although written in scheme, it could also be re-written in python, by re-arranging the parenthesis. (This isn't hard, just tedious.)
Changedir to the scheme directory and use the Guile interpreter
to run the demo:
$ guile -s reaction.scm
In order to monkey with the example, it can be more convenient to work at the command prompt, and cut-n-paste portions of the example into the guile REPL:
$ guile
(use-modules (opencog) (opencog cheminformatics))
(load "reaction.scm")
The current examples are:
- reaction.scm - An esterification reaction.
Change to the jupyter directory, start a Jupyter server and use the
automatically opened web GUI to inspect and run a notebook:
$ jupyter-notebook