Project for CAS741.
Developer Name: Jen Garner
This project implements conformer searching using evolutionary computation.
The main folders in the project are:
- docs (documentation)
- kaplan (source code)
There is also a test folder within the kaplan directory that contains:
- testfiles
- jupyter-notebooks
Kaplan has the following dependencies. Note sublists indicate that Kaplan does not directly import the dependency, but it is needed by its parent in the list.
The recommended installation process involves installing conda or miniconda.
Generate a new conda environment:
$ conda create -n kenv python=3.6 numpy
Turn on the environment:
$ source activate kenv
Your prompt should now reflect the environment name:
(kenv) $
With the environment active, install the dependencies:
- psi4
(kenv) $ conda install -c psi4 psi4 - openbabel
(kenv) $ conda install -c openbabel openbabel - pubchempy
(kenv) $ conda install -c mcs07 pubchempy - rmsd
(kenv) $ pip install rmsd - vetee
(kenv) $ pip install -i https://pypi.anaconda.org/kumrud/simple vetee
Do a git clone of the kaplan repo:
(kenv) $ git clone https://github.com/PeaWagon/Kaplan.git
Go into the Kaplan directory:
(kenv) $ cd Kaplan
Then do a pip install (development):
(kenv) $ pip install -e ./
To see installed packages:
(kenv) $ conda list
Turn off the environment:
(kenv) $ source deactivate kenv
$
(kenv) $ pip uninstall kaplan
Please see the README.md in the kaplan subdirectory for more information on how to run this program.
Please see the README.md in the kaplan/test subdirectory for information on how to run the tests for this program.
The following people have contributed in some way to the making of this project.
- Kumru Dikmenli
- Xiaomin Huang
- Laura Bickley
- Brooks MacLachlan
- Vajiheh Motamer
- Oluwaseun Owojaiye
- Karol Sekis
- Malavika Srinivasan
- Robert White
- Hanane Zlitni
- Dr. Spencer Smith
- Dr. Paul Ayers