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.

• python 3.6
• numpy
• rmsd
  • scipy
• psi4
• openbabel
• vetee
  • pubchempy

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:

1. psi4
   (kenv) $ conda install -c psi4 psi4
2. openbabel
   (kenv) $ conda install -c openbabel openbabel
3. pubchempy
   (kenv) $ conda install -c mcs07 pubchempy
4. rmsd
   (kenv) $ pip install rmsd
5. 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