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Kaplan

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

Dependencies

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.

How to install

Installing Dependencies

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

Installing Kaplan

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 ./

Working with the environment

To see installed packages:
(kenv) $ conda list

Turn off the environment:
(kenv) $ source deactivate kenv
$

Uninstall Kaplan

(kenv) $ pip uninstall kaplan

How to run Kaplan

Please see the README.md in the kaplan subdirectory for more information on how to run this program.

Running tests

Please see the README.md in the kaplan/test subdirectory for information on how to run the tests for this program.

Special Thanks

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