Automated conformational search with a genetic algorithm interfaced with a Psi4-input generator for conformers that requires only SMILES as input
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Smiles4Psi is a Python 3 program that automates the creation of Psi4 input files for 3D-structures obtained from a genetic algorithm conformational search. The conformers are generated via Open Babel. The only input Smiles4Psi requires is a SMILES string description of the molecule.
To run Smiles4Psi, the code requires Python 3.7 and its modules psi4, psi4-rt, openbabel, and psutil. So, the instructions to download and install Smiles4Psi and to create a conda environment that includes these modules are presented below.
Minimal set of commands to install Smiles4Psi on Linux, MacOS, or Windows (with the Windows Subsystem for Linux). Last tested on 16 August 2021:
If you have an installation of Conda in your system, please skip to step 2. Otherwise, Miniconda is required and the installer is available from the Anaconda website. To download the installer from the terminal (in Linux or the Windows Subsystem for Linux):
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
(Note) If you use MacOS, replace Linux by MacOSX in the previous command and the subsequent ones.
Run the installer following on-screen instructions:
bash Miniconda3-latest-Linux-x86_64.sh
After the installation is complete, close the terminal and start a new shell.
(Optional) Disable automatic activation of the base conda environment:
conda config --set auto_activate_base false
Smiles4Psi requires Python 3 and several modules. Conda offers the possibility of creating an environment that contains all the dependencies required by Smiles4Psi. To download and install the required software tools in a new S4P environment execute the command below and follow on-screen instructions:
conda create -n S4P psi4=1.3.2 psi4-rt=1.3 python=3.7 openbabel=3.1.0 psutil=5.8.0 -c psi4 -c conda-forge
To use the recently created S4P environment, activate it:
conda activate S4P
In your file system, navigate to the location where you would like to place the root directory of Smiles4Psi and clone it from its corresponding GitHub repository:
git clone https://github.com/carlosborca/Smiles4Psi.git
Documentation about the code and runtime options, including examples and defaults, can be found by executing with the -h or --help option.
python Smiles4Psi.py --help
The code uses the current working directory as a reference point for execution and will produce new files and directories on that current working directory upon execution. Therefore, one needs to navigate to the folder where the files are meant to be produced and execute the Python 3 code there, within the S4P environment.
conda activate S4P
cd /To/Directory/Where/The/Files/Are/Meant/To/Be/Created/
python /Path/to/Smiles4Psi/Smiles4Psi.py
The first and third command can be grouped and automated by doing something horrific like creating an alias in ~/.bashrc, for example:
alias Smiles4Psi="conda activate S4P; python ~/Gits/Smiles4Psi/Smiles4Psi.py; conda deactivate"
Copyright (c) 2021, Carlos H. Borca