Installing SparcleQC

Creating a SparcleQC Enviornment

To get started, you will need to install sparcleqc and its dependencies. We have provided a yaml file to create a conda environment containing all of the necessary packages.

First, clone the SparcleQC repository:

git clone https://github.com/carolinesargent/sparcleqc.git

Change your working directory to sparcleqc/:

cd sparcleqc

Create a conda environment from the yaml file provided in this repository:

conda env create -f sparcleqc.yaml

Command Line Usage

SparcleQC is now installed in this enviornment and can be called on the command line in any directory using the following syntax:

sparcleqc input_file.in

Python API

Alternatively, for more advanced scripting utilities, SparcleQC can be imported as a python package:

import sparcleqc

SparcleQC can be called by referencing an input file:

sparcleqc.run_sparcle(input_file = 'input_file.in')

or by passing a dictionary of inputs:

inputs = {
'input_filename': 'example.in',
'pdb_file': 'complex_pdb_file.pdb',
'cutoff': 6,
'seed': 'ligand',
'charge_scheme': 'Z2',
'ligand_charge': 0,
'method': 'hf',
'basis_set': 'aug-cc-pv(D+d)z',
'amber_ff': 'ff19SB',
'software': 'psi4',
}

sparcleqc.run_sparcle(user_options = inputs)

Running SparcleQC

To learn more about SparcleQC, check out Getting Started.