PathReducer is a tool that takes as input some set of molecular geometries in .xyz file format (e.g., an intrinsic reaction coordinate, a molecular dynamics trajectory, a relaxed potential energy surface scan) and outputs a reduced dimensional space for that set of molecular geometries.

PathReducer takes as input

1. the path to the .xyz file (or files) of interest, as a string
2. the number of dimensions to reduce to, as an integer
3. optionally (though often necessary for visualization when representing the molecular structures as interatomic distances) the indexes of atoms (with numbering starting at 1, not 0) surrounding a stereogenic center in the system, as a list of integers

Currently, dimensionality reduction is conducted using Principal Component Analysis (PCA), though other dimensionality reduction techniques will be implemented in the future.

To initially define a reduced dimensional space, use the pathreducer function. To transform new data into an already defined reduced dimensional space, use the transform_new_data function.

Dependencies can be found in requirements.txt. To install all dependencies, use pip install in Terminal:

pip install -r requirements.txt

Test scripts for using PathReducer's basic functions are provided in the test_scripts folder. Additionally, the Jupyter notebook PathReducer Walkthrough I.ipynb guides you through an example system. An interactive function is also available to lead you through the process step-by-step by calling

from dimensionality_reduction_functions import *

pathreducer_interactive()

in a Python 3 shell.