qm-tools-aw 1.4.5

Provides some functions that I have found value in reusing for quantum chemistry related tasks.

QM-Tools-AW

A collection of quantum mechanics and computational chemistry tools for data analysis, visualization, and manipulation.

Installation

pip install qm-tools-aw

Features

General Utilities

• File I/O operations (JSON, pickle)
• Molecular geometry manipulation and conversion
• Handling of various file formats (XYZ, PDB, Psi4 input)
• Distance calculations and molecular structure analysis
• Visualization helpers (e.g., PyMOL script generation)

Plot Utilities

• Violin plots for error analysis with customizable aesthetics
• Support for statistical visualizations of computational chemistry data

SAPT Analysis

• Symmetry-Adapted Perturbation Theory (SAPT) term computation for higher-order SAPT mimicking Psi4 but on a pandas DataFrame

Software Access

• Interface with external chemistry software
• Tools for working with checkmol for functional group analysis

Usage Examples

Create Violin Plots for Error Analysis

import pandas as pd
import numpy as np
from qm_tools_aw.plot import violin_plot

# Create sample data
df = pd.DataFrame({
    'MP2': np.random.normal(0.5, 5, 1000),
    'HF': np.random.normal(-0.5, 5, 1000),
})

# Create violin plot
violin_plot(
    df,
    {'MP2 Method': 'MP2', 'HF Method': 'HF'},
    output_filename="method_comparison",
    ylim=[-25, 25],
    plt_title="Method Error Comparison"
)

Results: Plotting method_comparison

Process Molecular Geometries

from qm_tools_aw.tools import read_xyz_to_pos_carts, write_cartesians_to_xyz, print_cartesians_pos_carts

# Read XYZ file
pos, carts = read_xyz_to_pos_carts("molecule.xyz")

# Manipulate coordinates
carts[:, 0] += 1.0  # Shift x coordinates

# Write modified structure
write_cartesians_to_xyz(pos, carts, "modified.xyz")
print_cartesians_pos_carts(pos, carts)

Results:

8	0.2978039460	-0.0560602560	0.0099422620
1	-0.0221932240	0.8467757820	-0.0114887140
1	1.2575210620	0.0421214960	0.0052189990

Documentation

For detailed documentation on all functions and classes, refer to the docstrings in the source code.

Dependencies

• NumPy
• Pandas
• Matplotlib
• QCElemental
• Other standard Python libraries

License

This project is licensed under the MIT License - see the LICENSE file for details.