DP4

Copyright (c) 2024 Alexander Howarth, Kristaps Ermanis, Jonathan M. Goodman, Benji Rowlands

Distributed under MIT license

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Contents

1. Release Notes
2. Requirements and Setup
3. Usage
4. NMR Description Format
5. Code Organization
6. Help and Contact Details

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Release Notes

This repository contains all the code necessary to reproduce the DP4* results in the paper "Towards automatically verifying chemical structures: the powerful combination of ¹H NMR and IR spectroscopy".

This package should be used in conjunction with the Apollo data repository in order to reproduce the DP4* results. Using the data from the Apollo repository, the results from the paper can be reproduced in roughly 5 minutes.

Scripts to reproduce the SCC plots from the paper are also available on GitHub.

Separately, the code necessary to reproduce the IR.Cai results from the paper is also available on GitHub

Functionality from other releases of DP4 (diastereoisomer generation, automatic interpretation of raw NMR data, conformational analysis of 5-membered rings, calculation of DP5 probabilities) has been removed to facilitate easy reproduction of the results in the paper.

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Requirements and Setup

Requirements

• Python 3.6+
• scipy (version 1.14.0)
• numpy (version 2.0.1)
• rdkit (version 2024.3.4)
• networkx (version 3.3)
• setuptools (version 72.1.0)

Setup Instructions

1. Clone or download the repository

   Clone or download the repository to your local machine. You can use the following git command to clone the repository:

   git clone https://github.com/jbr46/DP4.git
   

2. Create and activate a virtual environment Navigate to the directory where you cloned the repository and run the following command:

   python -m venv .venv
   

   This command creates a virtual environment named .venv in your DP4 directory.

3. Activate the virtual environment

   source .venv/bin/activate
   

4. Install the package With the virtual environment activated, install DP4 and its dependencies using pip:

   pip install .
   

Expected install time: around 1 minute, but this may vary depending on how fast the required packages download.

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NMR Description Format

Example NMR file:

59.58(any),127.88(any),... 4.81(any),7.18(any),...

Sections:

1. C shifts (e.g., 59.58(any)).
2. H shifts (e.g., 4.81(any)).

In this work, the shifts are always assumed to be unassigned, i.e., each one should be followed by (any).

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Code Organization

• dp4/: The main package directory.
• __init__.py: Initializes the dp4 package.
• ConfPrune.pyx: Cython file for conformer alignment and RMSD pruning.
• main.py: Main script for DP4 workflow.
• MacroModel.py: Handles MacroModel-specific calculations.
• Gaussian.py: Handles Gaussian-specific calculations.
• NWChem.py: Handles NWChem-specific calculations.
• DP4.py: Python implementation of DP4 probability calculation.
• StructureInput.py: Cleans structures, generates 3D geometries, reads SMILES and SMARTS formats.
• data/: Contains data files such as TMSdata.

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Help and Contact Details

For more information on using the scripts and additional options, refer to the in-script help by running:

pydp4 -h

In case of any questions or issues, please email Jonathan Goodman at [email protected].