https://github.com/andrewtarzia/simple_het_construction

Simple construction and analysis of heteroleptic cages
https://github.com/andrewtarzia/simple_het_construction

Last synced: 28 days ago
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Simple construction and analysis of heteroleptic cages

• Host: GitHub
• URL: https://github.com/andrewtarzia/simple_het_construction
• Owner: andrewtarzia
• License: mit
• Created: 2022-07-07T17:03:53.000Z (over 2 years ago)
• Default Branch: submission
• Last Pushed: 2024-09-07T22:00:59.000Z (2 months ago)
• Last Synced: 2024-09-07T23:19:27.736Z (2 months ago)
• Language: Python
• Size: 451 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# simple_het_construction

Python code for the construction and analysis of heteroleptic cages

DOI for publication: **AWAITING**.

DOI for ChemRxiv: [10.26434/chemrxiv-2024-s0mmw](https://doi.org/10.26434/chemrxiv-2024-s0mmw).

The library is built off of [`stk`](https://stk.readthedocs.io/en/stable/)

# Installation

I recommend installing the library with the following instructions and setting the paths in `env_set.py` appropriately. *E.g.*, the working directory for me is `/home/atarzia/projects/simple_het/`

The code can be installed following these steps:

1. clone the `submission` branch of `simple_het_construction` from [here](https://github.com/andrewtarzia/simple_het_construction)

2. Create a `conda` or `mamba` environment:

```

conda env create -f environment.yml

```

3. Update directories in `env_set.py`

For cage and ligand optimisation, this library uses:

`Gulp (6.1)`: Follow the instructions to download and install [GULP](https://gulp.curtin.edu.au/gulp/help/manuals.cfm)

`xTB (6.5.0=h9d67668_0)`: Installed using `conda` or `mamba` through `environment.yml`

# Usage for ligand-based modelling

`run_ligand_analysis.py`:

    Runs the ligand-based analysis (conformer generation and pairing).

`analyse_csd_survey.py`:

    This is a helper script for analysing the survery of Pd centres in the Cambridge Structural Database. The methods for extracting the data are not provided.

`plot_conformer_numbers.py`:

    Plots the number of conformers for each ligand at each stage of screening before performing ligand-based analysis.

`run_pdn_distance_tests.py`:

    Reruns some of the ligand-based analysis with varying Pd-N distances to see impact of this variable.

# Usage for cage modelling

`extract_m30l60.py`:

    Extracts the topology information from a given structure.

`build_ligands.py`:

    Build ligands for cage construction. Generates ligands lowest energy conformer and an appropriate conformer for cage construction.

`build_cages.py`:

    Builds and optimises homoleptic and heteroleptic cages. List of structures to build are defined in the script.

`analyse_cages.py`:

    Obtains structural and energetic analysis for all cages. Produces plots.

# Modules

`utilities.py`:

    Defines utilities for construction and analysis.

`optimisation.py`:

    Defines optimisation sequences.

`topologies.py`:

    Defines the new topology graph for M30L60.

`plotting.py`:

    Utilities and functions for plotting.

`pywindow_module.py`:

    Defines a class for using `pyWindow`.