`atom_access` is a python package for assessing the steric hinderance at any atom in a molecule or molecular fragment.
We request that any results obtained through the use of `atom_access` are accompanied by the following reference:
> A. J. McMillan, M. Sieńkowska, P. Di Lorenzo, G. K. Gransbury, N. F. Chilton, M. Salamone, A. Ruffoni, M. Bietti, D. Leonori, Angew. Chem. Int. Ed. **2021**, 60, 7132.
This code was developed under the ERC CoG-816268 grant with PI [David P. Mills](https://millsgroup.weebly.com/). We acknowledge Ken Gransbury for help conceptualising the `atom_access` logo.
# Web interface
The `atom_access` web interface is available on the [Magnetism Tools](https://magnetism-tools.manchester.ac.uk) website and has all the features of the command line interface and package, plus the ability to visualise rays/clsuters on top of molecular models.
# Installation via `pip`
The easiest way to install atom_access is to use `pip`
```shell
pip install atom_access
```
some users, such as those on shared machines, may need to use the `--user` argument after `install`
# Updating via `pip`
Update the code using `pip`
```shell
pip install --upgrade atom_access
```
some users, such as those on shared machines, may need to use the `--user` argument after `install`
# Usage
Use `atom_access -h` to see all available options
# Developers: Installation with `pip` editable install
Clone a copy of this repository, preferably while within a directory called git
```shell
mkdir -p git; cd git
git clone https://gitlab.com/jonkragskow/atom_access
```
Navigate to the package directory
```shell
cd atom_access
```
and install the package in editable mode
```shell
pip install -e .
```
some users, such as those on shared machines, may need to use the `--user` argument after `install`
To uninstall this editable copy, use
```shell
pip uninstall atom_access
```
# Building a `.whl` file (Advanced)
To build a copy of the `atom_access` `.whl` file, move to the `package` directory.
Now run
```shell
./build_binaries.sh
```
Then install the `.whl` file with `pip`
```shell
pip install dist/*.whl
```
some users, such as those on shared machines, may need to use the `--user` argument after `install`
# Documentation
The [documentation](https://jonkragskow.gitlab.io/atom_access/) for this package is hosted by gitlab, and is automatically generated whenever new code is committed to the `main` branch.
# Bugs
If you believe you have a bug, *please check that you are using the most up to date version of the code*.
If that does not fix the problem, please create an issue on GitLab detailing the following:
- The commands you entered
- The error message
If possible, try to simplify the problem as much as possible, e.g. providing an example for a small molecule rather than one with 1000 atoms.
