atom-access 2.3.1

atom_access is a ray tracing package for addressing the steric hindrance of molecules

atom_access is a python package for assessing the steric hindrance 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:

Gransbury, G. K.; Corner, S. C.; Kragskow, J. G. C., Evans, P.; Yeung, H. M.; Blackmore, W. J. A.; Whitehead, G. F. S.; Vitorica-Yrezabal, I. J.; Chilton, N. F.; Mills, D. P. AtomAccess: A predictive tool for molecular design and its application to the targeted synthesis of dysprosium single-molecule magnets. ChemRxiv 2023, DOI: 10.26434/chemrxiv-2023-28z84.

This code was developed under the ERC CoG-816268 grant with PI David P. Mills. We acknowledge Ken Gransbury for help conceptualising the atom_access logo.

Web interface

The atom_access web interface is available on the Magnetism Tools website and has all the features of the command line interface and package, plus the ability to visualise rays/clusters on top of molecular models.

Installation via pip

The easiest way to install atom_access is to use pip

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

pip install --upgrade atom_access

some users, such as those on shared machines, may need to use the --user argument after install

Usage

atom_access takes an xyz file as the input and can be run in the command line

atom_access <molecule.xyz>

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

mkdir -p git; cd git
git clone https://gitlab.com/chilton-group/atom_access

Navigate to the package directory

cd atom_access

and install the package in editable mode

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

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

./build_binaries.sh

Then install the .whl file with pip

pip install dist/*.whl

some users, such as those on shared machines, may need to use the --user argument after install

Documentation

The documentation 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.