Atom access is a ray tracing package for determining steric hinderance
Project description
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:
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. We acknowledge Ken Gransbury for help conceptualising the atom_access
logo.
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
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. The automatic generation of this documentation relies on PEP8 compliance and the use of numpy
style docstrings.
Chilton-Group Members: Development
Before making changes to this repository, please follow the steps outlined in the group wiki.
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.
Project details
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