Important: I am building this repository from pieces of a previous repository. This means I still have to run some tests to check I didn't mess up.
A3MDutils provides some useful classes and scripts that I developped for my main project, A3MD. You can employ it to:
- generate inputs for ORCA and Gaussian
- compile QM electron density information in H5 files
- rotate coordinates of MOL2 files
- extract forces from QM files
I am only providing manual build
python3 -m build
This generates some files in dist/ that you can install with pip.
To interact with these scripts, you can just call the a3mdutils script.
>>> a3mdutils
Usage: a3mdutils [OPTIONS] COMMAND [ARGS]...
a set of scripts to work with molecular representations and their electron densities
Options:
--help Show this message and exit.
Commands:
compile-mol2 Generates a json file containing molecular...
compile-wfn Generates an HDF5 file contaning all the...
convert-sample Converts a .csv file into an .npy file, and viceversa
extract-forces Extracts the values of forces from a G09 output...
many-compile-mol2 Generates a json file containing molecular...
many-compile-wfn Generates an HDF5 file contaning the information...
many-convert-sample Converts many .csv files into an .npy file, and...
many-extract-forces Extracts the values of forces from many G09...
many-prepare-qm Creates inputs for QM programs like Gaussian09 and...
many-relabel-mol2 Applies a relabelling of the atoms of many Mol2.
many-update-mol2 Generates new mol2 files by including charge...
merge-sources Generates and HDF5 containing the information of...
prepare-qm Creates inputs for QM programs like Gaussian09 and...
random-rotation Rotates a mol2 file
relabel-mol2 Applies a relabelling of the atoms of a Mol2.
update-mol2 Generates new mol2 files by including charge...
Right now, I cannot support this repository but from time to time. But don't hesistate to contact me if you find something that does not work at brunocuevaszuviria at gmail.com