xyzparser

A lightweight python API to read xyz files

A lightweight package of two classes for simple parsing of unimolecular and multimolecular chemical xyz files.

Install

You can either copy and paste the code in the xyzparser/base.py at the beginning of whatever script you are writing or if you want to install it as a package you can simply download this github repo and then pip install it.

For https:

git clone https://github.com/rperezsoto/xyzparser.git
python -m pip install xyzparser/

For ssh:

git clone git@github.com:rperezsoto/xyzparser.git
python -m pip install xyzparser/

If you want to add your own modifications to the code:

git clone git@github.com:rperezsoto/xyzparser.git
python -m pip install -e xyzparser/

Note

If you want to install it in your conda environment remember to have it activated before the pip installing it.

Example XYZMolecule

Lets assume that we want to read a file with a single molecule, change its title, print how the new file would look, and then translate the molecule on the (0,0,0), print how the final file looks and write it.

from xyzparser import XYZMolecule

path_to_xyzfile = 'my_existing_file_with_one_molecule.xyz'

mol = XYZMolecule(path_to_xyzfile)
mol.read()

mol.title = 'new_title'

print(mol.write())

# Now lets center the molecule around the (0,0,0)

centroid = mol.xyz.mean(axis=0)
mol.xyz = mol.xyz - centroid

print(mol.write())

# Now let's write it to a file:
path_to_outfile = 'centered_molecule.xyz'

mol.write(path_to_outfile)

Example XYZReader

In this example we will assume a large xyz file with over 100000 molecules and extract the molecule 13169th and write it into its own file.

from xyzparser import XYZReader

path_to_xyzfile = 'my_very_large_file.xyz'

xyzfile = XYZReader(path_to_xyzfile)

outfile = 'molecule_13169th.xyz'

for i,mol in enumerate(xyzfile):
   if i+1 == 13169:
       mol.write(outfile)
       break

xyzfile.close()

Developed with

• python 3.7
• Ubuntu 16.04 LTS, 18.04 LTS and 20.04 LTS

Authors

• Raúl Pérez-Soto - [rperezsoto](https://github.com/rperezsoto)

License

The code is freely available under an [Unlicense](https://unlicense.org)