hmcezar/clusttraj

Python script that receives a molecular dynamics or Monte Carlo trajectory and performs agglomerative clustering to classify similar structures.

clusttraj's Issues

Provide some examples/tests code

Hi, this repo seems nice to me, however, I could not found some demonstration files for testing and learning. Hope to add some examples/tests into this repo. 😄

Invalid literal related with atom symbol

Running with:

python clusttraj.py output.xyz 0.5 -e -cc xyz -p

I get the following error

  ...
  File "/usr/lib/python3.10/multiprocessing/pool.py", line 375, in starmap
    return self._map_async(func, iterable, starmapstar, chunksize).get()
  File "/usr/lib/python3.10/multiprocessing/pool.py", line 774, in get
    raise self._value
ValueError: invalid literal for int() with base 10: 'Sn'

output.xyz have Sn atoms...

citation

Hi thanks for this,

Is there a citation for this work that we can use?

Many thanks and take care,
Xinglong

Reorder after rotating considering the solute

Maybe it would be a good idea to receive the number of atoms in the solute, to perform previously to the reordering, a rotation with the Kabsch algorithm considering just the solute atoms.

After the coordinates would be rotated, it would be easier to perform the reordering of the solvent molecules.