Convert structure

This protocol converts the format of the files stored for a set of Small Molecules, an Atom Structure or a Molecular dynamics system (either coordinates, topology or trajectory files).

In order to do the conversions, we use RDKit or OpenBabel for small molecules, Biopython for Atom Structures and Parmed and MDTraj for Molecular Dynamics systems.

Input

Note

All parameters include a help button that gives further information for each of them.

Convert structure form 1

Convert structure form 2

The result of this protocol is object equal to the one in the input, but this time the files inside this object are in the desired format.

Test

This protocol has an integrated test that can be run using the following command:

scipion3 tests pwchem.tests.tests_general.TestConverter