PELE Converter

Prerequisites

Before launching the Converter, ensure you have PELE Platform (version 1.6.2 or higher) installed and activate the Python environment you normally use to run it.

To ensure everything is set up correctly, you can run the following command, which should print all available arguments.

python -m pele_platform.converter -h

Launching the tool

The most basic usage requires only three mandatory arguments:

  • the path to the trajectories to convert

  • format of the input files

  • desired output format.

However, you can influence the default behaviour using the parameters outlined in the arguments section.

Example 1. The tool will convert all trajectories in the output folder, generated trajectories in XTC format will be saved in the same folder.

python -m pele_platform.converter IK1_Pele/output -if pdb -of xtc

Example 2. The outputs will be saved in a custom folder converted_trajectories, additionally, the tool will verify the new trajectories and remove the original ones.

python -m pele_platform.converter IK1_Pele/output -if pdb -of xtc --delete --verify --output_path converted_trajectories

Arguments

Parameters

Optional

Functionality

input_path (positional)

No

Path to the directory containing PELE trajectories to convert,

this can be path the output folder, epoch folder or even

a specific trajectory file.

-if

--input_format

No

The original trajectory file format, pdb or xtc.

-of

--output_format

No

The destination format, pdb or xtc.

-o

--output_path

Yes

Path where converted trajectories will be saved.

-t

--topology

Yes

Path to the topology file in PDB format.

-d

--delete

Yes

Delete the original trajectory after conversion. Default: False.

-n

--n_processors

Yes

Number of processors to use. Default: 1.

--trajectory_name

Yes

Name of PELE’s trajectory files, e.g.

trajectory.pdb or trajectory.xtc.

--verify

Yes

Double-check the trajectories for consistency

after conversion.*

--dont_verify

Yes

Skip verification.*

* Verification involves checking if the original coordinates match the new ones. By default, the verification is performed only when the original trajectories are deleted after conversion. If the software was to identify any issues, it will not delete the old trajectories and raise a warning instead.