Getting Started

Installation

Poké is available on PyPI under the name poke-scouter. To install it with pip run:

python -m pip install poke-scouter

The package provides the poke command and the poke Python module.

Alternatively, the package can be installed directly from GitHub:

git clone https://github.com/SibyllaBiotech/poke
pip install ./poke

Basic Examples

Note

All input structures passed to Poké must be protonated and the atom names should match the CHARMM or Amber convention. Alternatively, use the --prepare flag to let Poké add the hydrogens itself (see Structure Preparation).

Single Structure

Poké can be used on a single structure (pdb, gro, or pdbqt) with the following command:

poke -dvp protein.pdb

The result will appear in a folder named after the input file (in this example protein) in the current working directory. The flags -dvp specify the desired output files:

  • -d for the descriptors CSV file (see Descriptors)

  • -v for the volumes, a PDB file with the grid points of each pocket

  • -p for a PyMOL script to visualize the pockets

The other output files are described in Outputs.

Multiple Structures

Poké can also be used on multiple files:

poke -dvp protein1.pdb protein2.pdb

In this case it will create two output folders called protein1 and protein2.

If the input is a long list of files, they can be listed in a text file (.txt, one path per line) and passed to Poké:

poke -dvp list.txt

MD Trajectory

To run the scouter on all the frames of a trajectory (xtc, trr, or dcd), a reference structure must be provided to define the atom types (its positions will not be used):

poke -dvp reference.pdb trajectory.xtc

Multiple trajectories can be concatenated:

poke -dvp reference.pdb trajectory1.xtc trajectory2.xtc

Normally Poké does not produce a new trajectory, but the frames with at least one pocket can be extracted into one with the -e flag. The pockets can be sorted by any property with the -s flag, in descending order, and -n keeps only the first ones. For example, to extract the frames with a pocket and keep the ten best pockets by score:

poke -dvp -e -s score -n 10 reference.pdb trajectory.xtc

Pockets can also be filtered by their properties or by the residues they involve; see Filters.

Options

poke -h prints every option with a short description. The same list, grouped by topic, is in the CLI Reference.