CLI Reference

Every option of the poke command, grouped as in the output of poke -h. This page is generated from the command-line parser of the installed Poké, so it always matches the program. In the Default column, “off” marks a switch that is off unless given, and a dash marks an option with no default.

usage: poke [-h] [-d] [--write-atoms] [-v] [-p] [-dx] [-e] [-k] [-g] [-ls]
            [-o PATH] [-q] [-nc N] [-z] [-ss SEL] [-so SEL] [-a SEL] [-r PATH]
            [-mv V] [-ac R] [-sf NAME] [-f EXPR] [-s EXPR] [-n N] [-ks]
            [--prepare] [--keep-hydrogens] [--selection-prepare SEL]
            [--caps-types TYPE N_TERM C_TERM [TYPE N_TERM C_TERM ...]]
            [--caps-exclude [NAME ...]] [--ignore-segid] [--max-other-len LEN]
            [--resid-threshold LEN] [--ter-indices [IX ...]] [--his TYPE]
            [--lys TYPE] [--arg TYPE] [--glu TYPE] [--asp TYPE] [--cys TYPE]
            [--custom-restype [IX TYPE ...]]
            structures [structures ...]

Positional arguments

Argument	Description
structures	Input structures (.pdb, .gro, .pdbqt, .xtc, …). List of proteins to search for pockets. When a coordinate-only file is passed, the previous structure is used to open it. A .txt file can be passed containing additional structures, one per line.

Output options

Flag	Default	Description
-d, --descriptors	off	Compute the descriptors and save them in a CSV file.
--write-atoms	off	Add the pocket atoms to the descriptors CSV file (requires -d).
-v, --volumes	off	Save the volumes in a multi-model PDB file.
-p, --pymol	off	Save a PyMOL script to open the pockets found.
-dx, --density	off	Save the density map of the pockets in a DX file.
-e, --extract	off	Save the results relative to a new trajectory containing only frames with at least one pocket.
-k, --pickle	off	Save a pickle with a list of pockets for each frame.
-g, --graph	off	Plot distributions of pocket descriptors.
-ls, --launch-script	off	Save the launch command in a bash script to be able to rerun with the same parameters.

General options

Flag	Default	Description
-h, --help	—	Show this help message and exit.
-o, --output PATH	current directory	Output path where to create the folders with the results.
-q, --quiet	off	Avoid writing the progress for long trajectories.
-nc, --ncores N	—	Number of cores used to parallelize the computation of trajectories or multi-model PDB files. By default it is chosen from the number of frames and the available cores.
-z, --compress	off	Compress the results using gzip; most programs can read them without problem.

Atom selection options

Flag	Default	Description
-ss, --selection-scouter SEL	—	Selection of atoms used by the scouter. Default is all the atoms, or the prepared atoms when –prepare is used.
-so, --selection-output SEL	all	Selection of atoms written in the output. It does not change the atoms used by the scouter; see –selection-scouter.

Alignment options

Flag	Default	Description
-a, --align SEL	—	Align the given atom selection to the reference.
-r, --reference PATH	—	Reference used for alignment. Default is the first structure.

Pocket detection options

Flag	Default	Description
-mv, --min-volume V	15	Minimum volume of the pocket core in cubic angstroms. Pockets with a smaller volume are discarded. Default is 15 ų.
-ac, --accessible-cutoff R	1.0	Distance in angstroms around the pocket core within which the low-energy points are counted as accessible volume. Default is 1.0 Å.

Scoring options

Flag	Default	Description
-sf, --scoring-function NAME	model	Scoring function used.

Filtering and sorting options

Flag	Default	Description
-f, --filter EXPR	—	Keep only the pockets for which the Python expression is true. The pocket properties and the filter functions can be used in the expression; see the Pocket Filtering section of the documentation.
-s, --sort EXPR	—	Sort the pockets by the value of a Python expression, in descending order. Same syntax as –filter.
-n, --max-output-frames N	—	Maximum number of pockets in the output. Only when –sort is used.
-ks, --keep-subpockets	off	Keep all pockets even if they share regions, instead of only the highest scoring one.

Structure preparation options

Flag	Default	Description
--prepare	off	Prepare the structures before scouting (select altLocs, add hydrogens and caps). Default is to NOT prepare the structures.
--keep-hydrogens	off	Try to keep the existing hydrogens during preparation, adding only the missing ones.
--selection-prepare SEL	—	Selection of atoms to prepare. Other atoms are kept as they are. If not provided, only proteins, nucleic acids, and common cofactors and structural ions are prepared.

Capping options

Flag	Default	Description
--caps-types TYPE N_TERM C_TERM	protein NH3+ COO- nucleic_acid 5TER 3TER	Types of caps to add to the structures.
--caps-exclude NAME	ACE NME	List of residue names to exclude from capping.
--ignore-segid	off	Do not use the segid (chain) value to split the structure for capping.
--max-other-len LEN	5	Maximum number of residues of type “other” before a chain is considered interrupted.
--resid-threshold LEN	50	Jump in residue numbers to consider a chain interrupted (used only if segid info is absent).
--ter-indices IX	—	Explicit list of 0-based indices of residues to be considered as terminal residues for splitting.

Protonation state options

Flag	Default	Description
--his TYPE	auto	Type of histidine to use. Options are “auto”, “bond”, “HSP”, “HSE”, “HSD”. Default is “auto” which uses the presence of HD1 and HE2 or hydrogen bonding detection.
--lys TYPE	auto	Type of lysine to use. Options are “auto”, “LYS”, “LSN”. Default is “auto”.
--arg TYPE	auto	Type of arginine to use. Options are “auto”, “ARG”, “ARGN”. Default is “auto”.
--glu TYPE	auto	Type of glutamate to use. Options are “auto”, “GLU”, “GLUP”. Default is “auto”.
--asp TYPE	auto	Type of aspartate to use. Options are “auto”, “ASP”, “ASPP”. Default is “auto”.
--cys TYPE	auto	Type of cysteine to use. Options are “auto”, “bond”, “CYS”, “CYS2”. Default is “auto” which uses the presence of HG1 or covalent bonding detection.
--custom-restype IX TYPE	—	Custom residue types to use at specific 0-based residue indices, given as pairs of index and type, e.g. 42 HSE 105 CYS2.

SEL is an atom selection in the MDAnalysis selection syntax, e.g. “protein”, “resid 10:50” or “not resname HOH”; see https://docs.mdanalysis.org/stable/documentation_pages/selections.html