Usage

Full list of arguments for fpocketR CLI.

Option / Argument	Type	Description
-pdb, --pdb (Required)	str	Path to a .pdb file, .cif file, or 4 character PDB identification code.
-ss, --ss	str	Path to an .ss or other secondary structure file for generating secondary structure figures.
-m	float	Minimum radius for an a-sphere (Default: 3.0).
-M	float	Maximum radius for an a-sphere (Default: 5.70).
-i	int	Minimum number of a-spheres per pocket (Default: 42).
-D	float	A-sphere clustering distance for forming pockets (Default: 1.65).
-A	int	Number of electronegative atoms required to define a polar a-sphere (Default: 3).
-p	float	Maximum ratio of apolar a-spheres in a pocket (Default: 0.0).
-o, --out	str	Path to the output parent directory (Default: “./fpocketR_out”).
-n, --name	str	Output filename prefix and output subdirectory name (Default: “{PDB}_clean_out”).
-y, --yes	bool	Answers yes to user prompts for overwriting files (Default: False).
-s, --state	int	Specify the NMR states/model to analyze. 0 for all (Default: None).
-c, --chain	str	Specify a chain from the input .pdb file (Default: <first_rna_chain>).
-l, --ligand	str	PDB ligand identification code (2-3 characters).
-lc, --ligandchain	str	Chain containing ligand from the input .pdb file (Default: <–chain input>).
-nt, --knownnt	list[int]	List residue IDs of nucleotides in known pocket (e.g. 1,2,3) (Default: None).
-off, --offset	int	Offset between starting nucleotide of RNA sequence and starting nucleotide of PDB structure (automatic).
-qf, --qualityfilter	float	Minimum fpocket score for pocket (Default: 0.0).
-dpi, --dpi	int	Figure resolution in dpi (Default: 300).
-z, --zoom	float	Zoom buffer (Å) for creating 3D figures (Default: 5.0).
-cp, --connectpocket	bool	Visually connects pockets in 2D figures (Default: False).
-al, --alignligand	str	bool

TIP: To see all these options in your terminal, run:

python -m fpocketR --help