GetCleft as a Python Package

A Python package designed to prepare arguments and run GetCleft.

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Example usage:

from getcleftpy import run_getcleft

result = run_getcleft("/path/to/myprotein.pdb")

#optional:
stdout = result.stdout
stderr = result.stderr
returncode = result.returncode

file_path_dict = result.file_path_dict
SPH_files = file_path_dict['SPH']


#Using arguments:
#run_getcleft("/path/to/myprotein.pdb", output_clf=True)

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Arguments

Argument	Type	Description	Default
pdb_file	str	PDB filename (e.g., myprotein.pdb).	Required
min_sphere_radius	float	Minimum sphere radius. Get_Cleft default is 1.50.	None
max_sphere_radius	float	Maximum sphere radius. Get_Cleft default is 4.00.	None
output_het_atoms	bool	Output hetero group atoms in the cleft. Corresponds to the -h flag in Get_Cleft.	False
output_all_het_atoms	bool	Output all atoms of hetero groups found in the cleft.	False
chain_ids	list	A list of chain IDs to be considered (e.g., ['A', 'B']). If None, all chains are included.	None
num_clefts	int	The maximum number of clefts to be generated. Get_Cleft default is 0 (all clefts).	5
anchor_residue_specifier	str	Specifies an anchor residue or hetero molecule as residue, number, chain, alternate location identifier. The placeholder - is used to indicate a blank character for the alternate location identifier (should be present if unsure) or the chain ID (e.g., LIG123A- or LYS128-).	None
anchor_mode	str	Mode for the anchor residue. Can be all, interacting, or both.	None
include_calpha	bool	Include C-alpha atoms of residues in certain outputs.	False
include_cbeta	bool	Include C-beta atoms of residues in certain outputs.	False
include_all_residue_atoms	bool	Include all atoms of the residue in certain outputs.	False
output_spheres	bool	Output the cleft spheres, including their center coordinates and radii.	True
output_clf	bool	Output the clf file.	False
contact_threshold	float	The threshold distance for defining contacts. Get_Cleft default is 5.0.	None
output_base	str	The full path and filename for the output, without the extension (e.g., /path/to/output/filename).	Folder of the input pdb_file
verbose	bool	Output filepaths to files written by GetCleft as a dictionary	True

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Returns

Type	Description
subprocess.CompletedProcess	An object containing returncode, stdout, stderr, and file_path_dict.

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Raises

Error	Condition
FileNotFoundError	Raised if the Get_Cleft executable or the specified input file cannot be found.
ValueError	Raised if anchor_mode is provided without an anchor_residue_specifier, or if an invalid anchor_mode is given.
subprocess.CalledProcessError	Raised if the Get_Cleft executable returns a non-zero exit code, indicating an error during its execution.