GetCleft as a Python Package
A Python package designed to prepare arguments and run GetCleft.
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)
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 |
Returns
| Type | Description |
|---|---|
subprocess.CompletedProcess |
An object containing returncode, stdout, stderr, and file_path_dict. |
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. |
1 maintainer
Metadata
1 maintainer
Release files for getcleft-py 1.0.5
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| getcleft_py-1.0.5.tar.gz | 5.7 kB | Details |
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| getcleft_py-1.0.5-py3-none-win_amd64.whl | Python 3 | none | Windows x86-64 | Details |
| getcleft_py-1.0.5-py3-none-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl | Python 3 | none | Linux glibc 2.17+ x86-64, Linux glibc 2.12+ x86-64 | Details |
| getcleft_py-1.0.5-py3-none-macosx_10_9_universal2.whl | Python 3 | none | macOS 10.9+ universal2 (ARM64, x86-64) | Details |
Total release size: 67.8 kB
Release files / getcleft_py-1.0.5.tar.gz
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