ProcessLigand as a Python Package
A Python package designed to prepare arguments and run ProcessLigand.
Example usage:
from processligandpy import run_processligand
# For a ligand
result_ligand = run_processligand(file_path='path/to/target_or_ligand', atom_index=90000)
# For a target:
# result_target = run_processligand(file_path='path/to/target_or_ligand', target=True)
# Using arguments:
# result = run_processligand(file_path='path/to/target_or_ligand', atom_index=1)
# Expanding the result:
output = result_ligand.stdout
error = result_ligand.stderr
returncode = result_ligand.returncode
file_path_dict = result_ligand.file_path_dict
Arguments
Required Argument
| Arg | Description |
|---|---|
file_path |
Input file (not listed in the provided dictionary) |
Optional Arguments
| Flag | Value Type | Description |
|---|---|---|
target |
<BOOL> |
Parse a target |
v |
<INT> |
Verbose level (0 prints nothing. 1 prints everything) |
o |
<STR> |
Output base filename |
e |
<STR> |
Residue to extract |
c |
<STR> |
Convert molecule to specified format |
atom_index |
<INT> |
Starting atom index |
res_name |
<STR> |
3-char ligand code |
res_chain |
<CHAR> |
Ligand chain |
res_number |
<INT> |
Ligand number |
force_gpa |
<INT> |
Force reference atom |
force_pcg |
<FLOAT FLOAT FLOAT> |
Force protein center of geometry |
d |
<BOOL> |
Deletes tmp files created when converting inout to mol2 |
pf |
<BOOL> |
Prints a line containing the filepath to every written file |
hf |
<BOOL> |
Include hydrogen flexible bonds |
wh |
<BOOL> |
Add hydrogen atoms in output |
ref |
<BOOL> |
Output final PDB from IC |
gen3D |
<BOOL> |
Generate 3D conformation |
Raises
| Exception | Description |
|---|---|
FileNotFoundError |
If the required input file 'f' does not exist. |
ProcessLigandError |
If the external process fails to execute. |
Returns
| Type | Description |
|---|---|
ProcessLigandResult |
A namedtuple containing stdout, stderr, returncode, and file_path_dict. |
Metadata
Release files for processligand-py 1.0.4
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| processligand_py-1.0.4.tar.gz | 4.9 kB | Details |
Built distributions (wheels)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| processligand_py-1.0.4-py3-none-win_amd64.whl | Python 3 | none | Windows x86-64 | Details |
| processligand_py-1.0.4-py3-none-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl | Python 3 | none | Linux glibc 2.5+ x86-64, Linux glibc 2.28+ x86-64 | Details |
| processligand_py-1.0.4-py3-none-macosx_10_9_universal2.whl | Python 3 | none | macOS 10.9+ universal2 (ARM64, x86-64) | Details |
Total release size: 30.5 MB
Release files / processligand_py-1.0.4.tar.gz
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