processligand-py 1.0.0

Python wheels and a wrapper for ProcessLigand, a tool to prepare target and ligand files for FlexAID

ProcessLigand as a Python Package

A Python package designed to prepare arguments and run ProcessLigand.

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Example usage:

from processligandpy import run_processligand

result = run_processligand(f='path/to/target_or_ligand')

# Using arguments:
# result = run_processligand(f='path/to/target_or_ligand', target=True, atom_index=1)

# Optional:
output = result.stdout
error = result.stderr
returncode = result.returncode

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Arguments

Required Argument

Arg	Description
f	Input file (not listed in the provided dictionary)

Optional Arguments

Flag	Value Type	Description
target	<BOOL>	Parse a target
v	<INT>	Verbose level
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
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

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Raises

Exception	Description
FileNotFoundError	If the required input file 'f' does not exist.
ProcessLigandError	If the external process fails to execute.

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Returns

Type	Description
ProcessLigandResult	A namedtuple containing stdout, stderr, and the returncode.