README.md

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

# 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

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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

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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, returncode, and file_path_dict.