Vcontacts in a Python Package

A lightweight Python package to simplify running Vcontacts,
a tool to compute surface areas in contact using the constrained Voronoi procedure from the paper:

Quantification of protein surfaces, volumes and atom-atom contacts using a constrained Voronoi procedure
(doi: 10.1093/bioinformatics/18.10.1365)

This makes it easy to run Vcontacts directly from Python, capture the output, and optionally return the result as a Python dictionary.

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Installation

pip install vcon-py

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Example Usage

from vconpy import run_vcon

# Run Vcontacts
result = run_vcon("/path/to/protein.pdb")

# Run Vcontacts and return a dictionary instead of outputting a file
result_with_dictionary = run_vcon("/path/to/protein.pdb", as_dictionary=True)

# NRGTEN requires setting showbonded as True
result_nrgten = run_vcon("/path/to/protein.pdb", as_dictionary=True, showbonded=True)

print(result_with_dictionary.surface_dictionary)

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Arguments

Argument	Type	Description	Default
pdb_filename	str	Path to the input PDB file.	Required
showbonded	bool	If True, include covalently bonded atoms in the contacts (-all flag).	False
normalize	bool	If True, normalize contacts to percent of total contact area. Otherwise, contacts are given in SAS units (Ų). (-norm flag).	False
planedef	str	Plane definition for analysis. Options: X (extended radical plane), R (radical plane), B (bisecting plane).	None
as_dictionary	bool	If True, returns a Python dictionary. The .vcon file is deleted after parsing.	False

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Returns

The function returns a VconResult namedtuple with the following fields:

Field	Type	Description
vcon_filename	str	Path to the generated .vcon file.
surface_dictionary	dict	Dictionary of atom-atom contact areas (only if as_dictionary=True).
stdout	str	Standard output from the Vcontacts process.
stderr	str	Standard error from the Vcontacts process.
returncode	int	Exit code from the Vcontacts process.

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Raises

Error	Condition
ValueError	Raised if the input file does not exist, or if vcon_type is invalid.
VconError	Raised if the Vcontacts executable is missing, not executable, or fails.

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