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.
Installation
pip install vcon-py
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)
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 |
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. |
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. |
Metadata
Release files for vcon-py 1.0.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| vcon_py-1.0.2.tar.gz | 24.3 kB | Details |
Built distributions (wheels)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| vcon_py-1.0.2-py3-none-win_amd64.whl | Python 3 | none | Windows x86-64 | Details |
| vcon_py-1.0.2-py3-none-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl | Python 3 | none | Linux glibc 2.17+ x86-64, Linux glibc 2.5+ x86-64 | Details |
| vcon_py-1.0.2-py3-none-macosx_10_9_universal2.whl | Python 3 | none | macOS 10.9+ universal2 (ARM64, x86-64) | Details |
Total release size: 114.8 kB
Release files / vcon_py-1.0.2.tar.gz
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