A package to caculate residue-residue contacts from MD trajectories
Project description
The presence of a contact between two residues in macromolecular systems, such as proteins and nucleic acids, is established when the minimum interresidue heavy atom pair distance falls within a specified cutoff (4-5 Å) for a given majority (for example, 75% or above snapshots) of the simulation time. This program can be untilized for extracting residue contacts from long MD simulation trajectories as well as PDB structures.
This is a command line program for linux systems and depends on MDTraj simulation analysis package (1): mdtraj.load() is used for trajectory/topology inputs and inter-atomic distances are calculated using mdtraj.distance().
After installation, type 'trajcontacts -h' for detailed options.
A simple 'trajcontacts -p topologyfile -f coordinatefile -n 10' will run the program on 10 processors and extract contacts with 4.5 angstrom cutoff. Both 'topologyfile' and 'coordinatefile' should be specified as same for extracting contactd from a PDB file.
Example: trajcontacts -p 3sn6.pdb -f 3sn6.pdb -n 10
While citing, please add:
(1) McGibbon, R., et al. "MDTraj: a modern open library for the analysis of molecular dynamics trajectories." Biophysical journal 109.8 (2015): 1528-1532.
(2) Madhu, M. K., et al. "Delineating the Biased Signaling Mechanism in Mutated Variants of β2-Adrenergic Receptor Using Molecular Dynamics Simulations"
Copyright: Computational Biophysics and Soft Matter Group (https://home.iiserb.ac.in/~rkm/)
Project details
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distributions
Hashes for trajcontacts-0.1.3-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 7457e4c606092aa741854e1ef7c30a5a27a656d3e9d1a0e24193bf1f2dbfcf4a |
|
MD5 | f82d39bc2738ce4fb229ac6a96f3af16 |
|
BLAKE2b-256 | 75f2b4e8acd5cb6d4d4f03f0e192ebb3d284b5cfb1a260eb5109de15c25bf89b |
Hashes for trajcontacts-0.1.3-py2.py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 58f13df1a387ae0bca2b3e802c409f4f1d84d0514f0bf9860de02190263ba5d6 |
|
MD5 | edf20d3dbba5949da2129ee9392edbe6 |
|
BLAKE2b-256 | e8c98bd05e68dd2eade345394618e13d47f29fdd425b64a67a84a44f1235a510 |