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MolHandler.jl Documentation

This is simple and intuitive package for handling Molecular dynamics(MD) trajectory data. Supported formats are xyz, pdb and dcd.

How to install

This package assumes julia 1.2.

pkg> add https://github.com/yutakasi634/MolHandler.jl.git
julia> using MolHandler

Example of use

Handling dcd file

julia> using MolHandler
julia> trj = read_dcd("trajectory.dcd")
julia> trj.coordinates[:,1] # get first snapshot as Coordinate object array.
julia> trj.coordinates[1,:] # get first atom coordinate time series by Coordinate object array.
julia> frame            = get_frame(1, trj)  # get first frame as Frame object.
julia> atom_time_series = get_atom(1, trj)   # get first atom time series as Atom object array.
julia> atom             = get_atom(2, frame) # get second atom as Atom object.
julia> atom.coordinate.x # return x element of atom  coordinate.
julia> com = center_of_mass(trj, geometric = ture)
julia> trj.coordinates .-= com[1] # move this trajectory to origin by first frame center of mass.
julia> write_dcd("com_fixed_trj.dcd", trj) # output this protein as dcd file.

Handling pdb file

ulia> using MolHandler
julia> trj = read_pdb("1aki.pdb", model = :AA) # read protein as all atom model.
julia> com = center_of_mass(trj)
julia> rg  = radius_of_gyration(trj)
julia> trj.coordinates .-= com # move this protein to origin.
julia> write_pdb("com_fixed_1aki.pdb", trj) # output this protein as pdb file.

Support Multi-Threading

julia> using Molhandler
julia> trj = read_dcd("trajectory.dcd")
julia> contact_map = contact_probability_matrix_parallel(10.0, trj) # get contact-map of which contact threshold is 10.0

You have to set the environment variable JULIA_NUM_THREADS before excution.

Functions list

Structs list