File IO

mdload(filename::AbstractString; index=nothing, top::TrjArray=nothing) -> ta::TrjArray

Function for reading bimolecular structure files or molecular dynamics trajectories. This function automatically detects files types from the filename extension of input filename. Currently, PDB, PSF, DCD, NetCDF, and namdbin(namd restart file) formats are available. For reading subset atoms from the trajectory files, the user can specify atom indices as index::AbstractVector{Int}. Returns a TrjArray variable ta.

If the user wants to attach a topology information read from PSF, PDB, or other files to MD trajectory, the user can give an addtional option top=ta:TrjArray. If the option is given the topology information is applied.

Example

julia> ta = mdload("1ake.psf")
julia> ta = mdload("1ake.dcd", top=ta)

mdsave(filename::AbstractString, ta::TrjArray)

Function for writing bimolecular structure files or molecular dynamics trajectories. This function automatically detects files types from the filename extension of input filename. Currently, PDB, PSF, NetCDF, and namdbin(namd restart file) formats are available.

Example

julia> ta = TrjArray(xyz=randn(100, 9))
julia> ta = mdsave("1ake.nc", ta)