avtraj 0.0.6

A tool to calculate FRET observables for MD trajectories by accessible volume calculations.Here, spatial density of flexible coupled dyes/labels is approximated by the sterically allowedspace for labels modeled by ellipsoids attached by a flexible cylinder.

avtraj

MDTrajFPS is tool to calculate FRET observables from MD-trajectories.

MDTrajFPS depends on MDTraj and utilizes the original libraries published together with the "FRET Positioning System" (FPS) in Nature Methods 9, 1218–1225 (2012) "A toolkit and benchmark study for FRET-restrained high-precision structural modeling".

The implicit model of the label is being improved to support the latest developments . Hence, the library for the calculation of the implicit labels are currently only provided as pre-compiled binaries for (Windows x32, x64, MacOS, and Linux x32, x64).

With MDTrajFPS, you can

• Process every MD format supported by MDTraj
• Calculate FRET efficienes using a fast implicit dye model
• Save calculated positional distributions of dyes for later vizualization

The original FPS-software package is available at http://www.mpc.hhu.de/software/fps.html.

Installation

Anaconda

conda --add channels tpeulen
conda install mdtraj_fps

Code Example

import mdtraj as md
from mdtraj_fps import fps

# First load an MD trajectory by mdtraj
traj = md.load('./examples/hGBP1_out_3.h5')

# Pass a trajectory to fps.AVTrajectory. This creates an object, which can be 
# accessed as a list. The objects within the "list" are accessible volumes  
av_traj = fps.AVTrajectory(traj, '18D', attachment_atom_selection='resSeq 7 and name CB')
# These accessible volumes can be saved as xyz-file
av_traj[0].save_xyz('test_344.xyz')

# The dye parameters can either be passed explicitly on creation of the object
av_traj = fps.AVTrajectory(traj, '18D', attachment_atom_selection='resSeq 7 and name CB', linker_length=25., linker_width=1.5, radius_1=6.0)

# or they can be selected from a predefined set of parameters found in the JSON file dye_definition.json located within
# the package directory 
av_traj = fps.AVTrajectory(traj, '18D', attachment_atom_selection='resSeq 7 and name CB', dye_parameter_set='D3Alexa488')

# To calculate a trajectory of distances and distance distributions first a labeling file and a "distance file" 
# needs to be specified. The distance file contains a set of labeling positions and distances and should be compatible
# to the labeling files used by the software "Olga". By default the 
av_dist = fps.AvDistanceTrajectory(traj, './examples/hGBP1_distance.json')

Dependencies

The windows dll requires the following redistributables (not included)

MS-visual studio 2005 vcredist_x64 vcredist_x86

Citations

• MDTraj -
• FPS -

License

GNU LGPL version 2.1, or at your option a later version of the license. Various sub-portions of this library may be independently distributed under different licenses. See those files for their specific terms.