A library to calculate FRET observables for MD trajectories by accessible volume (AV) simulations.In the AV simulations the sterically allowed conformation space of the labels is approximated the conformational space of flexible attached ellipsoids.
AvTraj is tool to calculate FRET observables from MD-trajectories. Read, write and analyze accessible volumes (AVs) using MD trajectories as an input with only a few lines of Python code. By the use of LabelLib AvTraj provides programmatic access to latest developments in implicit dye models for FRET experiments .
AvTraj is a python library that allows users to perform simulations of accessible volumes for molecular dynamics (MD) trajectories. AvTraj serves as a high-level interface for the development of new methodologies for structure-based fluorescence spectroscopy.
A wide support of diverse MD formats by the use of MDTraj. Extremely fast calculation of AVs by the use of LabelLib (e.g. xxxx the speed of yyyy). Extensive analysis functions including those that compute inter-dye distances, FRET-efficiencies, fluorescence decays, distance distributions, and an Pythonic API.
AVTraj includes a command-line application, avana, for screening and analyzing structural models.
Relation of other software and libraries
LabelLib serves as core low-level library for the software Olga and the higher-level Python library AvTraj. The deprecated software FPS is independent of LabelLib.
Olga is a software dedicated towards experimentalists. Olga provides a graphical user interface for the calculation of accessible volumes (AVs), screen a set of structural models against experimental observables, rigid-body docking, and the optimal design of new FRET experiments.
AvTraj AvTraj is a Python library for the calculation of accessible volumes (AVs), screening. AvTraj facilitates the development of new analytical approaches for FRET-based structural models. Avtraj facilitates processing of MD-simulations and the development of Python scripts handling FRET-based structural models.
FPS is a software with a graphical user interface for the FRET-based structural modeling. FPS can calculate accessible volumes (AVs), screen a set of structural models against experimental observables, and can generate new structural models by rigid-body docking using experimental FRET data.
conda --add channels tpeulen conda install avtraj
import mdtraj as md import avtraj as avt # 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 = avt.AVTrajectory(traj, '18D', attachment_atom_selection='resSeq 7 and name CB') # These accessible volumes can be saved as xyz-file av_traj.save_xyz('test_344.xyz') # The dye parameters can either be passed explicitly on creation of the object av_traj = avt.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 = avt.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 = avt.AvDistanceTrajectory(traj, './examples/hGBP1_distance.json')
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.