Tutorial

Define all parameters necessary for the calculation of an accessible volume (AV)

{
    "version": "0.0.1",
    "Distances": {
        "344-496": {
            "Forster_radius": 52.0,
            "distance": 54.8,
            "distance_type": "RDAMean",
            "error_neg": 6.3,
            "error_pos": 5.5,
            "position1_name": "344A",
            "position2_name": "496D",
            "distance_samples": 100000
        }
    },
    "Positions": {
        "344A": {
         "chain_identifier": "A",
         "residue_seq_number": 344,
         "atom_name": "CB",
         "linker_length": 20.0,
         "linker_width": 1.5,
         "radius1": 3.5,
         "strip_mask": "MDTraj: residue 344 and not (name CA or name C or name N or name O)",
         "contact_volume_thickness": 0.0,
         "contact_volume_trapped_fraction": 0.8,
         "simulation_type": "AV1",
         "simulation_grid_resolution": 0.5,
         "label_interaction_sites": [
            {
               "selection": "MDTraj: resSeq 344",
               "weight": 1.0,
               "radius": 6.0
            }
         ]
        },
        "496D": {
         "chain_identifier": "A",
         "residue_seq_number": 496,
         "atom_name": "CB",
         "linker_length": 20.0,
         "linker_width": 1.5,
         "radius1": 3.5,
         "strip_mask": "MDTraj: residue 496 and not (name CA or name C or name N or name O)",
         "contact_volume_thickness": 0.0,
         "contact_volume_trapped_fraction": 0.8,
         "simulation_type": "AV1",
         "simulation_grid_resolution": 0.5,
         "label_interaction_sites": [
            {
               "selection": "MDTraj: resSeq 496",
               "weight": 1.0,
               "radius": 6.0
            }
         ]
        }
    }
}

import mdtraj as md
import avtraj as avt
import json
import pylab as p

import avtraj.trajectory

traj = md.load('./examples/hGBP1_out_3.h5')
labeling = json.load(open('./examples/labeling.fps.json', 'r'))

# 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_1 = avtraj.trajectory.AVTrajectory(traj, '18D', attachment_atom_selection='resSeq 18 and name CB', strip_mask='resSeq 18')
av_traj_1 = avtraj.trajectory.AVTrajectory(traj, '18D', attachment_atom_selection='resSeq 18 and name CB', strip_mask='resSeq 7')

# These accessible volumes can be saved as xyz-file
av_traj_1[0].save_xyz('test_18_0.xyz')
av0 = av_traj_1[0]

# 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_2 = avtraj.AVTrajectory(traj, '18D', attachment_atom_selection='resSeq 550 and name CB', strip_mask='resSeq 550')
# These accessible volumes can be saved as xyz-file
av1 = av_traj_2[0]
x, y = av1.pRDA(av0)
p.plot(x, y)


# The dye parameters can either be passed explicitly on creation of the object
av_traj = avtraj.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 = avtraj.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"
av_dist = avtraj.AvDistanceTrajectory(traj, './examples/hGBP1_distance.json')

# For every frame the 'chi2' (for the provided set of distances), the FRET efficiency expressed in units of
# a distance 'rDAE', the distance between the mean dye positions 'rMP', and the donor-acceptor distance
# distribution 'pRDA' is calculated. 'pRDA' is a histogram. The histogram bins can be specified upon initialization
# of the AvDistanceTrajectory object and are returned as a value.
print av_dist[0]