Author: | Elizabeth Denning |
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Year: | 2013-2014 |
Copyright: | GNU Public License v2 |
With the help of this module, X3DNA_ can be run on frames in a trajectory. Data can be combined and analyzed. X3DNA_ [Lu2003] [Lu2008] must be installed separately.
References
[Lu2003] | Xiang-Jun Lu & Wilma K. Olson (2003). 3DNA: a software package for the analysis, rebuilding and visualization for three-dimensional nucleic acid structure Nucleic Acids Res. 31(17), 5108-21. |
[Lu2008] | Xiang-Jun Lu & Wilma K. Olson (2008). 3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures. Nat Protoc. 3(7), 1213-27. |
B-DNA structure:
from MDAnalysis.analysis.x3dna import X3DNA, X3DNAtraj
from MDAnalysis.tests.datafiles import PDB_X3DNA
# set path to your x3dna binary in bashrc file
H = X3DNA(PDB_X3DNA, executable="x3dna_ensemble analyze -b 355d.bps -p pdbfile")
H.run()
H.collect()
H.plot()
Analyzing a trajectory:
u = MDAnalysis.Universe(psf, trajectory)
H = X3DNAtraj(u, ...)
H.run()
H.plot()
H.save()
The profiles are available as the attribute X3DNAtraj.profiles (H.profiles in the example) and are indexed by frame number but can also be indexed by an arbitrary order parameter as shown in the next example.
Run X3DNA_ on a single frame or a DCD trajectory.
Only a subset of all X3DNA control parameters is supported and can be set with keyword arguments. For further details on X3DNA_ see the X3DNA docs.
Running X3DNA with the X3DNA class is a 3-step process:
- set up the class with all desired parameters
- run X3DNA with X3DNA.run()
- collect the data from the output file with X3DNA.collect()
The class also provides some simple plotting functions of the collected data such as X3DNA.plot() or X3DNA.plot3D().
New in version 0.8.
Set up parameters to run X3DNA_ on PDB filename.
Arguments: | filename
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Keywords: | executable
x3dna_param
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x3dna_ensemble analyze -b 355d.bps -p pdbfile attribute: After running X3DNA.collect(), this dict contains all the X3DNA profiles, indexed by the frame number. If only a single frame was analyzed then this will be X3DNA.profiles[0]. Note that the order is random; one needs to sort the keys first.
Parse the output from a X3DNA run into numpy recarrays.
Can deal with outputs containing multiple frames. Output format:
The method saves the result as X3DNA.profiles, a dictionary indexed by the frame number. Each entry is a numpy.recarray.
If the keyword outdir is supplied (e.g. ”.”) then each profile is saved to a gzipped data file.
Keywords: |
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H.mean() returns the mean value for the base parameters (order of base parameters:Shear,Stretch,Stagger,Buckle,Propeller,Opening,Shift,Slide,Rise,Tilt,Roll,Twist) for each nucleic acid pair.
H.mean_std() returns the mean and standard deviation of base parameters (order of base parameters:Shear,Stretch,Stagger,Buckle,Propeller,Opening,Shift,Slide,Rise,Tilt,Roll,Twist) for each nucleic acid pair.
Keywords: | Not available at this time |
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Save profiles as a Python pickle file filename.
Load profiles dictionary with
import cPickle
profiles = cPickle.load(open(filename))
Return an iterator over profiles sorted by frame/order parameter q.
The iterator produces tuples (q, profile).
H.std() returns the standard deviation of base parameters (order of base parameters:Shear,Stretch,Stagger,Buckle,Propeller,Opening,Shift,Slide,Rise,Tilt,Roll,Twist) for each nucleic acid pair.
Analyze all frames in a trajectory.
The X3DNA class provides a direct interface to X3DNA. X3DNA itself has limited support for analysing trajectories but cannot deal with all the trajectory formats understood by MDAnalysis. This class can take any universe and feed it to X3DNA. By default it sequentially creates a PDB for each frame and runs X3DNA on the frame.
Set up the class.
Arguments: |
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After running X3DNA.collect(), this dict contains all the X3DNA profiles, indexed by the frame number.
H.mean() returns the mean value for the base parameters (order of base parameters:Shear,Stretch,Stagger,Buckle,Propeller,Opening,Shift,Slide,Rise,Tilt,Roll,Twist) for each nucleic acid pair.
H.mean_std() returns the mean and standard deviation of base parameters (order of base parameters:Shear,Stretch,Stagger,Buckle,Propeller,Opening,Shift,Slide,Rise,Tilt,Roll,Twist) for each nucleic acid pair.
Keywords: | Not available at this time |
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Run X3DNA on the whole trajectory and collect profiles.
Keyword arguments start, stop, and step can be used to only analyse part of the trajectory.
Save profiles as a Python pickle file filename.
Load profiles dictionary with
import cPickle
profiles = cPickle.load(open(filename))
Return an iterator over profiles sorted by frame/order parameter q.
The iterator produces tuples (q, profile).
H.std() returns the standard deviation of base parameters (order of base parameters:Shear,Stretch,Stagger,Buckle,Propeller,Opening,Shift,Slide,Rise,Tilt,Roll,Twist) for each nucleic acid pair.