4.10.1.1.1. Generation and Analysis of X3DNA helicoidal parameter profiles — MDAnalysis.analysis.legacy.x3dna

Author:Elizabeth Denning
Year:2013-2014
Copyright:GNU Public License v2

New in version 0.8.

Changed in version 0.16.0: This module is difficult to test due to restrictions on the X3DNA code. It is therefore considered unmaintained and legacy code. It was moved to the MDAnalysis.analysis.legacy package (see issue 906)

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.

4.10.1.1.1.1. Example applications

4.10.1.1.1.1.1. Single structure

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()

4.10.1.1.1.1.2. Trajectory

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.

4.10.1.1.1.2. Analysis classes

class MDAnalysis.analysis.legacy.x3dna.X3DNA(filename, **kwargs)[source]

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:

  1. set up the class with all desired parameters
  2. run X3DNA with X3DNA.run()
  3. 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().

When methods return helicoidal basepair parameter as lists, then the order is always

index parameter
0 shear
1 stretch
2 stagger
3 buckle
4 propeller
5 opening
6 shift
7 slide
8 rise
9 tilt
10 roll
11 twist

New in version 0.8.

Set up parameters to run X3DNA on PDB filename.

Parameters:
  • filename (str) – The filename is used as input for X3DNA in the xdna_ensemble command. It specifies the name of a PDB coordinate file to be used. This must be in Brookhaven protein databank format or something closely approximating this.
  • executable (str (optional)) – Path to the xdna_ensemble executable directories (e.g. /opt/x3dna/2.1 and /opt/x3dna/2.1/bin) must be set and then added to export in bashrc file. See X3DNA documentation for set-up instructions.
  • x3dna_param (bool (optional)) – Determines whether base step or base pair parameters will be calculated. If True (default) then stacked base step parameters will be analyzed. If False then stacked base pair parameters will be analyzed.
  • logfile (str (optional)) – Write output from X3DNA to logfile (default: “bp_step.par”)

See also

X3DNAtraj

profiles

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.

collect(**kwargs)[source]

Parse the output from a X3DNA run into numpy recarrays.

Can deal with outputs containing multiple frames.

The method saves the result as X3DNA.profiles, a dictionary indexed by the frame number. Each entry is a np.recarray.

If the keyword outdir is supplied (e.g. “.”) then each profile is saved to a gzipped data file.

Parameters:
  • run (str, int (optional) – identifier, free form [1]
  • outdir (str (optional)) – save output data under outdir/run if set to any other value but None [None]
mean()

Returns the mean value for the base parameters.

Returns:The list contains the means for the helicoidal parameters. The order is [shear, stretch, stagger, buckle, propeller, opening, shift, slide, rise, tilt, roll, twist].
Return type:list
mean_std()

Returns the mean and standard deviation of base parameters.

Returns:The tuple contains two lists with the means and the standard deviations for the helicoidal parameters. The order for both lists is [shear, stretch, stagger, buckle, propeller, opening, shift, slide, rise, tilt, roll, twist].
Return type:(list, list)
plot(**kwargs)

Plot time-averaged base parameters for each basse pair in a 1D graph.

One plot is produced for each parameter. It shows the the mean and standard deviation for each individual base pair. Each plot is saved to PNG file with name “<parameter_name>.png”.

Parameters:ax (matplotlib.pyplot.Axes (optional)) – Provide ax to have all plots plotted in the same axes.
run(**kwargs)[source]

Run X3DNA on the input file.

save(filename=’x3dna.pickle’)

Save profiles as a Python pickle file filename.

Load profiles dictionary with

import cPickle
profiles = cPickle.load(open(filename))
sorted_profiles_iter()

Return an iterator over profiles sorted by frame/order parameter.

The iterator produces tuples (q, profile). Typically, q is the frame number.

std()

Returns the standard deviation for the base parameters.

Returns:The list contains the standard deviations for the helicoidal parameters. The order is [shear, stretch, stagger, buckle, propeller, opening, shift, slide, rise, tilt, roll, twist].
Return type:list
class MDAnalysis.analysis.legacy.x3dna.X3DNAtraj(universe, **kwargs)[source]

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.

Parameters:
  • universe (Universe) – The input trajectory as part of a Universe; the trajectory is converted to a sequence of PDB files and X3DNA is run on each individual file. (Use the start, stop, and step keywords to slice the trajectory.)
  • selection (str (optional)) – MDAnalysis selection string (default: “nucleic”) to select the atoms that should be analyzed.
  • start (int (optional)) –
  • stop (int (optional)) –
  • step (int (optional)) – frame indices to slice the trajectory as universe.trajectory[start, stop, step]; by default, the whole trajectory is analyzed.
  • x3dna_param (bool (optional)) – indicates whether stacked bases or stacked base-pairs will be analyzed. True is bases and False is stacked base-pairs [Default is True].
  • kwargs (keyword arguments (optional)) – All other keywords are passed on to X3DNA (see there for description).

See also

X3DNA

profiles

After running X3DNA.collect(), this dict contains all the X3DNA profiles, indexed by the frame number.

mean()

Returns the mean value for the base parameters.

Returns:The list contains the means for the helicoidal parameters. The order is [shear, stretch, stagger, buckle, propeller, opening, shift, slide, rise, tilt, roll, twist].
Return type:list
mean_std()

Returns the mean and standard deviation of base parameters.

Returns:The tuple contains two lists with the means and the standard deviations for the helicoidal parameters. The order for both lists is [shear, stretch, stagger, buckle, propeller, opening, shift, slide, rise, tilt, roll, twist].
Return type:(list, list)
plot(**kwargs)

Plot time-averaged base parameters for each basse pair in a 1D graph.

One plot is produced for each parameter. It shows the the mean and standard deviation for each individual base pair. Each plot is saved to PNG file with name “<parameter_name>.png”.

Parameters:ax (matplotlib.pyplot.Axes (optional)) – Provide ax to have all plots plotted in the same axes.
run(**kwargs)[source]

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. The defaults are the values provided to the class constructor.

run_x3dna(pdbfile, **kwargs)[source]

Run X3DNA on a single PDB file pdbfile.

save(filename=’x3dna.pickle’)

Save profiles as a Python pickle file filename.

Load profiles dictionary with

import cPickle
profiles = cPickle.load(open(filename))
sorted_profiles_iter()

Return an iterator over profiles sorted by frame/order parameter.

The iterator produces tuples (q, profile). Typically, q is the frame number.

std()

Returns the standard deviation for the base parameters.

Returns:The list contains the standard deviations for the helicoidal parameters. The order is [shear, stretch, stagger, buckle, propeller, opening, shift, slide, rise, tilt, roll, twist].
Return type:list

4.10.1.1.1.3. Utilities

exception MDAnalysis.analysis.legacy.x3dna.ApplicationError[source]

Raised when an external application failed.

The error code is specific for the application.

New in version 0.7.7.