4.5.2. Updated nucleic acid analysis — MDAnalysis.analysis.nucleicacids

Author:

Alia Lescoulie

Year:

2022

copyright:

GNU Public Licence v3

The module provides classes for analyzing nucleic acids structures. This is an updated, higher performance version of previous nucleic acid tools. For applications see [ᵇDenning2011, ᵇDenning2012].

References

[ᵇDenning2011]

Elizabeth J. Denning, U. Deva Priyakumar, Lennart Nilsson, and Alexander D. Mackerell Jr. Impact of 2-hydroxyl sampling on the conformational properties of rna: update of the charmm all-atom additive force field for rna. Journal of Computational Chemistry, 32(9):1929–1943, 2011. doi:10.1002/jcc.21777.

[ᵇDenning2012]

Elizabeth J. Denning and Alexander D. MacKerell. Intrinsic contribution of the 2\'-hydroxyl to rna conformational heterogeneity. Journal of the American Chemical Society, 134(5):2800–2806, 2012. PMID: 22242623. doi:10.1021/ja211328g.

4.5.2.1. Distances

class MDAnalysis.analysis.nucleicacids.NucPairDist(selection1: List[AtomGroup], selection2: List[AtomGroup], **kwargs)

Atom Pair distance calculation base class.

Takes two lists of AtomGroup and computes the distances between them over a trajectory. Used as a superclass for the other nucleic acid distances classes. The distance will be measured between atoms sharing an index in the two lists of AtomGroup.

Parameters:

• selection1 (List[AtomGroup]) – list of AtomGroup containing an atom of each nucleic acid being analyzed.

• selection1 – list of AtomGroup containing an atom of each nucleic acid being analyzed.

• kwargs (dict) – arguments for AnalysisBase

results

first index is selection second index is time

Type:

numpy.ndarray

results.times

times used in analysis

Type:

numpy.ndarray

Raises:

ValueError – if the selections given are not the same length

run(start=None, stop=None, step=None, frames=None, verbose=None)

Perform the calculation

Parameters:

• start (int, optional) – start frame of analysis

• stop (int, optional) – stop frame of analysis

• step (int, optional) – number of frames to skip between each analysed frame

• frames (array_like, optional) –

  array of integers or booleans to slice trajectory; frames can only be used instead of start, stop, and step. Setting both frames and at least one of start, stop, step to a non-default value will raise a ValueError.

  New in version 2.2.0.

• verbose (bool, optional) – Turn on verbosity

Changed in version 2.2.0: Added ability to analyze arbitrary frames by passing a list of frame indices in the frames keyword argument.

class MDAnalysis.analysis.nucleicacids.WatsonCrickDist(strand1: List[Residue], strand2: List[Residue], n1_name: str = 'N1', n3_name: str = 'N3', g_name: str = 'G', a_name: str = 'A', u_name: str = 'U', t_name: str = 'T', c_name: str = 'C', **kwargs)

Watson-Crick basepair distance for selected residues over a trajectory.

Takes two lists of Residue objects and calculates the Watson-Crick distance between them over the trajectory. Bases are matched by their index in the lists given as arguments.

Parameters:

• strand1 (List[Residue]) – First list of bases

• strand2 (List[Residue]) – Second list of bases

• n1_name (str (optional)) – Name of Nitrogen 1 of nucleic acids by default assigned to N1

• n3_name (str (optional)) – Name of Nitrogen 3 of nucleic acids by default assigned to N3

• g_name (str (optional)) – Name of Guanine in topology by default assigned to G

• a_name (str (optional)) – Name of Adenine in topology by default assigned to G

• u_name (str (optional)) – Name of Uracil in topology by default assigned to U

• t_name (str (optional)) – Name of Thymine in topology by default assigned to T

• c_name (str (optional)) – Name of Cytosine in topology by default assigned to C

• **kwargs (dict) – arguments for AnalysisBase

results

first index is selection second index is time

Type:

numpy.ndarray

results.times

times used in analysis

Type:

numpy.ndarray

Raises:

• ValueError – if the residues given are not amino acids

• ValueError – if the selections given are not the same length

run(start=None, stop=None, step=None, frames=None, verbose=None)

Perform the calculation

Parameters:

• start (int, optional) – start frame of analysis

• stop (int, optional) – stop frame of analysis

• step (int, optional) – number of frames to skip between each analysed frame

• frames (array_like, optional) –

  array of integers or booleans to slice trajectory; frames can only be used instead of start, stop, and step. Setting both frames and at least one of start, stop, step to a non-default value will raise a ValueError.

  New in version 2.2.0.

• verbose (bool, optional) – Turn on verbosity

Changed in version 2.2.0: Added ability to analyze arbitrary frames by passing a list of frame indices in the frames keyword argument.