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:https://doi.org/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)[source]

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)[source]

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.