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
AtomGroupand 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 ofAtomGroup.- Parameters
- times
Simulation times for analysis.
- Type
- results
Array of pair distances. First index is selection, second index is time.
Deprecated since version 2.4.0: Will be removed in MDAnalysis 2.5.0. Please use
results.pair_distancesinstead.- Type
- results.times
Simulation times used in analysis
Deprecated since version 2.4.0: Will be removed in MDAnalysis 2.5.0. Please use
timesinstead.- Type
- results.pair_distances
2D array of pair distances. First dimension is simulation time, second dimension contains the pair distances for each each entry pair in selection1 and selection2.
New in version 2.4.0.
- Type
- Raises
ValueError – If the selections given are not the same length
Deprecated since version 2.4.0: Accessing results by passing selection indices to
resultsis now deprecated and will be removed in MDAnalysis version 2.5.0. Please useresults.pair_distancesinstead. Theresults.timesis deprecated and will be removed in version 2.5.0. Please use the class attributetimesinstead.- 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
Residueobjects 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 A
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
- times
Simulation times for analysis.
- Type
- results
Array of Watson-Crick basepair distances. First index is selection, second index is time.
Deprecated since version 2.4.0: Will be removed in MDAnalysis 2.5.0. Please use
results.pair_distancesinstead.- Type
- results.times
Simulation times used in analysis
Deprecated since version 2.4.0: Will be removed in MDAnalysis 2.5.0. Please use
timesinstead.- Type
- results.pair_distances
2D array of Watson-Crick basepair distances. First dimension is simulation time, second dimension contains the pair distances for each each entry pair in strand1 and strand2.
New in version 2.4.0.
- Type
- Raises
ValueError – If the residues given are not amino acids
ValueError – If the selections given are not the same length
Deprecated since version 2.4.0: Accessing results by passing strand indices to
resultsis now deprecated and will be removed in MDAnalysis version 2.5.0. Please useresults.pair_distancesinstead. Theresults.timesis deprecated and will be removed in version 2.5.0. Please use the class attributetimesinstead.- 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.