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

Author:

Alia Lescoulie

Year:

2022-2023

copyright:

LGPLv2.1

The module provides classes for analyzing nucleic acids structures. This is an updated, higher performance version of previous nucleic acid tools. For applications see [1][2].

References

[1]

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.

[2]

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.

• selection2 (List[AtomGroup]) – List of AtomGroup containing an atom of each nucleic acid being analyzed.

• kwargs (dict) – Arguments for AnalysisBase

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.

Note

results.pair_distances is slated for deprecation in version 3.0.0, use results.distances instead.

Deprecated since version 2.7.0: results.pair_distances will be removed in version 3.0.0, use results.distances instead.

Type:

numpy.ndarray

results.distances

stored in a 2d numpy array with first index selecting the Residue pair, and the second index selecting the frame number Distances are stored in a 2d numpy array with axis 0 (first index) indexing the trajectory frame and axis 1 (second index) selecting the Residue pair.

New in version 2.7.0.

Type:

numpy.ndarray

times

Simulation times for analysis.

Type:

numpy.ndarray

Raises:

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

• ValueError – An AtomGroup in one of the strands not a valid nucleic acid

• ValueError – If a given residue pair from the provided strands returns an empty AtomGroup when selecting the atom pairs used in the distance calculations

Version Info

Changed in version 2.5.0: The ability to access by passing selection indices to results is now removed as of MDAnalysis version 2.5.0. Please use results.pair_distances instead. The results.times was deprecated and is now removed as of MDAnalysis 2.5.0. Please use the class attribute times instead.

Changed in version 2.7.0: Added static method select_strand_atoms as a helper for selecting atom pairs for distance analysis.

run(start=None, stop=None, step=None, frames=None, verbose=None, *, progressbar_kwargs=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

• progressbar_kwargs (dict, optional) – ProgressBar keywords with custom parameters regarding progress bar position, etc; see MDAnalysis.lib.log.ProgressBar for full list.

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

Changed in version 2.5.0: Add progressbar_kwargs parameter, allowing to modify description, position etc of tqdm progressbars

static select_strand_atoms(strand1: ResidueGroup, strand2: ResidueGroup, a1_name: str, a2_name: str, g_name: str = 'G', a_name: str = 'A', u_name: str = 'U', t_name: str = 'T', c_name: str = 'C') → Tuple[List[AtomGroup], List[AtomGroup]]

A helper method for nucleic acid pair distance analyses. Used for selecting specific atoms from two strands of nucleic acids.

Parameters:

• strand1 (List[Residue]) – The first nucleic acid strand

• strand2 (List[Residue]) – The second nucleic acid strand

• a1_name (str) – The selection for the purine base of the strand pair

• a2_name (str) – the selection for the pyrimidine base of the strand pair

• 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

Returns:

returns a tuple containing two lists of AtomGroups corresponding to the provided selections from each strand.

Return type:

Tuple[List[AtomGroup], List[AtomGroup]]

Raises:

• ValueError: – An AtomGroup in one of the strands not a valid nucleic acid

• ValueError: – An Residue returns an empty AtomGroup with the provided selection

New in version 2.7.0.

class MDAnalysis.analysis.nucleicacids.WatsonCrickDist(strand1: List[Residue] | ResidueGroup, strand2: List[Residue] | ResidueGroup, 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 base pair distance for selected residues over a trajectory.

Takes two ResidueGroup objects or two lists of Residue and calculates the distance between the nitrogen atoms in the Watson-Crick hydrogen bond over the trajectory. Bases are matched either by their index in the two ResidueGroup provided as arguments, or based on the indices of the provided lists of Residue objects depending on which is provided.

Note

Support for Residue is slated for deprecation and will raise a warning when used. It still works but ResidueGroup is preferred.

Parameters:

• strand1 (ResidueClass) –

  First list of bases

  Deprecated since version 2.7.0: Using a list of Residue will be removed in 3.0.0. Use a ResidueGroup.

• strand2 (ResidueClass) –

  Second list of bases

  Deprecated since version 2.7.0: Using a list of Residue will be removed in 3.0.0. Use a ResidueGroup.

• 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) – Key word arguments for AnalysisBase

results.distances

Distances are stored in a 2d numpy array with axis 0 (first index) indexing the trajectory frame and axis 1 (second index) selecting the Residue pair.

New in version 2.7.0.

Type:

numpy.ndarray

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.

Deprecated since version 2.7.0: results.pair_distances will be removed in version 3.0.0, use results.distances instead.

Type:

numpy.ndarray

times

Simulation times for analysis.

Type:

numpy.ndarray

Raises:

• TypeError – If the provided list of Residue contains non-Residue elements .. deprecated:: 2.7.0 Starting with version 3.0.0, this exception will no longer be raised because only ResidueGroup will be allowed.

• ValueError – If strand1 and strand2 are not the same length

• ValueError: – An AtomGroup in one of the strands not a valid nucleic acid

• ValueError – If a given residue pair from the provided strands returns an empty AtomGroup when selecting the atom pairs used in the distance calculations

Version Info

Changed in version 2.5.0: Accessing results by passing strand indices to results was deprecated and is now removed as of MDAnalysis version 2.5.0. Please use results.pair_distances instead. The results.times was deprecated and is now removed as of MDAnalysis 2.5.0. Please use the class attribute times instead.

Changed in version 2.7.0: strand1 and strand2 now also accept a ResidueGroup as input. The previous input type, List[Residue] is still supported, but it is deprecated and will be removed in release 3.0.0.

run(start=None, stop=None, step=None, frames=None, verbose=None, *, progressbar_kwargs=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

• progressbar_kwargs (dict, optional) – ProgressBar keywords with custom parameters regarding progress bar position, etc; see MDAnalysis.lib.log.ProgressBar for full list.

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

Changed in version 2.5.0: Add progressbar_kwargs parameter, allowing to modify description, position etc of tqdm progressbars

class MDAnalysis.analysis.nucleicacids.MinorPairDist(strand1: ResidueGroup, strand2: ResidueGroup, o2_name: str = 'O2', c2_name: str = 'C2', g_name: str = 'G', a_name: str = 'A', u_name: str = 'U', t_name: str = 'T', c_name: str = 'C', **kwargs)

Minor-Pair basepair distance for selected residues over a trajectory.

Takes two ResidueGroup objects and calculates the Minor-groove hydrogen bond length between the nitrogen and oxygen atoms over the trajectory. Bases are matched by their index in the two ResidueGroup provided as arguments.

Parameters:

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

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

• o2_name (str (optional)) – Name of Oxygen 2 of nucleic acids; by default assigned to “O2”;

• c2_name (str (optional)) – Name of Carbon 2 of nucleic acids; by default assigned to “C2”;

• 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 – keyword arguments for AnalysisBase

results.distances

stored in a 2d numpy array with first index selecting the Residue pair, and the second index selecting the frame number

Type:

numpy.ndarray

times

Simulation times for analysis.

Type:

numpy.ndarray

Raises:

• ValueError – If the selections given are not the same length A Residue in one of the strands not a valid nucleic acid

• ValueError – If a given residue pair from the provided strands returns an empty AtomGroup when selecting the atom pairs used in the distance calculations

New in version 2.7.0.

run(start=None, stop=None, step=None, frames=None, verbose=None, *, progressbar_kwargs=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

• progressbar_kwargs (dict, optional) – ProgressBar keywords with custom parameters regarding progress bar position, etc; see MDAnalysis.lib.log.ProgressBar for full list.

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

Changed in version 2.5.0: Add progressbar_kwargs parameter, allowing to modify description, position etc of tqdm progressbars

class MDAnalysis.analysis.nucleicacids.MajorPairDist(strand1: ResidueGroup, strand2: ResidueGroup, n4_name: str = 'N4', o6_name: str = 'O6', g_name: str = 'G', a_name: str = 'A', u_name: str = 'U', t_name: str = 'T', c_name: str = 'C', **kwargs)

Minor-Pair base pair distance for selected residues over a trajectory.

Takes two ResidueGroup objects and calculates the Major-groove hydrogen bond length between the nitrogen and oxygen atoms over the trajectory. Bases are matched by their index in the two ResidueGroup provided as arguments.

Parameters:

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

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

• o6_name (str (optional)) – Name of Oxygen 6 of nucleic acids; by default assigned to “O6”

• n4_name (str (optional)) – Name of Nitrogen 4 of nucleic acids; by default assigned to “N4”

• 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 – arguments for AnalysisBase

results.distances

Distances are stored in a 2d numpy array with axis 0 (first index) indexing the trajectory frame and axis 1 (second index) selecting the Residue pair.

Type:

numpy.ndarray

times

Simulation times for analysis.

Type:

numpy.ndarray

Raises:

• ValueError – A Residue in one of the strands not a valid nucleic acid

• ValueError – If a given residue pair from the provided strands returns an empty AtomGroup when selecting the atom pairs used in the distance calculations

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

New in version 2.7.0.

run(start=None, stop=None, step=None, frames=None, verbose=None, *, progressbar_kwargs=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

• progressbar_kwargs (dict, optional) – ProgressBar keywords with custom parameters regarding progress bar position, etc; see MDAnalysis.lib.log.ProgressBar for full list.

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

Changed in version 2.5.0: Add progressbar_kwargs parameter, allowing to modify description, position etc of tqdm progressbars