Source code for MDAnalysis.analysis.nucleicacids

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r"""
Updated nucleic acid analysis --- :mod:`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 :cite:p:`b-Denning2011,b-Denning2012`.

.. rubric:: References

.. bibliography::
    :filter: False
    :style: MDA
    :keyprefix: b-
    :labelprefix: ᵇ

    Denning2011
    Denning2012

Distances
---------

.. autoclass:: NucPairDist
    :members:
    :inherited-members:

.. autoclass:: WatsonCrickDist
    :members:
    :inherited-members:

.. versionadded 2.2.0

"""

from typing import List, Dict
import warnings

import numpy as np

import MDAnalysis as mda
from .distances import calc_bonds
from .base import AnalysisBase, Results
from MDAnalysis.core.groups import Residue


[docs]class NucPairDist(AnalysisBase): r"""Atom Pair distance calculation base class. Takes two lists of :class:`~MDAnalysis.core.groups.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 :class:`~MDAnalysis.core.groups.AtomGroup`. Parameters ---------- selection1: List[AtomGroup] List of :class:`~MDAnalysis.core.groups.AtomGroup` containing an atom of each nucleic acid being analyzed. selection2: List[AtomGroup] List of :class:`~MDAnalysis.core.groups.AtomGroup` containing an atom of each nucleic acid being analyzed. kwargs: dict Arguments for :class:`~MDAnalysis.analysis.base.AnalysisBase` Attributes ---------- times: numpy.ndarray Simulation times for analysis. results.pair_distances: numpy.ndarray 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. .. versionadded:: 2.4.0 Raises ------ ValueError If the selections given are not the same length .. versionchanged:: 2.5.0 The ability to access by passing selection indices to :attr:`results` is is now removed as of MDAnalysis version 2.5.0. Please use :attr:`results.pair_distances` instead. The :attr:`results.times` was deprecated and is now removed as of MDAnalysis 2.5.0. Please use the class attribute :attr:`times` instead. """ _s1: mda.AtomGroup _s2: mda.AtomGroup _n_sel: int _res_dict: Dict[int, List[float]] _times = List[float] def __init__(self, selection1: List[mda.AtomGroup], selection2: List[mda.AtomGroup], **kwargs) -> None: super(NucPairDist, self).__init__(selection1[0].universe.trajectory, **kwargs) if len(selection1) != len(selection2): raise ValueError("Selections must be same length") self._n_sel: int = len(selection1) self._s1 = selection1[0] self._s2 = selection2[0] for i in range(1, self._n_sel): self._s1 += selection1[i] self._s2 += selection2[i] def _prepare(self) -> None: self._res_array: np.ndarray = np.zeros([self.n_frames, self._n_sel]) def _single_frame(self) -> None: dist: np.ndarray = calc_bonds(self._s1.positions, self._s2.positions) self._res_array[self._frame_index, :] = dist def _conclude(self) -> None: self.results['pair_distances'] = self._res_array
[docs]class WatsonCrickDist(NucPairDist): r"""Watson-Crick basepair distance for selected residues over a trajectory. Takes two lists of :class:`~MDAnalysis.core.groups.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 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 :class:`~MDAnalysis.analysis.base.AnalysisBase` Attributes ---------- times: numpy.ndarray Simulation times for analysis. results.pair_distances: numpy.ndarray 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. .. versionadded:: 2.4.0 Raises ------ ValueError If the residues given are not amino acids ValueError If the selections given are not the same length .. versionchanged:: 2.5.0 Accessing results by passing strand indices to :attr:`results` is was deprecated and is now removed as of MDAnalysis version 2.5.0. Please use :attr:`results.pair_distances` instead. The :attr:`results.times` was deprecated and is now removed as of MDAnalysis 2.5.0. Please use the class attribute :attr:`times` instead. """ def __init__(self, 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) -> None: sel1: List[mda.AtomGroup] = [] sel2: List[mda.AtomGroup] = [] strand = zip(strand1, strand2) for s in strand: if s[0].resname[0] in [c_name, t_name, u_name]: a1, a2 = n3_name, n1_name elif s[0].resname[0] in [a_name, g_name]: a1, a2 = n1_name, n3_name else: raise ValueError(f"{s} are not valid nucleic acids") sel1.append(s[0].atoms.select_atoms(f'name {a1}')) sel2.append(s[1].atoms.select_atoms(f'name {a2}')) super(WatsonCrickDist, self).__init__(sel1, sel2, **kwargs)