iq^dZddlZddlmZmZmZmZmZddl m Z ddZ ddZ ddZ d Zd Zd Zd Zd ZdZdZdZdZdZdZ ddZdS)a: Nucleic acid analysis --- :mod:`MDAnalysis.analysis.nuclinfo` ============================================================= :Author: Elizabeth Denning :Year: 2011 :Copyright: Lesser GNU Public License v2.1+ The module provides functions to analyze nucleic acid structures, in particular - backbone dihedrals, - chi dihedrals, - AS or CP phase angles, - Watson-Crick N1-N3 distances, C2-O2 distances, N6-O4 distances, O6-N4 distances. For applications of this kind of analysis see :footcite:p:`Denning2011,Denning2012`. All functions take a :class:`~MDAnalysis.core.universe.Universe` as an argument together with further parameters that specify the base or bases in question. Angles are in degrees. The functions use standard CHARMM names for nucleic acids and atom names. .. rubric:: References .. footbibliography:: Distances --------- .. autofunction:: wc_pair .. autofunction:: minor_pair .. autofunction:: major_pair Phases ------ .. autofunction:: phase_cp .. autofunction:: phase_as Dihedral angles --------------- .. autofunction:: tors .. autofunction:: tors_alpha .. autofunction:: tors_beta .. autofunction:: tors_gamma .. autofunction:: tors_delta .. autofunction:: tors_eps .. autofunction:: tors_zeta .. autofunction:: tors_chi .. autofunction:: hydroxyl .. autofunction:: pseudo_dihe_baseflip N)pisincossqrtpow)mdamathSYSTEMc |d|jddvrd\}}|d|jddvrd\}}|d||||||}tj|dj|djz }|S) aWatson-Crick basepair distance for residue `i` with residue `bp`. The distance of the nitrogen atoms in a Watson-Crick hydrogen bond is computed. Parameters ---------- universe : Universe :class:`~MDAnalysis.core.universe.Universe` containing the trajectory i : int resid of the first base bp : int resid of the second base seg1 : str (optional) segment id for first base ["SYSTEM"] seg2 : str (optional) segment id for second base ["SYSTEM"] Returns ------- float Watson-Crick base pair distance Notes ----- If failure occurs be sure to check the segment identification. .. versionadded:: 0.7.6 resid {0!s} rDCDTUCTCYTTHYURA)N3N1DGDAAGADEGUA)rr](segid {0!s} and resid {1!s} and name {2!s}) or (segid {3!s} and resid {4!s} and name {5!s})  select_atomsformatresnamesrnormposition) universeibpseg1seg2a1a2wc_distwcs f/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/analysis/nuclinfo.pywc_pairr0es@_33A6677@C H  B_33A6677@CHB## ;;A6 !Rr2< < G gaj)GAJ,?? @ @B Ic |d|jddvrd\}}|d|jddvrd\}}|d||||||}tj|dj|djz }|S) aMinor-Groove basepair distance for residue `i` with residue `bp`. The distance of the nitrogen and oxygen atoms in a Minor-groove hydrogen bond is computed. Parameters ---------- universe : Universe :class:`~MDAnalysis.core.universe.Universe` containing the trajectory i : int resid of the first base bp : int resid of the second base seg1 : str (optional) segment id for first base ["SYSTEM"] seg2 : str (optional) segment id for second base ["SYSTEM"] Returns ------- float Minor groove base pair distance Notes ----- If failure occurs be sure to check the segment identification. .. versionadded:: 0.7.6 r rr )O2C2r)r4r3z\(segid {0!s} and resid {1!s} and name {2!s}) or (segid {3!s} and resid {4!s} and name {5!s})rr ) r&r'r(r)r*r+r, c2o2_distc2o2s r/ minor_pairr7s>_33A6677@C H  B_33A6677@CHB%% ::@& !Rr2; ; I < ! - ! 0EE F FD Kr1c |d|jddvr@|d|jddvrd\}}nd\}}|d|jddvr@|d|jddvrd \}}nd \}}|d ||||||}tj|dj|d jz }|S) aMajor-Groove basepair distance for residue `i` with residue `bp`. The distance of the nitrogen and oxygen atoms in a Major-groove hydrogen bond is computed. Parameters ---------- universe : Universe :class:`~MDAnalysis.core.universe.Universe` containing the trajectory i : int resid of the first base bp : int resid of the second base seg1 : str (optional) segment id for first base ["SYSTEM"] seg2 : str (optional) segment id for second base ["SYSTEM"] Returns ------- float Major groove base pair distance Notes ----- If failure occurs be sure to check the segment identification. .. versionadded:: 0.7.6 r r)r rrrrr)r rr)N4O6)r:r9)rrrrrrrr)rrrrr)O4N6)r<r;rrr ) r&r'r(r)r*r+r,no_distmajors r/ major_pairr?sp@_33A6677@CH  !7!7!:!: ; ; DQ GL    FBFB_33A6677@C H    !7!7!:!: ; ; DQ GL    FBFB## ;;A6 !Rr2< < G L,wqz/BB C CE Lr1c |d||}|d||}|d||}|d||}|d||}|j}|j} |j} |j} |j} || z| z| z| zdz} || z }| | z }| | z }| | z }| | z }|tdtzdzd z z|tdtzd zd z zz|tdtzd zd z zz|tdtzd zd z zz|tdtzd zd z zz}|t dtzdzd z z|t dtzd zd z zz|t dtzd zd z zz|t dtzd zd z zz|t dtzd zd z zz}t j|d|d}|tt|ddt|ddzt|ddzz }t j ||}t j ||}t j ||}t j ||}t j ||}|tdtzdzd z z|tdtzd zd z zz|tdtzd zd z zz|tdtzd zd z zz|tdtzd zd z zzdztdz}|t dtzdzd z z|t dtzd zd z zz|t dtzd zd z zz|t dtzd zd z zz|t dtzd zd z zztdz}t j ||td z zdztz }|dzS)aPseudo-angle describing the phase of the ribose pucker for residue `i` using the CP method. The angle is computed by the positions of atoms in the ribose ring. Parameters ---------- universe : Universe :class:`~MDAnalysis.core.universe.Universe` containing the trajectory seg : str segment id for base i : int resid of the first base Returns ------- float phase angle in degrees .. versionadded:: 0.7.6  atom {0!s} {1!s} O4'  atom {0!s} {1!s} C1'  atom {0!s} {1!s} C2'  atom {0!s} {1!s} C3'  atom {0!s} {1!s} C4' g?@?@@@rrg?f@h) r!r" positionsrrrnpcrossrrdotarctan2)r&segr'atom1atom2atom3atom4atom5data1data2data3data4data5r0r1r2r3r4r5R1R2xnr1_dr2_dr3_dr4_dr5_dDr phase_angs r/phase_cprr.s.  ! !":"A"A#q"I"I J JE  ! !":"A"A#q"I"I J JE  ! !":"A"A#q"I"I J JE  ! !":"A"A#q"I"I J JE  ! !":"A"A#q"I"I J JE OE OE OE OE OE %-% % '% /I >B B B B B B c!b&3,$%% % AFSL3&'' ' ) AFSL3&'' ' ) AFSL3&'' ' ) AFSL3&'' '  ) c!b&3,$%% % AFSL3&'' ' ) AFSL3&'' ' ) AFSL3&'' ' ) AFSL3&'' '  ) A1A DQqT1AaD! ,s1Q4||; < <>Df #tS? ?   C   8??aHH  C   9@@sKK  C   9@@qII  C      A  adQqTk1Q4!A$;!qt D DF Z  # %F Mr1)r r )r r r )__doc__numpyrRmathrrrrrMDAnalysis.librr0r7r?rrr|rrrrrrrrrrr1r/rs|0FFN(((((((((((((("""""";;;;|::::zKKKK\XXXvXXXv\;\;\;~@@@@@@$$$N(((X?G;;;;;;r1