i@ dZddlZdZdZdZdZdejded ejfd Z dejded efd Z d ejd ejfdZ eedfd ejde de de d ejf dZd ejd ejfdZdS)a A re-implementation of DSSP algorithm :footcite:p:`Kabsch1983`, taken from *pydssp* v.0.9.0 (https://github.com/ShintaroMinami/PyDSSP) by Shintaro Minami, distributed under MIT license. Current implementation doesn't use `einops` as a dependency, instead directly using `numpy` operations for axis rearrangement. However, this implementation does not allow for batch computation, in contrast with `pydssp`, since it's designed to be used in per-frame manner in protein trajectories. Ng/$?iLg?awindowreturncBtt||d|dS)aPerforms array upsampling with given window along given axis. Example ------- .. code-block:: python hbmap = np.arange(4*4).reshape(4,4) print(hbmap) # [[ 0 1 2 3] # [ 4 5 6 7] # [ 8 9 10 11] # [12 13 14 15]] print(_upsample(hbmap)) # [[[[ 0 1 2] # [ 4 5 6] # [ 8 9 10]] # [[ 1 2 3] # [ 5 6 7] # [ 9 10 11]]] # [[[ 4 5 6] # [ 8 9 10] # [12 13 14]] # [[ 5 6 7] # [ 9 10 11] # [13 14 15]]]] Parameters ---------- a : np.ndarray input array window : int upsample window Returns ------- np.ndarray unfolded array )_unfold)rrs o/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/analysis/dssp/pydssp_numpy.py _upsampler s#V 71fb))62 6 66axisctj|dddftj|j||z dzdddfz}tj|||}tj||dz dS)z'Helper function for 2D array upsamplingNr )nparangeshapetakemoveaxis)rrr idxunfoldeds r r r Bs &!!!T'" )AGDMF*Q. / /aaa 8 9wq#D)))H ;x2 . ..r coordcr|dddf|dddfz }|tj|ddz }|dddf|dddfz }|tj|ddz }||z}|tj|ddz }|dddfd|zzS) aFills in hydrogen atoms positions if they are abscent, under the assumption that C-N-H and H-N-CA angles are perfect 120 degrees, and N-H bond length is 1.01 A. Parameters ---------- coord : np.ndarray input coordinates in Angstrom, shape (n_atoms, 4, 3), where second axes corresponds to (N, CA, C, O) atom coordinates Returns ------- np.ndarray coordinates of additional hydrogens, shape (n_atoms-1, 3) .. versionadded:: 2.8.0 rNrrT)r keepdimsg)\(?)rlinalgnorm)rvec_cnvec_canvec_nhs r _get_hydrogen_atom_positionr"Ls:122q5\E#2#q&M )F binnV"tnDD DFABBElU122q5\)G wR$GGGG g F binnV"tnDD DF Q<$- ''r Fcutoffmarginreturn_ec|j\}}}|dvs Jd|dkrt|}n0|dkr|dddf}|ddddf}ntd|dddf|ddd f|ddd f} } }|dz } tj| | ddf} tj| | ddf} tj|dd| f| | d }tj|dd| f| | d }tj| |z d }tj| |z d }tj| |z d }tj| |z d }tjtd |z d |z zd |z z d |z z ztzddgddgg}|r|Stj |t }|tj tj|dz t dz}|tj tj|d z t dz}tj||z |z | |}tj||z tjzd z d zd z }||z}|S)aReturns hydrogen bond map Parameters ---------- coord : np.ndarray input coordinates in either (n, 4, 3) or (n, 5, 3) shape (without or with hydrogens). If hydrogens are not present, then ideal positions (see :func:_get_hydrogen_atom_positions) are used. cutoff : float, optional cutoff, by default DEFAULT_CUTOFF margin : float, optional margin, by default DEFAULT_MARGIN return_e : bool, optional if to return energy instead of hbond map, by default False Returns ------- np.ndarray output hbond map or energy depending on return_e param .. versionadded:: 2.8.0 )z8Number of atoms should be 4 (N,CA,C,O) or 5 (N,CA,C,O,H)r'r(rNrrrrr)dtype)kr)a_mina_max)rr" ValueErrorrtilereshaperrpad CONST_Q1Q2CONST_Feyebooldiagonesclipsinpi)rr#r$r%n_atoms n_atom_types_h_1n_1c_0o_0ncmapomapnmaphmapd_ond_chd_ohd_cne local_mask hbond_maps r get_hbond_maprNws: %{G\1    B    q)%00   ABBElaaa!e  F   !""a%L%"a.%"a.cC! A 73Aq " "D 73Aq " "D 73Aq " " * *1a 3 3D 73Aq " " * *1a 3 3D 9>>$+B> / /D 9>>$+B> / /D 9>>$+B> / /D 9>>$+B> / /D  :d "S4Z /#* < >   Q!Q   A&----J27277Q;d;;;rBBBBBJ27277Q;d;;;rBBBBBJ!+F7&IIII F*RU2Q677#=BIJ&I r cpt|}tj|dd}tj|ddk}tj|ddk}tj|ddk}tj|dd|d dzd dgg}tj|dd|d dzd dgg}tj|dd|d dzd dgg}|tj|d d ztj|d d ztj|dd z}|tj|dd z|z}|tj|dd z|z}|tj|d d ztj|d d z} |tj|d d ztj|d d ztj|dd ztj|dd z} t |ddk} tj| d d } | ddddd d f| ddddd d fz| ddddd d f| ddddd d fzz} tj| d d gd d gg} | ddddd d f| ddddd d fz| ddddd d f| ddddd d fzz}tj|d d gd d gg}| |zddk}| |z| zdk}|}||z}tj|||gd }|S) aiAssigns secondary structure for a given coordinate array, either with or without assigned hydrogens Parameters ---------- coord : np.ndarray input coordinates in either (n, 4, 3) or (n, 5, 3) shape, without or with hydrogens, respectively. Second dimension `k` represents (N, CA, C, O) atoms coordinates (if k=4), or (N, CA, C, O, H) coordinates (when k=5). Returns ------- np.ndarray output (n,) array with one-hot labels in C3 notation ('-', 'H', 'E'), representing loop, helix and sheet, respectively. .. versionadded:: 2.8.0 rrr))offsetgr'r(Nrrrr) rNrswapaxesdiagonalr1rollr sumstack)rhbmapturn3turn4turn5h3h4h5helix4helix3helix5 unfoldmap unfoldmap_revp_bridgea_bridgeladderhelixstrandlooponehots r assignris, % E Kr2 & &E Ka ( ( (3 .E Ka ( ( (3 .E Ka ( ( (3 .E crc U122Y&!Q 1 1B crc U122Y&!Q 1 1B crc U122Y&!Q 1 1B"'"a## #bgb!Q&7&7 7"'"a:K:K KF rwvr1%%% % /B rwvr1%%% % /B "'"a## #bgb!Q&7&7 7F '"a    '"a    '"a    '"a     %##c)IK 1a00M!!!QQQ1*% aaaAqj(AAaaaAqj!IaaaAqj$99Hvh!Q!Q 011H!!!QQQ1*% aaaAqj(AA!!!QQQ1* aaaAqj 99Hvh!Q!Q 011H! & &r * *S 0Ff_v % ,E F 6VG D XtUF+" 5 5 5F Mr )__doc__numpyrr2r3DEFAULT_CUTOFFDEFAULT_MARGINndarrayintr r r"floatr5rNrir r rrsJ    +7+7S+7RZ+7+7+7+7\/rz/3/c////((rz((bj((((((((Z#" SS :S S S S Z SSSSlG"*GGGGGGGr