idZddlZddlZddlZddlZddlZddlZddlZddlZ ddl m Z ddl m Z ddlmZmZmZdZdZd Zd Zd Zd ZiZiZd ZGddeZGddeeZGddeZGddeZ dZ!GddeZ"Gddee"Z#Gdde#Z$Gdde#Z%Gd d!e%Z&Gd"d#e%Z'Gd$d%e%Z(Gd&d'e#Z)Gd(d)e#Z*Gd*d+e#Z+Gd,d-e#Z,Gd.d/e#Z-Gd0d1e-Z.Gd2d3e-Z/Gd4d5e#Z0Gd6d7e#Z1Gd8d9e#Z2Gd:d;e#Z3Gd<d=e#Z4Gd>d?e#Z5Gd@dAe#Z6GdBdCe#Z7GdDdEe#Z8GdFdGe#Z9GdHdIe#Z:GdJdKe:Z;GdLdMe:Z<GdNdOe#Z=GdPdQe#Z>GdRdSe#Z?GdTdUe=Z@GdVdWe>ZAGdXdYe>ZBGdZd[e>ZCGd\d]e#ZDGd^d_e#ZEGd`daeZFeFZGejHeIdbdcdZJeJejKeJjI<deZLdS)faAtom selection Hierarchy --- :mod:`MDAnalysis.core.selection` ============================================================= This module contains objects that represent selections. They are constructed and then applied to the group. In general, :meth:`Parser.parse` creates a :class:`Selection` object from a selection string. This :class:`Selection` object is then passed an :class:`~MDAnalysis.core.groups.AtomGroup` through its :meth:`~MDAnalysis.core.groups.AtomGroup.apply` method to apply the ``Selection`` to the ``AtomGroup``. This is all invisible to the user through the :meth:`~MDAnalysis.core.groups.AtomGroup.select_atoms` method of an :class:`~MDAnalysis.core.groups.AtomGroup`. N) unique_int_1d) distances)SelectionError NoDataErrorSelectionWarningz-?\d*\.?\d*(?:e[-+]?\d+)?z-?\d+z\s*(?:[:-]| to )\s*c6|tvp|tvp|dvp|duS)aIs val a selection keyword? Returns False on any of the following strings: - keys in SELECTIONDICT (tokens from Selection objects) - keys in OPERATIONS (tokens from LogicOperations) - (Parentheses) - The value `None` (used as EOF in selection strings) ()N)_SELECTIONDICT _OPERATIONS)vals c/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/core/selection.py is_keywordrDs9 ~  +   *   $; cg}t|dsQ|}||dt|dQ|S)aPop tokens from the left until you hit a keyword Keywords can be escaped with a backslash to allow their use as names, e.g. '\protein' Parameters ---------- tokens : collections.deque deque of strings, some tokens some not Returns ------- values : list of strings All non keywords found until a keyword was hit Note ---- This function pops the values from the deque Examples -------- grab_not_keywords(['H', 'and','resname', 'MET']) >>> ['H'] grab_not_keywords(['H', 'Ca', 'N', 'and','resname', 'MET']) >>> ['H', 'Ca' ,'N'] grab_not_keywords(['and','resname', 'MET']) >>> [] r\)rpopleftappend removeprefix)tokensvaluesrs rgrab_not_keywordsrUsi>F##.nn c&&t,,---##. Mrcgd}|r|d}||vrx dd|d|dd<n#t$rCdd|dd|}td|wxYwrD|dddvs'|dd kst fd |Drdd|d<n||S) a5Join range values that are separated by whitespace Parameters ---------- values: list list of value strings Returns ------- values: list of strings Examples -------- join_separated_values(['37', 'to', '22']) >>> ['37 to 22'] .. versionadded:: 2.0.0 )to:-r zInvalid expression given: Nr)z--rrc3NK|]}d|V dS)rN)endswith).0x_valuess r z(join_separated_values..s5??q72;''**??????r)pop IndexErrorjoinranyr)r DELIMITERSvgivenr%s @rjoin_separated_valuesr.|s^&G!J  JJqMM ?? K!(BBqBB6::a==BB  K K K88G,,EEqEE388F3C3CEE$%I%%I%IJJJ K  bqbE\ ! !ts{{????J?????%R[..1..GBKK NN1   ! " Ns &A A B)updatingceZdZdZdS)_Operationmetactt||| |t|d<dS#t$rYdSwxYwNtoken)type__init__rKeyErrorclsnamebases classdicts rr6z_Operationmeta.__init__sV dD%333 .1K '* + + +    DD s6 AAN__name__ __module__ __qualname__r6rrr1r1s#rr1ceZdZdZdZdS)LogicOperationc0||_||_||_dSN)rsellselparser)selfrGrFrHs rr6zLogicOperation.__init__s   rcX|j|i||jjSN)sorted_applyasuniquerHrLrIargskwargss rapplyzLogicOperation.apply/t{D+F++44DKr?r@r6rSrArrrCrCs7 PPPPPrrC) metaclassceZdZdZdZdZdS) AndOperationandc|j|}|j|}tj|j|j}||SrE)rFrSrGnpisinindices)rIgrouprFrGmasks rrNzAndOperation._applysIyu%%yu%%wt|T\22DzrNr>r?r@r4 precedencerNrArrrXrXs- EJrrXceZdZdZdZdZdS) OrOperationorrZc|j|}|j|}tj|j|jtj}|jj |SrE) rGrSrFr\union1dr^astypeint32universeatoms)rIr_rGrFidxs rrNzOrOperation._applys_yu%%yu%%jt|44;;BHEE~#C((rNrarArrrdrds- EJ)))))rrdcFtjfd}|S)zb Decorator to return empty AtomGroups from the apply() function without evaluating it cFt|dkr|S||S)Nr)len)rIr_funcs rrNz%return_empty_on_apply.._applys) u::??LtD%   r) functoolswraps)rprNs` rreturn_empty_on_applyrss: _T!!!!! MrceZdZdZdS)_Selectionmetactt||| |t|d<|t|d<dS#t$rYdSwxYwr3)r5r6r lowerr7r8s rr6z_Selectionmeta.__init__sq dD%333 14N9W- .9r?r@r4rNrArrr}r}s( Err}ceZdZfdZxZS)UnarySelectionct||||j}||_dSrEsuperr6parse_expressionrbsel)rIrHrr __class__s rr6zUnarySelection.__init__s= (((%%do66r)r>r?r@r6 __classcell__rs@rrrs8rrceZdZdZdZdZdS) NotSelectionnotc|j|}|tj|j|jSrE)rrSr\r]r^)rIr_notsels rrNzNotSelection._applys3&&bgemV^<<<==rNrarArrrrs- EJ>>>>>rrceZdZdZdZdZdS)GlobalSelectionglobalrcT|j|jjjSrE)rrSrjrkuniquers rrNzGlobalSelection._apply"sx~~en233::rNrarArrrrs- EJ;;;;;rrc eZdZdZdZdZdZdS)ByResSelectionz Selects all atoms that are in the same segment and residue as selection .. versionchanged:: 1.0.0 Use :code:`"resindices"` instead of :code:`"resids"` (see #2669 and #2672) byresc|j|}t|j}t j|j|}||SrE)rrSr resindicesr\r])rIr_res unique_resr`s rrNzByResSelection._apply1sBhnnU##"3>22 wu'44T{rN)r>r?r@__doc__r4rbrNrArrrr&s9 EJrrc<eZdZdZdZfdZedZxZS)AroundSelectionaroundrct|||j|_t||_||j|_dSrE rr6periodicfloatrcutoffrrbrrIrHrrs rr6zAroundSelection.__init__=Z ((( FNN,,-- **4?;;rcg}|j|}|tj|j|j}|r|s|gS|jr|jnd}tj|j |j |j |d}|j dkrtj |dddf}|tj |tjSNFboxreturn_distancesrrdtype)rrSr\r]r^r dimensionsrcapped_distance positionsrsizesortasarrayint64)rIr_r^rsysrpairss rrNzAroundSelection._applyCshnnU##RWU]CK8889 # r7N"&-9eT) M M K"     :>>geAAAqDk**G2:gRX66677r r>r?r@r4rbr6rsrNrrs@rrr9s^ EJ<<<<< 8888888rrc<eZdZdZdZfdZedZxZS)SphericalLayerSelectionsphlayerrc:t|||j|_t||_t||_||j|_ dSrE rr6rrrinRadiusexRadiusrrbrrs rr6z SphericalLayerSelection.__init___s ((( fnn..// fnn..// **4?;;rc g}|j|}t|dkr|gS|jr|jnd}|ddtj }tj ||j |j |j|d}|jdkrtj|dddf}|tj|tjS)NrrrZF) min_cutoffrrr)rrSrorrcenter_of_geometryreshaperhr\float32rrrrrrrrrrIr_r^rrrefrs rrNzSphericalLayerSelection._applyfshnnU## s88q==9 "&-9eT$$&&..q!44;;BJGG)  O M}"     :>>geAAAqDk**GRZrx88899rrrs@rrr[s^ EJ<<<<<:::::::rrc<eZdZdZdZfdZedZxZS)IsoLayerSelectionisolayerrc:t|||j|_t||_t||_||j|_ dSrErrs rr6zIsoLayerSelection.__init__rrcg}|j|}|tj|j|j}|r|s|gS|jr|jnd}tj|j |j |j |d}tj|j |j |j |d}|j dkrtj tj|dddf}|j dkrMtj tj|dddf} |tj|| }n|}|tj|tjSr)rrSr\r]r^rrrrrrrrrrrr) rIr_r^rrr pairs_outer pairs_inner sys_ind_outer sys_ind_inners rrNzIsoLayerSelection._applyschnnU##RWU]CK8889 # r7N"&-9eT/ M M M"     / M M M"      a  GBIk!!!Q$.?$@$@AAM!## " +aaad2C(D(D E E ' )N)N(NO'2:gRX66677rrrs@rrr}s^ EJ<<<<<!8!8!8!8!8!8!8rrc<eZdZdZdZfdZedZxZS)SphericalZoneSelectionsphzonerct|||j|_t||_||j|_dSrErrs rr6zSphericalZoneSelection.__init__rrcg}|j|}t|dkr|gS|jr|jnd}|ddtj }tj ||j |j |d}|jdkrtj|dddf}|tj|tjS)NrrrZFrr)rrSrorrrrrhr\rrrrrrrrrrs rrNzSphericalZoneSelection._applyshnnU## s88q==9 "&-9eT$$&&..q!44;;BJGG) $+3    :>>geAAAqDk**GRZrx88899rrrs@rrrs^ EJ<<<<< :::::::rrc$eZdZedZdS)CylindricalSelectionc|j|}t|dkr|gS|j|z }|jr|j|jdd}|j|jz }d|j z|dkr1td d|j z|dd|j z|dkr1td d|j z|d||dkr)td ||dtj |jdddkr.||ddtj||ddz zz}n|jjjj}||dtj|dddf|ddz dddfzz}||dtj|dddf|ddz dddfzz}||dtj|dddf|ddz dddfzz}|dddf|jk|dddf|jkz}||}||}|dddfdz|dddfdzz}||j dzk} |||jdzkz}n#t($rYnwxYw||S) NrrZrzThe diameter of the cylinder selection ({:.3f}) is larger than the unit cell's x dimension ({:.3f}). Can only do selections where it is smaller or equal.rzThe diameter of the cylinder selection ({:.3f}) is larger than the unit cell's y dimension ({:.3f}). Can only do selections where it is smaller or equal.zThe total length of the cylinder selection in z ({:.3f}) is larger than the unit cell's z dimension ({:.3f}). Can only do selections where it is smaller or equal.gV@)rrSrorrrrzmaxzminrNotImplementedErrorformatr\r~rintrj trajectorytstriclinic_dimensionsrAttributeError) rIr_rvecsr cyl_z_hheighttriboxr`radiis rrNzCylindricalSelection._applysChnnU## s88q==9 !7!7!9!99 =" P!1!9"2A2&C I 1M4= 3q6)))va$-/Q88  4= 3q6)))va$-/Q88  s1v%%)vmSV44 ve&qrr*d233 PBQB"'$RaR."9"99925Jq BGDAJ1,E$F$Fqqq$w$OOOq BGDAJ1,E$F$Fqqq$w$OOOq BGDAJ1,E$F$Fqqq$w$OOOQQQT TY&41: +ABDzd QQQT a$qqq!t*/1t}a''  EDM1,, ,DD    D T{sK,, K98K9N)r>r?r@rsrNrArrrrs.:::::rrc&eZdZdZdZfdZxZS)CylindricalZoneSelectioncyzonerct|||j|_t||_t||_t||_||j |_ dSrE) rr6rrrrrrrrbrrs rr6z!CylindricalZoneSelection.__init__ s ((( fnn..// &..**++ &..**++ **4?;;rr>r?r@r4rbr6rrs@rrrsB EJ<<<<<<<<>geAAAqDk**GRZrx88899r)r>r?r@r4r6rsrNrrs@rrr#sY E.....:::::::rrc(eZdZdZfdZdZxZS) AtomSelectionatomct||||_t ||_||_dSrE)rr6rsegidintresidr:rs rr6zAtomSelection.__init__Ds\ (((^^%% ))** NN$$ rc||j|jk}|r||j|jk}|r||j|jk}|jSrE)namesr:residsrsegidsrr)rIr_subs rrNzAtomSelection._applyJsSEK49,-  0cjDJ./C  0cjDJ./Czrr>r?r@r4r6rNrrs@rrrAsL E%%%%% rrc,eZdZdZdZfdZdZxZS)BondedSelectionbondedrct||||j|_dSrErrs rr6zBondedSelection.__init__Ws8 (((**4?;;rcP|j|}|jstjd|gS|j}t j|j}g}| |dddft j |dddf|| |dddft j |dddf|t j |}|j j t j|S)NzBonded selection has 0 bondsrr)rrSbondswarningswarnr^r\r to_indicesrr]rgrjrkr)rIr_grpgrpidxbixrls rrNzBondedSelection._apply[shnnU##{  M8 9 9 99 hu{--//00 3qqq!t9RWSAY778999 3qqq!t9RWSAY778999j#~#BIcNN33r)r>r?r@r4rbr6rNrrs@rrrSsQ EJ<<<<<4444444rrc(eZdZdZfdZdZxZS)SelgroupSelectionr_c6t|||}|tvr"t d| |j||_dS#t$rd|}t|dwxYw)NzJThe '{}' keyword is reserved and cannot be used as a selection group name.zFailed to find group: ) rr6r_RESERVED_KWARGS TypeErrorr selgroupsrr7 ValueError)rIrHrgrpnameerrmsgrs rr6zSelgroupSelection.__init__us (((.."" & & &228&//  /'0DHHH / / /7g77FV$$$ . /s $A88 BcZtj|j|jj}||SrE)r\r]r^r)rIr_r`s rrNzSelgroupSelection._applys$wu}dh&677T{rrrs@rrrrsL E / / / / /rrc8eZdZdZfdZedZxZS)SingleCharSelectionzbfor when an attribute is just a single character, eg RSChirality .. versionadded:: 2.1.0 ct||t|}|s(td|d||_dSNzUnexpected token '{0}'rrr6rrrrrIrHrvalsrs rr6zSingleCharSelection.__init___ ((( (( I5<r?r@rr6rsrNrrs@rrrs^ rrc8eZdZdZfdZedZxZS)_ProtoStringSelectionz}Selections based on text attributes .. versionchanged:: 1.0.0 Supports multiple wildcards, based on fnmatch ct||t|}|s(td|d||_dSrr r!s rr6z_ProtoStringSelection.__init__r#rcdt|jj|j}g}|jD]:\}t fd|jDr||;|j t||j }|tj ||S)Nc3BK|]}tj|VdSrE)fnmatch fnmatchcase)r#rnms rr&z/_ProtoStringSelection._apply..s0GGC7&r3//GGGGGGr) r%rj _topologyr&namedictitemsr*rrnmidxlevelr\r])rIr_nmattrmatchesixr4r0s @rrNz_ProtoStringSelection._applys14:>>o++-- # #FBGGGG4;GGGGG #r""" WUDJ778RWUG,,--rr(rs@rr*r*s^  . . . . . . .rr*c eZdZdZdZdZdZdS)AromaticSelectionz}Select aromatic atoms. Aromaticity is available in the `aromaticities` attribute and is made available through RDKitaromatic aromaticitiesc||jSrE)r<rs rrNzAromaticSelection._applysU())rN)r>r?r@rr4r&rNrArrr:r:s9 E E*****rr:c,eZdZdZdZfdZdZxZS)SmartsSelectionatSelect atoms based on SMARTS queries. Uses RDKit to run the query and converts the result to MDAnalysis. Supports chirality. .. versionchanged:: 2.2.0 ``rdkit_wargs`` and ``smarts_kwargs`` can now be passed to control the behaviour of the RDKit converter and RDKit's ``GetSubstructMatches`` respectively. The default ``maxMatches`` value passed to ``GetSubstructMatches`` has been changed from ``1000`` to ``max(1000, n_atoms * 10)`` in order to limit cases where too few matches were generated. A warning is now also thrown if ``maxMatches`` has been reached. smartsc t||g}ddd}|ddvst|ds|ddvr5||dxxdz cc<|ddkr|d|dkrnH|}|||ddvrt|dd||_|j|_|j|_dS)Nrr rr r ) rr6rrrr)pattern rdkit_kwargs smarts_kwargs)rIrHrrCcounterrrs rr6zSmartsSelection.__init__s (((""Qi:%%Zq -B-B%ayJ&&q """a'"""!9##  (E(E..""C NN3   Qi:%%Zq -B-B%www'' "/#1rc  ddlm}n#t$rtdwxYw||j}|st |jd|jd i|j}|j dd|j dtd t|d z|j |fi|j}t||jdkrtjd tjd |D}tjt%|j|}||S)Nr)ChemzRDKit is required for SMARTS-based atom selection but it's not installed. Try installing it with conda install -c conda-forge rdkitz is not a valid SMARTS queryRDKIT useChiralityT maxMatchesi aJYour smarts-based atom selection returned the maxnumber of matches. This indicates that not allmatching atoms were selected. When callingatom_group.select_atoms(), the default valueof maxMatches is max(100, len(atom_group * 10)). To fix this, add the following argument to select_atoms: smarts_kwargs={maxMatches: }cg|] }|D]}| SrArA)r#matchrls r z*SmartsSelection._apply..s%GGGUGG#SGGGGr)rI)rdkitrH ImportError MolFromSmartsrCr convert_torDrE setdefaultmaxroGetSubstructMatchesr r r\rr]rangen_atoms)rIr_rHrCmolr7r^r`s rrNzSmartsSelection._applys|  " " " " " " "   5  $$T\22 N LLLMM Me<<$*;<< %%nd;;; %%lCc%jj2o4N4NOOO)#)'HHT5GHH w<<4-l; ; ; M=   )GGgGGGHHwuU]++W55T{s #)r>r?r@rr4r6rNrrs@rr?r?sX   E222226       rr?c8eZdZdZdZfdZdZdZdZxZ S)ResidSelectionzSelect atoms based on numerical fields Allows the use of ':', '-' and 'to' to specify a range of values For example resid 1:10 rc^t||t|}|s(td|dt |}g}g}|D]+}t jdtddz|}|4| }t|d|df} d} ndtdt} | dtdz } t j| |} | "td || }t|d|df} t|d |d f} | | | | -||_ ||_dS) NUnexpected token: '{0}'rr r z(\w?)$r)NNz)(\w?)zFailed to parse value: {0}rrZ)rr6rrrr.rerN INT_PATTERNgroupsr RANGE_PATTERNrlowersuppers)rIrHrrrcrbrm1rrwupperrCselrangers rr6zResidSelection.__init__'s ((("6** J6==fQiHHII I&v.. ! !C,k,,,y8#>>B:iikkCF SV+"BkAA-AA3{33338GS11#$%A%H%H%M%MNNNoo''CF SV+CF SV+ MM% MM%   rc\|j} |j}ng#ttf$rSd}t d|jDst d|jDrd}t|dYnwxYw||||}n| |}||S)Nc3&K|] }|dV dSrNrAr#r,s rr&z(ResidSelection._apply..Ts&--A1Q4------rc3&K|] }|dV dSrirArjs rr&z(ResidSelection._apply..Ts755!555555rz@Selection specified icodes, while the topology doesn't have any.) ricodesrrr*rcrbr_sel_with_icodes_sel_without_icodes)rIr_r"rlrr`s rrNzResidSelection._applyLs| 3\FF , 3 3 3F------- 355"k55522 3(!((d2 3 3 3~((v66DD++D11DT{sA!A54A5ctjt|t}t |j|jD](\\}}\}}|||k}|||kz}n||k}||z})|Sr)r\zerosroboolziprcrb)rIr"r`u_resid_l_residthismasks rrnz"ResidSelection._sel_without_icodesdsxD ...*-dk4;*G*G   &LWa,7A"7?DGO+7? H DD rctjt|t}t |j|jD]\\}}\}}|||kr||k}|||kz}|||kz}n||k} | ||kz} | }tj|dz|} t| r$| d| d} } || k} | || kz} || z}||k}|||kz}||z}n||k}|||kz}||z}|S)Nrrrr)r\rprorqrrrcrbarange)rIr"rlr`rsu_icoderul_icoderv startmaskmidmid_begmid_endmidmaskendmasks rrmzResidSelection._sel_with_icodesssPxD ...69 K7 7 & &  2 Wg 2'"g%%#wH' 11H' 11HH!%I7!22I(H)GaK99C3xx,+.q63r7"&'/47?2 G+#goGv00G'HH7?Fg-- H DD r) r>r?r@rr4r6rNrnrmrrs@rr[r[sw E#####J0   ,,,,,,,rr[c(eZdZdZfdZdZxZS) BoolSelectionzSelection for boolean valuesc2t||t|}|sdg}g|_|D]U}|}|dkrd}n|dkrd}nt d|d|j|VdS)NtruefalseFT'zB' is an invalid value for boolean selection. Use 'True' or 'False')rr6rrrwrr)rIrHrrrrwbvalrs rr6zBoolSelection.__init__s ((("6** XF  % %CIIKKE& ,,,, K  t $ $ $ $ % %rct||j}tjt |t }|jD] }|||kz} ||Sr)r%r&r\rprorqr)rIr_r"r`rs rrNzBoolSelection._applysXudj))xD ...;  C DCK DDT{r)r>r?r@rr6rNrrs@rrrsM&&%%%%%*rrcHeZdZdZdZdedededZeZ fdZ dZ xZ S)RangeSelectionzRange selection for int valuesrr r ct|||j|_|j|_t |}|s(t d|dt|}g}g}|D]} ||}d}nk#t $r^tj |j |} | sd|} t | dt|j| \}}YnwxYw||||||_||_dS)Nr]rzFailed to parse number: )rr6rtolatolrrrr.rr^rNrCmapr`rrbrc) rIrHrrrcrbrrwrerfrrs rr6zRangeSelection.__init__s] (((K K "6** J6==fQiHHII I&v.. ! !C B 3 B B B8DL#667===F$V,,$6"4:x/@/@AA uuu  B MM% MM%   s B%%A%D  D ctjt|t}t ||j|jz}t|j|j D]"\}}|||k}|||kz}n||k}||z}#||Sr) r\rprorqr%r& value_offsetrrrcrb)rIr_r`r"rerwrvs rrNzRangeSelection._applysxE $///udj))D,== T[99  LE5 5=DEM)5= H DDT{r) r>r?r@rrr_rarCrrr6rNrrs@rrrsx((L>+>> >> >>>G E@       rrc4eZdZdZdedededZeZdZ dS)FloatRangeSelectionz Range selection for float valuesr r c tjt|t}t ||j|jz}t|j|j D]y\}}|||k}|||kz}n]|dz |dz}}d} d| d|j d|d|d } tj | t tj|||j|j }||z}z||S) Nrrz7https://docs.python.org/3.8/tutorial/floatingpoint.htmlzUsing float equality to select atoms is not recommended because of inherent limitations in representing numbers on computers (see zA for more). Instead, we recommend using a range to select, e.g. 'r z to zt'. If you still want to compare floats, use the `atol` and `rtol` keywords to modify the tolerance for `np.isclose`.)categoryrr)r\rprorqr%r&rrrrcrbr4r r riscloserr) rIr_r`r"rerwrvlowhighfpmsgs rrNzFloatRangeSelection._applys,xE $///udj))D,== T[99  LE5 5=DEM)!AIuqyTN(')(( )- (( 69 (( ?C ((( c,<====:%didi H DDT{rN) r>r?r@r FLOAT_PATTERNrarCrrrNrArrrrsN**B-BB-BB-BBBG ErrceZdZdZdZdZdS)ByNumSelectionbynumr^rN)r>r?r@r4r&rrArrrrs E ELLLrrc$eZdZdZdZhdZdZdS)ProteinSelectionaConsists of all residues with recognized residue names. Recognized residue names in :attr:`ProteinSelection.prot_res`. * from the CHARMM force field:: awk '/RESI/ {printf "'"'"%s"'"',",$2 }' top_all27_prot_lipid.rtf * manually added special CHARMM, OPLS/AA and Amber residue names. See Also -------- :func:`MDAnalysis.lib.util.convert_aa_code` .. versionchanged:: 1.0.1 prot_res changed to set (from numpy array) performance improved by ~100x on larger systems protein>hACEALAARGASFASHASNASPCMECYMCYSCYXDABGLHGLNGLUGLYHIDHIEHIPHISHSDHSEHSPHYPILELEULYNLYSMETMSENMEORNPHEPROQLNSERTHRTRPTYRVALALADARGNASN1ASPHCALACARGCASFCASNCASPCCYSCCYXCGLNCGLUCGLYCHIDCHIECHIPCILECLEUCLYSCMETCPHECPROCSERCTHRCTRPCTYRCVALCYS1CYS2CYSHGLUHHIS1HIS2HISAHISBHISDHISEHISHLYSHNALANARGNASNNASPNCYSNCYXNGLNNGLUNGLYNHIDNHIENHIPNILENLEUNLYSNMETNPHENPRONSERNTHRNTRPNTYRNVALPGLUc|jjj}fd|jD}|j|j}|tj||S)Nc,g|]\}}|jv|SrAprot_resr#r0r8rIs rrOz+ProteinSelection._apply..s4   RT]"" """r) rjr1resnamesr2r3r4rr\r])rIr_ resname_attrr7r4s` rrNzProteinSelection._applysp~/8     (17799    "5#34RWUG,,--rN)r>r?r@rr4r rNrArrrr#sI& EpppHd . . . . .rrc$eZdZdZdZhdZdZdS)NucleicSelectionaAll atoms in nucleic acid residues with recognized residue names. Recognized residue names: * from the CHARMM force field :: awk '/RESI/ {printf "'"'"%s"'"',",$2 }' top_all27_prot_na.rtf * recognized: 'ADE', 'URA', 'CYT', 'GUA', 'THY' * recognized (CHARMM in Gromacs): 'DA', 'DU', 'DC', 'DG', 'DT' .. versionchanged:: 0.8 additional Gromacs selections .. versionchanged:: 1.0.1 nucl_res changed to set (from numpy array) performance improved by ~100x on larger systems nucleic>"ACGTUDADCDGDTRARCRGRUADECYTDA3DA5DC3DC5DG3DG5DT3DT5GUARA3RA5RC3RC5RG3RG5RU3RU5THYURAc|jjj}|j|j}fd|jD}tj||}||S)Nc,g|]\}}|jv|SrAnucl_resrs rrOz+NucleicSelection._apply..s0   BB$-+4u/0    '06688   wug&&T{rN)r>r?r@rr4r9rNrArrrrsF E###HJ     rrc$eZdZdZdZhdZdZdS)WaterSelectiona5All atoms in water residues with recognized water residue names. Recognized residue names: * recognized 3 Letter resnames: 'H2O', 'HOH', 'OH2', 'HHO', 'OHH' 'TIP', 'T3P', 'T4P', 'T5P', 'SOL', 'WAT' * recognized 4 Letter resnames: 'TIP2', 'TIP3', 'TIP4' .. versionadded:: 2.9.0 water>H2OHHOHOHOH2OHHSOLT3PT4PT5PTIPWATTIP2TIP3TIP4c|jjj}|j|j}fd|jD}tj||}||S)Nc,g|]\}}|jv|SrA) water_resrs rrOz)WaterSelection._apply.."s4   RT^## ###rr:r;s` rrNzWaterSelection._applyss>+4u/0    $-3355    wug&&T{rN)r>r?r@rr4rOrNrArrr=r=sE   EI"     rr=c$eZdZdZdZhdZdZdS)BackboneSelectiona1A BackboneSelection contains all atoms with name 'N', 'CA', 'C', 'O'. This excludes OT* on C-termini (which are included by, eg VMD's backbone selection). .. versionchanged:: 1.0.1 bb_atoms changed to set (from numpy array) performance improved by ~100x on larger systems backbone>rNOCAc|jjj}|jjj}fd|jD}|j|j}|tj ||}fd|jD}|j|j }|tj ||}|j S)Nc,g|]\}}|jv|SrAbb_atomsrs rrOz,BackboneSelection._apply..@4   RT]"" """rc,g|]\}}|jv|SrAr rs rrOz,BackboneSelection._apply..I0   BB$-+4    %.4466   )bge\223    '06688   u/0bge_556|rNr>r?r@rr4rYrNrArrrQrQ,s?   E$$$HrrQc$eZdZdZdZhdZdZdS)NucleicBackboneSelectiona6Contains all atoms with name "P", "C5'", C3'", "O3'", "O5'". These atoms are only recognized if they are in a residue matched by the :class:`NucleicSelection`. .. versionchanged:: 1.0.1 bb_atoms changed to set (from numpy array) performance improved by ~100x on larger systems nucleicbackbone>C5'O3'O5'PC3'c|jjj}|jjj}fd|jD}|j|j}|tj ||}fd|jD}|j|j }|tj ||}|j S)Nc,g|]\}}|jv|SrArXrs rrOz3NucleicBackboneSelection._apply..frZrc,g|]\}}|jv|SrAr8rs rrOz3NucleicBackboneSelection._apply..or\rr]r^s` rrNzNucleicBackboneSelection._applyarbrNrcrArrrereRs?   E000Hrrec$eZdZdZdZhdZdZdS) BaseSelectionaBSelection of atoms in nucleobases. Recognized atom names (from CHARMM): 'N9', 'N7', 'C8', 'C5', 'C4', 'N3', 'C2', 'N1', 'C6', 'O6','N2','N6', 'O2','N4','O4','C5M' .. versionchanged:: 1.0.1 base_atoms changed to set (from numpy array) performance improved by ~100x on larger systems nucleicbase>C2C4C5C6C8N1N2N3N4N6N7N9O2O4O6C5Mc|jjj}|jjj}fd|jD}|j|j}|tj ||}fd|jD}|j|j }|tj ||}|j S)Nc,g|]\}}|jv|SrA) base_atomsrs rrOz(BaseSelection._apply..s4   RT_$$ $$$rc,g|]\}}|jv|SrAr8rs rrOz(BaseSelection._apply..r\rr]r^s` rrNzBaseSelection._applyrbrN)r>r?r@rr4rrNrArrrprpxsE   EJ&rrpc$eZdZdZdZhdZdZdS)NucleicSugarSelectionzContains all atoms with name C1', C2', C3', C4', O2', O4', O3'. .. versionchanged:: 1.0.1 sug_atoms changed to set (from numpy array) performance improved by ~100x on larger systems nucleicsugar>C1'C2'C4'O4'rkc|jjj}|jjj}fd|jD}|j|j}|tj ||}fd|jD}|j|j }|tj ||}|j S)Nc,g|]\}}|jv|SrA) sug_atomsrs rrOz0NucleicSugarSelection._apply..s4   RT^## ###rc,g|]\}}|jv|SrAr8rs rrOz0NucleicSugarSelection._apply..r\rr]r^s` rrNzNucleicSugarSelection._applyrbrN)r>r?r@rr4rrNrArrrrs? E333Irrc eZdZdZdZedejfdejfdej fdej fdej fdej fgZ d Zddddddd Zd d d d Zfd ZdZxZS)PropertySelectionzSome of the possible properties: x, y, z, radius, mass, .. versionchanged:: 2.0.0 changed == operator to use np.isclose instead of np.equals. Added ``atol`` and ``rtol`` keywords to control ``np.isclose`` tolerance. prop><>=<===!=)rrrrrr)rrrrrrrr$rrcht|||}d}d}|dkrd|_|}nd|_|jD]3} ||\}}|}||z}n#t $rY0wxYw||}|jD]&}||vr ||\}}|r|}|}n'||}||jvr||}}|j|}||_ |j ||_ |dkr+tj |j |j|j|_ n>#t $r1d|d|j d } t | dwxYwt%||_dS) z~ Possible splitting around operator: prop x < 5 prop x< 5 prop x <5 prop x<5 NabsTFrrzInvalid operator : 'z' Use one of : 'r)rr6rabsolute _op_symbolssplitrprops opposite_opsropsoperatorrqpartialrrr7keysrvalue) rIrHrroperrpossibler$rrrs rr6zPropertySelection.__init__s# (((~~ 5== DM>>##DD!DM(  H zz(++1 !|      <>>##D(  H4zz(++1#DE   =NN$$E DJ  %D$T*D   HTNDMt|| ) 1M &+!!!  / / /'t''HMMOO''' V$$$ .  /5\\ s/B BBE ;Fc t||j|j}nx#t$r:dt |j}t |dt$r)|j|j}d|d}t |dwxYw dddd|j}|dd|f}n#t$rYnwxYw|jrtj |}| ||j }||S)NzExpected one of zThis Universe does not contain z informationrrrr) r%rrr7listrrrrr\rrr)rIr_rrr'colr`s rrNzPropertySelection._apply>s7 3UDJty$9::FF 3 3 3ATZ__->->(?(?AAF ((d 2 3 3 3:di(DItIIIF ((d 2 3  $**495CAAAsF^FF    D  = $VF^^F}}VTZ00T{s #A5BB:: CC)r>r?r@rr4dictr\greaterless greater_equal less_equalr not_equalrrrrr6rNrrs@rrrs E $ "*  "'N 2# $ 2= ! 2:  2<    C5K    LKk B BEB"B"B"B"B"HrrceZdZdZdZdZiddddddddd d d d d ddddddddddddddddddd Zfd!Zd"ZxZ S)# SameSelectionz Selects all atoms that have the same subkeyword value as any atom in selection .. versionchanged:: 1.0.0 Map :code:`"residue"` to :code:`"resindices"` and :code:`"segment"` to :code:`"segindices"` (see #2669 and #2672) samerfragmentNr$rrresiduersegment segindicesr:rr5typesresnamerrrrrmassmasseschargechargesradiusrbfactorbfactorsresnumresnumsc~t|||}||jvr:t d||j||_|d| |j |_ ||_dS)Nz.Unknown same property : {0}Choose one of : {1}as) rr6r prop_transrrrrexpectrrbr)rIrHrrrs rr6zSameSelection.__init__vs (((~~ t & &6$ 4 4 6 677    d**4?;; rc|j|}|s|gS|jdkrBtjd|j}t j|j|j}||S dddd|j}|j dd|f}|j dd|ft j fd|D d}||S#t$rP|j |j}t||}t jt|||}||cYSwxYw) Nrc ||zSrErA)r$rs rz&SameSelection._apply..s QUrrrrrc:g|]}tj|SrA)r\r)r#r,poss rrOz(SameSelection._apply..s%???Qbja00???r)axis)rrSrrqreduce fragmentsr\r]r^rvstackr*r7rr%) rIr_rallfragsr`pos_idxr"attrnamers @rrNzSameSelection._applys^hnnU## 9  9 " "!'(:(:CMJJH75=(*:;;D;  AA..ty9G=G,D/!!!W*-C9????$???@@DD!DLLD;    ty1H3))D775(33T::D;    s4C##AD=<D=) r>r?r@rr4rbrr6rNrrs@rrrWs  EJD T T T  <  <    :    ) ' : )!J&     rrcBeZdZdZiZdZdZ d dZd Zd Z dS) SelectionParseraA small parser for selection expressions. Demonstration of recursive descent parsing using Precedence climbing (see http://www.engr.mun.ca/~theo/Misc/exp_parsing.htm). Transforms expressions into nested Selection tree. For reference, the grammar that we parse is :: E(xpression)--> Exp(0) Exp(p) --> P {B Exp(q)} P --> U Exp(q) | "(" E ")" | v B(inary) --> "and" | "or" U(nary) --> "not" T(erms) --> segid [value] | resname [value] | resid [value] | name [value] | type [value] cHtj|g|Ri|}|j|_|SrE)object__new__ _shared_state__dict__)r9pkrIs rrzSelectionParser.__new__s0~c+A+++++)  rc|jd|kr|jdStd|jd|)z#Anticipate and remove a given tokenrz'Unexpected token: '{0}' Expected: '{1}'N)rrrr)rIr4s rrzSelectionParser.expectsY ;q>U " " K   ! ! ! ! ! 6$+a.%00 rN:0yE>h㈵>Tc ||_||_||_||_|pi|_|pi|_||_||_|dddd} tj | dgz|_ | d} |j d-td|j d| S)aCreate a Selection object from a string. Parameters ---------- selectstr : str The string that describes the selection selgroups : AtomGroups AtomGroups to be used in `group` selections periodic : bool, optional for distance based selections, whether to consider periodic boundary conditions atol : float, optional The absolute tolerance parameter for float comparisons. Passed to :func:`numpy.isclose`. rtol : float, optional The relative tolerance parameter for float comparisons. Passed to :func:`numpy.isclose`. sorted : bool, optional Whether to sorted the output AtomGroup. rdkit_kwargs : dict, optional Arguments passed to the RDKitConverter when using selection based on SMARTS queries smarts_kwargs : dict, optional Arguments passed internally to RDKit's `GetSubstructMatches `_. Returns ------- The appropriate Selection object. Use the .apply method on this to perform the selection. Raises ------ SelectionError If anything goes wrong in creating the Selection object. .. versionchanged:: 2.0.0 Added `atol` and `rtol` keywords to select float values. Added `rdkit_kwargs` to pass arguments to the RDKitConverter .. versionchanged:: 2.2.0 Added ``smarts_kwargs`` argument, allowing users to pass a a dictionary of arguments to RDKit's ``GetSubstructMatches``. r z ( r z ) Nrz2Unexpected token at end of selection string: '{0}')rrrrLrDrE selectstrrreplace collectionsdequerrrrr) rIrrrrrrLrDrEr parsetrees rparsezSelectionParser.parsesn!    (.B*0b""""3..66sEBB!' $(?@@ ))!,, ;q> % 6$+a.)) rc|}|jdtvrt|jdj|krt|j}d|jz}||}||||}|jdtvr!t|jdj|k|S)Nrr) _parse_subexprrrbrr)rIrexp1opqexp2s rrz SelectionParser.parse_expressions!!## KNk ) )DKN+6!;;T[00223BBM!A((++D2dD$''D KNk ) )DKN+6!;;  rc^|j}|dkr,|d}|d|S t |||jS#t $rd|d}t |dt$r}d|d}t |dd}~wwxYw)Nr rr zUnknown selection token: 'rzSelection failed: ')rrrrr r7rr)rIrexpres rrzSelectionParser._parse_subexp#s [ " " 99''**C KK   J 3!"%dDK88 8 3 3 37"777F ((d 2 3 3 3/1///F ((d 2 3s A(()B,B''B,)NrrTNN) r>r?r@rrrrrrrrArrrrs(M   HHHHT   33333rrz ._selectorsz!Automatically generated selectors)doccF||tjd}|d}|dkrt}nt |t rt }ntj|tj rt}ntj|tj rt}nXt |ts |tkr%t}|dkrd|d<n%|dkrd|d<nd |d<nt!d |d t#||f|}t%t|||S) afSelection class factory for arbitrary TopologyAttrs. Normally this should not be used except within the codebase or by developers; it is called by the metaclass :class:`MDAnalysis.core.topologyattrs._TopologyAttrMeta` to auto-generate suitable selection classes by creating a token with the topology attribute (singular) name. The function uses the provided ``dtype`` to choose which Selection class to subclass: * :class:`BoolSelection` for booleans * :class:`RangeSelection` for integers * :class:`FloatRangeSelection` for floats * :class:`_ProtoStringSelection` for strings Other value types are not yet supported and will raise a ValueError. The classes are created in the :mod:`_selectors` module to avoid namespace clashes. Parameters ---------- singular: str singular name of TopologyAttr attrname: str attribute name of TopologyAttr dtype: type type of TopologyAttr per_object: str level of TopologyAttr Returns ------- selection: subclass of Selection Raises ------ ValueError If ``dtype`` is not one of the supported types Example ------- The function creates a class inside ``_selectors`` and returns it. Normally it should not need to be manually called, as it is created for each TopologyAttr:: >>> gen_selection_class("resname", "resnames", object, "residue") Simply generating this selector is sufficient for the keyword to be accessible by :meth:`~MDAnalysis.core.universe.Universe.select_atoms`, as that is automatically handled by :class:`~MDAnalysis.core.selections._Selectionmeta`. See also -------- :class:`MDAnalysis.core.topologyattrs._TopologyAttrMeta` .. versionadded:: 2.0.0 )r4r&r?ryU1rrr5rrr8z No base class defined for dtype zK. Define a Selection class manually by subclassing core.selection.Selection) _selectorsr> capitalizer issubclassrqrr\ issubdtypeintegerrfloatingrstrrr*rr5setattr)singularrr per_objectbasedctr:baseclsr9s rgen_selection_classr@sL~ ) G !!## . . .D }}% E4   ubj ) )   ubk * * % E3    5F??'  " "+GG   9 $ $+GG  #GG   3u 3 3 3   tgZ ) )C Jc""" Jr)Mrrr^r.rqrrr numpyr\lib.utilrlibr exceptionsrrrrr_rarrr.r rrr5r1rrCrXrdrsruryr}rrrrrrrrrrrrrrrrr*r:r?r[rrrrrrr=rQrerprrrrParser ModuleTyper>rmodulesrrArrrs0"  %$$$$$FFFFFFFFFF-  ' "$$$N&&&R ! TPPPPPV~PPPP     >    ) ) ) ) ). ) ) )   TPPPPP.PPPP     9   Y>>>>>>>>>;;;;;n;;;^&88888i888D:::::i:::D-8-8-8-8-8 -8-8-8`:::::Y:::8<<<<<9<<<~ < < < < <3 < < < < < < < < 4 < < <:::::Y:::<I$44444i444> ,)......I...@ * * * * * * * *MMMMMiMMM`CCCCCYCCCLI@33333Y333l"""""."""J^ S.S.S.S.S.yS.S.S.lAAAAAyAAAH,,,,,Y,,,^#####(###L#####/###L66666$666r     ,   F@@@@@ @@@FMMMMMIMMM`K3K3K3K3K3fK3K3K3^   U "E $. J  _____r