RiJHdZddlZddlmZddlmZddlmZddlmZddlmZddlm Z dd lm Z dd lm Z ddl Z dd lmZdd lmZe rdd lmZe de dZe dedZe ddZGddeeefZGddZy)zBase class for Residue, Chain, Model and Structure classes. It is a simple container class, with list and dictionary like properties. N)deque)copy)Any)Generic)Optional) TYPE_CHECKING)TypeVar)Union)BiopythonWarning)PDBConstructionException)Atom_Child)Entityr )bound_Parentr_SelfzEntity[Any, Any]c leZdZUdZedzed<eeed<ee efed<e ed<dZ dZ d Z d Zd Zd Zd ZdZdZdZdZdZdZdZdZedZej8dZ d.dedededefdZdZ defdZ!d Z"d!Z#defd"Z$d#e%defd$Z&d%Z'd&Z(d'Z)d(Z*d)Z+d*Z,d+Z-d.d,Z.d-Z/y)/rzBasic container object for PDB hierarchy. Structure, Model, Chain and Residue are subclasses of Entity. It deals with storage and lookup. Nparent child_list child_dictlevelcX||_d|_d|_g|_i|_i|_yzInitialize the class.N)_idfull_idrrrxtraselfids F/home/agent/.friday_env/lib/python3.12/site-packages/Bio/PDB/Entity.py__init__zEntity.__init__/s,   c,t|jSzReturn the number of children.)lenrrs r __len__zEntity.__len__;s4??##r"c |j|S)zReturn the child with given id.rrs r __getitem__zEntity.__getitem__?sr""r"c$|j|S)Remove a child.) detach_childrs r __delitem__zEntity.__delitem__Cs  $$r"c||jvS)z4Check if there is a child element with the given id.r)rs r __contains__zEntity.__contains__GT__$$r"c#8K|jEd{y7w)zIterate over children.Nrr&s r __iter__zEntity.__iter__K??"" ct|t|rD|j|j|jk(S|jdd|jddk(St S)zJTest for equality. This compares full_id including the IDs of all parents.N isinstancetyperrrNotImplementedrothers r __eq__z Entity.__eq__QT eT$Z ({{"ww%((**||AB'5==+<<<! !r"ct|t|rD|j|j|jk7S|jdd|jddk7St S)zTest for inequality.Nr8r9r=s r __ne__z Entity.__ne__[r@r"ct|t|rD|j|j|jkDS|jdd|jddkDSt S)zTest greater than.Nr8r9r=s r __gt__z Entity.__gt__eT eT$Z ({{"ww))||AB'%--*;;;! !r"ct|t|rD|j|j|jk\S|jdd|jddk\St S)zTest greater or equal.Nr8r9r=s r __ge__z Entity.__ge__or@r"ct|t|rD|j|j|jkS|jdd|jddkSt S)zTest less than.Nr8r9r=s r __lt__z Entity.__lt__yrEr"ct|t|rD|j|j|jkS|jdd|jddkSt S)zTest less or equal.Nr8r9r=s r __le__z Entity.__le__r@r"c,t|jS)z&Hash method to allow uniqueness (set).)hashrr&s r __hash__zEntity.__hash__sDLL!!r"c||D]} |j|j|_y#t$rY7wxYw)zReset the full_id (PRIVATE). Resets the full_id of this entity and recursively of all its children based on their ID. N)_reset_full_idAttributeError_generate_full_idrrchilds r rPzEntity._reset_full_idsJ  E $$&  --/ "  s / ;;c|j}|g}|j}|4|j}|j||j}|4|jt |S)zGenerate full_id (PRIVATE). Generate the full_id of the Entity based on its Id and the IDs of the parents. )get_id get_parentappendreversetuple)r entity_idpartsrs r rRzEntity._generate_full_idsj KKM  "  I LL #&&(F   U|r"c|jS)zReturn identifier.)rr&s r rz Entity.ids xxr"c j||jk(ry|j||jjvr.tjd|d|jd|dt |jj|j=||jj|<||_|j y)zChange the id of this entity. This will update the child_dict of this entity's parent and invalidate all cached full ids involving this entity. @raises: ValueError NzThe id `zB` is already used for a sibling of this entity. Changing id from `z` to `zG` might create access inconsistencies to children of the parent entity.)rrrwarningswarnr rP)rvalues r rz Entity.ids DHH   ;; " ... ug&))- &@HH%   &&txx0,0DKK " "5 ) r"rr>compare_coordinatesreturncPt|t|sy|j|jk7ryt|jt|jk7ryt |j|jD]'\}}t |dsJ|j||r'yy)aCompare this entity to the other entity for equality. Recursively compare the children of this entity to the other entity's children. Compare most properties including names and IDs. :param other: The entity to compare this entity with :type other: Entity :param compare_coordinates: Whether to compare atomic coordinates :type compare_coordinates: bool :return: Whether the two entities are strictly equal :rtype: bool Fstrictly_equalsT)r:r;rr%rziphasattrre)rr>rb left_child right_childs r rezEntity.strictly_equalss%d, 77ehh  t 3u'7'7#8 8'*4??E >:%$=  "Aww**A//11ALL((011qww1G1/)h7QWW7rzzJ FZZ :A :"**MFzz&q&9928!;s3D&"D+$D0ct|}g|_i|_t|j|_|j |jD]!}|j |j#|S)zCopy entity recursively.)rrrrrrryrshallowrTs r rz Entity.copys`t*DII __ &E KK % &r"F)0__name__ __module__ __qualname____doc__r__annotations__listrdictrstrr!r'r*r.r0r4r?rBrDrGrIrKrNrPrRpropertyrsetterrboolrerkrnrrr-ryintr|r~rrxrWrVrrrrr"r rr#s< dNV S&[!! J$#%%# """"""" 0$YY4@E!8< >  &,&,,#,v,#%%0#.:B r"ceZdZdZdZdZdZdZdZdZ dZ d Z d Z d Z d Zd ZdZdZ d dddedefdZdZdZdZdZdZdZdZdZdZd!dZdZy)"DisorderedEntityWrapperaWrapper class to group equivalent Entities. This class is a simple wrapper class that groups a number of equivalent Entities and forwards all method calls to one of them (the currently selected object). DisorderedResidue and DisorderedAtom are subclasses of this class. E.g.: A DisorderedAtom object contains a number of Atom objects, where each Atom object represents a specific position of a disordered atom in the structure. c<||_i|_d|_d|_yr)rrselected_childrrs r r!z DisorderedEntityWrapper.__init__s" r"ch|dk(rtt|dstt|j|S)z.Forward the method call to the selected child. __setstate__r)rQrggetattrr)rmethods r __getattr__z#DisorderedEntityWrapper.__getattr__s6 ^ # t-.! t**F33r"c |j|S)z#Return the child with the given id.rrs r r*z#DisorderedEntityWrapper.__getitem__s""2&&r"c"||j|<y)z*Add a child, associated with a certain id.Nr)rus r __setitem__z#DisorderedEntityWrapper.__setitem__s#r"c||jvS)z$Check if the child has the given id.rrs r r0z$DisorderedEntityWrapper.__contains__sT((((r"c,t|jSr$)iterrr&s r r4z DisorderedEntityWrapper.__iter__sD''((r"c,t|jSr$)r%rr&s r r'zDisorderedEntityWrapper.__len__s4&&''r"c |j|z S)z Subtraction with another object.rr=s r __sub__zDisorderedEntityWrapper.__sub__""U**r"c |j|kDS)z&Return if child is greater than other.rr=s r rDzDisorderedEntityWrapper.__gt__rr"c |j|k\S)z/Return if child is greater or equal than other.rr=s r rGzDisorderedEntityWrapper.__ge__""e++r"c |j|kS)z#Return if child is less than other.rr=s r rIzDisorderedEntityWrapper.__lt__rr"c |j|kS)z,Return if child is less or equal than other.rr=s r rKzDisorderedEntityWrapper.__le__rr"ct|}i|_|j|jD]!}|j |j#|S)z"Copy disorderd entity recursively.)rrrrdisordered_get_listdisordered_addrs r rzDisorderedEntityWrapper.copysRt*--/ 1E  " "5::< 0 1r"c|jSrrr&s r rVzDisorderedEntityWrapper.get_idrr"r>rbrcct|t|sy|j|jk7ry|jj |jj k(sy|j j |j j k7ry|j j D]0}|j |j|j ||r0yy)a-Compare this entity to the other entity using a strict definition of equality. Recursively compare the children of this entity to the other entity's children. Compare most properties including the selected child, names, and IDs. :param other: The entity to compare this entity with :type other: DisorderedEntityWrapper :param compare_coordinates: Whether to compare atomic coordinates :type compare_coordinates: bool :return: Whether the two entities are strictly equal :rtype: bool FT)r:r;rrrVrkeysre)rr>rbkeys r rez'DisorderedEntityWrapper.strictly_equalss%d, 77ehh ""))+u/C/C/J/J/LL ??   !U%5%5%:%:%< <??'') C??3'77  %':   r"c||jvS)zsdoo&&r"Nc<| |jS|j|S)zsGet the child object associated with id. If id is None, the currently selected child is returned. )rrrs r disordered_getz&DisorderedEntityWrapper.disordered_getCs$ :&& &r""r"cHt|jjS)zReturn list of children.)rrvaluesr&s r rz+DisorderedEntityWrapper.disordered_get_listLsDOO**,--r"r)N)rrrrr!rr*rr0r4r'rrDrGrIrKrrVrrerrrrWrnrrrrrrrrr"r rrs  4' $))(+ +,+,  MR#.#EI# #J%" % 2""' #.r"r)rr_ collectionsrrtypingrrrrr r numpyrBior Bio.PDB.PDBExceptionsr Bio.PDB.Atomr rrrrrrr"r rs   :! '7!8 9 )8H#5 612jWWf_ %jZ ~.~.r"