o RŀgMH@sdZddlZddlmZddlmZddlmZddlmZddlmZddlm Z dd lm Z dd lm Z ddl Z dd lmZdd lmZe rNdd lmZe de ddZe deddZe dddZGdddeeefZGdddZdS)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 @seZdZUdZeeed<eeed<e e efed<e ed<ddZ dd Z d d Zd d ZddZddZddZddZddZddZddZddZddZd d!Zd"d#Zed$d%Zejd&d%Z 'dOd(ed)ed*ed+efd,d-Z d.d/Z!d0efd1d2Z"d3d4Z#d5d6Z$d0efd7d8Z%d9e&d0efd:d;Z'dd?Z)d@dAZ*dBdCZ+dDdEZ,dFdGZ-dHdIZ.dOdJdKZ/dLdMZ0dNS)PrzBasic container object for PDB hierarchy. Structure, Model, Chain and Residue are subclasses of Entity. It deals with storage and lookup. parent child_list child_dictlevelcCs(||_d|_d|_g|_i|_i|_dSzInitialize the class.N)_idfull_idrrrxtraselfidrB/var/www/html/myenv/lib/python3.10/site-packages/Bio/PDB/Entity.py__init__/s  zEntity.__init__cC t|jSzReturn the number of children.)lenrrrrr__len__; zEntity.__len__cC |j|S)zReturn the child with given id.rrrrr __getitem__?r%zEntity.__getitem__cCs ||S)Remove a child.) detach_childrrrr __delitem__Cr%zEntity.__delitem__cC ||jvS)z4Check if there is a child element with the given id.r'rrrr __contains__Gr%zEntity.__contains__cc|jEdHdS)zIterate over children.Nrr#rrr__iter__KzEntity.__iter__cCsDt|t|r |jdur|j|jkS|jdd|jddkStS)zJTest for equality. This compares full_id including the IDs of all parents.N isinstancetyperrrNotImplementedrotherrrr__eq__Q   z Entity.__eq__cCsDt|t|r |jdur|j|jkS|jdd|jddkStS)zTest for inequality.Nr2r3r7rrr__ne__[r:z Entity.__ne__cCsDt|t|r |jdur|j|jkS|jdd|jddkStS)zTest greater than.Nr2r3r7rrr__gt__er:z Entity.__gt__cCsDt|t|r |jdur|j|jkS|jdd|jddkStS)zTest greater or equal.Nr2r3r7rrr__ge__or:z Entity.__ge__cCsDt|t|r |jdur|j|jkS|jdd|jddkStS)zTest less than.Nr2r3r7rrr__lt__yr:z Entity.__lt__cCsDt|t|r |jdur|j|jkS|jdd|jddkStS)zTest less or equal.Nr2r3r7rrr__le__r:z Entity.__le__cCr )z&Hash method to allow uniqueness (set).)hashrr#rrr__hash__r%zEntity.__hash__c Cs6|D]}z|WqtyYqw||_dS)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_idrrchildrrrrBs  zEntity._reset_full_idcCsP|}|g}|}|dur |}|||}|dus|t|S)zGenerate full_id (PRIVATE). Generate the full_id of the Entity based on its Id and the IDs of the parents. N)get_id get_parentappendreversetuple)r entity_idpartsrrrrrDs zEntity._generate_full_idcC|jS)zReturn identifier.)rr#rrrrsz Entity.idc Csp||jkrdS|jdur/||jjvr#td|d|jd|dt|jj|j=||jj|<||_|dS)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 rB)rvaluerrrrs      Frr8compare_coordinatesreturncCsvt|t|s dS|j|jkrdSt|jt|jkrdSt|j|jD]\}}t|ds/J|||s8dSq$dS)aCompare this entity to the other entity for equality. Recursively compare the children of this entity to the other entity's children. 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A - atom R - residue C - chain M - model S - structure rr#rrr get_levels zEntity.get_levelentitycCs||_|dS)zSet the parent Entity object.N)rrB)rr[rrr set_parents zEntity.set_parentcCs d|_dSzDetach the parent.Nrr#rrr detach_parentr%zEntity.detach_parentcCs*|j|}||j|=|j|dS)r)N)rr_rremoverrrFrrrr*s zEntity.detach_childcCsD|}||rt|d|||j|||j|<dS)zAdd a child to the Entity. defined twiceN)rGhas_idr r\rrIr)rr[rLrrradd s    z Entity.addposcCsH|}||rt|d|||g|j||<||j|<dS)z2Add a child to the Entity at a specified position.rbN)rGrcr r\rr)rrer[rLrrrinserts   z Entity.insertccr.)zReturn iterator over children.Nr/r#rrr get_iteratorr1zEntity.get_iteratorcCr )z&Return a copy of the list of children.)rrr#rrrget_list!r%zEntity.get_listcCr,)z&Check if a child with given id exists.r'rrrrrc%r%z Entity.has_idcCrN)z Return the parent Entity object.r^r#rrrrH)zEntity.get_parentcCrNzReturn the id.rr#rrrrG-riz Entity.get_idcCs|jdur ||_|jS)akReturn the full id. 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N)rrDr#rrr get_full_id1s  zEntity.get_full_idcCs|D]}|||qdS)aFApply rotation and translation to the atomic coordinates. :param rot: A right multiplying rotation matrix :type rot: 3x3 NumPy array :param tran: the translation vector :type tran: size 3 NumPy array Examples -------- This is an incomplete but illustrative example:: from numpy import pi, array from Bio.PDB.vectors import Vector, rotmat rotation = rotmat(pi, Vector(1, 0, 0)) translation = array((0, 0, 1), 'f') entity.transform(rotation, translation) N)rh transform)rrottranorrrrmIs zEntity.transformc Cst|s t|dddh}dh}t|g} |}|j|vr(||7}n||j7}dd|D}||kr9nqtjdd |Dtj d }|rLd }n tjd d |Dtj d }tj |d |dS)zReturn the center of mass of the Entity as a numpy array. If geometric is True, returns the center of geometry instead. z does not have childrenRCATcSsh|]}|jqSrrY).0errr uz(Entity.center_of_mass..cSg|]}|jqSr)coordrtarrr yrwz)Entity.center_of_mass..)dtypeNcSrxr)massrzrrrr|}rwr)axisweights) r" ValueErrorrpopleftrget_unpacked_listrnpasarrayfloat32average) r geometricmaybe_disorderedonly_atom_levelentitiesruelevelscoordsmassesrrrcenter_of_mass`s&    zEntity.center_of_masscCsFt|}g|_i|_t|j|_||jD] }||q|S)zCopy entity recursively.)rrrrr_rdrshallowrFrrrrs  z Entity.copyNF)1__name__ __module__ __qualname____doc__rr__annotations__listr dictrstrrr$r(r+r-r0r9r;r<r=r>r?rArBrDpropertyrsetterrboolrTrZr\r_r*rdintrfrgrhrcrHrGrlrmrrrrrrr#sd                   !c@seZdZdZddZddZddZdd Zd d Zd d Z ddZ ddZ ddZ ddZ ddZddZddZddZ d;ddd ed!efd"d#Zd$d%Zd&d'Zd(d)Zd*d+Zd,d-Zd.d/Zd0d1Zd2d3Zd4d5Zdr%zDisorderedEntityWrapper.__lt__cCs |j|kS)z,Return if child is less or equal than other.rr7rrrr?r%zDisorderedEntityWrapper.__le__cCs6t|}i|_||D] }||q|S)z"Copy disorderd entity recursively.)rrr_disordered_get_listdisordered_addrrrrrs  zDisorderedEntityWrapper.copycCrNrjrkr#rrrrGrizDisorderedEntityWrapper.get_idFr8rRrScCst|t|s dS|j|jkrdS|j|jksdS|j|jkr)dS|jD]}|j||j||s?dSq.dS)a-Compare this entity to the other entity using a strict definition of equality. Recursively compare the children of this entity to the other entity's children. Compare most properties including the selected child, names, and IDs. :param other: The entity to compare this entity with :type other: DisorderedEntityWrapper :param compare_coordinates: Whether to compare atomic coordinates :type compare_coordinates: bool :return: Whether the two entities are strictly equal :rtype: bool FT)r4r5rrrGrkeysrT)rr8rRkeyrrrrTs   z'DisorderedEntityWrapper.strictly_equalscCr,)zs z.DisorderedEntityWrapper.disordered_get_id_listNcCs|dur|jS|j|S)zsGet the child object associated with id. If id is None, the currently selected child is returned. N)rrrrrrdisordered_getCs z&DisorderedEntityWrapper.disordered_getcCst|jS)zReturn list of children.)rrvaluesr#rrrrLrz+DisorderedEntityWrapper.disordered_get_listr)N)rrrrrrr(rr-r0r$rr<r=r>r?rrGrrTrr_rHr\rrrrrrrrrrrrsF     %  r)rrO collectionsrrtypingrrrrrr numpyrBior Bio.PDB.PDBExceptionsr Bio.PDB.Atomr r rrrrrrrrs,            o