:>"^*5@sVdZddlmZddlmZGdddeZGdddeZdS) zBase class for Residue, Chain, Model and Structure classes. It is a simple container class, with list and dictionary like properties. )copy)PDBConstructionExceptionc@seZdZdZddZddZddZdd Zd d Zd d Z ddZ ddZ ddZ ddZ ddZddZddZddZddZed d!Zejd"d!Zd#d$Zd%d&Zd'd(Zd)d*Zd+d,Zd-d.Zd/d0Zd1d2Zd3d4Zd5d6Zd7d8Z d9d:Z!d;d<Z"d=d>Z#d?S)@EntityzBasic container object for PDB heirachy. Structure, Model, Chain and Residue are subclasses of Entity. It deals with storage and lookup. cCs:||_d|_d|_g|_i|_i|_dS)zInitialize the class.N)_idfull_idparent child_list child_dictxtra)selfidr 3/tmp/pip-build-ww9dw3qa/biopython/Bio/PDB/Entity.py__init__s      zEntity.__init__cCs t|jS)zReturn the number of children.)lenr)r r r r__len__$szEntity.__len__cCs |j|S)zReturn the child with given id.)r )r r r r r __getitem__(szEntity.__getitem__cCs |j|S)zRemove a child.) detach_child)r r r r r __delitem__,szEntity.__delitem__cCs ||jkS)z4Check if there is a child element with the given id.)r )r r r r r __contains__0szEntity.__contains__ccsx|jD] }|Vq WdS)zIterate over children.N)r)r childr r r__iter__4szEntity.__iter__cCsct|t|r[|jdkr4|j|jkS|jdd|jddkSntSdS)zJTest for equality. This compares full_id including the IDs of all parents.N) isinstancetyperr rNotImplemented)r otherr r r__eq__;s 'z Entity.__eq__cCsct|t|r[|jdkr4|j|jkS|jdd|jddkSntSdS)zTest for inequality.Nr)rrrr rr)r rr r r__ne__Es 'z Entity.__ne__cCsct|t|r[|jdkr4|j|jkS|jdd|jddkSntSdS)zTest greater than.Nr)rrrr rr)r rr r r__gt__Os 'z Entity.__gt__cCsct|t|r[|jdkr4|j|jkS|jdd|jddkSntSdS)zTest greater or equal.Nr)rrrr rr)r rr r r__ge__Ys 'z Entity.__ge__cCsct|t|r[|jdkr4|j|jkS|jdd|jddkSntSdS)zTest less than.Nr)rrrr rr)r rr r r__lt__cs 'z Entity.__lt__cCsct|t|r[|jdkr4|j|jkS|jdd|jddkSntSdS)zTest less or equal.Nr)rrrr rr)r rr r r__le__ms 'z Entity.__le__cCs t|jS)z&Hash method to allow uniqueness (set).)hashr)r r r r__hash__wszEntity.__hash__c CsGx1|D])}y|jWqtk r/YqXqW|j|_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_idr)r rr r rr%}s    zEntity._reset_full_idcCsm|j}|g}|j}x5|dk rX|j}|j||j}q$W|jt|S)zGenerate full_id (PRIVATE). Generate the full_id of the Entity based on its Id and the IDs of the parents. N)get_id get_parentappendreversetuple)r entity_idpartsrr r rr's      zEntity._generate_full_idcCs|jS)zReturn identifier.)r)r r r rr sz Entity.idcCs||jkrdS|jrl||jjkrLtdj|j|||jj|j=||jj|<||_|jdS)zChange the id of this entity. This will update the child_dict of this entity's parent and invalidate all cached full ids involving this entity. @raises: ValueError Nz]Cannot change id from `{}` to `{}`. The id `{}` is already used for a sibling of this entity.)rrr ValueErrorformatr%)r valuer r rr s   cCs|jS)zReturn level in hierarchy. A - atom R - residue C - chain M - model S - structure )level)r r r r get_levels zEntity.get_levelcCs||_|jdS)zSet the parent Entity object.N)rr%)r entityr r r set_parents zEntity.set_parentcCs d|_dS)zDetach the parent.N)r)r r r r detach_parentszEntity.detach_parentcCs5|j|}|j|j|=|jj|dS)zRemove a child.N)r r6rremove)r r rr r rrs   zEntity.detach_childcCsY|j}|j|r+td||j||jj|||j|r?rr r r rrs@                  rc@s-eZdZdZddZddZddZdd Zd d Zd d Z ddZ ddZ ddZ ddZ ddZddZddZddZddZd d!Zd"d#Zd$d%Zd&d'Zd(d)Zd*d+Zd,d-d.Zd/d0Zd,S)1DisorderedEntityWrapperaWrapper 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. cCs(||_i|_d|_d|_dS)zInitialize the class.N)r r selected_childr)r r r r rrDs   z DisorderedEntityWrapper.__init__cCs7|dkrtt|ds'tt|j|S)z.Forward the method call to the selected child. __setstate__rH)r&hasattrgetattrrH)r methodr r r __getattr__Ms  z#DisorderedEntityWrapper.__getattr__cCs |j|S)z#Return the child with the given id.)rH)r r r r rrXsz#DisorderedEntityWrapper.__getitem__cCs||j| s (