B b;@sPdZddlmZddlmZddlZddlmZGdddZGdd d Z dS) zBase class for Residue, Chain, Model and Structure classes. It is a simple container class, with list and dictionary like properties. )deque)copyN)PDBConstructionExceptionc@seZdZdZddZddZddZdd Zd d Zd d Z ddZ ddZ ddZ ddZ ddZddZddZddZddZed d!Zejd"d!Zd#d$Zd%d&Zd'd(Zd)d*Zd+d,Zd-d.Zd/d0Zd1d2Zd3d4Zd5d6Zd7d8Z d9d:Z!d;d<Z"dCd>d?Z#d@dAZ$dBS)DEntityzBasic 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-lib/python3.7/site-packages/Bio/PDB/Entity.py__init__s zEntity.__init__cCs t|jS)zReturn the number of children.)lenr )r rrr__len__'szEntity.__len__cCs |j|S)zReturn the child with given id.)r )r r rrr __getitem__+szEntity.__getitem__cCs ||S)zRemove a child.) detach_child)r r rrr __delitem__/szEntity.__delitem__cCs ||jkS)z4Check if there is a child element with the given id.)r )r r rrr __contains__3szEntity.__contains__ccs|jEdHdS)zIterate over children.N)r )r rrr__iter__7szEntity.__iter__cCsJt|t|rB|jdkr$|j|jkS|jdd|jddkSntSdS)zJTest for equality. This compares full_id including the IDs of all parents.N) isinstancetyperr rNotImplemented)r otherrrr__eq__=s   z Entity.__eq__cCsJt|t|rB|jdkr$|j|jkS|jdd|jddkSntSdS)zTest for inequality.Nr)rrrr rr)r rrrr__ne__Gs   z Entity.__ne__cCsJt|t|rB|jdkr$|j|jkS|jdd|jddkSntSdS)zTest greater than.Nr)rrrr rr)r rrrr__gt__Qs   z Entity.__gt__cCsJt|t|rB|jdkr$|j|jkS|jdd|jddkSntSdS)zTest greater or equal.Nr)rrrr rr)r rrrr__ge__[s   z Entity.__ge__cCsJt|t|rB|jdkr$|j|jkS|jdd|jddkSntSdS)zTest less than.Nr)rrrr rr)r rrrr__lt__es   z Entity.__lt__cCsJt|t|rB|jdkr$|j|jkS|jdd|jddkSntSdS)zTest less or equal.Nr)rrrr rr)r rrrr__le__os   z Entity.__le__cCs t|jS)z&Hash method to allow uniqueness (set).)hashr)r rrr__hash__yszEntity.__hash__c Cs>x.|D]&}y |Wqtk r*YqXqW||_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 childrrrr%s    zEntity._reset_full_idcCsN|}|g}|}x&|dk r<|}|||}qW|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_idpartsrrrrr's   zEntity._generate_full_idcCs|jS)zReturn identifier.)r)r rrrr sz Entity.idcCsh||jkrdS|jrV||jjkr>td|jd|d|d|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 NzCannot change id from `z` to `z `. The id `z/` is already used for a sibling of this entity.)rrr ValueErrorr%)r valuerrrr s    cCs|jS)zReturn level in hierarchy. A - atom R - residue C - chain M - model S - structure )level)r rrr get_levels zEntity.get_levelcCs||_|dS)zSet the parent Entity object.N)rr%)r entityrrr set_parentszEntity.set_parentcCs d|_dS)zDetach the parent.N)r)r rrr detach_parentszEntity.detach_parentcCs*|j|}||j|=|j|dS)zRemove a child.N)r r6r remove)r r r(rrrrs zEntity.detach_childcCsD|}||r t|d|||j|||j|<dS)zAdd a child to the Entity.z defined twiceN)r)has_idrr5r r+r )r r4r.rrradds    z Entity.addcCsH|}||r t|d|||g|j||<||j|<dS)z2Add a child to the Entity at a specified position.z defined twiceN)r)r8rr5r r )r posr4r.rrrinserts   z Entity.insertccs|jEdHdS)zReturn iterator over children.N)r )r rrr get_iteratorszEntity.get_iteratorcCs t|jS)z&Return a copy of the list of children.)rr )r rrrget_listszEntity.get_listcCs ||jkS)z&Check if a child with given id exists.)r )r r rrrr8sz Entity.has_idcCs|jS)z Return the parent Entity object.)r)r rrrr*szEntity.get_parentcCs|jS)zReturn the id.)r )r rrrr)sz Entity.get_idcCs|jdkr||_|jS)akReturn the full id. The full id is a tuple containing all id's starting from the top object (Structure) down to the current object. A full id for a Residue object e.g. is something like: ("1abc", 0, "A", (" ", 10, "A")) This corresponds to: Structure with id "1abc" Model with id 0 Chain with id "A" Residue with id (" ", 10, "A") The Residue id indicates that the residue is not a hetero-residue (or a water) because it has a blank hetero field, that its sequence identifier is 10 and its insertion code "A". N)rr')r rrr get_full_ids  zEntity.get_full_idcCs"x|D]}|||q WdS)aJApply rotation and translation to the atomic coordinates. :param rot: A right multiplying rotation matrix :type rot: 3x3 Numeric array :param tran: the translation vector :type tran: size 3 Numeric 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)r= transform)r ZrotZtranorrrr?szEntity.transformFc Cst|st|dddh}dh}t|g}xF|}|j|krP||7}n ||j7}dd|D}||kr0Pq0Wtjdd|Dtj d }|rd }ntjd d|Dtj d }tj |d |d S)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 childrenRCAcSsh|] }|jqSr)r2).0errr ?sz(Entity.center_of_mass..cSsg|] }|jqSr)Zcoord)rDarrr Csz)Entity.center_of_mass..)ZdtypeNcSsg|] }|jqSr)Zmass)rDrGrrrrHGsr)ZaxisZweights) rr0rpopleftr2Zget_unpacked_listr npZasarrayZfloat32Zaverage) r Z geometricZmaybe_disorderedZonly_atom_levelZentitiesrEZelevelsZcoordsZmassesrrrcenter_of_mass*s$   zEntity.center_of_masscCsJt|}g|_i|_t|j|_|x|jD]}||q0W|S)zCopy entity recursively.)rr r r r6r9)r shallowr(rrrrKs  z Entity.copyN)F)%__name__ __module__ __qualname____doc__rrrrrrrrrr r!r"r$r%r'propertyr setterr3r5r6rr9r;r<r=r8r*r)r>r?rKrrrrrrsB             !rc@seZdZdZddZddZddZdd Zd d Zd d Z ddZ ddZ ddZ ddZ ddZddZddZddZddZd d!Zd"d#Zd$d%Zd&d'Zd(d)Zd*d+Zd,d-Zd.d/Zd5d1d2Zd3d4Zd0S)6DisorderedEntityWrapperaWrapper 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 rrrrfsz DisorderedEntityWrapper.__init__cCs&|dkr tt|dstt|j|S)z.Forward the method call to the selected child. __setstate__rT)r&hasattrgetattrrT)r methodrrr __getattr__os  z#DisorderedEntityWrapper.__getattr__cCs |j|S)z#Return the child with the given id.)rT)r r rrrrzsz#DisorderedEntityWrapper.__getitem__cCs||j|<dS)z*Add a child, associated with a certain id.N)r )r r r(rrr __setitem__sz#DisorderedEntityWrapper.__setitem__cCs ||jkS)z$Check if the child has the given id.)rT)r r rrrrsz$DisorderedEntityWrapper.__contains__cCs t|jS)zReturn the number of children.)iterrT)r rrrrsz DisorderedEntityWrapper.__iter__cCs t|jS)zReturn the number of children.)rrT)r rrrrszDisorderedEntityWrapper.__len__cCs |j|S)z Subtraction with another object.)rT)r rrrr__sub__szDisorderedEntityWrapper.__sub__cCs |j|kS)z&Return if child is greater than other.)rT)r rrrrrszDisorderedEntityWrapper.__gt__cCs |j|kS)z/Return if child is greater or equal than other.)rT)r rrrrr szDisorderedEntityWrapper.__ge__cCs |j|kS)z#Return if child is less than other.)rT)r rrrrr!szDisorderedEntityWrapper.__lt__cCs |j|kS)z,Return if child is less or equal than other.)rT)r rrrrr"szDisorderedEntityWrapper.__le__cCs:t|}i|_|x|D]}||q W|S)z"Copy disorderd entity recursively.)rr r6disordered_get_listdisordered_add)r rLr(rrrrs zDisorderedEntityWrapper.copycCs|jS)zReturn the id.)r )r rrrr)szDisorderedEntityWrapper.get_idcCs ||jkS)z s   H