o RŀgF@shdZddlmZddlmZddlmZddlmZer(ddlm Z ddl m Z Gdd d ed Z d S) z'Chain class, used in Structure objects.)Optional) TYPE_CHECKING)Entity)IC_Chain)Model)Residuec@seZdZdZddZddZddZdd Zd d Zd d Z ddZ ddZ ddZ ddZ ddZddZddZddZd(ded d!fd"d#Z  ! !d)ded$eed%eefd&d'Zd!S)*ChainzDefine Chain class. Chain is an object of type Entity, stores residues and includes a method to access atoms from residues. cCsd|_d|_t||dS)zInitialize the class.CN)levelinternal_coordr__init__selfidrA/var/www/html/myenv/lib/python3.10/site-packages/Bio/PDB/Chain.pyr szChain.__init__cCsJt|tr#|jdkr|jdkrdS|jdkr|jdkrdS|j|jkStS)z(Validate if id is greater than other.id. r isinstancerrNotImplementedrotherrrr__gt__#  z Chain.__gt__cCsJt|tr#|jdkr|jdkrdS|jdkr|jdkrdS|j|jkStS)z1Validate if id is greater or equal than other.id.rrrrrrrr__ge__/rz Chain.__ge__cCsJt|tr#|jdkr|jdkrdS|jdkr|jdkrdS|j|jkStS)z%Validate if id is less than other.id.rrrrrrrr__lt__;rz Chain.__lt__cCsJt|tr#|jdkr|jdkrdS|jdkr|jdkrdS|j|jkStS)z.Validate if id is less or equal than other id.rrrrrrrr__le__Grz Chain.__le__cCst|tr d|df}|S)aTranslate sequence identifier to tuple form (PRIVATE). A residue id is normally a tuple (hetero flag, sequence identifier, insertion code). Since for most residues the hetero flag and the insertion code are blank (i.e. " "), you can just use the sequence identifier to index a residue in a chain. The _translate_id method translates the sequence identifier to the (" ", sequence identifier, " ") tuple. Arguments: - id - int, residue resseq r)rintr rrr _translate_idSs  zChain._translate_idcC||}t||S)a!Return the residue with given id. The id of a residue is (hetero flag, sequence identifier, insertion code). If id is an int, it is translated to (" ", id, " ") by the _translate_id method. Arguments: - id - (string, int, string) or int )rr __getitem__r rrrr!es zChain.__getitem__cCr )zCheck if a residue with given id is present in this chain. Arguments: - id - (string, int, string) or int )rr __contains__r rrrr"s  zChain.__contains__cCr )zWDelete item. Arguments: - id - (string, int, string) or int )rr __delitem__r rrrr$}r#zChain.__delitem__cCsd|dS)zReturn the chain identifier.z )get_idrrrr__repr__szChain.__repr__cCsFg}|D]}|dkr|D]}||qq||q|S)zReturn a list of undisordered residues. Some Residue objects hide several disordered residues (DisorderedResidue objects). This method unpacks them, ie. it returns a list of simple Residue objects. )get_list is_disordereddisordered_get_listappend)r unpacked_listresiduedresiduerrrget_unpacked_lists     zChain.get_unpacked_listcCr )a0Return 1 if a residue with given id is present. The id of a residue is (hetero flag, sequence identifier, insertion code). If id is an int, it is translated to (" ", id, " ") by the _translate_id method. Arguments: - id - (string, int, string) or int )rrhas_idr rrrr2s z Chain.has_idccs|EdHdS)zReturn residues.Nrr'rrr get_residuesszChain.get_residuesccs|D]}|EdHqdS)zReturn atoms from residues.N)r3)rrrrr get_atomss  zChain.get_atomsFverbosereturnNcCs$|js t|||_|jj|ddS)zCreate/update internal coordinates from Atom X,Y,Z coordinates. Internal coordinates are bond length, angle and dihedral angles. :param verbose bool: default False describe runtime problems )r6N)r ratom_to_internal_coordinates)rr6rrrr8s z"Chain.atom_to_internal_coordinatesstartfincCsB|jr|jj|||ddS|jdurdn|jj}td||f)aCreate/update atom coordinates from internal coordinates. :param verbose bool: default False describe runtime problems :param: start, fin integers optional sequence positions for begin, end of subregion to process. N.B. this activates serial residue assembly, residue CA will be at origin :raises Exception: if any chain does not have .internal_coord attribute )r6r9r:Nzs