:>"^N:ã@sšdZddlZddlZddlZddlmZddlmZddlm Z ddl m Z Gdd„de ƒZ Gd d „d eƒZdS) z&Atom class, used in Structure objects.éN)ÚDisorderedEntityWrapper)ÚPDBConstructionWarning)ÚVector)Ú IUPACDatac@seZdZdZddd„Zdd„Zdd„Zd d „Zd d „Zd d„Z dd„Z dd„Z dd„Z dd„Z dd„Zdd„Zdd„Zdd„Zdd „Zd!d"„Zd#d$„Zd%d&„Zd'd(„Zd)d*„Zd+d,„Zd-d.„Zd/d0„Zd1d2„Zd3d4„Zd5d6„Zd7d8„Zd9d:„Zd;d<„Z d=d>„Z!d?d@„Z"dAdB„Z#dCdD„Z$dEdF„Z%dGdH„Z&dIdJ„Z'dKdL„Z(dMdN„Z)dOdP„Z*dQdR„Z+dSdT„Z,dS)UÚAtomaDefine Atom class. The Atom object stores atom name (both with and without spaces), coordinates, B factor, occupancy, alternative location specifier and (optionally) anisotropic B factor and standard deviations of B factor and positions. Nc Csûd|_d|_||_||_||_||_||_||_d|_||_ d|_ d|_ d|_ d|_ ||_i|_| sµ||jƒksµt|ƒ‚|j|ƒ|_|jƒ|_ddddddd d i|_dS) a:Initialize Atom object. :param name: atom name (eg. "CA"). Note that spaces are normally stripped. :type name: string :param coord: atomic coordinates (x,y,z) :type coord: Numeric array (Float0, size 3) :param bfactor: isotropic B factor :type bfactor: number :param occupancy: occupancy (0.0-1.0) :type occupancy: number :param altloc: alternative location specifier for disordered atoms :type altloc: string :param fullname: full atom name, including spaces, e.g. " CA ". Normally these spaces are stripped from the atom name. :type fullname: string :param element: atom element, e.g. "C" for Carbon, "HG" for mercury, :type element: uppercase string (or None if unknown) ÚANrÚNÚCAéÚCéÚOé)ÚlevelÚparentÚnameÚfullnameÚcoordÚbfactorÚ occupancyÚaltlocÚfull_idÚidÚdisordered_flagÚ anisou_arrayÚ siguij_arrayÚ sigatm_arrayÚ serial_numberÚxtraÚupperÚAssertionErrorÚ_assign_elementÚelementÚ_assign_atom_massZmassÚ _sorting_keys) Úselfrrrrrrrr"©r&ú1/tmp/pip-build-ww9dw3qa/biopython/Bio/PDB/Atom.pyÚ__init__s(#                %z Atom.__init__cCs;t|tƒr3|jdd…|jdd…kStSdS)zTest equality.r N)Ú isinstancerrÚNotImplemented)r%Úotherr&r&r'Ú__eq__\s$z Atom.__eq__cCs;t|tƒr3|jdd…|jdd…kStSdS)zTest inequality.r N)r)rrr*)r%r+r&r&r'Ú__ne__cs$z Atom.__ne__cCs´t|tƒr¬|j|jkr1|j|jkS|jj|jdƒ}|jj|jdƒ}||krw||kS|j|jkr™|j|jkS|j|jkSntSdS)zTest greater than.éN)r)rrr$Úgetrrr*)r%r+Úorder_sÚorder_or&r&r'Ú__gt__js  z Atom.__gt__cCs´t|tƒr¬|j|jkr1|j|jkS|jj|jdƒ}|jj|jdƒ}||krw||kS|j|jkr™|j|jkS|j|jkSntSdS)zTest greater or equal.r.N)r)rrr$r/rrr*)r%r+r0r1r&r&r'Ú__ge__zs  z Atom.__ge__cCs´t|tƒr¬|j|jkr1|j|jkS|jj|jdƒ}|jj|jdƒ}||krw||kS|j|jkr™|j|jkS|j|jkSntSdS)zTest less than.r.N)r)rrr$r/rrr*)r%r+r0r1r&r&r'Ú__lt__Šs  z Atom.__lt__cCs´t|tƒr¬|j|jkr1|j|jkS|jj|jdƒ}|jj|jdƒ}||krw||kS|j|jkr™|j|jkS|j|jkSntSdS)zTest less or equal.r.N)r)rrr$r/rrr*)r%r+r0r1r&r&r'Ú__le__šs  z Atom.__le__cCst|jƒƒS)zReturn atom full identifier.)ÚhashÚ get_full_id)r%r&r&r'Ú__hash__«sz Atom.__hash__cCsï| s|jƒtjkrë|jdjƒr[|jdd…jƒ r[|jjƒ}n0|jdjƒr~|jd}n |jd}|jƒtjkr¿d||j|f}|}nd||j|f}d}tj |t ƒ|S)z9Guess element from atom name if not recognised (PRIVATE).rr Nr z8Used element %r for Atom (name=%s) with given element %rzDCould not assign element %r for Atom (name=%s) with given element %rÚ) Ú capitalizerÚ atom_weightsrÚisalphaÚisdigitrÚstripÚwarningsÚwarnr)r%r"Zputative_elementÚmsgr&r&r'r!¯s"-   zAtom._assign_elementcCs+|jrtj|jjƒStdƒSdS)zReturn atom weight (PRIVATE).ÚNaNN)r"rr;r:Úfloat)r%r&r&r'r#Ñs zAtom._assign_atom_masscCsd|jƒS)z&Print Atom object as .z )Úget_id)r%r&r&r'Ú__repr__Ûsz Atom.__repr__cCs)|j|j}tjtj||ƒƒS)zôCalculate distance between two atoms. :param other: the other atom :type other: L{Atom} Examples -------- This is an incomplete but illustrative example:: distance = atom1 - atom2 )rÚnumpyÚsqrtÚdot)r%r+Zdiffr&r&r'Ú__sub__ßs z Atom.__sub__cCs ||_dS)zSet serial number.N)r)r%Únr&r&r'Úset_serial_numberñszAtom.set_serial_numbercCs ||_dS)zSet isotroptic B factor.N)r)r%rr&r&r'Ú set_bfactorõszAtom.set_bfactorcCs ||_dS)zSet coordinates.N)r)r%rr&r&r'Ú set_coordùszAtom.set_coordcCs ||_dS)z#Set alternative location specifier.N)r)r%rr&r&r'Ú set_altlocýszAtom.set_altloccCs ||_dS)zSet occupancy.N)r)r%rr&r&r'Ú set_occupancyszAtom.set_occupancycCs ||_dS)a@Set standard deviation of atomic parameters. The standard deviation of atomic parameters consists of 3 positional, 1 B factor and 1 occupancy standard deviation. :param sigatm_array: standard deviations of atomic parameters. :type sigatm_array: Numeric array (length 5) N)r)r%rr&r&r'Ú set_sigatms zAtom.set_sigatmcCs ||_dS)zÏSet standard deviations of anisotropic temperature factors. :param siguij_array: standard deviations of anisotropic temperature factors. :type siguij_array: Numeric array (length 6) N)r)r%rr&r&r'Ú set_siguijszAtom.set_siguijcCs ||_dS)z‹Set anisotropic B factor. :param anisou_array: anisotropic B factor. :type anisou_array: Numeric array (length 6) N)r)r%rr&r&r'Ú set_anisouszAtom.set_anisoucCs d|_dS)ztSet the disordered flag to 1. The disordered flag indicates whether the atom is disordered or not. r N)r)r%r&r&r'Ú flag_disorder#szAtom.flag_disordercCs|jS)z:Return the disordered flag (1 if disordered, 0 otherwise).)r)r%r&r&r'Ú is_disordered*szAtom.is_disorderedcCs||_|jƒ|_dS)zXSet the parent residue. Arguments: - parent - Residue object N)rr7r)r%rr&r&r'Ú set_parent.s zAtom.set_parentcCs d|_dS)zRemove reference to parent.N)r)r%r&r&r'Ú detach_parent8szAtom.detach_parentcCs|jS)z/Return standard deviation of atomic parameters.)r)r%r&r&r'Ú get_sigatm<szAtom.get_sigatmcCs|jS)z>Return standard deviations of anisotropic temperature factors.)r)r%r&r&r'Ú get_siguij@szAtom.get_siguijcCs|jS)zReturn anisotropic B factor.)r)r%r&r&r'Ú get_anisouDszAtom.get_anisoucCs|jS)zReturn parent residue.)r)r%r&r&r'Ú get_parentHszAtom.get_parentcCs|jS)zReturn the serial number.)r)r%r&r&r'Úget_serial_numberLszAtom.get_serial_numbercCs|jS)zReturn atom name.)r)r%r&r&r'Úget_namePsz Atom.get_namecCs|jS)z3Return the id of the atom (which is its atom name).)r)r%r&r&r'rDTsz Atom.get_idcCs |jjƒ|j|jffS)z Return the full id of the atom. The full id of an atom is the tuple (structure id, model id, chain id, residue id, atom name, altloc). )rr7rr)r%r&r&r'r7XszAtom.get_full_idcCs|jS)zReturn atomic coordinates.)r)r%r&r&r'Ú get_coord`szAtom.get_coordcCs|jS)zReturn B factor.)r)r%r&r&r'Ú get_bfactordszAtom.get_bfactorcCs|jS)zReturn occupancy.)r)r%r&r&r'Ú get_occupancyhszAtom.get_occupancycCs|jS)z)rD)r%r&r&r'rEÁszDisorderedAtom.__repr__cCsn|jƒ|jƒ}|j|ƒ|jƒ}|jƒ}|||<||jkrj||_|j|ƒdS)zAdd a disordered atom.N)rSrZrUrar_rnZdisordered_select)r%ZatomZresiduerrr&r&r'Údisordered_addÅs       zDisorderedAtom.disordered_addN)rirjrkrlr(rprErqr&r&r&r'rm¤s   rm)rlrFr?rhZBio.PDB.EntityrZBio.PDB.PDBExceptionsrZBio.PDB.vectorsrZBio.DatarÚobjectrrmr&r&r&r'Ús   ÿ‘