o RŀgN@sdZddlZddlZddlZddlmZddlmZddlmZddlZ ddl Z ddl m Z ddlmZddlmZdd lmZerHdd lmZed d d ZGdd d ZGdddeZdS)z&Atom class, used in Structure objects.N)Optional) TYPE_CHECKING)TypeVar) IUPACData)DisorderedEntityWrapper)PDBConstructionWarning)Vector)Residue_AtomTAtom)boundc@seZdZdZ   dmdedejdeedeededed eed eed eefd d Z ddZ ddZ ddZ ddZ ddZddZddZddZddZd d!Zd"d#Z $dnd%ed&ed'ed(efd)d*Zd+d,Zd-d.Zd/d0Zd1d2Zd3d4Zd5d6Zd7d8Zd9d:Zd;d<Z d=d>Z!d?d@Z"dAdBZ#dCdDZ$dEdFZ%dGdHZ&dIdJZ'dKdLZ(dMdNZ)dOdPZ*dQdRZ+dSdTZ,dUdVZ-dWdXZ.dYdZZ/d[d\Z0d]d^Z1d_d`Z2dadbZ3dcddZ4dedfZ5dgdhZ6didjZ7dkdlZ8dS)or agDefine 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. In the case of PQR files, B factor and occupancy are replaced by atomic charge and radius. Nnamecoordbfactor occupancyaltlocfullnameelement pqr_chargeradiusc Csd|_d|_||_||_||_||_||_||_d|_||_ d|_ d|_ d|_ d|_ ||_i|_|r<||ks.z)get_idrFr.r.r/__repr__sz Atom.__repr__cCs|j|j}tt||S)zCalculate distance between two atoms. :param other: the other atom :type other: L{Atom} Examples -------- This is an incomplete but illustrative example:: distance = atom1 - atom2 )rnpsqrtdot)r-r5diffr.r.r/__sub__s z Atom.__sub__Fr-r5compare_coordinatesreturncCst|t|s dS|j|jkoZt|j|joZt|j|joZ|j|jkoZ|j|jkoZ|r5t |j |j ndoZt |ddt |ddkoZt |ddt |ddkoZt |ddt |ddkS)afCompare this atom to the other atom using a strict definition of equality. Indicates whether the atoms have the same name, B factor, occupancy, alternate location indicator (altloc), fullname, element, charge, and radius. If ``compare_coordinates`` is true, then the coordinates are also compared. :param other: The atom to compare this atom with :type other: Atom :param compare_coordinates: Whether to compare the coordinates of the atoms :type compare_coordinates: bool :return: Whether the atoms are strictly equal :rtype: bool FTrNrr) r2typer rYiscloserrrrallclosergetattr)r-r5r^r.r.r/strictly_equalss&   zAtom.strictly_equalscC ||_dS)zSet serial number.Nr&)r-nr.r.r/set_serial_number3 zAtom.set_serial_numbercCre)zSet isotroptic B factor.Nr)r-rr.r.r/ set_bfactor7rizAtom.set_bfactorcCre)zSet coordinates.Nr)r-rr.r.r/ set_coord;rizAtom.set_coordcCre)z#Set alternative location specifier.Nr)r-rr.r.r/ set_altloc?rizAtom.set_altloccCre)zSet occupancy.Nr)r-rr.r.r/ set_occupancyCrizAtom.set_occupancycCre)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: NumPy array (length 5) Nr%)r-r%r.r.r/ set_sigatmGs zAtom.set_sigatmcCre)zSet standard deviations of anisotropic temperature factors. :param siguij_array: standard deviations of anisotropic temperature factors. :type siguij_array: NumPy array (length 6) Nr$)r-r$r.r.r/ set_siguijS zAtom.set_siguijcCre)zSet anisotropic B factor. :param anisou_array: anisotropic B factor. :type anisou_array: NumPy array (length 6) Nr#)r-r#r.r.r/ set_anisou[rvzAtom.set_anisoucCre)z Set charge.Nr)r-rr.r.r/ set_chargecrizAtom.set_chargecCre)z Set radius.Nr)r-rr.r.r/ set_radiusgrizAtom.set_radiuscCs d|_dS)ztSet the disordered flag to 1. The disordered flag indicates whether the atom is disordered or not. rNr"rFr.r.r/ flag_disorderms zAtom.flag_disordercC|jS)z:Return the disordered flag (1 if disordered, 0 otherwise).r}rFr.r.r/ is_disorderedtzAtom.is_disorderedcCs||_||_dS)zXSet the parent residue. Arguments: - parent - Residue object N)rrEr )r-rr.r.r/ set_parentxszAtom.set_parentcCs d|_dS)zRemove reference to parent.NrrFr.r.r/ detach_parentrizAtom.detach_parentcCr)z/Return standard deviation of atomic parameters.rrrFr.r.r/ get_sigatmrzAtom.get_sigatmcCr)z>Return standard deviations of anisotropic temperature factors.rtrFr.r.r/ get_siguijrzAtom.get_siguijcCr)zReturn anisotropic B factor.rwrFr.r.r/ get_anisourzAtom.get_anisoucCr)zReturn parent residue.rrFr.r.r/ get_parentrzAtom.get_parentcCr)zReturn the serial number.rfrFr.r.r/get_serial_numberrzAtom.get_serial_numbercCr)zReturn atom name.)r rFr.r.r/get_namerz Atom.get_namecCr)z3Return the id of the atom (which is its atom name).)r!rFr.r.r/rWrz Atom.get_idc CsBz |j|j|jffWSty dddd|j|jfYSw)zReturn the full id of the atom. The full id of an atom is a tuple used to uniquely identify the atom and consists of the following elements: (structure id, model id, chain id, residue id, atom name, altloc) N)rrEr rrSrFr.r.r/rEs  zAtom.get_full_idcCr)zReturn atomic coordinates.rlrFr.r.r/ get_coordrzAtom.get_coordcCr)zReturn B factor.rjrFr.r.r/ get_bfactorrzAtom.get_bfactorcCr)zReturn occupancy.rprFr.r.r/ get_occupancyrzAtom.get_occupancycCr)z*sz1DisorderedAtom.center_of_mass..)dtyperN)axisweights)r ValueErrorrYasarrayfloat32average)r-childrencoordsr.r.r/center_of_mass s zDisorderedAtom.center_of_masscCst|jdddS)zeReturn list of atom instances. Sorts children by altloc (empty, then alphabetical). cSs t|jSN)ordrrr.r.r/2s z4DisorderedAtom.disordered_get_list..key)sortedrvaluesrFr.r.r/r-sz"DisorderedAtom.disordered_get_listcCsT||}|||}|}|||<||jkr(||_||dSdS)zAdd a disordered atom.N)r~rrrrrdisordered_select)r-atomresiduerrr.r.r/disordered_add4s  zDisorderedAtom.disordered_addcCsv|j|}|j|u}|j|=||r,|jr,t|jdddd}||jdS|js9d|_tj |_ dSdS)zRemove a child atom altloc from the DisorderedAtom. Arguments: - altloc - name of the altloc to remove, as a string. cSrrrprr.r.r/rRsz2DisorderedAtom.disordered_remove..rN) rselected_childrrrrrrrr)r-rr is_selectedchildr.r.r/disordered_removeBs   z DisorderedAtom.disordered_removecCs"|D] }t|j|||_qdS)zvApply rotation and translation to all children. See the documentation of Atom.transform for details. Nr)r-rrrr.r.r/rXszDisorderedAtom.transformN) rrrrr0rrXrrrrrr.r.r.r/rs     r)rrrrNtypingrrrnumpyrY Bio.PDB.AtomBioBio.DatarBio.PDB.EntityrBio.PDB.PDBExceptionsrBio.PDB.vectorsrBio.PDB.Residuer r r rr.r.r.r/s*         ^