Ic@s_ddlZddlmZddlmZdZdd dYZdefdYZdS( iN(tDisorderedEntityWrapper(tVectors&Atom class, used in Structure objects.tAtomcBseZdZdZdZdZdZdZdZdZ dZ d Z d Z d Z d Zd ZdZdZdZdZdZdZdZdZdZdZdZdZdZdZdZdZdZ RS(cCsd|_d|_||_||_||_||_||_||_d|_ ||_ d|_ d|_ d|_ d|_||_i|_dS(s Atom object. 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. @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 tAiN(tleveltNonetparenttnametfullnametcoordtbfactort occupancytaltloctfull_idtidtdisordered_flagt anisou_arrayt siguij_arrayt sigatm_arrayt serial_numbertxtra(tselfRR R R R RR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Atom.pyt__init__s                cCsd|jS(s&Print Atom object as .s (tget_id(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Atom.pyt__repr__BscCs)|j|j}tjtj||S(s Calculate distance between two atoms. Example: >>> distance=atom1-atom2 @param other: the other atom @type other: L{Atom} (R tnumpytsqrttdot(Rtothertdiff((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Atom.pyt__sub__Fs cCs ||_dS(N(R(Rtn((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Atom.pytset_serial_numberUscCs ||_dS(N(R (RR ((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Atom.pyt set_bfactorXscCs ||_dS(N(R (RR ((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Atom.pyt set_coord[scCs ||_dS(N(R (RR ((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Atom.pyt set_altloc^scCs ||_dS(N(R (RR ((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Atom.pyt set_occupancyascCs ||_dS(sJ 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(RR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Atom.pyt set_sigatmds cCs ||_dS(s Set standard deviations of anisotropic temperature factors. @param siguij_array: standard deviations of anisotropic temperature factors. @type siguij_array: Numeric array (length 6) N(R(RR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Atom.pyt set_siguijqscCs ||_dS(s Set anisotropic B factor. @param anisou_array: anisotropic B factor. @type anisou_array: Numeric array (length 6) N(R(RR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Atom.pyt set_anisouzscCs d|_dS(stSet the disordered flag to 1. The disordered flag indicates whether the atom is disordered or not. iN(R(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Atom.pyt flag_disorderscCs|jS(s:Return the disordered flag (1 if disordered, 0 otherwise).(R(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Atom.pyt is_disorderedscCs ||_dS(sVSet the parent residue. Arguments: o parent - Residue object N(R(RR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Atom.pyt set_parentscCs d|_dS(sRemove reference to parent.N(RR(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Atom.pyt detach_parentscCs|jS(s/Return standard deviation of atomic parameters.(R(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Atom.pyt get_sigatmscCs|jS(s>Return standard deviations of anisotropic temperature factors.(R(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Atom.pyt get_siguijscCs|jS(sReturn anisotropic B factor.(R(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Atom.pyt get_anisouscCs|jS(sReturn parent residue.(R(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Atom.pyt get_parentscCs|jS(N(R(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Atom.pytget_serial_numberscCs|jS(sReturn atom name.(R(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Atom.pytget_namescCs|jS(s3Return the id of the atom (which is its atom name).(R(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Atom.pyRscCs |jj|j|jffS(sReturn 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). (Rt get_full_idRR (R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Atom.pyR2scCs|jS(sReturn atomic coordinates.(R (R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Atom.pyt get_coordscCs|jS(sReturn B factor.(R (R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Atom.pyt get_bfactorscCs|jS(sReturn occupancy.(R (R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Atom.pyt get_occupancyscCs|jS(s<Return the atom name, including leading and trailing spaces.(R(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Atom.pyt get_fullnamescCs|jS(s&Return alternative location specifier.(R (R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Atom.pyt get_altlocscCs|jS(N(R(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Atom.pyt get_levelscCs tj|j|||_dS(s Apply rotation and translation to the atomic coordinates. Example: >>> rotation=rotmat(pi, Vector(1,0,0)) >>> translation=array((0,0,1), 'f') >>> atom.transform(rotation, translation) @param rot: A right multiplying rotation matrix @type rot: 3x3 Numeric array @param tran: the translation vector @type tran: size 3 Numeric array N(RRR (Rtrotttran((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Atom.pyt transformscCs"|j\}}}t|||S(sq Return coordinates as Vector. @return: coordinates as 3D vector @rtype: Vector (R R(Rtxtytz((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Atom.pyt get_vectors(!t__name__t __module__RRRR R!R"R#R$R%R&R'R(R)R*R+R,R-R.R/R0R1RR2R3R4R5R6R7R8R;R?(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Atom.pyRs> 2                          tDisorderedAtomcBs)eZdZdZdZdZRS(s This class contains all Atom objects that represent the same disordered atom. One of these atoms is "selected" and all method calls not caught by DisorderedAtom are forwarded to the selected Atom object. In that way, a DisorderedAtom behaves exactly like a normal Atom. By default, the selected Atom object represents the Atom object with the highest occupancy, but a different Atom object can be selected by using the disordered_select(altloc) method. cCsd|_tj||dS(s= Arguments: o id - string, atom name iN(tlast_occupancyRR(RR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Atom.pyRs cCsd|jS(Ns(R(R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Atom.pyRscCsq|j|j}|j||j}|j}|||<||jkrm||_|j|ndS(sAdd a disordered atom.N(R(R/R*R7R5RCtdisordered_select(RtatomtresidueR R ((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Atom.pytdisordered_add s       (R@RAt__doc__RRRG(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Atom.pyRBs  ((RtEntityRRRHRRB(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Atom.pyts