ó ø™xTc@ sŒddlmZddlmZddlmZddlmZddlm Z ddl m Z de fd„ƒYZ eeed „Zd S( iÿÿÿÿ(tdivision(tmatrix(t unit_cell(t space_group(tspace_group_symbols(tcrystal_orientationt crystal_modelcB s7eZdZd!d!d!ed„Zed„ƒZed!d„Z d„Z d„Z d„Z d„Z d„Zd „Zd „Zd „Zd „Zd „Zd„Zd„Zd„Z d„Zd„Zd„Zd„Zed„Zed„Zd„Zdd„Zddddd„Zd„Zd„Z d „Z!RS("sÖSimple model for the crystal lattice geometry and symmetry A crystal is initialised from the elements of its real space axes a, b, and c. Space group information must also be provided, either in the form of a symbol, or an existing cctbx.sgtbx.space_group object. If space_group_symbol is provided, it is passed to the cctbx.sgtbx.space_group_symbols constructor. This accepts either extended Hermann Mauguin format, or Hall format with the prefix 'Hall:'. E.g. space_group_symbol = "P b a n:1" or space_group_symbol = "Hall:P 2 2 -1ab" Optionally the crystal mosaicity value may be set, with the deg parameter controlling whether this value is treated as being an angle in degrees or radians.c C s||gjdƒdks!t‚|r?tt|ƒƒ|_n ||_|dk rj|j|d|ƒn d|_tj |ƒ}tj |ƒ}tj |ƒ}tj |j |j |j ƒj ƒ}|j |||ƒ|jƒ||jj ƒ|_|jƒdS(Nitdegg(tcounttNonetAssertionErrortSGRt_sgt set_mosaicityt _mosaicityRtcoltsqrtelemstinverset set_unit_cellt _update_Bt_Bt_Utreset_scan_points( tselft real_space_at real_space_bt real_space_ctspace_group_symbolRt mosaicityRtA((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/model/crystal.pyt__init__s"!     cC s|jS(N(t_num_scan_points(R((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/model/crystal.pytnum_scan_pointsAscC s|dkr$ddl}|j}n|jƒjƒ}t|jƒjƒƒ}|jƒj dddt ƒj ƒ}|j ƒj dddt ƒj ƒ}|jƒ|j ƒj dddt ƒj ƒ}dg} | j dd|ƒ| j d|ƒ| j d |d ƒ| j d |d ƒ| j d |d ƒ| j d|d ƒ| j d |d ƒ| j d |d ƒ| j d|d ƒ| j d |d ƒ| j d |d ƒ|jd kr†| j dt|jƒdƒ|r†xt|jƒD]‰} |j| ƒ} |j| ƒ} |j| ƒ} |j| ƒjƒ}| j dddt ƒj ƒ}| j dddt ƒj ƒ}| j dddt ƒj ƒ}| j d| d ƒ| j dd|ƒ| j d |d ƒ| j d |d ƒ| j d |d ƒ| j d|d ƒ| j d |d ƒ| j d |d ƒ| j d|d ƒ| j d |d ƒ| j d |d ƒqóWq†n|dj| ƒIJdS(Niÿÿÿÿtformats% 5.4ftone_row_per_linesCrystal:s Unit cell: s*(%5.3f, %5.3f, %5.3f, %5.3f, %5.3f, %5.3f)s Space group: s U matrix: is iis B matrix: s A = UB: s A sampled at s scan pointss Scan point #%i:s (R tsyststdoutt get_unit_cellt parameterststrtget_space_grouptinfotget_Utmathematica_formtTruet splitlinestget_BtappendR!trangetget_A_at_scan_pointtget_B_at_scan_pointtget_U_at_scan_pointtget_unit_cell_at_scan_pointtjoin(Rtshow_scan_varyingtoutR$tuctsgtumattbmattamattmsgtiRtBtU((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/model/crystal.pytshowEsd    cC sBddlm}|ƒ}|jd|ƒ}|jdƒ|jƒS(Niÿÿÿÿ(tStringIOR8i(t cStringIORCRBtseektread(RRCtsR>((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/model/crystal.pyt__str__zs   c C st|jƒ|jƒ|jƒ|j|dtƒ|j|dtƒ|j|dtƒf}t|ƒ|_|jƒdS(NR(tlengthtangleR-Rt_ucR(RRRRtcell((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/model/crystal.pyRs   cC s%|j|ƒ}t|ƒ}|jƒS(N(R3RR(RttR@tco((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/model/crystal.pyR5‹s cC s%tj|jjƒƒjƒ|_dS(N(RRRKtfractionalization_matrixt transposeR(R((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/model/crystal.pyRscC s)|jƒst‚||_|jƒdS(N(tis_r3_rotation_matrixR RR(RRA((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/model/crystal.pytset_U“s cC s|jS(N(R(R((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/model/crystal.pyR+œscC s|jS(N(R(R((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/model/crystal.pyR/ŸscC sMt|tƒ}|jƒ|_tj|jjƒƒjƒ|_|j ƒdS(N( RR-RRKRRRORPRR(RR@RN((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/model/crystal.pytset_B¢s!cC s8g|D]}tj|ƒ^q|_t|ƒ|_dS(s¡Set the setting matrix A at a series of checkpoints within a rotation scan. There would typically be n+1 points, where n is the number of images in the scan. The first point is the state at the beginning of the rotation scan. The final point is the state at the end of the rotation scan. Intervening points give the state at the start of the rotation at the 2nd to the nth image. This data is held separately from the 'static' U and B because per-image setting matrices may be refined whilst restraining to a previously determined best-fit static UB. The values will be reset if any changes are made to the static U and B matrices. N(RRt_A_at_scan_pointstlenR (RtA_listte((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/model/crystal.pytset_A_at_scan_points¬s%cC s |j|S(spReturn the setting matrix with index t. This will typically have been set with reference to a particular scan, such that it equals the UB matrix appropriate at the start of the rotation for the image with array index t :param t: index into the list of scan points. :returns: The A matrix at index t :rtype: :py:class:`scitbx.matrix.sqr` (RT(RRM((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/model/crystal.pyR2½s cC s*|j|ƒ}|j|}||jƒS(sµ Return orientation matrix with index t. :param t: index into the list of scan points. :returns: The U matrix at index t :rtype: :py:class:`scitbx.matrix.sqr` (R3RTR(RRMtBttAt((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/model/crystal.pyR4Ìs  cC sA|j|}td|jƒjƒƒ}tj|jƒƒjƒS(s» Return orthogonalisation matrix with index t. :param t: index into the list of scan points. :returns: The B matrix at index t :rtype: :py:class:`scitbx.matrix.sqr` torthogonalization_matrix(RTRRPRRRRO(RRMRZR9((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/model/crystal.pyR3Ûs cC s,|j|}td|jƒjƒƒ}|S(s Return unit cell with index t. :param t: index into the list of scan points. :type t: int :returns: The unit cell at index t :rtype: :py:class:`cctbx.uctbx.unit_cell` R[(RTRRPR(RRMRZR9((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/model/crystal.pyR5ês cC sd|_d|_dS(Ni(R R RT(R((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/model/crystal.pyRús cC s|jS(sO :returns: The unit cell :rtype: :py:class:`cctbx.uctbx.unit_cell` (RK(R((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/model/crystal.pyR&þscC s ||_dS(sL :param space_group: :type space_group: cctbx.sgtbx.space_group N(R (RR((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/model/crystal.pytset_space_groupscC s|jS(s[ :returns: The current space group :rtype: :py:class:`cctbx.sgtbx.space_group` (R (R((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/model/crystal.pyR) scC s2ddlm}|tkr+|jd|S|jS(sì Get the current value of the mosaicity. :param deg: If True, return the mosaicity in degrees, else return the mosaicity in radians. :type deg: bool :returns: The mosaicity :rtype: float or None iÿÿÿÿ(tpig€f@(tmathR]R-R(RRR]((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/model/crystal.pyt get_mosaicitys  cC s=ddlm}|tkr0||d|_n ||_dS(s- Update the value of the mosaicity. :param mosaicity: The mosaicity :type mosaicity: float :param deg: If True, assume the mosaicity is given in degrees, else assume it is given in radians. :type deg: bool :returns: The mosaicity :rtype: float or None iÿÿÿÿ(R]g€f@N(R^R]R-R(RRRR]((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/model/crystal.pyR #s  cC s|j|jS(N(RR(R((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/model/crystal.pytget_A5sgH¯¼šò×z>cC s‚t|tƒr~t|j|jƒ}tgt|j|jƒD]\}}t||ƒ^q>ƒ}tgt|j|jƒD]\}}t||ƒ^q|ƒ} |jdkrJ|j|jkrÆt Sxt |jƒD]m} |j | ƒ|j | ƒ} } tgt| | ƒD]\} }t| |ƒ^qƒ}||krÖt SqÖWn||ko}||ko}| |ko}|j |j kSt S(Ni(t isinstanceRtabsRtsumtzipRRR!tFalseR1R2R tNotImplemented(Rtothertepst d_mosaicitytu1tu2td_Utb1tb2td_BR?tA1tA2ta1ta2td_A((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/model/crystal.pyt__eq__8s">>8    g{®Gáz„?gš™™™™™é?gð?cC s‰|jƒ|jƒkrtS|jdtƒ|jdtƒ}}t||ƒt||ƒ}} |dkr| dkr“tSn|| |kr“tS|jƒ|jƒ} } | jƒs¾t‚| jƒsÐt‚| | j ƒ} | j ƒ} | j dtƒd}t |ƒ|krtS|j ƒ|j ƒ}}|j|d|d|ƒsPtS|jdkr…|j|jkrutSx t|jƒD]ù}|j|ƒ|j|ƒ} } | jƒs¼t‚| jƒsÎt‚| | j ƒ} | j ƒ} | j dtƒd}t |ƒ|krtS|j|ƒ|j|ƒ}}t|tƒjƒ}t|tƒjƒ}|j|d|d|ƒs…tSq…WntS(s, Test similarity of this to another crystal model :param other: the crystal model to test against :type other: crystal_model :param angle_tolerance: maximum tolerated orientation difference in degrees :type angle_tolerance: float :param mosaicity_tolerance: minimum tolerated fraction of the larger mosaicity for the smaller mosaicity to retain similarity :type mosaicity_tolerance:float :param uc_rel_length_tolerance: relative length tolerance to pass to unit_cell.is_similar_to :type uc_rel_length_tolerance: float :param uc_abs_angle_tolerance: absolute angle tolerance to pass to unit_cell.is_similar_to :type uc_abs_angle_tolerance: float :returns: Whether the other crystal model is similar to this :rtype: bool Rgitrelative_length_tolerancetabsolute_angle_tolerance(R)ReR_R-tmintmaxR+RQR RPt%r3_rotation_matrix_as_unit_quaterniont!unit_quaternion_as_axis_and_angleRbR&t is_similar_toR!R1R4R3RR(RRgtangle_tolerancetmosaicity_tolerancetuc_rel_length_tolerancetuc_abs_angle_tolerancetm_atm_btmin_mtmax_mtU_atU_btR_abtuqRJtuc_atuc_bR?tB_atB_b((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/model/crystal.pyR|IsT%        cC sL|jƒjƒ}tj|d ƒtj|dd!ƒtj|dd!ƒfS(s™ Get the real space unit cell basis vectors. :returns: Real space unit cell basis vectors :rtype: list of :py:class:`scitbx.matrix.col` iii (R`RRR(RtA_inv((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/model/crystal.pytget_real_space_vectorsŽsc C sû|jƒjƒ}tj|jƒjƒjƒjƒƒ}||}|d }|dd!}|dd!}t|||d|j ƒj |ƒd|j ƒƒ}|j dkr÷|jƒ} |j g|jD]} | | ^qŃ|j |j ks÷t‚n|S(sI Returns a copy of the current crystal model transformed by the given change of basis operator to the new basis. :param change_of_basis_op: The change of basis operator. :type cctbx.sgtbx.change_of_basis_op: :returns: The crystal model transformed to the new basis. :rtype: :py:class:`crystal_model` iii RRi(R`RRRtc_invtrRPt as_doubleRR)t change_basisR_R!RXRTR ( Rtchange_of_basis_opt direct_matrixtMtnew_direct_matrixRRRRgtM_invRZ((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/model/crystal.pyR’šs$'       !cC sX|j|_|j|_|j|_|j|_|j|_|j|_|j|_dS(sš Update the current crystal model such that self == other. :param other: A crystal model to update self with. :type other: crystal_model N(RRRTR R RKR(RRg((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/model/crystal.pytupdateÍs      N("t__name__t __module__t__doc__R R-RtpropertyR!ReRBRHRR5RRRR+R/RSRXR2R4R3RR&R\R)R_R R`RuR|RŽR’R˜(((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/model/crystal.pyRs@$5                   C 3c C s|stdƒ}ntj|ƒ}|jƒ}|r||jƒ}tj|jdd!ƒ}|d|jƒ}||9}n|r||9}n|jdd!}|jdd!}|jdd!} tjd ƒ} | |} | |} | | } t| | | d|ƒS( s Create a crystal_model from a Mosflm A matrix (a*, b*, c*); N.B. assumes the mosflm coordinate frame:: /! Y-axis / ! ^ / ! ! / ! ! / ! ! / / Xd ! ! / / * ^ ! ! / ! 3 ! ! !/ X-ray beam ! ! ! /------------------------/--!---->X-axis / ! / *1! <-/- ! / ! / \+ve phi ! Yd / / / ! 2 / / ! * / Z-axis Ys ^ _/ Rotation ! /| Xs axis !/ O Also assume that the mosaic spread is 0. :param mosflm_A_matrix: The A matrix in Mosflm convention. :type mosflm_A_matrix: tuple of floats :param unit_cell: The unit cell parameters which are used to determine the wavelength from the Mosflm A matrix. :type unit_cell: cctbx.uctbx.unit_cell :param wavelength: The wavelength to scale the A matrix :type wavelength: float :param space_group: If the space group is None then the space_group will be assigned as P1 :type space_group: cctbx.sgtbx.space_group :returns: A crystal model derived from the given Mosflm A matrix :rtype: :py:class:`crystal_model` tP1iiii iiÿÿÿÿR( iiiiiiiÿÿÿÿii( R RRRR'RRRIR(tmosflm_A_matrixRt wavelengthRtA_starRtunit_cell_constantstatbtctrotate_mosflm_to_imgCIFt_at_bt_c((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/model/crystal.pyt crystal_model_from_mosflm_matrixÜs&,       N(t __future__RtscitbxRt cctbx.uctbxRt cctbx.sgtbxRR Rtcctbx.crystal_orientationRtobjectRR R©(((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/dxtbx/model/crystal.pytsÿÖ