xTc @ sddlmZddlZddlmZddlZddlmZddlm Z ddl Zddl m Z ddl Z ddlZdddZdddZd Zd Zddd Zed Zeed ZdddZdddZddddddZdddddddddZddeedZeddZgdZdZ dZ!dZ"dZ#dZ$dZ%dZ&dZ'dZ(dddd d!Z)d"Z*d#Z+d$Z,dS(%i(tdivisionN(tflex(tmonomer_library(tmatrix(txraycC sg}| r"|r"|j}n|rxW|D]L}xC|jD]8}|jttd|jjt|jjq?Wq/Wntj |S(s  Concatenate rotation angles, corresponding to the rotation matrices and scaled translation vectors to a single long flex.double object Args: transforms_obj : (mmtbx.refinement.minimization_ncs_constraints ncs_group_object) containing information on Rotation matrices (lists of objects matrix.rec) and Translation vectors (lists of objects matrix.rec) ncs_restraints_group_list : a list of ncs_restraint_group objects Returns: flex.double : [(alpha_1,beta_1,gamma_1,Tx_1,Ty_1,Tz_1)...] trotation( tget_ncs_restraints_group_listtcopiestextendtlisttrotation_to_anglestrtelemsttRtdouble(ttransforms_objtncs_restraints_group_listtxtgrttr((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_utils.pytconcatenate_rot_tran s  cC sg}g}| r(|r(|j}n|rvxE|D]:}x1|jD]&}|j|j|j|jqEWq5Wn||fS(s Get rotations and translations vectors from ncs_restraints_group_list or transforms_obj Returns: r (list): list of rotation matrices t (list): list of translation vectors (RRtappendR R (RRR R tnrgR((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_utils.pyt get_rotation_translation_as_list&s   cC st|jt|ks!tt|t|ks?txFt|j||D]/\}}}||j|_||j|_qUW|S(sV Update transforms_obj with the rotation matrices (rm) and translation vectors (tv) (tlenttransform_ordertAssertionErrortzipt ncs_transformR R (RtrmttvRR R ((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_utils.pytupdate_transforms;s !%cC s~t|t|kstg}xS|D]K}x5|jD]*}|jd|_|jd|_q;W|j|q+W|S(sa Update ncs_restraints_group_list with the rotation matrices (rm) and translation vectors (tv) i(RRRtpopR R R(RRRtnew_listRR((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_utils.pyt update_ncs_restraints_group_listEs c C s7t|t| kst|r4|j}n|r3d}x|D]}g}x|jD]}||d|dd!\}}} tjjd|d|d| dt} tj ||dd|dd!d } | j |_ | |_ |j ||d7}q]W||_qGW|r,|j||S|Snd S( sx Convert the refinable parameters, rotations angles and scaled translations, back to rotation matrices and translation vectors and updates the transforms_obj (ncs_restraints_group_list) Args: x : a flex.double of the form (theta_1,psi_1,phi_1,tx_1,ty_1,tz_1,.. theta_n,psi_n,phi_n,tx_n/s,ty_n/s,tz_n/s). where n is the number of transformations. transforms_obj : (ncs_group_object) containing information on Rotation matrices, Translation vectors and NCS ncs_restraints_group_list : a list of ncs_restraint_group objects Returns: The same type of input object with converted transforms iiitthetpsitphitdegiN(ii(tboolRRRtscitbxt rigid_bodyt rb_mat_xyztFalseRtrectrot_matR R Rt&update_using_ncs_restraints_group_list( RRRtiRRRR#R$R%trotttran((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_utils.pytupdate_rot_tranQs, " )   c C st|ttjs-tj|}n|jd\ }}}}}}}} } |d krtj|} tj| tj| | tj| } tj| tj| |tj| } nv|dkrtj d} tj||} d} nB|dkr9tj d} tj| |} d} n t dtj| | | f}|rd|tj }|jd}n|S( sO Get the rotation angles around the axis x,y,z for rotation r Such that r = Rx*Ry*Rz Those angles are the Tait-Bryan angles form of Euler angles Note that typically there are two solutions, and this function will return only one. In the case that cos(beta) == 0 there are infinite number of solutions, the function returns the one where gamma = 0 Args: r : (flex.double) of the form (Rxx,Rxy,Rxz,Ryx,Ryy,Ryz,Rzx,Rzy,Rzz) deg : When False use radians, when True use degrees Returns: angles (flex.double): (alpha, beta, gamma) rotation angles around the x,y,z iiiiisCan't calculate rotation anglesii(ii( t isinstancettypeRRtroundtmathtasintatan2tcostpitArithmeticError(RR&tRxxtRxytRxztRyxtRyytRyztRzxtRzytRzztbetatalphatgammatangles((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_utils.pyR zs** -0      c C st|dkst|\}}}tjjd|d|d|d|}|j}|rid}nd}|r|j|jStj |j|SdS( ss Calculate rotation matrix R, such that R = Rx(alpha)*Ry(beta)*Rz(gamma) Args: angles_xyz : (flex.double) (alpha,beta,gamma) deg : (bool) When False use radians, when True degrees rotation_is_tuple : (bool) when False, return flxe.double object, when True return tuple Returns: R : (tuple or flex.double) the components of a rotation matrix iR#R$R%R&iiN( RRR(R)R*R-R5R RR( t angles_xyzR&trotation_is_tupleRFRERGR0tRR/((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_utils.pytangles_to_rotations '  gQ?g?cC stj}xtdt|dD]}|jtj||d||jtj||d||jtj||d||jtj||d||jtj||d||jtj||d|q%W|S(s Shake rotation matrices and translation vectors of a rotation matrices and translation vectors from the MTRIX records in a PDB file. Args: x (flex.double): [(alpha_1,beta_1,gamma_1,Tx_1/s,Ty_1/s,Tz_1/s)...] shake_angles_sigma (float): the sigma (in radians) of the random gaussian shaking of the rotation angles shake_translation_sigma (float): the sigma (in angstrom) of the random gaussian shaking of the translation Return: new_x (flex.double): The shaken x iiiiiii(RRtxrangeRRtrandomtgauss(Rtshake_angles_sigmatshake_translation_sigmatnew_xR/((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_utils.pytshake_transformationss !!!!!%c C st|t| kst|r4|j}ng}tj|}d}x|D]}|j|j}|j} tj|jgd| } |tjt | | } x5|j D]*} |j| j } | | jkstt | j}| j | }t j|}||d|dd!\}}}tjjd|d|d|dt}||jjj}||jjj}||jjj}|j|||g|j||d7}qWqVWtj|S( s| Compute gradient in respect to the rotation angles and the translation vectors. R = Rx(the)Ry(psi)Rz(phi) Args: grad_wrt_xyz (flex.double): gradients with respect to xyz. ncs_restraints_group_list: list containing ncs_restraint_group objects transforms_obj (ncs_group_object): containing information in rotation matrices and to which chains they apply xyz_asu (flex.vec3): The coordinates sites cart of the complete ASU x (flex double): The angles, in the form (theta_1,psi_1,phi_1,tx_1,ty_1,tz_1,.. theta_n,psi_n,phi_n,tx_n/s,ty_n/s,tz_n/s) Returns: g (flex.double): the gradient iiiiR#R$R%R&(R'RRRt vec3_doubletselecttmaster_iselectiontsizetsumR Rt iselectionttranspose_multiplyRtsqrR(R)R*R+tr_thet transposettracetr_psitr_phiRR(t grad_wrt_xyztxyz_asuRRRtgR/Rtxyz_ncs_transformtxyz_lentmu_ctxyz_cmtnrg_copytgrad_ncs_wrt_xyzt grad_wrt_ttmR#R$R%R0tg_thetg_psitg_phi((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_utils.pytcompute_transform_grads6   "  cC s |rt|dr!|j}n |s-tt|drO|jj|St|dr}|jjj|}|jSt|ds|r|jj}|j|SnW|r|j|S|r|jj|}|jS|r|j}|j|SdS(s Args:: ncs_obj: an object that contains fmodel, sites_cart or xray_structure and an atom selection flags for a single NCS copy. Returns: (flex.vec3): coordinate sites cart of the single NCS copy textended_ncs_selectiont sites_carttfmodeltxray_structureN(thasattrRpRRqRURrRs(tncs_objRrRsRqRpt xrs_one_ncs((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_utils.pytget_ncs_sites_carts(      c C s|}d} |rl|} | j}| j}| j}| j}| j}| j}t| drl| j} qln| st d|d|} nt |st dt |st d|||gj t dkst d|gk} |j} |r| jjdd nO|r.| jjn9|rg| rgtd|} td | d d d d} n| jd| jdt | jjjdt|s|r tjd| jjdt tj| jdt j}|jd| jjdt j }n|rddl!}|j"j#j$}|j%j&}|jd| jjdt j }tjd| jjdt | jdt j'}|j(d| jd|d|j)dtdt j }n|r<| r<t*d|j'd|d| jjd | }t*d|j'd|d| jjd | }nd}|j+}|j+}|dkrs||}nt,|d }|S(!sN Calculates weights for refinements by slightly shaking the minimized parameters and taking the ratio: (restraint manager grad norm / parameters gradient norm) When calling this function during refinement macro cycle, the minimized object, "minimized_obj" , may contains fmodel, restraints_manager, refinement type info (sites, transformations, u_iso) and ncs_restraints_group_list. Args: fmodel : F-model object restraints_manager: Restraints manager object sites (bool): Refine by sites u_iso (bool): Refine using u_iso transformations (bool): Refine using transformations rotations, translations (matrix objects): ncs_restraints_group_list: list of ncs_restraint_group objects refine_selection (flex.size_t): selection of all ncs related copies and non ncs related parts to be included in selection (to be refined) minimized_obj:Minimization object containing all the other parameters above Returns: weight (int): Example: >>>get_weight(minimized_obj=minimized_obj) or >>>get_weight(fmodel=fmodel, restraints_manager=grm, sites=sites, transformations=transformations, u_iso=u_iso, ncs_restraints_group_list=ncs_restraints_group_list, refine_selection=refine_selection) RpRtrefine_selectionsF-model is not provideds$F-restraints_manager is not providedisRefinement type Errort mean_distanceg333333?RRPgQ?RQg?Rst update_f_calctstatet scattererstsiteRqtcompute_gradientsiNtu_isot parameterstuse_u_local_onlytuse_hdRaRbg?gg.A(-tNoneRrtgrmtsitesttransformationsRRRtRptget_extended_ncs_selectionR'RtcounttTruet deep_copyRstshake_sites_in_placet shake_adpRRStupdate_xray_structureR|tflags_set_gradsR+Rtset_scatterer_grad_flagsRRTt(one_time_gradients_wrt_atomic_parameterstpackedtenergies_sitesRqt gradientstmmtbx.refinement.adp_refinementt refinementtadp_refinementtadp_restraints_master_paramstextracttisot as_doubletenergies_adp_isoRRotnormtmin(Rrtrestraints_managerRRRRRxt minimized_objRRptmothave_transformstfmdcRtgxctgctmmtbxttemptiso_restraintstweighttgc_normtgxc_norm((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_utils.pyt get_weight;s1       *                         c C sA||gjddks!ttjj}tjj}|rT|j}nd}tjjd|d|d|d|dt }|j dt dd }t j jd |d |} |r9gt|D](} d | kr| d dkr| ^q} d} tg| D]} t| | ^q} | | fS| SdS(s Generate restraint manager from a PDB file or a PDB string Args: return_data_num (bool): when True, return the number of restraints it mon_lib_srvtener_libt file_namet raw_recordstforce_symmetryt show_energiestplain_pairs_radiusg@tgeometryt normalizationtproxiesit_cS s d|dS(NRt.s .__sizeof__()s geometry.((R((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_utils.pytsN(RRRRtserverRt splitlinestpdb_interpretationtprocessRtgeometry_restraints_managerR+Rt restraintstmanagertdirRXteval(t pdb_file_namet pdb_stringRtreturn_data_numRRt pdb_linestppfRRRRtlen_strtn_data((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_utils.pytget_restraints_managers.!     ; + c C stjdg|}|j||t|rJtd|d|}nx|D]z}tj||j}x\|jD]Q} tj|| j} |j|} | j j | | j } |j| | qvWqQW|rtj|j dStj|SdS(sM Apply transformation to ncs_coordinates, and round the results if round_coordinates is True Args: ncs_coordinates (flex.vec3): master ncs coordinates ncs_restraints_group_list: list of ncs_restraint_group objects total_asu_length (int): Complete ASU length extended_ncs_selection (flex.size_t): master ncs and non-ncs related parts center_of_coordinates : when not None, contains the center of coordinate of the master for each ncs copy Returns: (flex.vec3_double): Asymmetric or biological unit parts that are related via ncs operations itshiftsRiN(iii( RRTt set_selectedR'tshift_translation_back_to_placeRVRRYRUR R R R5( tncs_coordinatesRttotal_asu_lengthRptround_coordinatestcenter_of_coordinatestasu_xyzRtmaster_ncs_selectiontncs_copytcopy_selectiontncs_xyzt new_sites((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_utils.pytapply_transformss    c C st|}t}t}xZ|D]R}|j}|jt|x-|jD]"}|j}|jt|qQWq%W|r||B}d} t|| st| ||} tjt | Stjt |SdS(s` Args: ncs_restraints_group_list: list of ncs_restraint_group objects refine_selection (flex.siz_t): of all ncs related copies and non ncs related parts to be included in selection (to be refined) Returns: (flex.siz_t): selection of all ncs groups master ncs selection and non ncs related portions that are being refined s7refine_selection does not contain all ncs related atomsN( tsetRVtupdateRRYR'RRtsize_tR ( RRxttotal_master_ncs_selectionttotal_ncs_related_selectionRRRt asu_selectiontall_ncstmsgRp((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_utils.pyRs        c C st}t}xZ|D]R}|j}|jt|x-|jD]"}|j}|jt|qEWqW|j|tjt|}tj||} | S(s Args: ncs_restraints_group_list (list): list of ncs_restraint_group objects asu_size (int): the total size of the ASU Returns: selection (flex.bool): selection of all ncs related atom in the ASU ( RRVRRRYRRR R'( Rtasu_sizeRRRRRRttst selection((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_utils.pytget_ncs_related_selection8s      cC st|rt|}d}xj|D]_}xV|jD]K}||}|d7}|jj||j|}tj|d|_q5Wq%Wn|S(sw Add shifts to the translation component of ncs_restraints_group_list towards the center of coordinates Args: shifts (list): [mu_1, mu_1, mu_2...] where the mu stands for the shift of the master copy to the coordinate center mu is (dx,dy,dz) ncs_restraints_group_list (list): ncs_restraints_group_list Returns: ncs_restraints_group_list (list): ii(R'tncs_restraints_group_list_copyRR R R Rtcol(RRR!R/RRtmuR ((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_utils.pytshift_translation_to_centerOs     !cC st|rd}t|}xp|D]_}xV|jD]K}||}|d7}||jj||j}tj|d|_q5Wq%Wn|}|S(s shifts to the translation component of ncs_restraints_group_list from the center of coordinates back to place Args: shifts (list): [mu_1, mu_1, mu_2...] where the mu stands for the shift of the master copy to the coordinate center mu is (dx,dy,dz) ncs_restraints_group_list: ncs_restraints_group_list Returns: new_list (list): list of ncs_restraints_group objects ii(R'RRR R R RR(RRR/R!RRRR ((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_utils.pyRhs     !c C sg}|j}x{|D]s}|j}|j|}tj|jt|}tj|j g}x|j D]}|j |quWqW|S(s calculate the center of coordinate for the master of each ncs copy Args: xray_structure ncs_restraints_group_list Returns: shifts (list): [mu_1, mu_1, mu_2...] where the mu stands for the shift of the master copy to the coordinate center mu is (dx,dy,dz) ( RqRVRURRRXRRRTR RR( RsRRRRRt master_xyztmu_mR((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_utils.pytget_ncs_gorups_centerss    c C sddlm}ddlm}g}xr|D]j}||j}xE|jD]:}|d|jd|jd|j}|jj|qLW|j|q-W|S(s Deep copy of ncs_restraints_group_list Args: ncs_restraints_group_list: list of ncs_restraint_group Returns: new_list: a deep copy of ncs_restraints_group_list i(tncs_restraint_group(Rtcopy_iselectionR0R1( tiotbx.ncs.ncs_preprocessRRRVRRYR R R(RRRR!Rtnew_nrgtncst new_ncs_copy((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_utils.pyRs     c st|tjr!|j}nt|}t|}xw|D]o}t|j}gtt|jD]\}}||f^qk}|j |fd|D} x|j D]} t| j} gtt| jD]\}}||f^q} | j |fd| D} | j | t| sPqqWt |j| \|_}t ||}x;|j D]0} t | j| \| _}t ||}q{Wq@W|S(s4 Modifies the selections of master and copies according the "selection" - Keep the order of selected atoms - Keep only atoms that appear in master and ALL copies Also modify "selection" to include ncs related atoms only if selected in both master and ALL ncs copies (The modified selection is not returned in current version) Args: ncs_restraints_group_list (list): list of ncs_restraints_group objects selection (flex.bool or flex.size_t): atom selection Returns: new_nrg_list (list): list of modified ncs_restraints_group objects c s(h|]\}}|kr|qS(((t.0tpostindx(tm_in_sel(sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_utils.pys s c s(h|]\}}|kr|qS(((RRR(t copy_in_sel(sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_utils.pys s (R3RR'RYRRRVt enumerateR t intersectionRtintersection_updatetselected_positionstremove_items_from_selection(RRtsel_sett new_nrg_listRRkRRtm_listtcommon_selection_posRtctc_listt include_sett not_included((RRsA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_utils.pytncs_groups_selections2   44  cC st|tjstt|tr?tjt|}nt|tr`tj|}ntj|j|}|}|j||j|fS(s Returns only the selected indices in the positions specified in "positions" keeping the order Args: selection (flex.size_t): Atoms selection positions (set or list): the allowed positions in the selections Returns: (flex.size_t, flex.size_t): (selected atoms, atoms, not selected) Examples:: >>>a = flex.size_t([1,2,5,6,4]) >>>pos = {0,3,4} >>>s,d = selected_positions(a,pos) >>>list(s) [1,6,4] >>>list(d) [2,5] ( R3RRRRR R'RWRU(Rt positionstincludet not_include((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_utils.pyRscC sJt|}t|}g|D]}||kr|^q}tj|S(sk Remove a set of atoms from "selection" Args: selection (flex.size_t): atom selection remove (flex.size_t): atoms to remove from selection Returns: (flex.size_t): modified atom selection Examples:: >>>a = flex.size_t([1,2,5,6,4]) >>>r = flex.size_t([2,5]) >>>s = remove_items_from_selection(a,r,10) >>>list(s) [1,6,4] (R RRR(RtremoveRt new_selection((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_utils.pyRs  %c C sdt|tstt|t|ks3tx*t||D]\}}|dkraqCn|d}|j|j|j|_|j|_|j|jj }|j|_|j|j |j|j }|j|_ xvt |jD]e\}}||kr|j|j||j|j |j|_ |j|j||j|_qqWqCW|S(sE Switch master NCS copy with one of the copies, as specified in the new_masters Args: ncs_restraints_group_list: list of ncs restraints group objects new_masters (list of integers): the number of the copy, in each group, that will become the new master Returns: Modified ncs_restraints_group_list ii( R3R RRRRRYRVR R]R R( Rt new_mastersRRtc_iR R R/R((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_utils.pytchange_ncs_groups_masters   '$- ,)g?c C sg}tjjjd|d|d|d|}xv|D]n}g}|j|jx!|jD]} |j| jq]W|jd|} |j| j t | q7W|S(ss Finds the copy with best map correlation in each ncs group Args: ncs_restraints_group_list: list of ncs restraints group objects xray_structure (object): fmodel (object): map_data (object): d_min (float): min data resolution Returns: best_list (list of int): list of the copy with the best map correlation. (the master copy is 0) RsRrtmap_datatd_mint selections( Rtmapst correlationt%from_map_and_xray_structure_or_fmodelRRVRRYtcctindextmax( RRsRrR R t best_listtmpRRRR((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_utils.pyt)get_list_of_best_ncs_copy_map_correlation3s   cC s:t|s6t|jj}tj|}n|S(sD populate refine_selection with all atoms if no selection is given (R'trangeRqRWRR(RxRstselection_list((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_utils.pytget_refine_selectionWs c C s|jj}|jj}|d|}|j|}|j}tt|}||7}tj ||}|jS(s Convert iselection of NCS related atoms in the NCS copy to the ASU iselection Args: ncs_len (int) ncs_chain_id (str) iselection_ncs (flex.size_t) hierarchy_asu hierarchy object) Returns: iselection_asu (flex.size_t) schain ( tatomsRWtatom_selection_cacheRRURYRR RR'( tiselection_ncst ncs_chain_idt hierarchy_asutasu_lent atom_cachetselt hierarchy_ncstoffsettselection_bool((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_utils.pytiselection_ncs_to_asu_s   cC s?|j}|jd|}tt|j}||S(s Convert iselection of NCS related atoms in the NCS copy to the ASU iselection Args: ncs_chain_id (str) iselection_asu (flex.size_t) hierarchy_ncs (hierarchy object) Returns: iselection_ncs (flex.size_t) schain (RRRR RY(tiselection_asuRRR!t ph_ncs_selectt chain_start((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_utils.pytiselection_asu_to_ncsvs (-t __future__Rtmmtbx.maps.correlationRtscitbx.array_familyRtmmtbx.monomer_library.serverRR(Rtscitbx.rigid_bodytcctbxRRNR6RRRRR"R2R+R RLRSRoRwRRRRRRRRRRRRRR RRR&R*(((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ncs/ncs_utils.pytsp        ) 2  2 ! ' %      ,   $