|xTc@ sddlmZddlmZddlmZddlmZddlm Z ddl m Z ddl m Z ddlmZdd lmZdd lZdd l mZdd lmZdd lmZdd lZdd lZdd lZdd lZdd lZedZdefdYZdZ dZ!dZ"dZ#dddZ$dddZ%dZ&dZ'dZ(dZ)dZ*dZ+dZ,d Z-d!Z.d"Z/d#Z0d$Z1d%Z2e3e3e4d&d'd(Z5d)Z6d*Z7d+Z8d,Z9d-Z:d.Z;d/Z<d0Z=d1Z>d2Z?d3fd4YZ@d5efd6YZAd7efd8YZBd9efd:YZCd;efd<YZDd S(=i(tdivision(tget_ncs_object_from_pdb(tapply_transforms(t eigensystem(tflex(t superpose(t ncs_search(tSorry(tparseN(tncs(tmatrix(tpdbs0 ncs_group .multiple = True { master_selection = '' .type = str .help = 'Residue selection string for the complete master NCS copy' copy_selection = '' .type = str .help = 'Residue selection string for each NCS copy location in ASU' .multiple = True } tncs_group_objectcB seZdZd!d!d!d!d!d!d!d!dddded!d!eeedeedddZd!d!d!dZd!d!d!eddZeeededdd Z d Z d!ddded!ged Z d Z d Z dZdZdZdZdddZdZdZdZedZdZd!dZdZdZdZd!ed!d!d!d!d!d!eejd Zd!d!d!d!ejeeedZeejdZ ed Z!RS("cC sd|_i|_i|_i|_i|_i|_d|_i|_i|_ g|_ i|_ d|_ d|_ tj|_tj|_g|_t|_t|_g|_t|_g|_d|_i|_t|_d|_dS(s process MTRIX, BOIMT and PHIL parameters and produce an object with information for NCS refinement Argument: transform_info: an object produced from the PDB MTRIX or BIOMT records ncs_refinement_params: an object produced by the PHIL parameters itN(tNonettotal_asu_lengthtncs_to_asu_maptasu_to_ncs_maptncs_to_asu_selectiontncs_copies_chains_namesttr_id_to_selectiontnumber_of_ncs_groupst ncs_group_mapt ncs_transformttransform_chain_assignmentttransform_to_ncstncs_atom_selectiontncs_selection_strRtsize_ttnon_ncs_region_selectiontall_master_ncs_selectionstncs_chain_selectionttupletmodel_unique_chains_idstsett selection_idstmodel_order_chain_idsttransform_to_be_usedttransform_ordert hierarchytcommon_res_dicttFalsetfound_ncs_transformstmessages(tself((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyt__init__'s2                      R g{Gz?g?i cC sd}|r%tjj|d}n|rXd}t|tjjjst|n-|r|j }tjjj ||}n|j d#krtjjd|}n@| r|s| r|r|}n| }tjjd |}n|r;| r;|jj d d }|j dkr,d"}q;t|}n|sG|rt|sY|r~|jd |d |d|d|q||gjtdkst|jd |d|d|d|d|d|d|d|n|s|r |jd|d|d |d|n|j dks1| s1| s1|rh|jd|d| d| d| d |d|d| nO|r|jd |d|d|d|d|d|d|d|n td t|jdk|_|r|jdkrtd!n|jdkrt|jqnd"S($s Select method to build ncs_group_object order of implementation: 1) rotations,translations 2) transform_info 3) ncs_selection_params 4) ncs_phil_groups 5) spec file 6) iotbx.pdb.hierarchy.input object Args: ----- pdb_hierarchy_inp: iotbx.pdb.hierarchy.input transform_info: object containing MTRIX or BIOMT transformation info rotations: matrix.sqr 3x3 object translations: matrix.col 3x1 object ncs_selection_params: Phil parameters Phil structure ncs_group (multiple) { master_selection = '' copy_selection = '' (multiple) } ncs_phil_groups: a list of ncs_groups_container object, containing master NCS selection and a list of NCS copies selection file_name: (str) .ncs_spec or .mmcif or .pdb file name file_path: (str) spec_file_str: (str) spec format data spec_source_info: quiet: (bool) When True -> quiet output when processing files spec_ncs_groups: ncs_groups object as produced by simple_ncs_from_pdb cif_string: (str) string of cif type data use_cctbx_find_ncs_tools: (bool) Enable using of chain base NCS search use_simple_ncs_from_pdb: (bool) Enable using use_simple_ncs_from_pdb use_minimal_master_ncs: (bool) use maximal or minimal common chains in master ncs groups rms_eps (float): limit of rms difference between chains to be considered as copies error_msg_on (bool): When True, raise error if chains that are nearly the same length (but not exactly the same) and are NCS related. Raise error if NCS relations are not found process_similar_chains (bool): When True, process chains that are close in length without raising errors min_fraction_domain (float): Threshold for similarity between chains similarity define as: (number of matching res) / (number of res in longer chain) min_contig_length (int): minimum length of matching chain segments R is:pdb_hierarchy_inp is not iotbx.pdb.hierarchy.input object s.pdbs.cifs.mmcifs.gzt file_namet pdb_stringtepsg{Gz?tpdb_hierarchy_inpt rotationst translationsttransform_infoituse_cctbx_find_ncs_toolstuse_simple_ncs_from_pdbtuse_minimal_master_ncstprocess_similar_chainstmin_fraction_domaintmin_contig_lengthtrms_epstncs_selection_paramstncs_phil_groupss .ncs_spect file_pathtfile_strt source_infotspec_ncs_groupstquiets)Please provide one of the supported inputsNo NCS relation were found !!!N(s.pdbs.cifs.mmcifs.gz(tostpathtsplitextt isinstancetiotbxR R'tinputtAssertionErrortconstruct_hierarchytinput_hierarchy_pairtlowertprocess_mtrix_recordst as_pdb_stringRt$insure_identity_is_in_transform_infotncs_onlytbuild_ncs_obj_from_pdb_ncstcounttTruetbuild_ncs_obj_from_pdb_asutbuild_ncs_obj_from_philtbuild_ncs_obj_from_spec_fileRtlenR%R*R+(R,R1tpdb_inpR4R2R3R<R=R.R>t spec_file_strtspec_source_infot cif_stringRBRAR/R5R6R7R;t error_msg_onR8R9R:t extensiontmsgtpht input_str((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pytpreprocess_ncs_obj[sI'       !          c C s|jd|d}t|p(|o(|s:t||rY|jd|d|n|jd|t|j|_|jd|jd|j |_ xi|jD]^}d|j |}|j d d }||f|j | ASU mapping using PDB file containing a single NCS copy and MTRIX or BIOMT records Args: pdb_hierarchy_inp : iotbx.pdb.hierarchy.input transform_info : an object containing MTRIX or BIOMT transformation info rotations : matrix.sqr 3x3 object translations : matrix.col 3x1 object R1sNo NCS transform information R2R3R4ttransform_assignmenttunique_chain_namesschain t_itdtktvN(tcollect_basic_info_from_pdbtboolRIt'add_transforms_to_ncs_refinement_groupst process_pdbtget_transform_orderRRtmake_chains_namesR!RtsplitRt add_to_dictRtfinalize_pre_process( R,R1R4R2R3R^Rft selection_strtkey((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyRQs&$    cC s|rtt|tr$t|}ntjd|dt}|dj}|dgkshtd|j}n|d$k st|j dkstt }d} d} xY|D]Q} | j } |j j| t|| }td|d| } | d7} | d7} |jd | d | d | t| }|jd | d | d||j| | |g}x| jD]y}t||}td|d|}td| d|ddd|d|\}}}}|j|7_|jrd}n|j|| d7} t| }|j| ||td|d|d| dtd | d|}|jd|d|d| td|jd | d| d||_|jj| st||j|<|jj | |jd | d |d|quW||j!| <| |_"qWd |j dd!|_ x>t#dt$|j D]$}|j d"|j |d!7_ q=Wt%|j&|_'|j(d#|d$S(%s/ Build transforms objects and NCS <-> ASU mapping using phil selection strings and complete ASU Args: ncs_selection_params : Phil parameters pdb_hierarchy_inp : iotbx.pdb.hierarchy.input process_similar_chains (bool): When True, process chains that are close in length without raising errors min_fraction_domain (float): similarity between chains when looking for ncs relations Phil structure ncs_group (multiple) { master_selection = '' copy_selection = '' (multiple) } tsourcettrack_unused_definitionsiisCheck phil parameters... R R_Rqt ncs_selectiont ncs_group_idt transform_sntmasterstcopiesttr_idt master_ncs_pht ncs_copy_phR;idR8R9s=Master NCS and Copy are very poorly related, check selection.trotationt translationt serial_numtcoordinates_presenttrmsdt transform_idt transformt selection_idRR#t(t)s or (R1N()RFtstrRt master_philtfetchRStextractRIt ncs_groupRRR"tmaster_selectionRtappendtuniqueness_testtget_pdb_selectiontadd_identity_transformtformat_num_as_strtupdate_ncs_copies_chains_namestupdate_tr_id_to_selectiontcopy_selectiont get_rot_transR+tis_zeroRtbuild_transform_dicttupdate_ncs_group_mapRRthas_keyR#taddRRtrangeRWRlRRRp(R,R<R=R1R8R9t phil_paramt working_philtunique_selectionsRwRvtgrouptgnsR{Rrt asu_locationst asu_selectR|trttRR^terr_mttrti((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyRUs                         "g?c C s|r^tjd|jd|d|d|d|} |jjj|_|j| |nO|rtd|jd|j} | r| j } |j d|d | qnd S( s Build transforms objects and NCS <-> ASU mapping from a complete ASU Note that the MTRIX record are ignored, they are produced in the process of identifying the master NCS Args:: pdb_hierarchy_inp : iotbx.pdb.hierarchy.input use_cctbx_find_ncs_tools (bool): Enable using of chain base NCS search use_simple_ncs_from_pdb (bool): Enable using use_simple_ncs_from_pdb use_minimal_master_ncs (bool): indicate if using maximal or minimal NCS groups rms_eps (float): limit of rms difference between chains to be considered as copies process_similar_chains (bool): When True, process chains that are close in length without raising errors min_contig_length (int): minimum length of matching chain segments min_fraction_domain (float): Threshold for similarity between chains similarity define as: (number of matching res) / (number of res in longer chain) R_R:R9R7trmsd_epsRXR'R1RAN( Rtfind_ncs_in_hierarchyR'tatomstsizeRtbuild_ncs_obj_from_group_dictRRHt ncs_groupsRV( R,R1R5R6R7R;R8R:R9t group_dictt ncs_objectRA((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyRTs$       c" C s|}tjtg|j|_tjtg|j}t|}xt|D] \}}||}t} g|jdD]} t | D] } | ^qq} | j tj | } t || }g|j |t'dt(|jD]$}|j&d|j|d7_&qWt)|j*|_+|j,d|ndS(sv read .spec files and build transforms object and NCS <-> ASU mapping Arguments: spec file information using a file, file_str (str) of a source_info (str) quite: (bool) quite output when True pdb_hierarchy_inp: pdb hierarchy input spec_ncs_groups: ncs_groups object join_same_spec_groups: (bool) True: combine groups with similar transforms R R.tlinesR@RBiiiR}R~RRRvRRRRRR#RxRyRzRRs or (R1N(-RiRRCRDRt splitlinestisfileRIR tread_ncsRRFtget_ncs_group_selectiontchain_residue_idtlook_and_combine_groupsRRRt rota_matricesttranslations_orthtinverse_transformtroundt rmsd_listRRt is_identityRRSRRRRRR#RRRRRRRWRlRRRp(R,R.R>R?R@RBR1RAtjoin_same_spec_groupstfnRt spec_objectRwRvtgrtncs_group_selection_listtgst group_existRRtncs_copy_selectRRRRrR((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyRVs~  $               "cC sr|d}t}|j}|j}gt||D]\}}t||^q8} x/|jjD]\} \} } t|t| krqind gt| } t | }|j x|D]}|j |j }|j |j }xrt| D]d\}\}}| |d k r$qnt||||\}}|oI| }|r|| |t||D]-\}}|jdd|j|d|s cS si|]}d|qS(N(R(RR((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pys s is or chain schain N(R'tmodelstchainsR RR!RRRRRtpopR$RRRRIR( R,R1tmodelt chain_idsRtmodel_order_ch_idst ch_n_atomstchRRdtlast_ntselection_rangets((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyRhs&4 #cC sJt|j }t|j }t|j }|rF|rF|rF|jj}t|jj}|j|j |_|jj t }i}||kr||_ t jtg|} x|jD]} | jdd} |j| } |jj| s,d|| <| | B} | j|j| sRRRR*( RRIRGR Rdt"_mtrix_and_biomt_records_containerRRRRRRR( R,RPtresultt tr_sortedRrRRRt identity_testR.((R0sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pytbuild_MTRIX_objects        cC s4| s| riSt|}tttjt|}tttjt|}|j|j||}t||krH|t|}ttj |d}ttjttjttj } | | } tg| D]} | D]} | | ^qq} t| t|} | j|j | nt||ks`t || } t || }d|D}d|jD}x|jjD]\}}|d|}t|dkst |j}x?|dD]3}d|kr|jdd||d|s cS sh|]}t|qS((R(RR((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pys s is or schain R Rd(RWRR"tstringtascii_uppercasetascii_lowercaseRR+tmathtsqrttdigitstextendRIRR%RRR R(R,RbRcttotal_chains_numbert chr_list1t chr_list2tnew_names_listtn_namest chr_numbertchr_listRR7t extra_namestdictionary_valuest zippedliststnew_names_dictionaryRRfRgttr_strtch_sel((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyRms>     0    )cC sE|r/|jd||j|_|jnt|j|_dS(s@ Steps that are common to most method of transform info R1N(R%R'tset_common_res_dicttsort_dict_keysRR&(R,R1((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyRps   cC st|j}t}|jjt|jjjkrEt}n|jj }i}t |jj dkr|jj dj }x/|D]$}t d|d|jd|}qWnx|D]}|j|}|jj|s|jdd|jddf|j|tncs_restraint_groupRRRRRtncs_copyRyR(R,tncs_restraints_group_listt group_id_listRfRgt master_iselRrtnew_nrgRRRtncs_iselRt new_ncs_copy((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pytget_ncs_restraints_group_list&s(     c C st|t|jks!tt|j}x|D]}|j|}|jd}xtt|dD]}|jj|rp|j jd}|j |j |_ |j |j |_ t j}x)|j|D]} |j|j| qW|j|kstqpqpWq7WdS(s! Update ncs_group_object rotations and transformations. Note that to insure proper assignment the ncs_restraints_group_list should be produced using the get_ncs_restraints_group_list method Args: ncs_restraints_group_list: a list of ncs_restraint_group objects iiN(RWRRIRMR RRRRRyRRRRRR>RR( R,ReRfRfRgtnrgRRdRiR((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyt&update_using_ncs_restraints_group_listAs !   c C s| r| rt}t}nt|t| ks<t|rKt}n|jd|} d} d} |r{|j}n|rI|jrI| rI|j}|j}t|} |j j }|j }|j |j krt}|j |jj}|j }n|j |j ks3t|j j|n|r|}|rj|j}n|jd|}| st|} n|r|j |jj}n9d}t|jt|j kst||}|jdd} n|r| j}n|r*| j}n| r|rpt|d}|| IJ||IJ|| IJ|jq| | IJ| |IJ| | IJndj| || gS(s  Write to a file or prints transformation records. with or without PDB atoms and Cryst records. If no pdb_hierarchy, xray structure or fmodel are provided, the function will return only the MTRIX/BIOMT records Args: file_name: (str) output file name ncs_only: (bool) When False, the comple ASU will be printed (applicable only with MTRIX records) pdb_hierarchy: (pdb_hierarchy object) xrs: (xray structure) for crystal symmetry fmodel: (fmodel object) crystal_symmetry: crystal symmetry records mtrix: (bool) When True -> write MTRIX records biomt: (bool) When True -> write BIOMT records write: (bool) when False, will will not write to file or print Return: PDB string RPR tcrystal_symmetrys3The complete ASU hierarchy need to be provided !!! tws N(RSR)RiRIR6txray_structureR't as_pdb_filetget_pdb_headerRt extract_xyzt sites_cartRRRRtset_xyzRnRNRWRtformat_BOIMT_pdb_stringtopentcloseR(R,R.RPt pdb_hierarchytxrstfmodelRntmtrixtbiomttwritetlogt mtrix_objecttpdb_header_strt new_ph_strtpdb_strtxyztnew_xyzR_tnew_phR^t transform_rectf((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pytget_transform_records[sf       -       c &C stj} |r|j}n|r:| r:|j} n|jj} x|jjD]\} } x| dD]} i}xHt| D]:}x1| dD]%}|d|}|j||| :  P S)cC s4|j|r#||j|n |g||<|S(N(RR(ReRfRg((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyRo`s cC sTd}d}xA|D]9}||7}|d7}|dkrd}|d7}qqW|S(s Split string that is longer than 80 characters to several lines Args: s (str) Returns: ss (str): formatted string iR iiPs \ ((RRtssR((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyRgs     cC sHt|dr0|j|}|jj}n$|jj|}|jjj}t|tjru|j}nt |}|j dj }g}xD|D]<}d|j }t ||jj } | j|| k} g} d} d} | rx|jD]}|j}|d|}t ||jj } | j|| k}yt|}Wntk rd}nX|r0|dkr| dkr|} |} q-|| dkr| d7} q-t| | }| j||} |} qt| | | \} } } | jd|qt| | | \} } } d |d }g|jjD] }|^ql}d j|}| j||d qWt| | | \} } } nt|| }|j|qWg}|jx>|D]6}t|d kr$d|d}n|j|qWdj|}|S(s Convert a selection array to a selection string Args: pdb_hierarchy_inp : iotbx.pdb.hierarchy.input (or iotbx.pdb.hierarchy) selection (flex.bool or flex.size_t) Returns: sel_str (str): atom selection string Rischain is and resid iisresid s(resid s and (name s or name s))iRRs or N(thasattrRRRR'RFRRiRR"RR Rtas_intRRtresiduesROR+t ValueErrort resseq_stringRtupdate_res_selRt extract_nameRtget_clean_selection_stringRRW(R1RR_t atom_cahcet selection_setR tsel_listRRKta_seltcomplete_ch_not_presenttres_seltfirst_nt pre_res_nRR^t test_sel_strtall_atoms_presentRtres_seqRRt atom_nametatom_strts_ltsel_str((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyR|sp             %  cC sD|dkr7t||}d}d}|j|n|||fS(sE update the residue selection list and markers of continuous section iN(RRR(Rt first_res_nRR((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyRs  g?ic C st}d}x|jD]w\}}t|drI|j} |j} n|d\} } t||| | d|d|\} }| r||fSqW||fS(s( Check if the rotation r and translation t exist in the transform dictionary. Comparing rotations and the result of applying rotation and translation on a test vector Args: r (matrix.sqr): rotation t (matrix.col): translation transforms (dict): dictionary of all transforms angle_eps (float): allowed difference in similar rotations eps (float): allowed difference in the average distance between Returns: tr_num: (str) transform serial number is_transpose: (bool) True if the matching transform is transpose RiR0t angle_epsN(R)RRRRRR( RRRR0Rt is_transposettr_numRfRgtrrtttt is_the_same((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pytfind_same_transforms  $cC s|j r|j r|jdds2t|jddsJttjdddg}|j||j}t||\}} |j|| j} t|} t|} |j||j} || }|j |d | j }| | }|j |d | j }t | | }t |d |}||krf||krft tfS||kr||krt t fSttfSn ttfSdS(s Args: r1, r2: Rotation matrices t1, t2: Translation vectors eps, angle_eps: allowed numerical difference Returns: (bool,bool) (is_the_same, is_transpose) t rms_tolerancegMbP?i igi g@g@g$@ggX@gYg?iN(i igi (g@g@g$@(ggX@gY(Rtis_r3_rotation_matrixRIRt vec3_doubletelemst as_doubleRtget_rotation_vectdotRtangle_between_rotationsRRRSR)(RRRRR0RRta_reftrtRta_ref_transposetv1tv2taRetdttangtd_ang((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyRs,        cC s!|j}| |}||fS(N(R(RR((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyRs  cC s|jdd}|jdd}|jddd}gtjd|D]}|j^qM}g|D]}|||jd|!^ql}g|D]}d|^q}|S(s| Args: selection_str: (str) selection string Returns: (list of str) of the format ['chain X', 'chain Y',...] Rt tCHAINRWtChainschain (Rtretfinditertendtfind(RqtsstrRtpos_listRt ch_id_listt chain_list((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyR"s+,cC s|jdd|jdd|jdd|jdd|jdd|ddkr}|d d kr}|d }n|jd}g}xV|D]N}|j}|jd r|d }n|dkr|jd|qqW|S(NsChain schain sCHAIN s or chain s ) or (chain s )or(chain iRiRs oriR (R R(RRnRPtendswithR(Rts_listR((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyR2s      cC sZtj|j}|j}|j}t|jdjd}|||d!S(Niii(Rtreal_symmetrict as_sym_mat3tvectorstvaluesRRtindex(Rteigent eigenvectorst eigenvaluesR((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyRBs   cC s<|j|}tjtd|}|dtj9}|S(Nii(RR;tacosRRtpi(RRt cos_angleR3((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyRJscC sP|j}g}x.|D]&}|jdr2Pq|j|qWdj|S(s Collect CRYST and SCALE records Args: pdb_str: (str) pdb type string Returns: the portion of the pdb_str till the first ATOM tATOMs (Rt startswithRR(Rtpdb_header_linesR((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyRrQs  cC s|j|}|jS(s Args: xyz:(flex.vec3_double) the complete asu sites cart (atoms coordinates) selection: Returns: (flex.vec3_double) center of coordinates for the selected coordinates (Rtmean(RRR((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyRbs cC sk|dks|dkr'tdn@|d}|dd}|d}t|t|t|SdS(s return a 3 digit string of n iisInput out of the range 0 - 999.idi N(tIOErrorR(Rts1ts2ts3((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyRns   cC spt}|rk|}xVt|j|j|j|jD]0\}}}}t||s4|p^|}q4q4Wn| S(s Verify that all transforms are not present (excluding the identity transform) Args: transform_info: (transformation object) Returns: (bool): True if all transforms are not present (R)RRRR*RR(R4tpresentR-RRRR.((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyRPxs 4cC s|jo|jS(sD test if r, rotation matrix is identity, and t, translation is zero (tis_r3_identity_matrixt is_col_zero(RR((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyRscC s*t}x|jD]}|o|}qW|S(s Check if all transforms coordinates are present, if the complete ASU is present Args: transform_info: (transformation object) Returns: (bool) (RSR(R4RR.((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pytall_ncs_copies_presents cC st|ddS(s' set transformation application order RrcS st|dS(Ni(R+(Rr((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyR1s(R(R((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pytorder_transformsscC s-||krtdn|j||SdS(s When processing phil parameters. Insert new item to set, if not there, raise an error if already in set Args: unique_selection_set: (set) new_item: (str) Returns: unique_selection_set: updated set s)Phil selection strings are not unique !!!N(RR(tunique_selection_settnew_item((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyRs   g{Gz?g?c C sdd}tjdgd}tjdddg}d}|rP|rPtj|\} } tj|\} } g| D]\} }| ^qw}g| D]\} }| ^q}tjd|d|dddd\}}}|dkr||ddfS|jdjd}|jdjd}tj||||||\}}}}|j |j j }|j |j j }|j dkrt jd |d |}|j}|j}|j|j}||kr||ddfSn||kr7d }|jd d }|s7t|q7n||t|d|fS||ddfSdS(s; Get rotation and translation using superpose. Can raise "Sorry" if chains are not exactly the same length, but a large subset of them is NCS related. Return the subset of atoms indices used in such a case. Note that if the master and copy have the same length it will not check for similarity. Args: master_ncs_ph: pdb hierarchy input object ncs_copy_ph: pdb hierarchy input object process_similar_chains (bool): When True, process chains that are close in length without raising errors rms_eps (float): limit of rms difference between chains to be considered as copies min_fraction_domain (float): Threshold for similarity between chains Returns: r: rotation matrix t: translation vector rmsd (float): RMSD between master and copy msg (str): error messages R ii gtseq_atseq_bR:R9treference_sitest other_sitessBChains {0} and {1} appear to be NCS related but are dis-similar.. RtcopyiN(R R&R'Rtget_residue_sequencet res_alignmentRR tget_matching_atomsRRRsRRtleast_squares_fitRRtrms_differencetother_sites_best_fitRRR(R{R|R8R;R9R^tr_zerott_zeroRt chain_id_mtres_mt chain_id_ctres_cRR7tseq_mtseq_ct res_sel_mt res_sel_ct similaritytm_chaintc_chaintsel_mtsel_ct ref_sitesRt lsq_fit_objRR((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyRsH    $      cC stj}tj}| rt|r|jj}|d}|j|}|}|j}|j}|j}n$|rtjt|j }n|||fS(s Get the atoms to compare. Exclude water and alternative locations Args: hierarchy: pdb hierarchy input object atoms: (flex.vec3_double) master atoms sites cart Returns: atoms (flex.vec3_double): coordinates of atoms in hierarchy (Exclude water and alternative locations) selection (flex.size_t): used atoms not_selection (flex.size_t): unused atoms s (not resname hoh) and altloc " "( RRRiRRRRRRR(RR'Rt not_selectiont atom_cacheR_((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyt get_atomss     cC s|dk r|jj}|jd}tj}x*|D]"}|j|j|jq=Wtjt |}|jj |SdSdS(s Args: ph: pdb hierarchy input object selection_str (str): selection string Returns: portion of the hierarchy according to the selection s or N( RR'RRnRRR>RRRR(R_RqRtselection_str_listtselection_indicesRR((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyRs    cC s3||@jtdk}|s+td||BS(s Test for overlapping selection and then updates the selection_ref with the new_selection Both received and return arguments are flex.bool is5Overlapping atom selection. Check phil parameters... (RRRSRI(Rt new_selectionR((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyR,sc C s|d}|d}t|t|ks2tg}xt||D]\}}|j}|jddkstdd|}g|D]\}}dj||^q} ddj| d } |j|d | qHW|S( s Args: chain_residue_id: [[chain id's],[[[residues range]],[[...]]] Returns: selection lists, with selection string for each ncs copy in the group iiRs+Multiple chains in a single spec ncs group schain sresseq {0}:{1}Rs or Rs and (RWRIRRPRRRR( RR t res_rangesRuRRt ch_selectionRtet res_range((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyR7s   ! +cC sIt|}g}x0|D](}x||D]}|j|q*WqW|S(s1 order transforms mainly for proper chain naming (RR(RR&RRzt tr_selection((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyRlLs   cC szt|tr|g}n|j|r]||djt|||dj|nt||hg||<|S(s Update ncs_group_map that maps a group ID to a list: [master selection,list of objects containing transforms and copies selections] ii(RFRRtupdateR"R(RRvR#R((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyRUs c stdfdS(NRrc s|S(N((Rf(tdict(sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyR1es(R(RA((RAsF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyRMdscC s4||kr!dj||}ndj|}|S(Ns resseq {}:{}s resseq {}(R(t first_res_numtprevious_res_numR((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyRgs cC sy|rKt|dkr6|ddj|d}qQ|d|d}n|}|jdd}|jdd}|S( s Args: ch_sel (str): such as 'chain A' res_selection (list of str): such as ['resseq 1:10','resid 27c and name CA'] Returns: s (str): such as 'chain A and (resseq 1:10 or (resid 27c and name CA))' is and (s or Rs and is R(RWRR(RKt res_selectionR((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyRns c C s|}t|j|j|j|j}g}g}g}g}xt|D]\}\}} } } td|d| r|j|| g|dkr| dkr|j||j| |j| qqL|j||j| |j| qLW|ddggkr|S|jdt j dddddddddg |jdt j dddg|jdt d} gt t|D]}| j|d^q} ||_||_| |_||_|S(sQ Add the identity matrix in cases where the pdb or mmcif files do not contain it Args: transform_info (transformation object): contain rotation, translation, serial number and indication if present Return: transform_info : Add or reorder the transform_info so that the identity matrix has serial number 1 RRiis{0:3d}(RRRR*RRRRtinsertR R&R'RSRRWR(R4R-tti_zipt identity_sntt_rtt_ttt_cpRRRRR.Rtt_sn((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyROs8 !%    4"2    RdcB seZdZRS(cC s||_||_||_dS(N(RRR(R,R`RaRb((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyR-s  (RRR-(((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyRdsRccB seZdZRS(cC s||_g|_dS(N(tmaster_iselectionRy(R,RL((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyR-s (RRR-(((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyRcstncs_groups_containercB seZdZRS(cC sd|_g|_dS(NR (RR(R,((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyR-s (RRR-(((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyRMsRcB s#eZdddddddZRS(icC s@||_||_||_t||_||_||_dS(s Basic transformation properties Argument: rotation : Rotation matrix object translation: Translation matrix object serial_num : (int) Transform serial number coordinates_present: equals 1 when coordinates are presents in PDB file ncs_group_id : (int) ncs groups in, all the selections that the same transforms are being applied to N(RRRRiRRvR(R,R}R~RRRvR((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyR-s     N(RRRR-(((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyRs t selectionscB sAeZdZddejejejejdZRS(sN object for grouping multiple selection information for master ncs and copy R cC s:||_||_||_||_||_||_dS(s Arg: master_chain_id (str) opy_chain_id (str) master_sel (flex.size_t): master selection copy_sel (flex.size_t): copy selection not_in_master (flex.size_t): atoms in master to exclude not_in_copy (flex.size_t): atoms in copy to exclude N(tmaster_chain_idt copy_chain_idRRt not_in_mastert not_in_copy(R,RORPRRRQRR((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyR-s      (RRt__doc__RRR-(((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyRNs   (Et __future__Rtmmtbx.ncs.ncs_from_pdbRtmmtbx.ncs.ncs_utilsRt scitbx.linalgRtscitbx.array_familyRt scitbx.mathRt mmtbx.ncsRt libtbx.utilsRt libtbx.philRtiotbx.pdb.hierarchyRGR tscitbxR R R8R;RRCRRtobjectR RoRRRRRRRRRRRrRRRPRRRRRR)RR7RRRRlRRMRRRORdRcRMRRN(((sF/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/ncs/ncs_preprocess.pyts       @   R  %            C        -