xTc@ sddlmZddlZddlmZddlmZddlmZm Z ddl m Z ddl m Z ddl mZdd lmZmZdd lmZddlZdd lmZdd lmZmZdd lmZmZddlZddlmZdefdYZdZ de!fdYZ"e#dZ$dej%j&fdYZ'dZ(de!fdYZ)dZ*dej+j,fdYZ-de-fdYZ.dZ/dS( i(tdivisionN(tflex(tcrystal(t OrderedDictt OrderedSet(tdict_with_default_0(t group_args(t wrap_always(tnull_outtSorry(t format_value(t hierarchy(t hy36encodet hy36decode(t'refmac_range_to_phenix_string_selectionttls(tcrystal_symmetry_buildertpdb_hierarchy_buildercB seZdZRS(c5 C s tj||tj|_|jd}|jd}|dkr[|jd}n|jd}|jd}|jd}|dkr|}n|dkr|}n|jd}|dkr|jd}n|jd }|jd } | dkr|jd } n|||||| gjdd ksHt|dk sZt|jd } |jd} |jd} |jd} |jd}|jd}tj |jd}tj |jd}tj |jd}tj |jd}tj |jd}|jd}|jd}d}|dk rgd;D]'}|jd |d |d!f^qc}|jdd<kst|jdd kr|}n|jdd"kstgd=D]'}|jd#|d |d!f^q}|jdd>ks3t|jdd krZt j |}n|jdou|jd st|dk ry&g|D]}tj |^q}Wn)t k r}t d$t|nXtj|}qnd}d}d}d} d}!xt|jD]}"|}#| |"}|dk sKt||#kr|tjd%|}$|jj|$n|}%||"}|dk st|}&||"}|d&krd'}n|dk st||%krtjd%|}'|$j|'n||&kst| }(| |"} | dk s7t|!})| dk rk| |"}!|!d?krkd'}!qkn| |(ks|!|)ks||%krtjd)td*d+d,t| d-|!}*|'j|*t}+n||"},|,d&krd.},n||"}-|,|-f|+krgtjd/|,d0|-}.|.|+|,|-f<|,d.krW|*jd |.qw|*j|.n|+|,|-f}.tj}/|.j|/|/j ||"|/j!t"||"||"|/j#d1||"||"||"f|/j$||"|/j%||"|/j&td*d2d,t||"|/j'd3|dk ra||"d4krat(|/_)n|dk r||"}0|0d@kr|0j*d5s|0j+d5rd5}1nd6}1|0j,d7}0t|0}0|0d krd.}1n|/j-d8|0|1fqn| dk r;| |"}2|2dAkr;|/j.d9t/|2q;n| dk ry| |"}3|3dBkry|/j0d:t/|3qyn|dk r#|dk r#tj1||/j2j,}4|4dk r||4}|/j3|qq#q#Wt4|jj5d!kr d.|jj5d _6ndS(CNs_atom_site.type_symbols_atom_site.auth_atom_ids_atom_site.label_atom_ids_atom_site.label_alt_ids_atom_site.label_asym_ids_atom_site.auth_asym_ids_atom_site.auth_comp_ids_atom_site.label_comp_ids_atom_site.label_entity_ids_atom_site.auth_seq_ids_atom_site.label_seq_idis&_atom_site.phenix_scat_dispersion_reals&_atom_site.phenix_scat_dispersion_imags_atom_site.pdbx_PDB_ins_codes_atom_site.pdbx_PDB_model_nums _atom_site.ids_atom_site.group_PDBs_atom_site.B_iso_or_equivs_atom_site.Cartn_xs_atom_site.Cartn_ys_atom_site.Cartn_zs_atom_site.occupancys_atom_site.pdbx_formal_charges_atom_site_anisotrop.idt11t22t33t12t13t23s_atom_site_anisotrop.U[%s][%s]iis_atom_site_anisotrop.B[%s][%s]sError interpreting ADPs: tidt.t t?tresseqtwidthitvalueticodettaltloctresnametnew_xyzis tHETATMt-t+s -+s%i%stnew_fptnew_fdp(RRRRRR(ii(RRRRRR(ii(RRN(RR(RR(RR(7Rt__init__R troottgettNonetcounttAssertionErrorRtdoubletadptbxtb_as_ut ValueErrortCifBuilderErrortstrtsym_mat3_doubletrangetsizetmodelt append_modeltchaint append_chaint residue_groupR tinttappend_residue_groupRt atom_grouptinsert_atom_grouptappend_atom_grouptatomt append_atomt set_elementtset_nametformat_pdb_atom_nametset_xyztset_btset_occt set_serialt set_segidtTruetheterotendswitht startswithtstript set_chargetset_fptfloattset_fdpt first_indextserialtset_uijtlentmodelsR(5tselft cif_blockt type_symbolt atom_labelstalt_idt label_asym_idt auth_asym_idtcomp_idt entity_idtseq_idt atom_site_fpt atom_site_fdpt pdb_ins_codet model_idst atom_site_idt group_PDBtB_iso_or_equivtcart_xtcart_ytcart_ztoccut formal_charget anisotrop_idtadpstijtu_ijtb_ijtadptetcurrent_model_idtcurrent_label_asym_idtcurrent_auth_asym_idtcurrent_residue_idtcurrent_ins_codeti_atomt last_model_idR8tlast_label_asym_idtlast_auth_asym_idR:tlast_residue_idt last_ins_codeR<t atom_groupstcurrent_altloctcurrent_resnameR?RBtchargetsigntfptfdpt u_ij_index((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pyR)s(     - 1 1% &                                          (t__name__t __module__R)(((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pyRscC st|dkr|St|dkr,|S|j}t|dkrv|jd|jkrd|}qn:t|dkr|jd|jkr|}qnx t|dkrd|}qW|S(Niiis %sis%s (RXRPtupper(t atom_namet atom_type((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pyRFs  textract_tls_from_cif_blockcB seZdZdZRS(c!C sg|_t|_d|_|jd}gd(D]%\}}|jd||f^q1}gd)D]%\}}|jd ||f^qc}gd*D]%\}}|jd ||f^q}gdD]} |jd| ^q} t|trq|g}g|D]} | g^q}g|D]} | g^q!}g|D]} | g^q=}g| D]}|g^qY} n|jdd+kst |jdd,kst |jdd-kst | jdd.kst |jddkrdS|jd}|jd}|jd}|jd}|jd}|jd}|jd}|dk sqt t|trt j |g}|g}|g}|g}|g}|dk rt j |g}qn|j }xt |D]\}}g|D]} t| |^q}g|D]} t| |^q)}g|D]} t| |^qL}g| D]}t||^qo}||kj}g}x|D]}|dk r|jd r|j||j|j|dq|jtd|d||d||d ||d!||qWd"j|} |jjtd#|d$|d%|d&|d'| qWt|_dS(/Ns_pdbx_refine_tls.idRRRRRRs_pdbx_refine_tls.T[%s][%s]s_pdbx_refine_tls.L[%s][%s]t21t31t32s_pdbx_refine_tls.S[%s][%s]txyzs_pdbx_refine_tls.origin_%siii is_pdbx_refine_tls_group.ids$_pdbx_refine_tls_group.refine_tls_ids'_pdbx_refine_tls_group.beg_auth_asym_ids&_pdbx_refine_tls_group.beg_auth_seq_ids'_pdbx_refine_tls_group.end_auth_asym_ids&_pdbx_refine_tls_group.end_auth_seq_ids(_pdbx_refine_tls_group.selection_detailsRit pdb_hierarchyt chain_startt resseq_startt chain_endt resseq_ends or tttltstorigintselection_string(s11s22s33s12s13s23(s11s22s33s12s13s23( s11s12s13Rs22s23RRs33(ii(ii(ii (ii(t tls_paramstFalset tls_presentR,t error_stringR+t isinstancet basestringR-R.Rt std_stringtatom_selection_cachet enumerateRSt iselectiontall_eqtappendRPt selectionRtjoinRRL(!RZR[Rttls_idstitjtT_ijstL_ijstS_ijstxt origin_xyzstT_ijtL_ijtS_ijt origin_xyzt tls_group_idstrefine_tls_idst beg_chain_idst beg_seq_idst end_chain_idst end_seq_idstselection_detailstselection_cachettls_idtTtLtStorigin_xRti_groupst sel_stringsti_grouptsel_str((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pyR)sz   ///&       ####     &cC s|jS(N(R(RZ((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pytextract2s(RRR)R(((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pyRs Mc C sddl}|dkr-|jjj}nt|dkrct|dksWtdg}nt|t|kst|jjjdd'}|jjjdd(}xtt ||D]\}\}}|dd%d&g} | j t |j | j t |j | j t |j| j t |j|j| |j|d|dd%|fqW|j||j||S()Niiitalltheaders_pdbx_refine_tls.ids_pdbx_refine_tls.detailss_pdbx_refine_tls.methods_pdbx_refine_tls.origin_xs_pdbx_refine_tls.origin_ys_pdbx_refine_tls.origin_zs_pdbx_refine_tls.T[1][1]s_pdbx_refine_tls.T[2][2]s_pdbx_refine_tls.T[3][3]s_pdbx_refine_tls.T[1][2]s_pdbx_refine_tls.T[1][3]s_pdbx_refine_tls.T[2][3]s_pdbx_refine_tls.L[1][1]s_pdbx_refine_tls.L[2][2]s_pdbx_refine_tls.L[3][3]s_pdbx_refine_tls.L[1][2]s_pdbx_refine_tls.L[1][3]s_pdbx_refine_tls.L[2][3]s_pdbx_refine_tls.S[1][1]s_pdbx_refine_tls.S[1][2]s_pdbx_refine_tls.S[1][3]s_pdbx_refine_tls.S[2][1]s_pdbx_refine_tls.S[2][2]s_pdbx_refine_tls.S[2][3]s_pdbx_refine_tls.S[3][1]s_pdbx_refine_tls.S[3][2]s_pdbx_refine_tls.S[3][3]s_pdbx_refine_tls_group.ids$_pdbx_refine_tls_group.refine_tls_ids _pdbx_refine_tls_group.selections(_pdbx_refine_tls_group.selection_detailsRtrefined(s_pdbx_refine_tls.ids_pdbx_refine_tls.detailss_pdbx_refine_tls.methods_pdbx_refine_tls.origin_xs_pdbx_refine_tls.origin_ys_pdbx_refine_tls.origin_zs_pdbx_refine_tls.T[1][1]s_pdbx_refine_tls.T[2][2]s_pdbx_refine_tls.T[3][3]s_pdbx_refine_tls.T[1][2]s_pdbx_refine_tls.T[1][3]s_pdbx_refine_tls.T[2][3]s_pdbx_refine_tls.L[1][1]s_pdbx_refine_tls.L[2][2]s_pdbx_refine_tls.L[3][3]s_pdbx_refine_tls.L[1][2]s_pdbx_refine_tls.L[1][3]s_pdbx_refine_tls.L[2][3]s_pdbx_refine_tls.S[1][1]s_pdbx_refine_tls.S[1][2]s_pdbx_refine_tls.S[1][3]s_pdbx_refine_tls.S[2][1]s_pdbx_refine_tls.S[2][2]s_pdbx_refine_tls.S[2][3]s_pdbx_refine_tls.S[3][1]s_pdbx_refine_tls.S[3][2]s_pdbx_refine_tls.S[3][3](s_pdbx_refine_tls_group.ids$_pdbx_refine_tls_group.refine_tls_ids _pdbx_refine_tls_group.selections(_pdbx_refine_tls_group.selection_details(tiotbx.cif.modelR,tcifR8tblockRXR.tloopRtziptextendtlistRRRRtadd_rowtadd_loop( ttlsostselection_stringsR[tiotbxttls_loopttls_group_loopti_tlsttlsoRttls_row((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pyttls_as_cif_block6sf     ( %  t cif_inputcB s@eZddejjddedZdZe dZ dZ dZ dZ dZdZdedZd Zd Zd Zd Zd ZdZdZdZdZdZdZdZdZdZdZdZ dZ!dZ"e dZ#dZ$e ddZ%RS( cC s)|dk r6|dksttjjd|}n|dk ritjjd|}|j|_nT|dk rtjjddj |}|j|_n|dk r||_nt |jdkrt dn|jj d|_ t|j |_|jj|_d||_dS(Ntpdb_idt file_patht input_strings is/mmCIF file must contain at least one data blocksfile %s(R,R.Rtpdbtent_path_local_mirrorRtreaderR8t cif_modelRRXR tvaluesR[RtbuilderR t _source_info(RZt file_namet cif_objectt source_infotlinesRtraise_sorry_if_format_errorR((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pyR)ws"     cC sdS(Ntmmcif((RZ((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pyt file_typescC s|r|jjn|jS(N(R treset_atom_i_seqs(RZtset_atom_i_seq((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pytconstruct_hierarchyscC s|jS(N(R(RZ((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pyRscC s |jjS(N(R tatoms(RZ((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pyRscC s |jjS(N(R tatoms_with_labels(RZ((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pyRscC s/tjg|jjD]}|j^qS(N(Rtsize_tR RYt atoms_size(RZtm((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pyt model_indicesscC s tjS(N(RR(RZ((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pyt ter_indicesscC sC|jj}|dkr|S|dkr,|S|jd|d| S(Ntother_symmetrytforce(Rtcrystal_symmetryR,t join_symmetry(RZRt weak_symmetryt self_symmetry((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pyRs    cC s |jjS(N(RR(RZ((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pytcrystal_symmetry_from_cryst1scC s|jjdjdS(Nis _cell.Z_PDB(RRR+(RZ((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pytextract_cryst1_z_columnsscC sdS(NR ((RZ((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pytconnectivity_sectionscC sdS(NR ((RZ((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pytconnectivity_annotation_sectionscC sdS(NR ((RZ((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pytremark_sectionscC sdS(NR ((RZ((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pytheterogen_sectionscC sdS(NR ((RZ((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pytcrystallographic_sectionscC sdS(NR ((RZ((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pyt title_sectionscC s*|j}|dk r&t|d SdS(Ni(tdeposition_dateR,R=(RZtyyyymmdd((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pytextract_header_years  cC s}|jjd}|jd}|dk ry|jd}t|trP|Stj|d}|dk ry||SndS(Nis_database_PDB_rev.nums_database_PDB_rev.date_originalt1(RRR+R,RRRRU(RZR[trev_numt date_originalR((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pyR s  cC st|j|S(N(t_cif_get_r_rfree_sigma_objectR[(RZR((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pytget_r_rfree_sigmascC st|jjdS(Ns"_exptl_crystal.density_percent_sol(t_float_or_NoneR[R+(RZ((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pytget_solvent_contentscC st|jjdS(Ns_exptl_crystal.density_Matthews(RR[R+(RZ((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pytget_matthews_coeffscC s||jjd}|jjd}t|trC|dkrC|S|dk rxtj|d}|dkrx||SndS(Ns_software.names_software.classificationt refinementi(R[R+RRR,RRU(RZt software_nametsoftware_classificationR((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pytget_program_names   cC st|j|S(N(RR[(RZR ((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pytextract_tls_paramssc C sgdD](\}}|jjd ||f^q}|jdd krNdS|jdd ksitgd D]}|jjd|^qp}|jdd kstg|D]}t|^qg|D]}t|^qgS(NRRRRRRRRRs'_atom_sites.fract_transf_matrix[%s][%s]i it123s#_atom_sites.fract_transf_vector[%s]( s11s12s13s21s22s23s31s32s33(R[R+R-R,R.RS(RZRRtfractionalization_matrixtfractionalization_vector((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pyt scale_matrixs2)cC s,tjg|jjD]}|j^qS(N(RRR RYR(RZR8((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pyRgscC s t|jS(N(textract_f_model_core_constantsR[(RZ((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pyRscC s|jjd}t|jjd}|r|dk r@|S|dk rg|jdD]}t|j^q\}|dSn2|dk rg|jdD]}t|^qSdS(Ns#_diffrn_source.pdbx_wavelength_lists_diffrn_source.pdbx_wavelengtht,i(R[R+RR,tsplitRSRP(RZt first_onlyt wavelengthst wavelengthtf((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pytextract_wavelength s    .  &cC s|jjd}|S(Ns _exptl.method(R[R+(RZt exptl_method((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pytget_experiment_typesg-C6?c C sddlm}g}g}g}g}xt|jjdD]\}} |j| |f|j|jjd|dkgdD],\} } |jjd| | f|^q} |j|jtt| gdD] } |jjd| |^q} |j|j tt| qAW|j g|D]\}}|^q<}g|D]}||^q[}g|D]}||^qx}g|D]}||^q}g|D]\}}|^q}t j j j}xt||||D]\} } } }| jd|s9|r+tdq9tdGHn| joN| j}|jd| d| d|po|d| qW|S(s Read MTRIX records from a pdb file Arguments: ---------- error_handle -- True: will stop execution on improper rotation matrices False: will continue execution but will replace the values in the rotation matrix with [0,0,0,0,0,0,0,0,0] eps -- Rounding accuracy for avoiding numerical issue when when testing proper rotation error_handle can be use if one does not want a 'Sorry' to be raised. The program will continue to execute but all coordinates of the bad rotation matrix will zero out Returns: -------- result : object containing information on all NCS operations i(tmatrixs_struct_ncs_oper.ids_struct_ncs_oper.codetgivenRRRRRRRRRs_struct_ncs_oper.matrix[%s][%s]Rs_struct_ncs_oper.vector[%s]t rms_tolerances"Rotation matrices are not proper! trRtcoordinates_presentt serial_number( s11s12s13s21s22s23s31s32s33(tscitbxR'RR[R+RtsqrtmapRStcoltsortRRt_t"_mtrix_and_biomt_records_containerRtis_r3_rotation_matrixR tis_r3_identity_matrixt is_col_zerotadd(RZt error_handletepsR'ttranstrotsR,R+RtsnRtyR*RR2t items_orderRtresulttcptignore_transform((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pytprocess_mtrix_recordssB%6*# (    N(&RRR,RRtPlease_pass_string_or_NoneRR)RRLRRRRRRRRRRRRRRRR R RRRRRRRgRR$R&RB(((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pyRusH                          cC s6|dk r2|dks$|dkr(dSt|SdS(NRR(R,RS(R((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pyRTs RcB s&eZdZdZddZRS(cC s||_t|jd|_t|jd|_t|jd|_t|jd|_t|jd|_t|jd|_dS(Ns_refine.ls_R_factor_R_works_refine.ls_R_factor_R_frees_refine.pdbx_ls_sigma_Fs_refine.ls_d_res_highs_refine.ls_d_res_lows_reflns.d_resolution_high( RRR+tr_worktr_freetsigmathightlowt resolution(RZR[R((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pyR)\s c C sdtd|jtdt|jtdt|jtdt|jtdt|jtdt|jtdt|jf}|S(Ns%s %s %s %s %s %s %ss%6s( R RR4RDRERFRGRHRI(RZR?((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pytformatted_stringescC s,|dkrtj}n||jIJdS(N(R,tsyststdoutRJ(RZtlog((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pytshowps N(RRR)RJR,RN(((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pyR[s c C s&t|jd}t|jd}gdD]+\}}t|jd ||f^q1}|jddks}tt|jd }t|jd }t|jd}t|jd} d} d} d} td|d|d|d| d| d|d|d| d|d| S(Ns _refine.solvent_model_param_ksols _refine.solvent_model_param_bsolRRRRRRs_refine.aniso_B[%s][%s]iis$_refine.pdbx_solvent_vdw_probe_radiis$_refine.pdbx_solvent_shrinkage_radiis_refine.ls_R_factor_R_works_refine.ls_R_factor_R_freetk_soltb_soltb_cartt twin_fractionttwin_lawtr_solvtr_shrinktgrid_step_factorRDRE(s11s22s33s12s13s23(ii(RR+R-R,R.R( R[RORPRRRQRTRURDRERRRSRV((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pyRus.5tpdb_hierarchy_as_cif_blockcB s eZddddddZRS(iicPC s|dkrtj}ntjjj||ddd|}d|}d|} d|} tjjjdd4} tjjjdd5} | d} | d}| d}| d}| d }| d }| d }| d }| d }| d}| d}| d}| d}| d}| d}| d}| d}| d}| d}| d} | d}!| d}"| d}#| d}$| d}%| d}&| d}'| d }(| d!})| d"}*| d#}+| d$},| d%}-| d&}.t j }/t }0t j }1t j }2d'}3d(}4xJ|j D]<}5|5j }6|6d(krMd)}6nx|5jD]}7|7j }8|8jd(krd*}8nt|4}4x|7jD]}9|9jj}:|3d+7}3|9j};|;d,krd-};nx|9jD]r}<|<j}=|=d(kr d*}=n|<jj}>d-}?x6|<jD](}@d.}A|@jrKd/}Ang|@jD]}B||B^qU\}C}D}E|@j}F|Fdkrd-}Fn |Fj}F|Fd(krd-}Fn|@j|@j}G}H|Gd'kr|Hd'krd*}Gd*}Hnd0|G}Gd0|H}H| j|A|jttd1d2d3|@j |j|@j!j|j|=|j|>|j|8|j|:|j|;|j|C|j|D|j|E|j||@j"|j| |@j#|j|@j$j|j|F|j|G|j|H|j|4|j|?| jt|3|!j|6j|@j%r-g|@j&D]}B| |B^qo\}I}J}K}L}M}N|"j|@j j|#j|@j!j|$j|=|%j|>|&j|8|'j|:|(j|;|)j|I|*j|J|+j|K|,j|L|-j|M|.j|Nq-q-WqWqWqZWq)Wx+d6D]#}O| |Oj'd*rp| |O=qpqpW|j(j)| | j*d'kr|j(j)| ndS(7NtformatRs%%.%ifRs_atom_site.group_PDBs _atom_site.ids_atom_site.label_atom_ids_atom_site.label_alt_ids_atom_site.label_comp_ids_atom_site.auth_asym_ids_atom_site.auth_seq_ids_atom_site.pdbx_PDB_ins_codes_atom_site.Cartn_xs_atom_site.Cartn_ys_atom_site.Cartn_zs_atom_site.occupancys_atom_site.B_iso_or_equivs_atom_site.type_symbols_atom_site.pdbx_formal_charges&_atom_site.phenix_scat_dispersion_reals&_atom_site.phenix_scat_dispersion_imags_atom_site.label_asym_ids_atom_site.label_entity_ids_atom_site.label_seq_ids_atom_site.pdbx_PDB_model_nums_atom_site_anisotrop.ids&_atom_site_anisotrop.pdbx_auth_atom_ids&_atom_site_anisotrop.pdbx_label_alt_ids&_atom_site_anisotrop.pdbx_auth_comp_ids&_atom_site_anisotrop.pdbx_auth_asym_ids%_atom_site_anisotrop.pdbx_auth_seq_ids&_atom_site_anisotrop.pdbx_PDB_ins_codes_atom_site_anisotrop.U[1][1]s_atom_site_anisotrop.U[2][2]s_atom_site_anisotrop.U[3][3]s_atom_site_anisotrop.U[1][2]s_atom_site_anisotrop.U[1][3]s_atom_site_anisotrop.U[2][3]iR R RiRRtATOMR$s%.4fRiR(s_atom_site.group_PDBs _atom_site.ids_atom_site.label_atom_ids_atom_site.label_alt_ids_atom_site.label_comp_ids_atom_site.auth_asym_ids_atom_site.auth_seq_ids_atom_site.pdbx_PDB_ins_codes_atom_site.Cartn_xs_atom_site.Cartn_ys_atom_site.Cartn_zs_atom_site.occupancys_atom_site.B_iso_or_equivs_atom_site.type_symbols_atom_site.pdbx_formal_charges&_atom_site.phenix_scat_dispersion_reals&_atom_site.phenix_scat_dispersion_imags_atom_site.label_asym_ids_atom_site.label_entity_ids_atom_site.label_seq_ids_atom_site.pdbx_PDB_model_num( s_atom_site_anisotrop.ids&_atom_site_anisotrop.pdbx_auth_atom_ids&_atom_site_anisotrop.pdbx_label_alt_ids&_atom_site_anisotrop.pdbx_auth_comp_ids&_atom_site_anisotrop.pdbx_auth_asym_ids%_atom_site_anisotrop.pdbx_auth_seq_ids&_atom_site_anisotrop.pdbx_PDB_ins_codes_atom_site_anisotrop.U[1][1]s_atom_site_anisotrop.U[2][2]s_atom_site_anisotrop.U[3][3]s_atom_site_anisotrop.U[1][2]s_atom_site_anisotrop.U[1][3]s_atom_site_anisotrop.U[2][3](s&_atom_site.phenix_scat_dispersion_reals&_atom_site.phenix_scat_dispersion_imag(+R,RtsymmetryRRtcrystal_symmetry_as_cif_blockR)R8RRRtsetRYRtchainsRPtincrement_label_asym_idtresidue_groupsRRRR!R"RRMRt charge_tidyRRRR4R RVtnametocctbtelementtuij_is_definedtuijRR[RR7(PRZRRtcoordinate_precisiontoccupancy_precisiontb_iso_precisiontu_aniso_precisiont coord_fmt_strt occ_fmt_strt b_iso_fmt_strtu_aniso_fmt_strtatom_site_loopt aniso_looptatom_site_group_PDBRhtatom_site_label_atom_idtatom_site_label_alt_idtatom_site_label_comp_idtatom_site_auth_asym_idtatom_site_auth_seq_idtatom_site_pdbx_PDB_ins_codetatom_site_Cartn_xtatom_site_Cartn_ytatom_site_Cartn_ztatom_site_occupancytatom_site_B_iso_or_equivtatom_site_type_symboltatom_site_pdbx_formal_charget%atom_site_phenix_scat_dispersion_realt%atom_site_phenix_scat_dispersion_imagtatom_site_label_asym_idtatom_site_label_entity_idtatom_site_label_seq_idtatom_site_pdbx_PDB_model_numtatom_site_anisotrop_idt%atom_site_anisotrop_pdbx_auth_atom_idt%atom_site_anisotrop_pdbx_label_alt_idt%atom_site_anisotrop_pdbx_auth_comp_idt%atom_site_anisotrop_pdbx_auth_asym_idt$atom_site_anisotrop_pdbx_auth_seq_idt%atom_site_anisotrop_pdbx_PDB_ins_codetatom_site_anisotrop_U11tatom_site_anisotrop_U22tatom_site_anisotrop_U33tatom_site_anisotrop_U12tatom_site_anisotrop_U13tatom_site_anisotrop_U23Rgtunique_chain_idst auth_asym_idstlabel_asym_idst label_seq_idR_R8tmodel_idR:R`R<RcRR?R^RaRbRBt group_pdbRRR=tzt atom_chargeRRtu11tu22tu33tu12tu13tu23tkey((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pyR)sJ                                                         )         %              2          $ N(RRR,R)(((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pyRWs t(pdb_hierarchy_as_cif_block_with_sequencecB s#eZdddddddZRS(iic < C sO tj||d|d|d|d|d|ddl} | jjjd|d|d |d td t} tjj j d dO} tjj j d dP} tjj j d dQ} t }i}d}i}i}i}i}t }t }t }x| jD]}|jj}||kr<|d7}|||}*qL|2|1|0d)krLd?}*qLn| j||*|+d&d&t0d@j1|#dAdBj.t0d@j1|$dAdBj.dCj1||d"f q0WxR|jD]D\} }dD}3| dEkrdF}3n| j||3d"|| fqW|j2j3| |j2j3| |j2j3| |j2j4|j5|j2dG}4|j2dH}5|j2dI}6|j2dJ}7t6j7|5j8dK}8|6j9}6|6j:|6d"kd@x|jD]\}}|7|jj;k|6|j<j.k@|5|j=j.k@}9|8j:|9t>||4j:|9t>||jj;qWx|D]|}xs|jD]e}|7|jj;k|6|j<j.k@|5|j=j.k@}9|4j:|9t>||jdqo Wq\ W|8|j2dL<|j2dM}:|j2j'dN};|j2dM=|j2j3|:|;dk rK |j2dN=|j2j3|;ndS(TNRRgRhRiRjiRt sequencestparamstextract_residue_groupsRMRs _entity.ids _entity.types_entity.formula_weights _entity.pdbx_number_of_moleculess_entity_poly.entity_ids_entity_poly.types_entity_poly.nstd_chiralitys_entity_poly.nstd_linkages_entity_poly.nstd_monomers%_entity_poly.pdbx_seq_one_letter_codes)_entity_poly.pdbx_seq_one_letter_code_cans_entity_poly.pdbx_strand_ids_entity_poly.type_detailss_entity_poly_seq.entity_ids_entity_poly_seq.nums_entity_poly_seq.mon_ids_entity_poly_seq.heteroiiR%tpolymerR(tamino_acid_codestUNKs(%s)tnotntGLYg?spolypeptide(L)R=spolypeptide(D)tADtCDtGDtTDtDAtDCtDGtDTtAtCtGRs+As+Cs+Gs+Ttpolydeoxyribonucleotidetpolyribonucleotides1polydeoxyribonucleotide/polyribonucleotide hybridR RiPRs non-polymertHOHtwaters_atom_site.label_entity_ids_atom_site.auth_seq_ids_atom_site.pdbx_PDB_ins_codes_atom_site.auth_asym_idRs_atom_site.label_seq_idt _atom_sitet_atom_site_anisotrop(s _entity.ids _entity.types_entity.formula_weights _entity.pdbx_number_of_molecules( s_entity_poly.entity_ids_entity_poly.types_entity_poly.nstd_chiralitys_entity_poly.nstd_linkages_entity_poly.nstd_monomers%_entity_poly.pdbx_seq_one_letter_codes)_entity_poly.pdbx_seq_one_letter_code_cans_entity_poly.pdbx_strand_ids_entity_poly.type_details(s_entity_poly_seq.entity_ids_entity_poly_seq.nums_entity_poly_seq.mon_ids_entity_poly_seq.hetero(RRRRRRRR(RRRRs+As+Cs+Gs+T(?RWR)tmmtbx.validation.sequencet validationtsequenceRLRRRR8RRRRR]t alignmentRct setdefaultRtchain_idR7R_tparentRXtn_missing_startt n_missing_endR.R,Rtunique_resnamest iteritemsRt iotbx.pdbRtmatchestresnamest chain_typetPROTEINtthree_letter_given_one_letterR+tone_letter_given_three_letterRtcommon_residue_names_amino_acidt#three_letter_l_given_three_letter_dtsumt NUCLEIC_ACIDRPRRRR[Rtupdatet as_cif_blockRRR7t deep_copyt set_selectedRRRR4(<RZRRtalignment_paramsRRgRhRiRjtmmtbxRt entity_looptentity_poly_looptentity_poly_seq_looptsequence_countstsequence_to_chain_idsRbtsequence_to_entity_idtchain_id_to_entity_idtsequence_to_chainst residue_group_to_seq_num_mappingtaligned_pdb_chainstnon_polymer_countst non_polymer_resname_to_entity_idR:Rtunaligned_pdb_chainsR_Rtseq_numR<t pdb_chainR"R-tentity_poly_seq_numtpdbx_seq_one_letter_codetpdbx_seq_one_letter_code_canR]RRtone_letter_codet monomer_idtentity_poly_typetentity_nstd_chiralityt n_d_peptidest n_l_peptidestn_achiral_peptidest n_unknowntn_totaltn_dnatn_rnat entity_typetlabel_entity_idt auth_seq_idtins_codeR`RtselRotatom_site_aniso_loop((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pyR)Us              /% "           (                              %! %&     N(RRR,R)(((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/mmcif.pyRTs cC sddlm}t|dkr&dSt|}xtt|D]}||dkrd||<|dt|krdt|dSqEx9tr|j||}||d||s6    R ?  &