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Parameters ---------- file_name: path to PDB or mmCIF file source_info: string describing source of input (e.g. file name) lines: flex.std_string array of input lines pdb_id: PDB ID to automatically retrieve from local mirror raise_sorry_if_format_error: re-raise any low-level parser errors as a libtbx.utils.Sorry exception instance for clean user feedback Returns ------- An object representing the result of parsing, including an array of atom objects; the actual class will differ depending on the input format. Much of the API will be the same in either case. RRRRAR/(R-R@(RRRRAR/((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pyR"s tPEAKtSITER5t title_sectiontremark_sectiontprimary_structure_sectiontheterogen_sectiontsecondary_structure_sectiontconnectivity_annotation_sectiontmiscellaneous_features_sectiontcrystallographic_sectiontconnectivity_sectiontbookkeeping_sectiontpdb_input_mixinc B seZdedddZeeeeeeeedeed Zeeeeeeeeed Zdedeeedeeee d Z ededeedeeeee d Z RS(g?icC se|jd|d|}|dkr(dS|dk rO|j}|j}n|jd|d|S(Ntcrystal_symmetryt weak_symmetrytmin_distance_sym_equivtu_star_tolerance(RRRRTRUtspecial_position_settings(RRVRSRTRURR((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pyRVs      c C s| d kr-t} | tkrBt} qBn| tkrBt} n|tkr]|j}n|tkrx|j}n|d k s|d k r| td|d|d|IJn|jd| d|d|d|d|d || r| S| j S( s] Generate standard PDB format. Will use built-in crystal symmetry if available. RRtcryst1_ztwrite_scale_recordst cstringiot append_endt atom_hetatmtsigatmtanisoutsiguijN( RR R R)R RRtextract_cryst1_z_columnstformat_cryst1_and_scale_recordst_as_pdb_string_cstringiotgetvalue( RRRRWRXRZR[R\R]R^RYt link_recordstreturn_cstringio((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pyt as_pdb_strings2           c C s|tkr|j}n|tkr6|j}n|dk sN|dk r|r]d} nd} t|| td|d|d|IJt}n|jd|d|d|d |d |d | d | dS( NtabtwbRRRWRXRt open_appendRZR[R\R]R^(R RRR_RtopenR`R t_write_pdb_file( RRRhRRRWRXRZR[R\R]R^tmode((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pytwrite_pdb_files*      c C sV|jdtd|d|d|d|d|d|d|d |d | d | d | d S(sr Create a single cctbx.xray.structure object from the atom records, using only the first model found. tone_structure_for_each_modelRRRSt cryst1_substitution_buffer_layertunit_cube_pseudo_crystaltfractional_coordinatestuse_scale_matrix_if_availableRTt6non_unit_occupancy_implies_min_distance_sym_equiv_zerotscattering_type_exacttenable_scattering_type_unknownt atom_names_scattering_type_consti(txray_structures_simpleR)( RRRRSRnRoRpRqRTRrRsRtRu((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pytxray_structure_simple?s c  C sddlm} ddlm}ddlm}|ro|dkrN|dksTt|jdddd }n|jd |d |}|dkr|j}n|jdkr|j d|j d |j j d |}n|j dkr|j}n|j}d}d}|s| r|j}|dk rtgt|d|jD]\}}t||^qadkr|ddddgkr|j|dRTRVt scatterersRrN(iiiiZiZiZ( iiiiiiiii(iii(#tcctbxRxRyRzRRtsymmetryRRR{tcustomized_copytnon_crystallographic_unit_cellR&t extract_xyztspace_group_infotcell_equivalent_p1t scale_matrixtmaxRtfractionalization_matrixtabst xray_structures_simple_extensiontatoms_with_labelst model_indicestscitbxtstltsett stl_stringRVtnextRFt structureRR#R RA(RRmRRRSRnRoRpRTRrRqRsRtRuRxRyRzR{tscale_rtscale_tRRJRIRDtloopRVR6((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pyRv_s~           8          N( RRRR)RVR R ReRlt(default_atom_names_scattering_type_constRwRv(((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pyRQs^  &  RKcB s eZdZdZdZdZdZdZdZdZ dZ d Z de d Zd Zd efd YZeddZeddZddZdZdZdZdZdZedZdZdZdZRS(s This class parses PDB format, including non-ATOM records. Atom objects will be created as part of the parsing, but the full PDB hierarchy object requires calling the construct_hierarchy() method. c C stj}x+td D]}|jt||qWt}|jd|dtdtdtdtdt|jtj |j x+tdD]}|jt||qWd|fS( NiRYRZR[R\R]R^tpickle( RR#tinput_sectionsRRtgetattrR RaR)R RBRb(RRtsectiont pdb_string((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pyt__getinitargs__s   cC sdS(NR((R((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pyt file_typescC s4x-|jD]}|jdr t|Sq WdS(NsHEADER (RGRR+R(Rtline((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pytextract_header_yearscC sJg}d|}x3|jD]%}|j|r|j|qqW|S(Ns REMARK %3d (RHRRF(RtiiiRDtpatternR((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pytextract_remark_iii_recordss  cC s?ddlm}|j}|jdkr;|j|SdS(Ni(tsecondary_structurei(t iotbx.pdbRRKR't annotationR(RRR((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pytextract_secondary_structures   cC sOg}xB|jD]4}|jds7|jdr|j|qqW|S(s, Collect link records from PDB file tLINKtlink(RLRRF(RRDR((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pytextract_LINK_recordss cC sJddlm}x3|jD]%}|jdr|jd|SqWdS(Ni(tcryst1_interpretationRt cryst1_record(RRRNRRRR(RRR((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pytcrystal_symmetry_from_cryst1s cC sex^|jD]P}|jdr |d}t|dkrY|ddt|7}n|Sq WdS(NRiBit (RNRR9R(RRRD((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pyR_s cC s_ddlm}xH|jD]:}|jdr|jd|}|dk rW|SqqWdS(Ni(t pdb_remarkss REMARK sg=t pdb_record(t iotbx.cnsRRHRtextract_symmetryR(RRRRR((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pyt#crystal_symmetry_from_cns_remark_sgs  cC s^|j}|dkr'|j}n|dkr7|S|dkrG|S|jd|d| S(Ntother_symmetrytforce(RRRt join_symmetry(RRRRSt self_symmetry((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pyRR s     cC st|ds|j}t|dkr:d|}ndgddgdg|_t}g}x|jD]}|jdrs|dd!dkrstd |d |}|j |kr-x=t |j D],\}}||jd|j dd| group of lists extract REMARK 350 BIOMT information, information that provides rotation matrices and translation data, required for generating a complete multimer from the asymmetric unit. BIOMT data sample: REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 0.559048 -0.789435 0.253492 0.30000 REMARK 350 BIOMT2 2 0.722264 0.313528 -0.616470 0.00100 REMARK 350 BIOMT3 2 0.407186 0.527724 0.745457 0.05000 The data from every 3 lines will be combined to a list [[x11,x12,x13,x21,x22,x23,x31,x32,x33],[x1,x2,x3]] the first component, with the 9 numbers are the rotation matrix, and the second component, with the 3 numbers is the translation information x is the serial number of the operation Arguments: error_handle -- True: will stop execution on improper retation matrices False: will continue execution 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 for x=2 the transformation_data will be [[0.559048,-0.789435,0.253492,0.722264,0.313528,-0.616470,0.407186,0.527724,0.745457][0.30000,0.00100,0.05000]] the result is a list of libtx group_arg constructs, each one contains pdb_inp.process_BIOMT_records()[1].values # give a list containing float type numbers pdb_inp.process_BIOMT_records()[1].coordinates_present # True when transformatin included in pdb file pdb_inp.process_BIOMT_records()[1].serial_number # is an integer @author: Youval Dar (2013) i^itBIOMTiiiis?Improper or missing set of PDB BIOMAT records. Data length = %sg@s+Missing record sets in PDB BIOMAT records s%Actual number of BIOMT matrices: {} s)expected according to serial number: {} iit rms_tolerances"Rotation matrices are not proper! RRRR(RRR!tfindR9tmaptfloatR:RAR"tformattrangeRtsqrtcoltis_r3_rotation_matrixR tis_r3_identity_matrixt is_col_zeroR(Rt error_handletepsRRDtxt biomt_datattemptitjt rotation_datattranslation_datatrmttvtingnor_transform((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pytprocess_BIOMT_recordsPs:&  Z* 7/  c C s|j}t|dkr+d|}ni}xI|jD];}|jdr>|dd!dkr>td |d |}|j|j}|dkrdgd dgd g}dgd } dgd } || | f}||jq>W|j } xt|jD]}||\}} } tj|d}tj|d }|jd|s|rtdqtdGHnt| d dd gksCtt| d krVtd|n|jok|j}| jd|d|d| dd kp|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 is (%s)tMTRIXiiRRRRRi iiRs"Rotation matrices are not proper! is#Improper set of PDB MTRIX records%sRRRR(RRRN(RR9RNRtread_mtrix_recordRoRRRRRRRRRRRRRRR RR:RRR(RRRRtstorageRRtstoredR3tdonetpresentRRRDRRRtidentity_transform((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pytprocess_mtrix_recordssJ  "   ! 3   cC sEddlm}|jd}|j|jd|j||S(Ni(t"extract_rfactors_resolutions_sigmaii(RRRRRtget_r_rfree_sigma(RRRtremark_2_and_3_records((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pyRs cC s|jd}d}xB|D]:}|j}tjjjd|}|dk r|SqW|dk r~dj|j}n|S(NitstRK( RRRpRRtremark_3_interpretationt get_programR?R!(Rtremark_3_linesRDR((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pytget_program_names    cC s(|jd}g}x|D]}|j}|jddkr|jddkry|j|jdWqtk ry"|j||jddWqtk r|j|qXqXqqWd}t|dkr$yt |d}Wq$t k rq$t k r q$Xn|S(NitSOLVENTitCONTENTit:i( RRqR RFR!R%tindexRR9Rt IndexErrorR#(Rtremark_280_linestmctremarkRD((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pytget_solvent_contents,   "   cC s(|jd}g}x|D]}|j}|jddkr|jddkry|j|jdWqtk ry"|j||jddWqtk r|j|qXqXqqWd}t|dkr$yt |d}Wq$t k rq$t k r q$Xn|S(NitMATTHEWSit COEFFICIENTiRi( RRqR RFR!R%RRR9RRR#(RRRRRD((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pytget_matthews_coeffs,   "   cC sddl}|jd}g}x;|jD]-}x$|jD]}|j|jqAWq.W|jjjd|d|d|S(Niitremark_3_recordst pdb_hierarchyt chain_ids( t!iotbx.pdb.remark_3_interpretationRtmodelstchainsRFtidRRtextract_tls_parameters(RR RR R R2tchain((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pytextract_tls_paramss cC s(ddl}|jd}tj|S(Nii(RRRtextract_f_model_core_constants(RRR ((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pyRs cC s-x&|jD]}|jdr |jd}t|dksIt|djddjjd}g}x|D]~}|jdkrq{q{|jdkr|jdq{y|jt |jWq{t k r|jdq{Xq{W|r!t|d kr|d SdS|Sq WdS( NsREMARK 200 WAVELENGTH OR RANGERiit;t,RtNULLi( RHRR!R9RtreplaceRpRFRRR#(Rt first_onlyRR*t subfieldst wavelengthsR$((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pytextract_wavelength!s*%  cC s@x9|jD]+}|jdr tj|jjSq WdS(NtEXPDTA(RGRRtexpdtat techniqueRpR(RR((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pytget_experiment_type:sc C s@|j}t|dkr"dSddlm}|jt|jg}i}x9t|jD]%\}}|jj }|||sg?c C st|dkstt|}t}|jd|t|j}t|d}|j|j |j t |d|d|}|S(NiR twtsite_clash_cutoff( R9RRR R R>RDRitwriteRetclosetquick_clash_check( Rt output_fileRItlogtmerged_recordstwarningstmerged_hierarchyRIt n_clashes((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pyt!merge_files_and_check_for_overlaps     ic C std|}|j}|jdddt}|j}|j}|jd|} | j} | j} t | S(NRRni Rttdistance_cutoff( R"RRwR t sites_fracR{tpair_asu_tabletextract_pair_sym_tabletsimple_edge_listR9( RRIR t show_outliersR+t pdb_atomstxray_structureRUR{RVtpair_sym_tablet atom_pairs((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pyRLs         sR 3 :HsR 3 :RsR -3 :HsR -3 :RsR 3 2 :HsR 3 2 :RsR 3 m :HsR 3 m :RsR 3 c :HsR 3 c :Rs R -3 m :Hs R -3 m :Rs R -3 c :Hs R -3 c :RRcC s|jj}|tkr6|d|dd!}nd}||}t|dkr|jj rddlm}|d|dd d t}|dk r||j d d kr||}qn|S( NiiicS s&t|dkr"|jddS|S(Ni RR(R9R(RJ((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pytcompresssi (t ccp4_symbolRtlib_names syminfo.libtrequire_at_least_one_libRR( ttypet lookup_symbolt)standard_rhombohedral_space_group_symbolsR9tgroupt is_centrict#iotbx.mtz.extract_from_symmetry_libR_R)RR(RRDR^R_talt((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pytformat_cryst1_sgroups   % $cC sT|dkrd}n t|}d|jjtd|j|fjS(NRs2CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %-11.11s%4.4sR(RRAR{t parametersRiRR(RRR?((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pyRA's   icC s||gjddks!t|dk r<|j}nt|dksTt|}t|dksrtd|d|d|d|d|d|d|d|d|d |d |d |df jd d S(Nii iswSCALE1 %10.6f%10.6f%10.6f %10.5f SCALE2 %10.6f%10.6f%10.6f %10.5f SCALE3 %10.6f%10.6f%10.6f %10.5fiiiiiiis -0.000000s 0.000000(R RRRR9R(R{RRSRI((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pytformat_scale_records9s! c C sddlm}ddlm}ddlm}ddlm}|dkr[d} d} nt||jr|j } |j } nut||j j r|} d} nQt|t t frt|dkst|j |} d} n td| dkrK|dkr'|j d} qK|j d |j|j} n| dkrl|j d d } ntd |jd| d| d|} |r|dkr| j}n| dtd|d|7} n| S(Ni(Ry(tsgtbx(Rz(Risinvalid crystal_symmetry objectiiZtorthogonalization_matrixtsymbolsP 1RRR{RR?s RRS(iiiiZiZiZ(RRyRlRzRRRRCRR{RR!RQRDR9RR#RtinverseRARRk( RRRWRXtscale_fractionalization_matrixtscale_uRyRlRzRR{RRD((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pyR`OsJ              cC sd}d}d}xv|D]n\}}}}|d7}|||7}|d 7}|||7}|d7}|d7}|d7}|d 7}qW|S( s COLUMNS DATA TYPE FIELD DEFINITION ----------------------------------------------------------------------------- 1 - 6 Record name "LINK " 13 - 16 Atom name1 Atom name. 17 Character altLoc1 Alternate location indicator. 18 - 20 Residue name resName1 Residue name. 22 Character chainID1 Chain identifier. 23 - 26 Integer resSeq1 Residue sequence number. 27 AChar iCode1 Insertion code. 43 - 46 Atom name2 Atom name. 47 Character altLoc2 Alternate location indicator. 48 - 50 Residue name resName2 Residue name. 52 Character chainID2 Chain identifier. 53 - 56 Integer resSeq2 Residue sequence number. 57 AChar iCode2 Insertion code. 60 - 65 SymOP sym1 Symmetry operator atom 1. 67 - 72 SymOP sym2 Symmetry operator atom 2. 74 - 78 Real(5.2) Length Link distance s 1 2 3 4 5 6 7 8 12345678901234567890123456789012345678901234567890123456789012345678901234567890 LINK O GLY A 49 NA NA A6001 1555 1555 2.98 cS s2d|j|j|j|j|j|jf}|S(Ns%4s%s%-3s %s%4s%s(R(taltlocR0tchain_idtresseqticode(R,RD((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pyt_format_link_atoms  Rs LINK Ris 1555s %5.2fg333333@s s 2.90((t link_listttestRvRDR1R2tsym_op1tsym_op2((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pytformat_link_records}s      RcB s#eZdddgZddZRS(RRRRcC sLyt|dd!|_Wntk r6d|_nX|jdkritdt|d |fng}xddd d gD]}|||d!}t|jd krd }nbyt|}WnOtk rtd t|d |fd |ddd|dfnX|j |qW|d |d|_ |_ dS(NiiiiisUnknown PDB record %s%si iii-is-Not a floating-point value, PDB record %s%s: s s s %s%sRt^(iiis ^^^^^^^^^^( R"RR#RR:RR9RpRRFRR(tORRR3Rtfldtvalue((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pyRs&    ?(RRt __slots__R(((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pyRsRcB s'eZejddgZddZRS(RRRcC sRtj|d|d||dd!|_t|dkoH|ddk|_dS(NRRii i<i;R(RRRR9R(R}RR((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pyRs(RRRRR(((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pyRs cC sCytdddd|SWn!tk r>td|nXdS(NtwidthiRJs%4ss&invalid residue sequence number: "%4s"(t hy36decodeR#(RJ((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pyt resseq_decodes cC stddd|S(NRiR(t hy36encode(R((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pyt resseq_encodescC s]t|tr+t||ks't|St|trMtd|d|StddS(NRRs'serial number value must be str or int.(RCRAR9RR"RR:(RR((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pytencode_serial_numbers cC s|dkrtj}nt|jdks6t|dk rN||_n|dk rf||_n|dk r~||_n|dk r||_ n|dk r||_ n|dk r||_ n|dk r||_ n|dk r||_ n| dk r| |_n| dk r&| |_n| dk r>| |_n| dk rV| |_n| dk rn| |_n|dk r||_n|dk r||_n|dk r||_n|dk r||_n|dk r||_n|dk r||_n|dk r||_n|S(Ntatom_with_labels(RR9RRbRRtxyztsigxyztocctsigocctbtsigbtuijR^R/R&R(tsegidtelementtchargetmodel_idRsRtRuRrR0(RDRRRRRRRR^R/R&R(RRRRRsRtRuRrR0((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pytmake_atom_with_labelssX                     cC sB|dkr|j}n|j}g}xFt|jjD]/}|dkre|jdqC|j|qCWd|jfd|jfddj |fd|j fg}|j dkr|j d d |j fn|j }d |kr |jd |d fnd |ks$d|kr\|jd d |jdd }|jd|fnd|kr|jd|dfnd|krg}x9|jD].} tjj| dkr|j| qqWd|ddj |f} |jd| fnd|ksd|krg}x?|jD]4} tjj| } | d kr+|j| q+q+W|jdd |jdd }d|dj |f} |jd| fn|j} | j} tj| }tj| }tj| }|jdd|||ff|d krT| d kjt}|jdd|fn| j}tj|d kr|d kjt}|jdd|fn|j}|dk r>|j}|jdt|f|j}|dk r>dj g|j D]}d|^q }|jd|fq>n|S(!NRs' 'sNumber of atomssNumber of chainss Chain IDss, sAlternate conformationsiisNumber of modelstcommon_amino_acidsAmino acid residuestcommon_nucleic_acidtccp4_mon_lib_rna_dnasNucleic acid residuest common_watersWater moleculestcommon_elements%d (%s)sElemental ionstcommon_small_moleculetothersOther moleculessMean isotropic B-factors%.2f (range: %.2f - %.2f)sAtoms with iso. B <= 0s%d ***sAtoms with zero ocupancys Space groups%gs Unit cell(Rsother(!RR8toverall_countsRR RRFtn_atomstn_chainsR?tn_alt_conf_puretn_modelstinserttresname_classesRotresnamesRRtcommon_residue_names_get_classR&t extract_bRtmeantminRR R t extract_occRRRRAR{Rj(tpdb_inR9tcountsR Rt info_listtclRtnamesR(Rt res_classR&t b_factorstmean_btmin_btmax_bt n_bad_adpRt n_zero_occtsymmt space_groupR{Rtuc_str((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pytget_file_summarys|          "          ,c C s|dkrtj}nt||}tg|D]\}}t|^q1d}d|}x2|D]*\}} |||dt| fIJqgW|S(Nis %%-%ds %%sR(RRRRRR9RA( RR9R RRTRt label_widthRtlabelR((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pytshow_file_summarySs  / "c C sut|t|kst|dkrBtdt|}n|dkrdtgt|}ng}d}d}d}xt||||D]\}} } } d} | rd} n|j|t|| d| d| d| d| f|j|t|| d | d | d | d| f|j|t|| d | d | d| d| fqWdj|S(s MTRIX data sample REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 0.496590 -0.643597 0.582393 0.00000 MTRIX2 2 0.867925 0.376088 -0.324443 0.00000 MTRIX3 2 -0.010221 0.666588 0.745356 0.00000 is.MTRIX1 %2d%10.6f%10.6f%10.6f %10.5f %ss.MTRIX2 %2d%10.6f%10.6f%10.6f %10.5f %ss.MTRIX3 %2d%10.6f%10.6f%10.6f %10.5f %sRRiiiiiiiis N( R9RRRR)RRFR"R?( RRRRRRRRRRRtp_tflag((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pyR]s$     99=(Zt __future__Rtcctbx.array_familyRt boost.pythontboosttpythont import_extR!Rtiotbx.pdb.recordsRtiotbx.pdb.hierarchyRRt"iotbx.pdb.atom_name_interpretationRRtscitbx.array_family.sharedtscitbx.stl.settlibtbxRtlibtbx.str_utilsRt libtbx.utilsRR R R R t cStringIOR RR<tpathR>R-R7RERWRRRRnRsRRRRt#rna_dna_atom_names_backbone_aliasesR5RRRRR+R,R-RR)R3R"RRRQtinjectorRKR6tpdb_codes_fragment_filesR>RRSRLRdt __builtins__RiRARkR R`R{RRRRRRRRR(((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/pdb/__init__.pyts6      "      $                                                                                                                                                                                     (@3$ 8    %U'       ) /     C