xTc @sddlmZddlmZddlmZddlmZddlmZddlZddlm Z ddl m Z ddl Z ddl Z d Zd ZeejgZd Zd ZejjjZd ZdZied6ed6ZdZde_dZdeiejdededd6dd6ejdeddd6e_dZdeiejdededd6dd6ejdeddd6e_dZ de _ied 6ed!6ed"6e d#6Z!d$Z"d%e"_d&Z#d'e#_ie"d(6e#d)6Z$d*Z%d+e%_d,Z&d-eiejdededd6dd6ejdeddd6e&_ie%d.6e&d/6Z'd0Z(d1ed2e(_d3Z)d4ed5eiejdededd6dd6ejdeddd6fe)_d6Z*d7ed8e*_ie(d96e)d/6e*d:6Z+d;Z,d<Z-d=Z.ie,d>6e-d?6e.d96Z/d@Z0dAZ1dBZ2dCZ3dDZ4ie3dE6e4dF6Z5dGZ6e7dHZ8dIZ9dJZ:dKZ;i dLdM6dNdO6dPdQ6dRdS6dTdU6dVdW6dXdY6dZd[6d\d]6d^d_6d`da6dbdc6ddde6Z<ie<j=df6dMd[dcgdg6Z>iZ?dhZ@diZAdjZBdkZCdliejde5ddEdm6ZDdniejde/dd>do6ZEdpi ejde!dd dq6eBdre!ds6ejde$dddt6eBdre$du6ejde'dd.dv6eBdre'dw6ejde+dd9dx6eBdre+dy6ejdeGe jHgeD]%ZIgeIjJD]ZKeKjL^q^qddzd{6ZMd|ieMd}6eEd~6ZNdiejdeAddMd6eEd~6ZOdieMd}6ZPdZQejRjSdieCd6eDd6eNd 6eQd6deTZUeUe;fZVejRjSdieCd6eDd6eOd 6eQd6deTZWeWe:fZXeUZYdZZdZ[dZ\dZ]dZ^dZ_dZ`dZadZbdZcdZddeVejejfdZgde jhfdYZie jjdZkdZldZmdS(i(tchisel(tmmt(t tbx_utils(toutput(tbioinformaticsN(t runtime_utils(tSorrys0.3.3tsculptorsx calculation .help = "Normalized values (~1: perfect match; ~0: random sequence: ~-1: gap)" .short_caption = Sequence similarity calculation .help = "Configure sequence similarity calculation" .style = box auto_align { matrix = %(matrix)s .help = "Similarity matrix" .short_caption = Similarity matrix .type = choice .optional = False window = %(window)s .help = "Averaging window width" .type = int .optional = False weighting = %(weighting)s .help = "Weighting scheme" .type = choice .optional = False }s factor = %s .help = "Transform values by multiplying with a factor" .type = float .optional = False .short_caption = Scale current B-factors by .style = boldcCs,ddlm}|jdgd|dS(Ni(tflexii(tscitbx.array_familyRtdouble(twindowR((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/sculptor.pytget_unit_weights<scCsEddlm}|jtd|d|dgt|ddS(Ni(Rii(R RR trange(R R((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/sculptor.pytget_triangular_weightsBstuniformt triangularcCs tjS(N(RtMDAGap(tparams((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/sculptor.pytgap_mainchain_algorithmQss .short_caption = Filter by residue presence .help = "Delete residue if aligned with gap" .style = box auto_align { }c Csb|jj}t|jjd|}tjdtjd|jjddd|d|d|jS(NR tss_calctmatrixtunknownitweightst threshold( t calculationR tWEIGHTING_SCHEME_NAMEDt weightingRt MDASimilarityt LinearAveragedSequenceSimilarityRR(RtwR((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/sculptor.pytsimilarity_mainchain_algorithm^s     sk .short_caption = Filter by sequence similarity, truncate by specified threshold .help = "Delete residue if sequence similarity is low" .style = box auto_align { threshold = -0.2 .help = "Threshold to accept a residue" .short_caption = Threshold to accept a residue .type = float .optional = False %s }tpossibletdefaultiRiR Rc Csb|jj}t|jjd|}tjdtjd|jjddd|d|d|jS(NR RRRiRtoffset( RR RRRtMDAThresholdAdjustSimilarityRRR"(RRR((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/sculptor.pyt/threshold_adjust_similarity_mainchain_algorithms     s$ .short_caption = Filter by sequence similarity, truncate to target completeness .help = "Delete residues based on sequence similarity to get same number of gaps as the Schwarzenbacher algorithm" .style = box auto_align { offset = 0.0 .help = "Completeness in fraction of model length (0.0 = completeness from Schwarzenbacher algorithm, useful range: +/-0.05)" .short_caption = Model completeness wrt Schwarzenbacher-algorithm .type = float .optional = False %s }cCstjd|jS(Nt min_length(Rt MDARemoveLongR%(R((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/sculptor.pytremove_long_mainchain_algorithmss .short_caption = Filter by residue presence .help = "Delete residue if aligned with gap" .style = box auto_align { min_length = 3 .help = "Minimum length for mainchain segment to remove" .type = int .optional = False }tgaptthreshold_based_similaritytcompleteness_based_similarityt remove_longcCstjd|jS(NR%(RtMPARemoveShorttminimum_length(R((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/sculptor.pyt remove_short_polishing_algorithmss .help = "Delete short unconnected segments" { minimum_length = 3 .help = "Minimum length" .type = int .optional = False .short_caption = Minimum chain length to keep }cCstjd|jS(Nt max_length(RtMPAKeepRegulartmaximum_length(R((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/sculptor.pyt keep_regular_polishing_algorithmss .help = "Keep residues in secondary structure" { maximum_length = 1 .help = "Maximum length" .type = int .optional = False .short_caption = Maximum chain length to keep }t remove_shortt keep_regularcCstjd|jS(Ntlevel(RtSPASchwarzenbachert pruning_level(R((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/sculptor.pyt+schwarzenbacher_sidechain_pruning_algorithmss .help = "Truncate atoms if target residue != source residue" { pruning_level = 2 .help = "Level of truncation" .type = int .optional = False }c Cst|jj}t|jjd|}tjdtjd|jjddd|d|d|jd|j d |j S( NR RRRiRtlowertupperR5( RR RRRt SPASimilarityRRtfull_truncation_limittfull_length_limitR7(RRR((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/sculptor.pyt&similarity_sidechain_pruning_algorithms       s .help = "Truncate atoms based on sequence similarity" .short_caption = Similarity-based truncation .style = box auto_align { pruning_level = 2 .help = "Level of intermediate truncation" .type = int .optional = False full_length_limit = 0.2 .help = "Limit of no truncation" .type = float .optional = False full_truncation_limit = -0.2 .help = "Limit for full truncation" .type = float .optional = False %s }tschwarzenbachert similaritycCstjd|jS(Ntfactor(RtBPAOriginalBfactorRA(R((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/sculptor.pytoriginal_bfactor_algorithm@ss .help = "Use original bfactors to predict new B-values" .short_caption = Original B-factors .style = auto_align box { %s }ic Csb|jj}t|jjd|}tjdtjd|jjddd|d|d|jS(NR RRRiRRA( RR RRRtBPASequenceSimilarityRRRA(RRR((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/sculptor.pytsimilarity_bfactor_algorithmNs     s .help = "Use sequence similarity to predict new B-values" .short_caption = Sequence similarity-based .style = box auto_align { %s %s }icCs[|jdkrtdn|jdkr6tdntjd|jd|jd|jS(NisInvalid precision: >0 requiredis"Invalid probe_radius: >=0 requiredtprobet precisionRA(RGRt probe_radiusRtBPAAccessibleSurfaceAreaRA(R((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/sculptor.pytasa_bfactor_algorithmws     s .help = "Use accessible surface area to predict new B-values" .short_caption = Surface area-based .style = box auto_align { %s precision = 960 .help = "Number of points per atom" .type = int .optional = False probe_radius = 1.4 .help = "Radius for probing surface accessibility" .type = float .optional = False }itoriginaltasacCstjjd|jS(Ntstart(Rt MRASequencetTargetRM(R((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/sculptor.pyttarget_renumber_stepscCstjjd|jS(NRM(RRNtModelRM(R((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/sculptor.pytmodel_renumber_stepscCs tjS(N(Rt MRAOriginal(R((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/sculptor.pytno_renumber_stepsttargettmodelcCs|rtjStjS(N(RtSRSingleLetterTargett SRSequence(tkeep_ptm((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/sculptor.pyttarget_sequence_rename_stepscCs tjS(N(Rt SROriginal(((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/sculptor.pytmodel_sequence_rename_stepscCsx9|jD]+}|jdkr |jj|q q Wx|jD]}|jsn|j|qInx|jD]}|js|j|q{nxf|jD]X}|js|j |qx3|j D]"}|js|j |qqWqqWq{WqIW|j dS(Ng{Gzt?( tatomstocctparentt remove_atomtmodelst remove_modeltchainst remove_chaintresidue_groupstremove_residue_groupt atom_groupstremove_atom_grouptatoms_reset_serial(troottaRVtchaintrgtag((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/sculptor.pytregularize_hierarchys&       #cCs|jdd|jdd|j}tjd|}|jd|}|jddxf|D]^\} } | jd| } | jr|j| | jd| qg|jdd| qgW|jdd t d||jdd g} x|D]\} } | sqnt | j d |j }|sEt |d jd kr| jtjd |djjd| dqqW|jddd||f}t|d}x| D]}|jd|qW|jd|j|j|S(NtmsgsPDB output requesteds1Associate modifications with hierarchy objects...Rjt r_indexersApplying modifications...tentitys2%s - execution omitted because entity not attachedsRegularizing hierarchy...s'Generating sequence identity records...tindexeritmiditidentitygY@sPreparing output file...s %s_%s.pdbRs%s (tinfotdebugt deep_copyRtReverseIndexert instructionstlogt is_connectedtapply_toRotlistt as_entityt hierarchytAssertionErrorR5tappendRt get_phaser_model_identity_remarktobjecttidtfiletwritet as_pdb_stringtclose(Rjt blueprintt identitiest file_roottsuffixtloggert copy_rootRsRztitetmtremarkstdtht file_nametfouttr((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/sculptor.pytwrite_pdb_outputsF         cCsddl}|jdd|jdd|j}tjd|}|jd|} |jddg} g} g} tjj|j j j } tjj|j j j }tjj|j j j }x0| D](\}}t|tjrU|jdd|jd ||j| kr0| j|q|j|kr| j|qqt|tjr|jdd |jd ||j|kr| j||jjfn|jd |q|jdd |jd ||jd |qW|jdd td||jdd d||f}t|d}|jd|jdttjd||jdx+| D]#}|jdt|jqW|jd|jdx+| D]#}|jdt|jqW|jd|jdxJ| D]B\}}|jdt|j||jjjfqW|jd|jd|j |S(NiRpsCoot output requesteds1Associate modifications with hierarchy objects...RjRqs-Applying modifications (but not deletions)...s %s deferredRrs%s applied and loggeds %s appliedsRegularizing hierarchy...sPreparing output file...s %s_%s.cootRs( s%s, s %s, s ), s) (!t iotbx.pdbRvRwRxRRyRztEntityt LEVEL_FORtpdbRt residue_groupt atom_grouptatomt isinstancetDeleteInstructionR{R5RtAttachInstructiontdatatnameR}RoRRtstrtto_coot_s_expressiont coot_selectorRtaltloctstripR(RjRRRRRtiotbxRRsRztmoribund_residuestmoribund_atomstattached_atomstlevel_rgtlevel_agtlevel_aRRRRtn((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/sculptor.pytwrite_coot_outputsd       #  !   !  4   RtcootcCsEg|jD]7}||dt||r8t||nd^q S(NR(tusethasattrtgetattrtNone(t collectionRR((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/sculptor.pytget_algorithmsfscCstjdtdtd|dtdtd|dt|jd|dtdtd|dt|d|rt d |nt d tdt d|d |j S( Nt deletionsRRt polishingstrenumbertpruningst completionstrenameRYtbfactorst minimum_b( RtSculptorRtMAINCHAIN_ALGORITHM_NAMEDtPOLISHING_ALGORITHM_NAMEDtRENUMBER_STEP_BASED_ONRt!SIDECHAIN_PRUNING_ALGORITHM_NAMEDtsetRZR\tBFACTOR_ALGORITHM_NAMEDtminimum(tdeletiont polishingRtpruningt completionRtbfactorRY((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/sculptor.pytget_sculptor_objectns"      cCsf|sg}nGttjg|D].}g|jdD]}|j^q5^q}tjd|S(Nt,tkeep(treducetoperatortaddtsplitRRt Discarder(RtknowntindR((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/sculptor.pytget_discarder_objects  >cCsk|jddtjjt}t}xA|jjD]3}|tkr^|j t|q8|j |q8Wg}x|D]}|jdt j dd||j dtd|g}|jd|j|j}|jd|d|td |jjd |jjd |jjd |jjd |jjd|jjd|jjd|jjfq|W|S(NRps!Predefined protocols will be usedttexts Protocol %s:tsourcestkeys protocol %ss_%sRRRRRRRRY(RvtlibtbxtphiltparsetPHIL_PROTOCOL_MPRt macromoleculet protocolstPROTOCOL_COMBINATIONStupdateRRtheadingtfetchtget_protocol_philtas_strtextractRRRRRRRRRtkeep_ptm_if_base_residues_agree(RRt protocol_philt protocol_keysRRtmpptprot((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/sculptor.pytprocess_multiprotocol_phils4            cCs|jdd|jdtjtjjt}|jd|jd|g}|jd|j ddt d|j j d|j j d |j jd |j jd |j jd |j jd |j jd|j jfgS(NRps$User-specified protocol will be usedRt python_objectsuser defined protocoltRRRRRRRRY(RvRtblankRRRRRtformatRRRRRRRRRRR(RRRR((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/sculptor.pyt"process_user_defined_protocol_phils"        s macromolecule { deletion { use = gap } polishing { use = None } pruning { use = schwarzenbacher schwarzenbacher { pruning_level = 2 } } bfactor { use = original minimum = 10 } completion = cbeta } t1sU macromolecule { deletion { use = completeness_based_similarity completeness_based_similarity { offset = 0.0 calculation { matrix = blosum62 window = 5 weighting = triangular } } } polishing { use = None } pruning { use = schwarzenbacher schwarzenbacher { pruning_level = 2 } } bfactor { use = original minimum = 10 } completion = cbeta } t2s macromolecule { deletion { use = gap } polishing { use = None } pruning { use = similarity similarity { pruning_level = 2 full_length_limit = 0.2 full_truncation_limit = -0.2 calculation { matrix = blosum62 window = 1 weighting = triangular } } } bfactor { use = original minimum = 10 } completion = cbeta } t3s_ macromolecule { deletion { use = completeness_based_similarity completeness_based_similarity { offset = 0.0 calculation { matrix = blosum62 window = 5 weighting = triangular } } } polishing { use = None } pruning { use = similarity similarity { pruning_level = 2 full_length_limit = 0.2 full_truncation_limit = -0.2 calculation { matrix = blosum62 window = 1 weighting = triangular } } } bfactor { use = original minimum = 10 } completion = cbeta } t4s- macromolecule { deletion { use = gap } polishing { use = None } pruning { use = schwarzenbacher schwarzenbacher { pruning_level = 2 } } bfactor { use = similarity minimum = 10 similarity { factor = -80 calculation { matrix = blosum62 window = 5 weighting = triangular } } } completion = cbeta } t5so macromolecule { deletion { use = completeness_based_similarity completeness_based_similarity { offset = 0.0 calculation { matrix = blosum62 window = 5 weighting = triangular } } } polishing { use = None } pruning { use = schwarzenbacher schwarzenbacher { pruning_level = 2 } } bfactor { use = similarity minimum = 10 similarity { factor = -80 calculation { matrix = blosum62 window = 5 weighting = triangular } } } completion = cbeta } t6s macromolecule { deletion { use = gap } polishing { use = None } pruning { use = schwarzenbacher schwarzenbacher { pruning_level = 2 } } bfactor { use = asa minimum = 10 asa { factor = 12 precision = 960 probe_radius = 1.4 } } completion = cbeta } t7s macromolecule { deletion { use = completeness_based_similarity completeness_based_similarity { offset = 0.0 calculation { matrix = blosum62 window = 5 weighting = triangular } } } polishing { use = None } pruning { use = schwarzenbacher schwarzenbacher { pruning_level = 2 } } bfactor { use = asa minimum = 10 asa { factor = 12 precision = 960 probe_radius = 1.4 } } completion = cbeta } t8s macromolecule { deletion { use = gap } polishing { use = None } pruning { use = schwarzenbacher schwarzenbacher { pruning_level = 2 } } bfactor { use = similarity+asa minimum = 10 asa { factor = 8 precision = 960 probe_radius = 1.4 } similarity { factor = -60 calculation { matrix = blosum62 window = 5 weighting = triangular } } } completion = cbeta } t9s macromolecule { deletion { use = completeness_based_similarity completeness_based_similarity { offset = 0.0 calculation { matrix = blosum62 window = 5 weighting = triangular } } } polishing { use = None } pruning { use = schwarzenbacher schwarzenbacher { pruning_level = 2 } } bfactor { use = similarity+asa minimum = 10 asa { factor = 8 precision = 960 probe_radius = 1.4 } similarity { factor = -60 calculation { matrix = blosum62 window = 5 weighting = triangular } } } completion = cbeta } t10s macromolecule { deletion { use = gap } polishing { use = None } pruning { use = similarity similarity { pruning_level = 2 full_length_limit = 0.2 full_truncation_limit = -0.2 calculation { matrix = blosum62 window = 1 weighting = triangular } } } bfactor { use = similarity+asa minimum = 10 asa { factor = 8 precision = 960 probe_radius = 1.4 } similarity { factor = -60 calculation { matrix = blosum62 window = 5 weighting = triangular } } } completion = cbeta } t11s macromolecule { deletion { use = completeness_based_similarity completeness_based_similarity { offset = 0.0 calculation { matrix = blosum62 window = 5 weighting = triangular } } } polishing { use = None } pruning { use = similarity similarity { pruning_level = 2 full_length_limit = 0.2 full_truncation_limit = -0.2 calculation { matrix = blosum62 window = 1 weighting = triangular } } } bfactor { use = similarity+asa minimum = 10 asa { factor = 8 precision = 960 probe_radius = 1.4 } similarity { factor = -60 calculation { matrix = blosum62 window = 5 weighting = triangular } } } completion = cbeta } t12sS macromolecule { deletion { use = threshold_based_similarity threshold_based_similarity { threshold = -0.2 calculation { matrix = blosum62 window = 3 weighting = triangular } } } polishing { use = None } pruning { use = schwarzenbacher schwarzenbacher { pruning_level = 2 } } bfactor { use = original minimum = 10 } completion = cbeta } t13talltminimalcCsb|tkrZ|tkr=td|djttfntjjt|t|  "$     cCstjd|dtS(NRlR(RRDRO(RlRRR:R%R;R((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/sculptor.pytunaligned_chain_samplesc sddlm}ddlm}|jddj|jd|jddj} |jdd | |r,|jdd |j d |j d | d ddd|j } | j dkst |jd|j| tjddd| } d} tjddgd| g} nr|jdd|jdkrZtdn|jdd|jdd|jd| }|st t|}||kr|jdd |td!n|jdd"|gt||jD]\}}||kr|^q}dt|krZ|jdd#t||jdd$n|dd\} } |jdd%| j| f|jd| j|jdtjd&d'tjd(|d| jd)| d*d+|d,|j r|jdd-t!j }d.j"g|jD]}||kr@d/nd0^q(}tjd| gdd1g}|jd|j#d2d3d4d5d6|ngtj$j%D]*\}}|j&j'kr||f^q}tjdd.j"d7|Dd.j"fd8|Dgdd9d1g} | j(}|d:kr|jdd;|jdd<||j| ||krtd=qnS(>Ni(R9(tapplication_utilsRpsChain-sequence matching:trgstone_letter_forRsChain sequence: %ssTarget sequence providedtseq_atseq_btname_atMASTERtname_bsCHAIN_%sisAlignment with target:Rsphenix.alignmentt alignmentitnamestCHAINRIs$Select alignment from predefined setisNo alignments are availables$Pre-screening alignment sequences...s+Scoring sequences based on exact overlap...R:sGThe longest exact overlap is shorter than %s residues (min_hssp_length)s;No sufficiently similar alignment sequences have been foundsLongest overlap is %d residuess+There are %d sequences with longest overlapsThe first one will be selecteds$Best matching: name = %s, index = %sRsResidue mappingRlRLRtmin_hssp_lengthtmin_matching_fractionsUnaligned residues:Rt*t tPDBt aln_widthi<t caption_widthit middle_linecss|]}|dVqdS(iN((t.0tp((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/sculptor.pys =sc3sK|]A}|dr9j|djdjjn jjVqdS(iiN(RARgR%tunknown_one_letterR[R((RfRg(RPRRU(s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/sculptor.pys >stALIg?sSequence mismatchessMatching fraction: %.2fs:Unable to align: matching fraction < min_matching_fraction()R<R9RSRvRUtone_letter_sequenceReRhRwtcreate_alignmentR:Rt multiplicityRRtAlignmentObjectRtclustal_alignmenttcountRBtmatchingtmaxRCtzipRFR-RRRRRtAlignedChainSamplet unalignedRRRtmodel_sequencetalignedR[R(tidentity_fraction(RlRRR:R%R;RR9RSRMtali_objRKRLt chain_alit matchingstlongesttlRtbeststunknownsRmtmidlinetshow_aliR)tmappingRw((RPRRUs=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/sculptor.pytaligned_chain_samples                   7      4    "%$     cCsetd|Dr/|jddt}n2td|DsKt|jddt}|S(Ncss(|]}|djdtjVqdS(it sample_typeN(t processableRRD(RfRg((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/sculptor.pys SsRps%No chain-alignment matching necessarycss(|]}|djdtjVqdS(iRN(RRRs(RfRg((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/sculptor.pys Xss*Chain-alignment matching will be performed(RRvRRRR(t processorsRRG((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/sculptor.pytchain_sample_factoryQs  cCsg}x|D]}|jddt|jd|jd|jsOt|jdd|jd|d|}|jddt||j|q Wt j j d t t j|gd |}|S( NRpsProcessing '%s'...RvRs Finding modifications...tsampleRs (%d modifications found)RzRs(RvRRFRt __class__RtrunR-RRt Blueprinttfrom_instructionsRRR(Rstsamplest processorRRzRPtinstrtbp((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/sculptor.pytsample_process`s !  cCsUg}xH|D]@}tjj|jjd||jf}|j|q W|S(NRs(RRtChainRlt as_descriptorRuR(RsRRRRPR((s=/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/sculptor.pytidentity_processss  c Cs | jdtjddtd|d|jd|d|d|d |d | \} } tjd |j}| jdd | jdtjt d |d| d | }| r| jdtjddnt d |d| d|d | }| r| 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jj/D]u\}}|jdd%||jftj0jd|j}|j1dd+x'|jD]}|j1dt2|qUWd$t3|jkr|j4dd,n|j5dkrtd-|jnt7t8j9g|j5D]}|j:d.^qg}|jd/d0j;g|D]}t2|^q |j<t=g|D]}||jd1f^q6|jdtj.qWddl>}t?d2| d|}t@| jjA}|jdtjBdd3|jdd|j!|jCj:|j!\}} ytDd4|d5|d6|d7|d8| d9|d:| jEd;| jFd<|jCj;| jjG|jCjH| jjId=|jCjJ| d1d>|d| }!Wntk r} t| nX|!S(?NtstreamR5RpRs %s version %st master_phili(Rthandlert extensionsttemplatesinput.alignment.file_name=%ss.pdbs.entsinput.model.file_name=%st accumulatorsAll configuration options:sRequested protocolsRRsNo pdb files specifiedsReading PDB files File name: %sRRtnonesAtom selection: %ss"No atoms left after atom selectionRjRs#Removing alternate conformations...sRemoving occupancies > 1.0...s)Separating solvent from macromolecules...sReading alignment filesRMis%d. %ss#Assigning sequence #%d as target...RLs%s: %dsAlignment readsReading sequence filessSequences read:s=File contains multiple sequences, only the first will be usedsEmpty chain_id for %sRsApplicable chains: %ss, iRsProcessing PDB 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