9i[ SrSSKrSSKrSSKrSSKrSSKrSSKJrJrJ r J r J r J r J r \ \ \r\R "SS9"SS55r\R "SS9"SS 55rS \S \ \ \\ \44S jrS \S \4SjrS\S \4SjrS\ \S\S \\4SjrS4S\S\ \S\S \4SjjrS\S\ \S \4SjrS\S\S \4SjrS\S \4SjrS\S \4SjrS\S\S \ \ \4S jrS!\S"\S#\ \4S$jrS%\ \S \4S&jr S'\S \ \4S(jr!S)\S \\\"44S*jr#S!\S+\S \ \4S,jr$\R "SS9"S-S.55r%S/\S \%4S0jr&S5S1\S\S2\S \ \4S3jjr'g)6z+Functions for parsing various file formats.N)DictIterableListOptionalSequenceSetTupleT)frozenc^\rSrSr%Sr\\\S'\\S'\\\S'Sr Sr S\ 4S jr S r g ) Msaz%Class representing a parsed MSA file. sequencesdeletion_matrix descriptionsc 0[UR5[UR5s=:Xa[UR5:XdPO [ S[UR5S[UR5S[UR5S35eg)Nz5All fields for an MSA must have the same length. Got z sequences, z! rows in the deletion matrix and z descriptions.)lenrrr ValueErrorselfs m/var/www/html/land-doc-ocr/venv/lib/python3.13/site-packages/modelscope/models/science/unifold/msa/parsers.py __post_init__Msa.__post_init__!sDNN#s4+?+?'@#C!!E##4>>*+<t++,--Nt(()*.:; ;#c,[UR5$N)rrrs r__len__ Msa.__len__*s4>>""rmax_seqscf[URSUURSUURSUS9$)Nrrr)r rrr)rrs rtruncate Msa.truncate-s=nnYh/ 00(;**9H5  rN)__name__ __module__ __qualname____firstlineno____doc__rstr__annotations__DeletionMatrixrrintr!__static_attributes__r#rrr r s5/}##3-;#  rr c|\rSrSr%Sr\\S'\\S'\\S'\\ \S'\\S'\\S'\ \\S '\ \\S 'S r g ) TemplateHit5z"Class representing a template hit.indexname aligned_cols sum_probsquery hit_sequence indices_query indices_hitr#N) r$r%r&r'r(r,r*r)rfloatrr-r#rrr/r/5s>, J I J9crr/ fasta_stringreturnc/n/nSnUR5HjnUR5nURS5(a,US- nURUSS5 URS5 MUU(dM^X==U- ss'Ml X4$)a=Parses FASTA string and returns list of strings with amino-acid sequences. Arguments: fasta_string: The string contents of a FASTA file. Returns: A tuple of two lists: * A list of sequences. * A list of sequence descriptions taken from the comment lines. In the same order as the sequences. >N) splitlinesstrip startswithappend)r:rrr1lines r parse_fastarFCsIL E'')zz| ??3   QJE   QR )   R  D *  ""rstockholm_stringc,[R"5nUR5HYnUR5nU(aUR S5(aM2UR 5up4X1;aSX'X==U- ss'M[ /n/nSn/n[ UR55HupU S:Xa)Un[ U5V V s/sHupU S:wdM U PM nn n SRUV s/sHoU PM sn 5n URU 5 /nSn[XG5H4unnUS:wdUS:wdMUS:XaUS- nM!URU5 SnM6 URU5 M [UU[UR55S9$s sn n fs sn f)aParses sequences and deletion matrix from stockholm format alignment. Args: stockholm_string: The string contents of a stockholm file. The first sequence in the file should be the query sequence. Returns: A tuple of: * A list of sequences that have been aligned to the query. These might contain duplicates. * The deletion matrix for the alignment as a list of lists. The element at `deletion_matrix[i][j]` is the number of residues deleted from the aligned sequence i at residue position j. * The names of the targets matched, including the jackhmmer subsequence suffix. #//r@r-r?r ) collections OrderedDictrArBrCsplit enumeratevaluesjoinrDzipr listkeys)rGname_to_sequencerEr2sequencemsarr5 keep_columns seq_indexirescaligned_sequence deletion_vecdeletion_countseq_res query_ress rparse_stockholmrc`s"#..0 ++-zz|t{33   '%'  "(*. CO EL()9)@)@)BC >E,5e,<K,<&!s A,GHi^4iH #'! IsB6query_non_gapssto_seqc## [X5H,up#U(aUv MUS:wdMUR5v M. g7f)NrL)rSlower)rqrris_query_res_non_gap sequence_ress r_convert_sto_seq_to_a3mrws9.1..J*   S $$& & /Ks"??stockholm_format max_sequencesremove_first_row_gapsc^^0m0nSnUR5HxnU=(a [U5U:nUR5(dM1URS5(aMIUR SS9upgXc;a U(aMhSX6'X6==U- ss'Mz UR5HonUSSS:XdMUR S S9nUSS upi[U5S:XaUS OSn U S :waMBU(aXc;aMPU TU'[T5[U5:XdMo O 0mU(a6[ [ UR555n U V s/sHoS :gPM n n UR5H>upnURS S5nU(aSR[W U55nUTU'M@ UU4S jT5nSRU5S-$s sn f)z3Converts MSA in Stockholm format to the A3M format.FrIr?maxsplitr@N#=GSDErL.c3`># UH#nSUSTRUS5STU3v M% g7f)r> r@ N)get).0k a3m_sequencesrs r +convert_stockholm_to_a3m..s?,*s!L,,Q34B}Q7G6HI*s+.r) rArrBrCrOnextiterrQitemsreplacerRrw)rxryrzrreached_max_sequencesrEseqname aligned_seqcolumnsfeaturevaluequery_sequencer\rq sto_sequence out_sequence fasta_chunksrrs @@rconvert_stockholm_to_a3mrs LI! ++- -!(# 3'3( ::<< < <$(::q:#9 G'(%' "  + - .!++- 8v jj!j,G&q| G"%g,!"3GAJE$$)A$)L !< C N2. Md9#3#3#5670>?*?!*!2#++C4 77' EGL!- g "3,*,L 99\ "T ))@sG rEseqnamescPUR5(dgUR5S:XagURS5(agURS5(agUSSS:XaURSS 9up#nX1;$URS 5(ag URS 5S nX1;$)z'Function to decide which lines to keep.TrKz # STOCKHOLM#=GC RFNr~rr|rJFrr)rBrCrO partition)rEr_rs r _keep_liners ::<< zz|t }%% y!! BQx6 A . A""   ..%a(""r stockholm_msac[5n/nUR5HhnUR5(dMURS5(aM2UR S5SnUR U5 [ U5U:dMh O UR5H&n[XB5(dMURU5 M( SRU5S-$)z# UH nTUv M g7frr#)rr[processed_liness rr:remove_empty_columns_from_stockholm_msa..YsN2MQoa(2Ms) rPrArC rpartitionrangerrrDanyrR itertoolscompressrB)runprocessed_linesr[rEreference_annotation_ireference_annotation_linerfirst_alignmentmaskrlunprocessed_lineprefix alignment line_indexmasked_alignmentrs @r'remove_empty_columns_from_stockholm_msar/sO]5578 ??9 % %%& "(, %$(OOC$8 !AqD3/0+<+B+B+D'A+;+F+Fs+K(Fy |s* D) ,E KK&1+D & (#4J24OJ/#45F4K4K4M0J+;+F+Fs+K(Fy')ww!**9;(=$*02B1C&D$"$ 5N!#  ZZ\\$//+">">#'a !%OA K9L 99N%O8L2MN OOrc*[R"[5nUR5H`nUR 5(dMUR S5(aM2UR 5nUR 5up4X==U- ss'Mb [5n[5n[[UR555nUVs/sHoS:gPM n nUR5HSup4SR[R"XI55n X;aM1URU 5 URU5 MU /n UR5H&n[!X&5(dMU R#U5 M( SRU 5S-$s snf)z;Remove duplicate sequences (ignoring insertions wrt query).rIrLr@r)rM defaultdictr)rArBrCrOrrrrQrrRrrrrrD) r sequence_dictrErrseen_sequencesr query_alignr]rrrs rdeduplicate_stockholm_msar\sI++C0M((* ::<< < <::rrW start_index indices_listcxUnUH2nUS:XaURS5 MURU5 US- nM4 g)zUComputes the relative indices for each residue with respect to the original sequence.rLr=r?N)rD)rWrrcountersymbols r _update_hhr_residue_indices_listrs?G S=    #    ( qLG rdetailed_linesc [USR5S5nUSSSnSn[R"X0S5nUc[ SU<SUS<S 35eUR 5Vs/sHn[ U5PM snu pg phnS n S n /n /n Sn US SGHnURS 5(aURS 5(dURS5(dURS5(dSn[XSS5n[US5S- nUSn[US5n[UVs/sH oUS:XdM UPM sn5nUU- U-n U [U5:XdeU U- n [UUU 5 MURS5(dMURS5(aGMURS5(aGM*URS5(aGMCSn[XSS5n[US5S- nUSnU [U5:XdeU U- n [UUU 5 GM [UU[U5UU U U U S9$s snfs snf)aParses the detailed HMM HMM comparison section for a single Hit. This works on .hhr files generated from both HHBlits and HHSearch. Args: detailed_lines: A list of lines from a single comparison section between 2 sequences (which each have their own HMM's) Returns: A dictionary with the information from that detailed comparison section Raises: RuntimeError: If a certain line cannot be processed rr=r?NzProbab=(.*)[ ]*E-value=(.*)[ ]*Score=(.*)[ ]*Aligned_cols=(.*)[ ]*Identities=(.*)%[ ]*Similarity=(.*)[ ]*Sum_probs=(.*)[ ]*Template_Neff=(.*)rzCould not parse section: z. Expected this: z to contain summary.r@rzQ z Q ss_dsspz Q ss_predz Q Consensusz1[\t ]*([0-9]*) ([A-Z-]*)[\t ]*([0-9]*) \([0-9]*\)rLzT z T ss_dsspz T ss_predz T Consensusz/[\t ]*([0-9]*) ([A-Z-]*)[\t ]*[0-9]* \([0-9]*\)r1r2r3r4r5r6r7r8) r,rOrrrrr9rCrrrr/)r number_of_hitname_hitpatternrxrr3r4r5r6r7r8 length_blockrEpattrstart delta_queryendnum_insertionsdelta_hit_sequences r_parse_hhr_hitrs| q)//1"56Ma $H   HHWQ/ 0E }~a0 23 3#\\^ ,^58^ ,Q1Aq ELMKLqr" OOD ! !$//+*F*F 44 66HD/23i@Fq NQ&E )KfQi.C [!E[H![!EFN;7L3{#33 33 [ E ,[% O __T " "OOK00 OOK88 OOM::J3Drs)DF1I*%+AY"#s+='>>>> 22 01CU1<>Q#V  &!#  o -8"Fs/I6 I I hhr_stringc jUR5n[U5VVs/sHup#URS5(dMUPM! nnn/nU(a\UR[ U55 [ [ U5S- 5H'nUR[ XUXBS-55 M) U$s snnf)z)Parses the content of an entire HHR file.zNo r?)rArPrCrDrrr)rlinesr[rE block_startshitss r parse_hhrrs  ! ! #E#5))gaT__U-C) DCJ's<(1,-A KKu!_\a%5HIJ L. Ks B/B/tbloutcSS0nUR5Vs/sHo"SS:wdM UPM nnUH*nUR5nUSnUSn[U5X'M, U$s snf)zDParse target to e-value mapping parsed from Jackhmmer tblout string.r5rrJr~)rArOr9)re_valuesrErfieldse_value target_names rparse_e_values_from_tbloutr st|H$//1 D1d!W^T1E D)Qi %g  O Es A!A!rc/nUnUHNnUS:XaURS5 MUR5(aUS- nM8URU5 US- nMP U$)zHReturns indices for non-gap/insert residues starting at the given index.rLr=r?)rDrf)rWrindicesrrs r _get_indicesrs]GG S= NN2  ^^   qLG NN7 # qLG NrcR\rSrSr%\\S'\\S'\\S'\\S'\\S'\\S'Srg ) HitMetadatai*pdb_idchainrrlengthtextr#N)r$r%r&r'r)r*r,r-r#rrrr*s K J J H K Irr descriptionc [R"SUR55nU(d[SUS35e[ USUS[ US5[ US5[ US5US S 9$) z3Parses the hmmsearch A3M sequence description line.zF^>?([a-z0-9]+)_(\w+)/([0-9]+)-([0-9]+).*protein length:([0-9]+) *(.*)$zCould not parse description: "z".r?rrr~)rrrrrr)rrrBrrr,)rrs r_parse_hmmsearch_descriptionr4s~ HHQ E 9+bIJJ QxAh%(m aM58} 1X  rr skip_firstc [[[U565nU(aUSSn[USS9n/n[ USS9HunupxSU;aM[ U5n [ UV s/sHoR5=(a U S:gPM sn 5n [XyRS- S9n [UU RSU R3U SUUR5UU S9n URU 5 M U$s sn f) a Parses an a3m string produced by hmmsearch. Args: query_sequence: The query sequence. a3m_string: The a3m string produced by hmmsearch. skip_first: Whether to skip the first sequence in the a3m string. Returns: A sequence of `TemplateHit` results. r?Nr)rz mol:proteinrLrr)rTrSrFrrPrsumisupperrr/rrupperrD)rrdr parsed_a3mr7rr[r6hit_descriptionmetadatarr3r8hits rparse_hmmsearch_a3mrJsc;z234J^  q9M D.7 !.L* *L  / /@lKlIIK4AH4lKL "<~~7IJ OO$Ahnn%56% %++-'#   C%/M( KLs!%C1 )NT)T)(r(rM dataclassesrrrhtypingrrrrrrr r,r+ dataclassr r/r)rFrcrpboolrwrrrrrrrrrr9rrrrrr#rrr s2 GGG(3-( d#  $ 6 d#  $ #c#eHSM8C=,H&I#:;c;c;|$#$#$N'HTN'%('-5c]'$("&6*6*C=6* 6* 6*r#S#CH##(,#,c,c,(*P3*P3*PZ ,S ,S ,Fc%(-5hsm-D s  379 ^8C=^[^B#(;"7* s tCJ/? 3stCy$ d#$ck0,0))$')$()4<[4I)r