{"id":2144,"date":"2022-10-23T10:28:59","date_gmt":"2022-10-23T01:28:59","guid":{"rendered":"https:\/\/www.insilico.jp\/blog\/?p=2144"},"modified":"2023-01-05T14:53:54","modified_gmt":"2023-01-05T05:53:54","slug":"modify_resnumber_1st","status":"publish","type":"post","link":"https:\/\/www.insilico.jp\/blog\/2022\/10\/23\/modify_resnumber_1st\/","title":{"rendered":"PDB\u30d5\u30a1\u30a4\u30eb\u306e\u6b8b\u57fa\u756a\u53f7\u3092\u4fee\u6b63\u3059\u308b\u3000\u524d\u7de8"},"content":{"rendered":"\n

\u306f\u3058\u3081\u306b<\/h2>\n\n\n\n

RCSB Protein Data Bank (RCSB PDB) \u306b\u306f\u975e\u5e38\u306b\u591a\u304f\u306e\u30bf\u30f3\u30d1\u30af\u8cea\u306e\u69cb\u9020\u304c\u767b\u9332\u3055\u308c\u3066\u3044\u307e\u3059\u304c\u3001\u7a00\u306b\u6b8b\u57fa\u756a\u53f7\u304c\u305a\u308c\u3066\u3044\u308b\u5834\u5408\u304c\u3042\u308a\u307e\u3059\u3002\u305d\u306e\u3088\u3046\u306aPDB\u30d5\u30a1\u30a4\u30eb\u306e\u5834\u5408\u3001\u3053\u308c\u306b\u7d10\u4ed8\u3044\u3066\u3044\u308b\u8ad6\u6587\u5185\u3067\u306f\u6b8b\u57fa\u756a\u53f7\u306b\u77db\u76fe\u304c\u7121\u3044\u306e\u3067\u3059\u304c\u3001\u4ed6\u306e\u8ad6\u6587\u306b\u66f8\u304b\u308c\u3066\u3044\u308b\u6b8b\u57fa\u756a\u53f7\u3068\u306f\u7570\u306a\u3063\u3066\u3044\u3066\u9762\u5012\u3067\u3059\u3002\u7279\u306b\u30bf\u30f3\u30d1\u30af\u8cea\u306b\u5909\u7570\u3092\u5165\u308c\u3066\u30ea\u30ac\u30f3\u30c9\u3068\u306e\u6d3b\u6027\u3092\u8272\u3005\u3068\u6e2c\u5b9a\u3057\u3066\u3044\u308b\u8ad6\u6587\u306a\u3069\u3092\u8aad\u3080\u3068\u304d\u306f\u3001\u540c\u6642\u306b\u30bf\u30f3\u30d1\u30af\u8cea\u306e\u7acb\u4f53\u69cb\u9020\u3082\u78ba\u8a8d\u3059\u308b\u306e\u3067\u3001\u756a\u53f7\u304c\u305a\u308c\u3066\u3044\u308b\u3068\u30a4\u30e9\u30a4\u30e9\u3057\u307e\u3059\u3002\u306a\u305c\u6b8b\u57fa\u756a\u53f7\u304c\u305a\u308c\u308b\u306e\u304b\u7406\u7531\u306f\u3088\u304f\u5206\u304b\u308a\u307e\u305b\u3093\u304c\u3001\u4e0a\u8a18\u306e\u3088\u3046\u306a\u5834\u5408\u306b\u4fee\u6b63\u3057\u305f\u3044\u3068\u601d\u3046\u306e\u3067\u306f\u306a\u3044\u3067\u3057\u3087\u3046\u304b\u3002\u4eca\u56de\u306fPDB\u306e\u6b8b\u57fa\u756a\u53f7\u4fee\u6b63\u3059\u308b\u30d7\u30ed\u30b0\u30e9\u30e0\u3092OpenBabel\u3092\u5229\u7528\u3057\u3066\u4f5c\u6210\u3057\u305f\u3044\u3068\u601d\u3044\u307e\u3059\u3002<\/p>\n\n\n\n

\u8a08\u7b97\u5bfe\u8c61\u306a\u3069<\/h2>\n\n\n\n

\u4eca\u56de\u306fPDB code\u304c1LKE\u306e\u3082\u306e\u3092\u4f8b\u306b\u3057\u307e\u3059\u3002\u4eca\u307e\u3067\u79c1\u304c\u6271\u3063\u3066\u6765\u305f\u6b8b\u57fa\u756a\u53f7\u306e\u30ba\u30ec\u305fPDB\u304c\u3069\u308c\u306a\u306e\u304b\u63a2\u3057\u305f\u306e\u3067\u3059\u304c\u3001\u6b8b\u57fa\u756a\u53f7\u304c\u30ba\u30ec\u3066\u3044\u308b\u306e\u306f\u7a00\u306a\u306e\u3067\u3001\u3053\u308c\u306f\u30cd\u30c3\u30c8\u3067\u8272\u3005\u3068\u691c\u7d22\u3057\u3066\u3084\u3063\u3068\u898b\u3064\u3051\u305f\u30bf\u30f3\u30d1\u30af\u8cea\u69cb\u9020(PDB)\u3067\u3059\u3002\u4e0b\u56f3\u306fPyMOL\u30671LKE\u306ePDB\u30d5\u30a1\u30a4\u30eb\u3092\u8aad\u307f\u8fbc\u3093\u3060\u3068\u304d\u306e\u753b\u9762\u3067\u3059\u3002\u753b\u9762\u306e\u4e0a\u90e8\u304c\u30a2\u30df\u30ce\u9178\u914d\u5217\u304c\u4e00\u6587\u5b57\u7565\u53f7\u3067\u8868\u793a\u3055\u308c\u3066\u307e\u3059\u304c\u3001\u30a2\u30b9\u30d1\u30e9\u30ae\u30f3\u9178\u304c5\u756a\u76ee\u304b\u3089\u59cb\u307e\u3063\u3066\u307e\u3059\u3002
\u3057\u304b\u3057UniProt<\/a>\u3067\u30a2\u30df\u30ce\u9178\u914d\u5217\u3092\u8abf\u3079\u3066\u307f\u308b\u3068\u30015\u756a\u76ee\u306f\u30a4\u30bd\u30ed\u30a4\u30b7\u30f3\u3067\u3042\u308b\u3053\u3068\u304c\u308f\u304b\u308a\u307e\u3059\u3002
\u5b9f\u306f\u3053\u306e\u30a2\u30b9\u30d1\u30e9\u30ae\u30f3\u9178\u306fUniProt\u306e\u30a2\u30df\u30ce\u9178\u914d\u5217\u7684\u306b\u306f20\u756a\u76ee\u306b\u76f8\u5f53\u3057\u307e\u3059\u3002<\/p>\n\n\n\n

\u8a08\u7b97\u306e\u65b9\u91dd<\/h2>\n\n\n\n

\u3053\u306e\u3088\u3046\u306aPDB\u306e\u6b8b\u57fa\u756a\u53f7\u306e\u30ba\u30ec\u3092\u4fee\u6b63\u3059\u308b\u30d7\u30ed\u30b0\u30e9\u30e0\u3092\u4f5c\u6210\u3059\u308b\u306b\u3042\u305f\u308a\u3001\u4ee5\u4e0b\u306e\u3088\u3046\u306a\u30b9\u30c6\u30c3\u30d7\u3092\u8003\u3048\u307e\u3059\u3002<\/p>\n\n\n\n

  1. PDB\u30d5\u30a1\u30a4\u30eb\u4e2d\u306e\u30a2\u30df\u30ce\u9178\u914d\u5217\u3092FASTA\u30d5\u30a1\u30a4\u30eb\u306b\u51fa\u529b\u3057\u3001UniProt\u304b\u3089\u57fa\u6e96\u3068\u306a\u308b\u30a2\u30df\u30ce\u9178\u914d\u5217\u306eFASTA\u30d5\u30a1\u30a4\u30eb\u3092\u53d6\u5f97\u3059\u308b\u3002<\/li>
  2. 2\u3064\u306e\u30a2\u30df\u30ce\u9178\u914d\u5217\u3092Clustal Omega\u3092\u5229\u7528\u3057\u3066\u30a2\u30e9\u30a4\u30e1\u30f3\u30c8\u3059\u308b\u3002<\/li>
  3. \u30a2\u30e9\u30a4\u30e1\u30f3\u30c8\u6e08\u307f\u306eFASTA\u30d5\u30a1\u30a4\u30eb\u3068PDB\u30d5\u30a1\u30a4\u30eb\u3092\u8aad\u307f\u8fbc\u3080\u3002<\/li>
  4. FASTA\u30d5\u30a1\u30a4\u30eb\u306b\u5f93\u3063\u3066PDB\u30d5\u30a1\u30a4\u30eb\u4e2d\u306e\u6b8b\u57fa\u756a\u53f7\u3092\u4fee\u6b63\u3059\u308b\u3002<\/li>
  5. \u4fee\u6b63\u5f8c\u306ePDB\u30d5\u30a1\u30a4\u30eb\u3092\u51fa\u529b\u3059\u308b\u3002<\/li><\/ol>\n\n\n\n

    \u4e0a\u8a18\u624b\u9806\u306e\u3046\u30611\u30682\u306f\u30d7\u30ed\u30b0\u30e9\u30e0\u3067\u81ea\u52d5\u5316\u305b\u305a\u306b\u30de\u30cb\u30e5\u30a2\u30eb\u3067\u5b9f\u884c\u3059\u308b\u3053\u3068\u3068\u3057\u307e\u3059\u3002\u3057\u305f\u304c\u3063\u3066\u30d7\u30ed\u30b0\u30e9\u30e0\u3092\u4f5c\u6210\u3059\u308b\u306e\u306f3\u4ee5\u964d\u3068\u306a\u308a\u307e\u3059\u3002PDB\u30d5\u30a1\u30a4\u30eb\u306fOpenBabel\u306e\u30e9\u30a4\u30d6\u30e9\u30ea\u3092\u5229\u7528\u3059\u308c\u3070\u7c21\u5358\u306b\u8aad\u307f\u8fbc\u3080\u30d7\u30ed\u30b0\u30e9\u30e0\u3092\u4f5c\u6210\u3067\u304d\u307e\u3059\u3002\u3055\u3089\u306bOpenBabel\u306fFASTA\u30d5\u30a1\u30a4\u30eb\u306b\u3082\u5bfe\u5fdc\u3057\u3066\u3044\u307e\u3059\u3002\u3057\u304b\u3057\u306a\u304c\u3089\u30a2\u30e9\u30a4\u30e1\u30f3\u30c8\u6e08\u307f\u306eFASTA\u30d5\u30a1\u30a4\u30eb\u4e2d\u306b\u306f\u30ae\u30e3\u30c3\u30d7\u3092\u793a\u3059”-“\u8a18\u53f7\u304c\u542b\u307e\u308c\u307e\u3059\u304c\u3001OpenBabel\u306f\u30ae\u30e3\u30c3\u30d7\u8a18\u53f7\u306b\u306f\u5bfe\u5fdc\u3057\u3066\u3044\u306a\u3044\u3088\u3046\u306a\u306e\u3067\u3001FASTA\u30d5\u30a1\u30a4\u30eb\u3092\u53d6\u308a\u6271\u3046\u90e8\u5206\u306b\u3064\u3044\u3066\u306f\u81ea\u4f5c\u3059\u308b\u3053\u3068\u3068\u3057\u307e\u3059\u3002\u524d\u7de8\u3067\u306fFASTA\u30d5\u30a1\u30a4\u30eb\u3092\u53d6\u308a\u6271\u3046\u90e8\u5206\u306b\u3064\u3044\u3066\u898b\u3066\u3044\u304f\u3053\u3068\u3068\u3057\u307e\u3057\u3087\u3046\u3002<\/p>\n\n\n\n

    \u30a2\u30df\u30ce\u9178\u914d\u5217\u306e\u30a2\u30e9\u30a4\u30e1\u30f3\u30c8<\/h2>\n\n\n\n

    \u5148\u305a\u306fPDB\u30d5\u30a1\u30a4\u30eb\u4e2d\u306e\u30a2\u30df\u30ce\u9178\u914d\u5217\u3068UniProt\u304b\u3089\u306e\u30a2\u30df\u30ce\u9178\u914d\u5217\u3092\u30a2\u30e9\u30a4\u30e1\u30f3\u30c8\u3057\u307e\u3059\u3002\u4ee5\u4e0b\u306e\u3088\u3046\u306aOpenBabel\u306e\u30b3\u30de\u30f3\u30c9\u3067PDB\u30d5\u30a1\u30a4\u30eb<\/a>\u304b\u3089\u30a2\u30df\u30ce\u9178\u914d\u5217\u3092\u53d6\u308a\u51fa\u3057\u307e\u3059\u3002<\/p>\n\n\n\n

    $ obabel 1lke.pdb -O 1lke.fasta<\/code><\/pre>\n\n\n\n
    \u51fa\u529b\u3055\u308c\u305fFASTA\u30d5\u30a1\u30a4\u30eb\u306f\u6b21\u306e\u3088\u3046\u306b\u306a\u308a\u307e\u3059\u3002<\/p>\n\n\n\n
    >1lke.pdb 216 bp; generated with OpenBabel 3.1.0\nDGACPEVKPVDNFDWSQYHGKWWQVAAYPDHITKYGKCGWAEYTPEGKSVKVSRYSVIHG\nKEYFSEGTAYPVGDSKIGKIYHSYTIGGVTQEGVFNVLSTDNKNYIIGYFCSYGHMDLVW\nVLSRSMVLTGEAKTAVENYLIGSPVVDSQKLVYSDFSX<\/code><\/pre>\n\n\n\n
    \u305d\u3057\u3066UniProt\u304b\u3089FASTA\u30d5\u30a1\u30a4\u30eb<\/a>\u3092\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3057\u307e\u3059\u3002\u3053\u306eFASTA\u30d5\u30a1\u30a4\u30eb\uff08\u30d5\u30a1\u30a4\u30eb\u540d”P09464.fasta”\uff09\u306e\u5185\u5bb9\u306f\u6b21\u306e\u901a\u308a\u3067\u3059\u3002<\/p>\n\n\n\n
    >sp|P09464|BBP_PIEBR Bilin-binding protein OS=Pieris brassicae OX=7116 PE=1 SV=2\nMQYLIVLALVAAASANVYHDGACPEVKPVDNFDWSNYHGKWWEVAKYPNSVEKYGKCGWA\nEYTPEGKSVKVSNYHVIHGKEYFIEGTAYPVGDSKIGKIYHKLTYGGVTKENVFNVLSTD\nNKNYIIGYYCKYDEDKKGHQDFVWVLSRSKVLTGEAKTAVENYLIGSPVVDSQKLVYSDF\nSEAACKVNN<\/code><\/pre>\n\n\n\n
    2\u3064\u306eFASTA\u30d5\u30a1\u30a4\u30eb\u3092\u7528\u610f\u3067\u304d\u305f\u3089\u7d50\u5408\u3057\u307e\u3059\u3002<\/p>\n\n\n\n
    $ cat 1lke.fasta P09464.fasta > All.fasta<\/code><\/pre>\n\n\n\n
    2\u3064\u306e\u914d\u5217\u3092\u7d50\u5408\u3057\u305f\u3053\u306e\u30d5\u30a1\u30a4\u30eb\u3092Clustal Omega\u3092\u5229\u7528\u3057\u3066\u30a2\u30e9\u30a4\u30e1\u30f3\u30c8\u3057\u307e\u3059\u3002<\/p>\n\n\n\n
    $ clustalo -i All.fasta -o aligned.fasta<\/code><\/pre>\n\n\n\n
    \u3061\u306a\u307f\u306bClustal Omega\u306fAnaconda\u3092\u5229\u7528\u3059\u308b\u3068\u3001\u6b21\u306e\u30b3\u30de\u30f3\u30c9\u306b\u3088\u308a\u7c21\u5358\u306b\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3067\u304d\u307e\u3059\u3002<\/p>\n\n\n\n
    $ conda install -c bioconda clustalo<\/code><\/pre>\n\n\n\n
    \u6700\u5f8c\u306bClustal Omega\u306b\u3088\u3063\u3066\u30a2\u30e9\u30a4\u30e1\u30f3\u30c8\u3055\u308c\u305fFASTA\u30d5\u30a1\u30a4\u30eb\u306f\u6b21\u306e\u3088\u3046\u306a\u7121\u3044\u3088\u3046\u306b\u306a\u308a\u307e\u3059\u3002\u4e0a\u306e\u65b9\u304cPDB\u30d5\u30a1\u30a4\u30eb\u306e\u30a2\u30df\u30ce\u9178\u914d\u5217\u3067\u3001\u6240\u3005\u306b\u30ae\u30e3\u30c3\u30d7\u304c\u5165\u308b\u3053\u3068\u306b\u3088\u3063\u3066UniProt\u306e\u30a2\u30df\u30ce\u9178\u914d\u5217\u3092\u57fa\u6e96\u3068\u3057\u305f\u6b8b\u57fa\u756a\u53f7\u306b\u4fee\u6b63\u3067\u304d\u307e\u3059\u3002<\/p>\n\n\n\n
    $ cat aligned.fasta\n>1lke.pdb 216 bp; generated with OpenBabel 3.1.0\n-------------------DGACPEVKPVDNFDWSQYHGKWWQVAAYPDHITKYGKCGWA\nEYTPEGKSVKVSRYSVIHGKEYFSEGTAYPVGDSKIGKIYHSYTIGGVTQEGVFNVLSTD\nNKNYIIGYFCSY-----GHMDLVWVLSRSMVLTGEAKTAVENYLIGSPVVDSQKLVYSDF\nSX-------\n>sp|P09464|BBP_PIEBR Bilin-binding protein OS=Pieris brassicae OX=7116 PE=1 SV=2\nMQYLIVLALVAAASANVYHDGACPEVKPVDNFDWSNYHGKWWEVAKYPNSVEKYGKCGWA\nEYTPEGKSVKVSNYHVIHGKEYFIEGTAYPVGDSKIGKIYHKLTYGGVTKENVFNVLSTD\nNKNYIIGYYCKYDEDKKGHQDFVWVLSRSKVLTGEAKTAVENYLIGSPVVDSQKLVYSDF\nSEAACKVNN<\/code><\/pre>\n\n\n\n
    \u30d7\u30ed\u30b0\u30e9\u30e0\u89e3\u8aac<\/h2>\n\n\n\n
    \u4eca\u56de\u306e\u30d6\u30ed\u30b0\u3067\u7d39\u4ecb\u3059\u308b\u30d7\u30ed\u30b0\u30e9\u30e0\uff08\u30d7\u30ed\u30b0\u30e9\u30e0\u540d\u3092read_fasta.cpp\u3068\u3057\u307e\u3059\uff09\u306fclustalo\u30b3\u30de\u30f3\u30c9\u304b\u3089\u51fa\u529b\u3055\u308c\u305fFASTA\u30d5\u30a1\u30a4\u30eb\uff08aligned.fasta\uff09\u304b\u3089\u6700\u521d\u306e\u914d\u5217\u3092\u8aad\u307f\u8fbc\u3093\u3067\u3001\u305d\u306e\u307e\u307eFASTA\u5f62\u5f0f\u3067\u51fa\u529b\u3059\u308b\u3068\u3044\u3046\u3082\u306e\u3067\u3059\u3002\u3053\u306e\u30d7\u30ed\u30b0\u30e9\u30e0\u306e\u30b3\u30f3\u30d1\u30a4\u30eb\u3068\u5b9f\u884c\u65b9\u6cd5\u306f\u4ee5\u4e0b\u306e\u901a\u308a\u3067\u3059\u3002<\/p>\n\n\n\n
    read_fasta.cpp<\/a>\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9<\/a><\/div>\n\n\n\n
    $ g++ read_fasta.cpp\n$ .\/a.out\n>1lke.pdb 216 bp; generated with OpenBabel 3.1.0\n-------------------DGACPEVKPVDNFDWSQYHGKWWQVAAYPDHITKYGKCGWA\nEYTPEGKSVKVSRYSVIHGKEYFSEGTAYPVGDSKIGKIYHSYTIGGVTQEGVFNVLSTD\nNKNYIIGYFCSY-----GHMDLVWVLSRSMVLTGEAKTAVENYLIGSPVVDSQKLVYSDF\nSX-------<\/code><\/pre>\n\n\n\n
    \u305d\u308c\u3067\u306f\u30d7\u30ed\u30b0\u30e9\u30e0\u3092\u898b\u3066\u3044\u304d\u307e\u3057\u3087\u3046\u3002
    C++\u306e\u30bd\u30fc\u30b9\u30b3\u30fc\u30c9\u306f\u4ee5\u4e0b\u306e\u901a\u308a\u3067\u3059\u3002<\/p>\n\n\n\n
      1 #include <iostream>\n  2 #include <fstream>\n  3 #include <sstream>\n  4 #include <string>\n  5 #include <vector>\n  6 #include <map>\n  7 \n  8 using namespace std;\n  9 \n 10 \/\/ 1\u6587\u5b57\u30923\u6587\u5b57\u306b\u5909\u63db\u3059\u308b\u305f\u3081\u306e\u5909\u6570\u8a2d\u5b9a\n 11 map<char, string> aa3;\n 12 \n 13 void init(void) {\n 14   aa3['A'] = \"ALA\";\n 15   aa3['R'] = \"ARG\";\n 16   aa3['N'] = \"ASN\";\n 17   aa3['D'] = \"ASP\";\n 18   aa3['C'] = \"CYS\";\n 19   aa3['E'] = \"GLU\";\n 20   aa3['Q'] = \"GLN\";\n 21   aa3['G'] = \"GLY\";\n 22   aa3['H'] = \"HIS\";\n 23   aa3['I'] = \"ILE\";\n 24   aa3['L'] = \"LEU\";\n 25   aa3['K'] = \"LYS\";\n 26   aa3['M'] = \"MET\";\n 27   aa3['F'] = \"PHE\";\n 28   aa3['P'] = \"PRO\";\n 29   aa3['S'] = \"SER\";\n 30   aa3['T'] = \"THR\";\n 31   aa3['W'] = \"TRP\";\n 32   aa3['Y'] = \"TYR\";\n 33   aa3['V'] = \"VAL\";\n 34   aa3['-'] = \"GAP\";\n 35   aa3['X'] = \"ANY\";\n 36 }\n 37 \n 38 class SEQ {\n 39   string name;\n 40   string seq;\n 41   vector<pair<string, int> > seq3l;\n 42   int pos;\n 43 \n 44  public:\n 45   SEQ() : pos(0) {}  \/\/ \u30b3\u30f3\u30b9\u30c8\u30e9\u30af\u30bf\n 46 \n 47   SEQ(const SEQ& Obj) {  \/\/ \u30b3\u30d4\u30fc\u30b3\u30f3\u30b9\u30c8\u30e9\u30af\u30bf\n 48     name = Obj.name;\n 49     seq = Obj.seq;\n 50     seq3l = Obj.seq3l;\n 51     pos = Obj.pos;\n 52   }\n 53 \n 54   ~SEQ() {}  \/\/ \u30c7\u30b9\u30c8\u30e9\u30af\u30bf\n 55 \n 56   bool ReadFASTA(istream* ist) {\n 57     bool _f = false;\n 58     string line;\n 59     pos = 0;\n 60 \n 61     name.clear();\n 62     while (getline(*ist, line)) {\n 63       if (line[0] == '>') {\n 64         name = line.substr(1);\n 65         _f = true;\n 66         break;\n 67       }\n 68     }\n 69     if (!_f) {\n 70       return false;\n 71     }\n 72 \n 73     seq.clear();\n 74     streampos spos;\n 75     while (getline(*ist, line)) {\n 76       if (line[0] == '>') {\n 77         break;\n 78       }\n 79       seq = seq + line;\n 80       spos = ist->tellg();\n 81     }\n 82     ist->seekg(spos);\n 83 \n 84     this->ToTLC();\n 85 \n 86     return (true);\n 87   }\n 88 \n 89   void ToTLC(void) {\n 90     seq3l.clear();\n 91     for (int i = 0; i < seq.size(); i++) {\n 92       seq3l.push_back(pair<string, int>(aa3[seq[i]], i + 1));\n 93     }\n 94   }\n 95 \n 96   string GetName(void) { return name; }\n 97 \n 98   void SetName(string s) { name = s; }\n 99 \n100   int length(void) { return seq.size(); }\n101 \n102   void Reset(void) { pos = 0; }\n103 \n104   char GetChar(int p) {\n105     if (p > seq.size()) return '\\0';\n106     return seq[p - 1];\n107   }\n108 \n109   string GetTLC(int p) {\n110     if (p > seq.size()) return \"END\";\n111     return seq3l[p - 1].first;\n112   }\n113 \n114   pair<string, int> Next(void) {\n115     if (pos >= seq.size()) return pair<string, int>(\"END\", pos);\n116     return seq3l[pos++];\n117   }\n118 \n119   void print_seq(ostream* ost) {\n120     string x;\n121     *ost << \">\" << name << endl;\n122     int i = 0;\n123     for (; i < seq.size() \/ 60; i++) {\n124       x = seq.substr(i * 60, 60);\n125       *ost << x << endl;\n126     }\n127     x = seq.substr(i * 60);\n128     *ost << x << endl;\n129   }\n130 };\n131 \n132 int main(int argc, char* argv[]) {\n133   init();\n134   SEQ s;\n135   ifstream ifs(\"aligned.fasta\");\n136   s.ReadFASTA(&ifs);\n137   s.print_seq(&cout);\n138 \n139   return 0;\n140 }<\/code><\/pre>\n\n\n\n
    \u305d\u308c\u3067\u306f\u7c21\u5358\u306b\u8aac\u660e\u3057\u307e\u3057\u3087\u3046\u300210\u301c36\u884c\u76ee\u3067\u306f\u30a2\u30df\u30ce\u9178\u306e1\u6587\u5b57\u8868\u8a18\u304b\u30893\u6587\u5b57\u8868\u8a18\u3078\u5909\u63db\u3059\u308b\u305f\u3081\u306e\u30c7\u30fc\u30bf\u3092map\u3092\u5229\u7528\u3057\u3066\u8a2d\u5b9a\u3057\u3066\u3044\u307e\u3059\u300238\u884c\u76ee\u3067\u30a2\u30df\u30ce\u9178\u914d\u5217\u3092\u6271\u3046\u30af\u30e9\u30b9\u3092\u5b9a\u7fa9\u304c\u59cb\u307e\u308a\u307e\u3059\u300245\u301c54\u884c\u76ee\u3067\u30b3\u30f3\u30b9\u30c8\u30e9\u30af\u30bf\u3001\u30b3\u30d4\u30fc\u30b3\u30f3\u30b9\u30c8\u30e9\u30af\u30bf\u3001\u30c7\u30b9\u30c8\u30e9\u30af\u30bf\u306e3\u3064\u306e\u30e1\u30bd\u30c3\u30c9\u3092\u5b9a\u7fa9\u3057\u3066\u3044\u307e\u3059\u3002C++\u3067\u30af\u30e9\u30b9\u3092\u4f5c\u6210\u3059\u308b\u969b\u306b\u3053\u306e3\u3064\u306e\u30e1\u30bd\u30c3\u30c9\u304c\u5b9a\u7fa9\u3055\u308c\u3066\u3044\u308b\u3053\u3068\u304c\u5927\u5207\u3067\u3059\u3002\u7121\u304f\u3066\u3082\u51e6\u7406\u7cfb\u306e\u65b9\u3067\u4f55\u3068\u304b\u3057\u3066\u304f\u308b\u3053\u3068\u304c\u591a\u3044\u3067\u3059\u304c\u3001\u7a00\u306b\u60f3\u5b9a\u5916\u306e\u52d5\u4f5c\u3057\u3066\u30d0\u30b0\u308b\u3053\u3068\u304c\u3042\u308b\u306e\u3067\u3001\u9762\u5012\u3067\u3059\u304c\u3061\u3083\u3093\u3068\u5b9a\u7fa9\u3057\u307e\u3057\u3087\u3046\u3002\u3068\u306f\u8a00\u3063\u3066\u3082\u3053\u306e\u4f8b\u3067\u306f\u5927\u3057\u305f\u3053\u3068\u306f\u8a18\u8ff0\u3057\u3066\u3044\u307e\u305b\u3093\u3051\u3069\u306d\u300256\u301c87\u884c\u76ee\u3067\u306fFASTA\u30d5\u30a1\u30a4\u30eb\u304b\u30891\u3064\u5206\u306e\u30a2\u30df\u30ce\u914d\u5217\u3092\u8aad\u307f\u8fbc\u3080\u30e1\u30bd\u30c3\u30c9\u3092\u8a18\u8ff0\u3057\u3066\u3044\u307e\u3059\u3002\u3053\u306e\u30e1\u30bd\u30c3\u30c9\u3067\u306fFASTA\u30d5\u30a1\u30a4\u30eb\u3092\u8aad\u307f\u8fbc\u3093\u3067\u304b\u30891\u6587\u5b57\u8868\u8a18\u30923\u6587\u5b57\u8868\u8a18\u306b\u5909\u63db\u3057\u3066\u3044\u307e\u3059\u3002\u5909\u63db\u3059\u308b\u90e8\u5206\u306f\u76f4\u3050\u4e0b\u306e89\u301c94\u884c\u76ee\u306e”ToTLC”\u3068\u3044\u3046\u30e1\u30bd\u30c3\u30c9\u306b\u8a18\u8ff0\u3057\u3066\u3044\u307e\u3059\u300296\u301c117\u884c\u76ee\u3067\u306fSEQ\u30af\u30e9\u30b9\u4e2d\u306e\u30d7\u30ed\u30d1\u30c6\u30a3\u306b\u30a2\u30af\u30bb\u30b9\u3059\u308b\u305f\u3081\u306e\u8272\u3005\u306a\u30e1\u30bd\u30c3\u30c9\u3092\u8a18\u8ff0\u3057\u3066\u3044\u307e\u3059\u3002\u305d\u3057\u3066119\u301c129\u884c\u76ee\u3067\u306fFASTA\u5f62\u5f0f\u3067\u51fa\u529b\u3059\u308b\u90e8\u5206\u3092\u8a18\u8ff0\u3057\u3066\u3044\u307e\u3059\u3002<\/p>\n\n\n\n
    \u6700\u5f8c\u306e\u65b9\u306e132\u301c140\u884c\u76ee\u306bmain\u95a2\u6570\u304c\u8a18\u8ff0\u3055\u308c\u3066\u3044\u307e\u3059\u3002\u305f\u3060\u5358\u306bFASTA\u3092\u8aad\u307f\u8fbc\u3093\u3067\u304b\u3089\u3001\u305d\u306e\u307e\u307eFASTA\u5f62\u5f0f\u3067\u6a19\u6e96\u51fa\u529b\u3059\u308b\u3068\u3044\u3046\u5185\u5bb9\u3067\u3059\u3002\u51fa\u529b\u5148\u3092\u30d5\u30a1\u30a4\u30eb\u306b\u3057\u305f\u3044\u5834\u5408\u306fofstream\u3067\u51fa\u529b\u5148\u3092\u5b9a\u7fa9\u3057\u3066\u3001\u305d\u306e\u30dd\u30a4\u30f3\u30bf\u3092print_seq\u30e1\u30bd\u30c3\u30c9\u306e\u5f15\u6570\u306b\u5165\u308c\u3066\u3042\u3052\u308c\u3070OK\u3067\u3059\u3002<\/p>\n\n\n\n
    \u3056\u3063\u304f\u308a\u3068\u3057\u305f\u8aac\u660e\u3067\u3057\u305f\u304c\u3001PDB\u30d5\u30a1\u30a4\u30eb\u306e\u6b8b\u57fa\u756a\u53f7\u3092\u4fee\u6b63\u3059\u308b\u305f\u3081\u306e\u6e96\u5099\u304c\u3053\u308c\u3067\u6574\u3044\u307e\u3057\u305f\u3002\u5f8c\u7de8\u3067\u306f\u3053\u306e\u30d7\u30ed\u30b0\u30e9\u30e0\u306b\u3055\u3089\u306bOpenBabel\u3092\u4f7f\u7528\u3059\u308b\u90e8\u5206\u3092\u4ed8\u3051\u8db3\u3057\u3066\u30d7\u30ed\u30b0\u30e9\u30e0\u3092\u5b8c\u6210\u3055\u305b\u305f\u3044\u3068\u601d\u3044\u307e\u3059\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"
    \u306f\u3058\u3081\u306b RCSB Protein Data Bank (RCSB PDB) \u306b\u306f\u975e\u5e38\u306b\u591a\u304f\u306e\u30bf\u30f3\u30d1\u30af\u8cea\u306e\u69cb\u9020\u304c\u767b\u9332\u3055\u308c\u3066\u3044\u307e\u3059\u304c\u3001\u7a00\u306b\u6b8b\u57fa\u756a\u53f7\u304c\u305a\u308c\u3066\u3044\u308b\u5834\u5408\u304c\u3042\u308a\u307e\u3059\u3002\u305d\u306e\u3088\u3046\u306aPDB\u30d5\u30a1\u30a4\u30eb\u306e\u5834\u5408\u3001\u3053\u308c\u306b\u7d10\u4ed8\u3044\u3066\u3044…<\/p>\n","protected":false},"author":5,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[32,15],"tags":[122],"class_list":["post-2144","post","type-post","status-publish","format-standard","hentry","category-openbabel","category-15","tag-pdb"],"yoast_head":"\nPDB\u30d5\u30a1\u30a4\u30eb\u306e\u6b8b\u57fa\u756a\u53f7\u3092\u4fee\u6b63\u3059\u308b\u3000\u524d\u7de8 - In Silico \u5275\u85ac<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.insilico.jp\/blog\/2022\/10\/23\/modify_resnumber_1st\/\" \/>\n<meta property=\"og:locale\" content=\"ja_JP\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"PDB\u30d5\u30a1\u30a4\u30eb\u306e\u6b8b\u57fa\u756a\u53f7\u3092\u4fee\u6b63\u3059\u308b\u3000\u524d\u7de8 - 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