ConstructBuilder/builder.py

G = 'MVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITLGMDELYK'
L2 = 'XXXXXXX'
T = 'LEENLYFQS'
L1 = 'GGSGGGSGGGSGGGS'
H = 'HHHHHH'
soluTag = {
    'MBP': 'MKIKTGARILALSALTTMMFSASALAKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTRITK',
    'SUMO': 'MSDQEAKPSTEDLGDKKEGEYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTGGHSTV',
    'Fh8': 'MPSVQEVEKLLHVLDRNGDGKVSAEELKAFADDSKCPLDSNKIKAFIKEHDKNKDGKLDLKELVSILSS',
    'GST': 'MKLFYKPGACSLASHITLRESGKDFTLVSVDLMKKRLENGDDYFAVNPKGQVPALLLDDGTLLTEGVAIMQYLADSVPDRQLLAPVNSISRYKTIEWLNYIATELHKGFTPLFRPDTPEEYKPTVRAQLEKKLQYVNEALKDEHWICGQRFTIADAYLFTVLRWAYAVKLNLEGLEHIAAFMQRMAERPEVQDALSAEGLK',
    'MBP': 'MKIKTGARILALSALTTMMFSASALAKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTRITK',
    'NusA': 'MNKEILAVVEAVSNEKALPREKIFEALESALATATKKKYEQEIDVRVQIDRKSGDFDTFRRWLVVDEVTQPTKEITLEAARYEDESLNLGDYVEDQIESVTFDRITTQTAKQVIVQKVREAERAMVVDQFREHEGEIITGVVKKVNRDNISLDLGNNAEAVILREDMLPRENFRPGDRVRGVLYSVRPEARGAQLFVTRSKPEMLIELFRIEVPEIGEEVIEIKAAARDPGSRAKIAVKTNDKRIDPVGACVGMRGARVQAVSTELGGERIDIVLWDDNPAQFVINAMAPADVASIVVDEDKHTMDIAVEAGNLAQAIGRNGQNVRLASQLSGWELNVMTDDLQAKHQAEAHAAIDTFTKYLDIDEDFATVLVEEGFSTLEELAYVPMKELLEIEGLDEPTVEALRERAKNALATIAQAQEESLGDNKPADDLLNLEGVDRDLAFKLAARGVCTLEDLAEQGIDDLADIEGLTDEKAGALIMAARNICWFGDEA',
    'Thioredoxin': 'SDKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANLA',
    'FLAG': 'DYKDDDDK',
    'S-tag': 'KETAAAKFERQHMDS',
    'CBP': 'KRRWKKNFIAVSAANRFKKISSSGAL',
    'SUMO': 'MSDQEAKPSTEDLGDKKEGEYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTGGHSTV',
    'STREPII': 'WSHPQFEK',
    'BAP': 'GLNDIFEAQKIEWHE',
    'NT11': 'VSEPHDYNYEK',
    'Fh8': 'MPSVQEVEKLLHVLDRNGDGKVSAEELKAFADDSKCPLDSNKIKAFIKEHDKNKDGKLDLKELVSILSS',
    'Tab2': 'VVSHFND',
    'Z-basic': 'VDNKFNKEQQNAFYEILHLPNLNEEQRNAFIQSLKDDPSQSANLLAEAKKLNDAQPK',
    'ProteinA': 'MKKKNIYSIRKLGVGIASVTLGTLLISGGVTPAANAAQHDEAQQNAFYQVLNMPNLNADQRNGFIQSLKDDPSQSANVLGEAQKLNDSQAPKADAQQNNFNKDQQSAFYEILNMPNLNEAQRNGFIQSLKDDPSQSTNVLGEAKKLNESQAPKADNNFNKEQQNAFYEILNMPNLNEEQRNGFIQSLKDDPSQSANLLSEAKKLNESQAPKADNKFNKEQQNAFYEILHLPNLNEEQRNGFIQSLKDDPSQSANLLAEAKKLNDAQAPKADNKFNKEQQNAFYEILHLPNLTEEQRNGFIQSLKDDPSVSKEILAEAKKLNDAQAPKEEDNNKPGKEDNNKPGKEDNNKPGKEDNNKPGKEDNNKPGKEDGNKPGKEDNKKPGKEDGNKPGKEDNKKPGKEDGNKPGKEDGNKPGKEDGNGVHVVKPGDTVNDIAKANGADKIAADNKLADKNMIKPGQELVVDKKQPANHADANKAQALPETGEENPFIGTTVFGGLSLALGAALLEL',
    'IMPACT': 'TNPGVSAWQVNTAYTAGQLVTYNGKTYKCLQPHTSLAGWEPSNVPALWQLQ',
    'mysB': 'MTMYATLEEAIDAAREEFLADNPGIDAEDANVQQFNAQKYVLQDGDIMWQVEFFADEGEEGECLPMLSGEAAQSVFDGDYDEIEIRQEWQEENTLHEWDEGEFQLEPPLDTEEGRAAADEWDER',
    'PolyR': 'RRRRR',
    'c-myc': 'EQKLISEEDL',
    'S': 'KETAAAKFERQHMDS',
    'SBP-tag': 'MDEKTTGWRGGHVVEGLAGELEQLRARLEHHPQGQREP',
    'Strep-tag': 'WRHPQFGG',
    'Twin-Strep-tag': 'SAWSHPQFEKGGGSGGGSGGSAWSHPQFEK',
    'HAT': 'KDHLIHNVHKEFHAHAHNK',
    'BCCP': 'MDIRKIKKLIELVEESGISELEISEGEESVRISRAAPAASFPVMQQAYAAPMMQQPAQSNAAAPATVPSMEAPAAAEISGHIVRSPMVGTFYRTPSPDAKAFIEVGQKVNVDTLCIVEAMKMMNQIEADKSGTVKAILVESGQPVEFDEPLVVIE',
    'HaloTag': 'SGSAEIGTGFPFDPHYVEVLGERMHYVDVGPRDGTPVLFLHGNPTSSYVWRNIIPHVAPTHRCIAPDLIGMGKSDKPDLGYFFDDHVRFMDAFIEALGLEEVVLVIHDWGSALGFHWAKRNPERVKGIAFMEFIRPIPTWDEWPEFARETFQAFRTTDVGRKLIIDQNVFIEGTLPCGVVRPLTEVEMDHYREPFLNPVDREPLWRFPNELPIAGEPANIVALVEEYMDWLHQSPVPKLLFWGTPGVLIPPAEAARLAKSLPNCKAVDIGPGLNLLQEDNPDLIGSEIARWLSTLEISG'
    }

def run_N(P:str, gfp:bool, solu_tag:list)->dict:
    const = {}
    if gfp:
        for f in solu_tag:
            F = soluTag[f]
            const[f"con_gfp_N_{f}"] = P+T+L1+F+L2+G+H
        if not solu_tag:
            const[f"con_gfp_N"] = P+T+L2+G+H
    else:
        for f in solu_tag:
            F = soluTag[f]
            const[f"con_N_{f}"] = P+T+L1+F+H
        if not solu_tag:
            const[f"con_N"] = P+T+H # TODO: verify this one
    return const

def run_C(P:str, gfp:bool, solu_tag:list)->dict:
    const = {}
    if gfp:
        for f in solu_tag:
            F = soluTag[f]
            const[f"con_gfp_C_{f}"] = H+G+L2+F+L1+T+P
        if not solu_tag:
            const[f"con_gfp_C"] = H+G+L2+T+P
    else:
        for f in solu_tag:
            F = soluTag[f]
            const[f"con_C_{f}"] = H+F+L1+T+P
        if not solu_tag:
            const[f"con_C"] = H+T+P #TODO verify this
    return const

def build(P:str, solu_tag:list, GFP:bool, P_pos:str)->dict:
    """
    This function calculate constructs to Protera's LAB considering:
        -orientation N to C terminal, or reverse
        -With/withou GFP
        -Fusion Proteins
    
    usage = build( amino_sequence, solutags, GFP:True/false, P_pos:"N+C","N","C")    
    solutags availables:
            'MBP', 'SUMO', 'Fh8', 'GST', 'NusA', 'Thioredoxin', 'FLAG', 'S-tag', 'CBP', 'STREPII', 'BAP', 'NT11', 'Tab2', 'Z-basic', 'ProteinA', 'IMPACT', 'mysB', 'PolyR', 'c-myc', 'S', 'SBP-tag', 'Strep-tag', 'Twin-Strep-tag', 'HAT', 'BCCP', 'HaloTag'
    
    """
    if "all" in solu_tag:
        solu_tag = list(soluTag.keys())
    
    d1 = {}
    d2 = {}
    
    if  "C" in P_pos:
        d2 = run_C(P, GFP, solu_tag)
        
    if "N" in P_pos:
        d1 = run_N(P, GFP, solu_tag)
        
    return {**d1,**d2}