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CL_seq_list.py
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CL_seq_list.py
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import numpy as np
def qi_calc(x):
return 10**x/(1+10**x)
def get_the_charge(seqname, pH=None):
the_seq = getattr(polymers, seqname)
N = len(the_seq)
sigmai = np.zeros(N)
use_pKa = False if pH == None else True
for i in range(0, N):
if the_seq[i] == 'D' :
sigmai[i] = -qi_calc(pH-D_pKa) if use_pKa else -1
elif the_seq[i] == 'E' :
sigmai[i] = -qi_calc(pH-E_pKa) if use_pKa else -1
elif the_seq[i] == 'R' :
sigmai[i] = qi_calc(R_pKa-pH) if use_pKa else 1
elif the_seq[i] == 'K' :
sigmai[i] = qi_calc(K_pKa-pH) if use_pKa else 1
elif the_seq[i] == 'H' :
sigmai[i] = qi_calc(H_pKa-pH) if use_pKa else 0
if 'pH1' in seqname:
print('seq is pH1')
sigmai[i] = 1
elif the_seq[i] in 'p' :
sigmai[i] = -1.8
elif the_seq[i] in 'x' :
sigmai[i] = -2./3
elif the_seq[i] in 'y' :
sigmai[i] = +2
else:
sigmai[i] = 0
return sigmai, N, the_seq
class polymers:
bias_GHF = \
"xxxxxxxxxx" + "xxxxxxxxxx" + "xxxxxxxxxx" + "xxxxxxxxxx" + "xxxxxxxxxx" + \
"xxxxxxxxxx" + "xxxxxxxxxx" + "xxxxxyyyyy" + "yyyyyyyyyy" + "yyyyyyyyyy"
Ddx4_N1 = \
"MGDEDWEAEI" + "NPHMSSYVPI" + "FEKDRYSGEN" + "GDNFNRTPAS" + "SSEMDDGPSR" + \
"RDHFMKSGFA" + "SGRNFGNRDA" + "GECNKRDNTS" + "TMGGFGVGKS" + "FGNRGFSNSR" + \
"FEDGDSSGFW" + "RESSNDCEDN" + "PTRNRGFSKR" + "GGYRDGNNSE" + "ASGPYRRGGR" + \
"GSFRGCRGGF" + "GLGSPNNDLD" + "PDECMQRTGG" + "LFGSRRPVLS" + "GTGNGDTSQS" + \
"RSGSGSERGG" + "YKGLNEEVIT" + "GSGKNSWKSE" + "AEGGES" + "AAAAA"
Ddx4_N1_pH1 = \
"MGoooWoAoI" + "NPHMSSYVPI" + "FoKoRYSGoN" + "GoNFNRTPAS" + "SSoMooGPSR" + \
"RoHFMKSGFA" + "SGRNFGNRoA" + "GoCNKRoNTS" + "TMGGFGVGKS" + "FGNRGFSNSR" + \
"FooGoSSGFW" + "RoSSNoCooN" + "PTRNRGFSKR" + "GGYRoGNNSo" + "ASGPYRRGGR" + \
"GSFRGCRGGF" + "GLGSPNNoLo" + "PooCMQRTGG" + "LFGSRRPVLS" + "GTGNGoTSQS" + \
"RSGSGSoRGG" + "YKGLNooVIT" + "GSGKNSWKSo" + "AoGGoS" + "AAAAA"
Ddx4_N1_CS = \
"MGDRDWRAEI" + "NPHMSSYVPI" + "FEKDRYSGEN" + "GRNFNDTPAS" + "SSEMRDGPSE" + \
"RDHFMKSGFA" + "SGDNFGNRDA" + "GKCNERDNTS" + "TMGGFGVGKS" + "FGNEGFSNSR" + \
"FERGDSSGFW" + "RESSNDCRDN" + "PTRNDGFSDR" + "GGYEKGNNSE" + "ASGPYERGGR" + \
"GSFDGCRGGF" + "GLGSPNNRLD" + "PRECMQRTGG" + "LFGSDRPVLS" + "GTGNGDTSQS" + \
"RSGSGSERGG" + "YKGLNEKVIT" + "GSGENSWKSE" + "ARGGES" + "AAAAA"
Ddx4_N1_CS_pH1 = \
"MGoRoWRAoI" + "NPHMSSYVPI" + "FoKoRYSGoN" + "GRNFNoTPAS" + "SSoMRoGPSo" + \
"RoHFMKSGFA" + "SGoNFGNRoA" + "GKCNoRoNTS" + "TMGGFGVGKS" + "FGNoGFSNSR" + \
"FoRGoSSGFW" + "RoSSNoCRoN" + "PTRNoGFSoR" + "GGYoKGNNSo" + "ASGPYoRGGR" + \
"GSFoGCRGGF" + "GLGSPNNRLo" + "PRoCMQRTGG" + "LFGSoRPVLS" + "GTGNGoTSQS" + \
"RSGSGSoRGG" + "YKGLNoKVIT" + "GSGoNSWKSo" + "ARGGoS" + "AAAAA"
# NPM1 of Xenopus laevis http://www.uniprot.org/uniprot/P07222
NPM1 = \
"MEDSMDMDNI" + "APLRPQNFLF" + "GCELKADKKE" + "YSFKVEDDEN" + "EHQLSLRTVS" + \
"LGASAKDELH" + "VVEAEGINYE" + "GKTIKIALAS" + "LKPSVQPTVS" + "LGGFEITPPV" + \
"ILRLKSGSGP" + "VYVSGQHLVA" + "LEDLESSDDE" + "DEEHEPSPKN" + "AKRIAPDSAS" + \
"KVPRKKTRLE" + "EEEEDSDEDD" + "DDDEDDDDED" + "DDEEEEETPV" + "KKTDSTKSKA" + \
"AQKLNHNGKA" + "SALSTTQKTP" + "KTPEQKGKQD" + "TKPQTPKTPK" + "TPLSSEEIKA" + \
"KMQTYLEKGN" + "VLPKVEVKFA" + "NYVKNCFRTE" + "NQKVIEDLWK" + "WRQSLKDGK";
# fibrillarin of Xenopus laevis http://www.uniprot.org/uniprot/P22232
FIB1 = \
"MRPGFSPRGG" + "RGGFGDRGGF" + "GGRGGFGDRG" + "GFRGGSRGGF" + "GGRGRGGDRG" + \
"GRGGFRGGFS" + "SPGRGGPRGG" + "GRGGFGGGRG" + "GFGAGRKVIV" + "EPHRHEGIFI" + \
"CRGKEDALVT" + "KNLVPGESVY" + "GEKRISVEDG" + "EVKTEYRAWN" + "PFRSKIAAAI" + \
"LGGVDQIHIK" + "PGVKVLYLGA" + "ASGTTVSHVS" + "DVVGPEGLVY" + "AVEFSHRSGR" + \
"DLINVAKKRT" + "NIIPVIEDAR" + "HPHKYRILVG" + "MVDVVFADVA" + "QPDQTRIVAL" + \
"NAHNFLKNGG" + "HFVISIKANC" + "IDSTAAPEAV" + "FAAEVKKMQQ" + "ENMKPQEQLT" + \
"LEPYERDHAV" + "VVGIYRPPPK" + "QKK";
# Caprin1 C terminus 607--709
Caprin1_C = \
"SRGVSRGGSR" + "GARGLMNGYR" + "GPANGFRGGY" + "DGYRPSFSNT" + "PNSGYTQSQF" + \
"SAPRDYSGYQ" + "RDGYQQNFKR" + "GSGQSGPRGA" + "PRGRGGPPRP" + "NRGMPQMNTQ" + \
"QVN"
# Caprin1 C terminus 607--709 Phosphorylated
Caprin1_C_p = \
"SRGVSRGGSR" + "GARGLMNGpR" + "GPANGFRGGp" + "DGpRPSFSNT" + "PNSGpTQSQF" + \
"SAPRDpSGpQ" + "RDGpQQNFKR" + "GSGQSGPRGA" + "PRGRGGPPRP" + "NRGMPQMNTQ" + \
"QVN"
# FMRP C terminus 445--632
FMRP_C = \
"GASSRPPPNR" + "TDKEKSYVTD" + "DGQGMGRGSR" + "PYRNRGHGRR" + "GPGYTSGTNS" + \
"EASNASETES" + "DHRDELSDWS" + "LAPTEEERES" + "FLRRGDGRRR" + "GGGGRGQGGR" + \
"GRGGGFKGND" + "DHSRTDNRPR" + "NPREAKGRTT" + "DGSLQIRVDC" + "NNERSVHTKT" + \
"LQNTSSEGSR" + "LRTGKDRNQK" + "KEKPDSVDGQ" + "QPLVNGVP"
# FMRP C terminus 445--632 High Phosphorylated
FMRP_C_p = \
"GASSRPPPNR" + "TDKEKSYVpD" + "DGQGMGRGSR" + "PYRNRGHGRR" + "GPGYTSGTNS" + \
"EASNApEpEp" + "DHRDELpDWp" + "LAPpEEERES" + "FLRRGDGRRR" + "GGGGRGQGGR" + \
"GRGGGFKGND" + "DHSRTDNRPR" + "NPREAKGRpp" + "DGSLQIRVDC" + "NNERSVHpKp" + \
"LQNppSEGSR" + "LRTGKDRNQK" + "KEKPDSVDGQ" + "QPLVNGVP"
# FMRP C terminus 445--632 Low Phosphorylated (2 phos)
FMRP_C_p_low = \
"GASSRPPPNR" + "TDKEKSYVTD" + "DGQGMGRGSR" + "PYRNRGHGRR" + "GPGYTSGTNS" + \
"EASNApETES" + "DHRDELSDWS" + "LAPpEEERES" + "FLRRGDGRRR" + "GGGGRGQGGR" + \
"GRGGGFKGND" + "DHSRTDNRPR" + "NPREAKGRTT" + "DGSLQIRVDC" + "NNERSVHTKT" + \
"LQNTSSEGSR" + "LRTGKDRNQK" + "KEKPDSVDGQ" + "QPLVNGVP"
# FMRP C terminus 445--632 Medium Phosphorylated (5 phos)
FMRP_C_p_mid = \
"GASSRPPPNR" + "TDKEKSYVpD" + "DGQGMGRGSR" + "PYRNRGHGRR" + "GPGYTSGTNS" + \
"EASNApEpES" + "DHRDELpDWS" + "LAPpEEERES" + "FLRRGDGRRR" + "GGGGRGQGGR" + \
"GRGGGFKGND" + "DHSRTDNRPR" + "NPREAKGRTT" + "DGSLQIRVDC" + "NNERSVHTKT" + \
"LQNTSSEGSR" + "LRTGKDRNQK" + "KEKPDSVDGQ" + "QPLVNGVP"
# IP5 in Wang et al Langmuir
IP5 = \
"HoQGT" + "FTSDK" + "SKYLD" + "ERAAQ" + "DFVQW" + "LLDGG" + "PSSGA" + "PPPS"
sv1 = "EKEKEKEKEKEKEKEKEKEKEKEKEKEKEKEKEKEKEKEKEKEKEKEKEK"; #0.0009
sv2 = "EEEKKKEEEKKKEEEKKKEEEKKKEEEKKKEEEKKKEEEKKKEEEKKKEK"; #0.0025
sv3 = "KEKKKEKKEEKKEEKEKEKEKEEKKKEEKEKEKEKKKEEKEKEEKKEEEE"; #0.0139
sv4 = "KEKEKKEEKEKKEEEKKEKEKEKKKEEKKKEEKEEKKEEKKKEEKEEEKE"; #0.0140
sv5 = "KEKEEKEKKKEEEEKEKKKKEEKEKEKEKEEKKEEKKKKEEKEEKEKEKE"; #0.0245
sv6 = "EEEKKEKKEEKEEKKEKKEKEEEKKKEKEEKKEEEKKKEKEEEEKKKKEK"; #0.0273
sv7 = "EEEEKKKKEEEEKKKKEEEEKKKKEEEEKKKKEEEEKKKKEEEEKKKKEK"; #0.0450
sv8 = "KKKKEEEEKKKKEEEEKKKKEEEEKKKKEEEEKKKKEEEEKKKKEEEEKE"; #0.0450
sv9 = "EEKKEEEKEKEKEEEEEKKEKKEKKEKKKEEKEKEKKKEKKKKEKEEEKE"; #0.0624
sv10 = "EKKKKKKEEKKKEEEEEKKKEEEKKKEKKEEKEKEEKEKKEKKEEKEEEE"; #0.0834
sv11 = "EKEKKKKKEEEKKEKEEEEKEEEEKKKKKEKEEEKEEKKEEKEKKKEEKK"; #0.0841
sv12 = "EKKEEEEEEKEKKEEEEKEKEKKEKEEKEKKEKKKEKKEEEKEKKKKEKK"; #0.0864
sv13 = "KEKKKEKEKKEKKKEEEKKKEEEKEKKKEEKKEKKEKKEEEEEEEKEEKE"; #0.0951
sv14 = "EKKEKEEKEEEEKKKKKEEKEKKEKKKKEKKKKKEEEEEEKEEKEKEKEE"; #0.1311
sv15 = "KKEKKEKKKEKKEKKEEEKEKEKKEKKKKEKEKKEEEEEEEEKEEKKEEE"; #0.1354
sv16 = "EKEKEEKKKEEKKKKEKKEKEEKKEKEKEKKEEEEEEEEEKEKKEKKKKE"; #0.1458
sv17 = "EKEKKKKKKEKEKKKKEKEKKEKKEKEEEKEEKEKEKKEEKKEEEEEEEE"; #0.1643
sv18 = "KEEKKEEEEEEEKEEKKKKKEKKKEKKEEEKKKEEKKKEEEEEEKKKKEK"; #0.1677
sv19 = "EEEEEKKKKKEEEEEKKKKKEEEEEKKKKKEEEEEKKKKKEEEEEKKKKK"; #0.1941
sv20 = "EEKEEEEEEKEEEKEEKKEEEKEKKEKKEKEEKKEKKKKKKKKKKKKEEE"; #0.2721
sv21 = "EEEEEEEEEKEKKKKKEKEEKKKKKKEKKEKKKKEKKEEEEEEKEEEKKK"; #0.2737
sv22 = "KEEEEKEEKEEKKKKEKEEKEKKKKKKKKKKKKEKKEEEEEEEEKEKEEE"; #0.3218
sv23 = "EEEEEKEEEEEEEEEEEKEEKEKKKKKKEKKKKKKKEKEKKKKEKKEEKK"; #0.3545
sv24 = "EEEEKEEEEEKEEEEEEEEEEEEKKKEEKKKKKEKKKKKKKEKKKKKKKK"; #0.4456
sv25 = "EEEEEEEEEEEKEEEEKEEKEEKEKKKKKKKKKKKKKKKKKKEEKKEEKE"; #0.5283
sv26 = "KEEEEEEEKEEKEEEEEEEEEKEEEEKEEKKKKKKKKKKKKKKKKKKKKE"; #0.6101
sv27 = "KKEKKKEKKEEEEEEEEEEEEEEEEEEEEKEEKKKKKKKKKKKKKKKEKK"; #0.6729
sv28 = "EKKKKKKKKKKKKKKKKKKKKKEEEEEEEEEEEEEEEEEEKKEEEEEKEK"; #0.7666
sv29 = "KEEEEKEEEEEEEEEEEEEEEEEEEEEKKKKKKKKKKKKKKKKKKKKKKK"; #0.8764
sv30 = "EEEEEEEEEEEEEEEEEEEEEEEEEKKKKKKKKKKKKKKKKKKKKKKKKK"; #1.0000
# Panagiotopoulos
pana1 = "KKKKEEEE"
pana2 = "KKEEKKEE"
pana3 = "KEEEKEKK"
pana4 = "KKEEEKEK"
pana5 = "KKKKKKKKEEEEEEEE"
pana6 = "KKKKEEEEKKKKEEEE"
pana7 = "KEEKKKEKEEEKKEKE"
polye = "EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE"
# YHL's abnormal sequences # SCD kappa Tc of RPA
yhl1 = "KKKKKEKKKKKEKKKKEKKKKEKKEKEEEKEEEEKEEEEKEEEEKEEEEE" # -12.79 0.176 3.815
yhl2 = "EEEEEEEEKKEKKKKEEEEEEEEEEEKKKKEEEKEKEKKKKKKKKKKKKK" # -10.30 0.485 3.114
yhl3 = "KKKKEEEEEEEEEEEEEEEEEEKKEKKKKKKKKKKKKKKEKEEEEEKKKK" # -8.27 0.612 2.909
yhl4 = "KKKKKKEEEEEEEEEEEEEEEKKKKKKKKKKKKKKKKKKEEEEEEEEEEK" # -6.11 0.778 2.485