rfdiffusion/scoring.py

##
## lk and lk term
#(LJ_RADIUS LJ_WDEPTH LK_DGFREE LK_LAMBDA LK_VOLUME)
type2ljlk = {
    "CNH2":(1.968297,0.094638,3.077030,3.5000,13.500000),
    "COO":(1.916661,0.141799,-3.332648,3.5000,14.653000),
    "CH0":(2.011760,0.062642,1.409284,3.5000,8.998000),
    "CH1":(2.011760,0.062642,-3.538387,3.5000,10.686000),
    "CH2":(2.011760,0.062642,-1.854658,3.5000,18.331000),
    "CH3":(2.011760,0.062642,7.292929,3.5000,25.855000),
    "aroC":(2.016441,0.068775,1.797950,3.5000,16.704000),
    "Ntrp":(1.802452,0.161725,-8.413116,3.5000,9.522100),
    "Nhis":(1.802452,0.161725,-9.739606,3.5000,9.317700),
    "NtrR":(1.802452,0.161725,-5.158080,3.5000,9.779200),
    "NH2O":(1.802452,0.161725,-8.101638,3.5000,15.689000),
    "Nlys":(1.802452,0.161725,-20.864641,3.5000,16.514000),
    "Narg":(1.802452,0.161725,-8.968351,3.5000,15.717000),
    "Npro":(1.802452,0.161725,-0.984585,3.5000,3.718100),
    "OH":(1.542743,0.161947,-8.133520,3.5000,10.722000),
    "OHY":(1.542743,0.161947,-8.133520,3.5000,10.722000),
    "ONH2":(1.548662,0.182924,-6.591644,3.5000,10.102000),
    "OOC":(1.492871,0.099873,-9.239832,3.5000,9.995600),
    "S":(1.975967,0.455970,-1.707229,3.5000,17.640000),
    "SH1":(1.975967,0.455970,3.291643,3.5000,23.240000),  
    "Nbb":(1.802452,0.161725,-9.969494,3.5000,15.992000),
    "CAbb":(2.011760,0.062642,2.533791,3.5000,12.137000),
    "CObb":(1.916661,0.141799,3.104248,3.5000,13.221000),
    "OCbb":(1.540580,0.142417,-8.006829,3.5000,12.196000),
    "HNbb":(0.901681,0.005000,0.0000,3.5000,0.0000),
    "Hapo":(1.421272,0.021808,0.0000,3.5000,0.0000),
    "Haro":(1.374914,0.015909,0.0000,3.5000,0.0000),
    "Hpol":(0.901681,0.005000,0.0000,3.5000,0.0000),
    "HS":(0.363887,0.050836,0.0000,3.5000,0.0000),
}

# hbond donor/acceptors
class HbAtom:
    NO = 0
    DO = 1 # donor
    AC = 2 # acceptor
    DA = 3 # donor & acceptor
    HP = 4 # polar H

type2hb = {
    "CNH2":HbAtom.NO, "COO":HbAtom.NO,  "CH0":HbAtom.NO,  "CH1":HbAtom.NO,
    "CH2":HbAtom.NO,  "CH3":HbAtom.NO,  "aroC":HbAtom.NO, "Ntrp":HbAtom.DO,
    "Nhis":HbAtom.AC, "NtrR":HbAtom.DO, "NH2O":HbAtom.DO, "Nlys":HbAtom.DO,
    "Narg":HbAtom.DO, "Npro":HbAtom.NO, "OH":HbAtom.DA,   "OHY":HbAtom.DA,
    "ONH2":HbAtom.AC, "OOC":HbAtom.AC,  "S":HbAtom.NO,    "SH1":HbAtom.NO,  
    "Nbb":HbAtom.DO,  "CAbb":HbAtom.NO, "CObb":HbAtom.NO, "OCbb":HbAtom.AC,
    "HNbb":HbAtom.HP, "Hapo":HbAtom.NO, "Haro":HbAtom.NO, "Hpol":HbAtom.HP,
    "HS":HbAtom.HP, # HP in rosetta(?)
}

##
## hbond term
class HbDonType:
    PBA = 0
    IND = 1
    IME = 2
    GDE = 3
    CXA = 4
    AMO = 5
    HXL = 6
    AHX = 7
    NTYPES = 8

class HbAccType:
    PBA = 0
    CXA = 1
    CXL = 2
    HXL = 3
    AHX = 4
    IME = 5
    NTYPES = 6

class HbHybType:
    SP2 = 0
    SP3 = 1
    RING = 2
    NTYPES = 3

type2dontype = {
    "Nbb": HbDonType.PBA,
    "Ntrp": HbDonType.IND,
    "NtrR": HbDonType.GDE,
    "Narg": HbDonType.GDE,
    "NH2O": HbDonType.CXA,
    "Nlys": HbDonType.AMO,
    "OH": HbDonType.HXL,
    "OHY": HbDonType.AHX,
}

type2acctype = {
    "OCbb": HbAccType.PBA,
    "ONH2": HbAccType.CXA,
    "OOC": HbAccType.CXL,
    "OH": HbAccType.HXL,
    "OHY": HbAccType.AHX,
    "Nhis": HbAccType.IME,
}

type2hybtype = {
    "OCbb": HbHybType.SP2,
    "ONH2": HbHybType.SP2,
    "OOC": HbHybType.SP2,
    "OHY": HbHybType.SP3,
    "OH": HbHybType.SP3,
    "Nhis": HbHybType.RING,
}

dontype2wt = {
    HbDonType.PBA: 1.45,
    HbDonType.IND: 1.15,
    HbDonType.IME: 1.42,
    HbDonType.GDE: 1.11,
    HbDonType.CXA: 1.29,
    HbDonType.AMO: 1.17,
    HbDonType.HXL: 0.99,
    HbDonType.AHX: 1.00,
}

acctype2wt = {
    HbAccType.PBA: 1.19,
    HbAccType.CXA: 1.21,
    HbAccType.CXL: 1.10,
    HbAccType.HXL: 1.15,
    HbAccType.AHX: 1.15,
    HbAccType.IME: 1.17,
}

class HbPolyType:
    ahdist_aASN_dARG = 0
    ahdist_aASN_dASN = 1
    ahdist_aASN_dGLY = 2
    ahdist_aASN_dHIS = 3
    ahdist_aASN_dLYS = 4
    ahdist_aASN_dSER = 5
    ahdist_aASN_dTRP = 6
    ahdist_aASN_dTYR = 7
    ahdist_aASP_dARG = 8
    ahdist_aASP_dASN = 9
    ahdist_aASP_dGLY = 10
    ahdist_aASP_dHIS = 11
    ahdist_aASP_dLYS = 12
    ahdist_aASP_dSER = 13
    ahdist_aASP_dTRP = 14
    ahdist_aASP_dTYR = 15
    ahdist_aGLY_dARG = 16
    ahdist_aGLY_dASN = 17
    ahdist_aGLY_dGLY = 18
    ahdist_aGLY_dHIS = 19
    ahdist_aGLY_dLYS = 20
    ahdist_aGLY_dSER = 21
    ahdist_aGLY_dTRP = 22
    ahdist_aGLY_dTYR = 23
    ahdist_aHIS_dARG = 24
    ahdist_aHIS_dASN = 25
    ahdist_aHIS_dGLY = 26
    ahdist_aHIS_dHIS = 27
    ahdist_aHIS_dLYS = 28
    ahdist_aHIS_dSER = 29
    ahdist_aHIS_dTRP = 30
    ahdist_aHIS_dTYR = 31
    ahdist_aSER_dARG = 32
    ahdist_aSER_dASN = 33
    ahdist_aSER_dGLY = 34
    ahdist_aSER_dHIS = 35
    ahdist_aSER_dLYS = 36
    ahdist_aSER_dSER = 37
    ahdist_aSER_dTRP = 38
    ahdist_aSER_dTYR = 39
    ahdist_aTYR_dARG = 40
    ahdist_aTYR_dASN = 41
    ahdist_aTYR_dGLY = 42
    ahdist_aTYR_dHIS = 43
    ahdist_aTYR_dLYS = 44
    ahdist_aTYR_dSER = 45
    ahdist_aTYR_dTRP = 46
    ahdist_aTYR_dTYR = 47
    cosBAH_off = 48
    cosBAH_7 = 49
    cosBAH_6i = 50
    AHD_1h = 51
    AHD_1i = 52
    AHD_1j = 53
    AHD_1k = 54

# map donor:acceptor pairs to polynomials
hbtypepair2poly = {
  (HbDonType.PBA,HbAccType.PBA): (HbPolyType.ahdist_aGLY_dGLY,HbPolyType.cosBAH_off,HbPolyType.AHD_1j),
  (HbDonType.CXA,HbAccType.PBA): (HbPolyType.ahdist_aGLY_dASN,HbPolyType.cosBAH_off,HbPolyType.AHD_1j),
  (HbDonType.IME,HbAccType.PBA): (HbPolyType.ahdist_aGLY_dHIS,HbPolyType.cosBAH_off,HbPolyType.AHD_1j),
  (HbDonType.IND,HbAccType.PBA): (HbPolyType.ahdist_aGLY_dTRP,HbPolyType.cosBAH_off,HbPolyType.AHD_1j),
  (HbDonType.AMO,HbAccType.PBA): (HbPolyType.ahdist_aGLY_dLYS,HbPolyType.cosBAH_off,HbPolyType.AHD_1h),
  (HbDonType.GDE,HbAccType.PBA): (HbPolyType.ahdist_aGLY_dARG,HbPolyType.cosBAH_off,HbPolyType.AHD_1j),
  (HbDonType.AHX,HbAccType.PBA): (HbPolyType.ahdist_aGLY_dTYR,HbPolyType.cosBAH_off,HbPolyType.AHD_1k),
  (HbDonType.HXL,HbAccType.PBA): (HbPolyType.ahdist_aGLY_dSER,HbPolyType.cosBAH_off,HbPolyType.AHD_1k),
  (HbDonType.PBA,HbAccType.CXA): (HbPolyType.ahdist_aASN_dGLY,HbPolyType.cosBAH_off,HbPolyType.AHD_1k),
  (HbDonType.CXA,HbAccType.CXA): (HbPolyType.ahdist_aASN_dASN,HbPolyType.cosBAH_off,HbPolyType.AHD_1k),
  (HbDonType.IME,HbAccType.CXA): (HbPolyType.ahdist_aASN_dHIS,HbPolyType.cosBAH_off,HbPolyType.AHD_1k),
  (HbDonType.IND,HbAccType.CXA): (HbPolyType.ahdist_aASN_dTRP,HbPolyType.cosBAH_off,HbPolyType.AHD_1k),
  (HbDonType.AMO,HbAccType.CXA): (HbPolyType.ahdist_aASN_dLYS,HbPolyType.cosBAH_off,HbPolyType.AHD_1h),
  (HbDonType.GDE,HbAccType.CXA): (HbPolyType.ahdist_aASN_dARG,HbPolyType.cosBAH_off,HbPolyType.AHD_1k),
  (HbDonType.AHX,HbAccType.CXA): (HbPolyType.ahdist_aASN_dTYR,HbPolyType.cosBAH_off,HbPolyType.AHD_1k),
  (HbDonType.HXL,HbAccType.CXA): (HbPolyType.ahdist_aASN_dSER,HbPolyType.cosBAH_off,HbPolyType.AHD_1k),
  (HbDonType.PBA,HbAccType.CXL): (HbPolyType.ahdist_aASP_dGLY,HbPolyType.cosBAH_off,HbPolyType.AHD_1k),
  (HbDonType.CXA,HbAccType.CXL): (HbPolyType.ahdist_aASP_dASN,HbPolyType.cosBAH_off,HbPolyType.AHD_1k),
  (HbDonType.IME,HbAccType.CXL): (HbPolyType.ahdist_aASP_dHIS,HbPolyType.cosBAH_off,HbPolyType.AHD_1k),
  (HbDonType.IND,HbAccType.CXL): (HbPolyType.ahdist_aASP_dTRP,HbPolyType.cosBAH_off,HbPolyType.AHD_1k),
  (HbDonType.AMO,HbAccType.CXL): (HbPolyType.ahdist_aASP_dLYS,HbPolyType.cosBAH_off,HbPolyType.AHD_1h),
  (HbDonType.GDE,HbAccType.CXL): (HbPolyType.ahdist_aASP_dARG,HbPolyType.cosBAH_off,HbPolyType.AHD_1k),
  (HbDonType.AHX,HbAccType.CXL): (HbPolyType.ahdist_aASP_dTYR,HbPolyType.cosBAH_off,HbPolyType.AHD_1k),
  (HbDonType.HXL,HbAccType.CXL): (HbPolyType.ahdist_aASP_dSER,HbPolyType.cosBAH_off,HbPolyType.AHD_1k),
  (HbDonType.PBA,HbAccType.IME): (HbPolyType.ahdist_aHIS_dGLY,HbPolyType.cosBAH_7,HbPolyType.AHD_1i),
  (HbDonType.CXA,HbAccType.IME): (HbPolyType.ahdist_aHIS_dASN,HbPolyType.cosBAH_7,HbPolyType.AHD_1i),
  (HbDonType.IME,HbAccType.IME): (HbPolyType.ahdist_aHIS_dHIS,HbPolyType.cosBAH_7,HbPolyType.AHD_1h),
  (HbDonType.IND,HbAccType.IME): (HbPolyType.ahdist_aHIS_dTRP,HbPolyType.cosBAH_7,HbPolyType.AHD_1h),
  (HbDonType.AMO,HbAccType.IME): (HbPolyType.ahdist_aHIS_dLYS,HbPolyType.cosBAH_7,HbPolyType.AHD_1i),
  (HbDonType.GDE,HbAccType.IME): (HbPolyType.ahdist_aHIS_dARG,HbPolyType.cosBAH_7,HbPolyType.AHD_1h),
  (HbDonType.AHX,HbAccType.IME): (HbPolyType.ahdist_aHIS_dTYR,HbPolyType.cosBAH_7,HbPolyType.AHD_1i),
  (HbDonType.HXL,HbAccType.IME): (HbPolyType.ahdist_aHIS_dSER,HbPolyType.cosBAH_7,HbPolyType.AHD_1i),
  (HbDonType.PBA,HbAccType.AHX): (HbPolyType.ahdist_aTYR_dGLY,HbPolyType.cosBAH_6i,HbPolyType.AHD_1i),
  (HbDonType.CXA,HbAccType.AHX): (HbPolyType.ahdist_aTYR_dASN,HbPolyType.cosBAH_6i,HbPolyType.AHD_1i),
  (HbDonType.IME,HbAccType.AHX): (HbPolyType.ahdist_aTYR_dHIS,HbPolyType.cosBAH_6i,HbPolyType.AHD_1i),
  (HbDonType.IND,HbAccType.AHX): (HbPolyType.ahdist_aTYR_dTRP,HbPolyType.cosBAH_6i,HbPolyType.AHD_1h),
  (HbDonType.AMO,HbAccType.AHX): (HbPolyType.ahdist_aTYR_dLYS,HbPolyType.cosBAH_6i,HbPolyType.AHD_1i),
  (HbDonType.GDE,HbAccType.AHX): (HbPolyType.ahdist_aTYR_dARG,HbPolyType.cosBAH_6i,HbPolyType.AHD_1i),
  (HbDonType.AHX,HbAccType.AHX): (HbPolyType.ahdist_aTYR_dTYR,HbPolyType.cosBAH_6i,HbPolyType.AHD_1i),
  (HbDonType.HXL,HbAccType.AHX): (HbPolyType.ahdist_aTYR_dSER,HbPolyType.cosBAH_6i,HbPolyType.AHD_1i),
  (HbDonType.PBA,HbAccType.HXL): (HbPolyType.ahdist_aSER_dGLY,HbPolyType.cosBAH_6i,HbPolyType.AHD_1i),
  (HbDonType.CXA,HbAccType.HXL): (HbPolyType.ahdist_aSER_dASN,HbPolyType.cosBAH_6i,HbPolyType.AHD_1i),
  (HbDonType.IME,HbAccType.HXL): (HbPolyType.ahdist_aSER_dHIS,HbPolyType.cosBAH_6i,HbPolyType.AHD_1i),
  (HbDonType.IND,HbAccType.HXL): (HbPolyType.ahdist_aSER_dTRP,HbPolyType.cosBAH_6i,HbPolyType.AHD_1h),
  (HbDonType.AMO,HbAccType.HXL): (HbPolyType.ahdist_aSER_dLYS,HbPolyType.cosBAH_6i,HbPolyType.AHD_1i),
  (HbDonType.GDE,HbAccType.HXL): (HbPolyType.ahdist_aSER_dARG,HbPolyType.cosBAH_6i,HbPolyType.AHD_1i),
  (HbDonType.AHX,HbAccType.HXL): (HbPolyType.ahdist_aSER_dTYR,HbPolyType.cosBAH_6i,HbPolyType.AHD_1i),
  (HbDonType.HXL,HbAccType.HXL): (HbPolyType.ahdist_aSER_dSER,HbPolyType.cosBAH_6i,HbPolyType.AHD_1i),
}


# polynomials are triplets, (x_min, x_max), (y[x<x_min],y[x>x_max]), (c_9,...,c_0)
hbpolytype2coeffs = { # Parameters imported from rosetta sp2_elec_params @v2017.48-dev59886
    HbPolyType.ahdist_aASN_dARG: ((0.7019094761929999, 2.86820307153,),(1.1, 1.1,),( 0.58376113, -9.29345473, 64.86270904, -260.3946711, 661.43138077, -1098.01378958, 1183.58371466, -790.82929582, 291.33125475, -43.01629727,)),
    HbPolyType.ahdist_aASN_dASN: ((0.625841094801, 2.75107708444,),(1.1, 1.1,),( -1.31243015, 18.6745072, -112.63858313, 373.32878091, -734.99145504, 861.38324861, -556.21026097, 143.5626977, 20.03238394, -11.52167705,)),
    HbPolyType.ahdist_aASN_dGLY: ((0.7477341047139999, 2.6796350782799996,),(1.1, 1.1,),( -1.61294554, 23.3150793, -144.11313069, 496.13575, -1037.83809166, 1348.76826073, -1065.14368678, 473.89008925, -100.41142701, 7.44453515,)),
    HbPolyType.ahdist_aASN_dHIS: ((0.344789524346, 2.8303582266000005,),(1.1, 1.1,),( -0.2657122, 4.1073775, -26.9099632, 97.10486507, -209.96002602, 277.33057268, -218.74766996, 97.42852213, -24.07382402, 3.73962807,)),
    HbPolyType.ahdist_aASN_dLYS: ((0.542905671869, 2.45259389314,),(1.1, 1.1,),( 1.38531754, -18.48733797, 106.14444613, -344.70585054, 698.91577956, -917.0879402, 775.32787908, -403.09588787, 113.65054778, -11.66516403,)),
    HbPolyType.ahdist_aASN_dSER: ((1.0812774602500002, 2.6832123582599996,),(1.1, 1.1,),( -3.51524353, 47.54032873, -254.40168577, 617.84606386, -255.49935027, -2361.56230539, 6426.85797934, -7760.4403891, 4694.08106855, -1149.83549068,)),
    HbPolyType.ahdist_aASN_dTRP: ((0.6689984999999999, 3.0704254,),(1.1, 1.1,),( -0.5284840422, 8.3510150838, -56.4100479414, 212.4884326254, -488.3178610608, 703.7762350506, -628.9936994633999, 331.4294356146, -93.265817571, 11.9691623698,)),
    HbPolyType.ahdist_aASN_dTYR: ((1.08950268805, 2.6887046709400004,),(1.1, 1.1,),( -4.4488705, 63.27696281, -371.44187037, 1121.71921621, -1638.11394306, 142.99988401, 3436.65879147, -5496.07011787, 3709.30505237, -962.79669688,)),
    HbPolyType.ahdist_aASP_dARG: ((0.8100404642229999, 2.9851230124799994,),(1.1, 1.1,),( -0.66430344, 10.41343145, -70.12656205, 265.12578414, -617.05849171, 911.39378582, -847.25013928, 472.09090981, -141.71513167, 18.57721132,)),
    HbPolyType.ahdist_aASP_dASN: ((1.05401125073, 3.11129675908,),(1.1, 1.1,),( 0.02090728, -0.24144928, -0.19578075, 16.80904547, -117.70216251, 407.18551288, -809.95195924, 939.83137947, -593.94527692, 159.57610528,)),
    HbPolyType.ahdist_aASP_dGLY: ((0.886260952629, 2.66843608743,),(1.1, 1.1,),( -7.00699267, 107.33021779, -713.45752385, 2694.43092298, -6353.05100287, 9667.94098394, -9461.9261027, 5721.0086877, -1933.97818198, 279.47763789,)),
    HbPolyType.ahdist_aASP_dHIS: ((1.03597611139, 2.78208509117,),(1.1, 1.1,),( -1.34823406, 17.08925926, -78.75087193, 106.32795459, 400.18459698, -2041.04320193, 4033.83557387, -4239.60530204, 2324.00877252, -519.38410941,)),
    HbPolyType.ahdist_aASP_dLYS: ((0.97789485082, 2.50496946108,),(1.1, 1.1,),( -0.41300315, 6.59243438, -44.44525308, 163.11796012, -351.2307798, 443.2463146, -297.84582856, 62.38600547, 33.77496227, -14.11652182,)),
    HbPolyType.ahdist_aASP_dSER: ((0.542905671869, 2.45259389314,),(1.1, 1.1,),( 1.38531754, -18.48733797, 106.14444613, -344.70585054, 698.91577956, -917.0879402, 775.32787908, -403.09588787, 113.65054778, -11.66516403,)),
    HbPolyType.ahdist_aASP_dTRP: ((0.419155746414, 3.0486938610500003,),(1.1, 1.1,),( -0.24563471, 3.85598551, -25.75176874, 95.36525025, -214.13175785, 299.76133553, -259.0691378, 132.06975835, -37.15612683, 5.60445773,)),
    HbPolyType.ahdist_aASP_dTYR: ((1.01057521468, 2.7207545786900003,),(1.1, 1.1,),( -0.15808672, -10.21398871, 178.80080949, -1238.0583801, 4736.25248274, -11071.96777725, 16239.07550047, -14593.21092621, 7335.66765017, -1575.08145078,)),
    HbPolyType.ahdist_aGLY_dARG: ((0.499016667857, 2.9377031027599996,),(1.1, 1.1,),( -0.15923533, 2.5526639, -17.38788803, 65.71046957, -151.13491186, 218.78048387, -199.15882919, 110.56568974, -35.95143745, 6.47580213,)),
    HbPolyType.ahdist_aGLY_dASN: ((0.7194388032060001, 2.9303772333599998,),(1.1, 1.1,),( -1.40718342, 23.65929694, -172.97144348, 720.64417348, -1882.85420815, 3194.87197776, -3515.52467458, 2415.75238278, -941.47705161, 159.84784277,)),
    HbPolyType.ahdist_aGLY_dGLY: ((1.38403812683, 2.9981039433,),(1.1, 1.1,),( -0.5307601, 6.47949946, -22.39522814, -55.14303544, 708.30945242, -2619.49318162, 5227.8805795, -6043.31211632, 3806.04676175, -1007.66024144,)),
    HbPolyType.ahdist_aGLY_dHIS: ((0.47406840932899996, 2.9234200830400003,),(1.1, 1.1,),( -0.12881679, 1.933838, -12.03134888, 39.92691227, -75.41519959, 78.87968016, -37.82769801, -0.13178679, 4.50193019, 0.45408359,)),
    HbPolyType.ahdist_aGLY_dLYS: ((0.545347533475, 2.42624380351,),(1.1, 1.1,),( -0.22921901, 2.07015714, -6.2947417, 0.66645697, 45.21805416, -130.26668981, 176.32401031, -126.68226346, 43.96744431, -4.40105281,)),
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}