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Commit 679a15b6 by maarten
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fix in peptidedb 

git-svn-id: svn+ssh://gitlab/srv/svn-repos/pdb-redo/trunk@209 a1961a4f-ab94-4bcc-80e8-33b5a54de466
parent b4a52806
Showing with 462 additions and 14 deletions
src/AtomType.cpp
...@@ -149,6 +149,434 @@ struct WKSFData ...@@ -149,6 +149,434 @@ struct WKSFData
}; };
WKSFData kWKSFData[] = { WKSFData kWKSFData[] = {
//{ H, 0, {{ 0.493002, 0.322912, 0.140191, 0.040810, 0.003038 },
// { 10.510900, 26.125700, 3.142360, 57.799698, 0.000000 }}},
////{ D, 0, {{ 0.493002, 0.322912, 0.140191, 0.040810, 0.003038 },
//// { 10.510900, 26.125700, 3.142360, 57.799698, 0.000000 }}},
//{ H, -1, {{ 0.897661, 0.565616, 0.415815, 0.116973, 0.002389 },
// { 53.136799, 15.187000, 186.575989, 3.567090, 0.000000 }}},
//{ He, 0, {{ 0.873400, 0.630900, 0.311200, 0.178000, 0.006400 },
// { 9.103700, 3.356800, 22.927601, 0.982100, 0.000000 }}},
//{ Li, 0, {{ 1.128200, 0.750800, 0.617500, 0.465300, 0.037700 },
// { 3.954600, 1.052400, 85.390503, 168.261002, 0.000000 }}},
//{ Li, +1, {{ 0.696800, 0.788800, 0.341400, 0.156300, 0.016700 },
// { 4.623700, 1.955700, 0.631600, 10.095300, 0.000000 }}},
//{ Be, 0, {{ 1.591900, 1.127800, 0.539100, 0.702900, 0.038500 },
// { 43.642700, 1.862300, 103.483002, 0.542000, 0.000000 }}},
//{ Be, +2, {{ 6.260300, 0.884900, 0.799300, 0.164700, -6.109200 },
// { 0.002700, 0.831300, 2.275800, 5.114600, 0.000000 }}},
//{ B, 0, {{ 2.054500, 1.332600, 1.097900, 0.706800, -0.193200 },
// { 23.218500, 1.021000, 60.349800, 0.140300, 0.000000 }}},
//{ C, 0, {{ 2.310000, 1.020000, 1.588600, 0.865000, 0.215600 },
// { 20.843899, 10.207500, 0.568700, 51.651199, 0.000000 }}},
//{ C, AtomTypeTraits::kWKSFVal,
// {{ 2.260690, 1.561650, 1.050750, 0.839259, 0.286977 },
// { 22.690701, 0.656665, 9.756180, 55.594898, 0.000000 }}},
//{ N, 0, {{ 12.212600, 3.132200, 2.012500, 1.166300, -11.528999 },
// { 0.005700, 9.893300, 28.997499, 0.582600, 0.000000 }}},
//{ O, 0, {{ 3.048500, 2.286800, 1.546300, 0.867000, 0.250800 },
// { 13.277100, 5.701100, 0.323900, 32.908897, 0.000000 }}},
//{ O, -1, {{ 4.191600, 1.639690, 1.526730, -20.306999, 21.941200 },
// { 12.857300, 4.172360, 47.017899, -0.014040, 0.000000 }}},
//{ F, 0, {{ 3.539200, 2.641200, 1.517000, 1.024300, 0.277600 },
// { 10.282499, 4.294400, 0.261500, 26.147600, 0.000000 }}},
//{ F, -1, {{ 3.632200, 3.510570, 1.260640, 0.940706, 0.653396 },
// { 5.277560, 14.735300, 0.442258, 47.343700, 0.000000 }}},
//{ Ne, 0, {{ 3.955300, 3.112500, 1.454600, 1.125100, 0.351500 },
// { 8.404200, 3.426200, 0.230600, 21.718399, 0.000000 }}},
//{ Na, 0, {{ 4.762600, 3.173600, 1.267400, 1.112800, 0.676000 },
// { 3.285000, 8.842199, 0.313600, 129.423996, 0.000000 }}},
//{ Na, +1, {{ 3.256500, 3.936200, 1.399800, 1.003200, 0.404000 },
// { 2.667100, 6.115300, 0.200100, 14.039000, 0.000000 }}},
//{ Mg, 0, {{ 5.420400, 2.173500, 1.226900, 2.307300, 0.858400 },
// { 2.827500, 79.261101, 0.380800, 7.193700, 0.000000 }}},
//{ Mg, +2, {{ 3.498800, 3.837800, 1.328400, 0.849700, 0.485300 },
// { 2.167600, 4.754200, 0.185000, 10.141100, 0.000000 }}},
//{ Al, 0, {{ 6.420200, 1.900200, 1.593600, 1.964600, 1.115100 },
// { 3.038700, 0.742600, 31.547199, 85.088600, 0.000000 }}},
//{ Al, +3, {{ 4.174480, 3.387600, 1.202960, 0.528137, 0.706786 },
// { 1.938160, 4.145530, 0.228753, 8.285240, 0.000000 }}},
//{ Si, 0, {{ 6.291500, 3.035300, 1.989100, 1.541000, 1.140700 },
// { 2.438600, 32.333698, 0.678500, 81.693695, 0.000000 }}},
//{ Si, AtomTypeTraits::kWKSFVal,
// {{ 5.662690, 3.071640, 2.624460, 1.393200, 1.247070 },
// { 2.665200, 38.663399, 0.916946, 93.545799, 0.000000 }}},
//{ Si, +4, {{ 4.439180, 3.203450, 1.194530, 0.416530, 0.746297 },
// { 1.641670, 3.437570, 0.214900, 6.653650, 0.000000 }}},
//{ P, 0, {{ 6.434500, 4.179100, 1.780000, 1.490800, 1.114900 },
// { 1.906700, 27.157000, 0.526000, 68.164497, 0.000000 }}},
//{ S, 0, {{ 6.905300, 5.203400, 1.437900, 1.586300, 0.866900 },
// { 1.467900, 22.215099, 0.253600, 56.172001, 0.000000 }}},
//{ Cl, 0, {{ 11.460400, 7.196400, 6.255600, 1.645500, -9.557400 },
// { 0.010400, 1.166200, 18.519400, 47.778400, 0.000000 }}},
//{ Cl, -1, {{ 18.291500, 7.208400, 6.533700, 2.338600, -16.378000 },
// { 0.006600, 1.171700, 19.542400, 60.448601, 0.000000 }}},
//{ Ar, 0, {{ 7.484500, 6.772300, 0.653900, 1.644200, 1.444500 },
// { 0.907200, 14.840700, 43.898300, 33.392899, 0.000000 }}},
//{ K, 0, {{ 8.218599, 7.439800, 1.051900, 0.865900, 1.422800 },
// { 12.794900, 0.774800, 213.186996, 41.684097, 0.000000 }}},
//{ K, +1, {{ 7.957800, 7.491700, 6.359000, 1.191500, -4.997800 },
// { 12.633100, 0.767400, -0.002000, 31.912800, 0.000000 }}},
//{ Ca, 0, {{ 8.626600, 7.387300, 1.589900, 1.021100, 1.375100 },
// { 10.442100, 0.659900, 85.748398, 178.436996, 0.000000 }}},
//{ Ca, +2, {{ 15.634800, 7.951800, 8.437200, 0.853700, -14.875000 },
// { -0.007400, 0.608900, 10.311600, 25.990499, 0.000000 }}},
//{ Sc, 0, {{ 9.189000, 7.367900, 1.640900, 1.468000, 1.332900 },
// { 9.021299, 0.572900, 136.108002, 51.353100, 0.000000 }}},
//{ Sc, +3, {{ 13.400800, 8.027300, 1.659430, 1.579360, -6.666700 },
// { 0.298540, 7.962900, -0.286040, 16.066200, 0.000000 }}},
//{ Ti, 0, {{ 9.759500, 7.355800, 1.699100, 1.902100, 1.280700 },
// { 7.850800, 0.500000, 35.633801, 116.104996, 0.000000 }}},
//{ Ti, +2, {{ 9.114230, 7.621740, 2.279300, 0.087899, 0.897155 },
// { 7.524300, 0.457585, 19.536100, 61.655800, 0.000000 }}},
//{ Ti, +3, {{ 17.734400, 8.738160, 5.256910, 1.921340, -14.652000 },
// { 0.220610, 7.047160, -0.157620, 15.976800, 0.000000 }}},
//{ Ti, +4, {{ 19.511400, 8.234730, 2.013410, 1.520800, -13.280000 },
// { 0.178847, 6.670180, -0.292630, 12.946400, 0.000000 }}},
//{ V, 0, {{ 10.297100, 7.351100, 2.070300, 2.057100, 1.219900 },
// { 6.865700, 0.438500, 26.893799, 102.477997, 0.000000 }}},
//{ V, +2, {{ 10.106000, 7.354100, 2.288400, 0.022300, 1.229800 },
// { 6.881800, 0.440900, 20.300400, 115.122002, 0.000000 }}},
//{ V, +3, {{ 9.431410, 7.741900, 2.153430, 0.016865, 0.656565 },
// { 6.395350, 0.383349, 15.190800, 63.969002, 0.000000 }}},
//{ V, +5, {{ 15.688700, 8.142080, 2.030810, -9.576000, 1.714300 },
// { 0.679003, 5.401350, 9.972780, 0.940464, 0.000000 }}},
//{ Cr, 0, {{ 10.640600, 7.353700, 3.324000, 1.492200, 1.183200 },
// { 6.103800, 0.392000, 20.262600, 98.739899, 0.000000 }}},
//{ Cr, +2, {{ 9.540340, 7.750900, 3.582740, 0.509107, 0.616898 },
// { 5.660780, 0.344261, 13.307500, 32.422401, 0.000000 }}},
//{ Cr, +3, {{ 9.680900, 7.811360, 2.876030, 0.113575, 0.518275 },
// { 5.594630, 0.334393, 12.828800, 32.876099, 0.000000 }}},
//{ Mn, 0, {{ 11.281900, 7.357300, 3.019300, 2.244100, 1.089600 },
// { 5.340900, 0.343200, 17.867399, 83.754303, 0.000000 }}},
//{ Mn, +2, {{ 10.806100, 7.362000, 3.526800, 0.218400, 1.087400 },
// { 5.279600, 0.343500, 14.343000, 41.323502, 0.000000 }}},
//{ Mn, +3, {{ 9.845210, 7.871940, 3.565310, 0.323613, 0.393974 },
// { 4.917970, 0.294393, 10.817100, 24.128099, 0.000000 }}},
//{ Mn, +4, {{ 9.962530, 7.970570, 2.760670, 0.054447, 0.251877 },
// { 4.848500, 0.283303, 10.485200, 27.573000, 0.000000 }}},
//{ Fe, 0, {{ 11.769500, 7.357300, 3.522200, 2.304500, 1.036900 },
// { 4.761100, 0.307200, 15.353500, 76.880501, 0.000000 }}},
//{ Fe, +2, {{ 11.042400, 7.374000, 4.134600, 0.439900, 1.009700 },
// { 4.653800, 0.305300, 12.054600, 31.280899, 0.000000 }}},
//{ Fe, +3, {{ 11.176400, 7.386300, 3.394800, 0.072400, 0.970700 },
// { 4.614700, 0.300500, 11.672900, 38.556599, 0.000000 }}},
//{ Co, 0, {{ 12.284100, 7.340900, 4.003400, 2.348800, 1.011800 },
// { 4.279100, 0.278400, 13.535900, 71.169197, 0.000000 }}},
//{ Co, +2, {{ 11.229600, 7.388300, 4.739300, 0.710800, 0.932400 },
// { 4.123100, 0.272600, 10.244300, 25.646599, 0.000000 }}},
//{ Co, +3, {{ 10.337999, 7.881730, 4.767950, 0.725591, 0.286667 },
// { 3.909690, 0.238668, 8.355830, 18.349100, 0.000000 }}},
//{ Ni, 0, {{ 12.837600, 7.292000, 4.443800, 2.380000, 1.034100 },
// { 3.878500, 0.256500, 12.176300, 66.342102, 0.000000 }}},
//{ Ni, +2, {{ 11.416600, 7.400500, 5.344200, 0.977300, 0.861400 },
// { 3.676600, 0.244900, 8.873000, 22.162600, 0.000000 }}},
//{ Ni, +3, {{ 10.780600, 7.758680, 5.227460, 0.847114, 0.386044 },
// { 3.547700, 0.223140, 7.644680, 16.967300, 0.000000 }}},
//{ Cu, 0, {{ 13.337999, 7.167600, 5.615800, 1.673500, 1.191000 },
// { 3.582800, 0.247000, 11.396600, 64.812599, 0.000000 }}},
//{ Cu, +1, {{ 11.947500, 7.357300, 6.245500, 1.557800, 0.890000 },
// { 3.366900, 0.227400, 8.662500, 25.848700, 0.000000 }}},
//{ Cu, +2, {{ 11.816800, 7.111810, 5.781350, 1.145230, 1.144310 },
// { 3.374840, 0.244078, 7.987600, 19.896999, 0.000000 }}},
//{ Zn, 0, {{ 14.074300, 7.031800, 5.162500, 2.410000, 1.304100 },
// { 3.265500, 0.233300, 10.316299, 58.709702, 0.000000 }}},
//{ Zn, +2, {{ 11.971900, 7.386200, 6.466800, 1.394000, 0.780700 },
// { 2.994600, 0.203100, 7.082600, 18.099499, 0.000000 }}},
//{ Ga, 0, {{ 15.235400, 6.700600, 4.359100, 2.962300, 1.718900 },
// { 3.066900, 0.241200, 10.780500, 61.413498, 0.000000 }}},
//{ Ga, +3, {{ 12.691999, 6.698830, 6.066920, 1.006600, 1.535450 },
// { 2.812620, 0.227890, 6.364410, 14.412200, 0.000000 }}},
//{ Ge, 0, {{ 16.081600, 6.374700, 3.706800, 3.683000, 2.131300 },
// { 2.850900, 0.251600, 11.446800, 54.762501, 0.000000 }}},
//{ Ge, +4, {{ 12.917200, 6.700030, 6.067910, 0.859041, 1.455720 },
// { 2.537180, 0.205855, 5.479130, 11.603000, 0.000000 }}},
//{ As, 0, {{ 16.672300, 6.070100, 3.431300, 4.277900, 2.531000 },
// { 2.634500, 0.264700, 12.947900, 47.797199, 0.000000 }}},
//{ Se, 0, {{ 17.000599, 5.819600, 3.973100, 4.354300, 2.840900 },
// { 2.409800, 0.272600, 15.237200, 43.816299, 0.000000 }}},
//{ Br, 0, {{ 17.178900, 5.235800, 5.637700, 3.985100, 2.955700 },
// { 2.172300, 16.579599, 0.260900, 41.432800, 0.000000 }}},
//{ Br, -1, {{ 17.171799, 6.333800, 5.575400, 3.727200, 3.177600 },
// { 2.205900, 19.334499, 0.287100, 58.153500, 0.000000 }}},
//{ Kr, 0, {{ 17.355499, 6.728600, 5.549300, 3.537500, 2.825000 },
// { 1.938400, 16.562300, 0.226100, 39.397202, 0.000000 }}},
//{ Rb, 0, {{ 17.178400, 9.643499, 5.139900, 1.529200, 3.487300 },
// { 1.788800, 17.315100, 0.274800, 164.933990, 0.000000 }}},
//{ Rb, +1, {{ 17.581600, 7.659800, 5.898100, 2.781700, 2.078200 },
// { 1.713900, 14.795700, 0.160300, 31.208700, 0.000000 }}},
//{ Sr, 0, {{ 17.566299, 9.818399, 5.422000, 2.669400, 2.506400 },
// { 1.556400, 14.098800, 0.166400, 132.376007, 0.000000 }}},
//{ Sr, +2, {{ 18.087400, 8.137300, 2.565400, -34.193001, 41.402500 },
// { 1.490700, 12.696300, 24.565100, -0.013800, 0.000000 }}},
//{ Y, 0, {{ 17.775999, 10.294600, 5.726290, 3.265880, 1.912130 },
// { 1.402900, 12.800600, 0.125599, 104.353996, 0.000000 }}},
//{ Y, +3, {{ 17.926800, 9.153100, 1.767950, -33.108002, 40.260201 },
// { 1.354170, 11.214500, 22.659901, -0.013190, 0.000000 }}},
//{ Zr, 0, {{ 17.876499, 10.948000, 5.417320, 3.657210, 2.069290 },
// { 1.276180, 11.916000, 0.117622, 87.662697, 0.000000 }}},
//{ Zr, +4, {{ 18.166800, 10.056200, 1.011180, -2.647900, 9.414539 },
// { 1.214800, 10.148300, 21.605400, -0.102760, 0.000000 }}},
//{ Nb, 0, {{ 17.614201, 12.014400, 4.041830, 3.533460, 3.755910 },
// { 1.188650, 11.766000, 0.204785, 69.795700, 0.000000 }}},
//{ Nb, +3, {{ 19.881199, 18.065300, 11.017700, 1.947150, -12.912000 },
// { 0.019175, 1.133050, 10.162100, 28.338900, 0.000000 }}},
//{ Nb, +5, {{ 17.916300, 13.341700, 10.799000, 0.337905, -6.393400 },
// { 1.124460, 0.028781, 9.282060, 25.722799, 0.000000 }}},
//{ Mo, 0, {{ 3.702500, 17.235600, 12.887600, 3.742900, 4.387500 },
// { 0.277200, 1.095800, 11.004000, 61.658401, 0.000000 }}},
//{ Mo, +3, {{ 21.166401, 18.201700, 11.742300, 2.309510, -14.421000 },
// { 0.014734, 1.030310, 9.536590, 26.630699, 0.000000 }}},
//{ Mo, +5, {{ 21.014900, 18.099199, 11.463200, 0.740625, -14.316000 },
// { 0.014345, 1.022380, 8.788090, 23.345200, 0.000000 }}},
//{ Mo, +6, {{ 17.887100, 11.175000, 6.578910, 0.000000, 0.344941 },
// { 1.036490, 8.480610, 0.058881, 0.000000, 0.000000 }}},
//{ Tc, 0, {{ 19.130100, 11.094800, 4.649010, 2.712630, 5.404280 },
// { 0.864132, 8.144870, 21.570700, 86.847198, 0.000000 }}},
//{ Ru, 0, {{ 19.267399, 12.918200, 4.863370, 1.567560, 5.378740 },
// { 0.808520, 8.434669, 24.799700, 94.292801, 0.000000 }}},
//{ Ru, +3, {{ 18.563801, 13.288500, 9.326019, 3.009640, -3.189200 },
// { 0.847329, 8.371640, 0.017662, 22.886999, 0.000000 }}},
//{ Ru, +4, {{ 18.500299, 13.178699, 4.713040, 2.185350, 1.423570 },
// { 0.844582, 8.125340, 0.364950, 20.850399, 0.000000 }}},
//{ Rh, 0, {{ 19.295700, 14.350100, 4.734250, 1.289180, 5.328000 },
// { 0.751536, 8.217580, 25.874901, 98.606201, 0.000000 }}},
//{ Rh, +3, {{ 18.878500, 14.125900, 3.325150, -6.198900, 11.867800 },
// { 0.764252, 7.844380, 21.248699, -0.010360, 0.000000 }}},
//{ Rh, +4, {{ 18.854500, 13.980600, 2.534640, -5.652600, 11.283500 },
// { 0.760825, 7.624360, 19.331699, -0.010200, 0.000000 }}},
//{ Pd, 0, {{ 19.331900, 15.501699, 5.295370, 0.605844, 5.265930 },
// { 0.698655, 7.989290, 25.205200, 76.898598, 0.000000 }}},
//{ Pd, +2, {{ 19.170099, 15.209600, 4.322340, 0.000000, 5.291600 },
// { 0.696219, 7.555730, 22.505699, 0.000000, 0.000000 }}},
//{ Pd, +4, {{ 19.249300, 14.790000, 2.892890, -7.949200, 13.017400 },
// { 0.683839, 7.148330, 17.914400, 0.005127, 0.000000 }}},
//{ Ag, 0, {{ 19.280800, 16.688499, 4.804500, 1.046300, 5.179000 },
// { 0.644600, 7.472600, 24.660500, 99.815598, 0.000000 }}},
//{ Ag, +1, {{ 19.181200, 15.971900, 5.274750, 0.357534, 5.215720 },
// { 0.646179, 7.191230, 21.732599, 66.114700, 0.000000 }}},
//{ Ag, +2, {{ 19.164299, 16.245600, 4.370900, 0.000000, 5.214040 },
// { 0.645643, 7.185440, 21.407200, 0.000000, 0.000000 }}},
//{ Cd, 0, {{ 19.221399, 17.644400, 4.461000, 1.602900, 5.069400 },
// { 0.594600, 6.908900, 24.700800, 87.482498, 0.000000 }}},
//{ Cd, +2, {{ 19.151400, 17.253500, 4.471280, 0.000000, 5.119370 },
// { 0.597922, 6.806390, 20.252100, 0.000000, 0.000000 }}},
//{ In, 0, {{ 19.162399, 18.559601, 4.294800, 2.039600, 4.939100 },
// { 0.547600, 6.377600, 25.849899, 92.802902, 0.000000 }}},
//{ In, +3, {{ 19.104500, 18.110800, 3.788970, 0.000000, 4.996350 },
// { 0.551522, 6.324700, 17.359501, 0.000000, 0.000000 }}},
//{ Sn, 0, {{ 19.188900, 19.100500, 4.458500, 2.466300, 4.782100 },
// { 5.830300, 0.503100, 26.890900, 83.957100, 0.000000 }}},
//{ Sn, +2, {{ 19.109400, 19.054800, 4.564800, 0.487000, 4.786100 },
// { 0.503600, 5.837800, 23.375200, 62.206100, 0.000000 }}},
//{ Sn, +4, {{ 18.933300, 19.713100, 3.418200, 0.019300, 3.918200 },
// { 5.764000, 0.465500, 14.004900, -0.758300, 0.000000 }}},
//{ Sb, 0, {{ 19.641800, 19.045500, 5.037100, 2.682700, 4.590900 },
// { 5.303400, 0.460700, 27.907400, 75.282501, 0.000000 }}},
//{ Sb, +3, {{ 18.975500, 18.932999, 5.107890, 0.288753, 4.696260 },
// { 0.467196, 5.221260, 19.590200, 55.511299, 0.000000 }}},
//{ Sb, +5, {{ 19.868500, 19.030199, 2.412530, 0.000000, 4.692630 },
// { 5.448530, 0.467973, 14.125900, 0.000000, 0.000000 }}},
//{ Te, 0, {{ 19.964399, 19.013800, 6.144870, 2.523900, 4.352000 },
// { 4.817420, 0.420885, 28.528400, 70.840302, 0.000000 }}},
//{ I, 0, {{ 20.147200, 18.994900, 7.513800, 2.273500, 4.071200 },
// { 4.347000, 0.381400, 27.765999, 66.877602, 0.000000 }}},
//{ I, -1, {{ 20.233200, 18.997000, 7.806900, 2.886800, 4.071400 },
// { 4.357900, 0.381500, 29.525900, 84.930397, 0.000000 }}},
//{ Xe, 0, {{ 20.293301, 19.029800, 8.976700, 1.990000, 3.711800 },
// { 3.928200, 0.344000, 26.465900, 64.265800, 0.000000 }}},
//{ Cs, 0, {{ 20.389200, 19.106199, 10.662000, 1.495300, 3.335200 },
// { 3.569000, 0.310700, 24.387899, 213.903992, 0.000000 }}},
//{ Cs, +1, {{ 20.352400, 19.127800, 10.282100, 0.961500, 3.279100 },
// { 3.552000, 0.308600, 23.712799, 59.456497, 0.000000 }}},
//{ Ba, 0, {{ 20.336100, 19.297001, 10.888000, 2.695900, 2.773100 },
// { 3.216000, 0.275600, 20.207300, 167.201996, 0.000000 }}},
//{ Ba, +2, {{ 20.180700, 19.113600, 10.905399, 0.776340, 3.029020 },
// { 3.213670, 0.283310, 20.055799, 51.745998, 0.000000 }}},
//{ La, 0, {{ 20.577999, 19.598999, 11.372700, 3.287190, 2.146780 },
// { 2.948170, 0.244475, 18.772600, 133.123993, 0.000000 }}},
//{ La, +3, {{ 20.248899, 19.376301, 11.632299, 0.336048, 2.408600 },
// { 2.920700, 0.250698, 17.821100, 54.945297, 0.000000 }}},
//{ Ce, 0, {{ 21.167099, 19.769501, 11.851299, 3.330490, 1.862640 },
// { 2.812190, 0.226836, 17.608299, 127.112999, 0.000000 }}},
//{ Ce, +3, {{ 20.803600, 19.559000, 11.936900, 0.612376, 2.090130 },
// { 2.776910, 0.231540, 16.540800, 43.169201, 0.000000 }}},
//{ Ce, +4, {{ 20.323500, 19.818600, 12.123300, 0.144583, 1.591800 },
// { 2.659410, 0.218850, 15.799200, 62.235500, 0.000000 }}},
//{ Pr, 0, {{ 22.043999, 19.669701, 12.385600, 2.824280, 2.058300 },
// { 2.773930, 0.222087, 16.766899, 143.643997, 0.000000 }}},
//{ Pr, +3, {{ 21.372700, 19.749100, 12.132900, 0.975180, 1.771320 },
// { 2.645200, 0.214299, 15.323000, 36.406502, 0.000000 }}},
//{ Pr, +4, {{ 20.941299, 20.053900, 12.466800, 0.296689, 1.242850 },
// { 2.544670, 0.202481, 14.813700, 45.464298, 0.000000 }}},
//{ Nd, 0, {{ 22.684500, 19.684700, 12.774000, 2.851370, 1.984860 },
// { 2.662480, 0.210628, 15.885000, 137.903000, 0.000000 }}},
//{ Nd, +3, {{ 21.961000, 19.933899, 12.120000, 1.510310, 1.475880 },
// { 2.527220, 0.199237, 14.178300, 30.871700, 0.000000 }}},
//{ Pm, 0, {{ 23.340500, 19.609501, 13.123500, 2.875160, 2.028760 },
// { 2.562700, 0.202088, 15.100900, 132.720993, 0.000000 }}},
//{ Pm, +3, {{ 22.552700, 20.110800, 12.067100, 2.074920, 1.194990 },
// { 2.417400, 0.185769, 13.127500, 27.449100, 0.000000 }}},
//{ Sm, 0, {{ 24.004200, 19.425800, 13.439600, 2.896040, 2.209630 },
// { 2.472740, 0.196451, 14.399600, 128.007004, 0.000000 }}},
//{ Sm, +3, {{ 23.150400, 20.259899, 11.920200, 2.714880, 0.954586 },
// { 2.316410, 0.174081, 12.157100, 24.824200, 0.000000 }}},
//{ Eu, 0, {{ 24.627399, 19.088600, 13.760300, 2.922700, 2.574500 },
// { 2.387900, 0.194200, 13.754600, 123.173996, 0.000000 }}},
//{ Eu, +2, {{ 24.006300, 19.950399, 11.803400, 3.872430, 1.363890 },
// { 2.277830, 0.173530, 11.609600, 26.515600, 0.000000 }}},
//{ Eu, +3, {{ 23.749699, 20.374500, 11.850900, 3.265030, 0.759344 },
// { 2.222580, 0.163940, 11.311000, 22.996599, 0.000000 }}},
//{ Gd, 0, {{ 25.070900, 19.079800, 13.851800, 3.545450, 2.419600 },
// { 2.253410, 0.181951, 12.933100, 101.397995, 0.000000 }}},
//{ Gd, +3, {{ 24.346600, 20.420799, 11.870800, 3.714900, 0.645089 },
// { 2.135530, 0.155525, 10.578199, 21.702900, 0.000000 }}},
//{ Tb, 0, {{ 25.897600, 18.218500, 14.316700, 2.953540, 3.582240 },
// { 2.242560, 0.196143, 12.664800, 115.362000, 0.000000 }}},
//{ Tb, +3, {{ 24.955900, 20.327099, 12.247100, 3.773000, 0.691967 },
// { 2.056010, 0.149525, 10.049900, 21.277300, 0.000000 }}},
//{ Dy, 0, {{ 26.507000, 17.638300, 14.559600, 2.965770, 4.297280 },
// { 2.180200, 0.202172, 12.189899, 111.874001, 0.000000 }}},
//{ Dy, +3, {{ 25.539499, 20.286100, 11.981200, 4.500730, 0.689690 },
// { 1.980400, 0.143384, 9.349720, 19.580999, 0.000000 }}},
//{ Ho, 0, {{ 26.904900, 17.293999, 14.558300, 3.638370, 4.567960 },
// { 2.070510, 0.197940, 11.440700, 92.656601, 0.000000 }}},
//{ Ho, +3, {{ 26.129601, 20.099400, 11.978800, 4.936760, 0.852795 },
// { 1.910720, 0.139358, 8.800180, 18.590799, 0.000000 }}},
//{ Er, 0, {{ 27.656300, 16.428499, 14.977900, 2.982330, 5.920460 },
// { 2.073560, 0.223545, 11.360400, 105.703003, 0.000000 }}},
//{ Er, +3, {{ 26.722000, 19.774799, 12.150600, 5.173790, 1.176130 },
// { 1.846590, 0.137290, 8.362249, 17.897400, 0.000000 }}},
//{ Tm, 0, {{ 28.181900, 15.885099, 15.154200, 2.987060, 6.756210 },
// { 2.028590, 0.238849, 10.997499, 102.960999, 0.000000 }}},
//{ Tm, +3, {{ 27.308300, 19.332001, 12.333900, 5.383480, 1.639290 },
// { 1.787110, 0.136974, 7.967780, 17.292200, 0.000000 }}},
//{ Yb, 0, {{ 28.664101, 15.434500, 15.308700, 2.989630, 7.566720 },
// { 1.988900, 0.257119, 10.664700, 100.417000, 0.000000 }}},
//{ Yb, +2, {{ 28.120899, 17.681700, 13.333500, 5.146570, 3.709830 },
// { 1.785030, 0.159970, 8.183040, 20.389999, 0.000000 }}},
//{ Yb, +3, {{ 27.891700, 18.761400, 12.607200, 5.476470, 2.260010 },
// { 1.732720, 0.138790, 7.644120, 16.815300, 0.000000 }}},
//{ Lu, 0, {{ 28.947599, 15.220800, 15.100000, 3.716010, 7.976280 },
// { 1.901820, 9.985189, 0.261033, 84.329803, 0.000000 }}},
//{ Lu, +3, {{ 28.462799, 18.121000, 12.842899, 5.594150, 2.975730 },
// { 1.682160, 0.142292, 7.337270, 16.353500, 0.000000 }}},
//{ Hf, 0, {{ 29.143999, 15.172600, 14.758600, 4.300130, 8.581540 },
// { 1.832620, 9.599899, 0.275116, 72.028999, 0.000000 }}},
//{ Hf, +4, {{ 28.813099, 18.460100, 12.728500, 5.599270, 2.396990 },
// { 1.591360, 0.128903, 6.762320, 14.036600, 0.000000 }}},
//{ Ta, 0, {{ 29.202400, 15.229300, 14.513500, 4.764920, 9.243540 },
// { 1.773330, 9.370460, 0.295977, 63.364399, 0.000000 }}},
//{ Ta, +5, {{ 29.158699, 18.840700, 12.826799, 5.386950, 1.785550 },
// { 1.507110, 0.116741, 6.315240, 12.424400, 0.000000 }}},
//{ W, 0, {{ 29.081800, 15.430000, 14.432700, 5.119820, 9.887500 },
// { 1.720290, 9.225900, 0.321703, 57.056000, 0.000000 }}},
//{ W, +6, {{ 29.493599, 19.376301, 13.054399, 5.064120, 1.010740 },
// { 1.427550, 0.104621, 5.936670, 11.197200, 0.000000 }}},
//{ Re, 0, {{ 28.762100, 15.718900, 14.556400, 5.441740, 10.472000 },
// { 1.671910, 9.092270, 0.350500, 52.086098, 0.000000 }}},
//{ Os, 0, {{ 28.189400, 16.154999, 14.930500, 5.675890, 11.000500 },
// { 1.629030, 8.979480, 0.382661, 48.164700, 0.000000 }}},
//{ Os, +4, {{ 30.418999, 15.263700, 14.745800, 5.067950, 6.498040 },
// { 1.371130, 6.847060, 0.165191, 18.003000, 0.000000 }}},
//{ Ir, 0, {{ 27.304899, 16.729599, 15.611500, 5.833770, 11.472200 },
// { 1.592790, 8.865530, 0.417916, 45.001099, 0.000000 }}},
//{ Ir, +3, {{ 30.415600, 15.862000, 13.614500, 5.820080, 8.279030 },
// { 1.343230, 7.109090, 0.204633, 20.325399, 0.000000 }}},
//{ Ir, +4, {{ 30.705799, 15.551200, 14.232600, 5.536720, 6.968240 },
// { 1.309230, 6.719830, 0.167252, 17.491100, 0.000000 }}},
//{ Pt, 0, {{ 27.005899, 17.763901, 15.713100, 5.783700, 11.688300 },
// { 1.512930, 8.811740, 0.424593, 38.610298, 0.000000 }}},
//{ Pt, +2, {{ 29.842899, 16.722401, 13.215300, 6.352340, 9.853290 },
// { 1.329270, 7.389790, 0.263297, 22.942600, 0.000000 }}},
//{ Pt, +4, {{ 30.961201, 15.982900, 13.734800, 5.920340, 7.395340 },
// { 1.248130, 6.608340, 0.168640, 16.939199, 0.000000 }}},
//{ Au, 0, {{ 16.881901, 18.591299, 25.558201, 5.860000, 12.065800 },
// { 0.461100, 8.621600, 1.482600, 36.395599, 0.000000 }}},
//{ Au, +1, {{ 28.010899, 17.820400, 14.335899, 6.580770, 11.229900 },
// { 1.353210, 7.739500, 0.356752, 26.404301, 0.000000 }}},
//{ Au, +3, {{ 30.688599, 16.902901, 12.780100, 6.523540, 9.096800 },
// { 1.219900, 6.828720, 0.212867, 18.659000, 0.000000 }}},
//{ Hg, 0, {{ 20.680901, 19.041700, 21.657499, 5.967600, 12.608900 },
// { 0.545000, 8.448400, 1.572900, 38.324600, 0.000000 }}},
//{ Hg, +1, {{ 25.085300, 18.497299, 16.888300, 6.482160, 12.020500 },
// { 1.395070, 7.651050, 0.443378, 28.226200, 0.000000 }}},
//{ Hg, +2, {{ 29.564100, 18.059999, 12.837400, 6.899120, 10.626800 },
// { 1.211520, 7.056390, 0.284738, 20.748199, 0.000000 }}},
//{ Tl, 0, {{ 27.544600, 19.158400, 15.538000, 5.525930, 13.174600 },
// { 0.655150, 8.707510, 1.963470, 45.814899, 0.000000 }}},
//{ Tl, +1, {{ 21.398500, 20.472300, 18.747799, 6.828470, 12.525800 },
// { 1.471100, 0.517394, 7.434630, 28.848200, 0.000000 }}},
//{ Tl, +3, {{ 30.869499, 18.384100, 11.932800, 7.005740, 9.802700 },
// { 1.100800, 6.538520, 0.219074, 17.211399, 0.000000 }}},
//{ Pb, 0, {{ 31.061699, 13.063700, 18.441999, 5.969600, 13.411800 },
// { 0.690200, 2.357600, 8.618000, 47.257900, 0.000000 }}},
//{ Pb, +2, {{ 21.788601, 19.568199, 19.140600, 7.011070, 12.473400 },
// { 1.336600, 0.488383, 6.772700, 23.813200, 0.000000 }}},
//{ Pb, +4, {{ 32.124397, 18.800301, 12.017500, 6.968860, 8.084280 },
// { 1.005660, 6.109260, 0.147041, 14.714000, 0.000000 }}},
//{ Bi, 0, {{ 33.368900, 12.951000, 16.587700, 6.469200, 13.578199 },
// { 0.704000, 2.923800, 8.793700, 48.009300, 0.000000 }}},
//{ Bi, +3, {{ 21.805300, 19.502600, 19.105301, 7.102950, 12.471100 },
// { 1.235600, 6.241490, 0.469999, 20.318501, 0.000000 }}},
//{ Bi, +5, {{ 33.536400, 25.094601, 19.249699, 6.915550, -6.799400 },
// { 0.916540, 0.390420, 5.714140, 12.828500, 0.000000 }}},
//{ Po, 0, {{ 34.672600, 15.473300, 13.113800, 7.025880, 13.677000 },
// { 0.700999, 3.550780, 9.556419, 47.004501, 0.000000 }}},
//{ At, 0, {{ 35.316299, 19.021099, 9.498870, 7.425180, 13.710800 },
// { 0.685870, 3.974580, 11.382400, 45.471500, 0.000000 }}},
//{ Rn, 0, {{ 35.563099, 21.281601, 8.003700, 7.443300, 13.690500 },
// { 0.663100, 4.069100, 14.042200, 44.247299, 0.000000 }}},
//{ Fr, 0, {{ 35.929901, 23.054699, 12.143900, 2.112530, 13.724700 },
// { 0.646453, 4.176190, 23.105200, 150.644989, 0.000000 }}},
//{ Ra, 0, {{ 35.763000, 22.906399, 12.473900, 3.210970, 13.621099 },
// { 0.616341, 3.871350, 19.988701, 142.324997, 0.000000 }}},
//{ Ra, +2, {{ 35.215000, 21.670000, 7.913420, 7.650780, 13.543100 },
// { 0.604909, 3.576700, 12.601000, 29.843599, 0.000000 }}},
//{ Ac, 0, {{ 35.659698, 23.103199, 12.597700, 4.086550, 13.526600 },
// { 0.589092, 3.651550, 18.598999, 117.019997, 0.000000 }}},
//{ Ac, +3, {{ 35.173599, 22.111200, 8.192160, 7.055450, 13.463699 },
// { 0.579689, 3.414370, 12.918700, 25.944300, 0.000000 }}},
//{ Th, 0, {{ 35.564499, 23.421900, 12.747300, 4.807030, 13.431400 },
// { 0.563359, 3.462040, 17.830900, 99.172195, 0.000000 }}},
//{ Th, +4, {{ 35.100700, 22.441799, 9.785540, 5.294440, 13.375999 },
// { 0.555054, 3.244980, 13.466100, 23.953300, 0.000000 }}},
//{ Pa, 0, {{ 35.884701, 23.294800, 14.189100, 4.172870, 13.428699 },
// { 0.547751, 3.415190, 16.923500, 105.250999, 0.000000 }}},
//{ U, 0, {{ 36.022800, 23.412800, 14.949100, 4.188000, 13.396600 },
// { 0.529300, 3.325300, 16.092699, 100.612999, 0.000000 }}},
//{ U, +3, {{ 35.574699, 22.525900, 12.216499, 5.370730, 13.309200 },
// { 0.520480, 3.122930, 12.714800, 26.339399, 0.000000 }}},
//{ U, +4, {{ 35.371498, 22.532600, 12.029100, 4.798400, 13.267099 },
// { 0.516598, 3.050530, 12.572300, 23.458200, 0.000000 }}},
//{ U, +6, {{ 34.850899, 22.758400, 14.009900, 1.214570, 13.166500 },
// { 0.507079, 2.890300, 13.176700, 25.201700, 0.000000 }}},
//{ Np, 0, {{ 36.187401, 23.596399, 15.640200, 4.185500, 13.357300 },
// { 0.511929, 3.253960, 15.362200, 97.490799, 0.000000 }}},
//{ Np, +3, {{ 35.707397, 22.612999, 12.989799, 5.432270, 13.254400 },
// { 0.502322, 3.038070, 12.144899, 25.492800, 0.000000 }}},
//{ Np, +4, {{ 35.510300, 22.578699, 12.776600, 4.921590, 13.211599 },
// { 0.498626, 2.966270, 11.948400, 22.750200, 0.000000 }}},
//{ Np, +6, {{ 35.013599, 22.728600, 14.388400, 1.756690, 13.113000 },
// { 0.489810, 2.810990, 12.330000, 22.658100, 0.000000 }}},
//{ Pu, 0, {{ 36.525398, 23.808300, 16.770700, 3.479470, 13.381200 },
// { 0.499384, 3.263710, 14.945499, 105.979996, 0.000000 }}},
//{ Pu, +3, {{ 35.840000, 22.716900, 13.580700, 5.660160, 13.199100 },
// { 0.484936, 2.961180, 11.533100, 24.399200, 0.000000 }}},
//{ Pu, +4, {{ 35.649300, 22.646000, 13.359500, 5.188310, 13.155500 },
// { 0.481422, 2.890200, 11.316000, 21.830099, 0.000000 }}},
//{ Pu, +6, {{ 35.173599, 22.718100, 14.763500, 2.286780, 13.058200 },
// { 0.473204, 2.738480, 11.552999, 20.930300, 0.000000 }}},
//{ Am, 0, {{ 36.670601, 24.099199, 17.341499, 3.493310, 13.359200 },
// { 0.483629, 3.206470, 14.313600, 102.272995, 0.000000 }}},
//{ Cm, 0, {{ 36.648800, 24.409599, 17.399000, 4.216650, 13.288700 },
// { 0.465154, 3.089970, 13.434600, 88.483398, 0.000000 }}},
//{ Bk, 0, {{ 36.788101, 24.773600, 17.891899, 4.232840, 13.275400 },
// { 0.451018, 3.046190, 12.894600, 86.002998, 0.000000 }}},
//{ Cf, 0, {{ 36.918499, 25.199499, 18.331699, 4.243910, 13.267400 },
// { 0.437533, 3.007750, 12.404400, 83.788101, 0.000000}}},
{ H, 0, {{ 0.413048, 0.294953, 0.187491, 0.080701, 0.023736, 0.000049}, { H, 0, {{ 0.413048, 0.294953, 0.187491, 0.080701, 0.023736, 0.000049},
{ 15.569946, 32.398468, 5.711404, 61.889874, 1.334118, 0.000000}}}, { 15.569946, 32.398468, 5.711404, 61.889874, 1.334118, 0.000000}}},
{ He, 0, {{ 0.732354, 0.753896, 0.283819, 0.190003, 0.039139, 0.000487}, { He, 0, {{ 0.732354, 0.753896, 0.283819, 0.190003, 0.039139, 0.000487},
......
src/PDB2Cif.cpp
...@@ -5458,6 +5458,9 @@ int PDBFileParser::PDBChain::AlignResToSeqRes() ...@@ -5458,6 +5458,9 @@ int PDBFileParser::PDBChain::AlignResToSeqRes()
throw; throw;
} }
if (VERBOSE > 1)
printAlignment();
// assign numbers to the residues that don't have them yet // assign numbers to the residues that don't have them yet
stack<int> unnumbered; stack<int> unnumbered;
for (x = 0; x < dimX; ++x) for (x = 0; x < dimX; ++x)
......
src/PeptideDB.cpp
...@@ -55,8 +55,9 @@ const map<string,char> kBaseMap{ ...@@ -55,8 +55,9 @@ const map<string,char> kBaseMap{
// -------------------------------------------------------------------- // --------------------------------------------------------------------
struct PeptideDBImpl class PeptideDBImpl
{ {
public:
PeptideDBImpl(istream& data, PeptideDBImpl* next); PeptideDBImpl(istream& data, PeptideDBImpl* next);
~PeptideDBImpl() ~PeptideDBImpl()
...@@ -64,11 +65,13 @@ struct PeptideDBImpl ...@@ -64,11 +65,13 @@ struct PeptideDBImpl
delete mNext; delete mNext;
} }
/*unordered_*/set<string> mKnownPeptides; PeptideDBImpl* pop()
set<string> mKnownBases; {
cif::File mFile; auto result = mNext;
cif::Category& mChemComp; mNext = nullptr;
PeptideDBImpl* mNext; delete this;
return result;
}
string nameFor(const string& resName) const string nameFor(const string& resName) const
{ {
...@@ -113,6 +116,25 @@ struct PeptideDBImpl ...@@ -113,6 +116,25 @@ struct PeptideDBImpl
return result; return result;
} }
bool isKnownPeptide(const string& resName)
{
return mKnownPeptides.count(resName) or
(mNext != nullptr and mNext->isKnownPeptide(resName));
}
bool isKnownBase(const string& resName)
{
return mKnownBases.count(resName) or
(mNext != nullptr and mNext->isKnownBase(resName));
}
private:
/*unordered_*/set<string> mKnownPeptides;
set<string> mKnownBases;
cif::File mFile;
cif::Category& mChemComp;
PeptideDBImpl* mNext;
}; };
PeptideDBImpl::PeptideDBImpl(istream& data, PeptideDBImpl* next) PeptideDBImpl::PeptideDBImpl(istream& data, PeptideDBImpl* next)
...@@ -252,12 +274,7 @@ void PeptideDB::pushDictionary(boost::filesystem::path dict) ...@@ -252,12 +274,7 @@ void PeptideDB::pushDictionary(boost::filesystem::path dict)
void PeptideDB::popDictionary() void PeptideDB::popDictionary()
{ {
if (mImpl != nullptr) if (mImpl != nullptr)
{ mImpl = mImpl->pop();
auto i = mImpl;
mImpl = i->mNext;
i->mNext = nullptr;
delete i;
}
} }
PeptideDB::~PeptideDB() PeptideDB::~PeptideDB()
...@@ -267,12 +284,12 @@ PeptideDB::~PeptideDB() ...@@ -267,12 +284,12 @@ PeptideDB::~PeptideDB()
bool PeptideDB::isKnownPeptide(const string& resName) const bool PeptideDB::isKnownPeptide(const string& resName) const
{ {
return mImpl->mKnownPeptides.count(resName) > 0; return mImpl->isKnownPeptide(resName);
} }
bool PeptideDB::isKnownBase(const string& resName) const bool PeptideDB::isKnownBase(const string& resName) const
{ {
return mImpl->mKnownBases.count(resName) > 0; return mImpl->isKnownBase(resName);
} }
string PeptideDB::nameForResidue(const string& resName) const string PeptideDB::nameForResidue(const string& resName) const
......
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