leonarski_f
dd0bffb283
Build Packages / Unit tests (push) Skipped
Build Packages / build:windows:nocuda (push) Successful in 11m6s
Build Packages / build:rpm (rocky8_nocuda) (push) Successful in 10m27s
Build Packages / build:rpm (rocky9_nocuda) (push) Successful in 10m54s
Build Packages / build:rpm (ubuntu2204_nocuda) (push) Successful in 9m25s
Build Packages / build:rpm (ubuntu2404_nocuda) (push) Successful in 10m5s
Build Packages / build:rpm (rocky8_sls9) (push) Successful in 11m33s
Build Packages / build:rpm (rocky9_sls9) (push) Successful in 11m19s
Build Packages / build:rpm (rocky8) (push) Successful in 12m23s
Build Packages / build:rpm (rocky9) (push) Successful in 13m21s
Build Packages / build:rpm (ubuntu2204) (push) Successful in 12m30s
Build Packages / build:rpm (ubuntu2404) (push) Successful in 11m55s
Build Packages / DIALS test (push) Successful in 13m42s
Build Packages / XDS test (durin plugin) (push) Successful in 9m26s
Build Packages / XDS test (JFJoch plugin) (push) Successful in 6m41s
Build Packages / XDS test (neggia plugin) (push) Successful in 6m12s
Build Packages / Generate python client (push) Successful in 19s
Build Packages / Build documentation (push) Successful in 52s
Build Packages / Create release (push) Skipped
Build Packages / build:viewer-tgz:cpu (push) Successful in 5m29s
Build Packages / build:viewer-tgz:cuda (push) Successful in 6m12s
Build Packages / build:windows:cuda (push) Successful in 18m36s
This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * rugnux: Add `--model model.pdb` - score the merged data against an atomic model and compute initial maps. It reports R-work/R-free (scaling the model to the observed amplitudes with an overall scale, an anisotropic B and a flat bulk solvent - the standard few-parameter model, so a batch of maps stays directly comparable) and writes 2Fo-Fc / Fo-Fc electron-density maps (CCP4) plus a map-coefficient MTZ. The structure itself is not refined; the model is only re-fractionalised into the data cell. * rugnux: The merged reflection output now carries French-Wilson amplitudes (|F| and its sigma) next to the intensities - MTZ `F`/`SIGF`, mmCIF `_refln.F_meas_au`, and the text HKL - computed with the correct centric/acentric Wilson prior and epsilon multiplicity, so a downstream program (e.g. phenix.refine) can refine against amplitudes. The intensity columns are unchanged. * rugnux: R-free test-set flags are now assigned deterministically and consistently across symmetry - a Bijvoet pair I(+)/I(-) is never split between the work and free sets, and the assignment is a reproducible per-hkl hash that depends only on the reflection index, so every dataset of one crystal form gets the same ~5% free set (what a multi-dataset campaign such as PanDDA needs). On small data the fraction is floored so the test set stays large enough for a stable R-free (~500 reflections, capped at 10%); it stays flat at 5% on ordinary data. When a reference MTZ carries a `FreeR_flag` column its test set is imported instead, letting a whole campaign inherit one shared free set. * rugnux: A reference MTZ (`--reference-mtz`) can now fix the space group and cell for rotation data too (previously rejected), without being used to scale - the rotation merge stays self-consistent. When the crystal has an indexing (merohedral) ambiguity - a lattice symmetry higher than its Laue symmetry, e.g. P3/P4/P6/C2 - the reference also resolves it: each candidate reindexing (identity plus the twin-law cosets of the metric symmetry) is scored by its intensity correlation against the reference and the data are re-merged in the best-correlating one. This is a metric-preserving relabelling of hkl (the cell is unchanged) and a no-op for a holohedral crystal such as lysozyme. * rugnux: `--model` validation now aligns the data to the model before scoring - the observed reflections are reindexed into the model's enantiomorph when the two differ only by hand (indistinguishable from merged intensities). A merohedral indexing ambiguity is resolved against the reference MTZ when one is given (so a whole campaign shares one indexing convention); only with a model and no reference does validation fall back to fitting each candidate reindexing and keeping the lowest R-free. * rugnux: De-novo symmetry - recover a genuine high-symmetry group whose data are imperfectly scaled. Such a merge's within-orbit chi² lands just past the self-consistency bound (each real symmetry step adds a little systematic scatter), right where a merohedral twin also lands, so the chi² ratio alone cannot separate them. The candidate is now rescued when the extra intensity-proportional systematic error it invokes stays small relative to the confirmed subgroup - a genuine symmetry step gains multiplicity without inflating the merge error model's b, whereas a twin forces non-equivalent reflections together and b balloons. Fixes cubic insulin (I23 instead of I222) with no change to any other crystal in the test battery, including the twins that must stay in their lower symmetry. * Docs: Document the French-Wilson amplitude estimation, R-free flagging, reference-based space-group/ambiguity resolution, and model-based validation/maps in CPU_DATA_ANALYSIS.md. * Frontend: The status-bar pill now shows a progress bar during detector calibration (previously only during measurement), and the calibration state and its button are labelled "Calibration"/"CALIBRATE" (the internal `Pedestal` state name is unchanged for back-compatibility).Reviewed-on: #69 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
885 lines
31 KiB
C++
885 lines
31 KiB
C++
/// Copyright 2018-2022 Global Phasing Ltd.
|
|
|
|
#include <gemmi/resinfo.hpp>
|
|
#include <gemmi/atox.hpp> // for is_space
|
|
|
|
namespace gemmi {
|
|
|
|
using RI = ResidueKind;
|
|
|
|
|
|
|
|
size_t find_tabulated_residue_idx(const std::string& name) {
|
|
if (name.size() == 3) {
|
|
|
|
#define ID(s) (((s)[0] << 16 | (s)[1] << 8 | (s)[2]) & ~0x202020)
|
|
//printf(">>> %x %x %x\n", ID(name.c_str()), ID("ALA"), ID("GLX"));
|
|
switch (ID(name.c_str())) {
|
|
case ID("ALA"): return 0;
|
|
case ID("ARG"): return 1;
|
|
case ID("ASN"): return 2;
|
|
case ID("ABA"): return 3;
|
|
case ID("ASP"): return 4;
|
|
case ID("ASX"): return 5;
|
|
case ID("CYS"): return 6;
|
|
case ID("CSH"): return 7;
|
|
case ID("GLN"): return 8;
|
|
case ID("GLU"): return 9;
|
|
case ID("GLX"): return 10;
|
|
case ID("GLY"): return 11;
|
|
case ID("HIS"): return 12;
|
|
case ID("ILE"): return 13;
|
|
case ID("LEU"): return 14;
|
|
case ID("LYS"): return 15;
|
|
case ID("MET"): return 16;
|
|
case ID("MSE"): return 17;
|
|
case ID("ORN"): return 18;
|
|
case ID("PHE"): return 19;
|
|
case ID("PRO"): return 20;
|
|
case ID("SER"): return 21;
|
|
case ID("THR"): return 22;
|
|
case ID("TRY"):
|
|
case ID("TRP"): return 23;
|
|
case ID("TYR"): return 24;
|
|
case ID("UNK"): return 25;
|
|
case ID("VAL"): return 26;
|
|
case ID("SEC"): return 27;
|
|
case ID("PYL"): return 28;
|
|
case ID("SEP"): return 29;
|
|
case ID("TPO"): return 30;
|
|
case ID("PCA"): return 31;
|
|
case ID("CSO"): return 32;
|
|
case ID("PTR"): return 33;
|
|
case ID("KCX"): return 34;
|
|
case ID("CSD"): return 35;
|
|
case ID("LLP"): return 36;
|
|
case ID("CME"): return 37;
|
|
case ID("MLY"): return 38;
|
|
case ID("DAL"): return 39;
|
|
case ID("TYS"): return 40;
|
|
case ID("OCS"): return 41;
|
|
case ID("M3L"): return 42;
|
|
case ID("FME"): return 43;
|
|
case ID("ALY"): return 44;
|
|
case ID("HYP"): return 45;
|
|
case ID("CAS"): return 46;
|
|
case ID("CRO"): return 47;
|
|
case ID("CSX"): return 48;
|
|
case ID("DPR"): return 49;
|
|
case ID("DGL"): return 50;
|
|
case ID("DVA"): return 51;
|
|
case ID("CSS"): return 52;
|
|
case ID("DPN"): return 53;
|
|
case ID("DSN"): return 54;
|
|
case ID("DLE"): return 55;
|
|
case ID("HIC"): return 56;
|
|
case ID("NLE"): return 57;
|
|
case ID("MVA"): return 58;
|
|
case ID("MLZ"): return 59;
|
|
case ID("CR2"): return 60;
|
|
case ID("SAR"): return 61;
|
|
case ID("DAR"): return 62;
|
|
case ID("DLY"): return 63;
|
|
case ID("YCM"): return 64;
|
|
case ID("NRQ"): return 65;
|
|
case ID("CGU"): return 66;
|
|
case ID("0TD"): return 67;
|
|
case ID("MLE"): return 68;
|
|
case ID("DAS"): return 69;
|
|
case ID("DTR"): return 70;
|
|
case ID("CXM"): return 71;
|
|
case ID("TPQ"): return 72;
|
|
case ID("DCY"): return 73;
|
|
case ID("DSG"): return 74;
|
|
case ID("DTY"): return 75;
|
|
case ID("DHI"): return 76;
|
|
case ID("MEN"): return 77;
|
|
case ID("DTH"): return 78;
|
|
case ID("SAC"): return 79;
|
|
case ID("DGN"): return 80;
|
|
case ID("AIB"): return 81;
|
|
case ID("SMC"): return 82;
|
|
case ID("IAS"): return 83;
|
|
case ID("CIR"): return 84;
|
|
case ID("BMT"): return 85;
|
|
case ID("DIL"): return 86;
|
|
case ID("FGA"): return 87;
|
|
case ID("PHI"): return 88;
|
|
case ID("CRQ"): return 89;
|
|
case ID("SME"): return 90;
|
|
case ID("GHP"): return 91;
|
|
case ID("MHO"): return 92;
|
|
case ID("NEP"): return 93;
|
|
case ID("TRQ"): return 94;
|
|
case ID("TOX"): return 95;
|
|
case ID("ALC"): return 96;
|
|
case ID("3FG"): return 97;
|
|
case ID("SCH"): return 98;
|
|
case ID("MDO"): return 99;
|
|
case ID("MAA"): return 100;
|
|
case ID("GYS"): return 101;
|
|
case ID("MK8"): return 102;
|
|
case ID("CR8"): return 103;
|
|
case ID("KPI"): return 104;
|
|
case ID("SCY"): return 105;
|
|
case ID("DHA"): return 106;
|
|
case ID("OMY"): return 107;
|
|
case ID("CAF"): return 108;
|
|
case ID("0AF"): return 109;
|
|
case ID("SNN"): return 110;
|
|
case ID("MHS"): return 111;
|
|
case ID("MLU"): return 112;
|
|
case ID("SNC"): return 113;
|
|
case ID("PHD"): return 114;
|
|
case ID("B3E"): return 115;
|
|
case ID("MEA"): return 116;
|
|
case ID("MED"): return 117;
|
|
case ID("OAS"): return 118;
|
|
case ID("GL3"): return 119;
|
|
case ID("FVA"): return 120;
|
|
case ID("PHL"): return 121;
|
|
case ID("CRF"): return 122;
|
|
case ID("OMZ"): return 123;
|
|
case ID("BFD"): return 124;
|
|
case ID("MEQ"): return 125;
|
|
case ID("DAB"): return 126;
|
|
case ID("AGM"): return 127;
|
|
case ID("PSU"): return 128;
|
|
case ID("5MU"): return 129;
|
|
case ID("7MG"): return 130;
|
|
case ID("OMG"): return 131;
|
|
case ID("UR3"): return 132;
|
|
case ID("OMC"): return 133;
|
|
case ID("2MG"): return 134;
|
|
case ID("H2U"): return 135;
|
|
case ID("4SU"): return 136;
|
|
case ID("OMU"): return 137;
|
|
case ID("4OC"): return 138;
|
|
case ID("MA6"): return 139;
|
|
case ID("M2G"): return 140;
|
|
case ID("1MA"): return 141;
|
|
case ID("6MZ"): return 142;
|
|
case ID("CCC"): return 143;
|
|
case ID("2MA"): return 144;
|
|
case ID("1MG"): return 145;
|
|
case ID("5BU"): return 146;
|
|
case ID("MIA"): return 147;
|
|
case ID("DOC"): return 148;
|
|
case ID("8OG"): return 149;
|
|
case ID("5CM"): return 150;
|
|
case ID("3DR"): return 151;
|
|
case ID("BRU"): return 152;
|
|
case ID("CBR"): return 153;
|
|
case ID("WAT"):
|
|
case ID("H2O"):
|
|
case ID("HOH"): return 154;
|
|
case ID("DOD"): return 155;
|
|
case ID("HEM"): return 156;
|
|
case ID("SO4"): return 157;
|
|
case ID("GOL"): return 158;
|
|
case ID("EDO"): return 159;
|
|
case ID("NAG"): return 160;
|
|
case ID("PO4"): return 161;
|
|
case ID("ACT"): return 162;
|
|
case ID("PEG"): return 163;
|
|
case ID("MAN"): return 164;
|
|
case ID("FAD"): return 165;
|
|
case ID("BMA"): return 166;
|
|
case ID("ADP"): return 167;
|
|
case ID("DMS"): return 168;
|
|
case ID("ACE"): return 169;
|
|
case ID("NH2"): return 170;
|
|
case ID("MPD"): return 171;
|
|
case ID("MES"): return 172;
|
|
case ID("NAD"): return 173;
|
|
case ID("NAP"): return 174;
|
|
case ID("TRS"): return 175;
|
|
case ID("ATP"): return 176;
|
|
case ID("PG4"): return 177;
|
|
case ID("GDP"): return 178;
|
|
case ID("FUC"): return 179;
|
|
case ID("FMT"): return 180;
|
|
case ID("GAL"): return 181;
|
|
case ID("PGE"): return 182;
|
|
case ID("FMN"): return 183;
|
|
case ID("PLP"): return 184;
|
|
case ID("EPE"): return 185;
|
|
case ID("SF4"): return 186;
|
|
case ID("BME"): return 187;
|
|
case ID("CIT"): return 188;
|
|
case ID("BE7"): return 189;
|
|
case ID("MRD"): return 190;
|
|
case ID("MHA"): return 191;
|
|
case ID("BU3"): return 192;
|
|
case ID("PGO"): return 193;
|
|
case ID("BU2"): return 194;
|
|
case ID("PDO"): return 195;
|
|
case ID("BU1"): return 196;
|
|
case ID("PG6"): return 197;
|
|
case ID("1BO"): return 198;
|
|
case ID("PE7"): return 199;
|
|
case ID("PG5"): return 200;
|
|
case ID("TFP"): return 201;
|
|
case ID("DHD"): return 202;
|
|
case ID("PEU"): return 203;
|
|
case ID("TAU"): return 204;
|
|
case ID("SBT"): return 205;
|
|
case ID("SAL"): return 206;
|
|
case ID("IOH"): return 207;
|
|
case ID("IPA"): return 208;
|
|
case ID("PIG"): return 209;
|
|
case ID("B3P"): return 210;
|
|
case ID("BTB"): return 211;
|
|
case ID("NHE"): return 212;
|
|
case ID("C8E"): return 213;
|
|
case ID("OTE"): return 214;
|
|
case ID("PE4"): return 215;
|
|
case ID("XPE"): return 216;
|
|
case ID("PE8"): return 217;
|
|
case ID("P33"): return 218;
|
|
case ID("N8E"): return 219;
|
|
case ID("2OS"): return 220;
|
|
case ID("1PS"): return 221;
|
|
case ID("CPS"): return 222;
|
|
case ID("DMX"): return 223;
|
|
case ID("MPO"): return 224;
|
|
case ID("GCD"): return 225;
|
|
case ID("DXG"): return 226;
|
|
case ID("CM5"): return 227;
|
|
case ID("ACA"): return 228;
|
|
case ID("ACN"): return 229;
|
|
case ID("CCN"): return 230;
|
|
case ID("GLC"): return 231;
|
|
case ID("DR6"): return 232;
|
|
case ID("NH4"): return 233;
|
|
case ID("AZI"): return 234;
|
|
case ID("BNG"): return 235;
|
|
case ID("BOG"): return 236;
|
|
case ID("BGC"): return 237;
|
|
case ID("BCN"): return 238;
|
|
case ID("BRO"): return 239;
|
|
case ID("CAC"): return 240;
|
|
case ID("CBX"): return 241;
|
|
case ID("ACY"): return 242;
|
|
case ID("CBM"): return 243;
|
|
case ID("CLO"): return 244;
|
|
case ID("3CO"): return 245;
|
|
case ID("NCO"): return 246;
|
|
case ID("CU1"): return 247;
|
|
case ID("CYN"): return 248;
|
|
case ID("MA4"): return 249;
|
|
case ID("TAR"): return 250;
|
|
case ID("GLO"): return 251;
|
|
case ID("MTL"): return 252;
|
|
case ID("SOR"): return 253;
|
|
case ID("DMU"): return 254;
|
|
case ID("DDQ"): return 255;
|
|
case ID("DMF"): return 256;
|
|
case ID("DIO"): return 257;
|
|
case ID("DOX"): return 258;
|
|
case ID("12P"): return 259;
|
|
case ID("SDS"): return 260;
|
|
case ID("LMT"): return 261;
|
|
case ID("EOH"): return 262;
|
|
case ID("EEE"): return 263;
|
|
case ID("EGL"): return 264;
|
|
case ID("FLO"): return 265;
|
|
case ID("TRT"): return 266;
|
|
case ID("FCY"): return 267;
|
|
case ID("FRU"): return 268;
|
|
case ID("GBL"): return 269;
|
|
case ID("GPX"): return 270;
|
|
case ID("HTO"): return 271;
|
|
case ID("HTG"): return 272;
|
|
case ID("B7G"): return 273;
|
|
case ID("C10"): return 274;
|
|
case ID("16D"): return 275;
|
|
case ID("HEZ"): return 276;
|
|
case ID("IOD"): return 277;
|
|
case ID("IDO"): return 278;
|
|
case ID("ICI"): return 279;
|
|
case ID("ICT"): return 280;
|
|
case ID("TLA"): return 281;
|
|
case ID("LAT"): return 282;
|
|
case ID("LBT"): return 283;
|
|
case ID("LDA"): return 284;
|
|
case ID("MN3"): return 285;
|
|
case ID("MRY"): return 286;
|
|
case ID("MOH"): return 287;
|
|
case ID("BEQ"): return 288;
|
|
case ID("C15"): return 289;
|
|
case ID("MG8"): return 290;
|
|
case ID("POL"): return 291;
|
|
case ID("NO3"): return 292;
|
|
case ID("JEF"): return 293;
|
|
case ID("P4C"): return 294;
|
|
case ID("CE1"): return 295;
|
|
case ID("DIA"): return 296;
|
|
case ID("CXE"): return 297;
|
|
case ID("IPH"): return 298;
|
|
case ID("PIN"): return 299;
|
|
case ID("15P"): return 300;
|
|
case ID("CRY"): return 301;
|
|
case ID("PGR"): return 302;
|
|
case ID("PGQ"): return 303;
|
|
case ID("SPD"): return 304;
|
|
case ID("SPK"): return 305;
|
|
case ID("SPM"): return 306;
|
|
case ID("SUC"): return 307;
|
|
case ID("TBU"): return 308;
|
|
case ID("TMA"): return 309;
|
|
case ID("TEP"): return 310;
|
|
case ID("SCN"): return 311;
|
|
case ID("TRE"): return 312;
|
|
case ID("ETF"): return 313;
|
|
case ID("144"): return 314;
|
|
case ID("UMQ"): return 315;
|
|
case ID("URE"): return 316;
|
|
case ID("YT3"): return 317;
|
|
case ID("ZN2"): return 318;
|
|
case ID("FE2"): return 319;
|
|
case ID("3NI"): return 320;
|
|
case ID("SIA"): return 321;
|
|
case ID("XYP"): return 322;
|
|
case ID("A2G"): return 323;
|
|
case ID("GLA"): return 324;
|
|
case ID("NDG"): return 325;
|
|
case ID("NGA"): return 326;
|
|
#undef ID
|
|
}} else if (name.size() == 1) {
|
|
switch (name[0]& ~0x20) {
|
|
case 'A': return 327;
|
|
case 'C': return 328;
|
|
case 'G': return 329;
|
|
case 'I': return 330;
|
|
case 'U': return 331;
|
|
case 'N': return 332;
|
|
case 'F': return 333;
|
|
case 'K': return 334;
|
|
}
|
|
} else if (name.size() == 2) {
|
|
if (name[0] == 'D' || name[0] == '+')
|
|
switch (name[1]) {
|
|
case 'A': return 335;
|
|
case 'C': return 336;
|
|
case 'G': return 337;
|
|
case 'I': return 338;
|
|
case 'T': return 339;
|
|
case 'U': return 340;
|
|
case 'N': return 341;
|
|
}
|
|
#define ID(s) ((s)[0] << 8 | (s)[1])
|
|
switch (ID(name.c_str())) {
|
|
case ID("AG"): return 342;
|
|
case ID("AL"): return 343;
|
|
case ID("BA"): return 344;
|
|
case ID("BR"): return 345;
|
|
case ID("CA"): return 346;
|
|
case ID("CD"): return 347;
|
|
case ID("CL"): return 348;
|
|
case ID("CM"): return 349;
|
|
case ID("CN"): return 350;
|
|
case ID("CO"): return 351;
|
|
case ID("CS"): return 352;
|
|
case ID("CU"): return 353;
|
|
case ID("FE"): return 354;
|
|
case ID("HG"): return 355;
|
|
case ID("LI"): return 356;
|
|
case ID("MG"): return 357;
|
|
case ID("MN"): return 358;
|
|
case ID("NA"): return 359;
|
|
case ID("NI"): return 360;
|
|
case ID("NO"): return 361;
|
|
case ID("PB"): return 362;
|
|
case ID("RB"): return 363;
|
|
case ID("SR"): return 364;
|
|
case ID("Y1"): return 365;
|
|
case ID("ZN"): return 366;
|
|
}
|
|
#undef ID
|
|
}
|
|
return 367;
|
|
}
|
|
|
|
ResidueInfo& get_residue_info(size_t idx) {
|
|
static ResidueInfo array[368] = {
|
|
// hydrogen_count needs to be verified
|
|
{"ALA", RI::AA, 1, 'A', 7, 89.0932f },
|
|
{"ARG", RI::AA, 1, 'R', 15, 175.209f },
|
|
{"ASN", RI::AA, 1, 'N', 8, 132.118f },
|
|
{"ABA", RI::AA, 1, 'a', 9, 103.120f },
|
|
{"ASP", RI::AA, 1, 'D', 7, 133.103f },
|
|
{"ASX", RI::AA, 1, 'B', 6, 100.096f },
|
|
{"CYS", RI::AA, 1, 'C', 7, 121.158f }, // also BUF
|
|
{"CSH", RI::AA, 1, 's', 17, 283.284f },
|
|
{"GLN", RI::AA, 1, 'Q', 10, 146.144f },
|
|
{"GLU", RI::AA, 1, 'E', 9, 147.129f },
|
|
|
|
{"GLX", RI::AA, 1, 'Z', 8, 114.123f },
|
|
{"GLY", RI::AA, 1, 'G', 5, 75.0666f }, // also BUF
|
|
{"HIS", RI::AA, 1, 'H', 10, 156.162f },
|
|
{"ILE", RI::AA, 1, 'I', 13, 131.173f },
|
|
{"LEU", RI::AA, 1, 'L', 13, 131.173f },
|
|
{"LYS", RI::AA, 1, 'K', 15, 147.196f },
|
|
{"MET", RI::AA, 1, 'M', 11, 149.211f },
|
|
{"MSE", RI::AA, 1, 'm', 11, 196.106f },
|
|
{"ORN", RI::AA, 1, 'a', 12, 132.161f },
|
|
{"PHE", RI::AA, 1, 'F', 11, 165.189f },
|
|
//20
|
|
|
|
{"PRO", RI::AA, 1, 'P', 9, 115.130f },
|
|
{"SER", RI::AA, 1, 'S', 7, 105.093f },
|
|
{"THR", RI::AA, 1, 'T', 9, 119.119f },
|
|
{"TRP", RI::AA, 1, 'W', 12, 204.225f },
|
|
{"TYR", RI::AA, 1, 'Y', 11, 181.189f },
|
|
{"UNK", RI::AA, 1, 'X', 9, 103.120f },
|
|
{"VAL", RI::AA, 1, 'V', 11, 117.146f },
|
|
{"SEC", RI::AA, 1, 'U', 7, 168.053f },
|
|
{"PYL", RI::AA, 1, 'O', 21, 255.313f },
|
|
{"SEP", RI::AA, 1, 's', 8, 185.072f },
|
|
// 30
|
|
|
|
{"TPO", RI::AA, 1, 't', 10, 199.099f },
|
|
{"PCA", RI::AA, 1, 'e', 7, 129.114f },
|
|
{"CSO", RI::AA, 1, 'c', 7, 137.158f },
|
|
{"PTR", RI::AA, 1, 'y', 12, 261.168f },
|
|
{"KCX", RI::AA, 1, 'k', 14, 190.197f },
|
|
{"CSD", RI::AA, 1, 'c', 7, 153.157f },
|
|
{"LLP", RI::AA, 1, 'k', 22, 375.314f },
|
|
{"CME", RI::AA, 1, 'c', 11, 197.276f },
|
|
{"MLY", RI::AA, 1, 'k', 18, 174.241f },
|
|
{"DAL", RI::AAD, 1, 'a', 7, 89.0932f },
|
|
{"TYS", RI::AA, 1, 'y', 11, 261.252f },
|
|
{"OCS", RI::AA, 1, 'c', 7, 169.156f },
|
|
// 40
|
|
|
|
{"M3L", RI::AA, 1, 'k', 21, 189.275f },
|
|
{"FME", RI::AA, 1, 'm', 11, 177.221f },
|
|
{"ALY", RI::AA, 1, 'k', 16, 188.224f },
|
|
{"HYP", RI::AA, 1, 'p', 9, 131.130f },
|
|
{"CAS", RI::AA, 1, 'c', 12, 225.141f },
|
|
{"CRO", RI::AA, 1, 't', 17, 319.313f },
|
|
{"CSX", RI::AA, 1, 'c', 7, 137.158f },
|
|
{"DPR", RI::AAD, 1, 'p', 9, 115.130f }, // also BUF
|
|
{"DGL", RI::AAD, 1, 'e', 9, 147.129f },
|
|
{"DVA", RI::AAD, 1, 'v', 11, 117.146f },
|
|
{"CSS", RI::AA, 1, 'c', 7, 153.223f },
|
|
{"DPN", RI::AAD, 1, 'f', 11, 165.189f },
|
|
{"DSN", RI::AAD, 1, 's', 7, 105.093f },
|
|
// 50
|
|
|
|
{"DLE", RI::AAD, 1, 'l', 13, 131.173f },
|
|
{"HIC", RI::AA, 1, 'h', 11, 169.181f },
|
|
{"NLE", RI::AA, 1, 'l', 13, 131.173f },
|
|
{"MVA", RI::AA, 1, 'v', 13, 131.173f },
|
|
{"MLZ", RI::AA, 1, 'k', 16, 160.214f },
|
|
{"CR2", RI::AA, 1, 'g', 13, 275.260f },
|
|
{"SAR", RI::AA, 1, 'g', 7, 89.0932f },
|
|
{"DAR", RI::AAD, 1, 'r', 15, 175.209f },
|
|
{"DLY", RI::AAD, 1, 'k', 14, 146.188f },
|
|
{"YCM", RI::AA, 1, 'c', 10, 178.209f },
|
|
// 60
|
|
|
|
{"NRQ", RI::AA, 1, 'm', 17, 347.389f },
|
|
{"CGU", RI::AA, 1, 'e', 9, 191.139f },
|
|
{"0TD", RI::AA, 1, 'd', 9, 179.194f },
|
|
{"MLE", RI::AA, 1, 'l', 15, 145.200f },
|
|
{"DAS", RI::AAD, 1, 'd', 7, 133.103f },
|
|
{"DTR", RI::AAD, 1, 'w', 12, 204.225f },
|
|
{"CXM", RI::AA, 1, 'm', 11, 193.221f },
|
|
{"TPQ", RI::AA, 1, 'y', 9, 211.171f },
|
|
{"DCY", RI::AAD, 1, 'c', 7, 121.158f },
|
|
{"DSG", RI::AAD, 1, 'n', 8, 132.118f },
|
|
{"DTY", RI::AAD, 1, 'y', 11, 181.189f },
|
|
// 70
|
|
|
|
{"DHI", RI::AAD, 1, 'h', 10, 156.162f },
|
|
{"MEN", RI::AA, 1, 'n', 10, 146.144f },
|
|
{"DTH", RI::AAD, 1, 't', 9, 119.119f },
|
|
{"SAC", RI::AA, 1, 's', 9, 147.129f },
|
|
{"DGN", RI::AAD, 1, 'q', 10, 146.144f },
|
|
{"AIB", RI::AA, 1, 'a', 9, 103.120f },
|
|
{"SMC", RI::AA, 1, 'c', 9, 135.185f },
|
|
{"IAS", RI::AA, 1, 'd', 7, 133.103f },
|
|
{"CIR", RI::AA, 1, 'r', 13, 175.186f },
|
|
{"BMT", RI::AA, 1, 't', 19, 201.263f },
|
|
{"DIL", RI::AAD, 1, 'i', 13, 131.173f },
|
|
{"FGA", RI::AA, 1, 'e', 9, 147.129f },
|
|
//80
|
|
|
|
{"PHI", RI::AA, 1, 'f', 10, 291.086f },
|
|
{"CRQ", RI::AA, 1, 'q', 16, 344.322f },
|
|
{"SME", RI::AA, 1, 'm', 11, 165.211f },
|
|
{"GHP", RI::AA, 1, 'g', 9, 167.162f }, // d-peptide in CCD
|
|
{"MHO", RI::AA, 1, 'm', 11, 165.211f },
|
|
{"NEP", RI::AA, 1, 'h', 10, 235.134f },
|
|
{"TRQ", RI::AA, 1, 'w', 10, 234.208f },
|
|
{"TOX", RI::AA, 1, 'w', 12, 236.224f },
|
|
{"ALC", RI::AA, 1, 'a', 17, 171.237f },
|
|
{"3FG", RI::AA, 1, ' ', 9, 183.161f },
|
|
{"SCH", RI::AA, 1, 'c', 9, 167.250f },
|
|
{"MDO", RI::AA, 1, 'a', 11, 197.191f },
|
|
{"MAA", RI::AA, 1, 'a', 9, 103.120f },
|
|
//90
|
|
|
|
{"GYS", RI::AA, 1, 's', 15, 305.286f },
|
|
{"MK8", RI::AA, 1, 'l', 15, 145.200f },
|
|
{"CR8", RI::AA, 1, 'h', 16, 354.340f },
|
|
{"KPI", RI::AA, 1, 'k', 16, 216.234f },
|
|
{"SCY", RI::AA, 1, 'c', 9, 163.195f },
|
|
{"DHA", RI::AA, 1, 's', 5, 87.0773f },
|
|
{"OMY", RI::AA, 1, 'y', 10, 231.633f },
|
|
{"CAF", RI::AA, 1, 'c', 12, 241.140f },
|
|
{"0AF", RI::AA, 1, 'w', 12, 220.225f },
|
|
{"SNN", RI::AA, 1, 'n', 6, 114.103f },
|
|
// 100
|
|
|
|
{"MHS", RI::AA, 1, 'h', 11, 169.181f },
|
|
{"MLU", RI::AAD, 1, ' ', 15, 145.200f },
|
|
{"SNC", RI::AA, 1, 'c', 6, 150.156f },
|
|
{"PHD", RI::AA, 1, 'd', 8, 213.083f },
|
|
{"B3E", RI::AA, 1, 'e', 11, 161.156f },
|
|
{"MEA", RI::AA, 1, 'f', 13, 179.216f },
|
|
{"MED", RI::AAD, 1, 'm', 11, 149.211f },
|
|
{"OAS", RI::AA, 1, 's', 9, 147.129f },
|
|
{"GL3", RI::AA, 1, 'g', 5, 91.1322f },
|
|
{"FVA", RI::AA, 1, 'v', 11, 145.156f },
|
|
// 110
|
|
|
|
{"PHL", RI::AA, 1, 'f', 13, 151.206f },
|
|
{"CRF", RI::AA, 1, 't', 18, 342.349f },
|
|
{"OMZ", RI::AA, 1, ' ', 10, 231.633f }, // d-peptide in CCD
|
|
{"BFD", RI::AA, 1, 'd', 6, 198.102f },
|
|
{"MEQ", RI::AA, 1, 'q', 12, 160.171f },
|
|
{"DAB", RI::AA, 1, 'a', 10, 118.134f },
|
|
{"AGM", RI::AA, 1, 'r', 17, 189.235f },
|
|
{"PSU", RI::RNA, 2, 'u', 13, 324.181f },
|
|
{"5MU", RI::RNA, 2, 'u', 15, 338.208f },
|
|
{"7MG", RI::RNA, 2, 'g', 18, 379.263f },
|
|
// 120
|
|
|
|
{"OMG", RI::RNA, 2, 'g', 16, 377.247f },
|
|
{"UR3", RI::RNA, 2, 'u', 15, 338.208f },
|
|
{"OMC", RI::RNA, 2, 'c', 16, 337.223f },
|
|
{"2MG", RI::RNA, 2, 'g', 16, 377.247f },
|
|
{"H2U", RI::RNA, 2, 'u', 15, 326.197f },
|
|
{"4SU", RI::RNA, 2, 'u', 13, 340.247f },
|
|
{"OMU", RI::RNA, 2, 'u', 15, 338.208f },
|
|
{"4OC", RI::RNA, 2, 'c', 18, 351.250f },
|
|
{"MA6", RI::RNA, 2, 'a', 18, 375.274f },
|
|
{"M2G", RI::RNA, 2, 'g', 18, 391.274f },
|
|
// 130
|
|
|
|
{"1MA", RI::RNA, 2, 'a', 16, 361.248f },
|
|
{"6MZ", RI::RNA, 2, 'a', 16, 361.248f },
|
|
{"CCC", RI::RNA, 2, 'c', 13, 385.161f },
|
|
{"2MA", RI::RNA, 2, 'a', 16, 361.248f },
|
|
{"1MG", RI::RNA, 2, 'g', 16, 377.247f },
|
|
{"5BU", RI::RNA, 2, 'u', 12, 403.077f },
|
|
{"MIA", RI::RNA, 2, 'a', 24, 461.430f },
|
|
{"DOC", RI::DNA, 2, 'c', 14, 291.198f },
|
|
{"8OG", RI::DNA, 2, 'g', 14, 363.221f },
|
|
{"5CM", RI::DNA, 2, 'c', 16, 321.224f },
|
|
// 140
|
|
|
|
{"3DR", RI::DNA, 2, ' ', 11, 198.111f },
|
|
{"BRU", RI::DNA, 2, 'u', 12, 387.078f },
|
|
{"CBR", RI::DNA, 2, 'c', 13, 386.093f },
|
|
{"HOH", RI::HOH, 0, ' ', 2, 18.0153f },
|
|
{"DOD", RI::HOH, 0, ' ', 2, 20.0276f },
|
|
{"HEM", RI::ELS, 0, ' ', 32, 616.487f },
|
|
{"SO4", RI::BUF, 0, ' ', 0, 96.0626f },
|
|
{"GOL", RI::BUF, 0, ' ', 8, 92.0938f },
|
|
{"EDO", RI::BUF, 0, ' ', 6, 62.0678f },
|
|
{"NAG", RI::PYR, 0, ' ', 15, 221.208f },
|
|
// 150
|
|
|
|
{"PO4", RI::ELS, 0, ' ', 0, 94.9714f },
|
|
{"ACT", RI::BUF, 0, ' ', 3, 59.0440f },
|
|
{"PEG", RI::ELS, 0, ' ', 10, 106.120f },
|
|
{"MAN", RI::PYR, 0, ' ', 12, 180.156f }, // also BUF
|
|
{"FAD", RI::ELS, 0, ' ', 33, 785.550f },
|
|
{"BMA", RI::PYR, 0, ' ', 12, 180.156f }, // also BUF
|
|
{"ADP", RI::ELS, 0, ' ', 15, 427.201f },
|
|
{"DMS", RI::BUF, 0, ' ', 6, 78.1334f },
|
|
{"ACE", RI::ELS, 1, ' ', 4, 44.0526f },
|
|
{"NH2", RI::ELS, 1, ' ', 2, 16.0226f }, // ?
|
|
{"MPD", RI::BUF, 0, ' ', 14, 118.174f },
|
|
{"MES", RI::ELS, 0, ' ', 13, 195.237f },
|
|
// 160
|
|
|
|
{"NAD", RI::ELS, 0, ' ', 27, 663.425f },
|
|
{"NAP", RI::ELS, 0, ' ', 28, 743.405f },
|
|
{"TRS", RI::BUF, 0, ' ', 12, 122.143f },
|
|
{"ATP", RI::ELS, 0, ' ', 16, 507.181f },
|
|
{"PG4", RI::ELS, 0, ' ', 18, 194.226f },
|
|
{"GDP", RI::ELS, 2, 'g', 15, 443.201f }, // RNA in CCD
|
|
{"FUC", RI::PYR, 0, ' ', 12, 164.156f },
|
|
{"FMT", RI::BUF, 0, ' ', 2, 46.0254f },
|
|
{"GAL", RI::PYR, 0, ' ', 12, 180.156f },
|
|
{"PGE", RI::BUF, 0, ' ', 14, 150.173f },
|
|
{"FMN", RI::ELS, 0, ' ', 21, 456.344f },
|
|
// 170
|
|
|
|
{"PLP", RI::ELS, 0, ' ', 10, 247.142f },
|
|
{"EPE", RI::ELS, 0, ' ', 18, 238.305f },
|
|
{"SF4", RI::ELS, 0, ' ', 0, 351.640f },
|
|
{"BME", RI::ELS, 0, ' ', 6, 78.1334f },
|
|
{"CIT", RI::BUF, 0, ' ', 8, 192.124f },
|
|
{"BE7", RI::BUF, 0, ' ', 5, 357.156f },
|
|
{"MRD", RI::BUF, 0, ' ', 14, 118.174f },
|
|
{"MHA", RI::BUF, 0, ' ', 10, 190.154f },
|
|
{"BU3", RI::BUF, 0, ' ', 10, 90.1210f },
|
|
{"PGO", RI::BUF, 0, ' ', 8, 76.0944f },
|
|
{"BU2", RI::BUF, 0, ' ', 10, 90.1210f },
|
|
// 180
|
|
|
|
{"PDO", RI::BUF, 0, ' ', 8, 76.0944f },
|
|
{"BU1", RI::BUF, 0, ' ', 10, 90.1210f },
|
|
{"PG6", RI::BUF, 0, ' ', 26, 266.331f },
|
|
{"1BO", RI::BUF, 0, ' ', 10, 74.1216f },
|
|
{"PE7", RI::BUF, 0, ' ', 30, 342.449f },
|
|
{"PG5", RI::BUF, 0, ' ', 18, 178.226f },
|
|
{"TFP", RI::BUF, 0, ' ', 24, 407.496f },
|
|
{"DHD", RI::BUF, 0, ' ', 4, 160.082f },
|
|
{"PEU", RI::BUF, 0, ' ', 112, 1221.46f },
|
|
{"TAU", RI::BUF, 0, ' ', 7, 125.147f },
|
|
{"SBT", RI::BUF, 0, ' ', 10, 74.1216f },
|
|
// 180
|
|
|
|
{"SAL", RI::BUF, 0, ' ', 6, 138.121f },
|
|
{"IOH", RI::BUF, 0, ' ', 8, 60.0950f },
|
|
{"IPA", RI::BUF, 0, ' ', 8, 60.0950f },
|
|
{"PIG", RI::BUF, 0, ' ', 14, 150.173f },
|
|
{"B3P", RI::BUF, 0, ' ', 26, 282.334f },
|
|
{"BTB", RI::BUF, 0, ' ', 19, 209.240f },
|
|
{"NHE", RI::BUF, 0, ' ', 17, 207.290f },
|
|
{"C8E", RI::BUF, 0, ' ', 34, 306.438f },
|
|
{"OTE", RI::BUF, 0, ' ', 34, 306.438f },
|
|
{"PE4", RI::BUF, 0, ' ', 34, 354.436f },
|
|
{"XPE", RI::BUF, 0, ' ', 42, 458.541f },
|
|
// 200
|
|
|
|
{"PE8", RI::BUF, 0, ' ', 34, 370.436f },
|
|
{"P33", RI::BUF, 0, ' ', 30, 326.383f },
|
|
{"N8E", RI::BUF, 0, ' ', 38, 350.491f },
|
|
{"2OS", RI::BUF, 0, ' ', 36, 468.493f },
|
|
{"1PS", RI::BUF, 0, ' ', 11, 201.243f },
|
|
{"CPS", RI::BUF, 0, ' ', 58, 614.877f },
|
|
{"DMX", RI::BUF, 0, ' ', 19, 257.349f },
|
|
{"MPO", RI::BUF, 0, ' ', 15, 209.263f },
|
|
{"GCD", RI::PYR, 0, ' ', 8, 176.124f },
|
|
{"DXG", RI::BUF, 0, ' ', 8, 192.124f },
|
|
{"CM5", RI::BUF, 0, ' ', 42, 494.573f },
|
|
// 210
|
|
|
|
{"ACA", RI::BUF, 1, ' ', 13, 131.173f }, // peptide linking
|
|
{"ACN", RI::BUF, 0, ' ', 6, 58.0791f },
|
|
{"CCN", RI::BUF, 0, ' ', 3, 41.0519f },
|
|
{"GLC", RI::PYR, 0, ' ', 12, 180.156f },
|
|
{"DR6", RI::BUF, 0, ' ', 142, 1527.90f },
|
|
{"NH4", RI::BUF, 0, ' ', 4, 18.0385f },
|
|
{"AZI", RI::BUF, 0, ' ', 0, 42.0201f },
|
|
{"BNG", RI::PYR, 0, ' ', 30, 306.395f },
|
|
{"BOG", RI::PYR, 0, ' ', 28, 292.369f },
|
|
{"BGC", RI::PYR, 0, ' ', 12, 180.156f },
|
|
{"BCN", RI::BUF, 0, ' ', 13, 163.172f },
|
|
// 220
|
|
|
|
{"BRO", RI::BUF, 0, ' ', 0, 79.9040f },
|
|
{"CAC", RI::BUF, 0, ' ', 6, 136.989f },
|
|
{"CBX", RI::BUF, 0, ' ', 2, 46.0254f },
|
|
{"ACY", RI::BUF, 0, ' ', 4, 60.0520f },
|
|
{"CBM", RI::BUF, 0, ' ', 4, 60.0520f },
|
|
{"CLO", RI::BUF, 0, ' ', 0, 35.4530f },
|
|
{"3CO", RI::BUF, 0, ' ', 0, 58.9332f },
|
|
{"NCO", RI::BUF, 0, ' ', 18, 161.116f },
|
|
{"CU1", RI::BUF, 0, ' ', 0, 63.5460f },
|
|
{"CYN", RI::BUF, 0, ' ', 0, 26.0174f },
|
|
{"MA4", RI::BUF, 0, ' ', 44, 508.600f },
|
|
// 230
|
|
|
|
{"TAR", RI::BUF, 0, ' ', 6, 150.087f },
|
|
{"GLO", RI::BUF, 0, ' ', 12, 180.156f }, // d-saccharide
|
|
{"MTL", RI::BUF, 0, ' ', 14, 182.172f },
|
|
{"SOR", RI::BUF, 0, ' ', 14, 182.172f },
|
|
{"DMU", RI::BUF, 0, ' ', 42, 482.562f }, // d-saccharide
|
|
{"DDQ", RI::BUF, 0, ' ', 27, 201.349f },
|
|
{"DMF", RI::BUF, 0, ' ', 7, 73.0938f },
|
|
{"DIO", RI::BUF, 0, ' ', 8, 88.1051f },
|
|
{"DOX", RI::BUF, 0, ' ', 8, 88.1051f },
|
|
{"12P", RI::BUF, 0, ' ', 50, 546.646f },
|
|
{"SDS", RI::BUF, 0, ' ', 26, 266.397f },
|
|
// 240
|
|
|
|
{"LMT", RI::BUF, 0, ' ', 46, 510.615f }, // d-saccharide
|
|
{"EOH", RI::BUF, 0, ' ', 6, 46.0684f },
|
|
{"EEE", RI::BUF, 0, ' ', 8, 88.1051f },
|
|
{"EGL", RI::BUF, 0, ' ', 6, 62.0678f },
|
|
{"FLO", RI::BUF, 0, ' ', 0, 18.9984f },
|
|
{"TRT", RI::BUF, 0, ' ', 36, 352.508f },
|
|
{"FCY", RI::BUF, 0, ' ', 7, 121.158f },
|
|
{"FRU", RI::BUF, 0, ' ', 12, 180.156f }, // saccharide
|
|
{"GBL", RI::BUF, 0, ' ', 6, 86.0892f },
|
|
{"GPX", RI::BUF, 0, ' ', 14, 505.165f },
|
|
{"HTO", RI::BUF, 0, ' ', 16, 148.200f },
|
|
// 250
|
|
|
|
{"HTG", RI::BUF, 0, ' ', 26, 294.408f },
|
|
{"B7G", RI::BUF, 0, ' ', 26, 278.342f },
|
|
{"C10", RI::BUF, 0, ' ', 46, 422.596f },
|
|
{"16D", RI::BUF, 0, ' ', 16, 116.205f },
|
|
{"HEZ", RI::BUF, 0, ' ', 14, 118.174f },
|
|
{"IOD", RI::BUF, 0, ' ', 0, 126.904f },
|
|
{"IDO", RI::BUF, 0, ' ', 0, 126.904f },
|
|
{"ICI", RI::BUF, 0, ' ', 8, 192.124f },
|
|
{"ICT", RI::BUF, 0, ' ', 8, 192.124f },
|
|
{"TLA", RI::BUF, 0, ' ', 6, 150.087f },
|
|
{"LAT", RI::BUF, 0, ' ', 22, 342.296f }, // saccharide
|
|
// 260
|
|
|
|
{"LBT", RI::BUF, 0, ' ', 22, 342.296f }, // saccharide
|
|
{"LDA", RI::BUF, 0, ' ', 31, 229.402f },
|
|
{"MN3", RI::BUF, 0, ' ', 0, 54.9380f },
|
|
{"MRY", RI::BUF, 0, ' ', 10, 122.120f },
|
|
{"MOH", RI::BUF, 0, ' ', 4, 32.0419f },
|
|
{"BEQ", RI::BUF, 0, ' ', 38, 342.517f },
|
|
{"C15", RI::BUF, 0, ' ', 38, 336.554f },
|
|
{"MG8", RI::BUF, 0, ' ', 31, 321.410f },
|
|
{"POL", RI::BUF, 0, ' ', 8, 60.0950f },
|
|
{"NO3", RI::BUF, 0, ' ', 0, 62.0049f },
|
|
{"JEF", RI::BUF, 0, ' ', 63, 597.822f },
|
|
// 270
|
|
|
|
{"P4C", RI::BUF, 0, ' ', 28, 324.367f },
|
|
{"CE1", RI::BUF, 0, ' ', 58, 538.755f },
|
|
{"DIA", RI::BUF, 0, ' ', 20, 144.258f },
|
|
{"CXE", RI::BUF, 0, ' ', 42, 378.544f },
|
|
{"IPH", RI::BUF, 0, ' ', 6, 94.1112f },
|
|
{"PIN", RI::BUF, 0, ' ', 18, 302.368f },
|
|
{"15P", RI::BUF, 0, ' ', 140, 1529.83f },
|
|
{"CRY", RI::BUF, 0, ' ', 8, 92.0938f },
|
|
{"PGR", RI::BUF, 0, ' ', 8, 76.0944f },
|
|
{"PGQ", RI::BUF, 0, ' ', 8, 76.0944f },
|
|
{"SPD", RI::BUF, 0, ' ', 19, 145.246f },
|
|
// 270
|
|
|
|
{"SPK", RI::BUF, 0, ' ', 30, 206.372f },
|
|
{"SPM", RI::BUF, 0, ' ', 26, 202.340f },
|
|
{"SUC", RI::PYR, 0, ' ', 22, 342.296f },
|
|
{"TBU", RI::BUF, 0, ' ', 10, 74.1216f },
|
|
{"TMA", RI::BUF, 0, ' ', 12, 74.1448f },
|
|
{"TEP", RI::BUF, 0, ' ', 8, 180.164f },
|
|
{"SCN", RI::BUF, 0, ' ', 0, 58.0824f },
|
|
{"TRE", RI::PYR, 0, ' ', 22, 342.296f },
|
|
{"ETF", RI::BUF, 0, ' ', 3, 100.040f },
|
|
{"144", RI::BUF, 0, ' ', 12, 122.143f },
|
|
{"UMQ", RI::BUF, 0, ' ', 44, 496.589f },
|
|
// 280
|
|
|
|
{"URE", RI::BUF, 0, ' ', 4, 60.0553f },
|
|
{"YT3", RI::BUF, 0, ' ', 0, 88.9059f },
|
|
{"ZN2", RI::BUF, 0, ' ', 0, 65.3800f },
|
|
{"FE2", RI::BUF, 0, ' ', 0, 55.8450f },
|
|
{"3NI", RI::BUF, 0, ' ', 0, 58.6934f },
|
|
{"SIA", RI::PYR, 0, ' ', 0, 0.0f },
|
|
{"XYP", RI::PYR, 0, ' ', 0, 0.0f },
|
|
{"A2G", RI::PYR, 0, ' ', 0, 0.0f },
|
|
{"GLA", RI::PYR, 0, ' ', 0, 0.0f },
|
|
{"NDG", RI::PYR, 0, ' ', 0, 0.0f },
|
|
// 290
|
|
{"NGA", RI::PYR, 0, ' ', 0, 0.0f },
|
|
{"A", RI::RNA, 2, 'A', 14, 347.221f },
|
|
{"C", RI::RNA, 2, 'C', 14, 323.197f },
|
|
{"G", RI::RNA, 2, 'G', 14, 363.221f },
|
|
{"I", RI::RNA, 2, 'I', 13, 348.206f },
|
|
{"U", RI::RNA, 2, 'U', 13, 324.181f },
|
|
{"N", RI::RNA, 2, 'N', 11, 214.11f },
|
|
|
|
{"F", RI::BUF, 0, ' ', 0, 18.9984f },
|
|
{"K", RI::BUF, 0, ' ', 0, 39.0983f },
|
|
{"DA", RI::DNA, 2, 'A', 14, 331.222f },
|
|
// 300
|
|
{"DC", RI::DNA, 2, 'C', 14, 307.197f },
|
|
{"DG", RI::DNA, 2, 'G', 14, 347.221f },
|
|
{"DI", RI::DNA, 2, 'I', 13, 332.207f },
|
|
{"DT", RI::DNA, 2, 'T', 15, 322.208f },
|
|
{"DU", RI::DNA, 2, 'U', 13, 308.182f },
|
|
{"DN", RI::DNA, 2, 'N', 14, 198.111f }, // unknown DNA
|
|
{"AG", RI::BUF, 0, ' ', 0, 107.868f },
|
|
{"AL", RI::BUF, 0, ' ', 0, 26.9815f },
|
|
// 308
|
|
|
|
{"BA", RI::BUF, 0, ' ', 0, 137.327f },
|
|
{"BR", RI::BUF, 0, ' ', 0, 79.9040f },
|
|
{"CA", RI::BUF, 0, ' ', 0, 40.0780f },
|
|
{"CD", RI::BUF, 0, ' ', 0, 112.411f },
|
|
{"CL", RI::BUF, 0, ' ', 0, 35.4530f },
|
|
{"CM", RI::BUF, 0, ' ', 4, 60.0520f },
|
|
{"CN", RI::BUF, 0, ' ', 0, 27.0253f },
|
|
{"CO", RI::BUF, 0, ' ', 0, 58.9332f },
|
|
{"CS", RI::BUF, 0, ' ', 0, 132.905f },
|
|
{"CU", RI::BUF, 0, ' ', 0, 63.5460f },
|
|
{"FE", RI::BUF, 0, ' ', 0, 55.8450f },
|
|
// 318
|
|
|
|
{"HG", RI::BUF, 0, ' ', 0, 200.590f },
|
|
{"LI", RI::BUF, 0, ' ', 0, 6.94100f },
|
|
{"MG", RI::BUF, 0, ' ', 0, 24.3050f },
|
|
{"MN", RI::BUF, 0, ' ', 0, 54.9380f },
|
|
{"NA", RI::BUF, 0, ' ', 0, 22.9898f },
|
|
{"NI", RI::BUF, 0, ' ', 0, 58.6934f },
|
|
{"NO", RI::ELS, 0, ' ', 0, 30.0061f },
|
|
{"PB", RI::BUF, 0, ' ', 0, 207.200f },
|
|
{"RB", RI::BUF, 0, ' ', 0, 85.4678f },
|
|
{"SR", RI::BUF, 0, ' ', 0, 87.6200f },
|
|
{"Y1", RI::BUF, 0, ' ', 0, 88.9059f },
|
|
// 328
|
|
|
|
{"ZN", RI::BUF, 0, ' ', 0, 65.3800f },
|
|
{"", RI::UNKNOWN, 0, ' ', 0, 0.0f }
|
|
};
|
|
return array[idx];
|
|
}
|
|
|
|
ResidueInfo& find_tabulated_residue(const std::string& name) {
|
|
size_t idx = find_tabulated_residue_idx(name);
|
|
return get_residue_info(idx);
|
|
}
|
|
|
|
|
|
std::vector<std::string> expand_one_letter_sequence(const std::string& seq,
|
|
ResidueKind kind) {
|
|
|
|
std::vector<std::string> r;
|
|
r.reserve(seq.size());
|
|
auto kind_str = [&]() {
|
|
switch (kind) {
|
|
case ResidueKind::AA: return "peptide";
|
|
case ResidueKind::RNA: return "RNA";
|
|
case ResidueKind::DNA: return "DNA";
|
|
default: return "unknown";
|
|
}
|
|
};
|
|
for (size_t i = 0; i != seq.size(); ++i) {
|
|
char c = seq[i];
|
|
if (is_space(c))
|
|
continue;
|
|
if (c == '(') { // special case, e.g. (MSE)
|
|
size_t start = i + 1;
|
|
i = seq.find(')', start);
|
|
if (i == std::string::npos)
|
|
gemmi::fail("unmatched '(' in sequence");
|
|
r.emplace_back(seq, start, i - start);
|
|
} else {
|
|
const char* str = gemmi::expand_one_letter(c, kind);
|
|
if (str == nullptr)
|
|
gemmi::fail("unexpected letter in ", kind_str(), " sequence: ", c,
|
|
" (", std::to_string(int(c)), ')');
|
|
r.emplace_back(str);
|
|
}
|
|
}
|
|
return r;
|
|
}
|
|
}
|