Press n or j to go to the next uncovered block, b, p or k for the previous block.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 | 18x 60x 18x 17745x 16569x 12819x 18x 6x 6x 6x 6x 6x 6x 6x 6x 6x 6x 6x 6x 6x 6x 6x 6x 6x 6x 6x 6x 6x 6x 6x 6x 6x 6x 6x 6x 1x 1x 1x 1x 1x 6x 6x 6x 6x 6x 6x 30x 30x 6x 6x 6x 6x 6x 6x 6x 30x 30x 30x 30x 30x 30x 30x 3030x 3030x 3030x 3030x 3030x 3030x 3030x 3030x 3030x 216x 3030x 3030x 3030x 3030x 3030x 3030x 3030x 3030x 3030x 3030x 3030x 3030x 3030x 3030x 3030x 3030x 12126x 12126x 12126x 12126x 12126x 12126x 12126x 906x 12126x 12126x 12126x 12126x 435x 435x 11691x 11691x 11691x 11691x 11691x 11691x 11691x 11691x 11691x 11691x 3030x 3030x 9372x 9372x 9372x 9372x 9372x 9372x 9372x 9372x 8884x 8884x 8884x 8884x 3030x 30x 30x 3030x 30x 6x 6x 1368x 1368x 1368x 1368x 1368x 1368x 1368x 1368x 1368x 1359x 1359x 1359x 1359x 6x 6x 6x 1x 1x 6x 5x 6x | import { base64ToArray } from "../utilities"; import { Matrix4 } from "../WebGL"; import { computeSecondaryStructure } from "./utils/computeSecondaryStructure"; import { processSymmetries } from "./utils/processSymmetries"; interface MMTFobj { decode(data:Uint8Array|ArrayBuffer): any; } declare var MMTF: MMTFobj; var fromCharCode = function( charCodeArray ){ return String.fromCharCode.apply( null, charCodeArray ).replace(/\0/g, ''); }; var convertSS = function(val) { //convert mmtf code to 3dmol code /* 0: pi helix 1: bend 2: alpha helix 3: sheet extended 4: 3-10 helix 5: bridge 6: turn 7: coil */ if(val == 0 || val == 2 || val == 4) return 'h'; if(val == 3) return 's'; return 'c'; }; let mmtfHETATMtypes = new Set([ "D-SACCHARIDE", "D-SACCHARIDE 1,4 AND 1,4 LINKING", "D-SACCHARIDE 1,4 AND 1,6 LINKING", "L-SACCHARIDE", "L-SACCHARIDE 1,4 AND 1,4 LINKING", "L-SACCHARIDE 1,4 AND 1,6 LINKING", "NON-POLYMER", "OTHER", "PEPTIDE-LIKE", "SACCHARIDE" ]); /** @param bindata - binary UInt8Array buffer or a base64 encoded string * @param ParserOptionsSpec * @category Parsers */ export function MMTFparser(bindata, options) { var noH = !options.keepH; // suppress hydrogens by default var selAltLoc = options.altLoc ? options.altLoc : 'A'; //default alternate location to select if present var ignoreStruct = !!options.noSecondaryStructure; var computeStruct = !options.noComputeSecondaryStructure; //extract symmetries - only take first assembly, apply to all models (ignoring changes for now) var noAssembly = !options.doAssembly; // don't assemble by default var assemblyIndex = options.assemblyIndex ? options.assemblyIndex : 0; if(typeof(bindata) == "string") { //assume base64 encoded bindata = base64ToArray(bindata); } var mmtfData = MMTF.decode( bindata ); var atoms: any[][] & Record<string, any> = [[]]; var modelData: any[] = atoms.modelData = []; // setup index counters var modelIndex = 0; var chainIndex = 0; var groupIndex = 0; var atomIndex = 0; // setup optional fields var secStructList = mmtfData.secStructList; var insCodeList = mmtfData.insCodeList; var sequenceIndexList = mmtfData.sequenceIndexList; var bFactorList = mmtfData.bFactorList; var altLocList = mmtfData.altLocList; var occupancyList = mmtfData.occupancyList; var bondAtomList = mmtfData.bondAtomList; var bondOrderList = mmtfData.bondOrderList; var numModels = mmtfData.numModels; Iif (numModels == 0) return atoms; if (!options.multimodel) numModels = 1; //first only // hoisted loop variables var i, j, k, kl, m, n; var symmetries: Matrix4[] = []; if(!noAssembly && mmtfData.bioAssemblyList && mmtfData.bioAssemblyList.length > 0) { var transforms = mmtfData.bioAssemblyList[assemblyIndex].transformList; for(i = 0, n = transforms.length; i < n; i++) { var matrix = new Matrix4(transforms[i].matrix); matrix.transpose(); symmetries.push(matrix); } } var unitCell = null as Record<string, number> | null; //unit cell info if(mmtfData.unitCell) { var u = mmtfData.unitCell; unitCell = {'a' : u[0], 'b' : u[1], 'c' : u[2], 'alpha' : u[3], 'beta' : u[4], 'gamma' : u[5]}; } let chainIsPolymer: boolean[] = []; mmtfData.entityList.forEach(entity => { entity.chainIndexList.forEach(ch => { chainIsPolymer[ch] = entity.type == "polymer"; }); }); var bondAtomListStart = 0; //for current model //loop over models, for (m = 0; m < numModels; m++ ) { var modelChainCount = mmtfData.chainsPerModel[m]; var matoms = atoms[atoms.length-1]; var serialToIndex: number[] = []; // map to matoms index, needed for noh modelData.push({symmetries:symmetries, cryst: unitCell}); for( i = 0; i < modelChainCount; ++i ){ var chainGroupCount = mmtfData.groupsPerChain[ chainIndex ]; var chainId = fromCharCode( mmtfData.chainIdList.subarray( chainIndex * 4, chainIndex * 4 + 4 ) ); if(mmtfData.chainNameList) { chainId = fromCharCode( mmtfData.chainNameList.subarray( chainIndex * 4, chainIndex * 4 + 4 ) ); } var startGroup = groupIndex; var prevSS = ''; for( j = 0; j < chainGroupCount; ++j ){ //over residues (groups) var groupData = mmtfData.groupList[ mmtfData.groupTypeList[ groupIndex ] ]; var groupAtomCount = groupData.atomNameList.length; var secStruct = 0; var secStructBegin = false; var secStructEnd = false; if( secStructList ){ secStruct = secStructList[ groupIndex ]; var sscode = convertSS(secStruct); if(groupIndex == 0 || sscode != prevSS) { secStructBegin = true; } prevSS = sscode; var nextgroup = groupIndex+1; if(nextgroup >= secStructList.length || convertSS(secStructList[nextgroup] != sscode)) { secStructEnd = true; } } var insCode = null as string|null; if( mmtfData.insCodeList ){ insCode = String.fromCharCode( insCodeList[ groupIndex ] ); } var sequenceIndex = null; if( sequenceIndexList ){ sequenceIndex = sequenceIndexList[ groupIndex ]; } var groupId = mmtfData.groupIdList[ groupIndex ]; var groupName = groupData.groupName; let groupType = groupData.chemCompType; var startAtom = atomIndex; //note the following is not identical to respecting HETATM records //this information isn't available in MMTF. let isHETATM = mmtfHETATMtypes.has(groupType) || !chainIsPolymer[chainIndex]; for( k = 0; k < groupAtomCount; ++k ){ var element = groupData.elementList[ k ]; Iif(noH && element == 'H') { atomIndex += 1; continue; } var bFactor = ''; if( bFactorList ){ bFactor = bFactorList[ atomIndex ]; } var altLoc = ''; if( altLocList && altLocList[ atomIndex ]){ //not zero altLoc = String.fromCharCode( altLocList[ atomIndex ] ); } var occupancy = ''; if( occupancyList ){ occupancy = occupancyList[ atomIndex ]; } if (altLoc != '' && altLoc != selAltLoc && selAltLoc != '*') { atomIndex += 1; continue; } var atomId = mmtfData.atomIdList[ atomIndex ]; var atomName = groupData.atomNameList[ k ]; var atomCharge = 0; Iif(groupData.atomChargeList) atomCharge = groupData.atomChargeList[ k ]; var xCoord = mmtfData.xCoordList[ atomIndex ]; var yCoord = mmtfData.yCoordList[ atomIndex ]; var zCoord = mmtfData.zCoordList[ atomIndex ]; serialToIndex[atomIndex] = matoms.length; matoms.push({ 'resn' : groupName, 'x' : xCoord, 'y' : yCoord, 'z' : zCoord, 'elem' : element, 'hetflag' : isHETATM, 'chain' : chainId, 'resi' : groupId, 'icode' : altLoc, 'rescode' : groupId + (altLoc != ' ' ? "^" + altLoc : ""), // combo // resi // and // icode 'serial' : atomId, 'altLoc' : altLoc, 'index' : atomIndex, 'atom' : atomName, 'bonds' : [], 'ss' : convertSS(secStruct), 'ssbegin' : secStructBegin, 'ssend' : secStructEnd, 'bondOrder' : [], 'properties' : {charge: atomCharge, occupancy:occupancy}, 'b' : bFactor, }); atomIndex += 1; } // intra group bonds var groupBondAtomList = groupData.bondAtomList; for( k = 0, kl = groupData.bondOrderList.length; k < kl; ++k ){ var atomIndex1 = startAtom + groupBondAtomList[ k * 2 ]; var atomIndex2 = startAtom + groupBondAtomList[ k * 2 + 1 ]; var bondOrder = groupData.bondOrderList[ k ]; //I assume bonds are only recorded once var i1 = serialToIndex[atomIndex1]; var i2 = serialToIndex[atomIndex2]; var a1 = matoms[i1]; var a2 = matoms[i2]; if(a1 && a2) { a1.bonds.push(i2); a1.bondOrder.push(bondOrder); a2.bonds.push(i1); a2.bondOrder.push(bondOrder); } } groupIndex += 1; } //reset for bonds groupIndex = startGroup; for( j = 0; j < chainGroupCount; ++j ){ //over residues (groups) groupIndex += 1; } chainIndex += 1; } // inter group bonds if( bondAtomList ){ for(let k = bondAtomListStart, kl = bondAtomList.length; k < kl; k += 2 ){ let atomIndex1 = bondAtomList[ k ]; let atomIndex2 = bondAtomList[ k + 1 ]; let bondOrder = bondOrderList ? bondOrderList[ k / 2 ] : 1; Iif(atomIndex1 >= atomIndex) { bondAtomListStart = k; break; //on next model } //I assume bonds are only recorded once let i1 = serialToIndex[atomIndex1]; let i2 = serialToIndex[atomIndex2]; let a1 = matoms[i1]; let a2 = matoms[i2]; if(a1 && a2) { a1.bonds.push(i2); a1.bondOrder.push(bondOrder); a2.bonds.push(i1); a2.bondOrder.push(bondOrder); } } } Iif (options.multimodel) { Iif (!options.onemol) atoms.push([]); } modelIndex += 1; } if(!noAssembly) { for (let n = 0; n < atoms.length; n++) { processSymmetries(modelData[n].symmetries, atoms[n], options,modelData[n].cryst); } } if (computeStruct && !ignoreStruct) { computeSecondaryStructure(atoms,options.hbondCutoff); } return atoms; }; |