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 | 5x 5x 5x 5x 5x 5x 5x 5x 5x 5x 5x 5x 5x 9461x 9461x 9461x 3x 3x 3x 3x 9458x 4722x 4722x 4722x 4722x 4722x 4722x 4722x 4722x 4722x 4722x 4722x 4722x 4722x 4722x 4722x 4722x 4722x 4722x 4722x 4722x 4736x 4736x 4722x 4722x 4722x 4722x 4722x 18888x 18888x 18888x 18888x 9588x 9588x 9588x 9588x 9588x 14x 14x 14x 3x 3x 3x 3x 3x 3x 3x 11x 5x 5x 5x 5x 5x 5x 5x | import { Matrix4 } from "../../WebGL"; import { atomNameToElem } from "./atomNameToElem"; import { bondTable } from "./bondTable"; import { computeSecondaryStructure } from "./computeSecondaryStructure"; import { isEmpty } from "./isEmpty"; import { processSymmetries } from "./processSymmetries"; import { assignPDBBonds } from "./assignPDBBonds"; import { validateBonds } from "./validateBonds"; //return one model worth of pdb, returns atoms, modelData, and remaining lines export function getSinglePDB(lines, options, sslookup) { var atoms: any[] = []; var assignbonds = options.assignBonds === undefined ? true : options.assignBonds; var noH = !options.keepH; // suppress hydrogens by default var ignoreStruct = !!options.noSecondaryStructure; var computeStruct = !options.noComputeSecondaryStructure; var noAssembly = !options.doAssembly; // don't assemble by default var selAltLoc = options.altLoc ? options.altLoc : "A"; //default alternate location to select if present var modelData: Record<string, any> = { symmetries: [] }; var atom; var remainingLines = []; var hasStruct = false; var serialToIndex: number[] = []; // map from pdb serial to index in atoms var line; var seenbonds: Record<any, any> = {}; //sometimes connect records are duplicated as an unofficial means of relaying bond orders for (let i = 0; i < lines.length; i++) { line = lines[i].replace(/^\s*/, ""); // remove indent var recordName = line.substr(0, 6); var startChain, startResi, endChain, endResi; if (recordName.indexOf("END") == 0) { remainingLines = lines.slice(i + 1); if (recordName == "END") { //as opposed to ENDMDL //reset secondary structure for (var prop in sslookup) { Iif (sslookup.hasOwnProperty(prop)) { delete sslookup[prop]; } } } break; } else if (recordName == "ATOM " || recordName == "HETATM") { var resn, chain, resi, icode, x, y, z, hetflag, elem, serial, altLoc, b; altLoc = line.substr(16, 1); Iif (altLoc != " " && altLoc != selAltLoc && selAltLoc != "*") continue; serial = parseInt(line.substr(6, 5)); atom = line.substr(12, 4).replace(/ /g, ""); resn = line.substr(17, 3).replace(/ /g, ""); chain = line.substr(21, 1); resi = parseInt(line.substr(22, 4)); icode = line.substr(26, 1); x = parseFloat(line.substr(30, 8)); y = parseFloat(line.substr(38, 8)); z = parseFloat(line.substr(46, 8)); b = parseFloat(line.substr(60, 8)); elem = line.substr(76, 2).replace(/ /g, ""); Iif (elem === "" || typeof bondTable[elem] === "undefined") { // for some incorrect PDB files elem = atomNameToElem(line.substr(12, 2), line[0] == "A"); } else { elem = elem[0].toUpperCase() + elem.substr(1).toLowerCase(); } Iif (elem == "H" && noH) continue; Iif (recordName[0] == "H") hetflag = true; else hetflag = false; serialToIndex[serial] = atoms.length; atoms.push({ resn: resn, x: x, y: y, z: z, elem: elem, hetflag: hetflag, altLoc: altLoc, chain: chain, resi: resi, icode: icode, rescode: resi + (icode != " " ? "^" + icode : ""), // combo // resi // and // icode serial: serial, atom: atom, bonds: [], ss: "c", bondOrder: [], properties: {}, b: b, pdbline: line, }); } else Iif (recordName == "SHEET ") { hasStruct = true; startChain = line.substr(21, 1); startResi = parseInt(line.substr(22, 4)); endChain = line.substr(32, 1); endResi = parseInt(line.substr(33, 4)); Iif (!(startChain in sslookup)) { sslookup[startChain] = {}; } //mark start and end with additional character sslookup[startChain][startResi] = "s1"; for (var res = startResi + 1; res < endResi; res++) { sslookup[startChain][res] = "s"; } sslookup[startChain][endResi] = "s2"; } else if (recordName == "CONECT") { // MEMO: We don't have to parse SSBOND, LINK because both are // also // described in CONECT. But what about 2JYT??? var from = parseInt(line.substr(6, 5)); var fromindex = serialToIndex[from]; var fromAtom = atoms[fromindex]; var coffsets = [11, 16, 21, 26]; for (let j = 0; j < 4; j++) { var to = parseInt(line.substr(coffsets[j], 5)); var toindex = serialToIndex[to]; var toAtom = atoms[toindex]; if (fromAtom !== undefined && toAtom !== undefined) { // duplicated conect records indicate bond order // @ts-ignore if (!seenbonds[[fromindex, toindex]]) { // @ts-ignore seenbonds[[fromindex, toindex]] = 1; if ( fromAtom.bonds.length == 0 || fromAtom.bonds[fromAtom.bonds.length - 1] != toindex ) { fromAtom.bonds.push(toindex); fromAtom.bondOrder.push(1); } } else E{ //update bond order // @ts-ignore seenbonds[[fromindex, toindex]] += 1; for (let bi = 0; bi < fromAtom.bonds.length; bi++) { Iif (fromAtom.bonds[bi] == toindex) { // @ts-ignore var newbo = seenbonds[[fromindex, toindex]]; if (newbo >= 4) { //aromatic fromAtom.bondOrder[bi] = 1; } else { fromAtom.bondOrder[bi] = newbo; } } } } } } } else Iif (recordName == "HELIX ") { hasStruct = true; startChain = line.substr(19, 1); startResi = parseInt(line.substr(21, 4)); endChain = line.substr(31, 1); endResi = parseInt(line.substr(33, 4)); Iif (!(startChain in sslookup)) { sslookup[startChain] = {}; } sslookup[startChain][startResi] = "h1"; for (let res = startResi + 1; res < endResi; res++) { sslookup[startChain][res] = "h"; } sslookup[startChain][endResi] = "h2"; } else Iif ( !noAssembly && recordName == "REMARK" && line.substr(13, 5) == "BIOMT" ) { var n; var matrix = new Matrix4(); for (n = 1; n <= 3; n++) { line = lines[i].replace(/^\s*/, ""); if (parseInt(line.substr(18, 1)) == n) { // check for all // three lines // by matching # // @ end of // "BIOMT" to n matrix.elements[n - 1] = parseFloat(line.substr(23, 10)); matrix.elements[n - 1 + 4] = parseFloat(line.substr(33, 10)); matrix.elements[n - 1 + 8] = parseFloat(line.substr(43, 10)); matrix.elements[n - 1 + 12] = parseFloat(line.substr(53)); i++; } else { while (line.substr(13, 5) == "BIOMT") { i++; line = lines[i].replace(/^\s*/, ""); } } } matrix.elements[3] = 0; matrix.elements[7] = 0; matrix.elements[11] = 0; matrix.elements[15] = 1; modelData.symmetries.push(matrix); i--; // set i back } else if (recordName == "CRYST1") { let a, b, c, alpha, beta, gamma; a = parseFloat(line.substr(7, 8)); b = parseFloat(line.substr(16, 8)); c = parseFloat(line.substr(25, 8)); alpha = parseFloat(line.substr(34, 6)); beta = parseFloat(line.substr(41, 6)); gamma = parseFloat(line.substr(48, 6)); modelData.cryst = { a: a, b: b, c: c, alpha: alpha, beta: beta, gamma: gamma, }; } else Iif (recordName == "ANISOU") { let serial = parseInt(line.substr(6, 5)); var anisouAtomIndex = serialToIndex[serial]; var anisouAtom = atoms[anisouAtomIndex]; Iif (anisouAtom) { var vals = line.substr(30).trim().split(/\s+/); var uMat = { u11: parseInt(vals[0]), u22: parseInt(vals[1]), u33: parseInt(vals[2]), u12: parseInt(vals[3]), u13: parseInt(vals[4]), u23: parseInt(vals[5]), }; anisouAtom.uMat = uMat; } } } //fix any "one-way" bonds in CONECT records validateBonds(atoms, serialToIndex); // assign bonds - yuck, can't count on connect records if (assignbonds) assignPDBBonds(atoms); Iif (!noAssembly) processSymmetries(modelData.symmetries, atoms, options, modelData.cryst); if (computeStruct && !ignoreStruct) { computeSecondaryStructure(atoms, options.hbondCutoff); } // Assign secondary structures from pdb file Iif (!isEmpty(sslookup)) { for (let i = 0; i < atoms.length; i++) { atom = atoms[i]; Iif (atom === undefined) continue; Iif (atom.chain in sslookup && atom.resi in sslookup[atom.chain]) { var code = sslookup[atom.chain][atom.resi]; atom.ss = code[0]; Iif (code.length > 1) { if (code[1] == "1") atom.ssbegin = true; else Iif (code[1] == "2") atom.ssend = true; } } } } //console.log("assign structure " + ((new Date()).getTime() - starttime)); return [atoms, modelData, remainingLines]; } |