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 | 3x 3x 3x 3x 3x 3x 5x 5x 5x 5x 5x 2x 3x 3x 3x 3x 1x 3x | // parse pdb file from str and create atoms // if computeStruct is true will always perform secondary structure // analysis, // otherwise only do analysis of SHEET/HELIX comments are missing import { getSinglePDB } from "./utils/getSinglePDB"; /** * @param {string} str * @param {ParserOptionsSpec} options - keepH (do not strip hydrogens), noSecondaryStructure, * assignbonds (default true, calculate implicit bonds) * (do not compute ss), altLoc (which alternate location to select, if present; '*' to load all) * @category Parsers * */ export function PDB(str, options) { options = options || {}; var atoms: any[] & Record<string, any> = []; //a separate list for each model var sslookup = {}; //stores SHEET and HELIX info, which is shared across models atoms.modelData = []; var lines = str.split(/\r?\n|\r/); while (lines.length > 0) { var pdbinfo = getSinglePDB(lines, options, sslookup); var modelatoms = pdbinfo[0]; var modelData = pdbinfo[1]; lines = pdbinfo[2]; if (modelatoms.length == 0) { continue; //happens when there are blank lines } Iif (options.multimodel && options.onemol && atoms.length > 0) { //merge into existing atoms var inc = atoms[0].length; for (var i = 0; i < modelatoms.length; i++) { //renumber var atom = modelatoms[i]; atom.index = i; for (var b = 0; b < atom.bonds.length; b++) { atom.bonds[b] += inc; } atoms[0].push(atom); } } else { atoms.modelData.push(modelData); atoms.push(modelatoms); } if (!options.multimodel) { break; } } return atoms; } |