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 | 18x 9x 9x 9x 9x 11x 8x 8x 5x 5x 5x 4x 4x 4x 4x 76x 76x 76x 76x 76x 72x 72x 72x 72x 72x 72x 72x 72x 72x 72x 72x 4x 80x 80x 80x 80x 80x 76x 76x 76x 76x 4x 2x 2x 2x 2x 9x 18x 9x 9x 9x 4x 9x 9x | /* * @param {!Array.<string>} lines * @param {ParserOptionsSpec} options * @returns {!Array.<Array<Object>>} */ var parseV2000 = function (lines, options) { var atoms: any[][] & Record<string, any> = [[]]; var noH = false; if (typeof options.keepH !== "undefined") noH = !options.keepH; while (lines.length > 0) { if (lines.length < 4) break; var atomCount = parseInt(lines[3].substr(0, 3)); if (isNaN(atomCount) || atomCount <= 0) break; var bondCount = parseInt(lines[3].substr(3, 3)); var offset = 4; if (lines.length < 4 + atomCount + bondCount) break; // serial is atom's index in file; index is atoms index in 'atoms' var serialToIndex: number[] = []; var start = atoms[atoms.length - 1].length; var end = start + atomCount; var i, line; for (i = start; i < end; i++, offset++) { line = lines[offset]; var atom: Record<string, any> = {}; var elem = line.substr(31, 3).replace(/ /g, ""); atom.atom = atom.elem = elem[0].toUpperCase() + elem.substr(1).toLowerCase(); if (atom.elem !== "H" || !noH) { atom.serial = i; serialToIndex[i] = atoms[atoms.length - 1].length; atom.x = parseFloat(line.substr(0, 10)); atom.y = parseFloat(line.substr(10, 10)); atom.z = parseFloat(line.substr(20, 10)); atom.hetflag = true; atom.bonds = []; atom.bondOrder = []; atom.properties = {}; atom.index = atoms[atoms.length - 1].length; atoms[atoms.length - 1].push(atom); } } for (i = 0; i < bondCount; i++, offset++) { line = lines[offset]; var from = serialToIndex[parseInt(line.substr(0, 3)) - 1 + start]; var to = serialToIndex[parseInt(line.substr(3, 3)) - 1 + start]; var order = parseInt(line.substr(6, 3)); if (typeof from != "undefined" && typeof to != "undefined") { atoms[atoms.length - 1][from].bonds.push(to); atoms[atoms.length - 1][from].bondOrder.push(order); atoms[atoms.length - 1][to].bonds.push(from); atoms[atoms.length - 1][to].bondOrder.push(order); } } if (options.multimodel) { if (!options.onemol) atoms.push([]); while (lines[offset] !== "$$$$") offset++; lines.splice(0, ++offset); } else { break; } } return atoms; }; /* * @param {!Array.<string>} lines * @param {ParserOptionsSpec} options * @returns {!Array.<!Array<!Object>>} */ var parseV3000 = function (lines, options) { var atoms: any[][] & Record<string, any> = [[]]; var noH = false; Iif (typeof options.keepH !== "undefined") noH = !options.keepH; while (lines.length > 0) { Iif (lines.length < 8) break; Iif (!lines[4].startsWith("M V30 BEGIN CTAB")) break; Iif (!lines[5].startsWith("M V30 COUNTS") || lines[5].length < 14) break; var counts = lines[5].substr(13).match(/\S+/g); Iif (counts.length < 2) break; var atomCount = parseInt(counts[0]); Iif (isNaN(atomCount) || atomCount <= 0) break; var bondCount = parseInt(counts[1]); var offset = 7; Iif (lines.length < 8 + atomCount + bondCount) //header, bgn+end CTAB, counts, END break; // serial is atom's index in file; index is atoms index in 'atoms' var serialToIndex: number[] = []; var start = atoms[atoms.length - 1].length; var end = start + atomCount; var i, line; for (i = start; i < end; i++, offset++) { line = lines[offset]; var atomParts = line.substr(6).match(/\S+/g); Iif (atomParts.length > 4) { var atom: Record<string, any> = {}; var elem = atomParts[1].replace(/ /g, ""); atom.atom = atom.elem = elem[0].toUpperCase() + elem.substr(1).toLowerCase(); Iif (atom.elem !== "H" || !noH) { atom.serial = i; serialToIndex[i] = atoms[atoms.length - 1].length; atom.x = parseFloat(atomParts[2]); atom.y = parseFloat(atomParts[3]); atom.z = parseFloat(atomParts[4]); atom.hetflag = true; atom.bonds = []; atom.bondOrder = []; atom.properties = {}; atom.index = atoms[atoms.length - 1].length; atoms[atoms.length - 1].push(atom); } } } if (lines[offset] === "M V30 END ATOM") offset++; else break; if (bondCount !== 0 && lines[offset] === "M V30 BEGIN BOND") offset++; else break; for (i = 0; i < bondCount; i++, offset++) { line = lines[offset]; var bondParts = line.substr(6).match(/\S+/g); Iif (bondParts.length > 3) { var from = serialToIndex[parseInt(bondParts[2]) - 1 + start]; var to = serialToIndex[parseInt(bondParts[3]) - 1 + start]; var order = parseInt(bondParts[1]); Iif (typeof from != "undefined" && typeof to != "undefined") { atoms[atoms.length - 1][from].bonds.push(to); atoms[atoms.length - 1][from].bondOrder.push(order); atoms[atoms.length - 1][to].bonds.push(from); atoms[atoms.length - 1][to].bondOrder.push(order); } } } if (options.multimodel) { Iif (!options.onemol) { atoms.push([]); } while (lines[offset] !== "$$$$") { offset++; } lines.splice(0, ++offset); } else { break; } } return atoms; }; /** * @param {string} * str * @param {ParserOptionsSpec} * options * @category Parsers */ export function SDF(str, options) { var molformat = "V2000"; var lines = str.split(/\r?\n|\r/); if (lines.length > 3 && lines[3].length > 38) { molformat = lines[3].substr(34, 5); } if (molformat === "V2000") { return parseV2000(lines, options); } else IEif (molformat === "V3000") { return parseV3000(lines, options); } return [[]]; } |