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 | 18x 2x 2x 2x 2x 2x 2x 2x 2x 2x 2x 2x 2x 2x 2x 2x 8x 2x 2x 2x 2x 2x 86x 86x 86x 86x 86x 86x 86x 86x 86x 86x 86x 86x 86x 86x 86x 86x 86x 86x 86x 86x 86x 86x 86x 2x 2x 2x 2x 2x 2x 2x 90x 90x 90x 90x 90x 90x 90x 90x 90x 90x 90x 90x 90x 2x 2x 2x | let SYBYLtoElem = { 'C.1': 'C', 'C1': 'C', 'C.2': 'C', 'C2': 'C', 'C.3': 'C', 'C3': 'C', 'C.ar': 'C', 'Car': 'C', 'C.cat': 'C', 'Ccat': 'C', 'H.spc' :'H', 'Hspc':'H', 'H.t3p':'H', 'Ht3p': 'H', 'N.1':'N', 'N1':'N', 'N.2':'N', 'N2':'N', 'N.3':'N', 'N3':'N', 'N.4':'N', 'N4':'N', 'N.am':'N', 'Nam':'N', 'N.ar':'N', 'Nar':'N', 'N.p13':'N', 'Np13':'N', 'O.2':'O', 'O2':'O', 'O.3':'O', 'O3':'O', 'O.co2':'O', 'Oco2':'O', 'O.spc':'O', 'Ospc':'O', 'O.t3p':'O', 'Ot3p':'O', 'P.3':'P', 'P3':'P', 'S.2':'S', 'S2':'S', 'S.3':'S', 'S3':'S', 'S.o':'S', 'So':'S', 'S.o2':'S', 'So2':'S' }; // parse SYBYL mol2 file from string - assumed to only contain one molecule // tag /** * @param {string} * str * @param {ParserOptionsSpec} * options * @category Parsers */ export function MOL2(str, options) { var atoms: any[][] & Record<string,any> = [[]]; var noH = false; if (typeof options.keepH !== "undefined") noH = !options.keepH; // Note: these regex's work, though they don't match '<TRIPOS>' // correctly - something to do with angle brackets var mol_pos = str.search(/@<TRIPOS>MOLECULE/); var atom_pos = str.search(/@<TRIPOS>ATOM/); // Assuming both Molecule and Atom sections exist Iif (mol_pos == -1 || atom_pos == -1) return atoms; var lines = str.substr(mol_pos, str.length).split(/\r?\n|\r/); while (lines.length > 0) { // serial is atom's index in file; index is atoms index in 'atoms' var serialToIndex: number[] = []; var tokens = lines[2].replace(/^\s+/, "").replace(/\s+/g, " ").split(" "); var natoms = parseInt(tokens[0]); var nbonds = 0; if (tokens.length > 1) nbonds = parseInt(tokens[1]); var offset = 4; var i: number; // Continue until 'Atom' section for (i = 3; i < lines.length; i++) { if (lines[i] == "@<TRIPOS>ATOM") { offset = i + 1; break; } } var start = atoms[atoms.length - 1].length; var end = start + natoms; var line; // Process ATOMS for (i = start; i < end; i++) { line = lines[offset++]; tokens = line.replace(/^\s+/, "").replace(/\s+/g, " ").split(" "); var atom: Record<string, any> = {}; // get element var elem = tokens[5]; if(SYBYLtoElem[elem] !== undefined) { elem = SYBYLtoElem[elem]; } else E{ elem = elem.split(".")[0]; elem = elem[0].toUpperCase() + elem.substr(1).toLowerCase(); } atom.atom = tokens[1]; atom.elem = elem; Iif (atom.elem == "H" && noH) { // ignore } else { // 'index' is this atom's index in 'atoms'; 'serial' is this // atom's // serial id in mol2 file var index = atoms[atoms.length - 1].length; var serial = parseInt(tokens[0]); atom.serial = serial; // atom.serial = i; atom.x = parseFloat(tokens[2]); atom.y = parseFloat(tokens[3]); atom.z = parseFloat(tokens[4]); atom.atom = tokens[5]; var charge = parseFloat(tokens[8]); atom.index = index; atom.bonds = []; atom.bondOrder = []; atom.properties = { charge: charge, partialCharge: charge, }; serialToIndex[serial] = index; atoms[atoms.length - 1].push(atom); } } // Process BONDS var bonds_found = false; while (offset < lines.length) { if (lines[offset++] == "@<TRIPOS>BOND") { bonds_found = true; break; } } if (bonds_found && nbonds) { for (i = 0; i < nbonds; i++) { line = lines[offset++]; tokens = line.replace(/^\s+/, "").replace(/\s+/g, " ").split(" "); var from = parseInt(tokens[1]); var fromAtom = atoms[atoms.length - 1][serialToIndex[from]]; var to = parseInt(tokens[2]); var toAtom = atoms[atoms.length - 1][serialToIndex[to]]; // Won't be able to read aromatic bonds correctly... var order = parseInt(tokens[3]); if (isNaN(order)) order = 1; if (fromAtom !== undefined && toAtom !== undefined) { fromAtom.bonds.push(serialToIndex[to]); fromAtom.bondOrder.push(order); toAtom.bonds.push(serialToIndex[from]); toAtom.bondOrder.push(order); } } } Iif (options.multimodel) { Iif (!options.onemol) atoms.push([]); lines.splice(0, offset); str = lines.join("\n"); //update for str.search continue; } else { break; } } return atoms; } |