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 | 3x 3x 3x 3x 1x 67971x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1x 1402x 1402x 28026x 28026x 28026x 28026x 28026x 28026x 28026x 28026x 28026x 28026x 28026x 28026x 28026x 1402x 1x 1x 1x 1x 1x 1x 5606x 5606x 28026x 28026x 5606x 1x 1x 1x 1x 1x 1x 5606x 5606x 28026x 28026x 5606x 1x 1x 1x 1x 1x 1x 1x 572x 1x 572x 5716x 1906x 3810x 1905x 5716x 572x 1x 1x 1x 1x 1x 1x 1x 7849x 1x 7849x 78486x 26162x 52324x 26162x 78486x 7849x 2x 6x 42x 6x 6x 6x 6x 6x 6x 6x 2x 6x 1x | // @ts-nocheck /** * Parse a prmtop file from str and create atoms * * @param {string} * str * @param {ParserOptionsSpec} * options - noSecondaryStructure (do not compute ss) * * @category Parsers */ export function PRMTOP(str /*, options*/) { var atoms = []; var atomIndex; var count = 0; var lines = str.split(/\r?\n|\r/); if (lines.length > 0 && lines[0].includes("VERSION")) { var sectionList = lines.filter(function (line) { //store the relevant section lists return ( line.includes("POINTERS") || line.includes("ATOM_NAME") || line.includes("CHARGE") || line.includes("RADII") || line.includes("BONDS_INC_HYDROGEN") || line.includes("BONDS_WITHOUT_HYDROGEN") ); }); var index = getIndex("POINTERS"); Iif (index == -1) return []; var col = getColEleSize(index); var atomCount = parseInt(lines[index + 1].slice(0, col[1])); Iif (isNaN(atomCount) || atomCount <= 0) return []; index = getIndex("ATOM_NAME"); Iif (index == -1) return []; col = getColEleSize(index); var noOfCol = col[0]; for (let i = 0; i < atomCount / col[0]; i++) { if (i == parseInt(atomCount / col[0])) noOfCol = atomCount % col[0]; for (let j = 0; j < noOfCol; j++) { let atom = {}; let properties = { charge: "", radii: "" }; atom.serial = count; atom.x = 0; atom.y = 0; atom.z = 0; atom.atom = lines[index + 1].slice(col[1] * j, col[1] * (j + 1)); atom.elem = lines[index + 1].slice(col[1] * j, col[1] * j + 1); atom.properties = properties; atom.bonds = []; atom.bondOrder = []; atoms.push(atom); count++; } index++; } index = getIndex("CHARGE"); if (index != -1) { col = getColEleSize(index); count = 0; noOfCol = col[0]; for (let i = 0; i < atomCount / col[0]; i++) { if (i == parseInt(atomCount / col[0])) noOfCol = atomCount % col[0]; for (let j = 0; j < noOfCol; j++) { atoms[count].properties.charge = parseFloat( lines[index + 1].slice(col[1] * j, col[1] * (j + 1)) ); count++; } index++; } } index = getIndex("RADII"); if (index != -1) { col = getColEleSize(index); count = 0; noOfCol = col[0]; for (let i = 0; i < atomCount / col[0]; i++) { if (i == parseInt(atomCount / col[0])) noOfCol = atomCount % col[0]; for (let j = 0; j < noOfCol; j++) { atoms[count].properties.radii = parseFloat( lines[index + 1].slice(col[1] * j, col[1] * (j + 1)) ); count++; } index++; } } index = getIndex("BONDS_WITHOUT_HYDROGEN"); if (index != -1) { col = getColEleSize(index); count = 0; noOfCol = col[0]; index = index + 1; while (!lines[index].match(/^%FLAG/)) { if (lines[index + 1].match(/^%FLAG/)) //its the last line noOfCol = atomCount % col[0]; for (let j = 0; j < noOfCol; j++) { if (count % 3 == 0) { atomIndex = parseInt( lines[index].slice(col[1] * j, col[1] * (j + 1)) / 3 ); } else if (count % 3 == 1) { atoms[atomIndex].bonds.push( parseInt(lines[index].slice(col[1] * j, col[1] * (j + 1)) / 3) ); } count++; } index++; } } index = getIndex("BONDS_INC_HYDROGEN"); if (index != -1) { col = getColEleSize(index); count = 0; noOfCol = col[0]; index = index + 1; while (!lines[index].match(/^%FLAG/)) { if (lines[index + 1].match(/^%FLAG/)) //its the last line noOfCol = atomCount % col[0]; for (let j = 0; j < noOfCol; j++) { if (count % 3 == 0) { atomIndex = parseInt( lines[index].slice(col[1] * j, col[1] * (j + 1)) / 3 ); } else if (count % 3 == 1) { atoms[atomIndex].bonds.push( parseInt(lines[index].slice(col[1] * j, col[1] * (j + 1)) / 3) ); } count++; } index++; } } } else { return []; } function getIndex(section) { var index = lines.indexOf( sectionList.filter(function (line) { return line.includes(section); })[0] ); //returns the index of the line containing FLAG POINTERS if (Number.isInteger(index) && index > 0) { while (!lines[index].includes("FORMAT")) //doing this so as to take comments into consideration index++; return index; } else E{ return -1; } } function getColEleSize(i) { var numberOfCol = lines[i].match(/\((\d*)\S*/); // stores the number of columns var elementSize = lines[i].match(/[a-zA-Z](\d*)\)\s*/); if (elementSize == null) { elementSize = lines[i].match(/[a-zA-Z](\d*)\.\d*\)\s*/); //stores the element size } return [numberOfCol[1], elementSize[1]]; } return [atoms]; } |