# All files / src/parsers PRMTOP.ts

96.49% Statements 110/114
88.57% Branches 31/35
100% Functions 5/5
99% Lines 99/100

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];
    }