str+pdb2upl+lol

index.html

  <div class="container" id="app">
    <div class="input-group-prepend">
      <span class="input-group-text">.str file</span>
      <input type="file" @change="fileUpload($event, 'strdata')" />
    </div>
    <div class="input-group">
      <textarea v-model="strdata" class="form-control"></textarea>
    </div>
    <div class="input-group-prepend">
      <span class="input-group-text">.pdb file</span>
      <input type="file" @change="fileUpload($event, 'pdbdata')" />
    </div>
    <div class="input-group">
      <textarea v-model="pdbdata" class="form-control"></textarea>
    </div>
    <div class="btn-group m-4" role="group">
      <button type="button" class="btn btn-primary" v-on:click="goClick">.str .pdb convert to .upl .lol</button>
    </div>
    <div class="input-group-prepend">
      <span class="input-group-text">.upl file</span>
    </div>
    <div class="input-group">
      <textarea v-model="upldata" class="form-control"></textarea>
    </div>
    <div class="input-group-prepend">
      <span class="input-group-text">.lol file</span>
    </div>
    <div class="input-group">
      <textarea v-model="loldata" class="form-control"></textarea>
    </div>
    <div class="btn-group m-4" role="group">
      <button type="button" class="btn btn-primary" v-on:click="goDownload()"> Download </button>
    </div>
  </div>

script.js

function regexGet(regex, str) {
  var m;
  var matchs = [];
  while ((m = regex.exec(str)) !== null) {
    // This is necessary to avoid infinite loops with zero-width matches
    if (m.index === regex.lastIndex) {
      regex.lastIndex++;
    }
    matchs.push(m);
  }
  return matchs;
}

// https://stackoverflow.com/questions/3665115/create-a-file-in-memory-for-user-to-download-not-through-server?utm_medium=organic&utm_source=google_rich_qa&utm_campaign=google_rich_qa
function download(filename, text) {
  var element = document.createElement("a");
  element.setAttribute(
    "href",
    "data:text/plain;charset=utf-8," + encodeURIComponent(text)
  );
  element.setAttribute("download", filename);
  element.style.display = "none";
  document.body.appendChild(element);
  element.click();
  document.body.removeChild(element);
}

new Vue({
  el: "#app",
  data: {
    strdata: ` **testing**
assi sele resid    1 .and. type HT3  end -
     sele resid    2 .and. type HN   end -
 rmin  1.94190 rmax  5.94190 - 
 rexp @rexp fmax @fmax rswi @rswi sexp @sexp kmin @kmin kmax @kmax SUMR
assi sele resid    1 .and. type HT3  end -
     sele resid    2 .and. type HA2  end -
 rmin  2.58100 rmax  6.58100 - 
 rexp @rexp fmax @fmax rswi @rswi sexp @sexp kmin @kmin kmax @kmax SUMR`,
    pdbdata: `MODEL 1
ATOM     18 1HE2 GLN     1       3.477  -1.956   1.651  1.00  1.00      TAG
ATOM     19 2HE2 GLN     1       2.439  -2.764   0.524  1.00  1.00      TAG
ATOM     20  N   GLY     2      -0.652   2.217   0.763  1.00  1.00      TAG
ATOM     21  CA  GLY     2      -1.519   3.387   0.826  1.00  1.00      TAG`,
    upldata: "",
    loldata: ""
  },
  methods: {
    goClick: function() {
      // get dictionary
      var dict_num = {};
      this.pdbdata.split("\n").forEach(pdb => {
        var pdbs = pdb.split(/\s+/);
        if (pdbs.length > 4) dict_num[pdbs[4]] = pdbs[3];
      });

      // parse main
      this.upldata = this.loldata = "";
      var units = regexGet(/assi[\s\S]*?SUMR/gm, this.strdata);
      units.forEach(unit_match => {
        var id_data = regexGet(/resid\s*(\d+).*?type (\w+)/gm, unit_match);
        var min_max = regexGet(
          /rmin\s*([\.\d]+) rmax\s*([\.\d]+)/gm,
          unit_match
        );

        // possible error
        if (
          !(
            min_max.length === 1 &&
            min_max[0].length === 3 &&
            id_data[0].length === 3 &&
            id_data[1].length === 3 &&
            id_data.length === 2
          )
        )
          console.log(unit_match);
        min_max = [parseFloat(min_max[0][1]), parseFloat(min_max[0][2])];

        // transfer to this format
        // 109 GLU  HG3   110 GLN  H       5.90            #peak    13
        var resids = id_data.map(m =>
          [
            ("   " + m[1]).slice(-3),
            (dict_num[m[1]] + "    ").slice(0, 4),
            (m[2] + "     ").slice(0, 5)
          ].join(" ")
        );
        this.upldata +=
          resids.join(" ") + "   " + min_max[1].toPrecision(3) + "\n";
        this.loldata +=
          resids.join(" ") + "   " + min_max[0].toPrecision(3) + "\n";
      });
      console.log(123);
    },
    fileUpload: function(evt, data) {
      console.log(data);
      var files = evt.target.files || evt.dataTransfer.files;
      if (!files.length) return;
      var reader = new FileReader();
      reader.onload = event => {
        // The file's text will be printed here
        this[data] = event.target.result;
      };
      reader.readAsText(files[0]);
    },
    goDownload: function() {
      download("test.upl", this.upldata);
      download("test.lol", this.loldata);
    }
  }
});

scripts

<script src="https://cdnjs.cloudflare.com/ajax/libs/vue/2.5.13/vue.min.js"></script>

str-pdb2upl-lol.markdown

str+pdb2upl+lol

A Pen by linnil1 on CodePen.

License.

style.css

textarea {
  min-height: 20vh;
  font-family: monospace;
}

styles

<link href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.0.0/css/bootstrap.css" rel="stylesheet" />