mmcif-converter/index.js

A mmCIF file to JS Object parser that allows to create an object from the protein.cif file

const fs = require('fs');

/**
 * This is the only method in the package. Given the file path it returns an Object containing the mmCIF
 * file informations.
 * @param {String} file - file path
 */
function getObject(file) {

  var str = fs.readFileSync(file, 'utf8');

  //DELETE COMMENTS AND VOID
  var fileArray = str.split("\n").map(str => str.trim()).filter(v => v != '').filter(v => !v.startsWith("#"));


  //MERGE SEMICOLON LINES IN A UNIQUE ONE
  var semicolon = false;
  var sentence = "";

  for (let index = 0; index < fileArray.length; index++) {

    if (fileArray[index].startsWith(";") && semicolon === false) {
      semicolon = true;
      fileArray[index] = fileArray[index].substring(1, fileArray[index].length);
      sentence = sentence + fileArray[index];
      fileArray[index] = "";
    } else if (fileArray[index].startsWith(";") && semicolon === true) {
      semicolon = false;
      fileArray[index] = sentence;
      sentence = "";
    } else if (semicolon === true) {
      sentence = sentence + fileArray[index];
      fileArray[index] = "";
    }

  }

  fileArray = fileArray.filter(v => v != '');

  var fileObj = {};

  var datablockObj = {};
  var firstBlock = true;

  var isLoop = false;
  var dataname = "";
  var precArray = new Array();

  //THIS FOREACH DIVIDES THE SINGLE BLOCKS AND ELABORATE THEM ONE AFTER ONE
  fileArray.forEach(line => {

    line = line.trim();


    if (line.startsWith("data_") && firstBlock) {
      //IF THERE ARE MULTIPLE DATABLOCKS
      datablockObj["datablock"] = line.split("data_").join("");
      firstBlock = false;
    } else if ((line.startsWith("data_") && !firstBlock)) {

      fileObj[datablockObj.datablock] = datablockObj;
      datablockObj = {};
      datablockObj["datablock"] = line.split("data_").join("");

    } else {


      if (line === "loop_") { //LOOP START

        dataname = "";
        if (precArray.length > 0) datablockObj = {
          ...datablockObj,
          ...elaborate(precArray, isLoop)
        };
        precArray = new Array();
        isLoop = true;

      } else if (dataname === "" && line.startsWith("_")) { //NEW DATANAME IN LOOP OR FIRST DATANAME

        dataname = line.split(".")[0];
        precArray = new Array();
        precArray.push(line);

      } else if (dataname !== "" && dataname !== line.split(".")[0] && line.startsWith("_")) { //NEW DATANAME NO LOOP

        dataname = line.split(".")[0];
        datablockObj = {
          ...datablockObj,
          ...elaborate(precArray, isLoop)
        };
        precArray = new Array();
        precArray.push(line);
        isLoop = false;


      } else { //INSIDE DATANAME

        precArray.push(line);

      }
    }
  });

  fileObj[datablockObj.datablock] = datablockObj;

  return fileObj;

}


/**
 * This function elaborate the single block.
 * @param {String[]} dataArray - the various lines
 * @param {boolean} isLoop - is it a loop block?
 */
function elaborate(dataArray, isLoop) {

  var valueArray = new Array();
  var nameArray = new Array();

  var dataName = "";

  var JSONObj = {};

  if (isLoop) { //BLOCK IS LOOP

    var contArray = new Array();

    dataArray.forEach(line => {

      line = line.trim();

      if (line.startsWith("_")) { //DATANAME LINE
        dataName = line.split(".")[0];
        nameArray.push(line.split(".")[1]);
      } else { //VALUES LINES

        var field = "";
        var controlChar = " ";
        var pushed = false;

        for (let index = 0; index < line.length; index++) { //SPLIT BY WHITE SPACES EXEPT BETWEEN "" AND ''. P.S. I HATE REGEX.

          if (controlChar === " " && line.charAt(index) === "'") { // OPEN '

            controlChar = "'";
            pushed = false;

          } else if (controlChar === " " && line.charAt(index) === '"') { // OpEN "

            controlChar = '"';
            pushed = false;

          } else if (controlChar === " " && line.charAt(index) === " ") {

            if (field.trim() !== "") valueArray.push(field);
            field = "";
            pushed = true;

          } else if (controlChar === "'" && line.charAt(index) === "'") { // CLOSE '

            valueArray.push(field);
            field = "";
            controlChar = " ";
            pushed = true;

          } else if (controlChar === '"' && line.charAt(index) === '"') { // CLOSE "

            valueArray.push(field);
            field = "";
            controlChar = " ";
            pushed = true;
          } else {

            field = field + line.charAt(index);
            pushed = false;

          }

        }

        if (!pushed) valueArray.push(field);
      }

    });

    var i = 0;
    var obj = {};
    for (let increment = 0; increment < valueArray.length; increment++) {

      if (i === nameArray.length) {
        i = 0;
        contArray.push(obj);
        obj = {};

      }

      obj[nameArray[i]] = valueArray[increment];
      i++;
    }

    contArray.push(obj);

    JSONObj[dataName] = contArray;

  } else { //NOT LOOP DATA

    var dataName = dataArray.join("").trim().split(".")[0];

    dataArray = dataArray.join(" ").trim().split(dataName + ".").filter(v => v != '');

    var subObj = {};

    dataArray.forEach(line => {
      line = line.trim();
      var id = line.split(" ")[0];
      line = line.replace(id, "").trim();
      line = line.split("'").join("");
      subObj[id] = line;
    });

    JSONObj[dataName] = subObj;

  }

  return JSONObj;

}


module.exports = {
  getObject
}