# All files / src/parsers/utils getSinglePDB.ts

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49.29% Branches 35/71
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     import { Matrix4 } from "../../WebGL";
    import { atomNameToElem } from "./atomNameToElem";
    import { bondTable } from "./bondTable";
    import { computeSecondaryStructure } from "./computeSecondaryStructure";
    import { isEmpty } from "./isEmpty";
    import { processSymmetries } from "./processSymmetries";
    import { assignPDBBonds } from "./assignPDBBonds";
    import { validateBonds } from "./validateBonds";

    //return one model worth of pdb, returns atoms, modelData, and remaining lines
    export function getSinglePDB(lines, options, sslookup) {
      var atoms: any[] = [];
      var assignbonds =
        options.assignBonds === undefined ? true : options.assignBonds;
      var noH = !options.keepH; // suppress hydrogens by default
      var ignoreStruct = !!options.noSecondaryStructure;
      var computeStruct = !options.noComputeSecondaryStructure;
      var noAssembly = !options.doAssembly; // don't assemble by default
      var selAltLoc = options.altLoc ? options.altLoc : "A"; //default alternate location to select if present
      var modelData: Record<string, any> = { symmetries: [] };
      var atom;
      var remainingLines = [];

      var hasStruct = false;
      var serialToIndex: number[] = []; // map from pdb serial to index in atoms
      var line;
      var seenbonds: Record<any, any> = {}; //sometimes connect records are duplicated as an unofficial means of relaying bond orders

      for (let i = 0; i < lines.length; i++) {
        line = lines[i].replace(/^\s*/, ""); // remove indent
        var recordName = line.substr(0, 6);
        var startChain, startResi, endChain, endResi;

        if (recordName.indexOf("END") == 0) {
          remainingLines = lines.slice(i + 1);
          if (recordName == "END") {
            //as opposed to ENDMDL
            //reset secondary structure
            for (var prop in sslookup) {
              Iif (sslookup.hasOwnProperty(prop)) {
                delete sslookup[prop];
              }
            }
          }
          break;
        } else if (recordName == "ATOM  " || recordName == "HETATM") {
          var resn, chain, resi, icode, x, y, z, hetflag, elem, serial, altLoc, b;
          altLoc = line.substr(16, 1);
          Iif (altLoc != " " && altLoc != selAltLoc && selAltLoc != "*") continue;
          serial = parseInt(line.substr(6, 5));
          atom = line.substr(12, 4).replace(/ /g, "");
          resn = line.substr(17, 3).replace(/ /g, "");
          chain = line.substr(21, 1);
          resi = parseInt(line.substr(22, 4));
          icode = line.substr(26, 1);
          x = parseFloat(line.substr(30, 8));
          y = parseFloat(line.substr(38, 8));
          z = parseFloat(line.substr(46, 8));
          b = parseFloat(line.substr(60, 8));
          elem = line.substr(76, 2).replace(/ /g, "");
          Iif (elem === "" || typeof bondTable[elem] === "undefined") {
            // for some incorrect PDB files
            elem = atomNameToElem(line.substr(12, 2), line[0] == "A");
          } else {
            elem = elem[0].toUpperCase() + elem.substr(1).toLowerCase();
          }

          Iif (elem == "H" && noH) continue;
          Iif (recordName[0] == "H") hetflag = true;
          else hetflag = false;
          serialToIndex[serial] = atoms.length;
          atoms.push({
            resn: resn,
            x: x,
            y: y,
            z: z,
            elem: elem,
            hetflag: hetflag,
            altLoc: altLoc,
            chain: chain,
            resi: resi,
            icode: icode,
            rescode: resi + (icode != " " ? "^" + icode : ""), // combo
            // resi
            // and
            // icode
            serial: serial,
            atom: atom,
            bonds: [],
            ss: "c",
            bondOrder: [],
            properties: {},
            b: b,
            pdbline: line,
          });
        } else Iif (recordName == "SHEET ") {
          hasStruct = true;
          startChain = line.substr(21, 1);
          startResi = parseInt(line.substr(22, 4));
          endChain = line.substr(32, 1);
          endResi = parseInt(line.substr(33, 4));
          Iif (!(startChain in sslookup)) {
            sslookup[startChain] = {};
          }
          //mark start and end with additional character
          sslookup[startChain][startResi] = "s1";
          for (var res = startResi + 1; res < endResi; res++) {
            sslookup[startChain][res] = "s";
          }
          sslookup[startChain][endResi] = "s2";
        } else if (recordName == "CONECT") {
          // MEMO: We don't have to parse SSBOND, LINK because both are
          // also
          // described in CONECT. But what about 2JYT???
          var from = parseInt(line.substr(6, 5));
          var fromindex = serialToIndex[from];
          var fromAtom = atoms[fromindex];
          var coffsets = [11, 16, 21, 26];
          for (let j = 0; j < 4; j++) {
            var to = parseInt(line.substr(coffsets[j], 5));
            var toindex = serialToIndex[to];
            var toAtom = atoms[toindex];
            if (fromAtom !== undefined && toAtom !== undefined) {
              // duplicated conect records indicate bond order
              // @ts-ignore
              if (!seenbonds[[fromindex, toindex]]) {
                // @ts-ignore
                seenbonds[[fromindex, toindex]] = 1;
                if (
                  fromAtom.bonds.length == 0 ||
                  fromAtom.bonds[fromAtom.bonds.length - 1] != toindex
                ) {
                  fromAtom.bonds.push(toindex);
                  fromAtom.bondOrder.push(1);
                }
              } else E{
                //update bond order
                // @ts-ignore
                seenbonds[[fromindex, toindex]] += 1;

                for (let bi = 0; bi < fromAtom.bonds.length; bi++) {
                  Iif (fromAtom.bonds[bi] == toindex) {
                    // @ts-ignore
                    var newbo = seenbonds[[fromindex, toindex]];
                    if (newbo >= 4) {
                      //aromatic
                      fromAtom.bondOrder[bi] = 1;
                    } else {
                      fromAtom.bondOrder[bi] = newbo;
                    }
                  }
                }
              }
            }
          }
        } else Iif (recordName == "HELIX ") {
          hasStruct = true;
          startChain = line.substr(19, 1);
          startResi = parseInt(line.substr(21, 4));
          endChain = line.substr(31, 1);
          endResi = parseInt(line.substr(33, 4));
          Iif (!(startChain in sslookup)) {
            sslookup[startChain] = {};
          }
          sslookup[startChain][startResi] = "h1";
          for (let res = startResi + 1; res < endResi; res++) {
            sslookup[startChain][res] = "h";
          }
          sslookup[startChain][endResi] = "h2";
        } else Iif (
          !noAssembly &&
          recordName == "REMARK" &&
          line.substr(13, 5) == "BIOMT"
        ) {
          var n;
          var matrix = new Matrix4();
          for (n = 1; n <= 3; n++) {
            line = lines[i].replace(/^\s*/, "");
            if (parseInt(line.substr(18, 1)) == n) {
              // check for all
              // three lines
              // by matching #
              // @ end of
              // "BIOMT" to n
              matrix.elements[n - 1] = parseFloat(line.substr(23, 10));
              matrix.elements[n - 1 + 4] = parseFloat(line.substr(33, 10));
              matrix.elements[n - 1 + 8] = parseFloat(line.substr(43, 10));
              matrix.elements[n - 1 + 12] = parseFloat(line.substr(53));
              i++;
            } else {
              while (line.substr(13, 5) == "BIOMT") {
                i++;
                line = lines[i].replace(/^\s*/, "");
              }
            }
          }
          matrix.elements[3] = 0;
          matrix.elements[7] = 0;
          matrix.elements[11] = 0;
          matrix.elements[15] = 1;
          modelData.symmetries.push(matrix);
          i--; // set i back
        } else if (recordName == "CRYST1") {
          let a, b, c, alpha, beta, gamma;
          a = parseFloat(line.substr(7, 8));
          b = parseFloat(line.substr(16, 8));
          c = parseFloat(line.substr(25, 8));
          alpha = parseFloat(line.substr(34, 6));
          beta = parseFloat(line.substr(41, 6));
          gamma = parseFloat(line.substr(48, 6));
          modelData.cryst = {
            a: a,
            b: b,
            c: c,
            alpha: alpha,
            beta: beta,
            gamma: gamma,
          };
        } else Iif (recordName == "ANISOU") {
          let serial = parseInt(line.substr(6, 5));
          var anisouAtomIndex = serialToIndex[serial];
          var anisouAtom = atoms[anisouAtomIndex];
          Iif (anisouAtom) {
            var vals = line.substr(30).trim().split(/\s+/);
            var uMat = {
              u11: parseInt(vals[0]),
              u22: parseInt(vals[1]),
              u33: parseInt(vals[2]),
              u12: parseInt(vals[3]),
              u13: parseInt(vals[4]),
              u23: parseInt(vals[5]),
            };

            anisouAtom.uMat = uMat;
          }
        }
      }

      //fix any "one-way" bonds in CONECT records
      validateBonds(atoms, serialToIndex);
      // assign bonds - yuck, can't count on connect records
      if (assignbonds) assignPDBBonds(atoms);

      Iif (!noAssembly)
        processSymmetries(modelData.symmetries, atoms, options, modelData.cryst);

      if (computeStruct && !ignoreStruct) {
        computeSecondaryStructure(atoms, options.hbondCutoff);
      }

      // Assign secondary structures from pdb file
      Iif (!isEmpty(sslookup)) {
        for (let i = 0; i < atoms.length; i++) {
          atom = atoms[i];
          Iif (atom === undefined) continue;
          Iif (atom.chain in sslookup && atom.resi in sslookup[atom.chain]) {
            var code = sslookup[atom.chain][atom.resi];
            atom.ss = code[0];
            Iif (code.length > 1) {
              if (code[1] == "1") atom.ssbegin = true;
              else Iif (code[1] == "2") atom.ssend = true;
            }
          }
        }
      }
      //console.log("assign structure " + ((new Date()).getTime() - starttime));

      return [atoms, modelData, remainingLines];
    }