Updated Types for Parsers and Parser Utils

src/parsers/CDJSON.ts

@@ -1,3 +1,5 @@
+import { ParserOptionsSpec } from "./ParserOptionsSpec";
+
 /** 
  * This parses the ChemDoodle json file format. Although this is registered
  * for the json file extension, other chemical json file formats exist that
@@ -7,14 +9,15 @@
  * @param {string} str
  * @param {ParserOptionsSpec} options
  * @category Parsers
- */
-export function CDJSON(str, options) {
+*/
+
+export function CDJSON(str: string, options: ParserOptionsSpec) {
   var atoms: any[][] & Record<string, any> = [[]];
   if (typeof str === "string") {
     // Str is usually automatically parsed by JQuery
     str = JSON.parse(str);
   }
-  var molecules = str.m;
+  var molecules = (str as any).m;
   var atomsInFile = molecules[0].a; // Assumes there is at least one
   var bondsInFile = molecules[0].b; // molecule and ignores any more
   // Ignores any shapes

src/parsers/CIF.ts

@@ -1,17 +1,18 @@
 import { ParserOptionsSpec } from './ParserOptionsSpec';
-// puts atoms specified in mmCIF fromat in str into atoms
 
 import { assignBonds } from "./utils/assignBonds";
 import { computeSecondaryStructure } from "./utils/computeSecondaryStructure";
 import { processSymmetries } from "./utils/processSymmetries";
-import { conversionMatrix3, Matrix4, Vector3,  } from "../WebGL"
+import { conversionMatrix3, Matrix3, Matrix4, Vector3,  } from "../WebGL"
 
 /**
+ * Puts atoms specified in mmCIF fromat in str into atoms
+ * 
  * @param {string} str
  * @param {ParserOptionsSpec} options
  * @category Parsers
+*/
 
- */
 export function CIF(str: string, options: ParserOptionsSpec = {}) {
   var atoms: any[] & Record<string, any> = [];
   var noAssembly = !options.doAssembly; // don't assemble by default
@@ -20,12 +21,12 @@ export function CIF(str: string, options: ParserOptionsSpec = {}) {
     options.assignBonds === undefined ? true : options.assignBonds;
 
   //coordinate conversion
-  var fractionalToCartesian = function (cmat, x, y, z) {
+  var fractionalToCartesian = function (cmat: Matrix3, x: number, y: number, z: number) {
     return new Vector3(x, y, z).applyMatrix3(cmat);
   };
 
   // Used to handle quotes correctly
-  function splitRespectingQuotes(string, separator) {
+  function splitRespectingQuotes(string: string, separator: string | any[]) {
     var sections: any[] = [];
     var sectionStart = 0;
     var sectionEnd = 0;
@@ -318,7 +319,7 @@ export function CIF(str: string, options: ParserOptionsSpec = {}) {
         modelData[modelData.length - 1].symmetries.push(matrix);
       }
     }
-    var parseTerm = function (term) {
+    var parseTerm = function (term: string) {
       var negative = term.match("-");
       term = term.replace(/[-xyz]/g, "");
       var fractionParts = term.split("/");
@@ -342,7 +343,7 @@ export function CIF(str: string, options: ParserOptionsSpec = {}) {
           /["' ]/g,
           ""
         );
-        var componentStrings = transform.split(",").map(function (val) {
+        var componentStrings = transform.split(",").map(function (val: string) {
           return val.replace(/-/g, "+-");
         });
         let matrix = new Matrix4(

src/parsers/CUBE.ts

@@ -1,16 +1,16 @@
 import { Vector3, Matrix4 } from "../WebGL";
 import { assignBonds } from "./utils/assignBonds";
 import { anumToSymbol } from "./utils/anumToSymbol";
+import { ParserOptionsSpec } from "./ParserOptionsSpec";
 
 /**
-     * @param {string}
-     *            str
-     * @param {ParserOptionsSpec}
-     *            options
+ * @param {string}
+ *            str
+ * @param {ParserOptionsSpec}
+ *            options
  * @category Parsers
-
 */
-export function CUBE(str, options) {
+export function CUBE(str: string, options: ParserOptionsSpec) {
   options = options || {};
   var atoms: any[][] & Record<string, any> = [[]];
   var lines = str.split(/\r?\n/);
@@ -37,22 +37,22 @@ export function CUBE(str, options) {
   // always assume bohr: openbabel source code
   // always assume angstrom: http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/cubeplugin.html
   // we are going to go with n<0 means angstrom - note this is just the first n
-  var convFactor = (lineArr[0] > 0) ? 0.529177 : 1;
+  var convFactor = ((lineArr[0] as any) > 0) ? 0.529177 : 1;
   origin.multiplyScalar(convFactor);
 
-  var nX = Math.abs(lineArr[0]);
+  var nX = Math.abs((lineArr[0] as any));
   var xVec = new Vector3(parseFloat(lineArr[1]),
           parseFloat(lineArr[2]), parseFloat(lineArr[3]))
           .multiplyScalar(convFactor);
 
   lineArr = lines[4].replace(/^\s+/, "").replace(/\s+/g, " ").split(" ");
-  var nY = Math.abs(lineArr[0]);
+  var nY = Math.abs((lineArr[0] as any));
   var yVec = new Vector3(parseFloat(lineArr[1]),
           parseFloat(lineArr[2]), parseFloat(lineArr[3]))
           .multiplyScalar(convFactor);
 
   lineArr = lines[5].replace(/^\s+/, "").replace(/\s+/g, " ").split(" ");
-  var nZ = Math.abs(lineArr[0]);
+  var nZ = Math.abs((lineArr[0] as any));
   var zVec = new Vector3(parseFloat(lineArr[1]),
           parseFloat(lineArr[2]), parseFloat(lineArr[3]))
           .multiplyScalar(convFactor);

src/parsers/GRO.ts

@@ -3,15 +3,15 @@ import { atomNameToElem } from "./utils/atomNameToElem";
 
 /**
  * Parse a gro file from str and create atoms
-  * 
-  * @param {string}
-  *            str
-  * @param {ParserOptionsSpec}
-  *            options* 
-  * @category Parsers
+ * 
+ * @param {string}
+ *            str
+ * @param {ParserOptionsSpec}
+ *            options* 
+ * @category Parsers
+*/
 
- */
-export function GRO(str /*, options*/) {
+export function GRO(str: string /*, options*/) {
   var allatoms: any[][] & Record<string, any> = [];
   var lines = str.split(/\r?\n|\r/);
   while (lines.length > 0) {
@@ -53,7 +53,7 @@ export function GRO(str /*, options*/) {
       var box = last.trim().split(/\s+/);
       if (box.length == 3) {
         for (var b = 0; b < 3; b++) {
-          box[b] = parseFloat(box[b]) * 10.0;
+          (box[b] as any) = parseFloat(box[b]) * 10.0;
         }
         allatoms.box = box;
       }

src/parsers/LAMMPSTRJ.ts

@@ -1,13 +1,15 @@
+import { ParserOptionsSpec } from "./ParserOptionsSpec";
 import { assignBonds } from "./utils/assignBonds";
 
 /**
  * Parse a lammps trajectory file from str and create atoms
+ * 
  * @category Parsers
+*/
 
- */
-export function LAMMPSTRJ(str, options) {
+export function LAMMPSTRJ(str: string, options: ParserOptionsSpec) {
   var atoms: any[] = [];
-  var dic = {
+  var dic:any = {
     id: "serial",
     type: "atom",
     element: "elem",
@@ -43,7 +45,7 @@ export function LAMMPSTRJ(str, options) {
     atoms.push([]);
     for (let j = offset; j < offset + atomCount; j++) {
       var atom: Record<string, any> = {};
-      var properties = {};
+      var properties: any = {};
       var tokens = lines[j].split(" ");
       for (var k = 0; k < tokens.length; k++) {
         var prop = dic[types[k]];

src/parsers/MMTF.ts

@@ -1,5 +1,6 @@
 import { base64ToArray } from "../utilities";
 import { Matrix4 } from "../WebGL";
+import { ParserOptionsSpec } from "./ParserOptionsSpec";
 import { computeSecondaryStructure } from "./utils/computeSecondaryStructure";
 import { processSymmetries } from "./utils/processSymmetries";
 
@@ -8,12 +9,12 @@ interface MMTFobj {
 }
 declare var MMTF: MMTFobj;
 
-var fromCharCode = function (charCodeArray) {
+var fromCharCode = function (charCodeArray: any) {
     return String.fromCharCode.apply(null, charCodeArray).replace(/\0/g, '');
 };
 
-var convertSS = function (val) {
-    //convert mmtf code to 3dmol code
+var convertSS = function (val: number | boolean) {
+    // Convert mmtf code to 3dmol code
     /*    
       0:  pi helix
       1:  bend
@@ -41,11 +42,13 @@ let mmtfHETATMtypes = new Set([
     "PEPTIDE-LIKE",
     "SACCHARIDE"]);
 
-/** @param bindata - binary UInt8Array buffer or a base64 encoded string
- *  @param ParserOptionsSpec
- *  @category Parsers
+/** 
+ * @param bindata - binary UInt8Array buffer or a base64 encoded string
+ * @param ParserOptionsSpec
+ * @category Parsers
 */
-export function MMTFparser(bindata, options) {
+
+export function MMTFparser(bindata: any, options: ParserOptionsSpec) {
 
     var noH = !options.keepH; // suppress hydrogens by default
     var selAltLoc = options.altLoc ? options.altLoc : 'A'; //default alternate location to select if present
@@ -108,7 +111,7 @@ export function MMTFparser(bindata, options) {
     }
 
     let chainIsPolymer: boolean[] = [];
-    mmtfData.entityList.forEach(entity => {
+    mmtfData.entityList.forEach((entity: { chainIndexList: any[]; type: string; }) => {
         entity.chainIndexList.forEach(ch => {
             chainIsPolymer[ch] = entity.type == "polymer";
         });

src/parsers/MOL2.ts

@@ -1,5 +1,6 @@
+import { ParserOptionsSpec } from "./ParserOptionsSpec";
 
-let SYBYLtoElem = {
+let SYBYLtoElem:any = {
   'C.1': 'C',
   'C1': 'C',
   'C.2': 'C',
@@ -50,16 +51,17 @@ let SYBYLtoElem = {
   'So2':'S'
 };
 
-// parse SYBYL mol2 file from string - assumed to only contain one molecule
-// tag
+// Parse SYBYL mol2 file from string - assumed to only contain one molecule tag
+
 /**
  * @param {string}
  *            str
  * @param {ParserOptionsSpec}
  *            options
  * @category Parsers
- */
-export function MOL2(str, options) {
+*/
+
+export function MOL2(str: string, options: ParserOptionsSpec) {
   var atoms: any[][] & Record<string,any> = [[]];
   var noH = false;
   if (typeof options.keepH !== "undefined") noH = !options.keepH;

src/parsers/PDB.ts

@@ -1,24 +1,24 @@
-// parse pdb file from str and create atoms
-// if computeStruct is true will always perform secondary structure
-// analysis,
-// otherwise only do analysis of SHEET/HELIX comments are missing
-
+import { ParserOptionsSpec } from "./ParserOptionsSpec";
 import { getSinglePDB } from "./utils/getSinglePDB";
 
 /**
+ * Parse pdb file from str and create atoms if computeStruct is true will always perform secondary structure analysis, 
+ * otherwise only do analysis of SHEET/HELIX comments are missing
+ * 
  * @param {string} str
  * @param {ParserOptionsSpec} options - keepH (do not strip hydrogens), noSecondaryStructure,
  *            assignbonds (default true, calculate implicit bonds)
  *            (do not compute ss), altLoc (which alternate location to select, if present; '*' to load all)
  * @category Parsers
  * 
- */
-export function PDB(str, options) {
+*/
+
+export function PDB(str: string, options: ParserOptionsSpec) {
   options = options || {};
   var atoms: any[] & Record<string, any> = []; //a separate list for each model
   var sslookup = {}; //stores SHEET and HELIX info, which is shared across models
   atoms.modelData = [];
-  var lines = str.split(/\r?\n|\r/);
+  var lines: any = str.split(/\r?\n|\r/);
   while (lines.length > 0) {
     var pdbinfo = getSinglePDB(lines, options, sslookup);
     var modelatoms = pdbinfo[0];

src/parsers/PQR.ts

@@ -1,18 +1,19 @@
+import { ParserOptionsSpec } from "./ParserOptionsSpec";
 import { assignPDBBonds } from "./utils/assignPDBBonds";
 import { computeSecondaryStructure } from "./utils/computeSecondaryStructure";
 
-    /**
-     * Parse a pqr file from str and create atoms. A pqr file is assumed to be a
-     * whitespace delimited PDB with charge and radius fields.
-     *
-     * @param {string}
-     *            str
-     * @param {ParserOptionsSpec}
-     *            options - noSecondaryStructure (do not compute ss)
-    * @category Parsers 
-     */
-export function PQR(str, options) {
 
+/**
+ * Parse a pqr file from str and create atoms. A pqr file is assumed to be a whitespace delimited PDB with charge and radius fields.
+ * 
+ * @param {string}
+ *            str
+ * @param {ParserOptionsSpec}
+ *            options - noSecondaryStructure (do not compute ss)
+ * @category Parsers 
+*/
+
+export function PQR(str: string, options: ParserOptionsSpec) {
       var atoms: any[][] & Record<string, any> = [[]];
       var computeStruct = !options.noSecondaryStructure;
       atoms.modelData = [{symmetries:[]}];

src/parsers/PRMTOP.ts

@@ -1,16 +1,16 @@
 // @ts-nocheck
+
 /**
  * Parse a prmtop file from str and create atoms
  * 
-  * @param {string}
-  *            str
-  * @param {ParserOptionsSpec}
-  *            options - noSecondaryStructure (do not compute ss)
-  *  
+ * @param {string}
+ *            str
+ * @param {ParserOptionsSpec}
+ *            options - noSecondaryStructure (do not compute ss)
  * @category Parsers
+*/
 
- */
-export function PRMTOP(str /*, options*/) {
+export function PRMTOP(str: string /*, options*/) {
   var atoms = [];
   var atomIndex;
   var count = 0;