Added docstrings.

dist/Webina/Webina.js

@@ -0,0 +1,205 @@
+/**
+ * Webina Copyright 2019 Jacob Durrant
+ *
+ * Licensed under the Apache License, Version 2.0 (the License);
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an AS IS BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+// This file is part of Webina, released under the Apache 2.0 License. See
+// LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
+// details. Copyright 2019 Jacob D. Durrant.
+// There are a few variables and functions from vina.js that I want to easily
+// access from here.
+var VERSION = "1.0.0"; // Replaced by compile script.
+console.log("Webina JavaScript Library " + VERSION);
+var WEBINA_Module;
+// A shiv for decodeBase64.
+var decodeBase64 = "function" == typeof atob ? atob : function (r) {
+    var e, t, a, i, n, o, f = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/=", m = "", s = 0;
+    for (r = r.replace(/[^A-Za-z0-9\+\/\=]/g, ""); e = f.indexOf(r.charAt(s++)) << 2 | (i = f.indexOf(r.charAt(s++))) >> 4, t = (15 & i) << 4 | (n = f.indexOf(r.charAt(s++))) >> 2, a = (3 & n) << 6 | (o = f.indexOf(r.charAt(s++))), m += String.fromCharCode(e), 64 !== n && (m += String.fromCharCode(t)), 64 !== o && (m += String.fromCharCode(a)), s < r.length;)
+        return m;
+};
+// Make Webina global namespace.
+var Webina = (function () {
+    return {
+        WEBINA_ENVIRONMENT_IS_NODE: window["WEBINA_ENVIRONMENT_IS_NODE"],
+        WEBINA_lengthBytesUTF8: window["WEBINA_lengthBytesUTF8"],
+        WEBINA_stringToUTF8Array: window["WEBINA_stringToUTF8Array"],
+        WEBINA_assert: window["WEBINA_assert"],
+        WEBINA_ASSERTIONS: 1,
+        WEBINA_DATA_URI_PREFIX: "data:application/octet-stream;base64,",
+        WEBINA_BASE_URL: "./",
+        FS: window["FS"],
+        start: function start(vinaParams, receptorPDBQTTxt, ligandPDBQTTxt, onDone, onError, baseUrl) {
+            var _this = this;
+            // baseUrl = undefined;  // For debugging.
+            var baseUrlMsg = "\nWEBINA\n======\n\n";
+            if (baseUrl !== undefined) {
+                if (baseUrl.slice(baseUrl.length - 1) !== "/") {
+                    baseUrl += "/";
+                }
+                this.WEBINA_BASE_URL = baseUrl;
+                baseUrlMsg += "User specified baseUrl: " + baseUrl + "\n";
+            }
+            else {
+                baseUrlMsg += "No baseUrl specified, so using ./\n\n";
+                baseUrlMsg += "Use Webina.start() to specify the baseUrl:\n";
+                baseUrlMsg += "    function start(vinaParams, receptorPDBQTTxt, \n";
+                baseUrlMsg += "                   ligandPDBQTTxt, onDone, \n";
+                baseUrlMsg += "                   onError, baseUrl)\n";
+            }
+            baseUrlMsg += "\nExpecting files at the following locations:\n";
+            for (var i = 0; i < 5; i++) {
+                var fileName = ["Webina.min.js", "vina.html.mem",
+                    "vina.min.js", "vina.worker.min.js",
+                    "vina.wasm"][i];
+                baseUrlMsg += "    " + (baseUrl === undefined ? "./" : baseUrl) + fileName + "\n";
+            }
+            baseUrlMsg += "\n";
+            if (baseUrl !== undefined) {
+                console.log(baseUrlMsg);
+            }
+            else {
+                console.warn(baseUrlMsg);
+            }
+            if (onError === undefined) {
+                onError = function () {
+                    console.log("Webina encountered an error! Does your browser support WebAssembly?");
+                };
+            }
+            // Create a module object for WASM.
+            WEBINA_Module = {
+                "preRun": [],
+                "postRun": [],
+                "stdOut": "",
+                "stdErr": "",
+                "print": function () {
+                    return function (e) {
+                        1 < arguments.length && (e = Array.prototype.slice.call(arguments).join(" ")),
+                            window["WEBINA_Module"]["stdOut"] += e + "\n";
+                    };
+                }(),
+                "printErr": function (e) {
+                    // 1 < arguments.length && (e = Array.prototype.slice.call(arguments).join(" ")), console.error(e)
+                    1 < arguments.length && (e = Array.prototype.slice.call(arguments).join(" ")),
+                        window["WEBINA_Module"]["stdErr"] += e + "\n";
+                },
+                "setStatus": function (e) {
+                    if (e === "") {
+                        // This happens when it is done running.
+                        if (onDone !== undefined) {
+                            var outTxt = new TextDecoder("utf-8").decode(window["FS"]["readFile"]('ligand_out.pdbqt'));
+                            var stdOut = window["WEBINA_Module"]["stdOut"];
+                            var stdErr = window["WEBINA_Module"]["stdErr"];
+                            onDone(outTxt, stdOut, stdErr);
+                        }
+                    }
+                },
+                "onError": onError,
+                "catchError": function (n) {
+                    onError(n);
+                    // throw n;  // Don't throw the errr. You're catching it now.
+                },
+                "receptorPDBQTTxt": receptorPDBQTTxt,
+                "ligandPDBQTTxt": ligandPDBQTTxt
+            };
+            if (vinaParams["receptor"] !== undefined) {
+                console.warn("Webina does not support Vina's --receptor parameter. Instead, pass the content of the receptor file as a string to the webina.start() function.");
+            }
+            if (vinaParams["receptor"] !== undefined) {
+                console.warn("Webina does not support Vina's --ligand parameter. Instead, pass the content of the ligand file as a string to the webina.start() function.");
+            }
+            // Receptor and ligand files are always the same.
+            WEBINA_Module['arguments'] = [
+                '--receptor', '/receptor.pdbqt',
+                '--ligand', '/ligand.pdbqt',
+            ];
+            // For some reason, WebAssembly always uses one more processor
+            // than specified. Compensate for that here. But sometimes it
+            // doesn't, so commenting out... Confusing.
+            // if ((vinaParams["cpu"] !== undefined) && (vinaParams["cpu"] > 1)) {
+            //     vinaParams["cpu"] = vinaParams["cpu"] - 1;
+            // }
+            // Add in the remaining values. Note that there is no validation here.
+            var paramNames = Object.keys(vinaParams);
+            var paramNamesLen = paramNames.length;
+            for (var i = 0; i < paramNamesLen; i++) {
+                var key = paramNames[i];
+                var val = vinaParams[key];
+                WEBINA_Module['arguments'].push('--' + key);
+                if (typeof (val) !== "boolean") {
+                    WEBINA_Module['arguments'].push(String(val));
+                }
+            }
+            window["WEBINA_Module"] = WEBINA_Module;
+            // Initialize the memory
+            var memoryInitializer = this.WEBINA_BASE_URL + "vina.html.mem";
+            memoryInitializer = WEBINA_Module["locateFile"] ? WEBINA_Module["locateFile"](memoryInitializer, "") : memoryInitializer, WEBINA_Module["memoryInitializerRequestURL"] = memoryInitializer;
+            var meminitXHR = WEBINA_Module["memoryInitializerRequest"] = new XMLHttpRequest;
+            meminitXHR.onloadend = function () {
+                if (meminitXHR.status === 404) {
+                    var msg = "Unable to access " + memoryInitializer + ". See JavaScript console for warnings. The \"baseUrl\" variable passed to Webina is likely incorrect.";
+                    WEBINA_Module["catchError"]({ "message": msg });
+                    console.warn(msg);
+                }
+                else {
+                    var script = document.createElement("script");
+                    script.src = _this.WEBINA_BASE_URL + "vina.js";
+                    document.body.appendChild(script);
+                }
+            };
+            meminitXHR.open("GET", memoryInitializer, !0);
+            meminitXHR.responseType = "arraybuffer";
+            meminitXHR.send(null);
+        },
+        isDataURI: function (r) {
+            return String.prototype.startsWith ? r.startsWith(this.WEBINA_DATA_URI_PREFIX) : 0 === r.indexOf(this.WEBINA_DATA_URI_PREFIX);
+        },
+        intArrayFromBase64: function (e) {
+            if ("boolean" == typeof this.WEBINA_ENVIRONMENT_IS_NODE && this.WEBINA_ENVIRONMENT_IS_NODE) {
+                var t;
+                try {
+                    t = Buffer.from(e, "base64");
+                }
+                catch (r) {
+                    t = new Buffer(e, "base64");
+                }
+                return new Uint8Array(t.buffer, t.byteOffset, t.byteLength);
+            }
+            try {
+                for (var r = decodeBase64(e), a = new Uint8Array(r.length), i = 0; i < r.length; ++i)
+                    a[i] = r.charCodeAt(i);
+                return a;
+            }
+            catch (r) {
+                throw new Error("Converting base64 string to bytes failed.");
+            }
+        },
+        // Not used?
+        tryParseAsDataURI: function (r) {
+            if (this.isDataURI(r))
+                return this.intArrayFromBase64(r.slice(this.WEBINA_DATA_URI_PREFIX.length));
+        },
+        // Not used?
+        intArrayFromString: function (r, e, t) {
+            var a = 0 < t ? t : this.WEBINA_lengthBytesUTF8(r) + 1, i = new Array(a), n = this.WEBINA_stringToUTF8Array(r, i, 0, i.length);
+            return e && (i.length = n), i;
+        },
+        // Not used?
+        intArrayToString: function (r) {
+            for (var e = [], t = 0; t < r.length; t++) {
+                var a = r[t];
+                255 < a && (this.WEBINA_ASSERTIONS && this.WEBINA_assert(!1, "Character code " + a + " (" + String.fromCharCode(a) + ")  at offset " + t + " not in 0x00-0xFF."), a &= 255), e.push(String.fromCharCode(a));
+            }
+            return e.join("");
+        }
+    };
+})();