3dmol - npm Package Compare versions

Comparing version 1.7.1 to 1.8.0

3Dmol/3dmol.js

@@ -315,2 +315,13 @@
     var m = viewer.addModel();
+    
+    if (query.indexOf(':') < 0) {
+        //no type specifier, guess
+        if(query.length == 4) {
+            query = 'pdb:'+query;
+        } else if(!isNaN(query)) {
+            query = 'cid:'+query;
+        } else {
+            query = 'url:'+query;
+        }
+    }
     if (query.substr(0, 5) === 'mmtf:') {
@@ -385,3 +396,3 @@ pdbUri = options && options.pdbUri ? options.pdbUri : "https://mmtf.rcsb.org/v1.0/full/";
                     pdbUri = options && options.pdbUri ? options.pdbUri : "https://files.rcsb.org/view/";
-                    uri = pdbUri + query + "." + type;
+                    uri = pdbUri + query + ".pdb";
                     console.log("falling back to pdb format");
@@ -651,2 +662,10 @@ $.get(uri, function(ret) {
 //since we don't use the require optimizer to combine modules
+if(typeof(_3dmol_saved_define) !== 'undefined') {
+    /** When pulling in external sources, disable amd to ensure they
+     * populate the global namespace as expected.  Restore it so code
+     * using amd still works. */
+    /*global _3dmol_saved_define, _3dmol_saved_require, define:true, require:true */
+    define = _3dmol_saved_define;
+    require = _3dmol_saved_require;
+}
 if( typeof(define) === 'function' && define.amd) {
@@ -653,0 +672,0 @@ define('$3Dmol',[], function() { return $3Dmol; });

3Dmol/WebGL/shaders.js

@@ -604,3 +604,3 @@
 "         float t = dot(mvPosition.xyz-p1,n)/dot(pnorm,n);",
-"         mvPosition.xyz = p1+t*pnorm;",
+"         mvPosition.xyz = p1+t*pnorm;", 
 "       } else {", //orthographic
@@ -616,3 +616,3 @@ "         mvPosition.xyz = p1;",
 "         mvPosition.xyz = p2;",
-"       }",
+"       }", 
 "       mult *= -1.0;",
@@ -622,3 +622,3 @@ "    }",
 "    vec3 doublecr = normalize(cross(mvPosition.xyz,cr))*radius;",
-"    mvPosition.xy +=  mult*(cr + doublecr).xy;",
+"    mvPosition.xyz +=  mult*(cr + doublecr).xyz;",
 "    cposition = mvPosition.xyz;",
@@ -625,0 +625,0 @@ "    gl_Position = projectionMatrix * mvPosition;",

gulpfile.js

@@ -12,3 +12,3 @@ const { series, parallel, src, watch, dest} = require('gulp');
 coresrc = ['3Dmol/3dmol.js','3Dmol/WebGL/math.js','3Dmol/WebGL/shapes.js','3Dmol/WebGL/core.js','3Dmol/WebGL/**.js','3Dmol/**.js','!3Dmol/SurfaceWorker.js','3Dmol/SurfaceWorker.js'];
-extsrc = ['js/mmtf.js','node_modules/pako/dist/pako_inflate.js','node_modules/netcdfjs/dist/netcdfjs.js'];
+extsrc = ['js/disable_amd.js','js/mmtf.js','node_modules/pako/dist/pako.js','node_modules/netcdfjs/dist/netcdfjs.js','node_modules/upng-js/UPNG.js'];
 uisrc = ['3Dmol/ui/ui.js', '3Dmol/ui/state.js', '3Dmol/ui/icon.js', '3Dmol/ui/form.js', '3Dmol/ui/defaultValues.js'];
@@ -41,2 +41,3 @@ jqsrc = ['node_modules/jquery/dist/jquery.js'];
 		    'pako':false,
+		    'UPNG':false,
 		    'netcdfjs':false,
@@ -52,4 +53,7 @@ 'XMLHttpRequest':false,
 		    'TextDecoder': false,
-	            'define':false}}))
-    .pipe(jshint.reporter('default'));
+		    'FileReader': false,
+	            'define':false,
+		    'require':false}}))
+    .pipe(jshint.reporter('default'))
+    .pipe(jshint.reporter('fail'));
 }
@@ -56,0 +60,0 @@

package.json

 {
   "name": "3dmol",
-  "version": "1.7.1",
+  "version": "1.8.0",
   "description": "Object oriented Javascript molecular visualization library",
@@ -39,4 +39,5 @@ "repository": {
     "pako": "^2.0.4",
-    "yargs-parser": "^20.2.9"
+    "yargs-parser": "^20.2.9",
+    "upng-js": "^2.1.0"
   }
 }

New alerts

Uses eval

Supply chain risk

Package uses eval() which is a dangerous function. This prevents the code from running in certain environments and increases the risk that the code may contain exploits or malicious behavior.

Found 1 instance in 1 package

Long strings

Supply chain risk

Contains long string literals, which may be a sign of obfuscated or packed code.

Found 1 instance in 1 package

Minified code

Quality

This package contains minified code. This may be harmless in some cases where minified code is included in packaged libraries, however packages on npm should not minify code.

Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

81063038

increased by0.39%

Number of package files

271

increased by1.12%

Lines of code

306508

increased by2.61%

Worsened metrics

Dependency count

6

increased by20%

Number of low quality alerts

2

increased byInfinity%

Number of low supply chain risk alerts

51

increased by2450%

Number of medium supply chain risk alerts

7

increased by600%

Dependency changes

• + Addedupng-js@^2.1.0

• + Addedpako@1.0.11(transitive)

• + Addedupng-js@2.1.0(transitive)