Improve file reading strategy

Pass PDB and CIF files straight to ChemDoodle. For all other files, use Open Babel if available to convert to ChemDoodle JSON and pass that to ChemDoodle.
ghutchis · Feb 4, 2015 · 9908acd · 9908acd
1 parent 9b919c2
commit 9908acd
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Showing 3 changed files with 34 additions and 41 deletions.
diff --git a/Common.m b/Common.m
@@ -59,41 +59,40 @@
 
 NSString *PreviewURL(CFBundleRef bundle, NSURL *url, NSError *error) {
     NSString *extension = [[[url path] pathExtension] lowercaseString];
+    NSString *mol = nil;
 
-    // Use Open Babel to generate ChemDoodle JSON from file contents
-    NSString *options = @"-ocdjson -l 20 -c";
-    if ([@[@"smiles", @"smi", @"can", @"inchi"] containsObject:extension]) {
-        options = [options stringByAppendingString:@" --gen2d"];
+    // Read the raw file contents if ChemDoodle supports the format
+    if ([@[@"sdf", @"sd", @"mdl", @"mol", @"cif", @"pdb", @"xyz"] containsObject:extension]) {
+        mol = [NSString stringWithContentsOfURL:url encoding:NSUTF8StringEncoding error:&error];
     }
-    NSString *cdjson = MolDataFromOpenBabel(url, options);
 
-    // Read the raw file contents if Open Babel failed or if a cif (for unit cell info)
-    NSString *raw = nil;
-    if ((cdjson == nil) || [extension isEqualToString:@"cif"]) {
-        // Only worth reading the raw file contents if ChemDoodle supports the format
-        if ([@[@"sdf", @"sd", @"mdl", @"mol", @"cif", @"pdb", @"xyz"] containsObject:extension]) {
-            raw = [NSString stringWithContentsOfURL:url encoding:NSUTF8StringEncoding error:&error];
+    // Use Open Babel to generate ChemDoodle JSON from file (unless CIF or PDB)
+    if (![@[@"cif", @"pdb"] containsObject:extension]) {
+        NSString *options = @"-ocdjson -l 20 -c";
+        if ([@[@"smiles", @"smi", @"can", @"inchi"] containsObject:extension]) {
+            options = [options stringByAppendingString:@" --gen2d"];
+        }
+        NSString *cdjson = MolDataFromOpenBabel(url, options);
+        if (!(cdjson == nil)) {
+            extension = @"cdjson";
+            mol = cdjson;
         }
     }
-    if (cdjson == nil && raw == nil) {
-        return nil;
-    }
-
+
     // Escape strings to insert into template as javascript variables
-    raw = EscapeStringForJavascript(raw);
-    cdjson = EscapeStringForJavascript(cdjson);
+    mol = EscapeStringForJavascript(mol);
 
     // Load the template file as a string for substitution
     NSString *template = TextFromBundle(bundle, @"chemlook.html", error);
     NSString *css = TextFromBundle(bundle, @"style.css", error);
     NSString *chemdoodle = TextFromBundle(bundle, @"ChemDoodleWeb.js", error);
     NSString *js = TextFromBundle(bundle, @"script.js", error);
-    if (template == nil || chemdoodle == nil || css == nil || js == nil) {
+    if (mol == nil || extension == nil || template == nil || chemdoodle == nil || css == nil || js == nil) {
         return nil;
     }
 
     // Insert variables into template
-	NSString *output = [NSString stringWithFormat:template, css, chemdoodle, raw, cdjson, extension, js];
+    NSString *output = [NSString stringWithFormat:template, css, chemdoodle, extension, mol, js];
     return output;
 }
 

diff --git a/chemlook.html b/chemlook.html
@@ -15,9 +15,8 @@
     <a href="#transformer" id="threed" class="button active">3D</a>
 </div>
 <script>
-var raw = '%@';
-var cdjson = '%@';
-var extension = '%@';
+var extension = '%@',
+    molstring = '%@';
 %@
 </script>
 </body>

diff --git a/script.js b/script.js
@@ -39,26 +39,21 @@ ChemDoodle.lib.jQuery(document).ready(function($) {
     var viewer = new ChemDoodle.ViewerCanvas('viewer', width, height);
 
     // Construct ChemDoodle Molecule from molecule data
-    if (cdjson !== '') {
-        // If available, use the ChemDoodle JSON produced by Open Babel
-        var mol = ChemDoodle.readJSON(cdjson);
-        // TODO: Support previewing multiple molecules (for now we just take the first)
-        if (typeof(mol) !== 'undefined') {
-            mol = mol.molecules[0];
-        }
-    }
-
-    // If no ChemDoodle JSON, use the raw file contents instead with ChemDoodle reader
-    if (typeof(mol) === 'undefined' && raw !== '') {
-        if (extension === 'pdb') {
-            var mol = ChemDoodle.readPDB(raw);
-        } else if (extension === 'cif') {
-            var mol = ChemDoodle.readCIF(raw);
-        } else if (extension === 'xyz') {
-            var mol = ChemDoodle.readXYZ(raw);
-        } else {
-            var mol = ChemDoodle.readMOL(raw);
+    var mol = undefined,
+        unitcell = undefined;
+    if (extension === 'cdjson') {
+        var parsed = ChemDoodle.readJSON(molstring);
+        if (typeof parsed !== 'undefined' && typeof parsed.molecules[0] !== 'undefined') {
+            mol = parsed.molecules[0];
         }
+    } else if (extension === 'pdb') {
+        mol = ChemDoodle.readPDB(molstring);
+    } else if (extension === 'cif') {
+        var parsed = ChemDoodle.readCIF(molstring);
+        mol = parsed.molecule;
+        unitcell = parsed.unitCell;
+    } else {
+        mol = ChemDoodle.readMOL(molstring);
     }
     scaleMol(mol);