Ah yes, bad lines are read as empty

johnmay · johnmay · commit 28fdf639aa9a · 2021-01-10T19:41:31.000Z
diff --git a/storage/smiles/src/main/java/org/openscience/cdk/io/iterator/IteratingSMILESReader.java b/storage/smiles/src/main/java/org/openscience/cdk/io/iterator/IteratingSMILESReader.java
@@ -130,8 +130,6 @@ public boolean hasNext() {
                 }
 
                 hasNext = true;
-                final String suffix = suffix(line);
-
                 nextMolecule = readSmiles(line);
             } catch (Exception exception) {
                 logger.error("Unexpected problem: ", exception.getMessage());
@@ -154,7 +152,9 @@ public boolean hasNext() {
     private String suffix(final String line) {
         for (int i = 0; i < line.length(); i++) {
             char c = line.charAt(i);
-            if (c == ' ' || c == '\t') return line.substring(i + 1);
+            if (c == ' ' || c == '\t') {
+                return line.substring(i + 1);
+            }
         }
         return "";
     }
@@ -172,6 +172,7 @@ private IAtomContainer readSmiles(final String line) {
             logger.error("Error while reading the SMILES from: " + line + ", ", e);
             final IAtomContainer empty = builder.newInstance(IAtomContainer.class, 0, 0, 0, 0);
             empty.setProperty(BAD_SMILES_INPUT, line);
+            empty.setTitle(suffix(line));
             return empty;
         }
     }

Original file line number	Diff line number	Diff line change
`@@ -130,8 +130,6 @@ public boolean hasNext() {`
`130`	`130`	`}`
`131`	`131`
`132`	`132`	`hasNext = true;`
`133`		`- final String suffix = suffix(line);`
`134`		`-`
`135`	`133`	`nextMolecule = readSmiles(line);`
`136`	`134`	`} catch (Exception exception) {`
`137`	`135`	`logger.error("Unexpected problem: ", exception.getMessage());`
`@@ -154,7 +152,9 @@ public boolean hasNext() {`
`154`	`152`	`private String suffix(final String line) {`
`155`	`153`	`for (int i = 0; i < line.length(); i++) {`
`156`	`154`	`char c = line.charAt(i);`
`157`		`- if (c == ' ' \|\| c == '\t') return line.substring(i + 1);`
	`155`	`+ if (c == ' ' \|\| c == '\t') {`
	`156`	`+ return line.substring(i + 1);`
	`157`	`+ }`
`158`	`158`	`}`
`159`	`159`	`return "";`
`160`	`160`	`}`
`@@ -172,6 +172,7 @@ private IAtomContainer readSmiles(final String line) {`
`172`	`172`	`logger.error("Error while reading the SMILES from: " + line + ", ", e);`
`173`	`173`	`final IAtomContainer empty = builder.newInstance(IAtomContainer.class, 0, 0, 0, 0);`
`174`	`174`	`empty.setProperty(BAD_SMILES_INPUT, line);`
	`175`	`+ empty.setTitle(suffix(line));`
`175`	`176`	`return empty;`
`176`	`177`	`}`
`177`	`178`	`}`