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Ignore aromatic bonds by default. The option has be deprecated but sh…

…ould be removed in future. Global state, therefore impossible to test reliably.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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johnmay authored and egonw committed Mar 13, 2014
1 parent 9fa7f10 commit f66a59adb8308dfd9a6d1fba8ee216af6d44aa7b
@@ -74,7 +74,7 @@
/**
* If the CDK aromaticity flag should be ignored and the bonds treated solely as single and double bonds.
*/
- private boolean ignoreAromaticBonds = false;
+ private boolean ignoreAromaticBonds = true;
/**
* <p>Constructor for InChIGeneratorFactory. Ensures that native code
@@ -119,7 +119,12 @@ public static InChIGeneratorFactory getInstance() throws CDKException {
* http://www.inchi-trust.org/fileadmin/user_upload/html/inchifaq/inchi-faq.html#16.3
*
* @param ignore if aromatic bonds should be treated as bonds of type single and double
+ * @deprecated "the use of aromatic bonds is strongly discouraged" - InChI
+ * FAQ, the InChI will fail for many compounds if ignore
+ * aromatic bonds is not enabled and the compound have aromatic
+ * flags.
*/
+ @Deprecated
@TestMethod("testInChIGenerator_AromaticBonds")
public void setIgnoreAromaticBonds(boolean ignore) {
ignoreAromaticBonds = ignore;
@@ -130,6 +135,7 @@ public void setIgnoreAromaticBonds(boolean ignore) {
*
* @return if aromatic bonds are treated as bonds of type single and double
*/
+ @Deprecated
@TestMethod("testInChIGenerator_AromaticBonds")
public boolean getIgnoreAromaticBonds() {
return ignoreAromaticBonds;

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