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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 22, 2014
1 parent 9fa7f10 commit f66a59a
Showing 1 changed file with 7 additions and 1 deletion.
Expand Up @@ -74,7 +74,7 @@ public class InChIGeneratorFactory {
/**
* 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
Expand Down Expand Up @@ -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;
Expand All @@ -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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