Added a new contributor

Change-Id: I04ad1ea3b224cd65012b6b2111d565a11c49613b
Remove extra '}' from javadoc.

Change-Id: I7d49c4903169444ee06e183781d83d85031e36a1
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Removing testing of atom types on molecules which no longer exist.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Hotfix on beam, ring number 0 .. 99 inclusive - there are 100 rings not 99, doh.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Removing existing SmilesGenerator implementation.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Chiral SMILES = isomeric SMILES - this is now configured by the constructor and there is a single createSMILES method.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
API changes in other modules required to build - will come back and verify these work as expected later.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Don't set mass for default isotopes - incompatibilities between what CDK/SMILES define.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Updating API calls in SmilesGeneratorTest - no test assertions corrected.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Using Beam to generator the SMILES.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Actually we also want to include the isotope number if there was no major isotope found.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Remove errors due to hydrogen counts being null.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Intercept pseudo atoms and default null hydrogen counts to 0. The CDK will leave the nulls in place for pseudo atoms so we need this special exception,

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Unknown atom '*' doesn't need brackets - http://www.daylight.com/daycgi/depict?2a

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Bond symbol is now only writen on the ring open - recomeneded by OpenSMILES.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Bracket atoms must specify the number of hydrogens.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Ring numbering changed - numbering now starts from the first ring opening instead of the first ring closure.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
fixCarbonCount gave the wrong hydrogen count on one of the atoms.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Redundant brackets are no longer included in generated SMILES.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Bond symbol only written on opening of ring not closure.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>