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>
Atom typing doesn't preserve aromatic flags on atoms, doing aromaticity perception and then atom typing again (addImplicitHydrogens) removes the flags on the atoms. Moving the implicit hydrogen addition gives the correct output.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Generator now produces literal output - note this means the non-aromatic example are 6 singly bonded aliphatic carbons with 1 hydrogen (as specified).

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