Validator: Handle formulas in brackets

[tsufz]

@meier-rene,
In some cases, we need formulas in brackets, e.g. for charged compounds such as quaternary ammonia compounds. The validator needs to be fixed to handle such cases.

Formula from CH$IUPAC:   [C27H42NO2]+
Formula from CH$FORMULA: C27H42NO2

I suggest to check the inner formula only and to ignore the brackets.

Best wishes,
Tobias

[schymane]

PubChem handle charged formulas differently, without the brackets, just the charge afterwards. I don't recall seeing a charged formula with square brackets before, how are you producing them?

[tsufz]

RMassBank, well, I'll try with remove brackets and we should add the a handle in RMassBank to remove the brackets.

[meier-rene]

The formulas are created by cdk that way. I think its smart. The syntax for charged molecules in cdk is [Formula]Charge. This is a non ambiguous notation. Just consider a sulfate ion: [SO4]2- compared to SO42-. This means we have a incompatibility between java(CDK) and R. How can we solve that?