Improve sdf parsing

[ggutierrez-sunbright]

Current sdf parser doesn't take into account charges defined in the M CHG section (or any other properties defined with a M statement).

In order to preserve backwards compatibility, an extra parameter would be required. This creates a conflict with current initiatives to replace the argument parsing mechanism (see #82 )

This feature will be implemented for the first release after creating the dedicated branch for legacy version of rDock and implementing the new parsing with cxxopts

I consider parsing the M CHG lines is very important for correct molecule interpretation, so in the new version it will be the default behavior with a --sdf-ignore-m-chg flag to opt-out.

After fixing this, it would be nice to do a refactor on the RbtMdlFileSource class.

It would be also relevant to take a look at how the M CHG entries are (probably not) being handled for output (RbtMdlFileSink)

blocked by #82

• fix RbtMdlFileSource
• add opt-out flag --sdf-ignore-m-chg
• check RbtMdlFileSink and create an issue if necessary

There's also a problem identifying quaternary ammonium atoms (issue pending) that could be related to this