From-smiles-step

* Fixed an issue where the chemical name was handled as SMILES, causing the code to
crash.

* Added ability to ignore or discard a structure from e.g. optimization
* Added isomeric SMILES to the possible names for systems and configurations

* New configurations made from other systems could remove the atoms in those
systems.

* Using structure names is too dangerous to use by perceiving if text is a name of
SMILES and there is no easy test for valid SMILES. So change to only using names
if the user specifies names.

* Switched to standard structure handling, which adds more options
* Added getting structures from Pubchem using the chemical name.