From-smiles-step

* 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.

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* Updated the README file to give a better description.
* Updated the short description in setup.py to work with the new installer.
* Added keywords for better searchability.

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* Internal Changes

- Upgraded to be compatible with the improved version of the
MolSystem classes for describing the molecular system.