Configurable atom lines in write_input

[tovrstra]

A note from @tovrstra about a feature not supported in PR #188 when writing Gaussian input files:
"The format of the atom_lines should be configurable, with about the same level of flexibility as the template for the whole input file. See e.g. the Gaussian Molecule Specification: http:https://gaussian.com/molspec/. For some job types, more information than element and Cartesian coordinates needs to be added (fragment, charge, ...)."

Originally posted by @FarnazH in #43 (comment)