Fix/parsing lattice file (#18)

*  make references to original file instead of parsing them

* update code with respect to parsing of structures

* update unit tests

* debug energy landscape refinement

* debug adp

* update syntactic settings

* update wrapper tools for binding site calculation

* update defaults in syntactic settings

* make neighbour cut off optional in PES exploration

* update wrong variable

* update bad indent

* debug initializing mesoscale model

* mute neighbour cut off mapping for now

* update default value for neighbor cut off

* update wrong variable for process parallelization

* update retrieval of mechanisms

* update mode of temporary files

* add function to replace site types

* debug: print molar fractions and gas species

* uncomment unneeded code lines

* comment further lines for debug

* debug:comment unneeded lines for cluster expansion

* debug: comment unneeded lines

* debug:update list indexing

* move pz job out of get_rate-function

* debug: print lattice ids

* debug: print lattice ids

* debug:add seek mechanism while writing to temp file

* debug: update wrong variable

* debug: add example which imports the graph at mesoscopic level

* mute molar fraction for O2 in ADP

* remove printing, change CO2 to CO

* add needed comma to result output var

* add needed comma in tuple

* move from list to tuple

* debug: print resulting data from scan job

* debug:print settings

* update wrapping function for snapshots, uncomment pressure division

* remove float conversion in generic setting for zacros

* also remove float conversion from other generic settings

* move float conversion to other function and add asterisk

* remove print statements, successfully run adp

* update examples

* correct indentation

* add plot and update example

* update engine paths

* update function for mapping results

* update path variables

* update path keyword

* update path variable