move TransparentProxy to Tools namespace
fix reaction position links container
begining algorithm
fix SpecieGroupedNodes
fix specie backbone algorithm works with nodes now
add EntryNodes simple selector
a bit of comments
Revert "fix reaction position links container"

This reverts commit 05924b348710548780704fb783b27c0858c0a51c.
Merge branch 'code' into algorithm
fix storing similar specs to reaction or there object when analysis results optimizes collected data
fix comparing original specs with veiled spec
fix rehash reaction links when spec was swapped
fix duplication reactions for specie code generator
merge branch 'code' to 'algorithm'
fix sort children reactions of ubiquitos reaction by using atom
fix indent in specie find builder spec
add rspecs for algorithm species
add comments to SpecieGroupedNodes methods
fix collapse key nodes of backbonde if them have similar unique species
algorithm builds through units