Dealga McArdle

some debug images :) In 06_1L2Y_4GE.pdb 

more interim scripting: https://gist.github.com/zeffii/c864b5096bdc4a479703

> If I understand the number on each atom is the fi value associated, right? Yep! from the _values_fi_ lookup table, they are not yet remapped / normalized `[-3, +1]...

the red vertices indicate which vertices the search is limited to by passing a radius 

Right, i imagine there are vertices on the Connolly surface mesh which due to the blobby-ness of the surface are interpolation values and the nearest element is further away than...

probe radius could be this progressive thing, which first searches 2 times the max VdW radius , in most cases this will probably find something , if not then I...

https://gist.github.com/zeffii/95e09d1e94feb2c23a8a mostly left to do is the _choice + compare_ code now (interim code)

 https://gist.github.com/zeffii/37de8fde581c4fd98243 I just noticed not all elements are in the `scale_vdw` dictionary. for testing purposes the purple represents failed lookups for the radii of elements. ``` 06_1L2Y_4GE.pdb radii not...

please forgive in advance this, which is probably butchering chemistry terms.. These entities (NE, SD OE1...) need to be remapped back from specific _element in the chain_ to the _generic...

https://gist.github.com/zeffii/fa8f7530d28dcaca4c7a functional.. now to test on larger files..