updated pipeMif and pipeIsoMif from nrg
restored the original ff parameters
added pseudoatom placement in mif
added prototype automatic grid builder
added mif smoothing
updated the mifview and isomifview for pseudoatom
updated isomif matching stage for pseudoatoms
added ligand rmsd calculation in isomif
merge pseudoMif
restored pipeIsoMif and pipeMif
updated resnb to string
added -a argument for maxCliques in IsoMif
added burriedness score in mif
adapted mifView to show the buriedness of the 1 angstrom grid
changed env dist to 5 Angstrom
calculate cos difference of env
calculate euclidian distance of burried