select all
restrict none

define big  (*.n4,*.n6,*.n7, *.o4,*.o6, *.c5,*.c6, (*.c4,*.c7 and pyrimidine), (*.c8 and purine)) and dna
define bsmall  (*.o2,*.n3,*.n2,*.c2,(*.c4 and purine)) and dna
define dezox (*.C?*,*.O?*) and dna

define phos_polar *.O?P and dna
define phos_nonpolar *.P and dna

define pol *.O??, *.N??
define nonpol *.C??, *.P??, *.S??

define dez_polar (dezox and pol)
define dez_nonpolar (dezox and nonpol)

define big_polar (big and pol)   
define big_nonpolar (big and nonpol) 

define small_polar (bsmall and pol)
define small_nonpolar (bsmall and nonpol)

define protein_polar (protein and pol)
define protein_nonpolar (protein and nonpol)


define pol1 within(3.5,dez_polar)  and protein_polar
define pol2 within(3.5,phos_polar)  and protein_polar
define pol3 within(3.5,big_polar) and protein_polar
define pol4 within(3.5,small_polar) and protein_polar

define nonp1 within(4.5,dez_nonpolar) and protein_nonpolar
define nonp2 within(4.5,phos_nonpolar) and protein_nonpolar
define nonp3 within(4.5,big_nonpolar) and protein_nonpolar
define nonp4 within(4.5,small_nonpolar) and protein_nonpolar


