define polar_phosphate (*.O?P and dna)
echo polar_phosphate
pause
define nonpolar_phosphate (*.P? and dna)
echo nonpolar_phosphate
pause

define polar_doxribose (*.O?* and dna)
echo polar_doxribose
pause
define nonpolar_doxribose (*.C?* and dna)
echo nonpolar_doxribose
pause

define polar_bases ((*.N?, *.O?) and dna)
echo polar_bases
pause
define nonpolar_bases (*.C? and dna)
echo nonpolar_bases
pause

define polar_aacids ((*.N?, *.O?) and protein)
echo polar_aacids
pause
define nonpolar_aacids ((*.C?, *.S?) and protein)
echo nonpolar_aacids
pause

define minor_da ((*.C2, *.N3, *.C4, *.N9, *.C8) and da)

define minor_dt ((*.C7, *.C5, *.N1, *.C6) and dt)

define minor_dg ((*.C6, *.N1, *.C5, *.N7, *.C8, *.O6) and dg)

define minor_dc ((*.C5, *.N4, *.C4, *.C6) and dc)


define major_da ((*.C5, *.N6, *.C6, *.N7, *.N1) and da)

define major_dt ((*.C4, *.N3, *.C2, *.O4, *.O2) and dt)

define major_dg ((*.C2, *.N2, *.C4, *.N3, *.N9) and dg)

define major_dc ((*.C2, *.N1, *.O2, *.N3) and dc)


define polar_minor ((minor_da, minor_dt, minor_dg, minor_dc) and polar_bases)
echo polar_minor
pause
define nonpolar_minor ((minor_da, minor_dt, minor_dg, minor_dc) and nonpolar_bases)
echo nonpolar_minor
pause
define polar_major ((major_da, major_dt, major_dg, major_dc) and polar_bases)
echo polar_major
pause
define nonpolar_major ((major_da, major_dt, major_dg, major_dc) and nonpolar_bases)
echo nonpolar_major
pause

define nonpolar_contacts_phosphate within(4.5, nonpolar_phosphate) and nonpolar_aacids 
echo nonpolar_contacts_phosphate 
pause
define polar_contacts_phosphate within(3.5, polar_phosphate) and polar_aacids 
echo polar_contacts_phosphate 
pause

define nonpolar_contacts_sugar within(4.5, nonpolar_doxribose) and nonpolar_aacids  
echo nonpolar_contacts_sugar
pause
define polar_contacts_sugar within(3.5, polar_doxribose) and polar_aacids  
echo polar_contacts_sugar
pause

define nonpolar_contacts_major within(4.5, nonpolar_major) and nonpolar_aacids  
echo nonpolar_contacts_major
pause
define polar_contacts_major within(3.5, polar_major) and polar_aacids  
echo polar_contacts_major
pause

define nonpolar_contacts_minor within(4.5, nonpolar_minor) and nonpolar_aacids 
echo nonpolar_contacts_minor
pause
define polar_contacts_minor within(3.5, polar_minor) and polar_aacids 
echo polar_contacts_minor
pause


