define ahelix 19-36:A
echo The chosen alpha-helix is defined as "ahelix"
define nitrox (oxygen, nitrogen) and ahelix
echo The array of oxygen and nitrogen atoms from ahelix is defined as "nitrox"
define carbsulph (carbon, sulphur) and (not backbone) and ahelix
echo The array of side-chain carbon and sulphur atoms not from ahelix is defined as "carbsulph"                                                                                
define othnitrox (oxygen, nitrogen) and not ahelix                                                             
echo The array of oxygen and nitrogen atoms not from ahelix is defined as "othnitrox"               
define othcarbsulph (carbon, sulphur) and (not backbone) and not ahelix                                         
echo The array of side-chain carbon and sulphur atoms not from ahelix is defined as "othcarbsulph"
define hydbonds within (3.7, nitrox) and  othnitrox
echo The array of atoms not from ahelix connected with ahelix with hydrogen bonds defined as "hydbonds"
define hydrophob within (5.0, carbsulph) and othcarbsulph
echo The array of atoms not from ahelix connected with ahelix with hydrophobic bonds defined as "hydrophob"