define str 50-78:c
echo The chosen strands of alpha-spiral is defined as "str".
define oxy_nitro str and (oxygen, nitrogen)
echo The set of oxygen and nitrogen atoms of "alpha" is defined as "oxy_nitro".
define carb_sulph str and (carbon, sulphur) and not *.CA
echo The set of carbon and sulphur atoms of str's residues' side strands is defined as "carb_sulph".
define other_oxy_nitro not str and (oxygen, nitrogen) and protein
echo The set of oxygen and nitrogen atoms of none alpha is defined as "other_oxy_nitro".
define other_carb_sulph not str and (carbon, sulphur) and not *.CA
echo The set of carbon and sulphur atoms of none str's residues' side strands is defined as "other_carb_sulph".
define hydrobond oxy_nitro and within(3.7, (within(3.7, oxy_nitro) and not oxy_nitro and (oxygen,nitrogen)))
echo The set of oxygen and nitrogen atoms of str which make up hydrogen bonds with none str's oxygen and nitrogen atoms is defined as "hydrobond".
define carb (carbon and not *.CA,sulphur) and str
define hydrofob carb and within(5.0, within(5.0, carb) and not carb and (carbon and not *.CA, sulphur))
echo The set atoms of alpha which make up hydrophob interactions with none alpha's atoms is defined as "hydrofob".