pharmcas calculates your GPA in different subjects like physics, biology, chemistry, etc. they also group them together into science and non science. It's up to the individual school to make their own prepharmacy grouping.
Usually when you fill out a supplemental application for a school, they make you list all the prerequisite courses and sometimes have you calculate a pre-req gpa. It all depends on the school.
this is the thing that i hate that pharmcas calculates everything its extremely stupid and annoying and unfair bc someone who takes biochem and makes a B compared to someone who takes environmental science and makes an A will have a lower GPA. due to the fact there are so many applicants some school just fly thorugh applications and just look at gpa then once the see the 3.5 or more they look more into the classes and see if the pre-req is met while that student who met the pre-req and went beyond with harder classes is looked down upon.