The building has been so extensively remodeled that it's pretty much impossible to guess that a railroad was ever there.

The entrances to the old tunnel thru Potrero Hill are now sealed and hidden by apartments and condos.
A former yard at the north end is now the building that houses Bed & Bath Trader joes and other shops. The yard near the waterfront on the south east I believe is now the site of the Muni Metro east yard and shops.

I believe that in one of the Dirty Harry movies or maybe Streets of SF there was a chase scene that showed a WP switch engine working in the freight shed area.

The old Mission Bay yards are now the location of UCSF medical Center and all the old Santa Fe SP tracks down 16th are gone but there are still two former round end streamlined passenger cars converted to offices around 16th and deHaro partially visible from the street

just about all the tracks near the train station and south of market are gone and many other indusrial buildings have been remodeled or torn down and replaced by condos