refactor PDB loading
refactor PDB loading

The PDB loading logic has been split into smaller chunks which
makes it easier to extend. No intended functionality change.

biasmv/pv,CyrusBiotechnology/pv,CyrusBiotechnology/pv,yuhangwang/pv,yuhangwang/pv,biasmv/pv,biasmv/pv,Traksewt/pv,yuhangwang/pv,Traksewt/pv,Traksewt/pv,biasmv/pv,yuhangwang/pv,Traksewt/pv,CyrusBiotechnology/pv,CyrusBiotechnology/pv