def opm_mempos(opmpdbfn, geofn, ballfn):
""" get membrane position from opmdb pdb file
"""
geodat = IO.read_geo(geofn)
# an anchor residue used to find out the offset. it has no meaning
base_res_id = geodat['startingSNs'][0]
opmchain = IO.guess_chain(opmpdbfn, geodat)
for res in opmchain:
if res.get_id()[1] == base_res_id:
opm_base_z = res['CA'].get_coord()[2]
break
my_base_z = IO.read_balls(ballfn)[0].coords[2]
# offset from my ball coords to opm pdb coords
my_z_offset = opm_base_z - my_base_z
opm_half_thickness = abs( Bio.PDB.PDBParser().get_structure('MyStruct',opmpdbfn)[0] # structure and model
.get_list()[-1].get_list()[0] # last chain and first residue
.get_list()[0].get_coord()[2] ) # first atom and z coord
# my extracellular membrane position
my_extra_z = opm_half_thickness - my_z_offset
# my periplasm membrane position
my_peri_z = -opm_half_thickness - my_z_offset
return my_extra_z, my_peri_z, my_z_offset
