get_area calculates the surface area in square Angstroms of the selection given.
get_area sele [,state[, load_b ]]
cmd.get_area(string selection="(all)", load_b=0, state=0 )
# load components separately load my_ligand.pdb load my_target.pdb # get hydrogens onto everything (NOTE: must have valid valences on the ligand...) h_add # make sure all atoms within an object occlude one another flag ignore, none # use solvent-accessible surface with high sampling density set dot_solvent, 1 set dot_density, 3 # measure the components individually ligand_area=cmd.get_area("my_ligand") target_area=cmd.get_area("my_target") # create the complex create my_complex, my_ligand my_target # measure the complex complex_area=cmd.get_area("my_complex") # now print results print ligand_area print target_area print complex_area print (ligand_area + target_area) - complex_area
# example usage of load_b # select some organic small molecule select ligand, br. first organic # get its area and load it into it's b-factor column get_area ligand, load_b=1 # print out the b-factor/areas per atom iterate ligand, print b