import os
from chimera import openModels, Molecule
from chimera import runCommand as rc # use 'rc' as shorthand for runCommand
from chimera import replyobj # for emitting status messages
from chimera import selection

# change to folder with data files
os.chdir("C:/Users/Navya Shilpa/Desktop/thesis/All_Proteins/nr-bilogicalunits/working")

# gather the names of .pdb files in the folder
file_names = [fn for fn in os.listdir(".") if fn.endswith(".pdb1")]

# loop through the files, opening, processing, and closing each in turn
for fn in file_names:
        replyobj.status("Processing " + fn) 
        rc("open " + fn)
        rc("delete solvent")
        rc("select")
        rc("surf") # surface receptor
        outfn = open("testing.csv", "w")        
        residues = selection.currentResidues()
        for m in openModels.list(modelTypes=[Molecule]):
            for r in m.residues:
                for a in r.atoms:
                        try:
                                sas=a.areaSAS
                                bf=a.bfactor
                        except AttributeError:
                                continue        
                        print>>outfn, a, sas, bf        
        outfn.close()           
        rc("close all")