Extract SS with chain WITHOUT Biopython

Extract SS with chain WITHOUT Biopython

0

Hello, I have a list of 150 DSSP files from 150 PDB IDs with their chain that I need to obtain the SS from that are specific to the chain in question. I need to create a simple for loop by opening the file and parsing it. I have started here, but I am not sure how else to continue:

basepath = "/Users/data/Desktop/DSSP/"
for filename in os.listdir(basepath):
    if filename.endswith(".dssp"):
        # print(os.path.join("./DataFiles", filename))
        dssp = (filename)
        # dsspsplit = dssp.split()
        # print(type(dsspsplit))

        with open(basepath + filename) as openfile:
            for line in openfile:
                # extract sequence and secondary structure from the DSSP tuple
                sequence="".join(dssp.aa)
                sec_structure = []
                # for i in range(len(dsspsplit.aa)):
                #     s = dsspsplit.struct[i][2]
                #     if s == ' ':
                #         s="U"
                #     structs.append(s)

            ss="".join(structs)
            # tco = ','.join(dssp.getTCO())
            # kappa=",".join(dssp.getKAPPA())
            # alpha=",".join(dssp.getALPHA())
            # phi = ','.join(dssp.getPHI())
            # psi = ','.join(dssp.getPSI())


biopython


parse


dssp

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