secondary structure in pdb_class.py

[pbuslaev]

In def SecondaryStructure(file1): there is no need to identify prevStruct in a separate loop. It should be merged into the main loop.

[pbuslaev]

Could it potentially happen that there are two identical keys here 'phi[res+resid+segid] = phi_angle'?

[pbuslaev]

if ("Coil" in secStruct or "Turn" in secStruct) and (res=="GLY" and phi_angle > prs.ZERO_ANGLE and phi_angle!=prs.FULL_ANGLE):
     phiangle = phi_angle
     if phiangle==prs.FULL_ANGLE:
          phiangle=0

It looks like the inner if should not be accessible

[pbuslaev]

This could be merged in one elif

            elif secStruct != currentSecStructure:
                counter+=1
                phiangle = line[42:51].strip()
                if float(phiangle)==prs.FULL_ANGLE:
                    phiangle=0
                secStructure.write(res+resid+segid+"\t"+secStruct+str(counter)+"\t"+str(phiangle)+"\n")
                currentSecStructure = secStruct
            else:
                secStructure.write(res+resid+segid+"\t"+secStruct+str(counter)+"\t"+str(phi_angle)+"\n")
            currentAngle = phi_angle

[pbuslaev]

Why there are two versions of parsing phi files? Which is used in the end. We should remove unnecessary parts from the code.