Memory Error Python while processing large database

Question

When I run this on Pycharm 4 on windows I got an error in this code:

PDBSumWWW = urllib.urlopen("https://www.ebi.ac.uk/thornton-srv/databases/pdbsum/data/seqdata.dat")
PDBSum = PDBSumWWW.read().splitlines()
PDBSumWWW.close()

This is the error message:

Traceback (most recent call last): File "C:/Users/LuisAlberto/PycharmProjects/MSc/SeqPDBSumIRIndex.py", line 98, in main() File "C:/Users/LuisAlberto/PycharmProjects/MSc/SeqPDBSumIRIndex.py", line 40, in main PDBSum = PDBSumWWW.read().splitlines() MemoryError

However when running in on a Macbook Air it doesnt happen.

how do I get over this?

Answer 1

This is the most simple solution that I can think of to solve your problem.
In this solution the for loop will iterate over every line in the database.
every line will be assigned to the line variable.

PDBSumWWW = urllib.urlopen("https://www.ebi.ac.uk/thornton-srv/databases/pdbsum/data/seqdata.dat")
for line in PDBSumWWW:
    # Do necessary calculations. 
PDBSumWWW.close()