sdf.gz files as input with stream read? #13
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RyanArntzUU
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I'm calculating descriptors for a relatively big sets of molecules (~500.000). Due to limited space on the system we're working on, all the files are gzipped. Loading this amount of molecules in a script takes a lot of memory and I read that stream read uses less memory. Does stream read decrease memory usage significantly? or just by a small amount?
When I tried using
python3 -m mordred /path/to/file.sdf.gz -s -o path/to/output/file.csv.gz
for a certain set of molecules, I noticed I couldn't input .sdf.gz files (0it [00:00, ?it/s]WARNING:root:cannot detect file format: path/to/file.sdf.gz
). Is there a way to input these files without decompressing them?Thanks in advance,
Ryan (Utrecht University)
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