Computational Time for obspectrophore in Open Babel?

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10.3 years ago

dxu108 • 0

I apologize in advance if this question is naive/simple. I am currently running the Open Babel command obspectrophore as follows:

obspectrophore -i tester.sdf

where tester.sdf is an SDF file generated from the following FASTA sequence:

MDAATTRVGLTDLTFRLLRESFADAVSWVAKNLPARPAVPVLSGVLLTGSDNGLTISGFDYEVSAEAQVG

Running the command above took 5+ minutes to complete. Is this normal or is there some way (using a different file format/modifying settings) that I can obtain faster spectrophore results?

Thanks in advance!

feature extraction spectrophore open babel • 1.7k views

ADD COMMENT • link updated 10.2 years ago by Biostar 20 • written 10.3 years ago by dxu108 • 0

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"On a personal computer equipped with an i7-5500U processor with 12 GB of main memory, the Open Babel version runs fastest, with an average calculation speed of 36 ± 2 ms/molecule." https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5842169/ This is most likely the speed with small molecule not large ones.

ADD REPLY • link 5.5 years ago by db4 ▴ 10

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