Changes between Version 1 and Version 2 of Ticket #175, comment 7


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Timestamp:
Jan 4, 2016, 5:35:43 PM (10 years ago)
Author:
Greg Couch

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  • Ticket #175, comment 7

    v1 v2  
    1 Was able to speed up parse_mmCIF_file by 1% with improvements to the generic table reading code.  Turns out that the big cost is tokenizing the pdbx_poly_seq_scheme table.  In 3j3q there are 3,758,832 values, which takes ~3.4% of the total time in parse_mmCIF_file -- on my computer that is .334 seconds out of 10.1 seconds (compared to 9.54 seconds for 7/15/15 build, not tokenizing pdbx_poly_seq_scheme gives similar times, so to Python, the time is closer to .6 seconds).
     1Was able to speed up parse_mmCIF_file by 1% with improvements to the generic table reading code.  Turns out that the big cost is tokenizing the pdbx_poly_seq_scheme table.  In 3j3q there are 3,758,832 values, which takes ~3.4% of the total time in parse_mmCIF_file -- on my computer that is .334 seconds out of 10.1 seconds (compared to 9.54 seconds for 7/15/15 build, not tokenizing pdbx_poly_seq_scheme gives similar times, so to Python, the time is closer to .6 seconds, ie., ~6%).
    22
    33The next step is to try to eliminate the need for that table.  It is used to map the mmCIF file's internal chain ids to the author's chain ids that ChimeraX keeps.