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Add Bioexcel cv19 database #1853

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merged 20 commits into from
Apr 9, 2024
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jamesmkrieger
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We now have functions to fetch, convert (using mdtraj) and parse files from the BioExcel-CV19 simulation database.

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This needs tests too. We're also missing tests for parsePSF and writePSF that should be added too

@jamesmkrieger jamesmkrieger marked this pull request as draft March 28, 2024 14:50
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We now have tests for helper functions, structure functions and topology functions. We still need them for trajectory ones.

For convert xtc to dcd, we will also need a data file. It may also be good to move this more general function somewhere else, but probably it's fine.

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Try conda-forge mdtraj and find stringio fix

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Try conda-forge mdtraj and find stringio fix

conda-forge mdtraj was tried before. Python 2 just can't support either version.

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And there are still more places to check for seed alignment not full too

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Try conda-forge mdtraj and find stringio fix

not sure what happened with the stringio thing but it seems ok again

@jamesmkrieger jamesmkrieger marked this pull request as ready for review April 9, 2024 07:41
@jamesmkrieger jamesmkrieger merged commit 434c1ea into prody:master Apr 9, 2024
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@jamesmkrieger jamesmkrieger deleted the bioexcel_cv19 branch April 9, 2024 14:19
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