Feature PDBx/Gemmi #135
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Feature PDBx/Gemmi #135
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…IF files. This is an early stage, and currently only demonstrates that the package can be linked in and a file parsed. WIP
…er to fully interoperate with gemmi rather than hiding it in SireIO/PDBx. WIP
Have sorted the molecules by their entity type. WIP
This seems to work well. Now need to back-convert from sire to gemmi.
…ow need to actually create the gemmi::Structure from the System...
… gemmi or saving a pdbx file. Switched sire.load over to use cif for PDB codes if gemmi is supported. Also added support for the new PDB codes once they are available (automatically dropping back to the old codes for now)
… the way chains are handled
Added better tests that make sure a PDB and PDBx file give the same molecule (at least for the protein) Also check that conversion to and from gemmi gives the same number of atoms (more complex checks are difficult because of way chains and subchains are handled)
…erent platforms [ci skip]
…hen converting [ci skip]
the C++ library as it doesn't work on linux
PDBx/mmCIF format WIP [ci skip]
…into feature_format
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…ped by random numerical error [ci skip]
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Windows build failure is because the current Gemmi conda package has a static library that is built with whole program optimisation. This makes it binary incompatible with VS 2017. See this stackoverflow post: https://stackoverflow.com/questions/54664134/cannot-compile-unknown-flag-pdbrpc-in-p2 I’ll add a cmake compile Windows that checks for this and disables Gemmi until the dynamic library package is out (similar to how this is disabled in Linux and Mac) |
…re_format [ci skip]
neopentane to methane is correct [ci skip]
…this is useful! [ci skip]
…ad to weird
behaviour (the cutoff was silently ignored)
Now you can set the cutoff using strings, e.g. `cutoff="10 A"` or even
`cutoff="infinite"` or `cutoff="none"`
Added a `map.unset("option")` to unset options from a property map.
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…d a note about Gemmi support. [ci skip]
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This PR merges in the Gemmi conversion code. This allows interconversion between Gemmi and sire objects. This means we can now read and write PDBx/mmCIF files, including loading and saving custom metadata. The load function has been updated to use PDBx/mmCIF files by default is Gemmi is available, and support for new-style PDB codes is included.
develinto this branch before issuing this pull request (e.g. by runninggit pull origin devel): [y]Suggested reviewers:
@lohedges
Any additional context of information?
This PR includes the changes of
feature_optimise_leverso will minimise CI when we accept everything.This depends on the new Gemmi shared library package being created and uploaded to conda. That package isn't up yet, so some of the CI builds here will fail. You can test locally by building the gemmi conda package locally (the recipe builds the shared-library package). Ideally I'd like to get this code into the
2023.5.0release as it is self-contained and very useful. If the gemmi package isn't available then we may end up disabling it on unsupported platforms (MacOS, I think) and then enable it for all platforms in2023.5.1. Like OpenMM, Gemmi is only a runtime dependency - it only needs to be installed if the user wants PDBx/mmCIF support.(the LJ 12/6/4 code that is mentioned in the first commit was removed in later commit - it is not included at all in this PR)