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Feature format#126

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chryswoods wants to merge 26 commits intodevelOpenBioSim/sire:develfrom feature_formatOpenBioSim/sire:feature_formatCopy head branch name to clipboard

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Commits on Nov 11, 2023

• Working out how to add support for LJ C4 parameters

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• Adding in the stubs so I can play with writing a pdbx/cif parser

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• Added a PDBx parser which uses gemmi for reading and writing PDBx/mmCIF files. This

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• Using the gemmi structure object is much easier and will be more maintainable

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Commits on Nov 12, 2023

• Moved the gemmi integration to sire.convert, as it would be much better to fully interoperate

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• Have loaded the SireGemmi library and registered the reader and writer functions

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• Can now interoperate between (empty) sire.System and gemmi.Structure objects.

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• Cleaned up the interconversion - still only works for empty objects

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• Making progress - now beginning to add in all of the water molecules.

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• Not available for conda gemmi

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• Making a lot of progress now - can load up waters and non-proteins

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Commits on Nov 13, 2023

• Can now read a PDBx/mmcif file by converting it from a gemmi Structure.

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• Added in the calls to create a QStringList from a gemmi::Structure. Now need

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• Can now convert water molecules over to gemmi (and can save them to a .pdbx file)

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• Can use ensure_entities

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• Can now write molecules and proteins :-)

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• All multi-residue molecules are Polymers

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Commits on Nov 14, 2023

• Added proper (working) support for recording bonds when converting to gemmi

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• Adding in tests so that I can check the conversions. Need to clean up the way

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• Done a better job of handling entities

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• Pinned down version as gemmi is semverd, plus added more to the test

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Commits on Nov 15, 2023

• Attempting to fix some of the compile / link issues for gemmi on different platforms

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• Added a test if we need the extra files, which definitely fails well

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• Updating the docs - triggering a CI build :-)

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• Documented the gemmi integration, and also preserve the system name when converting

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• Manually adding in the C++ files we need from gemmi, and not linking to

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