Reimplementation of Recollect #148
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-Fixed to use variables `input_type` and `output_type`
-This required the creation of a separate `recollect_legacy` function. This is in the same format of the normal `recollect` function
-This has been updated to use the `ml.loads` function allowing implementation of any file types. For testing, I used zip files containing mol2, xyz, pdb, and sdf files successfully -In the event that non-native molli file formats are used with the molli parser, the code will correctly error out indicating that openbabel should be used.
…o molecule objects
… various objects: - Added `-iconv` option to indicate if files in directories and zip folders should be read in as a `ConformerEnsemble` or `Molecule` - Changed `converter` to `output_conv` - Added extra possibilities to `output_conv` when the input_conversion is being written to a `ConformerLibrary` and was read in as a `Molecule` or it is being written to a `MoleculeLibrary` and was read in as a `ConformerEnsemble` - Added `LegacyMolliWarning` to account for unexpected behavior when recollecting an ensemble to molecule or molecule to ensemble with the `recollect_legacy` -
…mmand is used incorrectly
…nd `ml.loads`. -In addition, the backends were fixed such that they work exclusively with bytes
…into recollect-fix
esalx
approved these changes
Oct 15, 2024
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| self._path = Path(path) | |||
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| if not self._path.is_file() and readonly: | |||
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This may need to be addressed in the future. I can definitely see how extension-less files and directories can conflict here, but let's hope for the best.
Non-issue for now.
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In a previous pull request, the changes made to the recollect had been accidentally removed. I have patched this problem and reimplemented all of the original functionality. Here are some of the changes:
recollect_legacy. This functionality has been extended to allow the use of either base geometries or conformer ensembles. It also offers a new warning to indicate if there may be unexpected behavior when requesting a recollection.ml.dumpsandml.loadsfunctions, offering the full functionality to write any file type to directories through the utilization of the openbabel interfaceiconv, which allows things from directories or zip files to be read in as aMoleculeorConformerEnsemble. This also allows for a separate output conversion if for example aConformerEnsembleis read in and the output is aMoleculeLibrary, the firstConformerof theConformerEnsemblewill be read into theMoleculeLibraryZipCollectionandDirCollectionassociated with reading/writing have been fixedI have attached a variety of the commands associated with the tests I have run. If requested, I can also include the testing folders and directories utilized in this test. All tests appeared to behave as expected.
test_commands.txt
This pull request takes care of the issues #107, #123, and #136