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Shuettel7/mol2 import export #29

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mol2 import and export implemented.

main use case in current state: converting json files for small molecules to mol2 SYBYL format

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mol2 import and export are now implemented only for MOLECULE, ATOM, and BOND sections.
Currently, its main use is for the validation of atomtyping with small molecules from PubChem in the json format. Older tools do not implement the json format. But also, the mol2 SUBSTRUCTURES section is not well implemented in most tools. Therefore, the BALLjl implementation in this branch has been reduced to the MOLECULE, ATOM, and BOND sections as these are most frequently used.

@tkemmer tkemmer marked this pull request as draft January 13, 2023 11:57
@shuettel7
mol2 import export
f81db51 
ToDo: tests have shown => need to make import more flexible
@shuettel7
line import more flexible
c3ae68a 
Signed-off-by: Samuel Hüttel <[email protected]>
@shuettel7
omit "_balljl_export" in export file naming
0adb839 
Signed-off-by: Samuel Hüttel <[email protected]>
@shuettel7
clean up, removed Revise from Project.toml
e667290 
Signed-off-by: Samuel Hüttel <[email protected]>
@shuettel7
adapted for new properties in atom and bond
888bd45
@shuettel7
intermittent commit
cc406d5
@shuettel7
Last work on substructure, probably not needed for ligands / json files
c934ad6 
Signed-off-by: Samuel Hüttel <[email protected]>
@shuettel7
change import to only small files, no substructures
ecba25f 
Signed-off-by: Samuel Hüttel <[email protected]>
@shuettel7
removed Substructure from export
7a2f544 
Signed-off-by: Samuel Hüttel <[email protected]>
@shuettel7
mol2 name adapted with basename method
3779053 
Signed-off-by: Samuel Hüttel <[email protected]>
@shuettel7
export_mol2 update to naming with basename
77fa981 
Signed-off-by: Samuel Hüttel <[email protected]>
@shuettel7
export_mol2 updated naming and Charge property
aab50f8 
Signed-off-by: Samuel Hüttel <[email protected]>
@shuettel7
export_mol2, naming adapted for more flexibility with file formats
7e5811e 
Signed-off-by: Samuel Hüttel <[email protected]>
@shuettel7
mol2, pubchem_json, mol2_export test update from validation branch
fcd8d02
@shuettel7
mol2 file cleanup
6c1c5e3 
Signed-off-by: Samuel Hüttel <[email protected]>
@shuettel7 shuettel7 force-pushed the shuettel7/mol2_import_export branch from 1ef60f5 to 6c1c5e3 Compare January 27, 2023 14:04
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