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Shuettel7/mol2 import export#29

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shuettel7 wants to merge 15 commits intohildebrandtlab:developfrom
shuettel7:shuettel7/mol2_import_export
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Shuettel7/mol2 import export#29
shuettel7 wants to merge 15 commits intohildebrandtlab:developfrom
shuettel7:shuettel7/mol2_import_export

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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
ToDo: tests have shown => need to make import more flexible
Signed-off-by: Samuel Hüttel <shuettel@students.uni-mainz.de>
Signed-off-by: Samuel Hüttel <shuettel@students.uni-mainz.de>
Signed-off-by: Samuel Hüttel <shuettel@students.uni-mainz.de>
Signed-off-by: Samuel Hüttel <shuettel@students.uni-mainz.de>
Signed-off-by: Samuel Hüttel <shuettel@students.uni-mainz.de>
Signed-off-by: Samuel Hüttel <shuettel@students.uni-mainz.de>
Signed-off-by: Samuel Hüttel <shuettel@students.uni-mainz.de>
Signed-off-by: Samuel Hüttel <shuettel@students.uni-mainz.de>
Signed-off-by: Samuel Hüttel <shuettel@students.uni-mainz.de>
Signed-off-by: Samuel Hüttel <shuettel@students.uni-mainz.de>
Signed-off-by: Samuel Hüttel <shuettel@students.uni-mainz.de>
@shuettel7 shuettel7 force-pushed the shuettel7/mol2_import_export branch from 1ef60f5 to 6c1c5e3 Compare January 27, 2023 14:04
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