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Mol2, SDF and XYZ File Parsers#418

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entropybit wants to merge 39 commits intobiotite-dev:mainbiotite-dev/biotite:mainfrom entropybit:masterentropybit/biotite:masterCopy head branch name to clipboard

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Commits on Aug 24, 2022

• XYZFile working with single model, some change with regards

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Commits on Aug 25, 2022

• XYZFile get_structure so far working (yet tests are not passing ...)

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Commits on Aug 26, 2022

• xyz file working with reading multiple models

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• XYZFile finally fully working with tests

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Commits on Aug 27, 2022

• XYZFile cleaning up for production code ...

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• Added some small molecule files for testing, specifically

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Commits on Aug 29, 2022

• Finally fucking (somewhat) finished the MOL2File class.

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Commits on Aug 30, 2022

• mol2 tests working again

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• Mol2File test expanded, charges and sybyl_atom type reading

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• forgot to commit changes on MOL2File before only pushed

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• Modified test_mol so that only pdbx residues are tested

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Commits on Aug 31, 2022

• all file formats somewhat working, at least reading works for

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Commits on Sep 1, 2022

• reading and writing of mol2 file now also works with atom_names

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Commits on Sep 2, 2022

• Mol test now passing without skipped for amino acids.

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• Small change in XYZFile and also added all docstrings for

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• XYZFile and MOL2File ready.

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• SD File read/write with AtomArray and AtomArrayStack,

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• removed small previous change in test_mol

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• Merge branch 'master' into master

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• removing get_header and set_header from test as apprently

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• Forgot to implement functionality in load_structure and

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Commits on Sep 4, 2022

• Update src/biotite/structure/io/ctab.py

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• Update src/biotite/structure/io/ctab.py

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• Update src/biotite/structure/io/general.py

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• Update src/biotite/structure/io/general.py

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• Update src/biotite/structure/io/general.py

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• Update src/biotite/structure/io/mol2/file.py

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• Bega pep8 checking + reformatting in file.py as well as

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• Merge branch 'master' of github.com:entropybit/biotite

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Commits on Sep 12, 2022

• PEP8 checking on file.py in xyz, also added myself

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• Added test for get_model_count in XYZFiles, found

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• Forgot contrib as well as changes to xyz file.

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• Retrieving file name from absolute path now done in a way

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• Typo in retrieve_file_name_from_path, hopefully working now

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• MOL2File all files have conformity to PEP8 now.

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Commits on Sep 13, 2022

• Changes in test_mol2 (now also covers using model parameter

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• Changes in sybyl_atom_type heuristic

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• Changed warning when MOLFile reads timestamp entry and

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Commits on Sep 14, 2022

• Date parsing now works in header test.

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