Mol2, SDF and XYZ File Parsers #418
Commits on Aug 24, 2022
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XYZFile working with single model, some change with regards
to model in get_structure function needed. MOL2File and SDFFile prepared now ...
Commits on Aug 25, 2022
Commits on Aug 27, 2022
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Added some small molecule files for testing, specifically
files with multiple models gained from conversion via openbabel
Commits on Aug 29, 2022
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Finally fucking (somewhat) finished the MOL2File class.
sybly atom types heuristic doesn't yet work though ...
Commits on Aug 30, 2022
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Mol2File test expanded, charges and sybyl_atom type reading
now seems to work. Also covering all elements in sybyl_atom_type now, although heuristic not fully working.
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forgot to commit changes on MOL2File before only pushed
changed tests ^^
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Modified test_mol so that only pdbx residues are tested
for pdbx residue consistency
Commits on Aug 31, 2022
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all file formats somewhat working, at least reading works for
xyz and sdf files. For mol2 files it works as long as the atom_name represents the element and not an atom_name like "CA"
Commits on Sep 1, 2022
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reading and writing of mol2 file now also works with atom_names
that are actual atom_names and not elements. Specifically this works with amino acids where the atom_names are written to the atom_name column. See TYR.mol2 for example in test cases.
Commits on Sep 2, 2022
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Mol test now passing without skipped for amino acids.
Before the logic for only doing that test when an amino acid in file name did create an empty list.
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Small change in XYZFile and also added all docstrings for
public functions. Internal functions and members have been made private.
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SD File read/write with AtomArray and AtomArrayStack,
as well as meta_information dictionaries working. Reading of datetime from header working. But besides that problems with read/write of header. These seem to stem from the fact that programs such as openbabel to not adher to the Chemical table file standard .. Omitting this for now as one can in principle get the header by acessing lines[1] -
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removing get_header and set_header from test as apprently
warning causes test suite to interpret this as failure..
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Forgot to implement functionality in load_structure and
save_structure. Cleaned up tests, also precision in XYZFiles did not match between loaded and stored.
Commits on Sep 4, 2022
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Update src/biotite/structure/io/ctab.py
Co-authored-by: Patrick Kunzmann <padix.key@gmail.com>
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Update src/biotite/structure/io/ctab.py
Co-authored-by: Patrick Kunzmann <padix.key@gmail.com>
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Update src/biotite/structure/io/general.py
Co-authored-by: Patrick Kunzmann <padix.key@gmail.com>
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Update src/biotite/structure/io/general.py
Co-authored-by: Patrick Kunzmann <padix.key@gmail.com>
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Update src/biotite/structure/io/general.py
Co-authored-by: Patrick Kunzmann <padix.key@gmail.com>
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Update src/biotite/structure/io/mol2/file.py
Co-authored-by: Patrick Kunzmann <padix.key@gmail.com>
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Bega pep8 checking + reformatting in file.py as well as
adding get_model_count function.
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Commits on Sep 12, 2022
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PEP8 checking on file.py in xyz, also added myself
to contributors list
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Added test for get_model_count in XYZFiles, found
some missing functionality with this (was not working properly before). Also made test_xyz.py conforming with PEP8 codestyle.
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Forgot contrib as well as changes to xyz file.
Made some changes also in conver to expose header get/set Also added tests for this.
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Retrieving file name from absolute path now done in a way
that it should also work with windows paths.
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Typo in retrieve_file_name_from_path, hopefully working now
with windows paths also...
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Commits on Sep 13, 2022
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Changes in test_mol2 (now also covers using model parameter
in get_structure for multi model files). Some cleanup...
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Changed warning when MOLFile reads timestamp entry and
datetime is not matching. Tried to negelect this warning in the test but somehow mark.filterwarnings has no effect.