Add O-Mannosylation to Sails #2
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Refined the statistical measures for alpha, beta, and gamma angles, as well as phi, psi, and omega torsions for several key residue linkages. Added new clusters for TRP-AMAN, MAN-SER, and MAN-THR with specific angle and torsion data to improve the accuracy and detail of molecular modeling.
Added the nodiscard attribute to the calculate_solvent_accessibility function to prevent ignoring its return value. This ensures critical solvent accessibility data is always utilized.
This commit introduces a new function, `find_o_mannosylation_sites`, which identifies O-mannosylation sites based on residue type and solvent accessibility. Additionally, minor formatting improvements for code readability were made.
Modified the donor_number initialization to check if the extracted character from donor_atom is a digit. If it is, convert the character to an integer; otherwise, set donor_number to 1. This prevents potential runtime errors from invalid conversions.
Included 'sails-solvent' header for solvent accessibility calculations. Modified test data paths and extended the test function to analyze solvent accessibility and O-mannosylation sites, recalculate the density maps, and save the updated structure to a file.
Added new residues SER and THR to data.json with their respective shapes, colors, and donor sets. Corrected the linkage pairs by swapping
Introduce an enum to manage glycosylation types and map respective functions for n_glycosylate, c_glycosylate, and o_mannosylate. Simplify argparse usage by replacing specific boolean options with a type selection.
This commit introduces a new function binding for `o_mannosylate_from_objects` in the Python Sails bindings. This will allow users to call the O-Mannosylation process directly from Python, similar to the existing N-Glycosylation and C-Glycosylation bindings.
Introduced a 'strict' parameter to refine thresholds for removing erroneous sugars in the `remove_erroneous_sugars` function. Added `o_mannosylate` function with solvent accessibility calculation. Updated the run_cycle function to accommodate the new strict mode parameter.
Eliminated redundant semicolons and cleaned up unused variables across multiple files for better code clarity and maintenance. Also improved error message formatting for consistency.
Clarified the term "Symbol Nomenclature for Glycans Diagram (SNFG)" and added an image example. Updated Automated Glycan Building with the new glycosylation type option and adjusted an example to reflect O-mannosylation.
Updated the function reference in the glycosylation test to use `sails.Type.c_glycosylate` instead of `sails.c_glycosylate_from_objects` to match the new structure of the sails module. This improves code clarity and consistency.
This change adds the `Type` class from the `glycosylate` module to the top-level imports in the `sails` package. This allows `Type` to be directly accessible, improving code modular
Deleted an unnecessary entry involving donorResidue "TRP" and acceptorResidue "AMAN" from the data.json file. This helps in reducing clutter and maintaining relevance in the dataset.
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Description
-typecommand line argument tosailsbinary to specify glycosylation type