v3.6.0 #43
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v3.6.0 #43
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This update includes the creation of new scripts to identify clashes between proteins and nucleic acids. It also combines the results from the Buccaneer and Nautilus prediction algorithms. This functionality has been integrated into the main model crafting process, further enhancing the prediction capabilities of our software. In addition, scores are calculated for each residue based on statistical data regarding Real Space Correlation Coefficients (RSCC) and B-factors.
This revision significantly alters the `combine_results.py` and `clashes.py` files, improving clash detection between protein and nucleic acid structures. It introduces an enumeration class for identifying structure types, helping to clarify the specification of residues to be removed. In addition, we've added explicit detection of clash 'zones' and included more detailed inline documentation for better understanding.
Clash and ClashZone classes were moved to separate file modelcraft/combine/types.py. The `identify_clash_zones` function is extended to group clashes in sequential keys and evaluate zones of clashes rather than individual pairs. New metrics for residues scoring were introduced in 'calculate_stats_per_residue' and 'score_from_key', which now consider differences in the electron density maps. In 'combine' residues are evaluated and removed by zones instead of individually.
Clash detection logic was refactored and moved to a separate file for better organization. Clash zones, groups of sequential keys where clashes occur, are now taken into account instead of individual clash pairs. Additionally, new scoring metrics have been introduced for residues within these zones, considering differences in the electron density maps. These changes have improved the efficiency and accuracy of clash detection and resolution.
…raft into combination-p-na
Changes to Xray Pipeline for better Protein Nucleic Acid Building
Merge 3.5.2 into complexes branch
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