Support ionic repulsion, parquet output, rename out file, and lots of bugfixes #10

y1zhou · 2025-02-17T02:58:50Z

Detection of repulsion between like charges
Support of parquet, json, and ndjson output formats
Added a -name flag in the CLI to rename the output file of contacts and sasa commands

Checks for polar contacts were skipped when hydrogen bond criteria are not satisfied
Better error messages when rings have missing atoms for finding the center and normal vector
Nomenclature mix of residue insertion codes and alternative locations; the two are now stored under separate columns (*_insertion and *_altloc) in the output files

Distance cutoff for T-shaped Pi-stacking lowered from 6Å to 5Å
Added hydrogen bond distance check to better differentiate Hbonds and polar contacts
Performance/memory footprint improvement by switching from 64-bit numbers to 32-bit
Logging is now less verbose

…tloc positions

y1zhou added 12 commits August 21, 2024 19:28

feat(contacts): add detection of repulsion between like charges

082e70c

fix(contacts): add check for hydrogen bond length upper limit

69e2407

refactor(contacts): reduce the amount of else None returns

3d976bb

fix(hbond): do not skip polar contact id when hbonds are not satisfied

772811d

feat(io): support parquet, json, and ndjson output formats

bcc5563

perf(io): no need to use f64 and i64 for saving results

38f3c09

feat(cli): allow renaming output file of contacts and sasa

4a4e816

feat(cli): modify logging levels to be less verbose by default

7121b57

fix(ring): skip ring calculation if atoms are missing

58a2f71

fix(parser): correctly parse residue insertion codes and conformer al…

d8b3239

…tloc positions

build(cargo): update dependencies

4f7c13f

docs: changelog for v0.4.0 release

d910d01

y1zhou merged commit c192255 into master Feb 17, 2025
1 check passed

y1zhou deleted the feat/pathology branch February 17, 2025 03:18

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