p2rank/breaking-changes.md

Breaking changes

Introduction

This file collects backwards incompatible changes that have potential to break code that uses P2Rank.

These include:

• changes in the command line interface
• changes in the input/output format
• changes in default behaviour

All changes of that type should be rare and should be all listed here.

List of changes

2.6

Evaluation

• Ligand detection was fixed (e7fc457f) to include nucleotide ligands (GDP, GTP, ATP — classified by BioJava as NUCLEOTIDE) and amino-acid-derivative ligands (SHR-like — classified as AMINOACID) that were previously skipped because only GroupType.HETATM qualified. Any non-water group in a NONPOLYMER chain now qualifies regardless of GroupType. This changes the relevant-ligand set on datasets containing such ligands, which moves DCA/DCC numerator and denominator and thus the reported success rates.
• For additional internal evaluation-criterion fixes during the 2.6 dev cycle see documentation/dev/evaluation-metric-fixes-2.6.md.

Pocket-descriptors export (opt-in feature)

• Per-pocket descriptors -export_pocket_descriptors underwent a multi-column interface migration. The shipped default list now contains seven descriptors (previously six), adds principal_moments (a 3-column descriptor emitting principal_moments.lambda1/lambda2/lambda3), and reorders the existing six so num_* come first. Scripts parsing the descriptors CSV/Arrow/Parquet output by column name are unaffected; scripts parsing by column index need updating. See documentation/export-pocket-descriptors.md.
• New opt-in -vis_pocket_grid (renamed from -export_pocket_grid_pml) emits both PyMOL .pml and ChimeraX .cxc overlay scripts. The two viz-tuning knobs were renamed for namespace consistency: pocket_grid_vis_volume_radius → vis_pocket_grid_volume_radius and pocket_grid_vis_gaussian_iso → vis_pocket_grid_gaussian_iso. Old names hard-fail at startup with no aliases.

2.5.1

none

2.5

none

2.4.2

none

2.4.1

Prediction

• Scripts that execute P2Rank (shell script distro/prank and distro/prank.bat) no longer redirect log (stderr stream) to the file distro/log/prank.log. Instead, they write stderr to the console. This was done to avoid P2Rank writing to the installation directory by default, which may be forbidden on some systems. See issue #59.

Training new models

• Type of parameter -ignore_het_groups changed from Set<String> to List<String>

2.4

Prediction

none

Training new models

• Removed deprecated parameters -conservation_origin and -load_conservation_paths

2.3

Prediction

none

Training new models

• parameter -extra_features was renamed to -features
• command line format of parameters values with type List<String> and List<List<String>> has changed
  • now only comas , are delimeters and inner parentheses are respected
  • before . was used as an alternative delimeter and delimeter for inner lists, now it is part of element value
  • Examples:
    • '(a.b.c)' was interpreted as list of 3 elements, now it defines list of 1 element: a.b.c
    • list of lists value '((a.b.c),(d.e))' should be changed to '((a,b,c),(d,e))'
• Changes in csv_file_feature
  • renamed to csv
  • introduced parameter -feat_csv_columns (type: List<String>). Names of enabled value columns from csv files must be listed here. Columns not listed are ignored.
    • Example: if you were working with one directory of csv files with one value column named pdbekb_conservation, you must now run the program with -feat_csv_columns '(pdbekb_conservation)'
  • introduced parameter -feat_csv_ignore_missing (type: boolean, default: false). If true, then feature ignores:
    • missing csv files for proteins
    • missing value columns
    • missing rows for atoms and residues

2.2

• parameter -conservation_dir (type: String) was renamed to -conservation_dirs (type: List<String>)
• column probability was added to *_predictions.csv output file