## 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`](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`](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