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87 lines
2.5 KiB
Markdown
87 lines
2.5 KiB
Markdown
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## Breaking changes
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### Introduction
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This file collects backwards incompatible changes that have potential to break code that uses P2Rank.
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These include:
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* changes in the command line interface
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* changes in the input/output format
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* changes in default behaviour
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All changes of that type should be rare and should be all listed here.
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## List of changes
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### 2.5.1
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none
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### 2.5
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none
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### 2.4.2
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none
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### 2.4.1
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###### Prediction
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* 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`.
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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.
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See issue #59.
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###### Training new models
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* Type of parameter `-ignore_het_groups` changed from `Set<String>` to `List<String>`
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### 2.4
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###### Prediction
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none
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###### Training new models
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* Removed deprecated parameters `-conservation_origin` and `-load_conservation_paths`
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### 2.3
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###### Prediction
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none
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###### Training new models
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* parameter `-extra_features` was renamed to `-features`
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* command line format of parameters values with type `List<String>` and `List<List<String>>` has changed
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* now only comas `,` are delimeters and inner parentheses are respected
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* before `.` was used as an alternative delimeter and delimeter for inner lists, now it is part of element value
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* Examples:
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* `'(a.b.c)'` was interpreted as list of 3 elements, now it defines list of 1 element: `a.b.c`
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* list of lists value `'((a.b.c),(d.e))'` should be changed to `'((a,b,c),(d,e))'`
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* Changes in `csv_file_feature`
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* renamed to `csv`
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* introduced parameter `-feat_csv_columns` (type: `List<String>`).
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Names of enabled value columns from csv files must be listed here.
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Columns not listed are ignored.
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* Example: if you were working with one directory of csv files with one value column named `pdbekb_conservation`,
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you must now run the program with `-feat_csv_columns '(pdbekb_conservation)'`
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* introduced parameter `-feat_csv_ignore_missing` (type: `boolean`, default: `false`). If true, then feature ignores:
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* missing csv files for proteins
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* missing value columns
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* missing rows for atoms and residues
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### 2.2
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* parameter `-conservation_dir` (type: `String`) was renamed to `-conservation_dirs` (type: `List<String>`)
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* column `probability` was added to `*_predictions.csv` output file
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