Audit cleanup: remove dead param, dead commented code, stale docs

- Drop dead mask_unknown_residues=true from default(_rescore).groovy
  (param removed from Params.groovy in 1b7809a6, 2019; configs missed)
- Rewrite distro/models/readme.md to match models on disk (add rescore_2024,
  rescore_conservation; remove nonexistent conservation.model)
- Remove broken documentation/rescoring.md link from distro/README.md
- distro/config/readme.md: drop nonexistent working.groovy reference,
  fix github link master->develop
- Delete dead commented-out method bodies in PdbUtils, RPlotter,
  PredictionVisualizer
- Fix typo in Main.groovy javadoc

distro/config/default.groovy

@@ -119,8 +119,6 @@ import cz.siret.prank.program.params.Params
      */
     neutral_points_margin = 5.5
 
-    mask_unknown_residues = true
-
     /**
      * chem. properties representation neighbourhood radius in A
      */

distro/config/default_rescore.groovy

@@ -111,8 +111,6 @@ import cz.siret.prank.program.params.Params
      */
     neutral_points_margin = 5.5
 
-    mask_unknown_residues = true
-
     /**
      * chem. properties representation neighbourhood radius in A
      */

distro/config/readme.md

@@ -11,7 +11,7 @@ Parameters can be then overridden in a custom config file (`-c <config.file>`) o
 
 Parameters can be set in 2 ways:
 1. on the command line `-<param_name> <value>`
-2. in config groovy file specified with `-c <config.file>` (see working.groovy for an example... `prank -c example.groovy`). 
+2. in config groovy file specified with `-c <config.file>` (see `example.groovy` for an example: `prank -c example.groovy`). 
 
 Parameters on the command line override those in the config file, which override defaults.
 
@@ -23,4 +23,4 @@ Parameter application priority (last wins):
 5. parameters on the command line
 
 To see a comprehensive list of all possible params see `Params.groovy` in the source code:
-https://github.com/rdk/p2rank/blob/master/src/main/groovy/cz/siret/prank/program/params/Params.groovy
+https://github.com/rdk/p2rank/blob/develop/src/main/groovy/cz/siret/prank/program/params/Params.groovy

distro/models/readme.md

@@ -1,22 +1,26 @@
 
 # Directory with pre-trained models
 
-Prank looks here for the model specified by (`-model`/`-m`) parameter.
+Prank looks here for the model specified by the `-model` / `-m` parameter.
 
-The model should be always used only in combination with the parameters or config file that was used to train it.
+The model should always be used only in combination with the parameters or config file that was used to train it.
 I.e.: the feature extraction has to be executed with the same parameters.
 
 ## List of models
 
 ### P2Rank (pocket prediction)
 
-* `default.model`      ... trained on `chen11-fpocket.ds` using config `default.groovy`
-* `conservation.model`  ... trained on `chen11-fpocket.ds` using config `conservation.groovy`
-* `conservation_hmm.model`  ... trained on `chen11-fpocket.ds` using config `conservation_hmm.groovy`
-* `alphafold.model`  ... trained on `chen11-fpocket.ds` using config `alphafold.groovy`
-* `alphafold_conservation_hmm.model`  ... trained on `chen11-fpocket.ds` using config `alphafold_conservation_hmm.groovy`
+* `default`                     ... config `default.groovy`
+* `conservation_hmm`            ... config `conservation_hmm.groovy` (uses HMMER-based sequence conservation)
+* `alphafold`                   ... config `alphafold.groovy` (tuned for AlphaFold / NMR / cryo-EM structures, no b-factor)
+* `alphafold_conservation_hmm`  ... config `alphafold_conservation_hmm.groovy`
 
 ### PRANK (pocket rescoring)
 
-* `default_rescore.model` ... trained on chen11-fpocket.ds using config `default_rescore.groovy`
+* `default_rescore`             ... config `default_rescore.groovy`
+* `rescore_2024`                ... config `rescore_2024.groovy` (newer model, recommended for AlphaFold / NMR / cryo-EM)
+* `rescore_conservation`        ... config `rescore_conservation.groovy` (rescoring with conservation features)
 
+## Auxiliary
+
+* `_score_transform/` — score-transformer JSON files (probability calibration, z-score) loaded by the models above.

src/main/groovy/cz/siret/prank/program/Main.groovy

@@ -462,7 +462,7 @@ class Main implements Parametrized, Writable {
     }
 
     /**
-     * @return false if successful, true it there was some (recoverable) error during execution
+     * @return false if successful, true if there was some (recoverable) error during execution
      */
     boolean run() {
 

src/main/groovy/cz/siret/prank/program/visualization/PredictionVisualizer.groovy

@@ -55,21 +55,6 @@ class PredictionVisualizer implements Parametrized {
         pdb.close()
     }
 
-//    void conditionallyZipVisualizations(List<File> fileList, String label) {
-//        if (params.zip_visualizations) {
-//            List<File> fileList = [new File(pmlf), new File(pointsf)]
-//            if (params.vis_copy_proteins) {
-//                fileList.add(new File(proteinfAbs))
-//            }
-//            File zipFile = new File("$outdir/${label}_visualization.zip")
-//            NameMapper mapper = { String fileName ->
-//                return fileName.endsWith(".pml") ? fileName : "data/".concat(fileName)
-//            }
-//            ZipUtil.packEntries(fileList.toArray(new File[0]) as File[], zipFile, mapper)
-//            fileList.forEach({ File f -> f.delete() })
-//        }
-//    }
-
 //===========================================================================================================//
 
     void generateVisualizations(Dataset.Item item, ModelBasedRescorer rescorer, PredictionPair pair) {

src/main/groovy/cz/siret/prank/utils/PdbUtils.groovy

@@ -391,78 +391,4 @@ class PdbUtils {
         return newS;
     }
 
-
-
-//    /**
-//     * Original code from Biojava 5.4 for comparison
-//     * see https://github.com/biojava/biojava/blob/9dcddeb0072ecc29aca8d8b1d43c3b18a430ac30/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java#L1286
-//     *
-//     * Reduce a structure to provide a smaller representation . Only takes the
-//     * first model of the structure. If chainName is provided only return a
-//     * structure containing that Chain ID. Converts lower case chain IDs to
-//     * upper case if structure does not contain a chain with that ID.
-//     *
-//     * @param s
-//     * @param chainId
-//     * @return Structure
-//     * @since 3.0
-//     * @deprecated Use {@link StructureIdentifier#reduce(Structure)} instead (v. 4.2.0)
-//     */
-//    @Deprecated
-//    public static Structure getReducedStructure(Structure s,
-//                                                String chainId) throws StructureException {
-//        // since we deal here with structure alignments,
-//        // only use Model 1...
-//
-//        Structure newS = new StructureImpl();
-//        newS.setPDBCode(s.getPDBCode());
-//        newS.setPDBHeader(s.getPDBHeader());
-//        newS.setName(s.getName());
-//        newS.setSSBonds(s.getSSBonds());
-//        newS.setDBRefs(s.getDBRefs());
-//        newS.setSites(s.getSites());
-//        newS.setBiologicalAssembly(s.isBiologicalAssembly());
-//        newS.setEntityInfos(s.getEntityInfos());
-//        newS.setSSBonds(s.getSSBonds());
-//        newS.setSites(s.getSites());
-//
-//        if (chainId != null)
-//            chainId = chainId.trim();
-//
-//        if (chainId == null || chainId.equals("")) {
-//            // only get model 0
-//            List<Chain> model0 = s.getModel(0);
-//            for (Chain c : model0) {
-//                newS.addChain(c);
-//            }
-//            return newS;
-//
-//        }
-//
-//        Chain c = null;
-//        try {
-//            c = s.getChainByPDB(chainId);
-//        } catch (StructureException e) {
-//            logger.warn(e.getMessage() + ". Chain id " + chainId
-//                    + " did not match, trying upper case Chain id.");
-//            c = s.getChainByPDB(chainId.toUpperCase());
-//
-//        }
-//        if (c != null) {
-//            newS.addChain(c);
-//            for (EntityInfo comp : s.getEntityInfos()) {
-//                if (comp.getChainIds() != null
-//                        && comp.getChainIds().contains(c.getChainID())) {
-//                    // found matching entity info. set description...
-//                    newS.getPDBHeader().setDescription(
-//                            "Chain " + c.getChainID() + " of " + s.getPDBCode()
-//                                    + " " + comp.getDescription());
-//                }
-//            }
-//        }
-//
-//        return newS;
-//    }
-
-
 }

src/main/groovy/cz/siret/prank/utils/rlang/RPlotter.groovy

@@ -132,39 +132,6 @@ class RPlotter implements Parametrized {
         rexec.runCode(rcode, label, outdir)
     }
 
-//    @Deprecated
-//    void plot1DVariableOld(String name) {
-//
-//        int column = header.indexOf(name)
-//
-//        String tabf = "../"+Futils.shortName(csvfile) //FileUtils.relativize(csvfile, outdir)
-//
-//        String rcode = """
-//            if (!require("ggplot2")) {
-//                  install.packages("ggplot2", dependencies = TRUE, repos = "http://cran.us.r-project.org")
-//                  library(ggplot2)
-//            }
-//            library(scales)
-//
-//            r <- c("green4","green3","yellow","gold","red3")
-//
-//            data <- read.csv("$tabf")
-//
-//            xx = names(data)[1]
-//            yy = names(data)[${column+1}]
-//
-//            p <- ggplot(data, aes_string(x=xx, y=yy, colour=yy, fill = yy))
-//
-//            p + geom_bar(stat="identity", position = 'dodge', alpha = 3/4, color="gray20") + scale_fill_gradientn(colours=r) + theme(axis.text.x = element_text(angle = 340, hjust = 0))
-//
-//            fname <- paste(yy,".png", sep="")
-//            ggsave(file=fname, dpi=$dpi)
-//        """
-//        // to add line plot: p  +  geom_line(size = 1, color="gray40") + geom_point(shape=18, size=4, color="gray20")
-//
-//        rexec.runCode(rcode, name, outdir)
-//    }
-
     /**
      *
      * @param tablef  2d csv table