fix pdbe's updated cifs parsing problem using forked biojava with new parseSites parsing param

build.gradle

@@ -22,7 +22,11 @@ apply plugin: "com.github.ben-manes.versions"   //  ./gradlew dependencyUpdates
 
 
 group = 'cz.siret'
+<<<<<<< HEAD
 version = '2.5.1-rc.1'
+=======
+version = '2.5.1-dev.3-parsFix'
+>>>>>>> 2e40ef0e (fix pdbe's updated cifs parsing problem using forked biojava with new parseSites parsing param)
 
 description = 'Ligand binding site prediction based on machine learning.'
 

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

@@ -28,13 +28,15 @@ class PdbUtils {
 
     static final FileParsingParameters PARSING_PARAMS = new FileParsingParameters()
     static {
-        PARSING_PARAMS.setAlignSeqRes(false);  // should the ATOM and SEQRES residues be aligned when creating the internal data model?
-        PARSING_PARAMS.setParseSecStruc(false);  // should secondary structure getByID parsed from the file
+        PARSING_PARAMS.setAlignSeqRes(false)  // should the ATOM and SEQRES residues be aligned when creating the internal data model?
+        PARSING_PARAMS.setParseSecStruc(false)  // should secondary structure getByID parsed from the file
 
         PARSING_PARAMS.setCreateAtomBonds(false)
         PARSING_PARAMS.setCreateAtomCharges(false)
         PARSING_PARAMS.setParseBioAssembly(false)
 
+        PARSING_PARAMS.parseSites = false  // using custom forked build with new parseSites param
+
         disableBiojavaFetching()
         //PARSING_PARAMS.setLoadChemCompInfo(Params.inst.biojava_load_chem_info); // info about modified amino acid residues, not available in BioJava4
     }

src/test/groovy/cz/siret/prank/domain/ProteinParsingTest.groovy

@@ -1,5 +1,6 @@
 package cz.siret.prank.domain
 
+import cz.siret.prank.utils.PdbUtils
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import org.junit.jupiter.api.Disabled
@@ -22,7 +23,10 @@ class ProteinParsingTest {
     void testParsePdbeUpdatedCif() {
         Protein protein = Protein.load("$DIR/4gqq.cif")
 
-        Protein protein2 = Protein.load("$DIR/4gqq_updated.cif")   // fails in 2.5, still fails with BioJava 7.1.4 and 7.2.0
+        PdbUtils.PARSING_PARAMS.parseSites = false  // using custom forked build with new parseSites param
+
+        //Protein protein2 = Protein.load("$DIR/4gqq_updated.cif")   // fails in 2.5, still fails with BioJava 7.1.4 and 7.2.2
+        Protein protein2 = Protein.load("$DIR/4gqq_updated_2025.cif")  // fails in 2.5, still fails with BioJava 7.1.4 and 7.2.2
     }
 
     @Test
@@ -35,7 +39,8 @@ class ProteinParsingTest {
     /**
      * https://github.com/rdk/p2rank/issues/77
      *
-     * 2.5 supposedly fails with org.rcsb.cif.EmptyColumnException: column pdbx_PDB_id_code is undefined
+     * P2Rank 2.5 (using BioJava 7.1.3) fails with org.rcsb.cif.EmptyColumnException: column pdbx_PDB_id_code is undefined
+     * Already fixed in BioJava 7.2.2
      */
     @Test
     void testParse8zz7Cif() {