update to AlphaFold v6 files

Author: Sebastian

README.md

@@ -146,7 +146,7 @@ not overloaded, but rather will only accept `String` values while in `entry.id`
 ```Java
 class Demo {
     public static void main(String[] args) {
-        String id = "AF-Q76EI6-F1-model_v4";
+        String id = "AF-Q76EI6-F1-model_v6";
 
         CifFile cifFile = CifIO.readFromURL(new URL("https://alphafold.ebi.ac.uk/files/" + id + ".cif"));
         MmCifFile mmCifFile = cifFile.as(StandardSchemata.MMCIF);

src/main/java/org/rcsb/cif/Demo.java

@@ -120,7 +120,7 @@ private static void buildModel() throws IOException {
     }
 
     private static void convertAlphaFold() throws IOException {
-        String id = "AF-Q76EI6-F1-model_v4";
+        String id = "AF-Q76EI6-F1-model_v6";
 
         CifFile cifFile = CifIO.readFromURL(new URL("https://alphafold.ebi.ac.uk/files/" + id + ".cif"));
         MmCifFile mmCifFile = cifFile.as(StandardSchemata.MMCIF);

src/test/java/org/rcsb/cif/ReaderTest.java

@@ -104,7 +104,7 @@ void shouldHonorFileFormatAndFailWhenMismatching2() throws ParsingException {
 
     @Test
     void whenReadingAlphaFoldText_thenConfidenceScoresAvailable() throws IOException {
-        String id = "AF-Q76EI6-F1-model_v4";
+        String id = "AF-Q76EI6-F1-model_v6";
         InputStream inputStream = TestHelper.getInputStream("cif/" + id + ".cif");
         MmCifFile cifFile = CifIO.readFromInputStream(inputStream).as(StandardSchemata.MMCIF);
 
@@ -119,11 +119,11 @@ void whenReadingAlphaFoldText_thenConfidenceScoresAvailable() throws IOException
 
     @Test
     void whenReadingStringWithEmptyQuotation_thenValueAvailable() throws IOException {
-        String id = "AF-O49373-F1-model_v4";
+        String id = "AF-O49373-F1-model_v4"; // this is a quirk in the v4 files only
         InputStream inputStream = TestHelper.getInputStream("cif/" + id + ".cif");
         MmCifFile cifFile = CifIO.readFromInputStream(inputStream).as(StandardSchemata.MMCIF);
 
-        String gene = cifFile.getFirstBlock().getCategory("ma_target_ref_db_details").getColumn("gene_name").getStringData(0);
+        String gene = cifFile.getFirstBlock().getMaTargetRefDbDetails().getGeneName().get(0);
         assertEquals("''cytochrome P450", gene, "Gene name with additional quotes not parsed correctly");
     }
 

src/test/java/org/rcsb/cif/WriterTest.java

@@ -254,7 +254,7 @@ void whenReading5E_thenNotTreatedAsScientificNumber() throws IOException {
     @Test
     void whenReadingChecksum_thenNotTreatedAsInt() throws IOException {
         // might treat the CRC64 in `_ma_target_ref_db_details.seq_db_sequence_checksum     0197355516942160` as int
-        MmCifFile cifFile = CifIO.readFromInputStream(TestHelper.getInputStream("cif/AF-P41068-F1-model_v4.cif"))
+        MmCifFile cifFile = CifIO.readFromInputStream(TestHelper.getInputStream("cif/AF-P41068-F1-model_v6.cif"))
                 .as(StandardSchemata.MMCIF);
         assertEquals("0197355516942160", cifFile.getFirstBlock().getMaTargetRefDbDetails().getSeqDbSequenceChecksum().get(0));
         assertNotNull(CifIO.writeBinary(cifFile));