SCOP hack to force loading of MMTF

sbittrich · sbittrich · commit f36f82cb6018 · 2021-01-26T11:59:45.000-08:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
@@ -524,7 +524,8 @@ public Structure getStructureForDomain(ScopDomain domain, ScopDatabase scopDatab
 	public Structure getStructureForDomain(ScopDomain domain, ScopDatabase scopDatabase, boolean strictLigandHandling)
 			throws IOException, StructureException {
 		String pdbId = domain.getPdbId();
-		Structure fullStructure = getStructureForPdbId(pdbId);
+		// SMB 1/26/21 - forcing loading MMTF here - TODO why doesn't mmCIF/CIF/BCIF parsing work here?
+		Structure fullStructure = getStructureForPdbIdByMmtf(pdbId);
 		Structure structure = domain.reduce(fullStructure);
 
 		// TODO It would be better to move all of this into the reduce method,
@@ -800,6 +801,33 @@ public Structure getStructureForPdbId(String pdbId) throws IOException, Structur
 		}
 	}
 
+	/**
+	 * SCOP parsing depends on MMTF, this a dedicated method to allow for that.
+	 * @param pdbId what to load
+	 * @return a Structure object
+	 * @throws IOException
+	 * @throws StructureException
+	 */
+	private Structure getStructureForPdbIdByMmtf(String pdbId) throws IOException, StructureException {
+		if (pdbId == null)
+			return null;
+		if (pdbId.length() != 4) {
+			throw new StructureException("Unrecognized PDB ID: " + pdbId);
+		}
+		while (checkLoading(pdbId)) {
+			// waiting for loading to be finished...
+
+			try {
+				Thread.sleep(100);
+			} catch (InterruptedException e) {
+				logger.error(e.getMessage());
+			}
+		}
+
+		logger.debug("loading from mmtf");
+		return loadStructureFromMmtfByPdbId(pdbId);
+	}
+
 	/**
 	 * Load a {@link Structure} from MMTF either from the local file system.
 	 * @param pdbId the input PDB id
