new utility classes to detect if a Group is polymeric, an amino acid, or a nucleotide group.

andreasprlic · andreasprlic · commit 46560c77ba07 · 2016-08-08T16:18:07.000-07:00
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/StructureUtil.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/StructureUtil.java
@@ -341,7 +341,18 @@ public static List<String> getAtomNames(Group group) {
 	 * @return
 	 */
 	public static List<Group> getAminoAcids(Chain chain) {
-		return chain.getAtomGroups(GroupType.AMINOACID);
+
+		List<Group> gs = new ArrayList<>();
+
+		for ( Group g : chain.getAtomGroups()){
+
+			if ( g.isAminoAcid())
+				gs.add(g);
+
+		}
+
+		return gs;
+
 	}
 
 }
diff --git a/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/ProteinModificationParserTest.java b/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/ProteinModificationParserTest.java
@@ -115,6 +115,8 @@ public static String[][] setUpShortTest() {
 				{"2HGD",null}, // X9Q
 				{"3LF4",null}, // 0YG
 
+				// {"2BF9","AA0099"}, // TYC this one needs a fix in the CCD before it can work
+
 		};
 		return strucs;
 	}
@@ -334,7 +336,9 @@ public void testParser() throws IOException, StructureException {
 	public void multiTest() throws IOException, StructureException {
 		for ( String[] name : strucs){
 			parserTest(name[0], (String)null);
-			parserTest(name[0], name[1]);
+
+			if ( name[1] != null)
+				parserTest(name[0], name[1]);
 
 		}
 	}
@@ -408,6 +412,7 @@ private void printResult(String pdbId, ProteinModificationIdentifier parser, boo
 		for (ModifiedCompound mc : mcs) {
 			sb.append("Modification #");
 			sb.append(++i);
+			sb.append(" ").append(mc.getDescription()).append(" ").append(mc.getModification().getId());
 			sb.append(":\n");
 			sb.append(mc.getAtomLinkages());
 			sb.append('\n');
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Group.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Group.java
@@ -178,6 +178,29 @@ public interface Group {
 	 */
 	public boolean hasAminoAtoms() ;
 
+
+	/** tests in the Chemical Component Dictionary, if this group is a polymeric group
+	 *
+	 * @return true if a polymeric group
+	 */
+	public boolean isPolymeric();
+
+
+	/** Tests in the Chemical Component Dictionary, if this group is an amino acid
+	 *
+	 * @return true if an amino acid
+     */
+	public boolean isAminoAcid();
+
+
+	/** Tests in the Chemical Component Dictionary, if this group is a nucleotide
+	 *
+	 * @return true if a nucleotide
+     */
+	public boolean isNucleotide();
+
+
+
 	/**
 	 * Properties of this amino acid. Currently available properties are:
 	 * phi
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/HetatomImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/HetatomImpl.java
@@ -25,6 +25,8 @@
 
 import org.biojava.nbio.structure.io.GroupToSDF;
 import org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory;
+import org.biojava.nbio.structure.io.mmcif.chem.PolymerType;
+import org.biojava.nbio.structure.io.mmcif.chem.ResidueType;
 import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -327,6 +329,71 @@ public boolean hasAminoAtoms(){
 
 	}
 
+	@Override
+	public boolean isPolymeric() {
+
+		ChemComp cc = getChemComp();
+
+		if ( cc == null)
+			return getType().equals(GroupType.AMINOACID) || getType().equals(GroupType.NUCLEOTIDE);
+
+		ResidueType rt = cc.getResidueType();
+
+		if ( rt.equals(ResidueType.nonPolymer))
+			return false;
+
+		PolymerType pt = rt.getPolymerType();
+
+		return pt.equals(PolymerType.peptide) ||
+				pt.equals(PolymerType.dna) ||
+				pt.equals(PolymerType.rna) ||
+				pt.equals(PolymerType.dnarna);
+
+
+	}
+
+	@Override
+	public boolean isAminoAcid() {
+
+		ChemComp cc = getChemComp();
+
+		if ( cc == null)
+			return getType().equals(GroupType.AMINOACID);
+
+
+		ResidueType rt = cc.getResidueType();
+
+		if ( rt.equals(ResidueType.nonPolymer))
+			return false;
+
+		PolymerType pt = rt.getPolymerType();
+
+		return pt.equals(PolymerType.peptide);
+
+	}
+
+	@Override
+	public boolean isNucleotide() {
+
+		ChemComp cc = getChemComp();
+
+		if ( cc == null)
+			return  getType().equals(GroupType.NUCLEOTIDE);
+
+		ResidueType rt = cc.getResidueType();
+
+		if ( rt.equals(ResidueType.nonPolymer))
+			return false;
+
+		PolymerType pt = rt.getPolymerType();
+
+		return pt.equals(PolymerType.dna) ||
+				pt.equals(PolymerType.rna) ||
+				pt.equals(PolymerType.dnarna) ;
+
+
+	}
+
 
 	/**
 	 * {@inheritDoc}
@@ -604,4 +671,7 @@ public void setHetAtomInFile(boolean isHetAtomInFile) {
 		this.isHetAtomInFile = isHetAtomInFile;
 	}
 
+
+
+
 }
