Full fix for biojava#148, all tests pass

- some improvement in exceptions and logging biojava#111 and biojava#155

biojava3-structure/src/main/java/org/biojava/bio/structure/AtomPositionMap.java

@@ -67,7 +67,7 @@ public static interface GroupMatcher {
 		@Override
 		public boolean matches(Group group) {
 			ResidueType type = group.getChemComp().getResidueType();
-			return group.hasAtom(StructureTools.caAtomName) || AMINO_ACID_NAMES.contains(group.getPDBName()) || type == ResidueType.lPeptideLinking || type == ResidueType.glycine || type == ResidueType.lPeptideAminoTerminus || type == ResidueType.lPeptideCarboxyTerminus || type == ResidueType.dPeptideLinking || type == ResidueType.dPeptideAminoTerminus || type == ResidueType.dPeptideCarboxyTerminus;
+			return group.hasAtom(StructureTools.CA_ATOM_NAME) || AMINO_ACID_NAMES.contains(group.getPDBName()) || type == ResidueType.lPeptideLinking || type == ResidueType.glycine || type == ResidueType.lPeptideAminoTerminus || type == ResidueType.lPeptideCarboxyTerminus || type == ResidueType.dPeptideLinking || type == ResidueType.dPeptideAminoTerminus || type == ResidueType.dPeptideCarboxyTerminus;
 		}
 	};
 

biojava3-structure/src/main/java/org/biojava/bio/structure/HetatomImpl.java

@@ -262,10 +262,10 @@ public boolean hasAminoAtoms(){
 		// if this method call is performed too often, it should become a
 		// private method and provide a flag for Group object ...
 
-		if (	hasAtom(StructureTools.caAtomName) && 
-				hasAtom(StructureTools.cAtomName) && 
-				hasAtom(StructureTools.nAtomName) && 
-				hasAtom(StructureTools.oAtomName)) {
+		if (	hasAtom(StructureTools.CA_ATOM_NAME) && 
+				hasAtom(StructureTools.C_ATOM_NAME) && 
+				hasAtom(StructureTools.N_ATOM_NAME) && 
+				hasAtom(StructureTools.O_ATOM_NAME)) {
 
 			// this is the minimun requirement for something to be considered an aminoacid with a backbone
 			// note that if the backbone is incomplete it won't be considered an aminoacid

biojava3-structure/src/main/java/org/biojava/bio/structure/StructureTools.java

@@ -62,29 +62,31 @@ public class StructureTools {
 	private static final Logger logger = LoggerFactory.getLogger(StructureTools.class);
 
 	/** 
-	 * The atom name of the C-alpha atom
+	 * The atom name of the backbone C-alpha atom.
+	 * Note that this can be ambiguous depending on the context since Calcium atoms
+	 * use the same name in PDB.
 	 */
-	public static final String caAtomName = "CA";
+	public static final String CA_ATOM_NAME = "CA";
 
 	/**
-	 * The atom name for the amide nitrogen
+	 * The atom name for the backbone amide nitrogen
 	 */
-	public static final String nAtomName = "N";
+	public static final String N_ATOM_NAME = "N";
 
 	/**
-	 * The atom name for the carbonyl carbon
+	 * The atom name for the backbone carbonyl
 	 */
-	public static final String cAtomName = "C";
+	public static final String C_ATOM_NAME = "C";
 
 	/**
-	 * The atom name for the carbonyl oxygen
+	 * The atom name for the backbone carbonyl oxygen
 	 */
-	public static final String oAtomName = "O";
+	public static final String O_ATOM_NAME = "O";
 
 	/**
-	 * The atom name of the C-beta atom
+	 * The atom name of the side-chain C-beta atom
 	 */
-	public static final String cbAtomName = "CB";
+	public static final String CB_ATOM_NAME = "CB";
 
 
 	public static final Character UNKNOWN_GROUP_LABEL = new Character('x');
@@ -470,8 +472,8 @@ public static final Atom[] getAtomCAArray(Chain c){
 		List<Atom> atoms = new ArrayList<Atom>();
 
 		for (Group g: c.getAtomGroups()) {
-			if (g.hasAtom(caAtomName) && g.getAtom(caAtomName).getElement()==Element.C) {
-				atoms.add(g.getAtom(caAtomName));
+			if (g.hasAtom(CA_ATOM_NAME) && g.getAtom(CA_ATOM_NAME).getElement()==Element.C) {
+				atoms.add(g.getAtom(CA_ATOM_NAME));
 			}
 		}
 
@@ -509,7 +511,7 @@ public static final Atom[] cloneCAArray(Atom[] ca) throws StructureException{
 
 			Group parentN = (Group)parentG.clone();
 
-			newCA[apos] = parentN.getAtom(caAtomName);
+			newCA[apos] = parentN.getAtom(CA_ATOM_NAME);
 			newChain.addGroup(parentN);
 		}
 		return newCA;
@@ -582,7 +584,7 @@ public static Atom[] duplicateCA2(Atom[] ca2) throws StructureException{
 			}
 
 			c.addGroup(g);
-			ca2clone[pos] = g.getAtom(caAtomName);
+			ca2clone[pos] = g.getAtom(CA_ATOM_NAME);
 
 			pos++;
 		}
@@ -606,7 +608,7 @@ public static Atom[] duplicateCA2(Atom[] ca2) throws StructureException{
 			}
 
 			c.addGroup(g);
-			ca2clone[pos] = g.getAtom(caAtomName);
+			ca2clone[pos] = g.getAtom(CA_ATOM_NAME);
 
 			pos++;
 		}
@@ -628,8 +630,8 @@ public static Atom[] getAtomCAArray(Structure s){
 
 		for (Chain c: s.getChains()) {
 			for (Group g: c.getAtomGroups()) {
-				if (g.hasAtom(caAtomName) && g.getAtom(caAtomName).getElement()==Element.C) {
-					atoms.add(g.getAtom(caAtomName));
+				if (g.hasAtom(CA_ATOM_NAME) && g.getAtom(CA_ATOM_NAME).getElement()==Element.C) {
+					atoms.add(g.getAtom(CA_ATOM_NAME));
 				}
 			}
 		}
@@ -653,10 +655,10 @@ public static Atom[] getBackboneAtomArray(Structure s){
 					// this means we will only take atoms grom groups that have complete backbones
 					for (Atom a:g.getAtoms()) {
 						// we do it this way instead of with g.getAtom() to be sure we always use the same order as original
-						if (a.getName().equals(caAtomName)) atoms.add(a);
-						if (a.getName().equals(cAtomName)) atoms.add(a);
-						if (a.getName().equals(nAtomName)) atoms.add(a);
-						if (a.getName().equals(oAtomName)) atoms.add(a);
+						if (a.getName().equals(CA_ATOM_NAME)) atoms.add(a);
+						if (a.getName().equals(C_ATOM_NAME)) atoms.add(a);
+						if (a.getName().equals(N_ATOM_NAME)) atoms.add(a);
+						if (a.getName().equals(O_ATOM_NAME)) atoms.add(a);
 					}
 				}
 			}
@@ -853,21 +855,25 @@ public static final Structure getReducedStructure(Structure s, int chainNr) thro
 
 
 
-	/** In addition to the functionality provided by getReducedStructure also provides a way to specify sub-regions of a structure with the following 
+	/** 
+	 * In addition to the functionality provided by {@link #getReducedStructure(Structure, int)} 
+	 * and {@link #getReducedStructure(Structure, String)}, also provides 
+	 * a way to specify sub-regions of a structure with the following 
 	 * specification:
 	 * 
-	 * 
-	 * ranges can be surrounded by ( and ). (but will be removed).
-	 * ranges are specified as
-	 * PDBresnum1 : PDBresnum2
-	 * 
-	 *  a list of ranges is separated by ,
+	 * <p>
+	 * <li>ranges can be surrounded by ( and ). (but will be removed).</li>
+	 * <li>ranges are specified as
+	 * PDBresnum1 : PDBresnum2</li>
 	 *  
-	 *  Example
+	 * <li>a list of ranges is separated by ,</li>
+	 * </p>
+	 * Example
+	 * <pre>
 	 *  4GCR (A:1-83)
 	 *  1CDG (A:407-495,A:582-686)
 	 *  1CDG (A_407-495,A_582-686)
-	 * 
+	 * </pre>
 	 * @param s The full structure
 	 * @param ranges A comma-seperated list of ranges, optionally surrounded by parentheses
 	 * @return Substructure of s specified by ranges
@@ -934,7 +940,7 @@ public static final Structure getSubRanges(Structure s, String ranges )
 				if(struc.size() != 1) {
 					// SCOP 1.71 uses this for some proteins with multiple chains
 					// Print a warning in this ambiguous case
-					logger.warn("Multiple possible chains match '_'. Using chain %s.%n",chain.getChainID());
+					logger.warn("Multiple possible chains match '_'. Using chain {}",chain.getChainID());
 				}
 			} else {
 				// Explicit chain

biojava3-structure/src/main/java/org/biojava/bio/structure/align/AFPTwister.java

@@ -353,7 +353,7 @@ private static void cloneAtomRange(Atom[] p1, Atom[] p2, int r1, int r2)
          Group g = p2[i].getGroup();
          Group newG = (Group)g.clone();
 
-         p1[i] = newG.getAtom(StructureTools.caAtomName);
+         p1[i] = newG.getAtom(StructureTools.CA_ATOM_NAME);
          Chain parentC = g.getChain();
 
          Chain newChain = null;

biojava3-structure/src/main/java/org/biojava/bio/structure/align/StrucAligParameters.java

@@ -34,7 +34,7 @@ public class StrucAligParameters {
 
 
     int initialK;
-    String[] usedAtomNames = { StructureTools.caAtomName, } ;
+    String[] usedAtomNames = { StructureTools.CA_ATOM_NAME, } ;
 
     // step 1
 

biojava3-structure/src/main/java/org/biojava/bio/structure/align/ce/CECalculator.java

@@ -269,14 +269,14 @@ private double getDistanceWithSidechain(Atom ca1, Atom ca2) throws StructureExce
 		double dist;
 		Group g1 = ca1.getGroup();
 		Atom cb1 = null;
-		if ( g1.hasAtom(StructureTools.cbAtomName)) {
-			cb1 = g1.getAtom(StructureTools.cbAtomName);
+		if ( g1.hasAtom(StructureTools.CB_ATOM_NAME)) {
+			cb1 = g1.getAtom(StructureTools.CB_ATOM_NAME);
 		}
 		//
 		Group g2 = ca2.getGroup();
 		Atom cb2 = null;
-		if ( g2.hasAtom(StructureTools.cbAtomName)) {
-			cb2 = g2.getAtom(StructureTools.cbAtomName);
+		if ( g2.hasAtom(StructureTools.CB_ATOM_NAME)) {
+			cb2 = g2.getAtom(StructureTools.CB_ATOM_NAME);
 		}
 
 
@@ -1241,7 +1241,7 @@ private void setStrBuf(Atom[] strBuf, int i, Atom[] ca, int j) {
 		//TODO
 		Group parent = ca[j].getGroup();
 		int pos = 0;
-		String atomName = StructureTools.caAtomName;
+		String atomName = StructureTools.CA_ATOM_NAME;
 
 		Atom a = null;
 
@@ -1856,7 +1856,7 @@ private void rot_mol(Atom[] caA, Atom[] caB, int nse2, Matrix m , Atom shift) th
 
 			Calc.rotate( g, m);
 			Calc.shift(  g, shift);
-			caB[l] = g.getAtom(" CA ");
+			caB[l] = g.getAtom(StructureTools.CA_ATOM_NAME);
 		}
 	}
 
@@ -1942,7 +1942,7 @@ private Atom[] getAtoms(Atom[] ca,  int length, boolean clone) throws StructureE
 			Atom a;
 			if ( clone ){
 				Group g = (Group)ca[i].getGroup().clone();
-				a = g.getAtom(" CA ");
+				a = g.getAtom(StructureTools.CA_ATOM_NAME);
 			}
 			else {
 				a = ca[i];

biojava3-structure/src/main/java/org/biojava/bio/structure/align/ce/CeCalculatorEnhanced.java

@@ -273,14 +273,14 @@ private double getDistanceWithSidechain(Atom ca1, Atom ca2) throws StructureExce
 		double dist;
 		Group g1 = ca1.getGroup();
 		Atom cb1 = null;
-		if ( g1.hasAtom(StructureTools.cbAtomName)) {
-			cb1 = g1.getAtom(StructureTools.cbAtomName);
+		if ( g1.hasAtom(StructureTools.CB_ATOM_NAME)) {
+			cb1 = g1.getAtom(StructureTools.CB_ATOM_NAME);
 		}
 		//
 		Group g2 = ca2.getGroup();
 		Atom cb2 = null;
-		if ( g2.hasAtom(StructureTools.cbAtomName)) {
-			cb2 = g2.getAtom(StructureTools.cbAtomName);
+		if ( g2.hasAtom(StructureTools.CB_ATOM_NAME)) {
+			cb2 = g2.getAtom(StructureTools.CB_ATOM_NAME);
 		}
 
 
@@ -1244,7 +1244,7 @@ private void setStrBuf(Atom[] strBuf, int i, Atom[] ca, int j) {
 		//TODO
 		Group parent = ca[j].getGroup();
 		int pos = 0;
-		String atomName = StructureTools.caAtomName;
+		String atomName = StructureTools.CA_ATOM_NAME;
 
 		Atom a = null;
 
@@ -1936,7 +1936,7 @@ private void rot_mol(Atom[] caA, Atom[] caB, int nse2, Matrix m , Atom shift) th
 
 			Calc.rotate( g, m);
 			Calc.shift(  g, shift);
-			caB[l] = g.getAtom(" CA ");
+			caB[l] = g.getAtom(StructureTools.CA_ATOM_NAME);
 		}
 	}
 
@@ -2028,7 +2028,7 @@ private Atom[] getAtoms(Atom[] ca,  int length, boolean clone) throws StructureE
 			Atom a;
 			if ( clone ){
 				Group g = (Group)ca[i].getGroup().clone();
-				a = g.getAtom(" CA ");
+				a = g.getAtom(StructureTools.CA_ATOM_NAME);
 			}
 			else {
 				a = ca[i];

biojava3-structure/src/main/java/org/biojava/bio/structure/align/ce/CeMain.java

@@ -106,7 +106,7 @@ public AFPChain align(Atom[] ca1, Atom[] ca2, Object param) throws StructureExce
 		for (Atom a : ca2){
 			Group g = (Group)a.getGroup().clone(); // works because each group has only a CA atom
 
-			ca2clone[pos] = g.getAtom(StructureTools.caAtomName);
+			ca2clone[pos] = g.getAtom(StructureTools.CA_ATOM_NAME);
 
 			pos++;
 		}

biojava3-structure/src/main/java/org/biojava/bio/structure/align/ce/CeSideChainMain.java

@@ -64,7 +64,7 @@ public static void main(String[] args){
 //      for (Atom a : ca2){
 //         Group g = (Group)a.getParent().clone();
 //
-//         ca2clone[pos] = g.getAtom(" CA ");
+//         ca2clone[pos] = g.getAtom(StructureTools.caAtomName);
 //
 //         pos++;
 //      }

biojava3-structure/src/main/java/org/biojava/bio/structure/align/fatcat/calc/StructureAlignmentOptimizer.java

@@ -103,15 +103,15 @@ public StructureAlignmentOptimizer(int b1, int end1, Atom[] c1, int b2, int end2
          //cod1[i] = (Atom)a.clone();
          Group parent = (Group)a.getGroup().clone();
          //cod1[i].setParent(parent);
-         cod1[i] = parent.getAtom(StructureTools.caAtomName);
+         cod1[i] = parent.getAtom(StructureTools.CA_ATOM_NAME);
          //cod1[i] = c1[i];
       }
       for(int i = 0; i < len2; i ++)      {
          Atom a = c2[i+b2];
          //cod2[i]= (Atom)a.clone();
          Group parent = (Group)a.getGroup().clone();
          //cod2[i].setParent(parent);
-         cod2[i] = parent.getAtom(StructureTools.caAtomName);
+         cod2[i] = parent.getAtom(StructureTools.CA_ATOM_NAME);
          //cod2[i] = c2[i];
       }
 

biojava3-structure/src/main/java/org/biojava/bio/structure/io/CAConverter.java

@@ -85,7 +85,7 @@ public static Chain getCAOnly(Chain chain){
 
             for (Atom a : atoms){
 
-                if ( a.getName().equals(StructureTools.caAtomName) && a.getElement()==Element.C){
+                if ( a.getName().equals(StructureTools.CA_ATOM_NAME) && a.getElement()==Element.C){
                     // we got a CA atom in this group!
                     AminoAcid n = new AminoAcidImpl();
                     n.setPDBName(g.getPDBName());

biojava3-structure/src/main/java/org/biojava/bio/structure/io/PDBFileReader.java

@@ -249,7 +249,7 @@ public static void main(String[] args){
 
 			}
 			 */
-		} catch (Exception e) {
+		} catch (IOException e) {
 			e.printStackTrace();
 		}
 	}
@@ -572,7 +572,7 @@ public InputStream getInputStreamBioAssembly(String pdbId)
 
 				InputStreamProvider isp = new InputStreamProvider();
 				inputStream = isp.getInputStream(fileName);
-				System.out.println("Loaded original PDB file as a fallback." + fileName);
+				logger.warn("Loaded original PDB file as a fallback." + fileName);
 				loadedBioAssembly = false;
 				return inputStream;
 
@@ -608,7 +608,7 @@ public InputStream getInputStreamBioAssembly(String pdbId)
 		if (bioAssemblyFallback) {	
 			inputStream = getInputStream(pdbId);		
 			if (inputStream != null) {
-				System.out.println("Biological assembly file for PDB ID: " + pdbId+  " is not available. " +
+				logger.warn("Biological assembly file for PDB ID: " + pdbId+  " is not available. " +
 						"Loaded original PDB file as a fallback from local cache.");
 				return getInputStream(pdbId);
 			}
@@ -660,7 +660,8 @@ private  File downloadPDB(String pdbId, String pathOnServer) throws IOException
 
 		String ftp = String.format("ftp://%s%s%s/pdb%s.ent.gz", serverName,pathOnServer,middle, pdbId);
 
-		//System.out.println("Fetching " + ftp);
+		logger.info("Fetching {}", ftp);
+		logger.info("Writing to {}",realFile.toString());
 
 
 		URL url = new URL(ftp);
@@ -699,7 +700,7 @@ private  File downloadPDBBiologicalAssembly(String pdbId, String pathOnServer) t
 
 		String ftp = String.format("ftp://%s%s%s/%s", serverName,pathOnServer,middle,fileName);
 
-		System.out.println("Fetching " + ftp);
+		logger.info("Fetching " + ftp);
 
 		URL url = null;
 		try {
@@ -724,7 +725,7 @@ private  File downloadPDBBiologicalAssembly(String pdbId, String pathOnServer) t
 
 			if (bioAssemblyFallback) {
 
-				System.out.println("Biological unit file for PDB ID: " + pdbId+  " is not available. " +
+				logger.warn("Biological unit file for PDB ID: " + pdbId+  " is not available. " +
 						"Downloading original PDB file as a fallback.");
 
 				loadedBioAssembly = false;