@@ -267,7 +267,9 @@ <li> atomserial (mandatory) : Atom serial number</li>
      * Return the connections value.
      * @return a List object representing the connections value
      * @see #setConnections
+     * @deprecated use {@link Atom#getBonds()} instead
      */
+    @Deprecated
     public List<Map<String,Integer>> getConnections();
 
     /** 
 
@@ -67,12 +67,6 @@ public class FileParsingParameters implements Serializable
 	 */
 	boolean alignSeqRes;
 
-	
-	/** Should we create connections instead of bonds for ligands?
-	 *
-	 */
-	boolean createConects;
-
 	/** Flag to control if the chemical component info should be downloaded while parsing the files. (files will be cached).
 	 * 
 	 */
@@ -158,8 +152,6 @@ public void setDefault(){
 		parseBioAssembly = false;
 
 		createAtomBonds = false;
-		
-		createConects = false;
 
 		createAtomCharges = true;
 
@@ -412,24 +404,6 @@ public void setCreateAtomCharges(boolean createAtomCharges) {
 		this.createAtomCharges = createAtomCharges;
 	}
 
-	/**Should we create Bonds for ligands when parsing an mmCIF file?
-	 * 
-	 * @return true if we should create bonds based on ChemComp information.
-	 */
-	public boolean isCreateLigandConects(){
-		return createConects;
-	}
-	
-	/**Should we create connections between atoms in ligands when parsing 
-	 * a file? Setting this to true must also set AlignSeqRes true.
-	 * 
-	 * @param createLigandConects boolean flag yes/no
-	 */
-	public void setCreateLigandConects(boolean createLigandConects){
-		this.createConects = createLigandConects;
-		this.alignSeqRes = true;
-	}
-
 	public boolean isUseInternalChainId() {
 		return useInternalChainId;
 	}
 
@@ -2758,10 +2758,6 @@ else if ( params.isParseSecStruc()) {
 		if ( params.shouldCreateAtomCharges()) {
 			addCharges();
 		}
-
-		if (params.isCreateLigandConects()){
-			addLigandConnections();
-		}
 
 		if ( params.isParseSecStruc() && !params.isHeaderOnly())
 			setSecStruc();
@@ -2831,12 +2827,6 @@ private void formBonds() {
 		maker.makeBonds();
 	}
 
-	//Builds a list of connections from ligands in a Structure
-	private void addLigandConnections(){
-		LigandConnectMaker maker = new LigandConnectMaker(structure);
-		maker.addLigandConnections();
-	}
-	
 	private void formLinkRecordBond(LinkRecord linkRecord) {
 		// only work with atoms that aren't alternate locations
 		if (linkRecord.getAltLoc1().equals(" ")
 
@@ -59,7 +59,6 @@
 import org.biojava.nbio.structure.io.BondMaker;
 import org.biojava.nbio.structure.io.ChargeAdder;
 import org.biojava.nbio.structure.io.FileParsingParameters;
-import org.biojava.nbio.structure.io.LigandConnectMaker;
 import org.biojava.nbio.structure.io.SeqRes2AtomAligner;
 import org.biojava.nbio.structure.io.mmcif.model.AtomSite;
 import org.biojava.nbio.structure.io.mmcif.model.AuditAuthor;
@@ -723,11 +722,6 @@ public void documentEnd() {
 			if ( params.shouldCreateAtomBonds()) {
 				addBonds();
 			}
-			
-			// Adds the equivalent CONECT-style records as a PDB has for ligands.
-			if ( params.isCreateLigandConects()) {
-				addLigandConnections();
-			}
 
 			if ( params.shouldCreateAtomCharges()) {
 				addCharges();
@@ -1039,11 +1033,6 @@ private void addBonds() {
 		maker.makeBonds();	
 	}
 
-	private void addLigandConnections(){
-		LigandConnectMaker maker = new LigandConnectMaker(structure);
-		maker.addLigandConnections();
-	}
-
 	private void alignSeqRes() {
 
 		logger.debug("Parsing mode align_seqres, will align to ATOM to SEQRES sequence");
 
@@ -20,7 +20,6 @@
  */
 package org.biojava.nbio.structure;
 
-import org.biojava.nbio.core.util.SoftHashMap;
 import org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory;
 import org.biojava.nbio.structure.io.mmcif.ChemCompProvider;
 import org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider;