Docs

josemduarte · josemduarte · commit d4dc3239b5fc · 2020-01-25T11:08:46.000-08:00
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/contact/TestInterfaceFinder.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/contact/TestInterfaceFinder.java
@@ -3,7 +3,6 @@
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureIO;
-import org.biojava.nbio.structure.contact.AtomContact;
 import org.biojava.nbio.structure.contact.AtomContactSet;
 import org.biojava.nbio.structure.contact.InterfaceFinder;
 import org.biojava.nbio.structure.contact.Pair;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/InterfaceFinder.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/InterfaceFinder.java
@@ -11,6 +11,11 @@
 import javax.vecmath.Point3d;
 import java.util.List;
 
+/**
+ * A class containing methods to find interfaces in a given structure.
+ * @author Jose Duarte
+ * @since 5.4.0
+ */
 public class InterfaceFinder {
 
     public static final double DEFAULT_CONTACT_CUTOFF = 6;
@@ -28,10 +33,20 @@ public InterfaceFinder(Structure structure) {
         this.cutoff = DEFAULT_CONTACT_CUTOFF;
     }
 
+    /**
+     * Set the contact distance cutoff.
+     * @param cutoff the distance value in Angstroms
+     */
     public void setCutoff(double cutoff) {
         this.cutoff = cutoff;
     }
 
+    /**
+     * Find all inter polymer-chain interfaces in the structure.
+     * Two chains will be considered in contact if at least a pair of atoms from each is within the
+     * contact cutoff.
+     * @return the list of all interfaces
+     */
     public StructureInterfaceList getAllInterfaces() {
         initBoundingBoxes();
 
