diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java
index e49bd22216..2d43a481bf 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java
@@ -260,7 +260,9 @@ private List<Location> parseLocationString(String string, int versus) {
 					l.setPartialOn3prime(true);
 				}
 
-				if (!(accession == null || "".equals(accession))) l.setAccession(new AccessionID(accession));
+				if (accession != null && !"".equals(accession)) {
+					l.setAccession(new AccessionID(accession));
+				}
 
 				boundedLocationsCollection.add(l);
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/Equals.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/Equals.java
index e8f78243ed..7e2c7128c9 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/Equals.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/Equals.java
@@ -49,7 +49,13 @@ public static boolean equal(boolean one, boolean two) {
 	 * @see #classEqual(Object, Object)
 	 */
 	public static boolean equal(Object one, Object two) {
-		return one == null && two == null || !(one == null || two == null) && (one == two || one.equals(two));
+		if (one == two) {
+			return true;
+		}
+		if (one == null || two == null) {
+			return false;
+		}
+		return one.equals(two);
 	}
 
 	/**
@@ -84,6 +90,12 @@ public static boolean equal(Object one, Object two) {
 	 *         equal at the class level
 	 */
 	public static boolean classEqual(Object one, Object two) {
-		return one == two || !(one == null || two == null) && one.getClass() == two.getClass();
+		if (one == two) {
+			return true;
+		}
+		if (one == null || two == null) {
+			return false;
+		}
+		return one.getClass() == two.getClass();
 	}
 }
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java
index 4163be2b56..a28f1019fb 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java
@@ -135,7 +135,7 @@ public static Location fromBio( int start, int end, char strand )
 		int s= start - 1;
 		int e= end;
 
-		if( !( strand == '-' || strand == '+' || strand == '.' ))
+		if( strand != '-' && strand != '+' && strand != '.' )
 		{
 			throw new IllegalArgumentException( "Strand must be '+', '-', or '.'" );
 		}
@@ -166,7 +166,7 @@ public static Location fromBioExt( int start, int length, char strand, int total
 		int s= start;
 		int e= s + length;
 
-		if( !( strand == '-' || strand == '+' || strand == '.' ))
+		if( strand != '-' && strand != '+' && strand != '.' )
 		{
 			throw new IllegalArgumentException( "Strand must be '+', '-', or '.'" );
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Author.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Author.java
index b0d7253507..bd5a01b885 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Author.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Author.java
@@ -62,7 +62,7 @@ public boolean equals(Object obj) {
 		if ((this.surname == null) ? (other.surname != null) : !this.surname.equals(other.surname)) {
 			return false;
 		}
-		return !((this.initials == null) ? (other.initials != null) : !this.initials.equals(other.initials));
+		return (this.initials == null) ? other.initials == null : this.initials.equals(other.initials);
 	}
 
 	@Override
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Element.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Element.java
index 2f534b2828..4e2d3e340a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Element.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Element.java
@@ -424,7 +424,7 @@ public boolean isHeavyAtom() {
 	 * @return <CODE>true</CODE> if Element is not Hydrogen and not Carbon.
 	 */
 	public boolean isHeteroAtom() {
-		return !(this == C || this == H);
+		return this != C && this != H;
 	}
 
 	/**
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java
index 6c045ba48e..83f16b7982 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java
@@ -1450,7 +1450,7 @@ private int optimizeSuperposition(AFPChain afpChain, int nse1, int nse2, int str
 			//afpChain.setTotalRmsdOpt(rmsd);
 			//System.out.println("rmsd: " + rmsd);
 
-			if(!(nAtom<strLen*0.95) && (!isRmsdLenAssigned)) {
+			if(nAtom >= strLen * 0.95 && !isRmsdLenAssigned) {
 				rmsdLen=rmsd;
 				isRmsdLenAssigned=true;
 			}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java
index 4f57161268..cab98b0113 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java
@@ -1455,7 +1455,7 @@ private int optimizeSuperposition(AFPChain afpChain, int nse1, int nse2, int str
 			//afpChain.setTotalRmsdOpt(rmsd);
 			//System.out.println("rmsd: " + rmsd);
 
-			if(!(nAtom<strLen*0.95) && (!isRmsdLenAssigned)) {
+			if(nAtom >= strLen * 0.95 && !isRmsdLenAssigned) {
 				rmsdLen=rmsd;
 				isRmsdLenAssigned=true;
 			}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java
index 7c359121de..f65f4617fe 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java
@@ -55,7 +55,7 @@ public static boolean isUnaryExpression(String expression) {
 		if (first < 0 || last < 0) {
 			return true;
 		}
-		return ! (first == 0 && last > first);
+		return first != 0 || last <= first;
 	}
 
 	public static List<String> parseUnaryOperatorExpression(String operatorExpression) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java
index 7732c04b80..42191d682d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java
@@ -57,7 +57,7 @@ public static List<SecStrucInfo> getSecStrucInfo(Structure s) {
 			Group g = iter.next();
 			if (g.hasAminoAtoms()) {
 				Object p = g.getProperty(Group.SEC_STRUC);
-				if (!(p == null)) {
+				if (p != null) {
 					SecStrucInfo ss = (SecStrucInfo) p;
 					listSSI.add(ss);
 				}