Less verbose logging in AsaCalculator

josemduarte · josemduarte · commit c11c0d20754b · 2017-01-21T11:33:08.000-08:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java
@@ -411,20 +411,16 @@ else if (atomCode.equals("CA") || atomCode.equals("CB") ||
 					else if (atomCode.equals("CG")) return TETRAHEDRAL_CARBON_VDW;
 
 				default:
-					logger.warn("Unexpected carbon atom "+atomCode+" for aminoacid "+aa+", assigning its standard vdw radius");
+					logger.info("Unexpected carbon atom "+atomCode+" for aminoacid "+aa+", assigning its standard vdw radius");
 					return Element.C.getVDWRadius();
 				}
 			}
 
 			// not any of the expected atoms
 		} else {
 			// non standard aas, (e.g. MSE, LLP) will always have this problem,
-			// thus we log at info level for them, at warn for others
-			if (amino.getChemComp()!=null && amino.getChemComp().isStandard()) {
-				logger.warn("Unexpected atom "+atomCode+" for aminoacid "+aa+ " ("+amino.getPDBName()+"), assigning its standard vdw radius");
-			} else {
-				logger.info("Unexpected atom "+atomCode+" for aminoacid "+aa+ " ("+amino.getPDBName()+"), assigning its standard vdw radius");
-			}
+			logger.info("Unexpected atom "+atomCode+" for aminoacid "+aa+ " ("+amino.getPDBName()+"), assigning its standard vdw radius");
+			
 
 			return atom.getElement().getVDWRadius();
 		}
@@ -449,7 +445,7 @@ private static double getRadiusForNucl(NucleotideImpl nuc, Atom atom) {
 
 		if (atom.getElement()==Element.O) return OXIGEN_VDW;
 
-		logger.warn("Unexpected atom "+atom.getName()+" for nucleotide "+nuc.getPDBName()+", assigning its standard vdw radius");
+		logger.info("Unexpected atom "+atom.getName()+" for nucleotide "+nuc.getPDBName()+", assigning its standard vdw radius");
 		return atom.getElement().getVDWRadius();
 	}
 
