Logging

josemduarte · josemduarte · commit 8e9535c070fd · 2021-01-27T22:52:22.000-08:00
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
@@ -568,16 +568,15 @@ else if (atomCode.equals("CA") || atomCode.equals("CB") ||
 					else if (atomCode.equals("CG")) return TETRAHEDRAL_CARBON_VDW;
 
 				default:
-					logger.info("Unexpected carbon atom "+atomCode+" for aminoacid "+aa+", assigning its standard vdw radius");
+					logger.info("Unexpected carbon atom {} for aminoacid {}, assigning its standard vdw radius", atomCode, aa);
 					return Element.C.getVDWRadius();
 				}
 			}
 
 			// not any of the expected atoms
 		} else {
 			// non standard aas, (e.g. MSE, LLP) will always have this problem,
-			logger.info("Unexpected atom "+atomCode+" for aminoacid "+aa+ " ("+amino.getPDBName()+"), assigning its standard vdw radius");
-
+			logger.debug("Unexpected atom {} for aminoacid {} ({}), assigning its standard vdw radius", atomCode, aa, amino.getPDBName());
 
 			return atom.getElement().getVDWRadius();
 		}

Original file line number	Diff line number	Diff line change
`@@ -568,16 +568,15 @@ else if (atomCode.equals("CA") \|\| atomCode.equals("CB") \|\|`
`568`	`568`	`else if (atomCode.equals("CG")) return TETRAHEDRAL_CARBON_VDW;`
`569`	`569`
`570`	`570`	`default:`
`571`		`- logger.info("Unexpected carbon atom "+atomCode+" for aminoacid "+aa+", assigning its standard vdw radius");`
	`571`	`+ logger.info("Unexpected carbon atom {} for aminoacid {}, assigning its standard vdw radius", atomCode, aa);`
`572`	`572`	`return Element.C.getVDWRadius();`
`573`	`573`	`}`
`574`	`574`	`}`
`575`	`575`
`576`	`576`	`// not any of the expected atoms`
`577`	`577`	`} else {`
`578`	`578`	`// non standard aas, (e.g. MSE, LLP) will always have this problem,`
`579`		`- logger.info("Unexpected atom "+atomCode+" for aminoacid "+aa+ " ("+amino.getPDBName()+"), assigning its standard vdw radius");`
`580`		`-`
	`579`	`+ logger.debug("Unexpected atom {} for aminoacid {} ({}), assigning its standard vdw radius", atomCode, aa, amino.getPDBName());`
`581`	`580`
`582`	`581`	`return atom.getElement().getVDWRadius();`
`583`	`582`	`}`