From: Egon W. <eg...@us...> - 2005-08-26 13:08:48
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Update of /cvsroot/cdk/cdk/src/org/openscience/cdk/tools In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv1181/src/org/openscience/cdk/tools Modified Files: ProteinBuilderTool.java Log Message: Removed code that was made obsolete by restoring the AminoAcids template behaviour of not including acidic oxygens (needed to fix the PDBReader). Index: ProteinBuilderTool.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/tools/ProteinBuilderTool.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- ProteinBuilderTool.java 19 Aug 2005 10:07:40 -0000 1.4 +++ ProteinBuilderTool.java 26 Aug 2005 13:08:11 -0000 1.5 @@ -62,13 +62,6 @@ public static BioPolymer addAminoAcidAtNTerminus( BioPolymer protein, AminoAcid aaToAdd, Strand strand, AminoAcid aaToAddTo) { - // remove the acidic oxygen which is to be replaced by the nitrogen - try { - AminoAcidManipulator.removeAcidicOxygen(aaToAdd); - } catch (Exception exception) { - logger.error("Could not remove acidic oxygen: ", exception.getMessage()); - logger.debug(exception); - } // then add the amino acid addAminoAcid(protein, aaToAdd, strand); // Now think about the protein back bone connection @@ -95,16 +88,6 @@ public static BioPolymer addAminoAcidAtCTerminus( BioPolymer protein, AminoAcid aaToAdd, Strand strand, AminoAcid aaToAddTo) { - // remove the acidic oxygen which might be removed by the next added amino - // acid... so we'll have a dangling carbonyl in the end - logger.debug("Before removal: ", aaToAdd); - try { - AminoAcidManipulator.removeAcidicOxygen(aaToAdd); - } catch (Exception exception) { - logger.error("Could not remove acidic oxygen: ", exception.getMessage()); - logger.debug(exception); - } - logger.debug("After removal: ", aaToAdd); // then add the amino acid addAminoAcid(protein, aaToAdd, strand); // Now think about the protein back bone connection |