Merge branch 'release-2.6.0' into develop

doxygen/Doxyfile.in

@@ -58,7 +58,7 @@ PROJECT_LOGO           =
 # entered, it will be relative to the location where doxygen was started. If
 # left blank the current directory will be used.
 
-OUTPUT_DIRECTORY       = doc
+OUTPUT_DIRECTORY       = @BUILD_DIR@/doc
 
 # If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub-
 # directories (in 2 levels) under the output directory of each output format and

modules/mol/alg/pymod/scoring.py

@@ -172,8 +172,8 @@ class Scorer:
                                            assign_elem=True)
         Molck(self._model, conop.GetDefaultLib(), molck_settings)
         Molck(self._target, conop.GetDefaultLib(), molck_settings)
-        self._model = model.Select("peptide=True or nucleotide=True")
-        self._target = target.Select("peptide=True or nucleotide=True")
+        self._model = self._model.Select("peptide=True or nucleotide=True")
+        self._target = self._target.Select("peptide=True or nucleotide=True")
 
         # catch models which have empty chain names
         for ch in self._model.chains: