Merge branch 'hotfix_fmodefaults'

CHANGES.md

@@ -1,3 +1,14 @@
+FragIt v1.6.1 Release Notes
+===========================
+
+This is a bug-fix and minor improvements release.
+
+Updates since  v1.6.0
+
+  * Fixes a default value in the base configuration
+    for FMO input files such that atom names are
+    ignored
+
 FragIt v1.6.0 Release Notes
 ===========================
 

src/config.py

@@ -61,7 +61,7 @@ def __init__(self, *args):
         self['output']['writepymol']=False
         self['output']['writejmol']=False
         self['output']['centralfragment']=0
-        self['output']['useatomnames'] = True
+        self['output']['useatomnames'] = False
 
         # Fragmentation patterns are set in the individual settings below
         self['fragmentpatterns'] = dict()
@@ -124,10 +124,6 @@ def __init__(self):
         # protection patterns are needed to remove small fragments
         self['protectpatterns']['nterminal']="[$([NH2]),$([NH3])]CC(=O)[$(NCC=O)]"
 
-        # don't use atom names when using FMO. This can cause
-        # annoying errors in GAMESS
-        self['output']['useatomnames'] = False
-
 class FragItDataPE(FragItDataBase):
     """ Initializes FragIt with options which are applicable to the
         polarizable embedding (PE) approach. This is mostly tuned
@@ -149,6 +145,9 @@ def __init__(self):
         # utilize the MFCC principle. Standard is cap-order 2 (for peptides)
         self['mfcc']['order'] = 2
 
+        # use atom names when using PE.
+        self['output']['useatomnames'] = True
+
 
 # export all config settings so they can be
 # loaded at a later time.

src/strings.py

@@ -2,7 +2,7 @@
 Copyright (C) 2011-2016 Casper Steinmann
 """
 
-version = ("1","6","0")
+version = ("1","6","1")
 version_str = ".".join(version)
 
 __doc__ = """FragIt fragments molecules for fragment based methods using in quantum chemistry.