src/py/aria/exportToCcpn.py   |   24 +++++++++++-------------
 src/py/aria/importFromCcpn.py |   32 ++++++++++++--------------------
 2 files changed, 23 insertions(+), 33 deletions(-)

diff --git a/src/py/aria/exportToCcpn.py b/src/py/aria/exportToCcpn.py
index c742a88..aae7b7d 100644
--- a/src/py/aria/exportToCcpn.py
+++ b/src/py/aria/exportToCcpn.py
@@ -1,5 +1,5 @@
 from ccpnmr.analysis.core.ConstraintBasic import makeNmrConstraintStore, makeStructureGeneration, getFixedResonance
-from ccpnmr.analysis.core.ExperimentBasic import getOnebondDataDims
+from ccpnmr.analysis.core.ExperimentBasic import getOnebondDataDims, getThroughSpaceDataDims
 from ccpnmr.analysis.core.AssignmentBasic import assignAtomsToRes, assignResToDim
 from ccpnmr.analysis.core.PeakBasic       import pickPeak, setManualPeakIntensity
 from ccpnmr.analysis.core.MoleculeBasic   import DEFAULT_ISOTOPES
@@ -791,12 +791,13 @@ def getPeakAssignmentsFromAria2(project, ariaRestraints, namesDict=None,
     ariaDims = ariaDimDict.get(spectrum)
     if not ariaDims:
       ariaDims = [] #[0,1,2]
+      throughSpaceDataDims = getThroughSpaceDataDims(spectrum)
 
       dataDims = spectrum.sortedDataDims()
       if len(dataDims) == 3:
         for dataDim in dataDims:
           expDimRef = dataDim.findFirstDataDimRef().expDimRef
-          if '1H' in expDimRef.isotopeCodes: # 0 or 2
+          if dataDim in throughSpaceDataDims: # 0 or 2
             if onebondDims.get(dataDim.dim):
               if ppmX1 is None:
                 ariaDims.append(2)
@@ -816,21 +817,18 @@ def getPeakAssignmentsFromAria2(project, ariaRestraints, namesDict=None,
               ariaDims.append(1)
 
       else:
-        transfer = spectrum.experiment.findFirstExpTransfer(transferType='through-space') or \
-                   spectrum.experiment.findFirstExpTransfer(transferType='NOESY')
 
+        i = 0
         for dataDim in dataDims:
-          expDimRefs = [dataDimRef.expDimRef for dataDimRef in dataDim.dataDimRefs]
-          i = 0
-          for expDimRef in transfer.sortedExpDimRefs():
-            if expDimRef in expDimRefs:
-              ariaDims.append(i)
-              boundDim = onebondDims.get(dataDim.dim)
-              if boundDim:
-                ariaDims.append(i+1)
-
+          if dataDim in throughSpaceDataDims:
+            ariaDims.append(i)
+            boundDim = onebondDims.get(dataDim.dim)
+            if boundDim:
+              ariaDims.append(i+1)
+            
             i += 2
 
+
       ariaDimDict[spectrum] = ariaDims
 
     if namesDict:
diff --git a/src/py/aria/importFromCcpn.py b/src/py/aria/importFromCcpn.py
index a65ae3e..f63ba16 100644
--- a/src/py/aria/importFromCcpn.py
+++ b/src/py/aria/importFromCcpn.py
@@ -165,7 +165,7 @@ def getStructureEnsembles(project, ccpChains):
             
     return ensembles
 
-def getNoesyPeakLists(project, molSystem=None):
+def getNoesyPeakLists(project, molSystem=None, excludeSimulated=True):
     """Descrn: Get the NOE peak lists from a CCPN project. Can filter if appropriate to a given
                molecular system if passed in.
        Inputs: Implementation.Project, ccp.molecule.MolSystem.MolSystem
@@ -196,19 +196,10 @@ def getNoesyPeakLists(project, molSystem=None):
  
         for spectrum in experiment.dataSources:
             if (spectrum.dataType == 'processed') and (spectrum.numDim > 1):
-
-                isotopes = []
-                for dataDim in spectrum.dataDims:
-                    for expDimRef in dataDim.expDim.expDimRefs:
-                        if expDimRef.measurementType in ('shift','Shift'):
-                            isotope = ','.join(expDimRef.isotopeCodes)
-                            isotopes.append(isotope)
-                            break
-
-                if isotopes.count('1H') > 1:
-                    for peakList in spectrum.peakLists:
-                        if peakList.findFirstPeak():
-                            peakLists.append(peakList)
+                for peakList in spectrum.sortedPeakLists():
+                    if excludeSimulated and peakList.isSimulated:
+                        continue
+                    peakLists.append(peakList)
 
 
     return peakLists
@@ -490,7 +481,10 @@ def makeAriaChain(ccpChain):
     # Does below work for DNA/RNA?
 
     aria_settings = ChainSettings()
-    aria_settings['type'] = chainTypeMapping[ccpChain.molecule.molType]
+    # wb104: below changed 31 Oct 2011 to try and get around case when molType is None
+    #aria_settings['type'] = chainTypeMapping[ccpChain.molecule.molType]
+    molType = ccpChain.molecule.molType or 'protein'
+    aria_settings['type'] = chainTypeMapping[molType]
 
     aria_chain = Chain(settings=aria_settings, segid=string_to_segid(ccpChain.code))
 
@@ -952,8 +946,6 @@ def makeAriaSpectrum(peakList, ariaMolecule, filterRejected=True):
     expDimRefDict = {}
 
     for expDimRef in transfer.sortedExpDimRefs():
-        if expDimRef.isotopeCodes != ('1H',):
-            raise Exception('Not an H-H experiment')
 
         onebondTransfer = expDimRef.findFirstExpTransfer(transferType='onebond')
 
@@ -1095,7 +1087,7 @@ def getAriaAtomsFromResonance(resonance, ariaMolecule, cache={}):
 
     # TJS modify to return just a list of atoms, rather than a list of list
     ariaAtoms = []
-    for atom in atomSet.sortedAtoms():
+    for atom in atomSet.atoms:
         ariaAtom = ariaResidue.atoms.get(atom.name)
         if not ariaAtom:
             messager.warning('Could not find ARIA Atom for CCPN atom %d%s %s' % (residue.seqCode,residue.ccpCode, atom.name))
@@ -1256,9 +1248,9 @@ def getAriaDistanceRestraintsList(constraint_list, constraint_type, aria_mol):
         restraint.setWeight(weight)
 
 
-        for constrItem in distConstr.sortedItems():
+        for constrItem in distConstr.items:
 
-            reso1, reso2 = constrItem.sortedResonances()
+            reso1, reso2 = constrItem.resonances
 
             # TJS fix for mapping prochirals
             # always use real resonnances where possible