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|
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
|
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