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-rw-r--r--sci-chemistry/aria/files/aria-2.3.2-python.patch30
-rw-r--r--sci-chemistry/aria/files/aria-2.3.2-through-space-2.patch139
-rw-r--r--sci-chemistry/aria/files/aria-2.3.2-through-space.patch118
3 files changed, 0 insertions, 287 deletions
diff --git a/sci-chemistry/aria/files/aria-2.3.2-python.patch b/sci-chemistry/aria/files/aria-2.3.2-python.patch
deleted file mode 100644
index 1f9ae1fcc5f..00000000000
--- a/sci-chemistry/aria/files/aria-2.3.2-python.patch
+++ /dev/null
@@ -1,30 +0,0 @@
- src/py/aria/legacy/QualityChecks/Descriptive.py | 5 +++--
- 1 files changed, 3 insertions(+), 2 deletions(-)
-
-diff --git a/src/py/aria/legacy/QualityChecks/Descriptive.py b/src/py/aria/legacy/QualityChecks/Descriptive.py
-index ae5913c..550d20c 100644
---- a/src/py/aria/legacy/QualityChecks/Descriptive.py
-+++ b/src/py/aria/legacy/QualityChecks/Descriptive.py
-@@ -1,3 +1,6 @@
-+from math import *
-+from numpy import *
-+
- class Descriptive:
- """
- some basic statistics
-@@ -55,7 +58,6 @@ class Descriptive:
-
- def getStdDev(self):
- if( len(self.myData) == 0): return None
-- from math import *
- if( (self.count - 1) > 0 ):
- return sqrt( self.pseudoVariance/ (self.count - 1))
- else:
-@@ -89,7 +91,6 @@ class Descriptive:
- def getMedian(self):
- if( len(self.myData) == 0): return None
- if( self.median == None ):
-- from numpy import *
- sort(self.myData)
- if( self.count%2 == 1):
- self.median = self.myData[(self.count-1)/2]
diff --git a/sci-chemistry/aria/files/aria-2.3.2-through-space-2.patch b/sci-chemistry/aria/files/aria-2.3.2-through-space-2.patch
deleted file mode 100644
index 6a363d09863..00000000000
--- a/sci-chemistry/aria/files/aria-2.3.2-through-space-2.patch
+++ /dev/null
@@ -1,139 +0,0 @@
- 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
diff --git a/sci-chemistry/aria/files/aria-2.3.2-through-space.patch b/sci-chemistry/aria/files/aria-2.3.2-through-space.patch
deleted file mode 100644
index bda76aa11c8..00000000000
--- a/sci-chemistry/aria/files/aria-2.3.2-through-space.patch
+++ /dev/null
@@ -1,118 +0,0 @@
- src/py/aria/exportToCcpn.py | 24 +++++++++++-------------
- src/py/aria/importFromCcpn.py | 25 +++++++------------------
- 2 files changed, 18 insertions(+), 31 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..91ad123 100644
---- a/src/py/aria/importFromCcpn.py
-+++ b/src/py/aria/importFromCcpn.py
-@@ -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
-@@ -952,8 +943,6 @@ 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 +1084,7 @@ 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 +1245,9 @@ 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