From 15122b09e87aea9cc833d02339faa23fce5cb38f Mon Sep 17 00:00:00 2001 From: "Michael Mair-Keimberger (asterix)" Date: Mon, 30 Jan 2017 17:54:57 +0100 Subject: sci-chemistry/aria: remove unused patches Closes: https://github.com/gentoo/gentoo/pull/3730 --- sci-chemistry/aria/files/aria-2.3.2-python.patch | 30 ----- .../aria/files/aria-2.3.2-through-space-2.patch | 139 --------------------- .../aria/files/aria-2.3.2-through-space.patch | 118 ----------------- 3 files changed, 287 deletions(-) delete mode 100644 sci-chemistry/aria/files/aria-2.3.2-python.patch delete mode 100644 sci-chemistry/aria/files/aria-2.3.2-through-space-2.patch delete mode 100644 sci-chemistry/aria/files/aria-2.3.2-through-space.patch (limited to 'sci-chemistry/aria') 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 1f9ae1fcc5f6..000000000000 --- 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 6a363d098632..000000000000 --- 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 bda76aa11c80..000000000000 --- 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 -- cgit v1.2.3-65-gdbad