sci-chemistry/aria: remove unused patches

Closes: https://github.com/gentoo/gentoo/pull/3730

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 (file)
index 1f9ae1f..0000000
--- 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 (file)
index 6a363d0..0000000
--- 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 (file)
index bda76aa..0000000
--- 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