pdb_eda
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Contents:
User Guide
The pdb_eda Tutorial
The pdb_eda API Reference
pdb_eda
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Index
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A
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B
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C
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D
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E
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F
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G
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L
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M
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N
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P
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R
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S
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T
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X
_
__eq__() (pdb_eda.ccp4.DensityBlob method)
__init__() (pdb_eda.ccp4.DensityBlob method)
(pdb_eda.ccp4.DensityHeader method)
(pdb_eda.ccp4.DensityMatrix method)
(pdb_eda.densityAnalysis.DensityAnalysis method)
(pdb_eda.pdbParser.Atom method)
(pdb_eda.pdbParser.PDBentry method)
(pdb_eda.pdbParser.PDBheader method)
(pdb_eda.utils.SymAtom method)
_calculateOrigin() (pdb_eda.ccp4.DensityHeader method)
_calculateSymmetryAtoms() (pdb_eda.densityAnalysis.DensityAnalysis method)
_testXyzWithinDistance() (in module pdb_eda.utils)
A
aggregateCloud() (pdb_eda.densityAnalysis.DensityAnalysis method)
asymmetryAtomCoords (pdb_eda.densityAnalysis.DensityAnalysis attribute)
asymmetryAtoms (pdb_eda.densityAnalysis.DensityAnalysis attribute)
Atom (class in pdb_eda.pdbParser)
atomCloudDescriptions (pdb_eda.densityAnalysis.DensityAnalysis attribute)
atomMetrics() (pdb_eda.densityAnalysis.DensityAnalysis method)
atomTypeOverlapCompleteness (pdb_eda.densityAnalysis.DensityAnalysis attribute)
atomTypeOverlapIncompleteness (pdb_eda.densityAnalysis.DensityAnalysis attribute)
B
blueBlobList (pdb_eda.densityAnalysis.DensityAnalysis attribute)
C
calculateAtomRegionDensity() (pdb_eda.densityAnalysis.DensityAnalysis method)
calculateAtomRegionDiscrepancies() (pdb_eda.densityAnalysis.DensityAnalysis method)
calculateAtomSpecificBlobStatistics() (pdb_eda.densityAnalysis.DensityAnalysis method)
calculateRegionDensity() (pdb_eda.densityAnalysis.DensityAnalysis method)
calculateRegionDiscrepancy() (pdb_eda.densityAnalysis.DensityAnalysis method)
calculateResidueRegionDensity() (pdb_eda.densityAnalysis.DensityAnalysis method)
calculateResidueRegionDiscrepancies() (pdb_eda.densityAnalysis.DensityAnalysis method)
calculateRsccRsrMetrics() (pdb_eda.densityAnalysis.DensityAnalysis method)
calculateSymmetryAtomRegionDensity() (pdb_eda.densityAnalysis.DensityAnalysis method)
calculateSymmetryAtomRegionDiscrepancies() (pdb_eda.densityAnalysis.DensityAnalysis method)
cleanPDBid() (in module pdb_eda.densityAnalysis)
clone() (pdb_eda.ccp4.DensityBlob method)
createBlobList() (pdb_eda.ccp4.DensityMatrix method)
createCrsLists() (in module pdb_eda.utils)
createFullBlobList() (pdb_eda.ccp4.DensityMatrix method)
createFullCrsList() (in module pdb_eda.utils)
createSymmetryAtoms() (in module pdb_eda.utils)
createTempJSONFile() (in module pdb_eda.fileUtils)
crs2xyzCoord() (pdb_eda.ccp4.DensityHeader method)
D
DensityAnalysis (class in pdb_eda.densityAnalysis)
DensityBlob (class in pdb_eda.ccp4)
densityElectronRatio (pdb_eda.densityAnalysis.DensityAnalysis attribute)
DensityHeader (class in pdb_eda.ccp4)
DensityMatrix (class in pdb_eda.ccp4)
domainCloudDescriptions (pdb_eda.densityAnalysis.DensityAnalysis attribute)
E
estimateF000() (pdb_eda.densityAnalysis.DensityAnalysis method)
F
F000 (pdb_eda.densityAnalysis.DensityAnalysis attribute)
fc (pdb_eda.densityAnalysis.DensityAnalysis attribute)
findAberrantBlobs() (pdb_eda.ccp4.DensityMatrix method)
findCoordContacts() (in module pdb_eda.crystalContacts)
fo (pdb_eda.densityAnalysis.DensityAnalysis attribute)
fromCrsList() (pdb_eda.ccp4.DensityBlob static method)
fromFile() (in module pdb_eda.densityAnalysis)
fromFileHeader() (pdb_eda.ccp4.DensityHeader class method)
fromPDBid() (in module pdb_eda.densityAnalysis)
G
getPointDensityFromCrs() (in module pdb_eda.utils)
(pdb_eda.ccp4.DensityMatrix method)
getPointDensityFromXyz() (pdb_eda.ccp4.DensityMatrix method)
getSphereCrsFromXyz() (in module pdb_eda.utils)
(pdb_eda.ccp4.DensityMatrix method)
getSphereCrsFromXyzList() (in module pdb_eda.utils)
getTotalAbsDensity() (pdb_eda.ccp4.DensityMatrix method)
getTotalDensityFromXyz() (pdb_eda.ccp4.DensityMatrix method)
greenBlobList (pdb_eda.densityAnalysis.DensityAnalysis attribute)
L
loadF000Parameters() (in module pdb_eda.densityAnalysis)
M
meanDensity (pdb_eda.ccp4.DensityMatrix attribute)
medianAbsFoFc() (pdb_eda.densityAnalysis.DensityAnalysis method)
medians (pdb_eda.densityAnalysis.DensityAnalysis attribute)
merge() (pdb_eda.ccp4.DensityBlob method)
N
numVoxelsAggregated (pdb_eda.densityAnalysis.DensityAnalysis attribute)
P
parse() (in module pdb_eda.ccp4)
(in module pdb_eda.pdbParser)
pdb_eda (module)
pdb_eda.ccp4 (module)
pdb_eda.crystalContacts (module)
pdb_eda.densityAnalysis (module)
pdb_eda.fileUtils (module)
pdb_eda.pdbParser (module)
pdb_eda.utils (module)
PDBentry (class in pdb_eda.pdbParser)
PDBheader (class in pdb_eda.pdbParser)
R
read() (in module pdb_eda.ccp4)
readFromPDBID() (in module pdb_eda.ccp4)
readFromURL() (in module pdb_eda.ccp4)
readPDBfile() (in module pdb_eda.pdbParser)
redBlobList (pdb_eda.densityAnalysis.DensityAnalysis attribute)
residueAtomName() (in module pdb_eda.densityAnalysis)
residueCloudDescriptions (pdb_eda.densityAnalysis.DensityAnalysis attribute)
residueMetrics() (pdb_eda.densityAnalysis.DensityAnalysis method)
S
setGlobals() (in module pdb_eda.densityAnalysis)
simulateCrystalNeighborCoordinates() (in module pdb_eda.crystalContacts)
stdDensity (pdb_eda.ccp4.DensityMatrix attribute)
sumOfAbs() (in module pdb_eda.utils)
SymAtom (class in pdb_eda.utils)
symmetryAtomCoords (pdb_eda.densityAnalysis.DensityAnalysis attribute)
symmetryAtoms (pdb_eda.densityAnalysis.DensityAnalysis attribute)
symmetryOnlyAtomCoords (pdb_eda.densityAnalysis.DensityAnalysis attribute)
symmetryOnlyAtoms (pdb_eda.densityAnalysis.DensityAnalysis attribute)
T
testCCP4URL() (in module pdb_eda.densityAnalysis)
testOverlap() (in module pdb_eda.utils)
(pdb_eda.ccp4.DensityBlob method)
testValidCrs() (in module pdb_eda.utils)
testValidCrsList() (in module pdb_eda.utils)
testValidXyz() (in module pdb_eda.utils)
testValidXyzList() (in module pdb_eda.utils)
totalAggregatedDensity (pdb_eda.densityAnalysis.DensityAnalysis attribute)
totalAggregatedElectrons (pdb_eda.densityAnalysis.DensityAnalysis attribute)
X
xyz2crsCoord() (pdb_eda.ccp4.DensityHeader method)
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