rhapsody
Contents
rhapsody package
Subpackages
rhapsody.features package
Submodules
rhapsody.features.BLOSUM module
rhapsody.features.EVmutation module
rhapsody.features.PDB module
rhapsody.features.Pfam module
rhapsody.features.PolyPhen2 module
rhapsody.features.Uniprot module
rhapsody.predict package
Submodules
rhapsody.predict.core module
rhapsody.predict.figures module
rhapsody.predict.main module
rhapsody.train package
Submodules
rhapsody.train.RFtraining module
rhapsody.train.figures module
rhapsody.utils package
Submodules
rhapsody.utils.misc module
rhapsody.utils.settings module
rhapsody
»
Index
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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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G
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I
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M
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P
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Q
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R
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S
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T
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U
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W
_
__init__() (rhapsody.features.PDB.PDBfeatures method)
(rhapsody.features.PDBfeatures method)
(rhapsody.features.Uniprot.UniprotMapping method)
(rhapsody.features.UniprotMapping method)
(rhapsody.PDBfeatures method)
(rhapsody.predict.core.Rhapsody method)
(rhapsody.predict.Rhapsody method)
(rhapsody.Rhapsody method)
(rhapsody.UniprotMapping method)
A
alignAllPDBs() (rhapsody.features.Uniprot.UniprotMapping method)
(rhapsody.features.UniprotMapping method)
(rhapsody.UniprotMapping method)
alignCustomPDB() (rhapsody.features.Uniprot.UniprotMapping method)
(rhapsody.features.UniprotMapping method)
(rhapsody.UniprotMapping method)
alignSinglePDB() (rhapsody.features.Uniprot.UniprotMapping method)
(rhapsody.features.UniprotMapping method)
(rhapsody.UniprotMapping method)
B
BLOSUM_FEATS (in module rhapsody.features.BLOSUM)
C
calcANM() (rhapsody.features.PDB.PDBfeatures method)
(rhapsody.features.PDBfeatures method)
(rhapsody.PDBfeatures method)
calcANMfeatures() (rhapsody.features.PDB.PDBfeatures method)
(rhapsody.features.PDBfeatures method)
(rhapsody.PDBfeatures method)
calcBLOSUMfeatures() (in module rhapsody)
(in module rhapsody.features)
(in module rhapsody.features.BLOSUM)
calcClassMetrics() (in module rhapsody)
(in module rhapsody.train)
(in module rhapsody.train.RFtraining)
calcDeltaSASA() (rhapsody.features.PDB.PDBfeatures method)
(rhapsody.features.PDBfeatures method)
(rhapsody.PDBfeatures method)
calcDSSP() (rhapsody.features.PDB.PDBfeatures method)
(rhapsody.features.PDBfeatures method)
(rhapsody.PDBfeatures method)
calcEvolProperties() (rhapsody.features.Uniprot.UniprotMapping method)
(rhapsody.features.UniprotMapping method)
(rhapsody.UniprotMapping method)
calcFeatures() (rhapsody.predict.core.Rhapsody method)
(rhapsody.predict.Rhapsody method)
(rhapsody.Rhapsody method)
calcGNM() (rhapsody.features.PDB.PDBfeatures method)
(rhapsody.features.PDBfeatures method)
(rhapsody.PDBfeatures method)
calcGNMfeatures() (rhapsody.features.PDB.PDBfeatures method)
(rhapsody.features.PDBfeatures method)
(rhapsody.PDBfeatures method)
calcPathogenicityProbs() (in module rhapsody)
(in module rhapsody.train)
(in module rhapsody.train.RFtraining)
calcPDBfeatures() (in module rhapsody)
(in module rhapsody.features)
(in module rhapsody.features.PDB)
calcPfamFeatures() (in module rhapsody)
(in module rhapsody.features)
(in module rhapsody.features.Pfam)
calcPolyPhen2features() (in module rhapsody)
(in module rhapsody.features)
(in module rhapsody.features.PolyPhen2)
calcPredictions() (in module rhapsody)
(in module rhapsody.predict)
(in module rhapsody.predict.core)
calcSASA() (rhapsody.features.PDB.PDBfeatures method)
(rhapsody.features.PDBfeatures method)
(rhapsody.PDBfeatures method)
calcScoreMetrics() (in module rhapsody)
(in module rhapsody.train)
(in module rhapsody.train.RFtraining)
calcSelFeatures() (rhapsody.features.PDB.PDBfeatures method)
(rhapsody.features.PDBfeatures method)
(rhapsody.PDBfeatures method)
D
delSettings() (in module rhapsody)
(in module rhapsody.utils)
(in module rhapsody.utils.misc)
(in module rhapsody.utils.settings)
DYN_FEATS (in module rhapsody.features.PDB)
E
EVMUT_FEATS (in module rhapsody.features.EVmutation)
exportTrainingData() (rhapsody.predict.core.Rhapsody method)
(rhapsody.predict.Rhapsody method)
(rhapsody.Rhapsody method)
extendDefaultTrainingDataset() (in module rhapsody)
(in module rhapsody.train)
(in module rhapsody.train.RFtraining)
G
getDefaultClassifiers() (in module rhapsody)
(in module rhapsody.utils)
(in module rhapsody.utils.misc)
(in module rhapsody.utils.settings)
getDefaultTrainingDataset() (in module rhapsody)
(in module rhapsody.utils)
(in module rhapsody.utils.misc)
(in module rhapsody.utils.settings)
getFullRecord() (rhapsody.features.Uniprot.UniprotMapping method)
(rhapsody.features.UniprotMapping method)
(rhapsody.UniprotMapping method)
getPDB() (rhapsody.features.PDB.PDBfeatures method)
(rhapsody.features.PDBfeatures method)
(rhapsody.PDBfeatures method)
getPDBcoords() (rhapsody.predict.core.Rhapsody method)
(rhapsody.predict.Rhapsody method)
(rhapsody.Rhapsody method)
getPDBmappings() (rhapsody.features.Uniprot.UniprotMapping method)
(rhapsody.features.UniprotMapping method)
(rhapsody.UniprotMapping method)
getPDBrecords() (rhapsody.features.Uniprot.UniprotMapping method)
(rhapsody.features.UniprotMapping method)
(rhapsody.UniprotMapping method)
getPredictions() (rhapsody.predict.core.Rhapsody method)
(rhapsody.predict.Rhapsody method)
(rhapsody.Rhapsody method)
getResAvgPredictions() (rhapsody.predict.core.Rhapsody method)
(rhapsody.predict.Rhapsody method)
(rhapsody.Rhapsody method)
getSAVcoords() (in module rhapsody)
(in module rhapsody.features)
(in module rhapsody.features.PolyPhen2)
(rhapsody.predict.core.Rhapsody method)
(rhapsody.predict.Rhapsody method)
(rhapsody.Rhapsody method)
getSettings() (in module rhapsody)
(in module rhapsody.utils)
(in module rhapsody.utils.misc)
(in module rhapsody.utils.settings)
getUniprot2PDBmap() (rhapsody.predict.core.Rhapsody method)
(rhapsody.predict.Rhapsody method)
(rhapsody.Rhapsody method)
getUniqueSAVcoords() (rhapsody.predict.core.Rhapsody method)
(rhapsody.predict.Rhapsody method)
(rhapsody.Rhapsody method)
I
importClassifiers() (rhapsody.predict.core.Rhapsody method)
(rhapsody.predict.Rhapsody method)
(rhapsody.Rhapsody method)
importDefaultClassifier() (in module rhapsody)
(in module rhapsody.utils)
(in module rhapsody.utils.misc)
(in module rhapsody.utils.settings)
importFeatMatrix() (rhapsody.predict.core.Rhapsody method)
(rhapsody.predict.Rhapsody method)
(rhapsody.Rhapsody method)
importPolyPhen2output() (rhapsody.predict.core.Rhapsody method)
(rhapsody.predict.Rhapsody method)
(rhapsody.Rhapsody method)
importPrecomputedExtraFeatures() (rhapsody.predict.core.Rhapsody method)
(rhapsody.predict.Rhapsody method)
(rhapsody.Rhapsody method)
initialSetup() (in module rhapsody)
(in module rhapsody.utils)
(in module rhapsody.utils.misc)
(in module rhapsody.utils.settings)
M
mapSAVs2PDB() (in module rhapsody)
(in module rhapsody.features)
(in module rhapsody.features.Uniprot)
mapSingleRes2CustomPDBs() (rhapsody.features.Uniprot.UniprotMapping method)
(rhapsody.features.UniprotMapping method)
(rhapsody.UniprotMapping method)
mapSingleResidue() (rhapsody.features.Uniprot.UniprotMapping method)
(rhapsody.features.UniprotMapping method)
(rhapsody.UniprotMapping method)
module
rhapsody
rhapsody.features
rhapsody.features.BLOSUM
rhapsody.features.EVmutation
rhapsody.features.PDB
rhapsody.features.Pfam
rhapsody.features.PolyPhen2
rhapsody.features.Uniprot
rhapsody.predict
rhapsody.predict.core
rhapsody.predict.figures
rhapsody.predict.main
rhapsody.train
rhapsody.train.figures
rhapsody.train.RFtraining
rhapsody.utils
rhapsody.utils.misc
rhapsody.utils.settings
P
parsePolyPhen2output() (in module rhapsody)
(in module rhapsody.features)
(in module rhapsody.features.PolyPhen2)
PDB_FEATS (in module rhapsody.features.PDB)
PDBfeatures (class in rhapsody)
(class in rhapsody.features)
(class in rhapsody.features.PDB)
PFAM_FEATS (in module rhapsody.features.Pfam)
PP2_FEATS (in module rhapsody.features.PolyPhen2)
print_feat_imp_figure() (in module rhapsody)
(in module rhapsody.train)
(in module rhapsody.train.figures)
print_path_prob_figure() (in module rhapsody)
(in module rhapsody.train)
(in module rhapsody.train.figures)
print_pred_distrib_figure() (in module rhapsody)
(in module rhapsody.train)
(in module rhapsody.train.figures)
print_ROC_figure() (in module rhapsody)
(in module rhapsody.train)
(in module rhapsody.train.figures)
print_sat_mutagen_figure() (in module rhapsody)
(in module rhapsody.predict)
(in module rhapsody.predict.figures)
printPredictions() (rhapsody.predict.core.Rhapsody method)
(rhapsody.predict.Rhapsody method)
(rhapsody.Rhapsody method)
printSAVlist() (in module rhapsody)
(in module rhapsody.features)
(in module rhapsody.features.Uniprot)
Q
queryPolyPhen2() (in module rhapsody)
(in module rhapsody.features)
(in module rhapsody.features.PolyPhen2)
(rhapsody.predict.core.Rhapsody method)
(rhapsody.predict.Rhapsody method)
(rhapsody.Rhapsody method)
queryUniprot() (in module rhapsody)
(in module rhapsody.features)
(in module rhapsody.features.Uniprot)
R
RandomForestCV() (in module rhapsody)
(in module rhapsody.train)
(in module rhapsody.train.RFtraining)
recoverEVmutFeatures() (in module rhapsody)
(in module rhapsody.features)
(in module rhapsody.features.EVmutation)
recoverPickle() (rhapsody.features.PDB.PDBfeatures method)
(rhapsody.features.PDBfeatures method)
(rhapsody.features.Uniprot.UniprotMapping method)
(rhapsody.features.UniprotMapping method)
(rhapsody.PDBfeatures method)
(rhapsody.UniprotMapping method)
refresh() (rhapsody.features.PDB.PDBfeatures method)
(rhapsody.features.PDBfeatures method)
(rhapsody.features.Uniprot.UniprotMapping method)
(rhapsody.features.UniprotMapping method)
(rhapsody.PDBfeatures method)
(rhapsody.UniprotMapping method)
resetTimestamp() (rhapsody.features.PDB.PDBfeatures method)
(rhapsody.features.PDBfeatures method)
(rhapsody.features.Uniprot.UniprotMapping method)
(rhapsody.features.UniprotMapping method)
(rhapsody.PDBfeatures method)
(rhapsody.UniprotMapping method)
rhapsody
module
Rhapsody (class in rhapsody)
(class in rhapsody.predict)
(class in rhapsody.predict.core)
rhapsody() (in module rhapsody)
(in module rhapsody.predict)
(in module rhapsody.predict.main)
rhapsody.features
module
rhapsody.features.BLOSUM
module
rhapsody.features.EVmutation
module
rhapsody.features.PDB
module
rhapsody.features.Pfam
module
rhapsody.features.PolyPhen2
module
rhapsody.features.Uniprot
module
rhapsody.predict
module
rhapsody.predict.core
module
rhapsody.predict.figures
module
rhapsody.predict.main
module
rhapsody.train
module
rhapsody.train.figures
module
rhapsody.train.RFtraining
module
rhapsody.utils
module
rhapsody.utils.misc
module
rhapsody.utils.settings
module
S
savePickle() (rhapsody.features.PDB.PDBfeatures method)
(rhapsody.features.PDBfeatures method)
(rhapsody.features.Uniprot.UniprotMapping method)
(rhapsody.features.UniprotMapping method)
(rhapsody.PDBfeatures method)
(rhapsody.predict.core.Rhapsody method)
(rhapsody.predict.Rhapsody method)
(rhapsody.Rhapsody method)
(rhapsody.UniprotMapping method)
seqScanning() (in module rhapsody)
(in module rhapsody.features)
(in module rhapsody.features.Uniprot)
setAlignAlgorithm() (rhapsody.features.Uniprot.UniprotMapping method)
(rhapsody.features.UniprotMapping method)
(rhapsody.UniprotMapping method)
setCustomPDB() (rhapsody.predict.core.Rhapsody method)
(rhapsody.predict.Rhapsody method)
(rhapsody.Rhapsody method)
setFeatSet() (rhapsody.predict.core.Rhapsody method)
(rhapsody.predict.Rhapsody method)
(rhapsody.Rhapsody method)
setNumModes() (rhapsody.features.PDB.PDBfeatures method)
(rhapsody.features.PDBfeatures method)
(rhapsody.PDBfeatures method)
setSAVs() (rhapsody.predict.core.Rhapsody method)
(rhapsody.predict.Rhapsody method)
(rhapsody.Rhapsody method)
setTrueLabels() (rhapsody.predict.core.Rhapsody method)
(rhapsody.predict.Rhapsody method)
(rhapsody.Rhapsody method)
STR_FEATS (in module rhapsody.features.PDB)
T
trainRFclassifier() (in module rhapsody)
(in module rhapsody.train)
(in module rhapsody.train.RFtraining)
U
UniprotMapping (class in rhapsody)
(class in rhapsody.features)
(class in rhapsody.features.Uniprot)
W
writePDBs() (rhapsody.predict.core.Rhapsody method)
(rhapsody.predict.Rhapsody method)
(rhapsody.Rhapsody method)
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