Index

A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W

A

Acceptor (class in prody.atomic.acceptor)
accession (DBRef attribute)
acidic
acyclic
addCoordset() (AtomGroup method)
(Ensemble method)
(PDBEnsemble method)
addEigenpair() (ANM method)
(EDA method)
(GNM method)
(NMA method)
(PCA method)
(RTB method)
(exANM method)
(exGNM method)
(imANM method)
addEnds() (in module prody.utilities.misctools)
addext() (in module prody.utilities.pathtools)
addFile() (Trajectory method)
addHandler() (PackageLogger method)
addModeSet() (ModeEnsemble method)
addNonstdAminoacid() (in module prody.atomic.flags)
alignByEnsemble() (in module prody.ensemble.functions)
alignChains() (in module prody.proteins.compare)
alignCoordsets() (in module prody.measure.transform)
alignSequencesByChain() (in module prody.sequence.analysis)
alignSequenceToMSA() (in module prody.sequence.analysis)
alignTwoSequencesWithBiopython() (in module prody.sequence.analysis)
aliphatic
all
alnum() (in module prody.utilities.misctools)
altloc
aminoacid
Angle (class in prody.atomic.angle)
anisou
ANM (class in prody.dynamics.anm)
apix (EMDMAP attribute)
apply() (Transformation method)
applyMutinfoCorr() (in module prody.sequence.analysis)
applyMutinfoNorm() (in module prody.sequence.analysis)
applyTransformation() (in module prody.measure.transform)
aromatic
Arrow3D (class in prody.utilities.drawtools)
assignSecstr() (in module prody.proteins.header)
at
Atom (class in prody.atomic.atom)
AtomGroup (class in prody.atomic.atomgroup)
Atomic (class in prody.atomic.atomic)
AtomMap (class in prody.atomic.atommap)
AtomPointer (class in prody.atomic.pointer)
AtomSubset (class in prody.atomic.subset)

B

backbone
backbonefull
backupFile() (in module prody.utilities.pathtools)
basic
BayesianGaussianMixture() (in module prody.chromatin.cluster)
bb
bbfull
bend
bestMatch() (in module prody.proteins.compare)
beta
bin2dec() (in module prody.utilities.misctools)
blastPDB() (in module prody.proteins.blastpdb)
Bond (class in prody.atomic.bond)
bridge
build_tree() (TreeConstructor method)
buildADPMatrix() (in module prody.measure.measure)
buildBiomolecules() (in module prody.proteins.header)
buildCovariance() (EDA method)
(PCA method)
buildDirectInfoMatrix() (in module prody.sequence.analysis)
buildDistMatrix() (in module prody.measure.measure)
buildHessian() (ANM method)
(RTB method)
(exANM method)
(imANM method)
buildKirchhoff() (exGNM method)
(GNM method)
buildMembrane() (exANM method)
(exGNM method)
buildMSA() (in module prody.sequence.analysis)
buildMutinfoMatrix() (in module prody.sequence.analysis)
buildOMESMatrix() (in module prody.sequence.analysis)
buildPCMatrix() (in module prody.sequence.analysis)
buildPDBEnsemble() (in module prody.ensemble.functions)
buildSCAMatrix() (in module prody.sequence.analysis)
buildSeqidMatrix() (in module prody.sequence.analysis)
buried

C

ca
calc2DSimilarity() (in module prody.compounds.functions)
calcAdaptiveANM() (in module prody.dynamics.adaptive)
calcADPAxes() (in module prody.measure.measure)
calcADPs() (in module prody.measure.measure)
calcAngle() (in module prody.measure.measure)
calcAnisousFromModel() (in module prody.dynamics.analysis)
calcANM() (in module prody.dynamics.anm)
calcCenter() (in module prody.measure.measure)
calcChainsNormDistFluct() (in module prody.dynamics.vmdfile)
calcCollectivity() (in module prody.dynamics.analysis)
calcCovariance() (in module prody.dynamics.analysis)
calcCovOverlap() (in module prody.dynamics.compare)
calcCrossCorr() (in module prody.dynamics.analysis)
calcCrossProjection() (in module prody.dynamics.analysis)
calcCumulOverlap() (in module prody.dynamics.compare)
calcDeepFunctionOverlaps() (in module prody.database.goa)
calcDeformVector() (in module prody.measure.measure)
calcDihedral() (in module prody.measure.measure)
calcDistance() (in module prody.measure.measure)
calcDistFlucts() (in module prody.dynamics.analysis)
calcENM() (in module prody.dynamics.functions)
calcEnsembleENMs() (in module prody.dynamics.signature)
calcEnsembleFunctionOverlaps() (in module prody.database.goa)
calcEnsembleSpectralOverlaps() (in module prody.dynamics.signature)
calcFractVariance() (in module prody.dynamics.analysis)
calcGNM() (HiC method)
(in module prody.dynamics.gnm)
calcGNMDomains() (in module prody.chromatin.cluster)
calcGoOverlap() (in module prody.database.goa)
calcGyradius() (in module prody.measure.measure)
calcHinges() (in module prody.dynamics.analysis)
calcHitTime() (in module prody.dynamics.analysis), [1]
calcInertiaTensor() (in module prody.measure.measure)
calcMechStiff() (in module prody.dynamics.mechstiff)
calcMechStiffStatistic() (in module prody.dynamics.mechstiff)
calcMeff() (in module prody.sequence.analysis)
calcMinBranchLength() (in module prody.database.goa)
calcModes() (ANM method)
(EDA method)
(GNM method)
(PCA method)
(RTB method)
(exANM method)
(exGNM method)
(imANM method)
calcMSAOccupancy() (in module prody.sequence.analysis)
calcMSF() (in module prody.measure.measure)
calcOccupancies() (in module prody.ensemble.functions)
calcOmega() (in module prody.measure.measure)
calcOverlap() (in module prody.dynamics.compare)
calcPairDeformationDist() (in module prody.dynamics.analysis)
calcPercentIdentities() (in module prody.sequence.analysis)
calcPerturbResponse() (in module prody.dynamics.perturb)
calcPhi() (in module prody.measure.measure)
calcPrincAxes() (in module prody.measure.measure)
calcProjection() (in module prody.dynamics.analysis)
calcPsi() (in module prody.measure.measure)
calcRankorder() (in module prody.sequence.analysis)
calcRMSD() (in module prody.measure.transform)
calcRMSF() (in module prody.measure.measure)
calcShannonEntropy() (in module prody.sequence.analysis)
calcSignatureCollectivity() (in module prody.dynamics.signature)
calcSignatureCrossCorr() (in module prody.dynamics.signature)
calcSignatureFractVariance() (in module prody.dynamics.signature)
calcSignatureModes() (in module prody.dynamics.signature)
calcSignatureOverlaps() (in module prody.dynamics.signature)
calcSignaturePerturbResponse() (in module prody.dynamics.signature)
calcSignatureSqFlucts() (in module prody.dynamics.signature)
calcSpecDimension() (in module prody.dynamics.analysis)
calcSpectralOverlap() (in module prody.dynamics.compare)
calcSqFlucts() (in module prody.dynamics.analysis)
calcSquareInnerProduct() (in module prody.dynamics.compare)
calcStiffnessRange() (in module prody.dynamics.mechstiff)
calcStiffnessRangeSel() (in module prody.dynamics.mechstiff)
calcSubfamilySpectralOverlaps() (in module prody.dynamics.signature)
calcSubspaceOverlap() (in module prody.dynamics.compare)
calcTempFactors() (in module prody.dynamics.analysis)
calcTransformation() (in module prody.measure.transform)
calcTree() (in module prody.utilities.catchall)
call (Field attribute)
calpha
carbon
CATHDB (class in prody.database.cath)
CATHElement (class in prody.database.cath)
center() (EMDMAP method)
cg
chain
(Chemical attribute)
Chain (class in prody.atomic.chain)
charge
charged
checkCoords() (in module prody.utilities.checkers)
checkIdentifiers() (in module prody.utilities.misctools)
checkTypes() (in module prody.utilities.checkers)
checkUpdates() (in module prody)
checkWeights() (in module prody.utilities.checkers)
Chemical (class in prody.proteins.header)
chid
(Polymer attribute)
chindex
clear() (PackageLogger method)
close() (DCDFile method)
(MSAFile method)
(PackageLogger method)
(TrajBase method)
(TrajFile method)
(Trajectory method)
closed (MSAFile attribute)
closeLogfile() (in module prody)
clusterMatrix() (in module prody.utilities.catchall)
clusterSubfamilies() (in module prody.utilities.catchall)
coil
combineAtomMaps() (in module prody.proteins.compare)
combineEnsembles() (in module prody.ensemble.functions)
comments (Polymer attribute)
Conformation (class in prody.ensemble.conformation)
confProDy() (in module prody)
Contacts (class in prody.measure.contacts)
coordinate() (EMDMAP method)
copy() (Atom method)
(AtomGroup method)
(AtomMap method)
(AtomPointer method)
(AtomSubset method)
(Atomic method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
(Sequence method)
copyFile() (in module prody.utilities.pathtools)
copyMap() (EMDMAP method)
countBytes() (in module prody.utilities.misctools)
countLabel() (MSA method)
critical() (PackageLogger method)
Crossterm (class in prody.atomic.crossterm)
cyclic

D

daliFilterMultimer() (in module prody.database.dali)
daliFilterMultimers() (in module prody.database.dali)
DaliRecord (class in prody.database.dali)
database (DBRef attribute)
dbabbr (DBRef attribute)
DBRef (class in prody.proteins.header)
dbrefs (Polymer attribute)
DCDFile (class in prody.trajectory.dcdfile)
debug() (PackageLogger method)
decToHybrid36() (in module prody.utilities.misctools)
deformAtoms() (in module prody.dynamics.sampling)
defSelectionMacro() (in module prody.atomic.select)
delCoordset() (AtomGroup method)
(Ensemble method)
(PDBEnsemble method)
delData() (AtomGroup method)
(Ensemble method)
(PDBEnsemble method)
delFlags() (AtomGroup method)
delHandler() (PackageLogger method)
delModeSet() (ModeEnsemble method)
delNonstdAminoacid() (in module prody.atomic.flags)
delSelectionMacro() (in module prody.atomic.select)
depr (Field attribute)
depr_pl (Field attribute)
desc (Field attribute)
description (Chemical attribute)
deselect() (Ensemble method)
(PDBEnsemble method)
dictElement() (in module prody.utilities.misctools)
diff (DBRef attribute)
Dihedral (class in prody.atomic.dihedral)
Discretize() (in module prody.chromatin.cluster)
DistanceMatrix (class in prody.utilities.TreeConstruction)
DistanceTreeConstructor (class in prody.utilities.TreeConstruction)
div0() (in module prody.utilities.misctools)
doc (Field attribute)
doc_pl (Field attribute)
Donor (class in prody.atomic.donor)
drawsample() (EMDMAP method)
drawsample_uniform() (EMDMAP method)
drawTree() (in module prody.utilities.drawtools)
dtype (Field attribute)
dummy

E

ec (Polymer attribute)
EDA (class in prody.dynamics.pca)
element
EMDMAP (class in prody.proteins.emdfile)
engineered (Polymer attribute)
Ensemble (class in prody.ensemble.ensemble)
environment variable
HOME
PATH, [1], [2], [3]
PYTHONPATH
error() (PackageLogger method)
ESSA (class in prody.dynamics.essa)
Everything (class in prody.utilities.misctools)
evol_coevol() (in module prody.apps.evol_apps.evol_coevol)
evol_conserv() (in module prody.apps.evol_apps.evol_conserv)
evol_fetch() (in module prody.apps.evol_apps.evol_fetch)
evol_filter() (in module prody.apps.evol_apps.evol_filter)
evol_merge() (in module prody.apps.evol_apps.evol_merge)
evol_occupancy() (in module prody.apps.evol_apps.evol_occupancy)
evol_rankorder() (in module prody.apps.evol_apps.evol_rankorder)
evol_refine() (in module prody.apps.evol_apps.evol_refine)
evol_search() (in module prody.apps.evol_apps.evol_search)
exANM (class in prody.dynamics.exanm)
execDSSP() (in module prody.proteins.dssp)
execSTRIDE() (in module prody.proteins.stride)
exGNM (class in prody.dynamics.exgnm)
exit() (PackageLogger method)
extend() (MSA method)
extendAtomicData() (in module prody.atomic.functions)
extendAtoms() (in module prody.atomic.functions)
extended
extendMode() (in module prody.dynamics.editing)
extendModel() (in module prody.dynamics.editing)
extendVector() (in module prody.dynamics.editing)

F

fetch() (DaliRecord method)
(PDBBlastRecord method)
(QuartataChemicalRecord method)
fetchBIRDviaFTP() (in module prody.compounds.bird)
fetchPDB() (in module prody.proteins.localpdb)
fetchPDBClusters() (in module prody.proteins.pdbclusters)
fetchPDBfromMirror() (in module prody.proteins.localpdb)
fetchPDBLigand() (in module prody.compounds.pdbligands)
fetchPDBviaFTP() (in module prody.proteins.wwpdb)
fetchPDBviaHTTP() (in module prody.proteins.wwpdb)
fetchPfamMSA() (in module prody.database.pfam)
Field (class in prody.atomic.fields)
filename (EMDMAP attribute)
Filenorm() (in module prody.chromatin.norm)
filter() (DaliRecord method)
(QuartataChemicalRecord method)
filterRankedPairs() (in module prody.sequence.analysis)
find() (CATHDB method)
findCommonParentGoIds() (in module prody.database.goa)
findDeepestCommonAncestor() (in module prody.database.goa)
findDeepestFunctions() (in module prody.database.goa)
findFragments() (in module prody.atomic.functions)
findNeighbors() (in module prody.measure.contacts)
findPDBFiles() (in module prody.proteins.localpdb)
findSubgroups() (in module prody.utilities.catchall)
first (DBRef attribute)
fixArraySize() (in module prody.utilities.misctools)
flagDefinition() (in module prody.atomic.flags)
flags (Field attribute)
flush() (DCDFile method)
format (MSAFile attribute)
format_phylip() (DistanceMatrix method)
formula (Chemical attribute)
fragindex
fragment
(Polymer attribute)
Frame (class in prody.trajectory.frame)

G

Gamma (class in prody.dynamics.gamma)
gamma() (Gamma method)
(GammaStructureBased method)
(GammaVariableCutoff method)
GammaStructureBased (class in prody.dynamics.gamma)
GammaVariableCutoff (class in prody.dynamics.gamma)
GaussianMixture() (in module prody.chromatin.cluster)
get() (PackageSettings method)
getAcceptors() (AtomGroup method)
getACSIndex() (Acceptor method)
(Angle method)
(Atom method)
(AtomGroup method)
(AtomMap method)
(AtomPointer method)
(AtomSubset method)
(Bond method)
(Chain method)
(Crossterm method)
(Dihedral method)
(Donor method)
(Improper method)
(NBExclusion method)
(Residue method)
(Segment method)
(Selection method)
getACSLabel() (Atom method)
(AtomGroup method)
(AtomMap method)
(AtomPointer method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
getAlignmentMethod() (in module prody.proteins.compare)
getAltloc() (Atom method)
getAltlocs() (AtomGroup method)
(AtomMap method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
getAngles() (AtomGroup method)
getAnisou() (Atom method)
getAnisous() (AtomGroup method)
(AtomMap method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
getAnistd() (Atom method)
getAnistds() (AtomGroup method)
(AtomMap method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
getApix() (EMDMAP method)
getArray() (ANM method)
(EDA method)
(GNM method)
(MSA method)
(Mode method)
(ModeEnsemble method)
(ModeSet method)
(NMA method)
(PCA method)
(RTB method)
(Sequence method)
(Vector method)
(exANM method)
(exGNM method)
(imANM method)
(sdarray method)
getArrayNx3() (Mode method)
(Vector method)
getAtom() (Residue method)
getAtomGroup() (Acceptor method)
(Angle method)
(Atom method)
(AtomMap method)
(AtomPointer method)
(AtomSubset method)
(Bond method)
(Chain method)
(Crossterm method)
(Dihedral method)
(Donor method)
(Improper method)
(NBExclusion method)
(Residue method)
(Segment method)
(Selection method)
getAtoms() (Acceptor method)
(Angle method)
(Bond method)
(Conformation method)
(Contacts method)
(Crossterm method)
(DCDFile method)
(Dihedral method)
(Donor method)
(Ensemble method)
(Frame method)
(HierView method)
(Improper method)
(ModeEnsemble method)
(NBExclusion method)
(PDBConformation method)
(PDBEnsemble method)
(TrajBase method)
(TrajFile method)
(Trajectory method)
getBest() (PDBBlastRecord method)
getBeta() (Atom method)
getBetas() (AtomGroup method)
(AtomMap method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
getBlockNumbersForRegionFromBinPosition() (in module prody.chromatin.straw)
getBonds() (AtomGroup method)
getBoolArray() (Select method)
getBySerial() (AtomGroup method)
getCanonicalSMILES() (PDBLigandRecord method)
getChain() (HierView method)
(Residue method)
(Segment method)
getCharge() (Atom method)
getCharges() (AtomGroup method)
(AtomMap method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
getChemicalList() (QuartataChemicalRecord method)
getChid() (Atom method)
(Chain method)
(Residue method)
getChids() (AtomGroup method)
(AtomMap method)
(AtomSubset method)
(Chain method)
(GammaStructureBased method)
(Residue method)
(Segment method)
(Selection method)
getChindex() (Atom method)
(Chain method)
getChindices() (AtomGroup method)
(AtomMap method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
getCombined() (exANM method)
(exGNM method)
getCompleteMap() (HiC method)
getConformation() (Ensemble method)
(PDBEnsemble method)
getCoords() (Atom method)
(AtomGroup method)
(AtomMap method)
(AtomSubset method)
(Chain method)
(Conformation method)
(DCDFile method)
(Ensemble method)
(Frame method)
(PDBConformation method)
(PDBEnsemble method)
(Residue method)
(Segment method)
(Selection method)
(TrajBase method)
(TrajFile method)
(Trajectory method)
getCoordsets() (Atom method)
(AtomGroup method)
(AtomMap method)
(AtomSubset method)
(Chain method)
(DCDFile method)
(Ensemble method)
(PDBEnsemble method)
(Residue method)
(Segment method)
(Selection method)
(TrajBase method)
(TrajFile method)
(Trajectory method)
getCount() (KDTree method)
getCovariance() (ANM method)
(EDA method)
(GNM method)
(ModeSet method)
(NMA method)
(PCA method)
(RTB method)
(exANM method)
(exGNM method)
(imANM method)
getCrossterms() (AtomGroup method)
getCSLabels() (Atom method)
(AtomGroup method)
(AtomMap method)
(AtomPointer method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
getCutoff() (ANM method)
(GNM method)
(exANM method)
(exGNM method)
getData() (Atom method)
(AtomGroup method)
(AtomMap method)
(AtomSubset method)
(Chain method)
(Conformation method)
(Ensemble method)
(PDBEnsemble method)
(Residue method)
(Segment method)
(Selection method)
(StarLoop method)
getDataLabels() (Atom method)
(AtomGroup method)
(AtomMap method)
(AtomPointer method)
(AtomSubset method)
(Chain method)
(Ensemble method)
(PDBEnsemble method)
(Residue method)
(Segment method)
(Selection method)
getDataType() (Atom method)
(AtomGroup method)
(AtomMap method)
(AtomPointer method)
(AtomSubset method)
(Chain method)
(Ensemble method)
(PDBEnsemble method)
(Residue method)
(Segment method)
(Selection method)
getDefvecs() (Ensemble method)
(PDBEnsemble method)
getDeviations() (Conformation method)
(Ensemble method)
(Frame method)
(PDBConformation method)
(PDBEnsemble method)
getDict() (StarDataBlock method)
(StarDict method)
(StarLoop method)
getDihedrals() (AtomGroup method)
getDistances() (KDTree method)
getDocstr() (Field method)
getDomainList() (HiC method)
(in module prody.chromatin.functions)
getDomains() (HiC method)
getDonors() (AtomGroup method)
getEigval() (Mode method)
(ModeEnsemble method)
getEigvals() (ANM method)
(EDA method)
(ESSA method)
(GNM method)
(Mode method)
(ModeEnsemble method)
(ModeSet method)
(NMA method)
(PCA method)
(RTB method)
(exANM method)
(exGNM method)
(imANM method)
getEigvec() (Mode method)
(ModeEnsemble method)
getEigvecs() (ANM method)
(EDA method)
(ESSA method)
(GNM method)
(Mode method)
(ModeEnsemble method)
(ModeSet method)
(NMA method)
(PCA method)
(RTB method)
(exANM method)
(exGNM method)
(imANM method)
getElement() (Atom method)
getElements() (AtomGroup method)
(AtomMap method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
getEnsemble() (Conformation method)
(PDBConformation method)
getESSAEnsemble() (ESSA method)
getESSAZscores() (ESSA method)
getFilename() (DCDFile method)
(MSAFile method)
(TrajFile method)
getFilenames() (Trajectory method)
getFilter() (MSAFile method)
getFilterList() (DaliRecord method)
(QuartataChemicalRecord method)
getFirstTimestep() (DCDFile method)
(TrajFile method)
(Trajectory method)
getFlag() (Atom method)
getFlagLabels() (Atom method)
(AtomGroup method)
(AtomMap method)
(AtomPointer method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
getFlags() (AtomGroup method)
(AtomMap method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
getFormat() (MSAFile method)
getFragindex() (Atom method)
getFragindices() (AtomGroup method)
(AtomMap method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
getFrame() (DCDFile method)
(TrajBase method)
(TrajFile method)
getFrameFreq() (DCDFile method)
(TrajFile method)
(Trajectory method)
getGamma() (ANM method)
(GNM method)
(GammaVariableCutoff method)
(exANM method)
(exGNM method)
getGapExtPenalty() (in module prody.proteins.compare)
getGapPenalty() (in module prody.proteins.compare)
getGoodCoverage() (in module prody.proteins.compare)
getGoodSeqId() (in module prody.proteins.compare)
getHandlers() (PackageLogger method)
getHessian() (ANM method)
(RTB method)
(exANM method)
(imANM method)
getHierView() (AtomGroup method)
(AtomMap method)
(Chain method)
(Segment method)
(Selection method)
getHits() (DaliRecord method)
(PDBBlastRecord method)
getIcode() (Atom method)
(Residue method)
getIcodes() (AtomGroup method)
(AtomMap method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
getImpropers() (AtomGroup method)
getIndex() (Atom method)
(Conformation method)
(Frame method)
(MSA method)
(Mode method)
(ModeEnsemble method)
(PDBConformation method)
(Sequence method)
getIndices() (Acceptor method)
(Angle method)
(Atom method)
(AtomMap method)
(AtomSubset method)
(Bond method)
(Chain method)
(Crossterm method)
(Dihedral method)
(Donor method)
(Ensemble method)
(Improper method)
(KDTree method)
(ModeEnsemble method)
(ModeSet method)
(NBExclusion method)
(PDBEnsemble method)
(Residue method)
(Segment method)
(Select method)
(Selection method)
getKirchhoff() (ANM method)
(GNM method)
(HiC method)
(exANM method)
(exGNM method)
getLabel() (MSA method)
(PDBConformation method)
(Sequence method)
getLabels() (ModeEnsemble method)
(MSA method)
(PDBEnsemble method)
(sdarray method)
getLength() (Acceptor method)
(Bond method)
(Donor method)
getLigandResidueCodes() (ESSA method)
getLigandResidueESSAZscores() (ESSA method)
getLigandResidueIndices() (ESSA method)
getLinkage() (in module prody.utilities.catchall)
getLinked() (DCDFile method)
(TrajBase method)
(TrajFile method)
(Trajectory method)
getLoop() (StarDataBlock method)
getMapping() (AtomMap method)
(DaliRecord method)
getMappings() (DaliRecord method)
getMass() (Atom method)
getMasses() (Atom method)
(AtomGroup method)
(AtomMap method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
getMatchingStatus() (ModeEnsemble method)
getMatchScore() (in module prody.proteins.compare)
getMatrix() (Transformation method)
getMembrane() (exANM method)
(exGNM method)
getMismatchScore() (in module prody.proteins.compare)
getModel() (ANM method)
(EDA method)
(GNM method)
(Mode method)
(ModeSet method)
(NMA method)
(PCA method)
(RTB method)
(exANM method)
(exGNM method)
(imANM method)
getModeSets() (ModeEnsemble method)
getMSA() (PDBEnsemble method)
(Sequence method)
getMSFs() (Ensemble method)
(PDBEnsemble method)
getName() (Atom method)
getNames() (AtomGroup method)
(AtomMap method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
getNBExclusions() (AtomGroup method)
getNext() (Residue method)
getNonstdProperties() (in module prody.atomic.flags)
getNormDistFluct() (exGNM method)
(GNM method)
getNormed() (Vector method)
getOccupancies() (AtomGroup method)
(AtomMap method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
getOccupancy() (Atom method)
getOrigin() (EMDMAP method)
getPackagePath() (in module prody.utilities.settings)
getParameters() (PDBBlastRecord method)
getParticularSMILES() (QuartataChemicalRecord method)
getPDBs() (DaliRecord method)
getPocketFeatures() (ESSA method)
getPocketRanks() (ESSA method)
getPocketZscores() (ESSA method)
getPrev() (Residue method)
getProjection() (imANM method)
(RTB method)
getRadii() (AtomGroup method)
(AtomMap method)
(AtomSubset method)
(Chain method)
(GammaVariableCutoff method)
(Residue method)
(Segment method)
(Selection method)
getRadius() (Atom method)
getRemarks() (DCDFile method)
getResidue() (Chain method)
(HierView method)
getResindex() (Atom method)
(Residue method)
getResindices() (AtomGroup method)
(AtomMap method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
getResname() (Atom method)
(Residue method)
getResnames() (AtomGroup method)
(AtomMap method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
getResnum() (Atom method)
(Residue method)
getResnums() (AtomGroup method)
(AtomMap method)
(AtomSubset method)
(Chain method)
(GammaStructureBased method)
(MSA method)
(Residue method)
(Segment method)
(Selection method)
(Sequence method)
getReweightingStatus() (ModeEnsemble method)
getRMSD() (Conformation method)
(Frame method)
(PDBConformation method)
getRMSDs() (Ensemble method)
(PDBEnsemble method)
getRMSFs() (Ensemble method)
(PDBEnsemble method)
getRotation() (Transformation method)
getSecclass() (Atom method)
getSecclasses() (AtomGroup method)
(AtomMap method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
getSecid() (Atom method)
getSecids() (AtomGroup method)
(AtomMap method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
getSecindex() (Atom method)
getSecindices() (AtomGroup method)
(AtomMap method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
getSecstr() (Atom method)
getSecstrs() (AtomGroup method)
(AtomMap method)
(AtomSubset method)
(Chain method)
(GammaStructureBased method)
(Residue method)
(Segment method)
(Selection method)
getSegindex() (Atom method)
getSegindices() (AtomGroup method)
(AtomMap method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
getSegment() (Chain method)
(HierView method)
(Residue method)
getSegname() (Atom method)
(Chain method)
(Residue method)
(Segment method)
getSegnames() (AtomGroup method)
(AtomMap method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
getSelectionMacro() (in module prody.atomic.select)
getSelstr() (Atom method)
(AtomMap method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
getSequence() (Atom method)
(AtomGroup method)
(AtomMap method)
(AtomPointer method)
(AtomSubset method)
(Atomic method)
(Chain method)
(PDBBlastRecord method)
(PDBConformation method)
(Residue method)
(Segment method)
(Selection method)
getSerial() (Atom method)
getSerials() (AtomGroup method)
(AtomMap method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
getSize() (Angle method)
(Crossterm method)
(Dihedral method)
(Improper method)
getSlice() (MSAFile method)
getSMILESList() (QuartataChemicalRecord method)
getTimestep() (DCDFile method)
(TrajFile method)
(Trajectory method)
getTitle() (ANM method)
(Atom method)
(AtomGroup method)
(AtomMap method)
(AtomPointer method)
(AtomSubset method)
(Atomic method)
(Chain method)
(DCDFile method)
(DaliRecord method)
(EDA method)
(EMDMAP method)
(Ensemble method)
(GNM method)
(HiC method)
(MSA method)
(MSAFile method)
(Mode method)
(ModeEnsemble method)
(ModeSet method)
(NMA method)
(PCA method)
(PDBEnsemble method)
(RTB method)
(Residue method)
(Segment method)
(Selection method)
(StarDataBlock method)
(StarDict method)
(StarLoop method)
(TrajBase method)
(TrajFile method)
(Trajectory method)
(Vector method)
(exANM method)
(exGNM method)
(imANM method)
(sdarray method)
getTrajectory() (Frame method)
getTransformation() (PDBConformation method)
getTransformations() (PDBEnsemble method)
getTranslation() (Transformation method)
getTreeFromLinkage() (in module prody.utilities.catchall)
getTrimedMap() (HiC method)
getType() (Atom method)
getTypes() (AtomGroup method)
(AtomMap method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
getUnitcell() (Contacts method)
(Frame method)
getVariance() (Mode method)
(ModeEnsemble method)
getVariances() (ANM method)
(EDA method)
(GNM method)
(Mode method)
(ModeEnsemble method)
(ModeSet method)
(NMA method)
(PCA method)
(RTB method)
(exANM method)
(exGNM method)
(imANM method)
getVector() (Acceptor method)
(Bond method)
(Donor method)
(NBExclusion method)
getVectors() (Angle method)
(Crossterm method)
(Dihedral method)
(Improper method)
getVelocities() (Frame method)
getVMDpath() (in module prody.dynamics.nmdfile)
getWeights() (Conformation method)
(DCDFile method)
(Ensemble method)
(Frame method)
(ModeEnsemble method)
(PDBConformation method)
(PDBEnsemble method)
(TrajBase method)
(TrajFile method)
(Trajectory method)
(sdarray method)
glob() (in module prody.utilities.pathtools)
GNM (class in prody.dynamics.gnm)
GOADictList (class in prody.database.goa)
goto() (DCDFile method)
(TrajBase method)
(TrajFile method)
(Trajectory method)
goToDownloads() (QuartataWebBrowser method)
goToWorkDir() (QuartataWebBrowser method)
gunzip() (in module prody.utilities.pathtools)

H

hasUnitcell() (DCDFile method)
(TrajBase method)
(TrajFile method)
(Trajectory method)
heavy
helix
helix310
helixpi
heme
hetatm
hetero
HiC (class in prody.chromatin.hic)
Hierarchy() (in module prody.chromatin.cluster)
HierView (class in prody.atomic.hierview)
HOME
hybrid36ToDec() (in module prody.utilities.misctools)
hydrogen
hydrophobic

I

icode
(Chemical attribute)
idcode (DBRef attribute)
imANM (class in prody.dynamics.imanm)
importLA() (in module prody.utilities.misctools)
Improper (class in prody.atomic.improper)
IndexFormatter (class in prody.utilities.drawtools)
inferBonds() (AtomGroup method)
info() (PackageLogger method)
inputMap() (TRNET method)
intorfloat() (in module prody.utilities.misctools)
ion
is3d() (ANM method)
(EDA method)
(GNM method)
(Mode method)
(ModeEnsemble method)
(ModeSet method)
(NMA method)
(PCA method)
(RTB method)
(Vector method)
(exANM method)
(exGNM method)
(imANM method)
(sdarray method)
isAligned() (MSA method)
(MSAFile method)
isDataLabel() (Atom method)
(AtomGroup method)
(AtomMap method)
(AtomPointer method)
(AtomSubset method)
(Chain method)
(Ensemble method)
(PDBEnsemble method)
(Residue method)
(Segment method)
(Selection method)
isExecutable() (in module prody.utilities.pathtools)
isFlagLabel() (Atom method)
(AtomGroup method)
(AtomMap method)
(AtomPointer method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
isLinked() (DCDFile method)
(TrajBase method)
(TrajFile method)
(Trajectory method)
isMatched() (ModeEnsemble method)
isPDB() (in module prody.utilities.misctools)
isReadable() (in module prody.utilities.pathtools)
isReserved() (in module prody.atomic.functions)
isReweighted() (ModeEnsemble method)
isSelected() (Ensemble method)
(PDBEnsemble method)
isSelectionMacro() (in module prody.atomic.select)
isSymmetric() (in module prody.utilities.misctools)
isURL() (in module prody.utilities.misctools)
isWritable() (in module prody.utilities.pathtools)
iterAcceptors() (Atom method)
(AtomGroup method)
(AtomMap method)
(AtomPointer method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
iterAngles() (Atom method)
(AtomGroup method)
(AtomMap method)
(AtomPointer method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
iterAtoms() (Atom method)
(AtomGroup method)
(AtomMap method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
iterBonded() (Atom method)
iterBonds() (Atom method)
(AtomGroup method)
(AtomMap method)
(AtomPointer method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
iterChains() (AtomGroup method)
(HierView method)
(Segment method)
iterCoordsets() (Atom method)
(AtomGroup method)
(AtomMap method)
(AtomSubset method)
(Chain method)
(DCDFile method)
(Ensemble method)
(PDBEnsemble method)
(Residue method)
(Segment method)
(Selection method)
(TrajBase method)
(TrajFile method)
(Trajectory method)
iterCrossterms() (Atom method)
(AtomGroup method)
(AtomMap method)
(AtomPointer method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
iterDihedrals() (Atom method)
(AtomGroup method)
(AtomMap method)
(AtomPointer method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
iterDonors() (Atom method)
(AtomGroup method)
(AtomMap method)
(AtomPointer method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
iterFragments() (AtomGroup method)
(in module prody.atomic.functions)
iterImpropers() (Atom method)
(AtomGroup method)
(AtomMap method)
(AtomPointer method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
iterLabels() (MSA method)
iterNBExclusions() (Atom method)
(AtomGroup method)
(AtomMap method)
(AtomPointer method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
iterNeighbors() (in module prody.measure.contacts)
iterPDBFilenames() (in module prody.proteins.localpdb)
iterpose() (Ensemble method)
(PDBEnsemble method)
iterResidues() (AtomGroup method)
(Chain method)
(HierView method)
iterSegments() (AtomGroup method)
(HierView method)

J

joinLinks() (in module prody.utilities.doctools)
joinRepr() (in module prody.utilities.doctools)
joinTerms() (in module prody.utilities.doctools)

K

KDTree (class in prody.kdtree.kdtree)
KMeans() (in module prody.chromatin.cluster)

L

large
last (DBRef attribute)
link() (DCDFile method)
(TrajBase method)
(TrajFile method)
(Trajectory method)
lipid
listNonstdAAProps() (in module prody.atomic.flags)
listPDBCluster() (in module prody.proteins.pdbclusters)
listReservedWords() (in module prody.atomic.functions)
load() (PackageSettings method)
loadAtoms() (in module prody.atomic.functions)
loadEnsemble() (in module prody.ensemble.functions)
loadHiC() (in module prody.chromatin.hic)
loadModeEnsemble() (in module prody.dynamics.signature)
loadModel() (in module prody.dynamics.functions)
loadPDBClusters() (in module prody.proteins.pdbclusters)
loadSignature() (in module prody.dynamics.signature)
loadVector() (in module prody.dynamics.functions)

M

makePath() (in module prody.utilities.pathtools)
makeSymmetric() (in module prody.utilities.misctools)
mapChainOntoChain() (in module prody.proteins.compare)
mapOntoChain() (in module prody.proteins.compare)
mapOntoChainByAlignment() (in module prody.proteins.compare)
mapOntoChains() (in module prody.proteins.compare)
mapped
mappings (DaliRecord attribute)
mass
match() (ModeEnsemble method)
matchAlign() (in module prody.proteins.compare)
matchChains() (in module prody.proteins.compare)
matchModes() (in module prody.dynamics.compare)
max() (sdarray method)
mean() (sdarray method)
medium
mergeMSA() (in module prody.sequence.msa)
meth (Field attribute)
meth_pl (Field attribute)
min() (sdarray method)
Mode (class in prody.dynamics.mode)
ModeEnsemble (class in prody.dynamics.signature)
ModeSet (class in prody.dynamics.modeset)
modified (Polymer attribute)
moveAtoms() (in module prody.measure.transform)
MSA (class in prody.sequence.msa)
MSAFile (class in prody.sequence.msafile)
multilap() (in module prody.utilities.laptools)
mutation (Polymer attribute)

N

name
(Chemical attribute)
(Field attribute)
(Polymer attribute)
natoms (Chemical attribute)
NBExclusion (class in prody.atomic.nbexclusion)
ndim (Field attribute)
neutral
next() (DCDFile method)
(TrajBase method)
(TrajFile method)
(Trajectory method)
nextCoordset() (DCDFile method)
(TrajBase method)
(TrajFile method)
(Trajectory method)
nextIndex() (DCDFile method)
(TrajBase method)
(TrajFile method)
(Trajectory method)
nitrogen
nj() (DistanceTreeConstructor method)
NMA (class in prody.dynamics.nma)
noh
none
(Field attribute)
nonstdaa
normalize() (HiC method)
nucleic
nucleobase
nucleoside
nucleotide
numAcceptors() (AtomGroup method)
numAngles() (AtomGroup method)
numAtoms() (ANM method)
(Atom method)
(AtomGroup method)
(AtomMap method)
(AtomSubset method)
(Chain method)
(Conformation method)
(DCDFile method)
(EDA method)
(Ensemble method)
(Frame method)
(GNM method)
(Mode method)
(ModeEnsemble method)
(ModeSet method)
(NMA method)
(PCA method)
(PDBConformation method)
(PDBEnsemble method)
(RTB method)
(Residue method)
(Segment method)
(Selection method)
(TrajBase method)
(TrajFile method)
(Trajectory method)
(Vector method)
(exANM method)
(exGNM method)
(imANM method)
(sdarray method)
numbonds
numBonds() (Atom method)
(AtomGroup method)
numBytes() (AtomGroup method)
numChains() (AtomGroup method)
(HierView method)
(Segment method)
numConfs() (Ensemble method)
(PDBEnsemble method)
numCoordsets() (Atom method)
(AtomGroup method)
(AtomMap method)
(AtomPointer method)
(AtomSubset method)
(Chain method)
(DCDFile method)
(Ensemble method)
(PDBEnsemble method)
(Residue method)
(Segment method)
(Selection method)
(TrajBase method)
(TrajFile method)
(Trajectory method)
numCrossterms() (AtomGroup method)
numDihedrals() (AtomGroup method)
numDOF() (ANM method)
(EDA method)
(GNM method)
(Mode method)
(ModeSet method)
(NMA method)
(PCA method)
(RTB method)
(Vector method)
(exANM method)
(exGNM method)
(imANM method)
numDonors() (AtomGroup method)
numDummies() (AtomMap method)
numEntries() (ANM method)
(EDA method)
(GNM method)
(Mode method)
(ModeSet method)
(NMA method)
(PCA method)
(RTB method)
(Vector method)
(exANM method)
(exGNM method)
(imANM method)
numFiles() (Trajectory method)
numFixed() (DCDFile method)
(TrajFile method)
(Trajectory method)
numFragments() (AtomGroup method)
numFrames() (DCDFile method)
(TrajBase method)
(TrajFile method)
(Trajectory method)
numGaps() (Sequence method)
numidx2matidx() (EMDMAP method)
numImpropers() (AtomGroup method)
numIndexed() (MSA method)
numMapped() (AtomMap method)
numModes() (ANM method)
(EDA method)
(GNM method)
(Mode method)
(ModeEnsemble method)
(ModeSet method)
(NMA method)
(PCA method)
(RTB method)
(Vector method)
(exANM method)
(exGNM method)
(imANM method)
numModeSets() (ModeEnsemble method)
(sdarray method)
numNBExclusions() (AtomGroup method)
numResidues() (AtomGroup method)
(Chain method)
(HierView method)
(MSA method)
(Sequence method)
numSegments() (AtomGroup method)
(HierView method)
numSelected() (Conformation method)
(DCDFile method)
(Ensemble method)
(Frame method)
(PDBConformation method)
(PDBEnsemble method)
(TrajBase method)
(TrajFile method)
(Trajectory method)
numSequences() (MSA method)

O

occupancy
openDB() (in module prody.utilities.pathtools)
openFile() (in module prody.utilities.pathtools)
openSQLite() (in module prody.utilities.pathtools)
openURL() (in module prody.utilities.pathtools)
origin (EMDMAP attribute)
outputEdges() (TRNET method)
oxygen

P

PackageLogger (class in prody.utilities.logger)
PackageSettings (class in prody.utilities.settings)
pairModes() (in module prody.dynamics.compare)
parseArray() (in module prody.dynamics.functions)
parseBIRD() (in module prody.compounds.bird)
parseCCD() (in module prody.compounds.ccd)
parseChainsList() (in module prody.proteins.pdbfile)
parseChemicals() (QuartataWebBrowser method)
parseDCD() (in module prody.trajectory.dcdfile)
parseDSSP() (in module prody.proteins.dssp)
parseEMD() (in module prody.proteins.emdfile)
parseEMDStream() (in module prody.proteins.emdfile)
parseGAF() (in module prody.database.goa)
parseHeatmap() (in module prody.dynamics.heatmapper)
parseHiC() (in module prody.chromatin.hic)
parseHiCStream() (in module prody.chromatin.hic)
parseImagesFromSTAR() (in module prody.proteins.starfile)
parseMMCIF() (in module prody.proteins.ciffile)
parseMMCIFStream() (in module prody.proteins.ciffile)
parseModes() (in module prody.dynamics.functions)
parseMSA() (in module prody.sequence.msafile)
parseNMD() (in module prody.dynamics.nmdfile)
parseOBO() (in module prody.database.goa)
parsePDB() (in module prody.proteins.pdbfile)
parsePDBHeader() (in module prody.proteins.header)
parsePDBLigand() (in module prody.compounds.pdbligands)
parsePDBs() (CATHElement method)
(UniprotRecord method)
parsePDBStream() (in module prody.proteins.pdbfile)
parsePfamPDBs() (in module prody.database.pfam)
parsePQR() (in module prody.proteins.pdbfile)
parsePSF() (in module prody.trajectory.psffile)
parseSparseMatrix() (in module prody.dynamics.functions)
parseSTAR() (in module prody.proteins.starfile)
parseSTRIDE() (in module prody.proteins.stride)
PATH, [1], [2], [3]
pathPDBFolder() (in module prody.proteins.localpdb)
pathPDBMirror() (in module prody.proteins.localpdb)
pathVMD() (in module prody.dynamics.nmdfile)
PCA (class in prody.dynamics.pca)
PDBBlastRecord (class in prody.proteins.blastpdb)
PDBConformation (class in prody.ensemble.conformation)
PDBEnsemble (class in prody.ensemble.pdbensemble)
pdbentry (Chemical attribute)
(Polymer attribute)
PDBLigandRecord (class in prody.compounds.pdbligands)
pdbter
performDSSP() (in module prody.proteins.dssp)
performSTRIDE() (in module prody.proteins.stride)
performSVD() (EDA method)
(PCA method)
pickCentral() (in module prody.measure.measure)
pickCentralAtom() (in module prody.measure.measure)
pickCentralConf() (in module prody.measure.measure)
pickle() (in module prody.utilities.pathtools)
pimshow() (in module prody.dynamics.plotting)
plog() (in module prody)
polar
Polymer (class in prody.proteins.header)
pop() (GOADictList method)
(PackageSettings method)
(StarDataBlock method)
(StarDict method)
pplot() (in module prody.dynamics.plotting)
prefix (PackageLogger attribute)
printData() (StarDataBlock method)
(StarDict method)
(StarLoop method)
printme() (in module prody.chromatin.straw)
printOverlapTable() (in module prody.dynamics.compare)
printRMSD() (in module prody.measure.transform)
private (Field attribute)
prody (module)
prody.apps (module)
prody.apps.evol_apps.evol_coevol (module)
prody.apps.evol_apps.evol_conserv (module)
prody.apps.evol_apps.evol_fetch (module)
prody.apps.evol_apps.evol_filter (module)
prody.apps.evol_apps.evol_merge (module)
prody.apps.evol_apps.evol_occupancy (module)
prody.apps.evol_apps.evol_rankorder (module)
prody.apps.evol_apps.evol_refine (module)
prody.apps.evol_apps.evol_search (module)
prody.apps.prody_apps.prody_align (module)
prody.apps.prody_apps.prody_anm (module)
prody.apps.prody_apps.prody_biomol (module)
prody.apps.prody_apps.prody_blast (module)
prody.apps.prody_apps.prody_catdcd (module)
prody.apps.prody_apps.prody_contacts (module)
prody.apps.prody_apps.prody_fetch (module)
prody.apps.prody_apps.prody_gnm (module)
prody.apps.prody_apps.prody_pca (module)
prody.apps.prody_apps.prody_select (module)
prody.atomic (module)
prody.atomic.acceptor (module)
prody.atomic.angle (module)
prody.atomic.atom (module)
prody.atomic.atomgroup (module)
prody.atomic.atomic (module)
prody.atomic.atommap (module)
prody.atomic.bond (module)
prody.atomic.chain (module)
prody.atomic.crossterm (module)
prody.atomic.dihedral (module)
prody.atomic.donor (module)
prody.atomic.fields (module)
prody.atomic.flags (module)
prody.atomic.functions (module)
prody.atomic.hierview (module)
prody.atomic.improper (module)
prody.atomic.nbexclusion (module)
prody.atomic.pointer (module)
prody.atomic.residue (module)
prody.atomic.segment (module)
prody.atomic.select (module)
prody.atomic.selection (module)
prody.atomic.subset (module)
prody.chromatin (module)
prody.chromatin.cluster (module)
prody.chromatin.functions (module)
prody.chromatin.hic (module)
prody.chromatin.norm (module)
prody.chromatin.straw (module)
prody.compounds (module)
prody.compounds.bird (module)
prody.compounds.ccd (module)
prody.compounds.functions (module)
prody.compounds.pdbligands (module)
prody.database (module)
prody.database.cath (module)
prody.database.dali (module)
prody.database.goa (module)
prody.database.pfam (module)
prody.database.quartataweb (module)
prody.database.uniprot (module)
prody.domain_decomposition (module)
prody.domain_decomposition.spectrus (module)
prody.dynamics (module)
prody.dynamics.adaptive (module)
prody.dynamics.analysis (module)
prody.dynamics.anm (module)
prody.dynamics.compare (module)
prody.dynamics.editing (module)
prody.dynamics.essa (module)
prody.dynamics.exanm (module)
prody.dynamics.exgnm (module)
prody.dynamics.functions (module)
prody.dynamics.gamma (module)
prody.dynamics.gnm (module)
prody.dynamics.heatmapper (module)
prody.dynamics.imanm (module)
prody.dynamics.mechstiff (module)
prody.dynamics.mode (module)
prody.dynamics.modeset (module)
prody.dynamics.nma (module)
prody.dynamics.nmdfile (module)
prody.dynamics.pca (module)
prody.dynamics.perturb (module)
prody.dynamics.plotting (module)
prody.dynamics.rtb (module)
prody.dynamics.sampling (module)
prody.dynamics.signature (module)
prody.dynamics.vmdfile (module)
prody.ensemble (module)
prody.ensemble.conformation (module)
prody.ensemble.ensemble (module)
prody.ensemble.functions (module)
prody.ensemble.pdbensemble (module)
prody.kdtree (module)
prody.kdtree.kdtree (module)
prody.measure (module)
prody.measure.contacts (module)
prody.measure.measure (module)
prody.measure.transform (module)
prody.proteins (module)
prody.proteins.blastpdb (module)
prody.proteins.ciffile (module)
prody.proteins.compare (module)
prody.proteins.dssp (module)
prody.proteins.emdfile (module)
prody.proteins.functions (module)
prody.proteins.header (module)
prody.proteins.localpdb (module)
prody.proteins.pdbclusters (module)
prody.proteins.pdbfile (module)
prody.proteins.starfile (module)
prody.proteins.stride (module)
prody.proteins.wwpdb (module)
prody.sequence (module)
prody.sequence.analysis (module)
prody.sequence.msa (module)
prody.sequence.msafile (module)
prody.sequence.plotting (module)
prody.sequence.sequence (module)
prody.trajectory (module)
prody.trajectory.dcdfile (module)
prody.trajectory.frame (module)
prody.trajectory.psffile (module)
prody.trajectory.trajbase (module)
prody.trajectory.trajectory (module)
prody.trajectory.trajfile (module)
prody.utilities (module)
prody.utilities.catchall (module)
prody.utilities.checkers (module)
prody.utilities.doctools (module)
prody.utilities.drawtools (module)
prody.utilities.eigtools (module)
prody.utilities.laptools (module)
prody.utilities.logger (module)
prody.utilities.misctools (module)
prody.utilities.pathtools (module)
prody.utilities.seqtools (module)
prody.utilities.settings (module)
prody.utilities.TreeConstruction (module)
prody_align() (in module prody.apps.prody_apps.prody_align)
prody_anm() (in module prody.apps.prody_apps.prody_anm)
prody_biomol() (in module prody.apps.prody_apps.prody_biomol)
prody_blast() (in module prody.apps.prody_apps.prody_blast)
prody_catdcd() (in module prody.apps.prody_apps.prody_catdcd)
prody_contacts() (in module prody.apps.prody_apps.prody_contacts)
prody_fetch() (in module prody.apps.prody_apps.prody_fetch)
prody_gnm() (in module prody.apps.prody_apps.prody_gnm)
prody_pca() (in module prody.apps.prody_apps.prody_pca)
prody_select() (in module prody.apps.prody_apps.prody_select)
progress() (PackageLogger method)
protein
psplot() (in module prody.dynamics.signature)
purine
pyrimidine
Python Enhancement Proposals
PEP 8, [1]
PEP 8#imports
PEP 8#whitespace-in-expressions-and-statements
PYTHONPATH

Q

QuartataChemicalRecord (class in prody.database.quartataweb)
QuartataWebBrowser (class in prody.database.quartataweb)
queryGOA() (in module prody.database.goa)
queryUniprot() (in module prody.database.uniprot)

R

radius
rangeString() (in module prody.utilities.misctools)
rankPockets() (ESSA method)
readBlock() (in module prody.chromatin.straw)
readFooter() (in module prody.chromatin.straw)
readHeader() (in module prody.chromatin.straw)
readMatrix() (in module prody.chromatin.straw)
readMatrixZoomData() (in module prody.chromatin.straw)
readNormalizationVector() (in module prody.chromatin.straw)
readonly (Field attribute)
reduceModel() (in module prody.dynamics.editing)
reduceModelByMask() (in module prody.dynamics.editing)
refineEnsemble() (in module prody.ensemble.functions)
refineMSA() (in module prody.sequence.msa)
relpath() (in module prody.utilities.pathtools)
reorder() (ModeEnsemble method)
reorderMatrix() (in module prody.utilities.catchall)
report() (PackageLogger method)
reset() (DCDFile method)
(MSAFile method)
(TrajBase method)
(TrajFile method)
(Trajectory method)
resetTicks() (in module prody.dynamics.plotting)
resid
Residue (class in prody.atomic.residue)
resindex
resname
(Chemical attribute)
resnum
(Chemical attribute)
reweight() (ModeEnsemble method)
RTB (class in prody.dynamics.rtb)
run() (TRNET method)
run_n_pause() (TRNET method)
runOnce() (TRNET method)

S

sameChid() (in module prody.proteins.compare)
sampleModes() (in module prody.dynamics.sampling)
save() (CATHDB method)
(PackageSettings method)
saveAtoms() (in module prody.atomic.functions)
saveEigvals() (ESSA method)
saveEigvecs() (ESSA method)
saveEnsemble() (in module prody.ensemble.functions)
saveESSAEnsemble() (ESSA method)
saveESSAZscores() (ESSA method)
saveHiC() (in module prody.chromatin.hic)
saveLigandResidueCodes() (ESSA method)
saveLigandResidueESSAZscores() (ESSA method)
saveModeEnsemble() (in module prody.dynamics.signature)
saveModel() (in module prody.dynamics.functions)
savePocketFeatures() (ESSA method)
savePocketRanks() (ESSA method)
savePocketZscores() (ESSA method)
saveSignature() (in module prody.dynamics.signature)
saveVector() (in module prody.dynamics.functions)
sc
scanPockets() (ESSA method)
scanResidues() (ESSA method)
SCN() (in module prody.chromatin.norm)
sdarray (class in prody.dynamics.signature)
search() (CATHDB method)
(KDTree method)
(StarDataBlock method)
(StarDict method)
(StarLoop method)
searchDali() (in module prody.database.dali)
searchPfam() (in module prody.database.pfam)
searchQuartataWeb() (in module prody.database.quartataweb)
searchUniprot() (in module prody.database.uniprot)
secclass
secid
secindex
secondary
secstr
segindex
segment
Segment (class in prody.atomic.segment)
segname
Select (class in prody.atomic.select)
select() (Atom method)
(AtomGroup method)
(AtomMap method)
(AtomPointer method)
(AtomSubset method)
(Atomic method)
(Chain method)
(Contacts method)
(Ensemble method)
(PDBEnsemble method)
(Residue method)
(Segment method)
(Select method)
(Selection method)
Selection (class in prody.atomic.selection)
SelectionError
SelectionWarning
selstr (Field attribute)
Sequence (class in prody.sequence.sequence)
sequence (Polymer attribute)
serial
setAcceptors() (AtomGroup method)
setACSIndex() (Acceptor method)
(Angle method)
(Atom method)
(AtomGroup method)
(AtomMap method)
(AtomPointer method)
(AtomSubset method)
(Bond method)
(Chain method)
(Crossterm method)
(Dihedral method)
(Donor method)
(Improper method)
(NBExclusion method)
(Residue method)
(Segment method)
(Selection method)
setACSLabel() (AtomGroup method)
setAlignmentMethod() (in module prody.proteins.compare)
setAltloc() (Atom method)
setAltlocs() (AtomGroup method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
setAngles() (AtomGroup method)
setAnisou() (Atom method)
setAnisous() (AtomGroup method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
setAnistd() (Atom method)
setAnistds() (AtomGroup method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
setApix() (EMDMAP method)
setAtoms() (DCDFile method)
(Ensemble method)
(ModeEnsemble method)
(PDBEnsemble method)
(TrajBase method)
(TrajFile method)
(Trajectory method)
setBeta() (Atom method)
setBetas() (AtomGroup method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
setBonds() (AtomGroup method)
setBrowserType() (QuartataWebBrowser method)
setCharge() (Atom method)
setCharges() (AtomGroup method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
setChid() (Atom method)
(Chain method)
setChids() (AtomGroup method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
setCoords() (Atom method)
(AtomGroup method)
(AtomMap method)
(AtomSubset method)
(Chain method)
(DCDFile method)
(Ensemble method)
(PDBEnsemble method)
(Residue method)
(Segment method)
(Selection method)
(TrajBase method)
(TrajFile method)
(Trajectory method)
setCovariance() (EDA method)
(PCA method)
setCrossterms() (AtomGroup method)
setCSLabels() (AtomGroup method)
setData() (Atom method)
(AtomGroup method)
(AtomSubset method)
(Chain method)
(Ensemble method)
(PDBEnsemble method)
(QuartataWebBrowser method)
(Residue method)
(Segment method)
(Selection method)
setDataSource() (QuartataWebBrowser method)
setDihedrals() (AtomGroup method)
setDomains() (HiC method)
setDonors() (AtomGroup method)
setDrugGroup() (QuartataWebBrowser method)
setEigens() (EDA method)
(NMA method)
(PCA method)
setElement() (Atom method)
setElements() (AtomGroup method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
setFilter() (MSAFile method)
setFlag() (Atom method)
setFlags() (AtomGroup method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
setGapExtPenalty() (in module prody.proteins.compare)
setGapPenalty() (in module prody.proteins.compare)
setGoodCoverage() (in module prody.proteins.compare)
setGoodSeqId() (in module prody.proteins.compare)
setHessian() (ANM method)
(RTB method)
(exANM method)
(imANM method)
setIcode() (Atom method)
(Residue method)
setIcodes() (AtomGroup method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
setImpropers() (AtomGroup method)
setInputType() (QuartataWebBrowser method)
setJObID() (QuartataWebBrowser method)
setKirchhoff() (exGNM method)
(GNM method)
setLabel() (PDBConformation method)
setLabels() (ModeEnsemble method)
setMass() (Atom method)
setMasses() (AtomGroup method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
setMatchingStatus() (ModeEnsemble method)
setMatchScore() (in module prody.proteins.compare)
setMismatchScore() (in module prody.proteins.compare)
setName() (Atom method)
setNames() (AtomGroup method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
setNBExclusions() (AtomGroup method)
setNumPredictions() (QuartataWebBrowser method)
setOccupancies() (AtomGroup method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
setOccupancy() (Atom method)
setOrigin() (EMDMAP method)
setPackagePath() (in module prody.utilities.settings)
setQueryType() (QuartataWebBrowser method)
setRadii() (AtomGroup method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
setRadius() (Atom method)
setResname() (Atom method)
(Residue method)
setResnames() (AtomGroup method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
setResnum() (Atom method)
(Residue method)
setResnums() (AtomGroup method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
setReweightingStatus() (ModeEnsemble method)
setRotation() (Transformation method)
setSecclass() (Atom method)
setSecclasses() (AtomGroup method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
setSecid() (Atom method)
setSecids() (AtomGroup method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
setSecindex() (Atom method)
setSecindices() (AtomGroup method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
setSecstr() (Atom method)
setSecstrs() (AtomGroup method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
setSegname() (Atom method)
(Segment method)
setSegnames() (AtomGroup method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
setSerial() (Atom method)
setSerials() (AtomGroup method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
setSlice() (MSAFile method)
setSystem() (ESSA method)
setTitle() (ANM method)
(AtomGroup method)
(AtomMap method)
(DCDFile method)
(EDA method)
(EMDMAP method)
(Ensemble method)
(GNM method)
(HiC method)
(MSA method)
(MSAFile method)
(NMA method)
(PCA method)
(PDBEnsemble method)
(RTB method)
(StarDataBlock method)
(StarDict method)
(StarLoop method)
(TrajBase method)
(TrajFile method)
(Trajectory method)
(Vector method)
(exANM method)
(exGNM method)
(imANM method)
setTranslation() (Transformation method)
setType() (Atom method)
setTypes() (AtomGroup method)
(AtomSubset method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
setVMDpath() (in module prody.dynamics.nmdfile)
setWeights() (DCDFile method)
(Ensemble method)
(ModeEnsemble method)
(PDBEnsemble method)
(TrajBase method)
(TrajFile method)
(Trajectory method)
(sdarray method)
showAlignment() (in module prody.sequence.analysis)
showAtomicLines() (in module prody.dynamics.plotting)
showAtomicMatrix() (in module prody.dynamics.plotting)
showContactMap() (in module prody.dynamics.plotting)
showCrossCorr() (in module prody.dynamics.plotting)
showCrossProjection() (in module prody.dynamics.plotting)
showCumulFractVars() (in module prody.dynamics.plotting)
showCumulOverlap() (in module prody.dynamics.plotting)
showDiffMatrix() (in module prody.dynamics.plotting)
showDirectInfoMatrix() (in module prody.sequence.plotting)
showDomainBar() (in module prody.dynamics.plotting)
showDomains() (in module prody.chromatin.functions)
showEllipsoid() (in module prody.dynamics.plotting)
showEmbedding() (in module prody.chromatin.functions)
showESSAProfile() (ESSA method)
showFigure() (in module prody.utilities.misctools)
showFractVars() (in module prody.dynamics.plotting)
showGoLineage() (in module prody.database.goa)
showHeatmap() (in module prody.dynamics.heatmapper)
showLines() (in module prody.utilities.catchall)
showLinkage() (in module prody.chromatin.cluster)
showMatrix() (in module prody.utilities.catchall)
showMeanMechStiff() (in module prody.dynamics.plotting)
showMechStiff() (in module prody.dynamics.plotting)
showMode() (in module prody.dynamics.plotting)
showMSAOccupancy() (in module prody.sequence.plotting)
showMutinfoMatrix() (in module prody.sequence.plotting)
showNormDistFunct() (in module prody.dynamics.plotting)
showNormedSqFlucts() (in module prody.dynamics.plotting)
showOccupancies() (in module prody.ensemble.functions)
showOverlap() (in module prody.dynamics.plotting)
showOverlaps() (in module prody.dynamics.plotting)
showOverlapTable() (in module prody.dynamics.plotting)
showPairDeformationDist() (in module prody.dynamics.plotting)
showPerturbResponse() (in module prody.dynamics.plotting)
showPocketZscores() (ESSA method)
showProjection() (in module prody.dynamics.plotting)
showProtein() (in module prody.proteins.functions)
showScaledSqFlucts() (in module prody.dynamics.plotting)
showSCAMatrix() (in module prody.sequence.plotting)
showShannonEntropy() (in module prody.sequence.plotting)
showSignature1D() (in module prody.dynamics.signature)
showSignatureAtomicLines() (in module prody.dynamics.signature)
showSignatureCollectivity() (in module prody.dynamics.signature)
showSignatureCrossCorr() (in module prody.dynamics.signature)
showSignatureDistribution() (in module prody.dynamics.signature)
showSignatureMode() (in module prody.dynamics.signature)
showSignatureOverlaps() (in module prody.dynamics.signature)
showSignatureSqFlucts() (in module prody.dynamics.signature)
showSignatureVariances() (in module prody.dynamics.signature)
showSqFlucts() (in module prody.dynamics.plotting)
showSubfamilySpectralOverlaps() (in module prody.dynamics.signature)
showTree() (in module prody.dynamics.plotting)
showTree_networkx() (in module prody.dynamics.plotting)
showVarianceBar() (in module prody.dynamics.signature)
sidechain
siguij
skip() (DCDFile method)
(TrajBase method)
(TrajFile method)
(Trajectory method)
sleep() (PackageLogger method)
sliceAtomicData() (in module prody.atomic.functions)
sliceAtoms() (in module prody.atomic.functions)
sliceMode() (in module prody.dynamics.editing)
sliceModel() (in module prody.dynamics.editing)
sliceModelByMask() (in module prody.dynamics.editing)
sliceVector() (in module prody.dynamics.editing)
small
sortAtoms() (in module prody.atomic.functions)
specMergeMSA() (in module prody.sequence.msa)
split (MSA attribute)
splitSeqLabel() (in module prody.sequence.msafile)
(in module prody.utilities.seqtools)
sqrtm() (in module prody.utilities.misctools)
SQRTVCnorm() (in module prody.chromatin.norm)
StarDataBlock (class in prody.proteins.starfile)
StarDict (class in prody.proteins.starfile)
StarLoop (class in prody.proteins.starfile)
start() (PackageLogger method)
startLogfile() (in module prody)
startswith() (in module prody.utilities.misctools)
std() (sdarray method)
stdaa
straw() (in module prody.chromatin.straw)
sugar
sulfur
superpose() (Ensemble method)
(Frame method)
(PDBEnsemble method)
(in module prody.measure.transform)
surface
sympath() (in module prody.utilities.pathtools)
synonym (Field attribute)
synonyms (Chemical attribute)
(Polymer attribute)

T

tabulate() (in module prody.utilities.doctools)
thresholdMap() (EMDMAP method)
timeit() (PackageLogger method)
timing() (PackageLogger method)
toAtomGroup() (Atom method)
(AtomGroup method)
(AtomMap method)
(AtomPointer method)
(AtomSubset method)
(Atomic method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
toTEMPyAtom() (Atom method)
toTEMPyAtoms() (Atom method)
(AtomGroup method)
(AtomMap method)
(AtomPointer method)
(AtomSubset method)
(Atomic method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
toTEMPyMap() (EMDMAP method)
toTEMPyStructure() (Atom method)
(AtomGroup method)
(AtomMap method)
(AtomPointer method)
(AtomSubset method)
(Atomic method)
(Chain method)
(Residue method)
(Segment method)
(Selection method)
TrajBase (class in prody.trajectory.trajbase)
Trajectory (class in prody.trajectory.trajectory)
TrajFile (class in prody.trajectory.trajfile)
Transformation (class in prody.measure.transform)
traverseMode() (in module prody.dynamics.sampling)
TreeConstructor (class in prody.utilities.TreeConstruction)
trimAtomsUsingMSA() (in module prody.sequence.analysis)
trimModel() (in module prody.dynamics.editing)
trimModelByMask() (in module prody.dynamics.editing)
trimPDBEnsemble() (in module prody.ensemble.functions)
TRNET (class in prody.proteins.emdfile)
turn
type

U

undoMatching() (ModeEnsemble method)
undoReweighting() (ModeEnsemble method)
UniprotRecord (class in prody.database.uniprot)
uniqueSequences() (in module prody.sequence.analysis)
unpickle() (in module prody.utilities.pathtools)
update() (CATHDB method)
(HierView method)
(PackageLogger method)
(PackageSettings method)
(Selection method)
updateHomePage() (QuartataWebBrowser method)
upgma() (DistanceTreeConstructor method)
userDefined() (in module prody.proteins.compare)

V

VCnorm() (in module prody.chromatin.norm)
Vector (class in prody.dynamics.mode)
verbosity (PackageLogger attribute)
view() (HiC method)
view3D() (in module prody.proteins.functions)
viewNMDinVMD() (in module prody.dynamics.nmdfile)
viewResults() (QuartataWebBrowser method)

W

warn() (PackageLogger method)
warning() (PackageLogger method)
water
weights (sdarray attribute)
which() (in module prody.utilities.pathtools)
wmean() (in module prody.utilities.misctools)
wrapAtoms() (in module prody.measure.transform)
wrapText() (in module prody.utilities.doctools)
write() (DCDFile method)
(MSAFile method)
(PackageLogger method)
writeArray() (in module prody.dynamics.functions)
writeChainsList() (in module prody.proteins.pdbfile)
writeDCD() (in module prody.trajectory.dcdfile)
writeDeformProfile() (in module prody.dynamics.vmdfile)
writeEMD() (in module prody.proteins.emdfile)
writeESSAZscoresToPDB() (ESSA method)
writeHeatmap() (in module prody.dynamics.heatmapper)
writeMap() (in module prody.chromatin.hic)
writeModes() (in module prody.dynamics.functions)
writeMSA() (in module prody.sequence.msafile)
writeNMD() (in module prody.dynamics.nmdfile)
writeOverlapTable() (in module prody.dynamics.compare)
writePDB() (in module prody.proteins.pdbfile)
writePDBStream() (in module prody.proteins.pdbfile)
writePocketRanksToCSV() (ESSA method)
writePQR() (in module prody.proteins.pdbfile)
writePQRStream() (in module prody.proteins.pdbfile)
writePSF() (in module prody.trajectory.psffile)
writeSequences() (PDBBlastRecord method)
writeSTAR() (in module prody.proteins.starfile)
writeVMDstiffness() (in module prody.dynamics.vmdfile)
wwPDBServer() (in module prody.proteins.wwpdb)