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Index

A

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) addext() (in module prody.utilities.pathtools) addFile() (Trajectory method) addHandler() (PackageLogger method) addNonstdAminoacid() (in module prody.atomic.flags) alignCoordsets() (in module prody.measure.transform) alignPDBEnsemble() (in module prody.ensemble.functions) aliphatic all alnum() (in module prody.utilities.misctools) altloc aminoacid

anisou ANM (class in prody.dynamics.anm) apply() (Transformation method) applyMutinfoCorr() (in module prody.sequence.analysis) applyMutinfoNorm() (in module prody.sequence.analysis) applyTransformation() (in module prody.measure.transform) aromatic 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 bb bbfull bend beta blastPDB() (in module prody.proteins.blastpdb) Bond (class in prody.atomic.bond) bridge 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) buildKirchhoff() (GNM method) buildMutinfoMatrix() (in module prody.sequence.analysis) buildOMESMatrix() (in module prody.sequence.analysis) buildSCAMatrix() (in module prody.sequence.analysis) buildSeqidMatrix() (in module prody.sequence.analysis) buried

C

ca calcADPAxes() (in module prody.measure.measure) calcADPs() (in module prody.measure.measure) calcAngle() (in module prody.measure.measure) calcANM() (in module prody.dynamics.anm) calcCenter() (in module prody.measure.measure) 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) calcDeformVector() (in module prody.measure.measure) calcDihedral() (in module prody.measure.measure) calcDistance() (in module prody.measure.measure) calcFractVariance() (in module prody.dynamics.analysis) calcGNM() (in module prody.dynamics.gnm) calcGyradius() (in module prody.measure.measure) calcMeff() (in module prody.sequence.analysis) calcModes() (ANM method) (EDA method) (GNM method) (PCA method) (RTB 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) calcPerturbResponse() (in module prody.dynamics.analysis) calcPhi() (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) calcSqFlucts() (in module prody.dynamics.analysis)

calcSubspaceOverlap() (in module prody.dynamics.compare) calcTempFactors() (in module prody.dynamics.analysis) calcTransformation() (in module prody.measure.transform) call (Field attribute) calpha carbon cg chain (Chemical attribute) Chain (class in prody.atomic.chain) charge charged checkCoords() (in module prody.utilities.checkers) 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) coil comments (Polymer attribute) Conformation (class in prody.ensemble.conformation) confProDy() (in module prody) Contacts (class in prody.measure.contacts) 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) countBytes() (in module prody.utilities.misctools) countLabel() (MSA method) critical() (PackageLogger method) cyclic

D

database (DBRef attribute) dbabbr (DBRef attribute) DBRef (class in prody.proteins.header) dbrefs (Polymer attribute) DCDFile (class in prody.trajectory.dcdfile) debug() (PackageLogger method) deformAtoms() (in module prody.dynamics.sampling) defSelectionMacro() (in module prody.atomic.select) delCoordset() (AtomGroup method) (Ensemble method) (PDBEnsemble method) delData() (AtomGroup method) delFlags() (AtomGroup method) delHandler() (PackageLogger 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) dictElement() (in module prody.utilities.misctools) diff (DBRef attribute) doc (Field attribute) doc_pl (Field attribute) dtype (Field attribute) dummy

E

ec (Polymer attribute) EDA (class in prody.dynamics.pca) element engineered (Polymer attribute) Ensemble (class in prody.ensemble.ensemble) environment variable HOME PATH, [1], [2], [3] PYTHONPATH error() (PackageLogger method) 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) execDSSP() (in module prody.proteins.dssp) execSTRIDE() (in module prody.proteins.stride) exit() (PackageLogger method) extended extendMode() (in module prody.dynamics.editing) extendModel() (in module prody.dynamics.editing) extendVector() (in module prody.dynamics.editing)

F

fetchPDB() (in module prody.proteins.localpdb) fetchPDBClusters() (in module prody.proteins.pdbclusters) fetchPDBfromMirror() (in module prody.proteins.localpdb) fetchPDBLigand() (in module prody.proteins.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) findFragments() (in module prody.atomic.functions) findNeighbors() (in module prody.measure.contacts)

findPDBFiles() (in module prody.proteins.localpdb) first (DBRef attribute) flagDefinition() (in module prody.atomic.flags) flags (Field attribute) flush() (DCDFile method) format (MSAFile attribute) 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) get() (PackageSettings method) getACSIndex() (Atom method) (AtomGroup method) (AtomMap method) (AtomPointer method) (AtomSubset method) (Bond method) (Chain 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) 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) getArray() (ANM method) (EDA method) (GNM method) (MSA method) (Mode method) (ModeSet method) (NMA method) (PCA method) (RTB method) (Vector method) getArrayNx3() (Mode method) (Vector method) getAtom() (Residue method) getAtomGroup() (Atom method) (AtomMap method) (AtomPointer method) (AtomSubset method) (Bond method) (Chain method) (Residue method) (Segment method) (Selection method) getAtoms() (Bond method) (Conformation method) (Contacts method) (DCDFile method) (Ensemble method) (Frame method) (HierView 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) getBoolArray() (Select method) getBySerial() (AtomGroup 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) 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) 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) (NMA method) (PCA method) (RTB 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) getData() (Atom method) (AtomGroup method) (AtomMap method) (AtomSubset method) (Chain method) (Residue method) (Segment method) (Selection method) getDataLabels() (Atom method) (AtomGroup method) (AtomMap method) (AtomPointer method) (AtomSubset method) (Chain method) (Residue method) (Segment method) (Selection method) getDataType() (Atom method) (AtomGroup method) (AtomMap method) (AtomPointer method) (AtomSubset method) (Chain method) (Residue method) (Segment method) (Selection method) getDeviations() (Conformation method) (Ensemble method) (Frame method) (PDBConformation method) (PDBEnsemble method) getDistances() (KDTree method) getDocstr() (Field method) getEigval() (Mode method) getEigvals() (ANM method) (EDA method) (GNM method) (ModeSet method) (NMA method) (PCA method) (RTB method) getEigvec() (Mode method) getEigvecs() (ANM method) (EDA method) (GNM method) (ModeSet method) (NMA method) (PCA method) (RTB method) getElement() (Atom method) getElements() (AtomGroup method) (AtomMap method) (AtomSubset method) (Chain method) (Residue method) (Segment method) (Selection method) getEnsemble() (Conformation method) (PDBConformation method) getFilename() (DCDFile method) (MSAFile method) (TrajFile method) getFilenames() (Trajectory method) getFilter() (MSAFile 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) getGapExtPenalty() (in module prody.proteins.compare) getGapPenalty() (in module prody.proteins.compare) getHandlers() (PackageLogger method) getHessian() (ANM method) (RTB method) getHierView() (AtomGroup method) (Selection method) getHits() (PDBBlastRecord method) getIcode() (Atom method) (Residue method) getIcodes() (AtomGroup method) (AtomMap method) (AtomSubset method) (Chain method) (Residue method) (Segment method) (Selection method)

getIndex() (Atom method) (Conformation method) (Frame method) (MSA method) (Mode method) (PDBConformation method) (Sequence method) getIndices() (Atom method) (AtomMap method) (AtomSubset method) (Bond method) (Chain method) (KDTree method) (ModeSet method) (Residue method) (Segment method) (Select method) (Selection method) getKirchhoff() (ANM method) (GNM method) getLabel() (MSA method) (PDBConformation method) (Sequence method) getLabels() (PDBEnsemble method) getLength() (Bond method) getLinked() (DCDFile method) (TrajBase method) (TrajFile method) (Trajectory method) getMapping() (AtomMap method) getMass() (Atom method) getMasses() (AtomGroup method) (AtomMap method) (AtomSubset method) (Chain method) (Residue method) (Segment method) (Selection method) getMatchScore() (in module prody.proteins.compare) getMatrix() (Transformation method) getMismatchScore() (in module prody.proteins.compare) getModel() (ANM method) (EDA method) (GNM method) (Mode method) (ModeSet method) (NMA method) (PCA method) (RTB method) getMSA() (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) getNext() (Residue method) getNonstdProperties() (in module prody.atomic.flags) getNormed() (Vector method) getOccupancies() (AtomGroup method) (AtomMap method) (AtomSubset method) (Chain method) (Residue method) (Segment method) (Selection method) getOccupancy() (Atom method) getPackagePath() (in module prody.utilities.settings) getParameters() (PDBBlastRecord method) getPrev() (Residue method) getProjection() (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) getRMSD() (Conformation method) (Frame method) (PDBConformation method) getRMSDs() (Ensemble method) (PDBEnsemble method) getRMSFs() (Ensemble method) (PDBEnsemble method) getRotation() (Transformation 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() (Chain method) (PDBBlastRecord method) getSerial() (Atom method) getSerials() (AtomGroup method) (AtomMap method) (AtomSubset method) (Chain method) (Residue method) (Segment method) (Selection method) getSlice() (MSAFile method) getTimestep() (DCDFile method) (TrajFile method) (Trajectory method) getTitle() (ANM method) (AtomGroup method) (AtomMap method) (DCDFile method) (EDA method) (Ensemble method) (GNM method) (MSA method) (MSAFile method) (Mode method) (ModeSet method) (NMA method) (PCA method) (PDBEnsemble method) (RTB method) (TrajBase method) (TrajFile method) (Trajectory method) (Vector method) getTrajectory() (Frame method) getTransformation() (PDBConformation method) getTranslation() (Transformation 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) getVariances() (ANM method) (EDA method) (GNM method) (ModeSet method) (NMA method) (PCA method) (RTB method) getVector() (Bond method) getVelocities() (Frame method) getVMDpath() (in module prody.dynamics.nmdfile) getWeights() (Conformation method) (DCDFile method) (Ensemble method) (Frame method) (PDBConformation method) (PDBEnsemble method) (TrajBase method) (TrajFile method) (Trajectory method) glob() (in module prody.utilities.pathtools) GNM (class in prody.dynamics.gnm) goto() (DCDFile method) (TrajBase method) (TrajFile method) (Trajectory method) gunzip() (in module prody.utilities.pathtools)

H

hasUnitcell() (DCDFile method) (TrajBase method) (TrajFile method) (Trajectory method) heavy helix helix310 helixpi heme

hetatm hetero HierView (class in prody.atomic.hierview) HOME hydrogen hydrophobic

I

icode (Chemical attribute) idcode (DBRef attribute) importLA() (in module prody.utilities.misctools) info() (PackageLogger method) intorfloat() (in module prody.utilities.misctools) ion is3d() (ANM method) (EDA method) (GNM method) (Mode method) (ModeSet method) (NMA method) (PCA method) (RTB method) (Vector method) isAligned() (MSA method) (MSAFile method) isDataLabel() (Atom method) (AtomGroup method) (AtomMap method) (AtomPointer method) (AtomSubset method) (Chain 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) isReadable() (in module prody.utilities.pathtools) isReserved() (in module prody.atomic.functions)

isSelectionMacro() (in module prody.atomic.select) isWritable() (in module prody.utilities.pathtools) 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) 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) iterFragments() (AtomGroup method) (in module prody.atomic.functions) iterLabels() (MSA 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)

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) loadModel() (in module prody.dynamics.functions) loadPDBClusters() (in module prody.proteins.pdbclusters) loadVector() (in module prody.dynamics.functions)

M

makePath() (in module prody.utilities.pathtools) mapOntoChain() (in module prody.proteins.compare) mapped mass matchAlign() (in module prody.proteins.compare) matchChains() (in module prody.proteins.compare) medium mergeMSA() (in module prody.sequence.msa) meth (Field attribute)

meth_pl (Field attribute) Mode (class in prody.dynamics.mode) 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) mutation (Polymer attribute)

N

name (Chemical attribute) (Field attribute) (Polymer attribute) natoms (Chemical attribute) 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 NMA (class in prody.dynamics.nma) noh none (Field attribute) nonstdaa nucleic nucleobase nucleoside nucleotide 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) (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) 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) numDOF() (ANM method) (EDA method) (GNM method) (Mode method) (ModeSet method) (NMA method) (PCA method) (RTB method) (Vector method) numDummies() (AtomMap 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) numIndexed() (MSA method) numMapped() (AtomMap method) numModes() (ANM method) (EDA method) (GNM method) (Mode method) (ModeSet method) (NMA method) (PCA method) (RTB method) (Vector 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) oxygen

P

PackageLogger (class in prody.utilities.logger) PackageSettings (class in prody.utilities.settings) parseArray() (in module prody.dynamics.functions) parseDCD() (in module prody.trajectory.dcdfile) parseDSSP() (in module prody.proteins.dssp) parseHeatmap() (in module prody.dynamics.heatmapper) parseModes() (in module prody.dynamics.functions) parseMSA() (in module prody.sequence.msafile) parseNMD() (in module prody.dynamics.nmdfile) parsePDB() (in module prody.proteins.pdbfile) parsePDBHeader() (in module prody.proteins.header) parsePDBStream() (in module prody.proteins.pdbfile) parsePQR() (in module prody.proteins.pdbfile) parsePSF() (in module prody.trajectory.psffile) parseSparseMatrix() (in module prody.dynamics.functions) 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) 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) plog() (in module prody) polar Polymer (class in prody.proteins.header) pop() (PackageSettings method) prefix (PackageLogger attribute) 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.atom (module) prody.atomic.atomgroup (module) prody.atomic.atomic (module) prody.atomic.atommap (module) prody.atomic.bond (module) prody.atomic.chain (module) prody.atomic.fields (module) prody.atomic.flags (module) prody.atomic.functions (module) prody.atomic.hierview (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.database (module) prody.database.pfam (module) prody.dynamics (module) prody.dynamics.analysis (module) prody.dynamics.anm (module) prody.dynamics.compare (module) prody.dynamics.editing (module) prody.dynamics.functions (module) prody.dynamics.gamma (module) prody.dynamics.gnm (module) prody.dynamics.heatmapper (module) prody.dynamics.mode (module) prody.dynamics.modeset (module) prody.dynamics.nma (module) prody.dynamics.nmdfile (module) prody.dynamics.pca (module) prody.dynamics.plotting (module) prody.dynamics.rtb (module) prody.dynamics.sampling (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.compare (module) prody.proteins.dssp (module) prody.proteins.functions (module) prody.proteins.header (module) prody.proteins.localpdb (module) prody.proteins.pdbclusters (module) prody.proteins.pdbfile (module) prody.proteins.pdbligands (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.checkers (module) prody.utilities.doctools (module) prody.utilities.logger (module) prody.utilities.misctools (module) prody.utilities.pathtools (module) prody.utilities.settings (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 purine pyrimidine Python Enhancement Proposals PEP 8, [1] PEP 8#imports PEP 8#whitespace-in-expressions-and-statements PYTHONPATH

R

radius rangeString() (in module prody.utilities.misctools) readonly (Field attribute) reduceModel() (in module prody.dynamics.editing) refineMSA() (in module prody.sequence.msa) relpath() (in module prody.utilities.pathtools) 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) RTB (class in prody.dynamics.rtb)

S

sampleModes() (in module prody.dynamics.sampling) save() (PackageSettings method) saveAtoms() (in module prody.atomic.functions) saveEnsemble() (in module prody.ensemble.functions) saveModel() (in module prody.dynamics.functions) saveVector() (in module prody.dynamics.functions) sc search() (KDTree method) searchPfam() (in module prody.database.pfam) 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) (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 setACSIndex() (Atom method) (AtomGroup method) (AtomMap method) (AtomPointer method) (AtomSubset method) (Bond method) (Chain 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) 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) setAtoms() (DCDFile method) (Ensemble 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) 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) setCSLabels() (AtomGroup method) setData() (Atom method) (AtomGroup method) (AtomSubset method) (Chain method) (Residue method) (Segment method) (Selection method) setEigens() (ANM method) (EDA method) (GNM method) (NMA method) (PCA method) (RTB 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) setHessian() (ANM method) (RTB method) setIcode() (Atom method) (Residue method) setIcodes() (AtomGroup method) (AtomSubset method) (Chain method) (Residue method) (Segment method) (Selection method) setKirchhoff() (GNM method) setLabel() (PDBConformation method) setMass() (Atom method) setMasses() (AtomGroup method) (AtomSubset method) (Chain method) (Residue method) (Segment method) (Selection 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) setOccupancies() (AtomGroup method) (AtomSubset method) (Chain method) (Residue method) (Segment method) (Selection method) setOccupancy() (Atom method) setPackagePath() (in module prody.utilities.settings)

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) setRotation() (Transformation 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) setTitle() (ANM method) (AtomGroup method) (AtomMap method) (DCDFile method) (EDA method) (Ensemble method) (GNM method) (MSA method) (MSAFile method) (NMA method) (PCA method) (PDBEnsemble method) (RTB method) (TrajBase method) (TrajFile method) (Trajectory method) (Vector 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) (PDBEnsemble method) (TrajBase method) (TrajFile method) (Trajectory method) 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) showEllipsoid() (in module prody.dynamics.plotting) showFigure() (in module prody.utilities.misctools) showFractVars() (in module prody.dynamics.plotting) showHeatmap() (in module prody.dynamics.heatmapper) showMode() (in module prody.dynamics.plotting) showMSAOccupancy() (in module prody.sequence.plotting) showMutinfoMatrix() (in module prody.sequence.plotting) showNormedSqFlucts() (in module prody.dynamics.plotting) showOccupancies() (in module prody.ensemble.functions) showOverlap() (in module prody.dynamics.plotting) showOverlapTable() (in module prody.dynamics.plotting) 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) showSqFlucts() (in module prody.dynamics.plotting) sidechain siguij skip() (DCDFile method) (TrajBase method) (TrajFile method) (Trajectory method) sleep() (PackageLogger method) sliceMode() (in module prody.dynamics.editing) sliceModel() (in module prody.dynamics.editing) sliceVector() (in module prody.dynamics.editing) small sortAtoms() (in module prody.atomic.functions) split (MSA attribute) splitSeqLabel() (in module prody.sequence.msafile) start() (PackageLogger method) startLogfile() (in module prody) startswith() (in module prody.utilities.misctools) stdaa 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) timeit() (PackageLogger method) timing() (PackageLogger 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) trimPDBEnsemble() (in module prody.ensemble.functions) turn type

U

uniqueSequences() (in module prody.sequence.analysis) unpickle() (in module prody.utilities.pathtools)

update() (HierView method) (PackageLogger method) (PackageSettings method) (Selection method)

V

Vector (class in prody.dynamics.mode) verbosity (PackageLogger attribute)

viewNMDinVMD() (in module prody.dynamics.nmdfile)

W

warn() (PackageLogger method) warning() (PackageLogger method) water which() (in module prody.utilities.pathtools) 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) writeDCD() (in module prody.trajectory.dcdfile) writeHeatmap() (in module prody.dynamics.heatmapper)

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) writePQR() (in module prody.proteins.functions) writePSF() (in module prody.trajectory.psffile) wwPDBServer() (in module prody.proteins.wwpdb)