Index

_

__init__() (biskit.AmberPrepParser method) (biskit.AmberResidueLibrary method) (biskit.AmberResidueType method) (biskit.ErrLog method) (biskit.LocalPath method) (biskit.LogFile method) (biskit.PDBCleaner method) (biskit.PDBModel method) (biskit.ProfileCollection method) (biskit.StdLog method)

A

aaAtoms (in module biskit.molUtils) aaAtomsH (in module biskit.molUtils) aaDic (in module biskit.molUtils) aaDicStandard (in module biskit.molUtils) aboveDiagonal() (in module biskit.mathUtils) absbinary() (in module biskit.tools) absfile() (in module biskit.tools) accumulate() (in module biskit.mathUtils) add() (biskit.LogFile method) add_nobreak() (biskit.LogFile method) addChainFromSegid() (biskit.PDBModel method) addChainId() (biskit.PDBModel method) addTopology() (biskit.AmberResidueLibrary method) allAA() (in module biskit.molUtils) allAACodes() (in module biskit.molUtils) AmberPrepParser (class in biskit) AmberResidueLibrary (class in biskit)

AmberResidueType (class in biskit) area() (in module biskit.mathUtils) argsort() (biskit.PDBModel method) array_or_list() (biskit.ProfileCollection method) arrayEqual() (in module biskit.mathUtils) atom2chainIndices() (biskit.PDBModel method) atom2chainMask() (biskit.PDBModel method) atom2resIndices() (biskit.PDBModel method) atom2resMask() (biskit.PDBModel method) atom2resProfile() (biskit.PDBModel method) atomDic (in module biskit.molUtils) atomkey() (biskit.AmberResidueLibrary method) (biskit.PDBModel method) atomLines() (biskit.AmberPrepParser method) atomMasses (in module biskit.molUtils) atomNames() (biskit.PDBModel method) atomRange() (biskit.PDBModel method) atomSynonyms (in module biskit.molUtils)

B

backup() (in module biskit.tools) binExists() (in module biskit.tools) biomodel() (biskit.PDBModel method) biskit.gnuplot (module) biskit.hist (module) biskit.match2seq (module) biskit.mathUtils (module)

biskit.molUtils (module) biskit.rmsFit (module) biskit.tools (module) BiskitError (class in biskit) boxPlot() (in module biskit.gnuplot) byAtoms() (biskit.AmberResidueLibrary method) byName() (biskit.AmberResidueLibrary method)

C

capACE() (biskit.PDBCleaner method) capNME() (biskit.PDBCleaner method) capTerminals() (biskit.PDBCleaner method) cartesian2D() (in module biskit.mathUtils) cartesianToPolar() (in module biskit.mathUtils) cbrt() (in module biskit.mathUtils) center() (biskit.PDBModel method) centered() (biskit.PDBModel method) centerOfMass() (biskit.PDBModel method) chain2atomIndices() (biskit.PDBModel method) chain2atomMask() (biskit.PDBModel method) chainBreaks() (biskit.PDBModel method) chainEndIndex() (biskit.PDBModel method) chainIndex() (biskit.PDBModel method) chainMap() (biskit.PDBModel method) clear() (biskit.ProfileCollection method) clipStr() (in module biskit.tools)

clone() (biskit.PDBModel method) (biskit.ProfileCollection method) cmdDict() (in module biskit.tools) cmpAtoms() (in module biskit.molUtils) colorSpectrum() (in module biskit.tools) compareAtoms() (biskit.PDBModel method) compareChains() (biskit.PDBModel method) compareModels() (in module biskit.match2seq) compareSequences() (in module biskit.match2seq) compress() (biskit.PDBModel method) (biskit.ProfileCollection method) concat() (biskit.PDBModel method) (biskit.ProfileCollection method) convertChainIdsCter() (biskit.PDBCleaner method) convertChainIdsNter() (biskit.PDBCleaner method) createResidue() (biskit.AmberPrepParser method) cubic() (in module biskit.mathUtils)

D

dataRoot() (in module biskit.tools) dateSortString() (in module biskit.tools) dateString() (in module biskit.tools) del2mask() (in module biskit.match2seq) density() (in module biskit.hist)

dictAdd() (in module biskit.tools) difference() (in module biskit.mathUtils) disconnect() (biskit.PDBModel method) dump() (biskit.LocalPath method) (in module biskit.tools)

E

EHandler (in module biskit) elements (in module biskit.molUtils) elementType() (in module biskit.molUtils) ensure() (in module biskit.tools) equals() (biskit.PDBModel method) ErrLog (class in biskit) errWrite() (in module biskit.tools) errWriteln() (in module biskit.tools)

eulerRotation() (in module biskit.mathUtils) exists() (biskit.LocalPath method) expand() (biskit.ProfileCollection method) expandRepeats() (in module biskit.match2seq) expandRepeatsLeft() (in module biskit.match2seq) expandRepeatsRight() (in module biskit.match2seq) extendIndex() (biskit.PDBModel method) extendMask() (biskit.PDBModel method)

F

f() (biskit.LogFile method) file2dic() (in module biskit.tools) fileLength() (in module biskit.tools) filter() (biskit.PDBModel method)

filterIndex() (biskit.PDBModel method) findTransformation() (in module biskit.rmsFit) fit() (biskit.PDBModel method) flushPrint() (in module biskit.tools) formatted() (biskit.LocalPath method)

G

get() (biskit.ProfileCollection method) get_cmdDict() (in module biskit.tools) get_local() (biskit.LocalPath method) get_substitution_pairs() (biskit.LocalPath method) getAtoms() (biskit.PDBModel method) getEqual() (in module biskit.match2seq)

getEqualLists() (in module biskit.match2seq) getInfo() (biskit.ProfileCollection method) getOpCodes() (in module biskit.match2seq) getPdbCode() (biskit.PDBModel method) getSkipLists() (in module biskit.match2seq) getXyz() (biskit.PDBModel method) gzopen() (in module biskit.tools)

H

hasNoneProfile() (biskit.ProfileCollection method) hex2int() (in module biskit.tools) hex2rgb() (in module biskit.tools)

hexColors() (in module biskit.tools) histogram() (in module biskit.hist) homefile() (in module biskit.tools)

I

index2map() (biskit.PDBModel method) indices() (biskit.PDBModel method) indicesFrom() (biskit.PDBModel method) info (biskit.PDBModel attribute) info() (in module biskit.tools) initVersion (biskit.PDBModel attribute)

intersection() (in module biskit.mathUtils) isBinary() (in module biskit.tools) isChanged() (biskit.ProfileCollection method) items() (biskit.ProfileCollection method) iterCrossViews() (biskit.ProfileCollection method) iterDicts() (biskit.ProfileCollection method) iteritems() (biskit.ProfileCollection method)

K

keep() (biskit.PDBModel method)

killViews() (biskit.ProfileCollection method)

L

lastError() (in module biskit.tools) lenAtoms() (biskit.PDBModel method) lenBiounits() (biskit.PDBModel method) lenChains() (biskit.PDBModel method) lenResidues() (biskit.PDBModel method) linfit() (in module biskit.mathUtils)

listToMatrix() (in module biskit.mathUtils) load() (biskit.LocalPath method) (in module biskit.tools) local() (biskit.LocalPath method) LocalPath (class in biskit) LocalPathError (class in biskit) LogFile (class in biskit)

M

magicFit() (biskit.PDBModel method) map2index() (biskit.PDBModel method) mask() (biskit.PDBModel method) maskBB() (biskit.PDBModel method) maskCA() (biskit.PDBModel method) maskCB() (biskit.PDBModel method) maskDNA() (biskit.PDBModel method) maskF() (biskit.PDBModel method) maskFrom() (biskit.PDBModel method) maskH() (biskit.PDBModel method) maskH2O() (biskit.PDBModel method) maskHeavy() (biskit.PDBModel method)

maskHetatm() (biskit.PDBModel method) maskNA() (biskit.PDBModel method) maskProtein() (biskit.PDBModel method) maskRNA() (biskit.PDBModel method) maskSolvent() (biskit.PDBModel method) mass() (biskit.PDBModel method) masses() (biskit.PDBModel method) match() (in module biskit.rmsFit) MathUtilError matrixToList() (in module biskit.mathUtils) mergeChains() (biskit.PDBModel method) mergeResidues() (biskit.PDBModel method) MolUtilError

N

nonredundant() (in module biskit.mathUtils)

nsDic (in module biskit.molUtils) nsDicStandard (in module biskit.molUtils)

O

original() (biskit.LocalPath method)

outliers() (in module biskit.mathUtils)

P

packageRoot() (in module biskit.tools) packBinaryMatrix() (in module biskit.mathUtils) pairwiseDistances() (in module biskit.mathUtils) parseResidue() (biskit.AmberPrepParser method) PDB_KEYS (biskit.PDBModel attribute) PDBCleaner (class in biskit) PDBError (class in biskit) PDBModel (class in biskit) PickleError platformFolder() (in module biskit.tools) plot() (biskit.PDBModel method) (biskit.ProfileCollection method) plotArray() (biskit.ProfileCollection method) plotHistogram() (biskit.ProfileCollection method) polar2D() (in module biskit.mathUtils)

polarToCartesian() (in module biskit.mathUtils) process() (biskit.PDBCleaner method) profile() (biskit.PDBModel method) (in module biskit.tools) profile2atomMask() (biskit.PDBModel method) profile2mask() (biskit.PDBModel method) (biskit.ProfileCollection method) profile2resList() (biskit.PDBModel method) profileChangedFromDisc() (biskit.PDBModel method) ProfileCollection (class in biskit) ProfileError (class in biskit) profileInfo() (biskit.PDBModel method) profLength() (biskit.ProfileCollection method) projectOnSphere() (in module biskit.mathUtils) projectRoot() (in module biskit.tools) PseudoClass (class in biskit.tools)

Q

quadratic() (in module biskit.mathUtils)

R

random2DArray() (in module biskit.mathUtils) randomMask() (in module biskit.mathUtils) randomRange() (in module biskit.mathUtils) randomRotation() (in module biskit.mathUtils) relpath() (in module biskit.tools) remove() (biskit.PDBModel method) (biskit.ProfileCollection method) remove_multi_occupancies() (biskit.PDBCleaner method) remove_non_standard_atoms() (biskit.PDBCleaner method) removeFromList() (in module biskit.mathUtils) removeProfile() (biskit.PDBModel method) removeRes() (biskit.PDBModel method) renameAmberRes() (biskit.PDBModel method) renumberResidues() (biskit.PDBModel method) replace_non_standard_AA() (biskit.PDBCleaner method) report() (biskit.PDBModel method) reportAtoms() (biskit.PDBModel method) res2atomIndices() (biskit.PDBModel method)

res2atomMask() (biskit.PDBModel method) res2atomProfile() (biskit.PDBModel method) resDic (in module biskit.molUtils) resDicStandard (in module biskit.molUtils) resEndIndex() (biskit.PDBModel method) residueDict() (biskit.AmberPrepParser method) residues (biskit.PDBModel attribute) residusMaximus() (biskit.PDBModel method) resIndex() (biskit.PDBModel method) resList() (biskit.PDBModel method) resMap() (biskit.PDBModel method) resMapOriginal() (biskit.PDBModel method) resModels() (biskit.PDBModel method) resType() (in module biskit.molUtils) rgb2hex() (in module biskit.tools) rms() (biskit.PDBModel method) rotateAxis() (in module biskit.mathUtils) rowDistances() (in module biskit.rmsFit) runningAverage() (in module biskit.mathUtils)

S

saveAs() (biskit.PDBModel method) SD() (in module biskit.mathUtils) sequence() (biskit.PDBModel method) set() (biskit.LocalPath method) (biskit.ProfileCollection method) set_fragments() (biskit.LocalPath method) set_path() (biskit.LocalPath method) set_string() (biskit.LocalPath method) setInfo() (biskit.ProfileCollection method) setMany() (biskit.ProfileCollection method) setPdbCode() (biskit.PDBModel method) setSource() (biskit.PDBModel method) setXyz() (biskit.PDBModel method)

single2longAA() (in module biskit.molUtils) singleAA() (in module biskit.molUtils) slim() (biskit.PDBModel method) sort() (biskit.PDBModel method) sortAtomsOfModel() (in module biskit.molUtils) sortString() (in module biskit.tools) sourceFile() (biskit.PDBModel method) splithome() (in module biskit.tools) StdLog (class in biskit) string2Fname() (in module biskit.tools) stripFilename() (in module biskit.tools) stripSuffix() (in module biskit.tools) structureFit() (biskit.PDBModel method)

T

take() (biskit.AmberResidueType method) (biskit.PDBModel method) (biskit.ProfileCollection method) takeChains() (biskit.PDBModel method) takeResidues() (biskit.PDBModel method) tempDir() (in module biskit.tools) testRoot() (in module biskit.tools) toCrossViews() (biskit.ProfileCollection method) toDicts() (biskit.ProfileCollection method) toInt() (in module biskit.tools)

toIntArray() (in module biskit.tools) toIntList() (in module biskit.tools) TOLERATE_MISSING (biskit.PDBCleaner attribute) toList() (in module biskit.tools) ToolsError toStr() (in module biskit.tools) transform() (biskit.PDBModel method) transformation() (biskit.PDBModel method) tryImport() (in module biskit.tools) tryImportModule() (in module biskit.tools) tryRemove() (in module biskit.tools)

U

unequalAtoms() (biskit.PDBModel method) union() (in module biskit.mathUtils) unpackBinaryMatrix() (in module biskit.mathUtils) unresolvedTerminals() (biskit.PDBCleaner method)

unsort() (biskit.PDBModel method) update() (biskit.PDBModel method) (biskit.ProfileCollection method) updateMissing() (biskit.ProfileCollection method)

V

validSource() (biskit.PDBModel method) values() (biskit.ProfileCollection method)

variance() (in module biskit.mathUtils) version() (biskit.ProfileCollection method)

W

wMean() (in module biskit.mathUtils) write() (biskit.LogFile method) writeln() (biskit.LogFile method)

writePdb() (biskit.PDBModel method) wSD() (in module biskit.mathUtils) wVar() (in module biskit.mathUtils)

X

xplor2amber() (biskit.PDBModel method) xxDic (in module biskit.molUtils)

xyzChanged (biskit.PDBModel attribute) xyzChangedFromDisc() (biskit.PDBModel method) xyzIsChanged() (biskit.PDBModel method)