Index

A

add() (labblouin.logfile.XMLfile method) AddAtom() (labblouin.PDBnet.PDBresidue method) AddChain() (labblouin.PDBnet.PDBmodel method) (labblouin.PDBnet.PDBstructure method) AddIndexOfResidue() (labblouin.PDBnet.PDBchain method) AddModel() (labblouin.PDBnet.PDBstructure method) addPDB() (labblouin.scop.scopItem method) AddRemark() (labblouin.PDBnet.PDBstructure method) AddResidue() (labblouin.PDBnet.PDBchain method) (labblouin.PDBnet.PDBmodel method)

AddResidueByIndex() (labblouin.PDBnet.PDBchain method) AddResidueToChain() (labblouin.PDBnet.PDBstructure method) AddResidueToModel() (labblouin.PDBnet.PDBstructure method) addSequence() (labblouin.FASTAnet.FASTAstructure method) allLower() (labblouin.FASTAnet.FASTAstructure method) allUpper() (labblouin.FASTAnet.FASTAstructure method) AsFASTA() (labblouin.PDBnet.PDBchain method)

C

calculateTime() (in module labblouin.logfile) call() (in module labblouin.psub) Centroid() (labblouin.PDBnet.PDBresidue method) ChainAsFASTA() (labblouin.PDBnet.PDBstructure method) chainNames (labblouin.PDBnet.PDBmodel attribute) chains (labblouin.PDBnet.PDBfile attribute) (labblouin.PDBnet.PDBmodel attribute) (labblouin.PDBnet.PDBstructure attribute) charge (labblouin.PDBnet.PDBatom attribute) (labblouin.PDBnet.PDBterminator attribute) check_if_is_align() (in module labblouin.RegExpress) CheckComplete() (labblouin.PDBnet.PDBstructure method) checkForFileCollision() (in module labblouin.homology) classes (labblouin.scop.scopHierarchy attribute) cleanFastaFile() (in module labblouin.homology) cleanModellerFolder() (in module labblouin.homology)

clear() (labblouin.memEfficient.memEfficientDictionary method) close() (labblouin.loadingBar.loadingBar method) (labblouin.PDBnet.PDBfile method) cluster() (labblouin.pfam.pfamFile method) compareStructures() (in module labblouin.homology) compile() (labblouin.logfile.XMLfile method) completePDB() (in module labblouin.homology) contactmap (labblouin.PDBnet.PDBstructure attribute) ContactMap() (labblouin.PDBnet.PDBchain method) Contacts() (labblouin.PDBnet.PDBstructure method) copyFile() (in module labblouin.IO) count() (labblouin.FASTAnet.FASTAsequence method) cross_validate (class in labblouin.svm)

D

decompressGzipFile() (in module labblouin.pfam) dict2array2matrix() (labblouin.Ordination.ORD method) dict2fasta() (in module labblouin.SeqMask) DistanceTo() (labblouin.PDBnet.PDBatom method)

domains (labblouin.scop.scopHierarchy attribute) doSequenceSearch() (in module labblouin.pfam) downloadFamilySequences() (in module labblouin.pfam)

E

ellipse() (labblouin.Ordination.ORD method) entries (labblouin.scop.scopHierarchy attribute) estimateRemainingTime() (in module labblouin.timer) expressoParser (class in labblouin.expresso)

extractPDBChain() (in module labblouin.pfam) extractPDBSequences() (in module labblouin.pfam) extractRandomFasta() (in module labblouin.homology)

F

families (labblouin.scop.scopHierarchy attribute) fasta (class in labblouin.homology) fasta2dict() (in module labblouin.SeqMask) FASTAsequence (class in labblouin.FASTAnet) FASTAstructure (class in labblouin.FASTAnet) FDmatrix() (labblouin.PDBnet.PDBstructure method)

fileHandle (labblouin.PDBnet.PDBfile attribute) filePath (labblouin.PDBnet.PDBfile attribute) filepath (labblouin.PDBnet.PDBstructure attribute) fixname() (labblouin.PDBnet.PDBatom method) folds (labblouin.scop.scopHierarchy attribute)

G

gdt() (labblouin.PDBnet.PDBstructure method) get() (labblouin.memEfficient.memEfficientDictionary method) getAlignedPDB() (labblouin.homstrad.homstradFolder method) getAlignmentLength() (labblouin.homstrad.homstradFolder method) (labblouin.mdsa.mdsaAlignment method) GetAllCentroid() (labblouin.PDBnet.PDBstructure method) GetAtoms() (labblouin.PDBnet.PDBchain method) (labblouin.PDBnet.PDBresidue method) GetAverage() (labblouin.PDBnet.PDBstructure method) GetCA() (labblouin.PDBnet.PDBresidue method) GetChain() (labblouin.PDBnet.PDBmodel method) (labblouin.PDBnet.PDBstructure method) GetChainByName() (labblouin.PDBnet.PDBmodel method) getChainNames() (labblouin.PDBnet.PDBfile method) GetChainNames() (labblouin.PDBnet.PDBmodel method) (labblouin.PDBnet.PDBstructure method) GetChains() (labblouin.PDBnet.PDBmodel method) getChecksum() (in module labblouin.pdbCompare) getDissimilar() (labblouin.scop.scopHierarchy method) getEllipses() (labblouin.Ordination.ORD method) getFailedCount() (labblouin.homstrad.homstradDatabase method) getFamilies() (labblouin.scop.scopHierarchy method) getFASTA() (labblouin.homstrad.homstradFolder method) getFASTAfor() (labblouin.homstrad.homstradFolder method) (labblouin.mdsa.mdsaAlignment method) GetFASTAIndices() (labblouin.PDBnet.PDBstructure method) getFileName() (in module labblouin.IO) getFiles() (labblouin.homstrad.homstradFolder method) (labblouin.mdsa.mdsaDatabase method) getFilesInFolder() (in module labblouin.IO) getFirstResidueNumber() (in module labblouin.homology) getFolderName() (in module labblouin.IO) getFolders() (labblouin.homstrad.homstradDatabase method) GetIndices() (labblouin.PDBnet.PDBchain method) GetMask() (in module labblouin.MATT2GM) GetModel() (labblouin.PDBnet.PDBstructure method)

getModellerPDB() (in module labblouin.homology) getModelNames() (labblouin.PDBnet.PDBfile method) GetModelNames() (labblouin.PDBnet.PDBstructure method) getNames() (labblouin.homstrad.homstradFolder method) (labblouin.mdsa.mdsaAlignment method) getNonEmptySequenceNames() (labblouin.expresso.expressoParser method) getNumSequences() (labblouin.homstrad.homstradFolder method) (labblouin.mdsa.mdsaAlignment method) getObject() (labblouin.mdsa.mdsaAlignment method) getPath() (labblouin.homstrad.homstradDatabase method) (labblouin.homstrad.homstradFolder method) (labblouin.mdsa.mdsaAlignment method) (labblouin.mdsa.mdsaDatabase method) getPDBcodes() (labblouin.expresso.expressoParser method) getPDBfor() (labblouin.homstrad.homstradFolder method) getPDBs() (labblouin.homstrad.homstradFolder method) (labblouin.scop.scopItem method) GetPosition() (labblouin.PDBnet.PDBatom method) GetPrimaryPropertiesFromBioPython() (labblouin.PDBnet.PDBchain method) getRandomPDBFragment() (in module labblouin.homology) GetRemarks() (labblouin.PDBnet.PDBstructure method) GetResidueByIndex() (labblouin.PDBnet.PDBchain method) getResidueNamesInChain() (labblouin.PDBnet.PDBfile method) GetResidues() (labblouin.PDBnet.PDBchain method) (labblouin.PDBnet.PDBmodel method) getSequenceByName() (labblouin.FASTAnet.FASTAstructure method) getSequenceLength() (labblouin.homstrad.homstradFolder method) (labblouin.mdsa.mdsaAlignment method) getSequenceNames() (labblouin.FASTAnet.FASTAstructure method) getSequences() (labblouin.FASTAnet.FASTAstructure method) (labblouin.homstrad.homstradFolder method) (labblouin.mdsa.mdsaAlignment method) getSimilar() (labblouin.scop.scopHierarchy method) getStrictlyUngappedPositions() (labblouin.FASTAnet.FASTAstructure method) getSucceededCount() (labblouin.homstrad.homstradDatabase method) getTime() (in module labblouin.timer) gm() (labblouin.PDBnet.PDBstructure method) grabNCBIAccessionMetadata() (in module labblouin.pfam) grabPDBFile() (in module labblouin.pfam) groups() (labblouin.sabmark.sabmarkDatabase method)

H

handle (labblouin.PDBnet.PDBstructure attribute) hasModels() (labblouin.PDBnet.PDBfile method) hasNoFolders() (in module labblouin.homstrad)

hasResidue() (labblouin.PDBnet.PDBfile method) homstradDatabase (class in labblouin.homstrad) homstradFolder (class in labblouin.homstrad)

I

InContactWith() (labblouin.PDBnet.PDBresidue method) incrementTimer() (labblouin.logfile.logfile method) IndexSeq() (labblouin.PDBnet.PDBstructure method) indices (labblouin.PDBnet.PDBchain attribute) (labblouin.PDBnet.PDBmodel attribute) InferSeqs_landmarks() (in module labblouin.SeqMask) InferSingleLettterCode() (in module labblouin.SeqMask) isLargeFile() (labblouin.PDBnet.PDBfile method) ismodel (labblouin.PDBnet.PDBstructure attribute)

items() (labblouin.memEfficient.memEfficientDictionary method) IterAllResidues() (labblouin.PDBnet.PDBstructure method) iteritems() (labblouin.memEfficient.memEfficientDictionary method) iterkeys() (labblouin.memEfficient.memEfficientDictionary method) iterResidueData() (labblouin.PDBnet.PDBfile method) IterResidues() (labblouin.PDBnet.PDBchain method) (labblouin.PDBnet.PDBmodel method) IterResiduesFor() (labblouin.PDBnet.PDBstructure method) itervalues() (labblouin.memEfficient.memEfficientDictionary method)

K

keys() (labblouin.memEfficient.memEfficientDictionary method)

L

labblouin (module) labblouin.expresso (module) labblouin.FASTAnet (module) labblouin.homology (module) labblouin.homstrad (module) labblouin.IO (module) labblouin.loadingBar (module) labblouin.logfile (module) labblouin.MATT2GM (module) labblouin.mdsa (module) labblouin.memEfficient (module) labblouin.Ordination (module) labblouin.passToqsub (module) labblouin.pdbCompare (module) labblouin.PDBnet (module) labblouin.pfam (module) labblouin.plotGM (module) labblouin.psub (module)

labblouin.RegExpress (module) labblouin.sabmark (module) labblouin.scop (module) labblouin.SeqMask (module) labblouin.svm (module) labblouin.timer (module) lastatom (labblouin.PDBnet.PDBterminator attribute) lastreschain (labblouin.PDBnet.PDBterminator attribute) lastresind (labblouin.PDBnet.PDBterminator attribute) lastresname (labblouin.PDBnet.PDBterminator attribute) LDA() (labblouin.Ordination.ORD method) list2txttable() (in module labblouin.pfam) load() (labblouin.svm.svm_model method) LoadDataGMfile() (labblouin.Ordination.ORD method) LoadFasta() (in module labblouin.MATT2GM) loadingBar (class in labblouin.loadingBar) logfile (class in labblouin.logfile)

M

main() (in module labblouin.MATT2GM) makeFolder() (in module labblouin.IO) manualModeller (class in labblouin.homology) Map2Protein() (labblouin.PDBnet.PDBstructure method) MaskAln() (in module labblouin.SeqMask) MDS() (labblouin.Ordination.ORD method) mdsaAlignment (class in labblouin.mdsa) mdsaDatabase (class in labblouin.mdsa) Mem2List2tuple() (in module labblouin.SeqMask)

memEfficientDictionary (class in labblouin.memEfficient) memHandle (labblouin.PDBnet.PDBfile attribute) ModelAsFASTA() (labblouin.PDBnet.PDBstructure method) modelIndices (labblouin.PDBnet.PDBfile attribute) models (labblouin.PDBnet.PDBstructure attribute) modseq2Fasta() (in module labblouin.SeqMask) moveFile() (in module labblouin.IO) mutation (labblouin.PDBnet.PDBstructure attribute)

N

name (labblouin.PDBnet.PDBatom attribute) (labblouin.PDBnet.PDBchain attribute) (labblouin.PDBnet.PDBmodel attribute) (labblouin.PDBnet.PDBterminator attribute) NewChain() (labblouin.PDBnet.PDBmodel method) (labblouin.PDBnet.PDBstructure method)

NewModel() (labblouin.PDBnet.PDBstructure method)

O

occupancy (labblouin.PDBnet.PDBatom attribute) (labblouin.PDBnet.PDBterminator attribute) open() (labblouin.loadingBar.loadingBar method) optimize() (labblouin.svm.svm_model method) ORD (class in labblouin.Ordination)

orderofchains (labblouin.PDBnet.PDBstructure attribute) orderofmodels (labblouin.PDBnet.PDBstructure attribute) organism (labblouin.PDBnet.PDBstructure attribute) outputResults() (in module labblouin.pdbCompare)

P

parent (labblouin.PDBnet.PDBatom attribute) (labblouin.PDBnet.PDBchain attribute) (labblouin.PDBnet.PDBterminator attribute) parse() (labblouin.pfam.pfamFile method) parseTime() (in module labblouin.logfile) PCA() (labblouin.Ordination.ORD method) PDBatom (class in labblouin.PDBnet) PDBchain (class in labblouin.PDBnet) pdbCrosscheck() (in module labblouin.pdbCompare) PDBfile (class in labblouin.PDBnet) PDBmodel (class in labblouin.PDBnet) PDBresidue (class in labblouin.PDBnet) PDBstructure (class in labblouin.PDBnet) PDBterminator (class in labblouin.PDBnet) perform() (labblouin.svm.cross_validate method)

pfamFile (class in labblouin.pfam) Plot() (labblouin.Ordination.ORD method) PlotXDA() (labblouin.Ordination.ORD method) pointsInEllipse() (labblouin.Ordination.ORD method) pop() (labblouin.PDBnet.PDBchain method) popitem() (labblouin.memEfficient.memEfficientDictionary method) populateHierarchy() (labblouin.scop.scopHierarchy method) postProcess() (labblouin.homology.manualModeller method) predict() (labblouin.svm.svm_model method) PrepData4PDBnet() (labblouin.Ordination.ORD method) printListToFile() (in module labblouin.pfam) processSequenceSearch() (in module labblouin.pfam)

Q

QDA() (labblouin.Ordination.ORD method)

query() (labblouin.scop.scopHierarchy method)

R

radiusOfGyration() (in module labblouin.homology) RadiusOfGyration() (labblouin.PDBnet.PDBstructure method) read() (labblouin.FASTAnet.FASTAstructure method) (labblouin.PDBnet.PDBfile method) (labblouin.PDBnet.PDBstructure method) (labblouin.homology.fasta method) (labblouin.logfile.XMLfile method) read_fasta() (in module labblouin.RegExpress) readFile() (labblouin.FASTAnet.FASTAstructure method) ReadFile() (labblouin.PDBnet.PDBstructure method) readPfamFile() (in module labblouin.pfam) readResidue() (labblouin.PDBnet.PDBfile method) reg_express() (in module labblouin.RegExpress) reg_express_col() (in module labblouin.RegExpress) remarks (labblouin.PDBnet.PDBstructure attribute) RemoveChain() (labblouin.PDBnet.PDBstructure method) removeFile() (in module labblouin.IO) removeGaps() (labblouin.FASTAnet.FASTAsequence method) (labblouin.FASTAnet.FASTAstructure method)

removeListDuplicates() (in module labblouin.pfam) RemoveModel() (labblouin.PDBnet.PDBstructure method) RemoveNonHomologous() (in module labblouin.MATT2GM) RemoveResidue() (labblouin.PDBnet.PDBchain method) removeSequence() (labblouin.FASTAnet.FASTAstructure method) Rename_fasta() (in module labblouin.MATT2GM) renameSequence() (labblouin.FASTAnet.FASTAstructure method) reorderSequences() (labblouin.FASTAnet.FASTAstructure method) residueIndices (labblouin.PDBnet.PDBfile attribute) residues (labblouin.PDBnet.PDBchain attribute) (labblouin.PDBnet.PDBmodel attribute) returnScript() (in module labblouin.passToqsub) rmsd() (in module labblouin.homology) (labblouin.PDBnet.PDBstructure method) rrmsd() (in module labblouin.homology) (labblouin.PDBnet.PDBstructure method) run() (labblouin.homology.manualModeller method)

S

sabmarkDatabase (class in labblouin.sabmark) sabmarkFile (class in labblouin.sabmark) sabmarkFolder (class in labblouin.sabmark) sabmarkSummary (class in labblouin.sabmark) save() (labblouin.svm.svm_model method) scopHierarchy (class in labblouin.scop) scopItem (class in labblouin.scop) serial (labblouin.PDBnet.PDBatom attribute) (labblouin.PDBnet.PDBterminator attribute) settitle() (labblouin.loadingBar.loadingBar method) setTotalNum() (labblouin.logfile.logfile method) size (labblouin.PDBnet.PDBfile attribute)

SortByNumericalIndices() (labblouin.PDBnet.PDBchain method) species (labblouin.scop.scopHierarchy attribute) startPymol() (in module labblouin.homology) Store() (labblouin.Ordination.ORD method) str2list() (in module labblouin.SeqMask) strip_gaps() (in module labblouin.RegExpress) structure (labblouin.PDBnet.PDBchain attribute) (labblouin.PDBnet.PDBmodel attribute) superfamilies (labblouin.scop.scopHierarchy attribute) svm_model (class in labblouin.svm) symbol (labblouin.PDBnet.PDBatom attribute) (labblouin.PDBnet.PDBterminator attribute) system() (in module labblouin.homology)

T

taxid (labblouin.PDBnet.PDBstructure attribute) tempFactor (labblouin.PDBnet.PDBatom attribute) (labblouin.PDBnet.PDBterminator attribute) tmscore() (in module labblouin.homology) (labblouin.PDBnet.PDBstructure method)

toLower() (labblouin.FASTAnet.FASTAsequence method) toUpper() (labblouin.FASTAnet.FASTAsequence method) traverse() (labblouin.homstrad.homstradDatabase method) (labblouin.mdsa.mdsaDatabase method) (labblouin.sabmark.sabmarkDatabase method)

U

update() (labblouin.loadingBar.loadingBar method) (labblouin.PDBnet.PDBchain method)

updateTimer() (labblouin.logfile.logfile method)

V

values() (labblouin.memEfficient.memEfficientDictionary method) view() (labblouin.PDBnet.PDBstructure method)

ViewStructure() (labblouin.PDBnet.PDBstructure method)

W

write() (labblouin.logfile.logfile method) (labblouin.logfile.XMLfile method) writeAlignmentFromFasta() (in module labblouin.homology) WriteAsPDB() (labblouin.PDBnet.PDBchain method) WriteContacts() (labblouin.PDBnet.PDBstructure method) writeElapsedTime() (labblouin.logfile.logfile method) writeFASTA() (labblouin.homstrad.homstradFolder method) (labblouin.mdsa.mdsaAlignment method) writeFile() (labblouin.FASTAnet.FASTAstructure method) WriteFile() (labblouin.PDBnet.PDBstructure method) writeFirstFromFasta() (in module labblouin.homology)

WriteGM() (labblouin.PDBnet.PDBstructure method) WriteLandmarks() (labblouin.PDBnet.PDBstructure method) writeModellerPIR() (in module labblouin.homology) writeNonEmpty() (labblouin.expresso.expressoParser method) writeSequencesToFasta() (in module labblouin.pfam) writeSequencesToFile() (in module labblouin.pfam) writeSequenceToFasta() (in module labblouin.pfam) writeSOAPSSAlignment() (in module labblouin.homology) writeTemporary() (labblouin.logfile.logfile method)

X

x (labblouin.PDBnet.PDBatom attribute) (labblouin.PDBnet.PDBterminator attribute)

XMLfile (class in labblouin.logfile)

Y

y (labblouin.PDBnet.PDBatom attribute) (labblouin.PDBnet.PDBterminator attribute)

Z

z (labblouin.PDBnet.PDBatom attribute) (labblouin.PDBnet.PDBterminator attribute)