Index

_

__abstractmethods__ (Bio.Align.a2m.AlignmentIterator attribute) (Bio.Align.a2m.AlignmentWriter attribute) (Bio.Align.Alignments attribute) (Bio.Align.AlignmentsAbstractBaseClass attribute) (Bio.Align.bed.AlignmentIterator attribute) (Bio.Align.bed.AlignmentWriter attribute) (Bio.Align.bigbed.AlignmentIterator attribute) (Bio.Align.bigbed.AlignmentWriter attribute) (Bio.Align.bigmaf.AlignmentIterator attribute) (Bio.Align.bigmaf.AlignmentWriter attribute) (Bio.Align.bigpsl.AlignmentIterator attribute) (Bio.Align.bigpsl.AlignmentWriter attribute) (Bio.Align.chain.AlignmentIterator attribute) (Bio.Align.chain.AlignmentWriter attribute) (Bio.Align.clustal.AlignmentIterator attribute) (Bio.Align.clustal.AlignmentWriter attribute) (Bio.Align.emboss.AlignmentIterator attribute) (Bio.Align.exonerate.AlignmentIterator attribute) (Bio.Align.exonerate.AlignmentWriter attribute) (Bio.Align.fasta.AlignmentIterator attribute) (Bio.Align.fasta.AlignmentWriter attribute) (Bio.Align.hhr.AlignmentIterator attribute) (Bio.Align.interfaces.AlignmentIterator attribute) (Bio.Align.interfaces.AlignmentWriter attribute) (Bio.Align.maf.AlignmentIterator attribute) (Bio.Align.maf.AlignmentWriter attribute) (Bio.Align.mauve.AlignmentIterator attribute) (Bio.Align.mauve.AlignmentWriter attribute) (Bio.Align.msf.AlignmentIterator attribute) (Bio.Align.nexus.AlignmentIterator attribute) (Bio.Align.nexus.AlignmentWriter attribute) (Bio.Align.PairwiseAlignments attribute) (Bio.Align.phylip.AlignmentIterator attribute) (Bio.Align.phylip.AlignmentWriter attribute) (Bio.Align.psl.AlignmentIterator attribute) (Bio.Align.psl.AlignmentWriter attribute) (Bio.Align.sam.AlignmentIterator attribute) (Bio.Align.sam.AlignmentWriter attribute) (Bio.Align.stockholm.AlignmentIterator attribute) (Bio.Align.stockholm.AlignmentWriter attribute) (Bio.Align.tabular.AlignmentIterator attribute) (Bio.Blast.Hit attribute) (Bio.Blast.Records attribute) (Bio.codonalign.codonseq.CodonSeq attribute) (Bio.motifs.meme.Instance attribute) (Bio.SearchIO.BlastIO.blast_tab.BlastTabIndexer attribute) (Bio.SearchIO.BlastIO.blast_xml.BlastXmlIndexer attribute) (Bio.SearchIO.BlatIO.BlatPslIndexer attribute) (Bio.SearchIO.ExonerateIO.exonerate_cigar.ExonerateCigarIndexer attribute) (Bio.SearchIO.ExonerateIO.exonerate_cigar.ExonerateCigarParser attribute) (Bio.SearchIO.ExonerateIO.exonerate_text.ExonerateTextIndexer attribute) (Bio.SearchIO.ExonerateIO.exonerate_text.ExonerateTextParser attribute) (Bio.SearchIO.ExonerateIO.exonerate_vulgar.ExonerateVulgarIndexer attribute) (Bio.SearchIO.ExonerateIO.exonerate_vulgar.ExonerateVulgarParser attribute) (Bio.SearchIO.FastaIO.FastaM10Indexer attribute) (Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextIndexer attribute) (Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmhitIndexer attribute) (Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmqueryIndexer attribute) (Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabIndexer attribute) (Bio.SearchIO.HmmerIO.hmmer3_text.Hmmer3TextIndexer attribute) (Bio.Seq.MutableSeq attribute) (Bio.Seq.Seq attribute) (Bio.Seq.SequenceDataAbstractBaseClass attribute) (Bio.SeqFeature.AfterPosition attribute) (Bio.SeqFeature.BeforePosition attribute) (Bio.SeqFeature.BetweenPosition attribute) (Bio.SeqFeature.CompoundLocation attribute) (Bio.SeqFeature.ExactPosition attribute) (Bio.SeqFeature.Location attribute) (Bio.SeqFeature.OneOfPosition attribute) (Bio.SeqFeature.Position attribute) (Bio.SeqFeature.SimpleLocation attribute) (Bio.SeqFeature.UncertainPosition attribute) (Bio.SeqFeature.UnknownPosition attribute) (Bio.SeqFeature.WithinPosition attribute) (Bio.SeqIO.AbiIO.AbiIterator attribute) (Bio.SeqIO.AceIO.AceIterator attribute) (Bio.SeqIO.AlignmentSequenceIterator attribute) (Bio.SeqIO.AlignmentSequenceWriter attribute) (Bio.SeqIO.FastaIO.FastaBlastIterator attribute) (Bio.SeqIO.FastaIO.FastaIterator attribute) (Bio.SeqIO.FastaIO.FastaPearsonIterator attribute) (Bio.SeqIO.FastaIO.FastaTwoLineIterator attribute) (Bio.SeqIO.FastaIO.FastaTwoLineWriter attribute) (Bio.SeqIO.FastaIO.FastaWriter attribute) (Bio.SeqIO.GckIO.GckIterator attribute) (Bio.SeqIO.GfaIO.Gfa1Iterator attribute) (Bio.SeqIO.GfaIO.Gfa2Iterator attribute) (Bio.SeqIO.IgIO.IgIterator attribute) (Bio.SeqIO.InsdcIO.EmblCdsFeatureIterator attribute) (Bio.SeqIO.InsdcIO.EmblIterator attribute) (Bio.SeqIO.InsdcIO.EmblWriter attribute) (Bio.SeqIO.InsdcIO.GenBankCdsFeatureIterator attribute) (Bio.SeqIO.InsdcIO.GenBankIterator attribute) (Bio.SeqIO.InsdcIO.GenBankWriter attribute) (Bio.SeqIO.InsdcIO.ImgtIterator attribute) (Bio.SeqIO.InsdcIO.ImgtWriter attribute) (Bio.SeqIO.Interfaces.SequenceIterator attribute) (Bio.SeqIO.Interfaces.SequenceWriter attribute) (Bio.SeqIO.NibIO.NibIterator attribute) (Bio.SeqIO.NibIO.NibWriter attribute) (Bio.SeqIO.PdbIO.CifAtomIterator attribute) (Bio.SeqIO.PdbIO.CifSeqresIterator attribute) (Bio.SeqIO.PdbIO.PdbAtomIterator attribute) (Bio.SeqIO.PdbIO.PdbSeqresIterator attribute) (Bio.SeqIO.PhdIO.PhdIterator attribute) (Bio.SeqIO.PhdIO.PhdWriter attribute) (Bio.SeqIO.PirIO.PirIterator attribute) (Bio.SeqIO.PirIO.PirWriter attribute) (Bio.SeqIO.QualityIO.FastqIlluminaIterator attribute) (Bio.SeqIO.QualityIO.FastqIlluminaWriter attribute) (Bio.SeqIO.QualityIO.FastqIteratorAbstractBaseClass attribute) (Bio.SeqIO.QualityIO.FastqPhredIterator attribute) (Bio.SeqIO.QualityIO.FastqPhredWriter attribute) (Bio.SeqIO.QualityIO.FastqSolexaIterator attribute) (Bio.SeqIO.QualityIO.FastqSolexaWriter attribute) (Bio.SeqIO.QualityIO.QualPhredIterator attribute) (Bio.SeqIO.QualityIO.QualPhredWriter attribute) (Bio.SeqIO.SeqXmlIO.SeqXmlIterator attribute) (Bio.SeqIO.SeqXmlIO.SeqXmlWriter attribute) (Bio.SeqIO.SffIO.SffIterator attribute) (Bio.SeqIO.SffIO.SffWriter attribute) (Bio.SeqIO.SnapGeneIO.SnapGeneIterator attribute) (Bio.SeqIO.SwissIO.SwissIterator attribute) (Bio.SeqIO.TabIO.TabIterator attribute) (Bio.SeqIO.TabIO.TabWriter attribute) (Bio.SeqIO.TwoBitIO.TwoBitIterator attribute) (Bio.SeqIO.UniprotIO.UniprotIterator attribute) (Bio.SeqIO.XdnaIO.XdnaIterator attribute) (Bio.SeqIO.XdnaIO.XdnaWriter attribute) __add__() (Bio.Align.Alignment method) (Bio.Align.MultipleSeqAlignment method) (Bio.codonalign.codonalignment.CodonAlignment method) (Bio.PDB.vectors.Vector method) (Bio.phenotype.phen_micro.PlateRecord method) (Bio.phenotype.phen_micro.WellRecord method) (Bio.SCOP.Raf.SeqMap method) (Bio.Seq.SequenceDataAbstractBaseClass method) (Bio.SeqFeature.AfterPosition method) (Bio.SeqFeature.BeforePosition method) (Bio.SeqFeature.BetweenPosition method) (Bio.SeqFeature.CompoundLocation method) (Bio.SeqFeature.ExactPosition method) (Bio.SeqFeature.OneOfPosition method) (Bio.SeqFeature.SimpleLocation method) (Bio.SeqFeature.UnknownPosition method) (Bio.SeqFeature.WithinPosition method) (Bio.SeqRecord.SeqRecord method) __annotations__ (Bio.Align.a2m.AlignmentIterator attribute) (Bio.Align.a2m.AlignmentWriter attribute) (Bio.Align.Alignments attribute) (Bio.Align.bed.AlignmentIterator attribute) (Bio.Align.bed.AlignmentWriter attribute) (Bio.Align.bigbed.AlignmentIterator attribute) (Bio.Align.bigbed.AlignmentWriter attribute) (Bio.Align.bigbed.AutoSQLTable attribute) (Bio.Align.bigmaf.AlignmentIterator attribute) (Bio.Align.bigmaf.AlignmentWriter attribute) (Bio.Align.bigpsl.AlignmentIterator attribute) (Bio.Align.bigpsl.AlignmentWriter attribute) (Bio.Align.chain.AlignmentIterator attribute) (Bio.Align.chain.AlignmentWriter attribute) (Bio.Align.clustal.AlignmentIterator attribute) (Bio.Align.clustal.AlignmentWriter attribute) (Bio.Align.emboss.AlignmentIterator attribute) (Bio.Align.exonerate.AlignmentIterator attribute) (Bio.Align.exonerate.AlignmentWriter attribute) (Bio.Align.fasta.AlignmentIterator attribute) (Bio.Align.fasta.AlignmentWriter attribute) (Bio.Align.hhr.AlignmentIterator attribute) (Bio.Align.interfaces.AlignmentIterator attribute) (Bio.Align.interfaces.AlignmentWriter attribute) (Bio.Align.maf.AlignmentIterator attribute) (Bio.Align.maf.AlignmentWriter attribute) (Bio.Align.mauve.AlignmentIterator attribute) (Bio.Align.mauve.AlignmentWriter attribute) (Bio.Align.msf.AlignmentIterator attribute) (Bio.Align.nexus.AlignmentIterator attribute) (Bio.Align.nexus.AlignmentWriter attribute) (Bio.Align.PairwiseAlignments attribute) (Bio.Align.phylip.AlignmentIterator attribute) (Bio.Align.phylip.AlignmentWriter attribute) (Bio.Align.psl.AlignmentIterator attribute) (Bio.Align.psl.AlignmentWriter attribute) (Bio.Align.sam.AlignmentIterator attribute) (Bio.Align.sam.AlignmentWriter attribute) (Bio.Align.stockholm.AlignmentIterator attribute) (Bio.Align.stockholm.AlignmentWriter attribute) (Bio.Align.tabular.AlignmentIterator attribute) (Bio.AlignIO.EmbossIO.EmbossIterator attribute) (Bio.AlignIO.Interfaces.AlignmentIterator attribute) (Bio.AlignIO.Interfaces.AlignmentWriter attribute) (Bio.AlignIO.Interfaces.SequentialAlignmentWriter attribute) (Bio.AlignIO.MafIO.MafWriter attribute) (Bio.AlignIO.MauveIO.MauveIterator attribute) (Bio.AlignIO.MauveIO.MauveWriter attribute) (Bio.AlignIO.MsfIO.MsfIterator attribute) (Bio.AlignIO.NexusIO.NexusWriter attribute) (Bio.AlignIO.PhylipIO.PhylipIterator attribute) (Bio.AlignIO.PhylipIO.PhylipWriter attribute) (Bio.AlignIO.PhylipIO.RelaxedPhylipIterator attribute) (Bio.AlignIO.PhylipIO.RelaxedPhylipWriter attribute) (Bio.AlignIO.PhylipIO.SequentialPhylipIterator attribute) (Bio.AlignIO.PhylipIO.SequentialPhylipWriter attribute) (Bio.AlignIO.StockholmIO.StockholmIterator attribute) (Bio.AlignIO.StockholmIO.StockholmWriter attribute) (Bio.BiopythonDeprecationWarning attribute) (Bio.BiopythonExperimentalWarning attribute) (Bio.BiopythonParserWarning attribute) (Bio.Blast.Hit attribute) (Bio.Blast.HSP attribute) (Bio.Blast.NCBIXML.Blast attribute) (Bio.Blast.NCBIXML.DescriptionExt attribute) (Bio.Blast.NCBIXML.PSIBlast attribute) (Bio.codonalign.codonalignment.CodonAlignment attribute) (Bio.codonalign.codonseq.CodonSeq attribute) (Bio.Data.CodonTable.AmbiguousCodonTable attribute) (Bio.Data.CodonTable.CodonTable attribute) (Bio.Data.CodonTable.NCBICodonTable attribute) (Bio.Data.CodonTable.NCBICodonTableDNA attribute) (Bio.Data.CodonTable.NCBICodonTableRNA attribute) (Bio.Entrez.Parser.DataHandlerMeta attribute) (Bio.ExPASy.ScanProsite.ContentHandler attribute) (Bio.GenBank.Scanner.EmblScanner attribute) (Bio.GenBank.Scanner.GenBankScanner attribute) (Bio.Graphics.BasicChromosome.AnnotatedChromosomeSegment attribute) (Bio.Graphics.BasicChromosome.Chromosome attribute) (Bio.Graphics.BasicChromosome.ChromosomeSegment attribute) (Bio.Graphics.BasicChromosome.SpacerSegment attribute) (Bio.Graphics.BasicChromosome.TelomereSegment attribute) (Bio.HMM.DynamicProgramming.LogDPAlgorithms attribute) (Bio.HMM.DynamicProgramming.ScaledDPAlgorithms attribute) (Bio.HMM.Trainer.BaumWelchTrainer attribute) (Bio.HMM.Trainer.KnownStateTrainer attribute) (Bio.MissingPythonDependencyError attribute) (Bio.motifs.jaspar.Motif attribute) (Bio.motifs.matrix.FrequencyPositionMatrix attribute) (Bio.motifs.matrix.PositionSpecificScoringMatrix attribute) (Bio.motifs.matrix.PositionWeightMatrix attribute) (Bio.motifs.meme.Instance attribute) (Bio.motifs.meme.Motif attribute) (Bio.motifs.transfac.Motif attribute) (Bio.Nexus.Trees.Tree attribute) (Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap attribute) (Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap attribute) (Bio.PDB.Chain.Chain attribute) (Bio.PDB.DSSP.DSSP attribute) (Bio.PDB.Entity.DisorderedEntityWrapper attribute) (Bio.PDB.Entity.Entity attribute) (Bio.PDB.HSExposure.ExposureCN attribute) (Bio.PDB.HSExposure.HSExposureCA attribute) (Bio.PDB.HSExposure.HSExposureCB attribute) (Bio.PDB.internal_coords.Dihedron attribute) (Bio.PDB.internal_coords.Hedron attribute) (Bio.PDB.internal_coords.IC_Chain attribute) (Bio.PDB.internal_coords.IC_Residue attribute) (Bio.PDB.mmcifio.MMCIFIO attribute) (Bio.PDB.mmtf.mmtfio.MMTFIO attribute) (Bio.PDB.Model.Model attribute) (Bio.PDB.NACCESS.NACCESS attribute) (Bio.PDB.NACCESS.NACCESS_atomic attribute) (Bio.PDB.PDBExceptions.PDBConstructionWarning attribute) (Bio.PDB.PDBIO.PDBIO attribute) (Bio.PDB.Polypeptide.PPBuilder attribute) (Bio.PDB.Residue.DisorderedResidue attribute) (Bio.PDB.Residue.Residue attribute) (Bio.PDB.ResidueDepth.ResidueDepth attribute) (Bio.PDB.Structure.Structure attribute) (Bio.Phylo.BaseTree.Clade attribute) (Bio.Phylo.BaseTree.Tree attribute) (Bio.Phylo.CDAO.Clade attribute) (Bio.Phylo.CDAO.Tree attribute) (Bio.Phylo.Newick.Clade attribute) (Bio.Phylo.Newick.Tree attribute) (Bio.Phylo.NeXML.Clade attribute) (Bio.Phylo.NeXML.Tree attribute) (Bio.Phylo.PAML.codeml.Codeml attribute) (Bio.Phylo.PAML.yn00.Yn00 attribute) (Bio.Phylo.PhyloXML.Accession attribute) (Bio.Phylo.PhyloXML.Annotation attribute) (Bio.Phylo.PhyloXML.BinaryCharacters attribute) (Bio.Phylo.PhyloXML.BranchColor attribute) (Bio.Phylo.PhyloXML.Clade attribute) (Bio.Phylo.PhyloXML.CladeRelation attribute) (Bio.Phylo.PhyloXML.Confidence attribute) (Bio.Phylo.PhyloXML.Date attribute) (Bio.Phylo.PhyloXML.Distribution attribute) (Bio.Phylo.PhyloXML.DomainArchitecture attribute) (Bio.Phylo.PhyloXML.Events attribute) (Bio.Phylo.PhyloXML.Id attribute) (Bio.Phylo.PhyloXML.MolSeq attribute) (Bio.Phylo.PhyloXML.Other attribute) (Bio.Phylo.PhyloXML.PhyloElement attribute) (Bio.Phylo.PhyloXML.Phylogeny attribute) (Bio.Phylo.PhyloXML.Phyloxml attribute) (Bio.Phylo.PhyloXML.PhyloXMLWarning attribute) (Bio.Phylo.PhyloXML.Point attribute) (Bio.Phylo.PhyloXML.Polygon attribute) (Bio.Phylo.PhyloXML.Property attribute) (Bio.Phylo.PhyloXML.ProteinDomain attribute) (Bio.Phylo.PhyloXML.Reference attribute) (Bio.Phylo.PhyloXML.Sequence attribute) (Bio.Phylo.PhyloXML.SequenceRelation attribute) (Bio.Phylo.PhyloXML.Taxonomy attribute) (Bio.Phylo.PhyloXML.Uri attribute) (Bio.Phylo.TreeConstruction.DistanceTreeConstructor attribute) (Bio.Phylo.TreeConstruction.NNITreeSearcher attribute) (Bio.Phylo.TreeConstruction.ParsimonyScorer attribute) (Bio.Phylo.TreeConstruction.ParsimonyTreeConstructor attribute) (Bio.SCOP.Domain attribute) (Bio.SearchIO.BlastIO.blast_tab.BlastTabIndexer attribute) (Bio.SearchIO.BlastIO.blast_xml.BlastXmlIndexer attribute) (Bio.SearchIO.BlatIO.BlatPslIndexer attribute) (Bio.SearchIO.ExonerateIO.exonerate_cigar.ExonerateCigarIndexer attribute) (Bio.SearchIO.ExonerateIO.exonerate_cigar.ExonerateCigarParser attribute) (Bio.SearchIO.ExonerateIO.exonerate_text.ExonerateTextIndexer attribute) (Bio.SearchIO.ExonerateIO.exonerate_text.ExonerateTextParser attribute) (Bio.SearchIO.ExonerateIO.exonerate_vulgar.ExonerateVulgarIndexer attribute) (Bio.SearchIO.ExonerateIO.exonerate_vulgar.ExonerateVulgarParser attribute) (Bio.SearchIO.FastaIO.FastaM10Indexer attribute) (Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextIndexer attribute) (Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmhitIndexer attribute) (Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmqueryIndexer attribute) (Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmqueryParser attribute) (Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmqueryWriter attribute) (Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabIndexer attribute) (Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabParser attribute) (Bio.SearchIO.HmmerIO.hmmer3_text.Hmmer3TextIndexer attribute) (Bio.Seq.MutableSeq attribute) (Bio.Seq.Seq attribute) (Bio.Seq.SequenceDataAbstractBaseClass attribute) (Bio.SeqFeature.AfterPosition attribute) (Bio.SeqFeature.BeforePosition attribute) (Bio.SeqFeature.BetweenPosition attribute) (Bio.SeqFeature.CompoundLocation attribute) (Bio.SeqFeature.ExactPosition attribute) (Bio.SeqFeature.Location attribute) (Bio.SeqFeature.OneOfPosition attribute) (Bio.SeqFeature.Position attribute) (Bio.SeqFeature.SimpleLocation attribute) (Bio.SeqFeature.UncertainPosition attribute) (Bio.SeqFeature.UnknownPosition attribute) (Bio.SeqFeature.WithinPosition attribute) (Bio.SeqIO.AbiIO.AbiIterator attribute) (Bio.SeqIO.AceIO.AceIterator attribute) (Bio.SeqIO.AlignmentSequenceIterator attribute) (Bio.SeqIO.AlignmentSequenceWriter attribute) (Bio.SeqIO.FastaIO.FastaBlastIterator attribute) (Bio.SeqIO.FastaIO.FastaIterator attribute) (Bio.SeqIO.FastaIO.FastaPearsonIterator attribute) (Bio.SeqIO.FastaIO.FastaTwoLineIterator attribute) (Bio.SeqIO.FastaIO.FastaTwoLineWriter attribute) (Bio.SeqIO.FastaIO.FastaWriter attribute) (Bio.SeqIO.GckIO.GckIterator attribute) (Bio.SeqIO.GfaIO.Gfa1Iterator attribute) (Bio.SeqIO.GfaIO.Gfa2Iterator attribute) (Bio.SeqIO.IgIO.IgIterator attribute) (Bio.SeqIO.InsdcIO.EmblCdsFeatureIterator attribute) (Bio.SeqIO.InsdcIO.EmblIterator attribute) (Bio.SeqIO.InsdcIO.EmblWriter attribute) (Bio.SeqIO.InsdcIO.GenBankCdsFeatureIterator attribute) (Bio.SeqIO.InsdcIO.GenBankIterator attribute) (Bio.SeqIO.InsdcIO.GenBankWriter attribute) (Bio.SeqIO.InsdcIO.ImgtIterator attribute) (Bio.SeqIO.InsdcIO.ImgtWriter attribute) (Bio.SeqIO.Interfaces.SequenceIterator attribute) (Bio.SeqIO.Interfaces.SequenceWriter attribute) (Bio.SeqIO.NibIO.NibIterator attribute) (Bio.SeqIO.NibIO.NibWriter attribute) (Bio.SeqIO.PdbIO.CifAtomIterator attribute) (Bio.SeqIO.PdbIO.CifSeqresIterator attribute) (Bio.SeqIO.PdbIO.PdbAtomIterator attribute) (Bio.SeqIO.PdbIO.PdbSeqresIterator attribute) (Bio.SeqIO.PhdIO.PhdIterator attribute) (Bio.SeqIO.PhdIO.PhdWriter attribute) (Bio.SeqIO.PirIO.PirIterator attribute) (Bio.SeqIO.PirIO.PirWriter attribute) (Bio.SeqIO.QualityIO.FastqIlluminaIterator attribute) (Bio.SeqIO.QualityIO.FastqIlluminaWriter attribute) (Bio.SeqIO.QualityIO.FastqIteratorAbstractBaseClass attribute) (Bio.SeqIO.QualityIO.FastqPhredIterator attribute) (Bio.SeqIO.QualityIO.FastqPhredWriter attribute) (Bio.SeqIO.QualityIO.FastqSolexaIterator attribute) (Bio.SeqIO.QualityIO.FastqSolexaWriter attribute) (Bio.SeqIO.QualityIO.InvalidCharError attribute) (Bio.SeqIO.QualityIO.QualPhredIterator attribute) (Bio.SeqIO.QualityIO.QualPhredWriter attribute) (Bio.SeqIO.SeqXmlIO.ContentHandler attribute) (Bio.SeqIO.SeqXmlIO.SeqXmlIterator attribute) (Bio.SeqIO.SeqXmlIO.SeqXmlWriter attribute) (Bio.SeqIO.SffIO.SffIterator attribute) (Bio.SeqIO.SffIO.SffWriter attribute) (Bio.SeqIO.SnapGeneIO.SnapGeneIterator attribute) (Bio.SeqIO.SwissIO.SwissIterator attribute) (Bio.SeqIO.TabIO.TabIterator attribute) (Bio.SeqIO.TabIO.TabWriter attribute) (Bio.SeqIO.TwoBitIO.TwoBitIterator attribute) (Bio.SeqIO.UniprotIO.UniprotIterator attribute) (Bio.SeqIO.XdnaIO.XdnaIterator attribute) (Bio.SeqIO.XdnaIO.XdnaWriter attribute) (Bio.SeqRecord.SeqRecord attribute) (Bio.SwissProt.FeatureTable attribute) (BioSQL.BioSeq.DBSeqRecord attribute) (BioSQL.BioSeqDatabase.MysqlConnectorAdaptor attribute) (BioSQL.DBUtils.Mysql_dbutils attribute) (BioSQL.DBUtils.Pgdb_dbutils attribute) (BioSQL.DBUtils.Psycopg2_dbutils attribute) (BioSQL.DBUtils.Sqlite_dbutils attribute) __array__() (Bio.Align.Alignment method) __array_finalize__() (Bio.Align.substitution_matrices.Array method) __array_prepare__() (Bio.Align.substitution_matrices.Array method) __array_ufunc__() (Bio.Align.substitution_matrices.Array method) __array_wrap__() (Bio.Align.substitution_matrices.Array method) __bool__() (Bio.Phylo.BaseTree.Clade method) (Bio.SeqFeature.SeqFeature method) (Bio.SeqRecord.SeqRecord method) __bytes__() (Bio.Align.bigbed.AutoSQLTable method) (Bio.Seq.SequenceDataAbstractBaseClass method) (Bio.SeqRecord.SeqRecord method) __call__() (Bio.pairwise2.affine_penalty method) (Bio.pairwise2.dictionary_match method) (Bio.pairwise2.identity_match method) __contains__() (Bio.Align.substitution_matrices.Array method) (Bio.Blast.Record method) (Bio.Data.CodonTable.AmbiguousForwardTable method) (Bio.PDB.AbstractPropertyMap.AbstractPropertyMap method) (Bio.PDB.Chain.Chain method) (Bio.PDB.Entity.DisorderedEntityWrapper method) (Bio.PDB.Entity.Entity method) (Bio.PDB.FragmentMapper.FragmentMapper method) (Bio.PDB.internal_coords.Edron method) (Bio.PDB.internal_coords.IC_Residue method) (Bio.PDB.vectors.Vector method) (Bio.phenotype.phen_micro.PlateRecord method) (Bio.Phylo.PhyloXML.Events method) (Bio.Seq.SequenceDataAbstractBaseClass method) (Bio.SeqFeature.CompoundLocation method) (Bio.SeqFeature.SeqFeature method) (Bio.SeqFeature.SimpleLocation method) (Bio.SeqRecord.SeqRecord method) (BioSQL.BioSeqDatabase.BioSeqDatabase method) (BioSQL.BioSeqDatabase.DBServer method) __dataclass_fields__ (Bio.SeqIO.QualityIO.InvalidCharError attribute) __dataclass_params__ (Bio.SeqIO.QualityIO.InvalidCharError attribute) __deepcopy__() (Bio.PDB.internal_coords.AtomKey method) (Bio.PDB.internal_coords.Edron method) (Bio.PDB.internal_coords.IC_Chain method) (Bio.PDB.internal_coords.IC_Residue method) __delitem__() (Bio.Align.MultipleSeqAlignment method) (Bio.PDB.Chain.Chain method) (Bio.PDB.Entity.Entity method) (Bio.phenotype.phen_micro.PlateRecord method) (Bio.Phylo.PhyloXML.Events method) (Bio.Seq.MutableSeq method) (BioSQL.BioSeqDatabase.BioSeqDatabase method) (BioSQL.BioSeqDatabase.DBServer method) __enter__() (Bio.Align.interfaces.AlignmentIterator method) (Bio.bgzf.BgzfReader method) (Bio.bgzf.BgzfWriter method) (Bio.Blast.Records method) (Bio.SeqIO.Interfaces.SequenceIterator method) __eq__() (Bio.Align.Alignment method) (Bio.Entrez.Parser.NoneElement method) (Bio.motifs.jaspar.Motif method) (Bio.Pathway.Reaction method) (Bio.Pathway.Rep.Graph.Graph method) (Bio.Pathway.Rep.MultiGraph.MultiGraph method) (Bio.PDB.Atom.Atom method) (Bio.PDB.Entity.Entity method) (Bio.PDB.internal_coords.AtomKey method) (Bio.PDB.internal_coords.Edron method) (Bio.phenotype.phen_micro.PlateRecord method) (Bio.phenotype.phen_micro.WellRecord method) (Bio.Seq.SequenceDataAbstractBaseClass method) (Bio.SeqFeature.CompoundLocation method) (Bio.SeqFeature.Reference method) (Bio.SeqFeature.SeqFeature method) (Bio.SeqFeature.SimpleLocation method) (Bio.SeqIO.QualityIO.InvalidCharError method) (Bio.SeqRecord.SeqRecord method) __exit__() (Bio.Align.interfaces.AlignmentIterator method) (Bio.bgzf.BgzfReader method) (Bio.bgzf.BgzfWriter method) (Bio.Blast.Records method) (Bio.SeqIO.Interfaces.SequenceIterator method) __format__() (Bio.Align.Alignment method) (Bio.Align.MultipleSeqAlignment method) (Bio.Align.substitution_matrices.Array method) (Bio.motifs.Motif method) (Bio.Phylo.BaseTree.Tree method) (Bio.SeqRecord.SeqRecord method) __ge__() (Bio.Align.Alignment method) (Bio.PDB.Atom.Atom method) (Bio.PDB.Chain.Chain method) (Bio.PDB.Entity.DisorderedEntityWrapper method) (Bio.PDB.Entity.Entity method) (Bio.PDB.internal_coords.AtomKey method) (Bio.PDB.internal_coords.Edron method) (Bio.Seq.SequenceDataAbstractBaseClass method) (Bio.SeqRecord.SeqRecord method) __getattr__() (Bio.Data.CodonTable.AmbiguousCodonTable method) (Bio.Graphics.GenomeDiagram.Feature method) (Bio.PDB.Entity.DisorderedEntityWrapper method) __getitem__() (Bio.Align.Alignment method) (Bio.Align.bigbed.AutoSQLTable method) (Bio.Align.interfaces.AlignmentIterator method) (Bio.Align.MultipleSeqAlignment method) (Bio.Align.PairwiseAlignments method) (Bio.Align.substitution_matrices.Array method) (Bio.Blast.Hit method) (Bio.Blast.Record method) (Bio.Blast.Records method) (Bio.codonalign.codonalignment.CodonAlignment method) (Bio.Data.CodonTable.AmbiguousForwardTable method) (Bio.Graphics.GenomeDiagram.Diagram method) (Bio.Graphics.GenomeDiagram.FeatureSet method) (Bio.Graphics.GenomeDiagram.GraphData method) (Bio.Graphics.GenomeDiagram.GraphSet method) (Bio.Graphics.GenomeDiagram.Track method) (Bio.motifs.mast.Record method) (Bio.motifs.matrix.GenericPositionMatrix method) (Bio.motifs.meme.Record method) (Bio.motifs.minimal.Record method) (Bio.motifs.Motif method) (Bio.motifs.transfac.Motif method) (Bio.Nexus.StandardData.StandardData method) (Bio.PDB.AbstractPropertyMap.AbstractPropertyMap method) (Bio.PDB.Chain.Chain method) (Bio.PDB.Entity.DisorderedEntityWrapper method) (Bio.PDB.Entity.Entity method) (Bio.PDB.FragmentMapper.FragmentMapper method) (Bio.PDB.vectors.Vector method) (Bio.phenotype.phen_micro.PlateRecord method) (Bio.phenotype.phen_micro.WellRecord method) (Bio.Phylo.BaseTree.Clade method) (Bio.Phylo.PhyloXML.Events method) (Bio.Phylo.PhyloXML.Phyloxml method) (Bio.SCOP.Cla.Index method) (Bio.SCOP.Raf.SeqMap method) (Bio.SCOP.Raf.SeqMapIndex method) (Bio.Seq.SequenceDataAbstractBaseClass method) (Bio.SeqIO.TwoBitIO.TwoBitIterator method) (Bio.SeqRecord.SeqRecord method) (BioSQL.BioSeqDatabase.BioSeqDatabase method) (BioSQL.BioSeqDatabase.DBServer method) __getnewargs__() (Bio.Align.bigbed.Field method) (Bio.pairwise2.Alignment method) (Bio.SeqFeature.BetweenPosition method) (Bio.SeqFeature.OneOfPosition method) (Bio.SeqFeature.WithinPosition method) __getstate__() (Bio.Align.PairwiseAligner method) __gt__() (Bio.Align.Alignment method) (Bio.PDB.Atom.Atom method) (Bio.PDB.Chain.Chain method) (Bio.PDB.Entity.DisorderedEntityWrapper method) (Bio.PDB.Entity.Entity method) (Bio.PDB.internal_coords.AtomKey method) (Bio.PDB.internal_coords.Edron method) (Bio.Seq.SequenceDataAbstractBaseClass method) (Bio.SeqRecord.SeqRecord method) __hash__ (Bio.Align.Alignment attribute) (Bio.Entrez.Parser.NoneElement attribute) (Bio.Pathway.Rep.Graph.Graph attribute) (Bio.Pathway.Rep.MultiGraph.MultiGraph attribute) (Bio.phenotype.phen_micro.PlateRecord attribute) (Bio.phenotype.phen_micro.WellRecord attribute) (Bio.SeqFeature.CompoundLocation attribute) (Bio.SeqFeature.Reference attribute) (Bio.SeqFeature.SeqFeature attribute) (Bio.SeqFeature.SimpleLocation attribute) (Bio.SeqIO.QualityIO.InvalidCharError attribute) (Bio.SeqRecord.SeqRecord attribute) __hash__() (Bio.motifs.jaspar.Motif method) (Bio.Pathway.Interaction method) (Bio.Pathway.Reaction method) (Bio.PDB.Atom.Atom method) (Bio.PDB.Entity.Entity method) (Bio.PDB.internal_coords.AtomKey method) (Bio.PDB.internal_coords.Edron method) (Bio.Seq.Seq method) (Bio.Seq.SequenceDataAbstractBaseClass method) (Bio.SeqFeature.UnknownPosition method) __iadd__() (Bio.SCOP.Raf.SeqMap method) __init__() (Bio.Affy.CelFile.ParserError method) (Bio.Affy.CelFile.Record method) (Bio.Align.AlignInfo.SummaryInfo method) (Bio.Align.Alignment method) (Bio.Align.AlignmentCounts method) (Bio.Align.Alignments method) (Bio.Align.bed.AlignmentWriter method) (Bio.Align.bigbed.AlignmentWriter method) (Bio.Align.bigbed.AutoSQLTable method) (Bio.Align.bigmaf.AlignmentIterator method) (Bio.Align.bigmaf.AlignmentWriter method) (Bio.Align.bigpsl.AlignmentWriter method) (Bio.Align.CodonAligner method) (Bio.Align.exonerate.AlignmentWriter method) (Bio.Align.interfaces.AlignmentIterator method) (Bio.Align.interfaces.AlignmentWriter method) (Bio.Align.mauve.AlignmentWriter method) (Bio.Align.MultipleSeqAlignment method) (Bio.Align.nexus.AlignmentWriter method) (Bio.Align.PairwiseAligner method) (Bio.Align.PairwiseAlignments method) (Bio.Align.psl.AlignmentWriter method) (Bio.Align.sam.AlignmentWriter method) (Bio.AlignIO.Interfaces.AlignmentIterator method) (Bio.AlignIO.Interfaces.AlignmentWriter method) (Bio.AlignIO.Interfaces.SequentialAlignmentWriter method) (Bio.AlignIO.MafIO.MafIndex method) (Bio.AlignIO.MauveIO.MauveWriter method) (Bio.bgzf.BgzfReader method) (Bio.bgzf.BgzfWriter method) (Bio.Blast.CorruptedXMLError method) (Bio.Blast.NCBIXML.Alignment method) (Bio.Blast.NCBIXML.Blast method) (Bio.Blast.NCBIXML.BlastParser method) (Bio.Blast.NCBIXML.DatabaseReport method) (Bio.Blast.NCBIXML.Description method) (Bio.Blast.NCBIXML.DescriptionExt method) (Bio.Blast.NCBIXML.DescriptionExtItem method) (Bio.Blast.NCBIXML.Header method) (Bio.Blast.NCBIXML.HSP method) (Bio.Blast.NCBIXML.MultipleAlignment method) (Bio.Blast.NCBIXML.Parameters method) (Bio.Blast.NCBIXML.PSIBlast method) (Bio.Blast.NCBIXML.Round method) (Bio.Blast.NotXMLError method) (Bio.Blast.Record method) (Bio.Blast.Records method) (Bio.CAPS.CAPSMap method) (Bio.CAPS.DifferentialCutsite method) (Bio.Cluster.Record method) (Bio.codonalign.codonalignment.CodonAlignment method) (Bio.codonalign.codonseq.CodonSeq method) (Bio.Compass.Record method) (Bio.Data.CodonTable.AmbiguousCodonTable method) (Bio.Data.CodonTable.AmbiguousForwardTable method) (Bio.Data.CodonTable.CodonTable method) (Bio.Data.CodonTable.NCBICodonTable method) (Bio.Emboss.Primer3.Primers method) (Bio.Emboss.Primer3.Record method) (Bio.Emboss.PrimerSearch.Amplifier method) (Bio.Emboss.PrimerSearch.InputRecord method) (Bio.Emboss.PrimerSearch.OutputRecord method) (Bio.Entrez.Parser.CorruptedXMLError method) (Bio.Entrez.Parser.DataHandler method) (Bio.Entrez.Parser.DataHandlerMeta method) (Bio.Entrez.Parser.DictionaryElement method) (Bio.Entrez.Parser.ErrorElement method) (Bio.Entrez.Parser.IntegerElement method) (Bio.Entrez.Parser.ListElement method) (Bio.Entrez.Parser.NoneElement method) (Bio.Entrez.Parser.NotXMLError method) (Bio.Entrez.Parser.OrderedListElement method) (Bio.Entrez.Parser.StringElement method) (Bio.Entrez.Parser.ValidationError method) (Bio.ExPASy.cellosaurus.Record method) (Bio.ExPASy.Enzyme.Record method) (Bio.ExPASy.Prodoc.Record method) (Bio.ExPASy.Prodoc.Reference method) (Bio.ExPASy.Prosite.Record method) (Bio.ExPASy.ScanProsite.ContentHandler method) (Bio.ExPASy.ScanProsite.Parser method) (Bio.ExPASy.ScanProsite.Record method) (Bio.GenBank.FeatureParser method) (Bio.GenBank.Iterator method) (Bio.GenBank.Record.Feature method) (Bio.GenBank.Record.Qualifier method) (Bio.GenBank.Record.Record method) (Bio.GenBank.Record.Reference method) (Bio.GenBank.RecordParser method) (Bio.GenBank.Scanner.InsdcScanner method) (Bio.GenBank.utils.FeatureValueCleaner method) (Bio.Geo.Record.Record method) (Bio.Graphics.BasicChromosome.AnnotatedChromosomeSegment method) (Bio.Graphics.BasicChromosome.Chromosome method) (Bio.Graphics.BasicChromosome.ChromosomeSegment method) (Bio.Graphics.BasicChromosome.Organism method) (Bio.Graphics.BasicChromosome.TelomereSegment method) (Bio.Graphics.ColorSpiral.ColorSpiral method) (Bio.Graphics.Comparative.ComparativeScatterPlot method) (Bio.Graphics.DisplayRepresentation.ChromosomeCounts method) (Bio.Graphics.Distribution.BarChartDistribution method) (Bio.Graphics.Distribution.DistributionPage method) (Bio.Graphics.Distribution.LineDistribution method) (Bio.Graphics.GenomeDiagram.ColorTranslator method) (Bio.Graphics.GenomeDiagram.CrossLink method) (Bio.Graphics.GenomeDiagram.Diagram method) (Bio.Graphics.GenomeDiagram.Feature method) (Bio.Graphics.GenomeDiagram.FeatureSet method) (Bio.Graphics.GenomeDiagram.GraphData method) (Bio.Graphics.GenomeDiagram.GraphSet method) (Bio.Graphics.GenomeDiagram.Track method) (Bio.Graphics.KGML_vis.KGMLCanvas method) (Bio.HMM.DynamicProgramming.AbstractDPAlgorithms method) (Bio.HMM.DynamicProgramming.LogDPAlgorithms method) (Bio.HMM.DynamicProgramming.ScaledDPAlgorithms method) (Bio.HMM.MarkovModel.HiddenMarkovModel method) (Bio.HMM.MarkovModel.MarkovModelBuilder method) (Bio.HMM.Trainer.AbstractTrainer method) (Bio.HMM.Trainer.BaumWelchTrainer method) (Bio.HMM.Trainer.KnownStateTrainer method) (Bio.HMM.Trainer.TrainingSequence method) (Bio.KEGG.Compound.Record method) (Bio.KEGG.Enzyme.Record method) (Bio.KEGG.Gene.Record method) (Bio.KEGG.KGML.KGML_parser.KGMLParser method) (Bio.KEGG.KGML.KGML_pathway.Component method) (Bio.KEGG.KGML.KGML_pathway.Entry method) (Bio.KEGG.KGML.KGML_pathway.Graphics method) (Bio.KEGG.KGML.KGML_pathway.Pathway method) (Bio.KEGG.KGML.KGML_pathway.Reaction method) (Bio.KEGG.KGML.KGML_pathway.Relation method) (Bio.motifs.alignace.Record method) (Bio.motifs.jaspar.db.JASPAR5 method) (Bio.motifs.jaspar.Motif method) (Bio.motifs.jaspar.Record method) (Bio.motifs.mast.Record method) (Bio.motifs.matrix.GenericPositionMatrix method) (Bio.motifs.matrix.PositionWeightMatrix method) (Bio.motifs.meme.Instance method) (Bio.motifs.meme.Motif method) (Bio.motifs.meme.Record method) (Bio.motifs.minimal.Record method) (Bio.motifs.Motif method) (Bio.motifs.thresholds.ScoreDistribution method) (Bio.motifs.transfac.Record method) (Bio.motifs.xms.XMSScanner method) (Bio.Nexus.Nexus.Block method) (Bio.Nexus.Nexus.CharBuffer method) (Bio.Nexus.Nexus.Commandline method) (Bio.Nexus.Nexus.Nexus method) (Bio.Nexus.Nexus.StepMatrix method) (Bio.Nexus.Nodes.Chain method) (Bio.Nexus.Nodes.Node method) (Bio.Nexus.StandardData.StandardData method) (Bio.Nexus.Trees.NodeData method) (Bio.Nexus.Trees.Tree method) (Bio.NMR.xpktools.Peaklist method) (Bio.NMR.xpktools.XpkEntry method) (Bio.pairwise2.affine_penalty method) (Bio.pairwise2.dictionary_match method) (Bio.pairwise2.identity_match method) (Bio.Pathway.Network method) (Bio.Pathway.Reaction method) (Bio.Pathway.Rep.Graph.Graph method) (Bio.Pathway.Rep.MultiGraph.MultiGraph method) (Bio.Pathway.System method) (Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap method) (Bio.PDB.AbstractPropertyMap.AbstractPropertyMap method) (Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap method) (Bio.PDB.Atom.Atom method) (Bio.PDB.Atom.DisorderedAtom method) (Bio.PDB.binary_cif.BinaryCIFParser method) (Bio.PDB.cealign.CEAligner method) (Bio.PDB.Chain.Chain method) (Bio.PDB.Dice.ChainSelector method) (Bio.PDB.DSSP.DSSP method) (Bio.PDB.Entity.DisorderedEntityWrapper method) (Bio.PDB.Entity.Entity method) (Bio.PDB.FragmentMapper.Fragment method) (Bio.PDB.FragmentMapper.FragmentMapper method) (Bio.PDB.HSExposure.ExposureCN method) (Bio.PDB.HSExposure.HSExposureCA method) (Bio.PDB.HSExposure.HSExposureCB method) (Bio.PDB.internal_coords.AtomKey method) (Bio.PDB.internal_coords.Dihedron method) (Bio.PDB.internal_coords.Edron method) (Bio.PDB.internal_coords.Hedron method) (Bio.PDB.internal_coords.IC_Chain method) (Bio.PDB.internal_coords.IC_Residue method) (Bio.PDB.MMCIF2Dict.MMCIF2Dict method) (Bio.PDB.mmcifio.MMCIFIO method) (Bio.PDB.MMCIFParser.FastMMCIFParser method) (Bio.PDB.MMCIFParser.MMCIFParser method) (Bio.PDB.mmtf.DefaultParser.StructureDecoder method) (Bio.PDB.mmtf.mmtfio.MMTFIO method) (Bio.PDB.Model.Model method) (Bio.PDB.NACCESS.NACCESS method) (Bio.PDB.NACCESS.NACCESS_atomic method) (Bio.PDB.NeighborSearch.NeighborSearch method) (Bio.PDB.PDBIO.PDBIO method) (Bio.PDB.PDBIO.StructureIO method) (Bio.PDB.PDBList.PDBList method) (Bio.PDB.PDBMLParser.PDBMLParser method) (Bio.PDB.PDBParser.PDBParser method) (Bio.PDB.Polypeptide.CaPPBuilder method) (Bio.PDB.Polypeptide.PPBuilder method) (Bio.PDB.PSEA.PSEA method) (Bio.PDB.qcprot.QCPSuperimposer method) (Bio.PDB.Residue.DisorderedResidue method) (Bio.PDB.Residue.Residue method) (Bio.PDB.ResidueDepth.ResidueDepth method) (Bio.PDB.SASA.ShrakeRupley method) (Bio.PDB.Structure.Structure method) (Bio.PDB.StructureAlignment.StructureAlignment method) (Bio.PDB.StructureBuilder.StructureBuilder method) (Bio.PDB.Superimposer.Superimposer method) (Bio.PDB.vectors.Vector method) (Bio.phenotype.phen_micro.JsonWriter method) (Bio.phenotype.phen_micro.PlateRecord method) (Bio.phenotype.phen_micro.WellRecord method) (Bio.Phylo.BaseTree.BranchColor method) (Bio.Phylo.BaseTree.Clade method) (Bio.Phylo.BaseTree.Tree method) (Bio.Phylo.CDAO.Clade method) (Bio.Phylo.CDAO.Tree method) (Bio.Phylo.CDAOIO.Parser method) (Bio.Phylo.CDAOIO.Writer method) (Bio.Phylo.Newick.Clade method) (Bio.Phylo.Newick.Tree method) (Bio.Phylo.NewickIO.Parser method) (Bio.Phylo.NewickIO.Writer method) (Bio.Phylo.NeXML.Clade method) (Bio.Phylo.NeXML.Tree method) (Bio.Phylo.NeXMLIO.Parser method) (Bio.Phylo.NeXMLIO.Writer method) (Bio.Phylo.PAML.baseml.Baseml method) (Bio.Phylo.PAML.codeml.Codeml method) (Bio.Phylo.PAML.yn00.Yn00 method) (Bio.Phylo.PhyloXML.Accession method) (Bio.Phylo.PhyloXML.Annotation method) (Bio.Phylo.PhyloXML.BinaryCharacters method) (Bio.Phylo.PhyloXML.BranchColor method) (Bio.Phylo.PhyloXML.Clade method) (Bio.Phylo.PhyloXML.CladeRelation method) (Bio.Phylo.PhyloXML.Date method) (Bio.Phylo.PhyloXML.Distribution method) (Bio.Phylo.PhyloXML.DomainArchitecture method) (Bio.Phylo.PhyloXML.Events method) (Bio.Phylo.PhyloXML.Id method) (Bio.Phylo.PhyloXML.MolSeq method) (Bio.Phylo.PhyloXML.Other method) (Bio.Phylo.PhyloXML.Phylogeny method) (Bio.Phylo.PhyloXML.Phyloxml method) (Bio.Phylo.PhyloXML.Point method) (Bio.Phylo.PhyloXML.Polygon method) (Bio.Phylo.PhyloXML.Property method) (Bio.Phylo.PhyloXML.ProteinDomain method) (Bio.Phylo.PhyloXML.Reference method) (Bio.Phylo.PhyloXML.Sequence method) (Bio.Phylo.PhyloXML.SequenceRelation method) (Bio.Phylo.PhyloXML.Taxonomy method) (Bio.Phylo.PhyloXML.Uri method) (Bio.Phylo.PhyloXMLIO.Parser method) (Bio.Phylo.PhyloXMLIO.Writer method) (Bio.Phylo.TreeConstruction.DistanceCalculator method) (Bio.Phylo.TreeConstruction.DistanceMatrix method) (Bio.Phylo.TreeConstruction.DistanceTreeConstructor method) (Bio.Phylo.TreeConstruction.NNITreeSearcher method) (Bio.Phylo.TreeConstruction.ParsimonyScorer method) (Bio.Phylo.TreeConstruction.ParsimonyTreeConstructor method) (Bio.PopGen.GenePop.FileParser.FileRecord method) (Bio.PopGen.GenePop.LargeFileParser.Record method) (Bio.PopGen.GenePop.Record method) (Bio.SCOP.Astral method) (Bio.SCOP.Cla.Index method) (Bio.SCOP.Cla.Record method) (Bio.SCOP.Des.Record method) (Bio.SCOP.Dom.Record method) (Bio.SCOP.Domain method) (Bio.SCOP.Hie.Record method) (Bio.SCOP.Node method) (Bio.SCOP.Raf.Res method) (Bio.SCOP.Raf.SeqMap method) (Bio.SCOP.Raf.SeqMapIndex method) (Bio.SCOP.Residues.Residues method) (Bio.SCOP.Scop method) (Bio.SearchIO.BlastIO.blast_tab.BlastTabIndexer method) (Bio.SearchIO.BlastIO.blast_tab.BlastTabParser method) (Bio.SearchIO.BlastIO.blast_tab.BlastTabWriter method) (Bio.SearchIO.BlastIO.blast_xml.BlastXmlIndexer method) (Bio.SearchIO.BlastIO.blast_xml.BlastXmlParser method) (Bio.SearchIO.BlastIO.blast_xml.BlastXmlWriter method) (Bio.SearchIO.BlatIO.BlatPslIndexer method) (Bio.SearchIO.BlatIO.BlatPslParser method) (Bio.SearchIO.BlatIO.BlatPslWriter method) (Bio.SearchIO.FastaIO.FastaM10Indexer method) (Bio.SearchIO.FastaIO.FastaM10Parser method) (Bio.SearchIO.HHsuiteIO.hhsuite2_text.Hhsuite2TextParser method) (Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser method) (Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmhitWriter method) (Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabParser method) (Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabWriter method) (Bio.SearchIO.HmmerIO.hmmer3_text.Hmmer3TextParser method) (Bio.SearchIO.InterproscanIO.interproscan_xml.InterproscanXmlParser method) (Bio.Seq.MutableSeq method) (Bio.Seq.Seq method) (Bio.Seq.SequenceDataAbstractBaseClass method) (Bio.SeqFeature.CompoundLocation method) (Bio.SeqFeature.Reference method) (Bio.SeqFeature.SeqFeature method) (Bio.SeqFeature.SimpleLocation method) (Bio.SeqIO.AbiIO.AbiIterator method) (Bio.SeqIO.AceIO.AceIterator method) (Bio.SeqIO.AlignmentSequenceIterator method) (Bio.SeqIO.FastaIO.FastaBlastIterator method) (Bio.SeqIO.FastaIO.FastaIterator method) (Bio.SeqIO.FastaIO.FastaPearsonIterator method) (Bio.SeqIO.FastaIO.FastaTwoLineIterator method) (Bio.SeqIO.FastaIO.FastaTwoLineWriter method) (Bio.SeqIO.FastaIO.FastaWriter method) (Bio.SeqIO.GckIO.GckIterator method) (Bio.SeqIO.GfaIO.Gfa1Iterator method) (Bio.SeqIO.GfaIO.Gfa2Iterator method) (Bio.SeqIO.IgIO.IgIterator method) (Bio.SeqIO.InsdcIO.EmblCdsFeatureIterator method) (Bio.SeqIO.InsdcIO.EmblIterator method) (Bio.SeqIO.InsdcIO.GenBankCdsFeatureIterator method) (Bio.SeqIO.InsdcIO.GenBankIterator method) (Bio.SeqIO.InsdcIO.ImgtIterator method) (Bio.SeqIO.Interfaces.SequenceIterator method) (Bio.SeqIO.Interfaces.SequenceWriter method) (Bio.SeqIO.NibIO.NibIterator method) (Bio.SeqIO.PdbIO.CifAtomIterator method) (Bio.SeqIO.PdbIO.CifSeqresIterator method) (Bio.SeqIO.PdbIO.PdbAtomIterator method) (Bio.SeqIO.PdbIO.PdbSeqresIterator method) (Bio.SeqIO.PhdIO.PhdIterator method) (Bio.SeqIO.PirIO.PirIterator method) (Bio.SeqIO.PirIO.PirWriter method) (Bio.SeqIO.QualityIO.FastqIlluminaIterator method) (Bio.SeqIO.QualityIO.FastqIteratorAbstractBaseClass method) (Bio.SeqIO.QualityIO.FastqPhredIterator method) (Bio.SeqIO.QualityIO.FastqSolexaIterator method) (Bio.SeqIO.QualityIO.InvalidCharError method) (Bio.SeqIO.QualityIO.QualPhredIterator method) (Bio.SeqIO.QualityIO.QualPhredWriter method) (Bio.SeqIO.SeqXmlIO.ContentHandler method) (Bio.SeqIO.SeqXmlIO.SeqXmlIterator method) (Bio.SeqIO.SeqXmlIO.SeqXmlWriter method) (Bio.SeqIO.SffIO.SffIterator method) (Bio.SeqIO.SffIO.SffWriter method) (Bio.SeqIO.SnapGeneIO.SnapGeneIterator method) (Bio.SeqIO.SwissIO.SwissIterator method) (Bio.SeqIO.TabIO.TabIterator method) (Bio.SeqIO.TwoBitIO.TwoBitIterator method) (Bio.SeqIO.UniprotIO.UniprotIterator method) (Bio.SeqIO.XdnaIO.XdnaIterator method) (Bio.SeqRecord.SeqRecord method) (Bio.Sequencing.Ace.ACEFileRecord method) (Bio.Sequencing.Ace.af method) (Bio.Sequencing.Ace.bs method) (Bio.Sequencing.Ace.Contig method) (Bio.Sequencing.Ace.ct method) (Bio.Sequencing.Ace.ds method) (Bio.Sequencing.Ace.qa method) (Bio.Sequencing.Ace.rd method) (Bio.Sequencing.Ace.Reads method) (Bio.Sequencing.Ace.rt method) (Bio.Sequencing.Ace.wa method) (Bio.Sequencing.Ace.wr method) (Bio.Sequencing.Phd.Record method) (Bio.SeqUtils.CodonAdaptationIndex method) (Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint method) (Bio.SeqUtils.ProtParam.ProteinAnalysis method) (Bio.SVDSuperimposer.SVDSuperimposer method) (Bio.SwissProt.KeyWList.Record method) (Bio.SwissProt.Record method) (Bio.SwissProt.Reference method) (Bio.SwissProt.SwissProtParserError method) (Bio.UniGene.ProtsimLine method) (Bio.UniGene.Record method) (Bio.UniGene.SequenceLine method) (Bio.UniGene.STSLine method) (BioSQL.BioSeq.DBSeqRecord method) (BioSQL.BioSeqDatabase.Adaptor method) (BioSQL.BioSeqDatabase.BioSeqDatabase method) (BioSQL.BioSeqDatabase.DBServer method) (BioSQL.DBUtils.Generic_dbutils method) (BioSQL.Loader.DatabaseLoader method) (BioSQL.Loader.DatabaseRemover method)

__iter__() (Bio.Align.AlignmentsAbstractBaseClass method) (Bio.Align.MultipleSeqAlignment method) (Bio.AlignIO.Interfaces.AlignmentIterator method) (Bio.bgzf.BgzfReader method) (Bio.Blast.Records method) (Bio.GenBank.Iterator method) (Bio.Nexus.StandardData.StandardData method) (Bio.PDB.AbstractPropertyMap.AbstractPropertyMap method) (Bio.PDB.Atom.DisorderedAtom method) (Bio.PDB.Entity.DisorderedEntityWrapper method) (Bio.PDB.Entity.Entity method) (Bio.phenotype.phen_micro.PlateRecord method) (Bio.phenotype.phen_micro.WellRecord method) (Bio.Phylo.BaseTree.Clade method) (Bio.Phylo.PhyloXML.Events method) (Bio.Phylo.PhyloXML.Other method) (Bio.Phylo.PhyloXML.Phyloxml method) (Bio.SearchIO.BlastIO.blast_tab.BlastTabIndexer method) (Bio.SearchIO.BlastIO.blast_tab.BlastTabParser method) (Bio.SearchIO.BlastIO.blast_xml.BlastXmlIndexer method) (Bio.SearchIO.BlastIO.blast_xml.BlastXmlParser method) (Bio.SearchIO.BlatIO.BlatPslIndexer method) (Bio.SearchIO.BlatIO.BlatPslParser method) (Bio.SearchIO.FastaIO.FastaM10Indexer method) (Bio.SearchIO.FastaIO.FastaM10Parser method) (Bio.SearchIO.HHsuiteIO.hhsuite2_text.Hhsuite2TextParser method) (Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextIndexer method) (Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser method) (Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabIndexer method) (Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabParser method) (Bio.SearchIO.HmmerIO.hmmer3_text.Hmmer3TextIndexer method) (Bio.SearchIO.HmmerIO.hmmer3_text.Hmmer3TextParser method) (Bio.SearchIO.InterproscanIO.interproscan_xml.InterproscanXmlParser method) (Bio.SeqFeature.CompoundLocation method) (Bio.SeqFeature.SeqFeature method) (Bio.SeqFeature.SimpleLocation method) (Bio.SeqIO.Interfaces.SequenceIterator method) (Bio.SeqRecord.SeqRecord method) (BioSQL.BioSeqDatabase.BioSeqDatabase method) (BioSQL.BioSeqDatabase.DBServer method) __le__() (Bio.Align.Alignment method) (Bio.PDB.Atom.Atom method) (Bio.PDB.Chain.Chain method) (Bio.PDB.Entity.DisorderedEntityWrapper method) (Bio.PDB.Entity.Entity method) (Bio.PDB.internal_coords.AtomKey method) (Bio.PDB.internal_coords.Edron method) (Bio.Seq.SequenceDataAbstractBaseClass method) (Bio.SeqRecord.SeqRecord method) __len__() (Bio.Align.Alignment method) (Bio.Align.Alignments method) (Bio.Align.AlignmentsAbstractBaseClass method) (Bio.Align.bigbed.AlignmentIterator method) (Bio.Align.hhr.AlignmentIterator method) (Bio.Align.interfaces.AlignmentIterator method) (Bio.Align.MultipleSeqAlignment method) (Bio.Align.PairwiseAlignments method) (Bio.AlignIO.MafIO.MafIndex method) (Bio.Emboss.Primer3.Primers method) (Bio.Graphics.GenomeDiagram.FeatureSet method) (Bio.Graphics.GenomeDiagram.GraphData method) (Bio.Graphics.GenomeDiagram.GraphSet method) (Bio.motifs.Motif method) (Bio.Nexus.StandardData.StandardData method) (Bio.PDB.AbstractPropertyMap.AbstractPropertyMap method) (Bio.PDB.Entity.DisorderedEntityWrapper method) (Bio.PDB.Entity.Entity method) (Bio.PDB.FragmentMapper.Fragment method) (Bio.phenotype.phen_micro.PlateRecord method) (Bio.phenotype.phen_micro.WellRecord method) (Bio.Phylo.BaseTree.Clade method) (Bio.Phylo.PhyloXML.Events method) (Bio.Phylo.PhyloXML.Phyloxml method) (Bio.Seq.SequenceDataAbstractBaseClass method) (Bio.SeqFeature.CompoundLocation method) (Bio.SeqFeature.SeqFeature method) (Bio.SeqFeature.SimpleLocation method) (Bio.SeqIO.TwoBitIO.TwoBitIterator method) (Bio.SeqRecord.SeqRecord method) (BioSQL.BioSeqDatabase.BioSeqDatabase method) (BioSQL.BioSeqDatabase.DBServer method) __lt__() (Bio.Align.Alignment method) (Bio.PDB.Atom.Atom method) (Bio.PDB.Chain.Chain method) (Bio.PDB.Entity.DisorderedEntityWrapper method) (Bio.PDB.Entity.Entity method) (Bio.PDB.internal_coords.AtomKey method) (Bio.PDB.internal_coords.Edron method) (Bio.Seq.SequenceDataAbstractBaseClass method) (Bio.SeqRecord.SeqRecord method) __match_args__ (Bio.Align.bigbed.Field attribute) (Bio.pairwise2.Alignment attribute) (Bio.SeqIO.QualityIO.InvalidCharError attribute) __mul__() (Bio.PDB.vectors.Vector method) (Bio.Seq.SequenceDataAbstractBaseClass method) __ne__() (Bio.Align.Alignment method) (Bio.Entrez.Parser.NoneElement method) (Bio.PDB.Atom.Atom method) (Bio.PDB.Entity.Entity method) (Bio.PDB.internal_coords.AtomKey method) (Bio.PDB.internal_coords.Edron method) (Bio.SeqRecord.SeqRecord method) __neg__() (Bio.PDB.vectors.Vector method) __new__() (Bio.Align.bigbed.Field static method) (Bio.Align.substitution_matrices.Array static method) (Bio.Entrez.Parser.ErrorElement static method) (Bio.Entrez.Parser.IntegerElement static method) (Bio.Entrez.Parser.StringElement static method) (Bio.pairwise2.Alignment static method) (Bio.Phylo.PhyloXML.Confidence static method) (Bio.SeqFeature.AfterPosition static method) (Bio.SeqFeature.BeforePosition static method) (Bio.SeqFeature.BetweenPosition static method) (Bio.SeqFeature.ExactPosition static method) (Bio.SeqFeature.OneOfPosition static method) (Bio.SeqFeature.WithinPosition static method) __next__() (Bio.Align.Alignments method) (Bio.Align.AlignmentsAbstractBaseClass method) (Bio.Align.interfaces.AlignmentIterator method) (Bio.Align.PairwiseAlignments method) (Bio.AlignIO.ClustalIO.ClustalIterator method) (Bio.AlignIO.EmbossIO.EmbossIterator method) (Bio.AlignIO.Interfaces.AlignmentIterator method) (Bio.AlignIO.MauveIO.MauveIterator method) (Bio.AlignIO.MsfIO.MsfIterator method) (Bio.AlignIO.PhylipIO.PhylipIterator method) (Bio.AlignIO.PhylipIO.SequentialPhylipIterator method) (Bio.AlignIO.StockholmIO.StockholmIterator method) (Bio.bgzf.BgzfReader method) (Bio.Blast.Records method) (Bio.GenBank.Iterator method) (Bio.Nexus.Nexus.CharBuffer method) (Bio.Nexus.StandardData.StandardData method) (Bio.SeqIO.AbiIO.AbiIterator method) (Bio.SeqIO.AceIO.AceIterator method) (Bio.SeqIO.AlignmentSequenceIterator method) (Bio.SeqIO.FastaIO.FastaBlastIterator method) (Bio.SeqIO.FastaIO.FastaIterator method) (Bio.SeqIO.FastaIO.FastaPearsonIterator method) (Bio.SeqIO.FastaIO.FastaTwoLineIterator method) (Bio.SeqIO.GckIO.GckIterator method) (Bio.SeqIO.GfaIO.Gfa1Iterator method) (Bio.SeqIO.GfaIO.Gfa2Iterator method) (Bio.SeqIO.IgIO.IgIterator method) (Bio.SeqIO.InsdcIO.EmblCdsFeatureIterator method) (Bio.SeqIO.InsdcIO.EmblIterator method) (Bio.SeqIO.InsdcIO.GenBankCdsFeatureIterator method) (Bio.SeqIO.InsdcIO.GenBankIterator method) (Bio.SeqIO.InsdcIO.ImgtIterator method) (Bio.SeqIO.Interfaces.SequenceIterator method) (Bio.SeqIO.NibIO.NibIterator method) (Bio.SeqIO.PdbIO.CifAtomIterator method) (Bio.SeqIO.PdbIO.CifSeqresIterator method) (Bio.SeqIO.PdbIO.PdbAtomIterator method) (Bio.SeqIO.PdbIO.PdbSeqresIterator method) (Bio.SeqIO.PhdIO.PhdIterator method) (Bio.SeqIO.PirIO.PirIterator method) (Bio.SeqIO.QualityIO.FastqIteratorAbstractBaseClass method) (Bio.SeqIO.QualityIO.QualPhredIterator method) (Bio.SeqIO.SeqXmlIO.SeqXmlIterator method) (Bio.SeqIO.SffIO.SffIterator method) (Bio.SeqIO.SnapGeneIO.SnapGeneIterator method) (Bio.SeqIO.SwissIO.SwissIterator method) (Bio.SeqIO.TabIO.TabIterator method) (Bio.SeqIO.TwoBitIO.TwoBitIterator method) (Bio.SeqIO.UniprotIO.UniprotIterator method) (Bio.SeqIO.XdnaIO.XdnaIterator method) __nonzero__() (Bio.SeqFeature.CompoundLocation method) (Bio.SeqFeature.SimpleLocation method) __orig_bases__ (Bio.PDB.Chain.Chain attribute) (Bio.PDB.Entity.Entity attribute) (Bio.PDB.Model.Model attribute) (Bio.PDB.Residue.Residue attribute) (Bio.PDB.Structure.Structure attribute) (Bio.SeqIO.Interfaces.SequenceIterator attribute) (Bio.SeqIO.Interfaces.SequenceWriter attribute) (Bio.SeqIO.QualityIO.FastqIteratorAbstractBaseClass attribute) __parameters__ (Bio.PDB.Chain.Chain attribute) (Bio.PDB.Entity.Entity attribute) (Bio.PDB.Model.Model attribute) (Bio.PDB.Residue.Residue attribute) (Bio.PDB.Structure.Structure attribute) (Bio.SeqIO.AbiIO.AbiIterator attribute) (Bio.SeqIO.AceIO.AceIterator attribute) (Bio.SeqIO.AlignmentSequenceIterator attribute) (Bio.SeqIO.AlignmentSequenceWriter attribute) (Bio.SeqIO.FastaIO.FastaBlastIterator attribute) (Bio.SeqIO.FastaIO.FastaIterator attribute) (Bio.SeqIO.FastaIO.FastaPearsonIterator attribute) (Bio.SeqIO.FastaIO.FastaTwoLineIterator attribute) (Bio.SeqIO.FastaIO.FastaTwoLineWriter attribute) (Bio.SeqIO.FastaIO.FastaWriter attribute) (Bio.SeqIO.GckIO.GckIterator attribute) (Bio.SeqIO.GfaIO.Gfa1Iterator attribute) (Bio.SeqIO.GfaIO.Gfa2Iterator attribute) (Bio.SeqIO.IgIO.IgIterator attribute) (Bio.SeqIO.InsdcIO.EmblCdsFeatureIterator attribute) (Bio.SeqIO.InsdcIO.EmblIterator attribute) (Bio.SeqIO.InsdcIO.EmblWriter attribute) (Bio.SeqIO.InsdcIO.GenBankCdsFeatureIterator attribute) (Bio.SeqIO.InsdcIO.GenBankIterator attribute) (Bio.SeqIO.InsdcIO.GenBankWriter attribute) (Bio.SeqIO.InsdcIO.ImgtIterator attribute) (Bio.SeqIO.InsdcIO.ImgtWriter attribute) (Bio.SeqIO.Interfaces.SequenceIterator attribute) (Bio.SeqIO.Interfaces.SequenceWriter attribute) (Bio.SeqIO.NibIO.NibIterator attribute) (Bio.SeqIO.NibIO.NibWriter attribute) (Bio.SeqIO.PdbIO.CifAtomIterator attribute) (Bio.SeqIO.PdbIO.CifSeqresIterator attribute) (Bio.SeqIO.PdbIO.PdbAtomIterator attribute) (Bio.SeqIO.PdbIO.PdbSeqresIterator attribute) (Bio.SeqIO.PhdIO.PhdIterator attribute) (Bio.SeqIO.PhdIO.PhdWriter attribute) (Bio.SeqIO.PirIO.PirIterator attribute) (Bio.SeqIO.PirIO.PirWriter attribute) (Bio.SeqIO.QualityIO.FastqIlluminaIterator attribute) (Bio.SeqIO.QualityIO.FastqIlluminaWriter attribute) (Bio.SeqIO.QualityIO.FastqIteratorAbstractBaseClass attribute) (Bio.SeqIO.QualityIO.FastqPhredIterator attribute) (Bio.SeqIO.QualityIO.FastqPhredWriter attribute) (Bio.SeqIO.QualityIO.FastqSolexaIterator attribute) (Bio.SeqIO.QualityIO.FastqSolexaWriter attribute) (Bio.SeqIO.QualityIO.QualPhredIterator attribute) (Bio.SeqIO.QualityIO.QualPhredWriter attribute) (Bio.SeqIO.SeqXmlIO.SeqXmlIterator attribute) (Bio.SeqIO.SeqXmlIO.SeqXmlWriter attribute) (Bio.SeqIO.SffIO.SffIterator attribute) (Bio.SeqIO.SffIO.SffWriter attribute) (Bio.SeqIO.SnapGeneIO.SnapGeneIterator attribute) (Bio.SeqIO.SwissIO.SwissIterator attribute) (Bio.SeqIO.TabIO.TabIterator attribute) (Bio.SeqIO.TabIO.TabWriter attribute) (Bio.SeqIO.TwoBitIO.TwoBitIterator attribute) (Bio.SeqIO.UniprotIO.UniprotIterator attribute) (Bio.SeqIO.XdnaIO.XdnaIterator attribute) (Bio.SeqIO.XdnaIO.XdnaWriter attribute) __pow__() (Bio.PDB.vectors.Vector method) __radd__() (Bio.Seq.SequenceDataAbstractBaseClass method) (Bio.SeqFeature.CompoundLocation method) (Bio.SeqFeature.SimpleLocation method) (Bio.SeqRecord.SeqRecord method) __reduce__() (Bio.Align.substitution_matrices.Array method) __repr__() (Bio.Align.Alignment method) (Bio.Align.AlignmentCounts method) (Bio.Align.bigbed.Field method) (Bio.Align.MultipleSeqAlignment method) (Bio.Align.substitution_matrices.Array method) (Bio.AlignIO.MafIO.MafIndex method) (Bio.Blast.Hit method) (Bio.Blast.HSP method) (Bio.Blast.Record method) (Bio.Blast.Records method) (Bio.Data.CodonTable.NCBICodonTable method) (Bio.Entrez.Parser.DictionaryElement method) (Bio.Entrez.Parser.ErrorElement method) (Bio.Entrez.Parser.IntegerElement method) (Bio.Entrez.Parser.ListElement method) (Bio.Entrez.Parser.NoneElement method) (Bio.Entrez.Parser.OrderedListElement method) (Bio.Entrez.Parser.StringElement method) (Bio.ExPASy.cellosaurus.Record method) (Bio.ExPASy.Enzyme.Record method) (Bio.GenBank.Record.Feature method) (Bio.GenBank.Record.Qualifier method) (Bio.GenBank.utils.FeatureValueCleaner method) (Bio.pairwise2.Alignment method) (Bio.Pathway.Interaction method) (Bio.Pathway.Network method) (Bio.Pathway.Reaction method) (Bio.Pathway.Rep.Graph.Graph method) (Bio.Pathway.Rep.MultiGraph.MultiGraph method) (Bio.Pathway.System method) (Bio.PDB.Atom.Atom method) (Bio.PDB.Atom.DisorderedAtom method) (Bio.PDB.Chain.Chain method) (Bio.PDB.FragmentMapper.Fragment method) (Bio.PDB.internal_coords.AtomKey method) (Bio.PDB.internal_coords.Dihedron method) (Bio.PDB.internal_coords.Edron method) (Bio.PDB.internal_coords.Hedron method) (Bio.PDB.internal_coords.IC_Residue method) (Bio.PDB.Model.Model method) (Bio.PDB.PDBIO.Select method) (Bio.PDB.Polypeptide.Polypeptide method) (Bio.PDB.Residue.DisorderedResidue method) (Bio.PDB.Residue.Residue method) (Bio.PDB.Structure.Structure method) (Bio.PDB.vectors.Vector method) (Bio.phenotype.phen_micro.PlateRecord method) (Bio.phenotype.phen_micro.WellRecord method) (Bio.Phylo.BaseTree.BranchColor method) (Bio.Phylo.BaseTree.TreeElement method) (Bio.SeqFeature.AfterPosition method) (Bio.SeqFeature.BeforePosition method) (Bio.SeqFeature.BetweenPosition method) (Bio.SeqFeature.CompoundLocation method) (Bio.SeqFeature.ExactPosition method) (Bio.SeqFeature.Location method) (Bio.SeqFeature.OneOfPosition method) (Bio.SeqFeature.Position method) (Bio.SeqFeature.Reference method) (Bio.SeqFeature.SeqFeature method) (Bio.SeqFeature.SimpleLocation method) (Bio.SeqFeature.UnknownPosition method) (Bio.SeqFeature.WithinPosition method) (Bio.SeqIO.QualityIO.InvalidCharError method) (Bio.SeqRecord.SeqRecord method) (Bio.UniGene.ProtsimLine method) (Bio.UniGene.Record method) (Bio.UniGene.SequenceLine method) (Bio.UniGene.STSLine method) (BioSQL.BioSeqDatabase.BioSeqDatabase method) (BioSQL.BioSeqDatabase.DBServer method) __setattr__() (Bio.Align.PairwiseAligner method) __setitem__() (Bio.Align.substitution_matrices.Array method) (Bio.PDB.Entity.DisorderedEntityWrapper method) (Bio.PDB.vectors.Vector method) (Bio.phenotype.phen_micro.PlateRecord method) (Bio.phenotype.phen_micro.WellRecord method) (Bio.Phylo.PhyloXML.Events method) (Bio.Phylo.TreeConstruction.DistanceMatrix method) (Bio.Seq.MutableSeq method) __setstate__() (Bio.Align.PairwiseAligner method) (Bio.Align.substitution_matrices.Array method) __slots__ (Bio.Align.AlignmentCounts attribute) (Bio.Align.bigbed.Field attribute) (Bio.pairwise2.Alignment attribute) (Bio.Seq.SequenceDataAbstractBaseClass attribute) __str__() (Bio.Align.Alignment method) (Bio.Align.bigbed.AutoSQLTable method) (Bio.Align.MultipleSeqAlignment method) (Bio.Align.substitution_matrices.Array method) (Bio.Blast.CorruptedXMLError method) (Bio.Blast.Hit method) (Bio.Blast.HSP method) (Bio.Blast.NCBIXML.Alignment method) (Bio.Blast.NCBIXML.Description method) (Bio.Blast.NCBIXML.DescriptionExtItem method) (Bio.Blast.NCBIXML.HSP method) (Bio.Blast.NotXMLError method) (Bio.Blast.Record method) (Bio.Blast.Records method) (Bio.codonalign.codonalignment.CodonAlignment method) (Bio.Data.CodonTable.CodonTable method) (Bio.Emboss.PrimerSearch.InputRecord method) (Bio.Entrez.Parser.CorruptedXMLError method) (Bio.Entrez.Parser.NotXMLError method) (Bio.Entrez.Parser.ValidationError method) (Bio.ExPASy.cellosaurus.Record method) (Bio.ExPASy.Enzyme.Record method) (Bio.GenBank.Record.Feature method) (Bio.GenBank.Record.Qualifier method) (Bio.GenBank.Record.Record method) (Bio.GenBank.Record.Reference method) (Bio.Geo.Record.Record method) (Bio.Graphics.GenomeDiagram.Diagram method) (Bio.Graphics.GenomeDiagram.FeatureSet method) (Bio.Graphics.GenomeDiagram.GraphData method) (Bio.Graphics.GenomeDiagram.GraphSet method) (Bio.Graphics.GenomeDiagram.Track method) (Bio.KEGG.Compound.Record method) (Bio.KEGG.Enzyme.Record method) (Bio.KEGG.Gene.Record method) (Bio.KEGG.KGML.KGML_pathway.Entry method) (Bio.KEGG.KGML.KGML_pathway.Pathway method) (Bio.KEGG.KGML.KGML_pathway.Reaction method) (Bio.KEGG.KGML.KGML_pathway.Relation method) (Bio.motifs.clusterbuster.Record method) (Bio.motifs.jaspar.db.JASPAR5 method) (Bio.motifs.jaspar.Motif method) (Bio.motifs.jaspar.Record method) (Bio.motifs.matrix.GenericPositionMatrix method) (Bio.motifs.Motif method) (Bio.motifs.pfm.Record method) (Bio.motifs.transfac.Record method) (Bio.motifs.xms.Record method) (Bio.Nexus.StandardData.StandardData method) (Bio.Nexus.Trees.Tree method) (Bio.Pathway.Interaction method) (Bio.Pathway.Network method) (Bio.Pathway.Reaction method) (Bio.Pathway.Rep.Graph.Graph method) (Bio.Pathway.Rep.MultiGraph.MultiGraph method) (Bio.Pathway.System method) (Bio.phenotype.phen_micro.PlateRecord method) (Bio.phenotype.phen_micro.WellRecord method) (Bio.Phylo.BaseTree.BranchColor method) (Bio.Phylo.BaseTree.Clade method) (Bio.Phylo.BaseTree.Tree method) (Bio.Phylo.BaseTree.TreeElement method) (Bio.Phylo.PhyloXML.Accession method) (Bio.Phylo.PhyloXML.Date method) (Bio.Phylo.PhyloXML.Id method) (Bio.Phylo.PhyloXML.MolSeq method) (Bio.Phylo.PhyloXML.Phyloxml method) (Bio.Phylo.PhyloXML.Polygon method) (Bio.Phylo.PhyloXML.Taxonomy method) (Bio.Phylo.PhyloXML.Uri method) (Bio.PopGen.GenePop.FileParser.FileRecord method) (Bio.PopGen.GenePop.Record method) (Bio.SCOP.Cla.Record method) (Bio.SCOP.Des.Record method) (Bio.SCOP.Dom.Record method) (Bio.SCOP.Domain method) (Bio.SCOP.Hie.Record method) (Bio.SCOP.Node method) (Bio.SCOP.Residues.Residues method) (Bio.SeqFeature.AfterPosition method) (Bio.SeqFeature.BeforePosition method) (Bio.SeqFeature.BetweenPosition method) (Bio.SeqFeature.CompoundLocation method) (Bio.SeqFeature.ExactPosition method) (Bio.SeqFeature.OneOfPosition method) (Bio.SeqFeature.Reference method) (Bio.SeqFeature.SeqFeature method) (Bio.SeqFeature.SimpleLocation method) (Bio.SeqFeature.WithinPosition method) (Bio.SeqIO.QualityIO.InvalidCharError method) (Bio.SeqRecord.SeqRecord method) (Bio.SeqUtils.CodonAdaptationIndex method) __sub__() (Bio.PDB.Atom.Atom method) (Bio.PDB.Entity.DisorderedEntityWrapper method) (Bio.PDB.FragmentMapper.Fragment method) (Bio.PDB.vectors.Vector method) (Bio.phenotype.phen_micro.PlateRecord method) (Bio.phenotype.phen_micro.WellRecord method) (Bio.SeqFeature.SimpleLocation method) __truediv__() (Bio.PDB.vectors.Vector method)

A

a (Bio.Graphics.ColorSpiral.ColorSpiral property) AAsiz (Bio.PDB.internal_coords.IC_Chain attribute) AbiIterator (class in Bio.SeqIO.AbiIO) AbstractAtomPropertyMap (class in Bio.PDB.AbstractPropertyMap) AbstractDPAlgorithms (class in Bio.HMM.DynamicProgramming) AbstractPropertyMap (class in Bio.PDB.AbstractPropertyMap) AbstractResiduePropertyMap (class in Bio.PDB.AbstractPropertyMap) AbstractTrainer (class in Bio.HMM.Trainer) accept_atom() (Bio.PDB.Dice.ChainSelector method) (Bio.PDB.PDBIO.Select method) accept_atoms (Bio.PDB.internal_coords.IC_Residue attribute) accept_backbone (Bio.PDB.internal_coords.IC_Residue attribute) accept_chain() (Bio.PDB.Dice.ChainSelector method) (Bio.PDB.PDBIO.Select method) accept_deuteriums (Bio.PDB.internal_coords.IC_Residue attribute) accept_hydrogens (Bio.PDB.internal_coords.IC_Residue attribute) accept_mainchain (Bio.PDB.internal_coords.IC_Residue attribute) accept_model() (Bio.PDB.Dice.ChainSelector method) (Bio.PDB.PDBIO.Select method) accept_residue() (Bio.PDB.Dice.ChainSelector method) (Bio.PDB.PDBIO.Select method) accept_resnames (Bio.PDB.internal_coords.IC_Residue attribute) accept_sidechain (Bio.PDB.internal_coords.IC_Residue attribute) Accession (class in Bio.Phylo.PhyloXML) accession() (Bio.Phylo.PhyloXMLIO.Parser method) (Bio.Phylo.PhyloXMLIO.Writer method) ACEFileRecord (class in Bio.Sequencing.Ace) AceIterator (class in Bio.SeqIO.AceIO) adam_consensus() (in module Bio.Phylo.Consensus) Adaptor (class in BioSQL.BioSeqDatabase) add() (Bio.Nexus.Nexus.StepMatrix method) (Bio.Nexus.Nodes.Chain method) (Bio.PDB.Entity.Entity method) (Bio.PDB.Residue.DisorderedResidue method) (Bio.PDB.Residue.Residue method) add_annotation() (Bio.Phylo.NeXMLIO.Parser method) add_component() (Bio.KEGG.KGML.KGML_pathway.Entry method) add_count() (Bio.Graphics.DisplayRepresentation.ChromosomeCounts method) add_edge() (Bio.Pathway.Rep.Graph.Graph method) (Bio.Pathway.Rep.MultiGraph.MultiGraph method) add_entry() (Bio.KEGG.KGML.KGML_pathway.Pathway method) add_feature() (Bio.Graphics.GenomeDiagram.FeatureSet method) add_graphics() (Bio.KEGG.KGML.KGML_pathway.Entry method) add_interaction() (Bio.Pathway.Network method) add_label() (Bio.Graphics.DisplayRepresentation.ChromosomeCounts method) add_node() (Bio.Pathway.Rep.Graph.Graph method) (Bio.Pathway.Rep.MultiGraph.MultiGraph method) add_point() (Bio.Graphics.GenomeDiagram.GraphData method) add_primer_set() (Bio.Emboss.PrimerSearch.InputRecord method) add_product() (Bio.KEGG.KGML.KGML_pathway.Reaction method) add_reaction() (Bio.KEGG.KGML.KGML_pathway.Pathway method) (Bio.Pathway.System method) add_relation() (Bio.KEGG.KGML.KGML_pathway.Pathway method) add_residue() (Bio.PDB.FragmentMapper.Fragment method) add_sequence() (Bio.Nexus.Nexus.Nexus method) add_set() (Bio.Graphics.GenomeDiagram.Track method) add_species() (Bio.Pathway.Network method) add_stmt_to_handle() (Bio.Phylo.CDAOIO.Writer method) add_substrate() (Bio.KEGG.KGML.KGML_pathway.Reaction method) add_succ() (Bio.Nexus.Nodes.Node method) add_track() (Bio.Graphics.GenomeDiagram.Diagram method) af (class in Bio.Sequencing.Ace) affine_penalty (class in Bio.pairwise2) AfterPosition (class in Bio.SeqFeature) align() (Bio.Align.CodonAligner method) (Bio.Align.PairwiseAligner method) (Bio.PDB.cealign.CEAligner method) aligned (Bio.Align.Alignment property) (Bio.Align.AlignmentCounts property) alignment (Bio.Align.MultipleSeqAlignment property) (Bio.Phylo.PhyloXML.Phylogeny property) Alignment (class in Bio.Align) (class in Bio.Blast.NCBIXML) (class in Bio.pairwise2) AlignmentCounts (class in Bio.Align) AlignmentHasDifferentLengthsError AlignmentIterator (class in Bio.Align.a2m) (class in Bio.Align.bed) (class in Bio.Align.bigbed) (class in Bio.Align.bigmaf) (class in Bio.Align.bigpsl) (class in Bio.Align.chain) (class in Bio.Align.clustal) (class in Bio.Align.emboss) (class in Bio.Align.exonerate) (class in Bio.Align.fasta) (class in Bio.Align.hhr) (class in Bio.Align.interfaces) (class in Bio.Align.maf) (class in Bio.Align.mauve) (class in Bio.Align.msf) (class in Bio.Align.nexus) (class in Bio.Align.phylip) (class in Bio.Align.psl) (class in Bio.Align.sam) (class in Bio.Align.stockholm) (class in Bio.Align.tabular) (class in Bio.AlignIO.Interfaces)

Alignments (class in Bio.Align) AlignmentsAbstractBaseClass (class in Bio.Align) AlignmentSequenceIterator (class in Bio.SeqIO) AlignmentSequenceWriter (class in Bio.SeqIO) AlignmentWriter (class in Bio.Align.a2m) (class in Bio.Align.bed) (class in Bio.Align.bigbed) (class in Bio.Align.bigmaf) (class in Bio.Align.bigpsl) (class in Bio.Align.chain) (class in Bio.Align.clustal) (class in Bio.Align.exonerate) (class in Bio.Align.fasta) (class in Bio.Align.interfaces) (class in Bio.Align.maf) (class in Bio.Align.mauve) (class in Bio.Align.nexus) (class in Bio.Align.phylip) (class in Bio.Align.psl) (class in Bio.Align.sam) (class in Bio.Align.stockholm) (class in Bio.AlignIO.Interfaces) all_ids() (Bio.Nexus.Nodes.Chain method) allow_all_transitions() (Bio.HMM.MarkovModel.MarkovModelBuilder method) allow_transition() (Bio.HMM.MarkovModel.MarkovModelBuilder method) alphabet (Bio.Align.substitution_matrices.Array property) alt() (Bio.Phylo.PhyloXMLIO.Writer method) altloc_match() (Bio.PDB.internal_coords.AtomKey method) AmbiguousCodonTable (class in Bio.Data.CodonTable) AmbiguousForwardTable (class in Bio.Data.CodonTable) amino_acids_percent (Bio.SeqUtils.ProtParam.ProteinAnalysis property) Amplifier (class in Bio.Emboss.PrimerSearch) angle (Bio.PDB.internal_coords.Dihedron property) (Bio.PDB.internal_coords.Hedron property) angle() (Bio.PDB.vectors.Vector method) angle_avg() (Bio.PDB.internal_coords.Dihedron static method) angle_dif() (Bio.PDB.internal_coords.Dihedron static method) angle_pop_sd() (Bio.PDB.internal_coords.Dihedron static method) annotate() (in module Bio.PDB.PSEA) AnnotatedChromosomeSegment (class in Bio.Graphics.BasicChromosome) Annotation (class in Bio.Phylo.PhyloXML) annotation() (Bio.Phylo.PhyloXMLIO.Parser method) (Bio.Phylo.PhyloXMLIO.Writer method) annotations (Bio.SeqRecord.SeqRecord attribute) (BioSQL.BioSeq.DBSeqRecord property) anticonsensus (Bio.motifs.matrix.GenericPositionMatrix property) (Bio.motifs.Motif property) append() (Bio.Align.MultipleSeqAlignment method) (Bio.SCOP.Raf.SeqMap method) (Bio.Seq.MutableSeq method) append_item() (Bio.Blast.NCBIXML.DescriptionExt method) append_sets() (Bio.Nexus.Nexus.Nexus method) apply() (Bio.PDB.qcprot.QCPSuperimposer method) (Bio.PDB.Superimposer.Superimposer method) applyMtx() (Bio.PDB.internal_coords.IC_Residue method) aromaticity() (Bio.SeqUtils.ProtParam.ProteinAnalysis method) Array (class in Bio.Align.substitution_matrices) artemis_color() (Bio.Graphics.GenomeDiagram.ColorTranslator method) as_fasta() (in module Bio.SeqIO.FastaIO) as_fasta_2line() (in module Bio.SeqIO.FastaIO) as_fastq() (in module Bio.SeqIO.QualityIO) as_fastq_illumina() (in module Bio.SeqIO.QualityIO) as_fastq_solexa() (in module Bio.SeqIO.QualityIO) as_handle() (in module Bio.File) as_phyloxml() (Bio.Phylo.BaseTree.Tree method) (Bio.Phylo.PhyloXML.Phylogeny method) as_qual() (in module Bio.SeqIO.QualityIO) as_tab() (in module Bio.SeqIO.TabIO) as_type (Bio.Align.bigbed.Field attribute) assemble() (Bio.PDB.internal_coords.IC_Residue method) assemble_residues() (Bio.PDB.internal_coords.IC_Chain method) assemble_residues_ser() (Bio.PDB.internal_coords.IC_Chain method) Astral (class in Bio.SCOP) atm() (Bio.PDB.internal_coords.AtomKey method) Atom (class in Bio.PDB.Atom) atom_chain (Bio.PDB.internal_coords.IC_Residue attribute) atom_re (Bio.PDB.internal_coords.AtomKey attribute) atom_sernum (Bio.PDB.internal_coords.IC_Residue attribute) atom_to_internal_coordinates() (Bio.PDB.Chain.Chain method) (Bio.PDB.internal_coords.IC_Chain method) (Bio.PDB.Model.Model method) (Bio.PDB.Structure.Structure method) atomArray (Bio.PDB.internal_coords.IC_Chain attribute) AtomIterator() (in module Bio.SeqIO.PdbIO) AtomKey (class in Bio.PDB.internal_coords) autocommit() (BioSQL.BioSeqDatabase.Adaptor method) (BioSQL.DBUtils.Generic_dbutils method) (BioSQL.DBUtils.Pgdb_dbutils method) (BioSQL.DBUtils.Psycopg2_dbutils method) AutoSQLTable (class in Bio.Align.bigbed)

B

b (Bio.Graphics.ColorSpiral.ColorSpiral property) back_table (Bio.Data.CodonTable.CodonTable attribute) back_transcribe() (in module Bio.Seq) background (Bio.motifs.Motif property) backward_algorithm() (Bio.HMM.DynamicProgramming.AbstractDPAlgorithms method) BarChartDistribution (class in Bio.Graphics.Distribution) BASE_FEATURE_FORMAT (Bio.GenBank.Record.Record attribute) BASE_FORMAT (Bio.GenBank.Record.Record attribute) base_id (Bio.motifs.jaspar.Motif property) Baseml (class in Bio.Phylo.PAML.baseml) BasemlError BaumWelchTrainer (class in Bio.HMM.Trainer) bc() (Bio.Phylo.PhyloXMLIO.Writer method) BeforePosition (class in Bio.SeqFeature) BetweenPosition (class in Bio.SeqFeature) bf_search() (in module Bio.Pathway.Rep.MultiGraph) bgcolor (Bio.KEGG.KGML.KGML_pathway.Graphics property) BgzfBlocks() (in module Bio.bgzf) BgzfReader (class in Bio.bgzf) BgzfWriter (class in Bio.bgzf) binary_characters() (Bio.Phylo.PhyloXMLIO.Parser method) (Bio.Phylo.PhyloXMLIO.Writer method) BinaryCharacters (class in Bio.Phylo.PhyloXML) BinaryCIFParser (class in Bio.PDB.binary_cif) Bio module Bio.Affy module Bio.Affy.CelFile module Bio.Align module Bio.Align.a2m module Bio.Align.AlignInfo module Bio.Align.analysis module Bio.Align.bed module Bio.Align.bigbed module Bio.Align.bigmaf module Bio.Align.bigpsl module Bio.Align.chain module Bio.Align.clustal module Bio.Align.emboss module Bio.Align.exonerate module Bio.Align.fasta module Bio.Align.hhr module Bio.Align.interfaces module Bio.Align.maf module Bio.Align.mauve module Bio.Align.msf module Bio.Align.nexus module Bio.Align.phylip module Bio.Align.psl module Bio.Align.sam module Bio.Align.stockholm module Bio.Align.substitution_matrices module Bio.Align.tabular module Bio.AlignIO module Bio.AlignIO.ClustalIO module Bio.AlignIO.EmbossIO module Bio.AlignIO.FastaIO module Bio.AlignIO.Interfaces module Bio.AlignIO.MafIO module Bio.AlignIO.MauveIO module Bio.AlignIO.MsfIO module Bio.AlignIO.NexusIO module Bio.AlignIO.PhylipIO module Bio.AlignIO.StockholmIO module Bio.bgzf module Bio.Blast module Bio.Blast.NCBIWWW module Bio.Blast.NCBIXML module Bio.CAPS module Bio.Cluster module Bio.codonalign module Bio.codonalign.codonalignment module Bio.codonalign.codonseq module Bio.Compass module Bio.Data module Bio.Data.CodonTable module Bio.Data.IUPACData module Bio.Data.PDBData module Bio.Emboss module Bio.Emboss.Primer3 module Bio.Emboss.PrimerSearch module Bio.Entrez module Bio.Entrez.Parser module Bio.ExPASy module Bio.ExPASy.cellosaurus module Bio.ExPASy.Enzyme module Bio.ExPASy.Prodoc module Bio.ExPASy.Prosite module Bio.ExPASy.ScanProsite module Bio.File module Bio.GenBank module Bio.GenBank.Record module Bio.GenBank.Scanner module Bio.GenBank.utils module Bio.Geo module Bio.Geo.Record module Bio.Graphics module Bio.Graphics.BasicChromosome module Bio.Graphics.ColorSpiral module Bio.Graphics.Comparative module Bio.Graphics.DisplayRepresentation module Bio.Graphics.Distribution module Bio.Graphics.GenomeDiagram module Bio.Graphics.KGML_vis module Bio.HMM module Bio.HMM.DynamicProgramming module Bio.HMM.MarkovModel module Bio.HMM.Trainer module Bio.HMM.Utilities module Bio.KEGG module Bio.KEGG.Compound module Bio.KEGG.Enzyme module Bio.KEGG.Gene module Bio.KEGG.KGML module Bio.KEGG.KGML.KGML_parser module Bio.KEGG.KGML.KGML_pathway module Bio.KEGG.Map module Bio.KEGG.REST module Bio.Medline module Bio.motifs module Bio.motifs.alignace module Bio.motifs.clusterbuster module Bio.motifs.jaspar module Bio.motifs.jaspar.db module Bio.motifs.mast module Bio.motifs.matrix module Bio.motifs.meme module Bio.motifs.minimal module Bio.motifs.pfm module Bio.motifs.thresholds module Bio.motifs.transfac module Bio.motifs.xms module Bio.Nexus module Bio.Nexus.Nexus module Bio.Nexus.Nodes module Bio.Nexus.StandardData module Bio.Nexus.Trees module Bio.NMR module Bio.NMR.NOEtools module Bio.NMR.xpktools module Bio.pairwise2 module Bio.Pathway module Bio.Pathway.Rep module Bio.Pathway.Rep.Graph module Bio.Pathway.Rep.MultiGraph module Bio.PDB module Bio.PDB.AbstractPropertyMap module Bio.PDB.alphafold_db module Bio.PDB.Atom module Bio.PDB.binary_cif module Bio.PDB.cealign module Bio.PDB.Chain module Bio.PDB.Dice module Bio.PDB.DSSP module Bio.PDB.Entity module Bio.PDB.FragmentMapper module Bio.PDB.HSExposure module Bio.PDB.ic_data module Bio.PDB.ic_rebuild module Bio.PDB.internal_coords module Bio.PDB.MMCIF2Dict module Bio.PDB.mmcifio module

Bio.PDB.MMCIFParser module Bio.PDB.mmtf module Bio.PDB.mmtf.DefaultParser module Bio.PDB.mmtf.mmtfio module Bio.PDB.Model module Bio.PDB.NACCESS module Bio.PDB.NeighborSearch module Bio.PDB.parse_pdb_header module Bio.PDB.PDBExceptions module Bio.PDB.PDBIO module Bio.PDB.PDBList module Bio.PDB.PDBMLParser module Bio.PDB.PDBParser module Bio.PDB.PICIO module Bio.PDB.Polypeptide module Bio.PDB.PSEA module Bio.PDB.qcprot module Bio.PDB.Residue module Bio.PDB.ResidueDepth module Bio.PDB.SASA module Bio.PDB.SCADIO module Bio.PDB.Selection module Bio.PDB.Structure module Bio.PDB.StructureAlignment module Bio.PDB.StructureBuilder module Bio.PDB.Superimposer module Bio.PDB.vectors module Bio.phenotype module Bio.phenotype.phen_micro module Bio.phenotype.pm_fitting module Bio.Phylo module Bio.Phylo.BaseTree module Bio.Phylo.CDAO module Bio.Phylo.CDAOIO module Bio.Phylo.Consensus module Bio.Phylo.Newick module Bio.Phylo.NewickIO module Bio.Phylo.NeXML module Bio.Phylo.NeXMLIO module Bio.Phylo.NexusIO module Bio.Phylo.PAML module Bio.Phylo.PAML.baseml module Bio.Phylo.PAML.chi2 module Bio.Phylo.PAML.codeml module Bio.Phylo.PAML.yn00 module Bio.Phylo.PhyloXML module Bio.Phylo.PhyloXMLIO module Bio.Phylo.TreeConstruction module Bio.PopGen module Bio.PopGen.GenePop module Bio.PopGen.GenePop.FileParser module Bio.PopGen.GenePop.LargeFileParser module Bio.Restriction module Bio.Restriction.PrintFormat module Bio.Restriction.Restriction_Dictionary module Bio.SCOP module Bio.SCOP.Cla module Bio.SCOP.Des module Bio.SCOP.Dom module Bio.SCOP.Hie module Bio.SCOP.Raf module Bio.SCOP.Residues module Bio.SearchIO module Bio.SearchIO.BlastIO module Bio.SearchIO.BlastIO.blast_tab module Bio.SearchIO.BlastIO.blast_xml module Bio.SearchIO.BlatIO module Bio.SearchIO.ExonerateIO module Bio.SearchIO.ExonerateIO.exonerate_cigar module Bio.SearchIO.ExonerateIO.exonerate_text module Bio.SearchIO.ExonerateIO.exonerate_vulgar module Bio.SearchIO.FastaIO module Bio.SearchIO.HHsuiteIO module Bio.SearchIO.HHsuiteIO.hhsuite2_text module Bio.SearchIO.HmmerIO module Bio.SearchIO.HmmerIO.hmmer2_text module Bio.SearchIO.HmmerIO.hmmer3_domtab module Bio.SearchIO.HmmerIO.hmmer3_tab module Bio.SearchIO.HmmerIO.hmmer3_text module Bio.SearchIO.InterproscanIO module Bio.SearchIO.InterproscanIO.interproscan_xml module Bio.Seq module Bio.SeqFeature module Bio.SeqIO module Bio.SeqIO.AbiIO module Bio.SeqIO.AceIO module Bio.SeqIO.FastaIO module Bio.SeqIO.GckIO module Bio.SeqIO.GfaIO module Bio.SeqIO.IgIO module Bio.SeqIO.InsdcIO module Bio.SeqIO.Interfaces module Bio.SeqIO.NibIO module Bio.SeqIO.PdbIO module Bio.SeqIO.PhdIO module Bio.SeqIO.PirIO module Bio.SeqIO.QualityIO module Bio.SeqIO.SeqXmlIO module Bio.SeqIO.SffIO module Bio.SeqIO.SnapGeneIO module Bio.SeqIO.SwissIO module Bio.SeqIO.TabIO module Bio.SeqIO.TwoBitIO module Bio.SeqIO.UniprotIO module Bio.SeqIO.XdnaIO module Bio.SeqRecord module Bio.Sequencing module Bio.Sequencing.Ace module Bio.Sequencing.Phd module Bio.SeqUtils module Bio.SeqUtils.CheckSum module Bio.SeqUtils.IsoelectricPoint module Bio.SeqUtils.lcc module Bio.SeqUtils.MeltingTemp module Bio.SeqUtils.ProtParam module Bio.SeqUtils.ProtParamData module Bio.SVDSuperimposer module Bio.SwissProt module Bio.SwissProt.KeyWList module Bio.TogoWS module Bio.UniGene module Bio.UniProt module Bio.UniProt.GOA module BiopythonDeprecationWarning BiopythonExperimentalWarning BiopythonParserWarning BiopythonWarning BioSeqDatabase (class in BioSQL.BioSeqDatabase) BioSQL module BioSQL.BioSeq module BioSQL.BioSeqDatabase module BioSQL.DBUtils module BioSQL.Loader module bits() (Bio.PDB.internal_coords.Dihedron method) Blast (class in Bio.Blast.NCBIXML) BlastParser (class in Bio.Blast.NCBIXML) BlastTabIndexer (class in Bio.SearchIO.BlastIO.blast_tab) BlastTabParser (class in Bio.SearchIO.BlastIO.blast_tab) BlastTabWriter (class in Bio.SearchIO.BlastIO.blast_tab) BlastXmlIndexer (class in Bio.SearchIO.BlastIO.blast_xml) BlastXmlParser (class in Bio.SearchIO.BlastIO.blast_xml) BlastXmlWriter (class in Bio.SearchIO.BlastIO.blast_xml) BlatPslIndexer (class in Bio.SearchIO.BlatIO) BlatPslParser (class in Bio.SearchIO.BlatIO) BlatPslWriter (class in Bio.SearchIO.BlatIO) BLOCK (Bio.SeqIO.SeqXmlIO.SeqXmlIterator attribute) Block (class in Bio.Nexus.Nexus) block_size (Bio.SearchIO.BlastIO.blast_xml.BlastXmlIndexer attribute) BLOCKS_PER_LINE (Bio.SeqIO.InsdcIO.EmblWriter attribute) blue() (Bio.Phylo.PhyloXMLIO.Writer method) bond_rotate() (Bio.PDB.internal_coords.IC_Residue method) bond_set() (Bio.PDB.internal_coords.IC_Residue method) bootstrap() (Bio.Nexus.Nexus.Nexus method) (in module Bio.Phylo.Consensus) bootstrap_consensus() (in module Bio.Phylo.Consensus) bootstrap_trees() (in module Bio.Phylo.Consensus) bounds (Bio.KEGG.KGML.KGML_pathway.Entry property) (Bio.KEGG.KGML.KGML_pathway.Graphics property) (Bio.KEGG.KGML.KGML_pathway.Pathway property) branch_length() (Bio.Phylo.PhyloXMLIO.Writer method) BranchColor (class in Bio.Phylo.BaseTree) (class in Bio.Phylo.PhyloXML) branchlength2support() (Bio.Nexus.Trees.Tree method) bs (class in Bio.Sequencing.Ace) build() (in module Bio.codonalign) build_atomArray() (Bio.PDB.internal_coords.IC_Chain method) build_edraArrays() (Bio.PDB.internal_coords.IC_Chain method) build_tree() (Bio.Phylo.TreeConstruction.DistanceTreeConstructor method) (Bio.Phylo.TreeConstruction.ParsimonyTreeConstructor method) (Bio.Phylo.TreeConstruction.TreeConstructor method)

C

ca_depth() (in module Bio.PDB.ResidueDepth) cal_dn_ds() (in module Bio.codonalign.codonseq) calc_affine_penalty() (in module Bio.pairwise2) calc_angle() (in module Bio.PDB.vectors) calc_dihedral() (in module Bio.PDB.vectors) calculate() (Bio.motifs.matrix.PositionSpecificScoringMatrix method) (Bio.SeqUtils.CodonAdaptationIndex method) calculate_consensus() (Bio.motifs.matrix.GenericPositionMatrix method) calculate_dn_ds() (in module Bio.Align.analysis) calculate_dn_ds_matrix() (in module Bio.Align.analysis) calculate_pseudocounts() (in module Bio.motifs.jaspar) CaPPBuilder (class in Bio.PDB.Polypeptide) CAPSMap (class in Bio.CAPS) cdao_to_obo() (in module Bio.Phylo.NeXMLIO) cdf_chi2() (in module Bio.Phylo.PAML.chi2) CEAligner (class in Bio.PDB.cealign) center_of_mass() (Bio.PDB.Atom.DisorderedAtom method) (Bio.PDB.Entity.Entity method) centre (Bio.KEGG.KGML.KGML_pathway.Graphics property) Chain (class in Bio.Nexus.Nodes) (class in Bio.PDB.Chain) ChainException ChainSelector (class in Bio.PDB.Dice) characterDataHandlerEscape() (Bio.Entrez.Parser.DataHandler method) characterDataHandlerRaw() (Bio.Entrez.Parser.DataHandler method) characters() (Bio.ExPASy.ScanProsite.ContentHandler method) (Bio.SeqIO.SeqXmlIO.ContentHandler method) CharBuffer (class in Bio.Nexus.Nexus) charge_at_pH() (Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint method) (Bio.SeqUtils.ProtParam.ProteinAnalysis method) chem_correction() (in module Bio.SeqUtils.MeltingTemp) child_dict (Bio.PDB.Entity.Entity attribute) child_edges() (Bio.Pathway.Rep.Graph.Graph method) (Bio.Pathway.Rep.MultiGraph.MultiGraph method) child_list (Bio.PDB.Entity.Entity attribute) children() (Bio.Pathway.Rep.Graph.Graph method) (Bio.Pathway.Rep.MultiGraph.MultiGraph method) Chromosome (class in Bio.Graphics.BasicChromosome) ChromosomeCounts (class in Bio.Graphics.DisplayRepresentation) ChromosomeSegment (class in Bio.Graphics.BasicChromosome) CifAtomIterator (class in Bio.SeqIO.PdbIO) CifSeqresIterator (class in Bio.SeqIO.PdbIO) clade (Bio.Phylo.BaseTree.Tree property) Clade (class in Bio.Phylo.BaseTree) (class in Bio.Phylo.CDAO) (class in Bio.Phylo.Newick) (class in Bio.Phylo.NeXML) (class in Bio.Phylo.PhyloXML) clade() (Bio.Phylo.PhyloXMLIO.Writer method) clade_relation() (Bio.Phylo.PhyloXMLIO.Parser method) (Bio.Phylo.PhyloXMLIO.Writer method) CladeRelation (class in Bio.Phylo.PhyloXML) clean() (Bio.AlignIO.Interfaces.AlignmentWriter method) (Bio.SeqIO.Interfaces.SequenceWriter method) clean_value() (Bio.GenBank.utils.FeatureValueCleaner method) clear_ic() (Bio.PDB.internal_coords.IC_Chain method) clear_transforms() (Bio.PDB.internal_coords.IC_Residue method) close() (Bio.AlignIO.MafIO.MafIndex method) (Bio.bgzf.BgzfReader method) (Bio.bgzf.BgzfWriter method) (BioSQL.BioSeqDatabase.Adaptor method) (BioSQL.BioSeqDatabase.DBServer method) ClustalIterator (class in Bio.AlignIO.ClustalIO) ClustalWriter (class in Bio.AlignIO.ClustalIO) clustercentroids() (Bio.Cluster.Record method) (in module Bio.Cluster) clusterdistance() (Bio.Cluster.Record method) (in module Bio.Cluster) Cmodulo (Bio.Restriction.PrintFormat.PrintFormat attribute) cmp_sccs() (in module Bio.SCOP) code() (Bio.Phylo.PhyloXMLIO.Writer method) Codeml (class in Bio.Phylo.PAML.codeml) CodemlError CodonAdaptationIndex (class in Bio.SeqUtils)

CodonAligner (class in Bio.Align) CodonAlignment (class in Bio.codonalign.codonalignment) CodonSeq (class in Bio.codonalign.codonseq) CodonTable (class in Bio.Data.CodonTable) collapse() (Bio.Nexus.Nodes.Chain method) (Bio.Phylo.BaseTree.TreeMixin method) collapse_all() (Bio.Phylo.BaseTree.TreeMixin method) collapse_genera() (Bio.Nexus.Trees.Tree method) color (Bio.Phylo.BaseTree.Clade property) color() (Bio.Phylo.PhyloXMLIO.Parser method) (Bio.Phylo.PhyloXMLIO.Writer method) color_names (Bio.Phylo.BaseTree.BranchColor attribute) color_to_reportlab() (in module Bio.Graphics.KGML_vis) ColorSpiral (class in Bio.Graphics.ColorSpiral) ColorTranslator (class in Bio.Graphics.GenomeDiagram) column_annotations (Bio.Align.MultipleSeqAlignment property) combine() (in module Bio.Nexus.Nexus) Commandline (class in Bio.Nexus.Nexus) comment (Bio.Align.bigbed.Field attribute) commit() (BioSQL.BioSeqDatabase.Adaptor method) (BioSQL.BioSeqDatabase.DBServer method) common_ancestor() (Bio.Nexus.Trees.Tree method) (Bio.Phylo.BaseTree.TreeMixin method) common_name() (Bio.Phylo.PhyloXMLIO.Writer method) ComparativeScatterPlot (class in Bio.Graphics.Comparative) compare_residues() (in module Bio.PDB.ic_rebuild) complement() (in module Bio.Seq) complement_rna() (in module Bio.Seq) Component (class in Bio.KEGG.KGML.KGML_pathway) CompoundLocation (class in Bio.SeqFeature) compounds (Bio.KEGG.KGML.KGML_pathway.Pathway property) compute() (Bio.PDB.SASA.ShrakeRupley method) confidence (Bio.Phylo.PhyloXML.Clade property) (Bio.Phylo.PhyloXML.Phylogeny property) Confidence (class in Bio.Phylo.PhyloXML) confidence() (Bio.Phylo.PhyloXMLIO.Parser method) (Bio.Phylo.PhyloXMLIO.Writer method) consensus (Bio.motifs.matrix.GenericPositionMatrix property) (Bio.motifs.Motif property) consensus() (in module Bio.Nexus.Trees) ConsoleWidth (Bio.Restriction.PrintFormat.PrintFormat attribute) constant() (Bio.Nexus.Nexus.Nexus method) ContentHandler (class in Bio.ExPASy.ScanProsite) (class in Bio.SeqIO.SeqXmlIO) Contig (class in Bio.Sequencing.Ace) convert() (in module Bio.AlignIO) (in module Bio.SearchIO) (in module Bio.SeqIO) (in module Bio.TogoWS) convert_absolute_support() (Bio.Nexus.Trees.Tree method) coord_space() (in module Bio.PDB.vectors) coords (Bio.KEGG.KGML.KGML_pathway.Graphics property) copy() (Bio.PDB.Atom.Atom method) (Bio.PDB.Entity.DisorderedEntityWrapper method) (Bio.PDB.Entity.Entity method) (Bio.PDB.vectors.Vector method) copy_initNCaCs() (Bio.PDB.internal_coords.IC_Chain method) CorruptedXMLError, [1] count() (Bio.Seq.SequenceDataAbstractBaseClass method) (Bio.SeqRecord.SeqRecord method) count_amino_acids() (Bio.SeqUtils.ProtParam.ProteinAnalysis method) count_terminals() (Bio.Nexus.Trees.Tree method) (Bio.Phylo.BaseTree.TreeMixin method) counts() (Bio.Align.Alignment method) cr_class() (Bio.PDB.internal_coords.AtomKey method) crc32() (in module Bio.SeqUtils.CheckSum) crc64() (in module Bio.SeqUtils.CheckSum) create() (in module Bio.motifs) crop_matrix() (Bio.Nexus.Nexus.Nexus method) CrossLink (class in Bio.Graphics.GenomeDiagram) cstatus() (Bio.Nexus.Nexus.Nexus method) CsvIterator() (in module Bio.phenotype.phen_micro) ct (class in Bio.Sequencing.Ace) cut() (Bio.Cluster.Tree method)

D

d2h (Bio.PDB.internal_coords.AtomKey attribute) darken() (in module Bio.Graphics.KGML_vis) data (Bio.Blast.Records property) data_generator() (Bio.PopGen.GenePop.LargeFileParser.Record method) data_quartiles() (Bio.Graphics.GenomeDiagram.GraphSet method) data_table() (in module Bio.NMR.xpktools) DatabaseLoader (class in BioSQL.Loader) DatabaseRemover (class in BioSQL.Loader) DatabaseReport (class in Bio.Blast.NCBIXML) DataHandler (class in Bio.Entrez.Parser) DataHandlerMeta (class in Bio.Entrez.Parser) Date (class in Bio.Phylo.PhyloXML) date() (Bio.Phylo.PhyloXMLIO.Parser method) (Bio.Phylo.PhyloXMLIO.Writer method) DBSeqRecord (class in BioSQL.BioSeq) DBServer (class in BioSQL.BioSeqDatabase) dbxrefs (Bio.SeqRecord.SeqRecord attribute) (BioSQL.BioSeq.DBSeqRecord property) dCoordSpace (Bio.PDB.internal_coords.IC_Chain attribute) dcsValid (Bio.PDB.internal_coords.IC_Chain attribute) decode() (Bio.Seq.SequenceDataAbstractBaseClass method) default (Bio.Align.bigbed.AutoSQLTable attribute) DEFAULT_PSEUDO (Bio.HMM.MarkovModel.MarkovModelBuilder attribute) defined (Bio.Seq.SequenceDataAbstractBaseClass property) defined_ranges (Bio.Seq.SequenceDataAbstractBaseClass property) degenerate_consensus (Bio.motifs.matrix.GenericPositionMatrix property) (Bio.motifs.Motif property) del_feature() (Bio.Graphics.GenomeDiagram.FeatureSet method) del_graph() (Bio.Graphics.GenomeDiagram.GraphSet method) del_set() (Bio.Graphics.GenomeDiagram.Track method) del_track() (Bio.Graphics.GenomeDiagram.Diagram method) deletions (Bio.Align.AlignmentCounts property) depths() (Bio.Phylo.BaseTree.TreeMixin method) desc() (Bio.Phylo.PhyloXMLIO.Writer method) Description (class in Bio.Blast.NCBIXML) description() (Bio.Phylo.PhyloXMLIO.Writer method) DescriptionExt (class in Bio.Blast.NCBIXML) DescriptionExtItem (class in Bio.Blast.NCBIXML) destroy_transition() (Bio.HMM.MarkovModel.MarkovModelBuilder method) detach_child() (Bio.PDB.Entity.Entity method) detach_parent() (Bio.PDB.Atom.Atom method) (Bio.PDB.Entity.DisorderedEntityWrapper method) (Bio.PDB.Entity.Entity method) details (Bio.SeqIO.QualityIO.InvalidCharError attribute) df_search() (in module Bio.Pathway.Rep.MultiGraph) Diagram (class in Bio.Graphics.GenomeDiagram) dictionary_match (class in Bio.pairwise2) DictionaryElement (class in Bio.Entrez.Parser) difference() (Bio.PDB.internal_coords.Dihedron method) DifferentialCutsite (class in Bio.CAPS) dihedral_signs() (Bio.PDB.internal_coords.IC_Chain method) Dihedron (class in Bio.PDB.internal_coords) directory (Bio.Entrez.Parser.DataHandlerMeta property) disordered_add() (Bio.PDB.Atom.DisorderedAtom method) (Bio.PDB.Entity.DisorderedEntityWrapper method) (Bio.PDB.Residue.DisorderedResidue method) disordered_get() (Bio.PDB.Entity.DisorderedEntityWrapper method)

disordered_get_id_list() (Bio.PDB.Entity.DisorderedEntityWrapper method) disordered_get_list() (Bio.PDB.Atom.DisorderedAtom method) (Bio.PDB.Entity.DisorderedEntityWrapper method) disordered_has_id() (Bio.PDB.Entity.DisorderedEntityWrapper method) disordered_remove() (Bio.PDB.Atom.DisorderedAtom method) (Bio.PDB.Entity.DisorderedEntityWrapper method) (Bio.PDB.Residue.DisorderedResidue method) disordered_select() (Bio.PDB.Entity.DisorderedEntityWrapper method) DisorderedAtom (class in Bio.PDB.Atom) DisorderedEntityWrapper (class in Bio.PDB.Entity) DisorderedResidue (class in Bio.PDB.Residue) display() (Bio.Nexus.Trees.Tree method) dist_pearson() (Bio.motifs.matrix.PositionSpecificScoringMatrix method) dist_pearson_at() (Bio.motifs.matrix.PositionSpecificScoringMatrix method) distance() (Bio.Nexus.Trees.Tree method) (Bio.Phylo.BaseTree.TreeMixin method) distance_plot() (Bio.PDB.internal_coords.IC_Chain method) distance_to_internal_coordinates() (Bio.PDB.internal_coords.IC_Chain method) DistanceCalculator (class in Bio.Phylo.TreeConstruction) DistanceMatrix (class in Bio.Phylo.TreeConstruction) distancematrix() (Bio.Cluster.Record method) (in module Bio.Cluster) DistanceTreeConstructor (class in Bio.Phylo.TreeConstruction) distplot_to_dh_arrays() (Bio.PDB.internal_coords.IC_Chain method) Distribution (class in Bio.Phylo.PhyloXML) distribution() (Bio.motifs.matrix.PositionSpecificScoringMatrix method) (Bio.Phylo.PhyloXMLIO.Parser method) (Bio.Phylo.PhyloXMLIO.Writer method) DistributionPage (class in Bio.Graphics.Distribution) dna_models (Bio.Phylo.TreeConstruction.DistanceCalculator attribute) Domain (class in Bio.SCOP) domain() (Bio.Phylo.PhyloXMLIO.Parser method) (Bio.Phylo.PhyloXMLIO.Writer method) domain_architecture() (Bio.Phylo.PhyloXMLIO.Parser method) (Bio.Phylo.PhyloXMLIO.Writer method) DomainArchitecture (class in Bio.Phylo.PhyloXML) domainsClusteredByEv() (Bio.SCOP.Astral method) domainsClusteredById() (Bio.SCOP.Astral method) download_all_assemblies() (Bio.PDB.PDBList.PDBList method) download_cif_for() (in module Bio.PDB.alphafold_db) download_entire_pdb() (Bio.PDB.PDBList.PDBList method) download_obsolete_entries() (Bio.PDB.PDBList.PDBList method) download_pdb_files() (Bio.PDB.PDBList.PDBList method) draw() (Bio.Graphics.BasicChromosome.Chromosome method) (Bio.Graphics.BasicChromosome.ChromosomeSegment method) (Bio.Graphics.BasicChromosome.Organism method) (Bio.Graphics.BasicChromosome.SpacerSegment method) (Bio.Graphics.Distribution.BarChartDistribution method) (Bio.Graphics.Distribution.DistributionPage method) (Bio.Graphics.Distribution.LineDistribution method) (Bio.Graphics.GenomeDiagram.Diagram method) (Bio.Graphics.KGML_vis.KGMLCanvas method) draw_to_file() (Bio.Graphics.Comparative.ComparativeScatterPlot method) ds (class in Bio.Sequencing.Ace) DSSP (class in Bio.PDB.DSSP) dssp_dict_from_pdb_file() (in module Bio.PDB.DSSP) duplications() (Bio.Phylo.PhyloXMLIO.Writer method)

E

ecitmatch() (in module Bio.Entrez) edges() (Bio.Pathway.Rep.Graph.Graph method) (Bio.Pathway.Rep.MultiGraph.MultiGraph method) Edron (class in Bio.PDB.internal_coords) edron_re (Bio.PDB.internal_coords.Edron attribute) efetch() (in module Bio.Entrez) egquery() (in module Bio.Entrez) einfo() (in module Bio.Entrez) element (Bio.KEGG.KGML.KGML_pathway.Component property) (Bio.KEGG.KGML.KGML_pathway.Entry property) (Bio.KEGG.KGML.KGML_pathway.Graphics property) (Bio.KEGG.KGML.KGML_pathway.Pathway property) (Bio.KEGG.KGML.KGML_pathway.Reaction property) (Bio.KEGG.KGML.KGML_pathway.Relation property) elementDecl() (Bio.Entrez.Parser.DataHandler method) elink() (in module Bio.Entrez) EMBL_INDENT (Bio.GenBank.Scanner.EmblScanner attribute) EMBL_SPACER (Bio.GenBank.Scanner.EmblScanner attribute) EmblCdsFeatureIterator (class in Bio.SeqIO.InsdcIO) EmblIterator (class in Bio.SeqIO.InsdcIO) EmblScanner (class in Bio.GenBank.Scanner) EmblWriter (class in Bio.SeqIO.InsdcIO) EmbossIterator (class in Bio.AlignIO.EmbossIO) empty_status_characters (Bio.Align.maf.AlignmentIterator attribute) end (Bio.pairwise2.Alignment attribute) (Bio.SeqFeature.CompoundLocation property) (Bio.SeqFeature.SimpleLocation property) endA (Bio.Graphics.GenomeDiagram.CrossLink property) endB (Bio.Graphics.GenomeDiagram.CrossLink property) endDBRefElement() (Bio.SeqIO.SeqXmlIO.ContentHandler method) endDescriptionElement() (Bio.SeqIO.SeqXmlIO.ContentHandler method) endElement() (Bio.ExPASy.ScanProsite.ContentHandler method) endElementHandler() (Bio.Entrez.Parser.DataHandler method) endEntryElement() (Bio.SeqIO.SeqXmlIO.ContentHandler method) endErrorElementHandler() (Bio.Entrez.Parser.DataHandler method) endIntegerElementHandler() (Bio.Entrez.Parser.DataHandler method) endNamespaceDeclHandler() (Bio.Entrez.Parser.DataHandler method) endPropertyElement() (Bio.SeqIO.SeqXmlIO.ContentHandler method) endRawElementHandler() (Bio.Entrez.Parser.DataHandler method) endSequenceElement() (Bio.SeqIO.SeqXmlIO.ContentHandler method) endSeqXMLElement() (Bio.SeqIO.SeqXmlIO.ContentHandler method) endSkipElementHandler() (Bio.Entrez.Parser.DataHandler method) endSpeciesElement() (Bio.SeqIO.SeqXmlIO.ContentHandler method) endStringElementHandler() (Bio.Entrez.Parser.DataHandler method) endswith() (Bio.Seq.SequenceDataAbstractBaseClass method)

Entity (class in Bio.PDB.Entity) entry (Bio.KEGG.KGML.KGML_pathway.Reaction property) Entry (class in Bio.KEGG.KGML.KGML_pathway) entry() (in module Bio.TogoWS) entry1 (Bio.KEGG.KGML.KGML_pathway.Relation property) entry2 (Bio.KEGG.KGML.KGML_pathway.Relation property) enumerate_atoms() (in module Bio.PDB.PICIO) epost() (in module Bio.Entrez) ErrorElement (class in Bio.Entrez.Parser) esearch() (in module Bio.Entrez) espell() (in module Bio.Entrez) estimate_params() (Bio.HMM.Trainer.AbstractTrainer method) esummary() (in module Bio.Entrez) Events (class in Bio.Phylo.PhyloXML) events() (Bio.Phylo.PhyloXMLIO.Parser method) (Bio.Phylo.PhyloXMLIO.Writer method) ExactPosition (class in Bio.SeqFeature) execute() (BioSQL.BioSeqDatabase.Adaptor method) (BioSQL.DBUtils.Generic_dbutils method) (BioSQL.DBUtils.Sqlite_dbutils method) execute_and_fetch_col0() (BioSQL.BioSeqDatabase.Adaptor method) (BioSQL.BioSeqDatabase.MysqlConnectorAdaptor method) execute_and_fetchall() (BioSQL.BioSeqDatabase.Adaptor method) (BioSQL.BioSeqDatabase.MysqlConnectorAdaptor method) execute_one() (BioSQL.BioSeqDatabase.Adaptor method) (BioSQL.BioSeqDatabase.MysqlConnectorAdaptor method) executemany() (BioSQL.BioSeqDatabase.Adaptor method) (BioSQL.DBUtils.Generic_dbutils method) (BioSQL.DBUtils.Sqlite_dbutils method) ExonerateCigarIndexer (class in Bio.SearchIO.ExonerateIO.exonerate_cigar) ExonerateCigarParser (class in Bio.SearchIO.ExonerateIO.exonerate_cigar) ExonerateTextIndexer (class in Bio.SearchIO.ExonerateIO.exonerate_text) ExonerateTextParser (class in Bio.SearchIO.ExonerateIO.exonerate_text) ExonerateVulgarIndexer (class in Bio.SearchIO.ExonerateIO.exonerate_vulgar) ExonerateVulgarParser (class in Bio.SearchIO.ExonerateIO.exonerate_vulgar) export_fasta() (Bio.Nexus.Nexus.Nexus method) export_phylip() (Bio.Nexus.Nexus.Nexus method) ExposureCN (class in Bio.PDB.HSExposure) extend() (Bio.Align.MultipleSeqAlignment method) (Bio.SCOP.Raf.SeqMap method) (Bio.Seq.MutableSeq method) externalEntityRefHandler() (Bio.Entrez.Parser.DataHandler method) extract() (Bio.SeqFeature.CompoundLocation method) (Bio.SeqFeature.SeqFeature method) (Bio.SeqFeature.SimpleLocation method) (in module Bio.PDB.Dice)

F

FastaBlastIterator (class in Bio.SeqIO.FastaIO) FastaIterator (class in Bio.SeqIO.FastaIO) FastaM10Indexer (class in Bio.SearchIO.FastaIO) FastaM10Iterator() (in module Bio.AlignIO.FastaIO) FastaM10Parser (class in Bio.SearchIO.FastaIO) FastaPearsonIterator (class in Bio.SeqIO.FastaIO) FastaTwoLineIterator (class in Bio.SeqIO.FastaIO) FastaTwoLineParser() (in module Bio.SeqIO.FastaIO) FastaTwoLineWriter (class in Bio.SeqIO.FastaIO) FastaWriter (class in Bio.SeqIO.FastaIO) FastMMCIFParser (class in Bio.PDB.MMCIFParser) FastqGeneralIterator() (in module Bio.SeqIO.QualityIO) FastqIlluminaIterator (class in Bio.SeqIO.QualityIO) FastqIlluminaWriter (class in Bio.SeqIO.QualityIO) FastqIteratorAbstractBaseClass (class in Bio.SeqIO.QualityIO) FastqPhredIterator (class in Bio.SeqIO.QualityIO) FastqPhredWriter (class in Bio.SeqIO.QualityIO) FastqSolexaIterator (class in Bio.SeqIO.QualityIO) FastqSolexaWriter (class in Bio.SeqIO.QualityIO) Feature (class in Bio.GenBank.Record) (class in Bio.Graphics.GenomeDiagram) FEATURE_END_MARKERS (Bio.GenBank.Scanner.EmblScanner attribute) (Bio.GenBank.Scanner.GenBankScanner attribute) (Bio.GenBank.Scanner.InsdcScanner attribute) FEATURE_HEADER (Bio.SeqIO.InsdcIO.EmblWriter attribute) (Bio.SeqIO.InsdcIO.ImgtWriter attribute) FEATURE_QUALIFIER_INDENT (Bio.GenBank.Scanner.EmblScanner attribute) (Bio.GenBank.Scanner.GenBankScanner attribute) (Bio.GenBank.Scanner.InsdcScanner attribute) FEATURE_QUALIFIER_SPACER (Bio.GenBank.Scanner.EmblScanner attribute) (Bio.GenBank.Scanner.GenBankScanner attribute) (Bio.GenBank.Scanner.InsdcScanner attribute) FEATURE_START_MARKERS (Bio.GenBank.Scanner.EmblScanner attribute) (Bio.GenBank.Scanner.GenBankScanner attribute) (Bio.GenBank.Scanner.InsdcScanner attribute) FeatureLocation (in module Bio.SeqFeature) FeatureParser (class in Bio.GenBank) features (BioSQL.BioSeq.DBSeqRecord property) FeatureSet (class in Bio.Graphics.GenomeDiagram) FeatureTable (class in Bio.SwissProt) FeatureValueCleaner (class in Bio.GenBank.utils) feed() (Bio.ExPASy.ScanProsite.Parser method) (Bio.GenBank.Scanner.InsdcScanner method) fetch_dbid_by_dbname() (BioSQL.BioSeqDatabase.Adaptor method) fetch_motif_by_id() (Bio.motifs.jaspar.db.JASPAR5 method) fetch_motifs() (Bio.motifs.jaspar.db.JASPAR5 method) fetch_motifs_by_name() (Bio.motifs.jaspar.db.JASPAR5 method) fetch_seqid_by_accession() (BioSQL.BioSeqDatabase.Adaptor method) fetch_seqid_by_display_id() (BioSQL.BioSeqDatabase.Adaptor method) fetch_seqid_by_identifier() (BioSQL.BioSeqDatabase.Adaptor method) fetch_seqid_by_version() (BioSQL.BioSeqDatabase.Adaptor method) fetch_seqids_by_accession() (BioSQL.BioSeqDatabase.Adaptor method) fgcolor (Bio.KEGG.KGML.KGML_pathway.Graphics property) Field (class in Bio.Align.bigbed) fieldNames (Bio.PDB.internal_coords.AtomKey attribute) fields (Bio.PDB.internal_coords.AtomKey attribute) fileno() (Bio.bgzf.BgzfReader method) (Bio.bgzf.BgzfWriter method) FileRecord (class in Bio.PopGen.GenePop.FileParser) fill_chromosome() (Bio.Graphics.DisplayRepresentation.ChromosomeCounts method) finalize_structure() (Bio.PDB.mmtf.DefaultParser.StructureDecoder method) find() (Bio.Seq.SequenceDataAbstractBaseClass method) find_any() (Bio.Phylo.BaseTree.TreeMixin method) find_clades() (Bio.Phylo.BaseTree.TreeMixin method) find_elements() (Bio.Phylo.BaseTree.TreeMixin method) find_start() (Bio.GenBank.Scanner.InsdcScanner method) fit() (Bio.phenotype.phen_micro.WellRecord method) (in module Bio.phenotype.pm_fitting) flag_disorder() (Bio.PDB.Atom.Atom method) flag_disordered() (Bio.PDB.Residue.Residue method) flexibility() (Bio.SeqUtils.ProtParam.ProteinAnalysis method) float1_color() (Bio.Graphics.GenomeDiagram.ColorTranslator method) flush() (Bio.bgzf.BgzfWriter method) fmt (Bio.Align.a2m.AlignmentIterator attribute) (Bio.Align.a2m.AlignmentWriter attribute) (Bio.Align.bed.AlignmentIterator attribute) (Bio.Align.bigbed.AlignmentIterator attribute) (Bio.Align.bigbed.AlignmentWriter attribute) (Bio.Align.bigmaf.AlignmentIterator attribute) (Bio.Align.bigmaf.AlignmentWriter attribute) (Bio.Align.bigpsl.AlignmentIterator attribute) (Bio.Align.bigpsl.AlignmentWriter attribute) (Bio.Align.chain.AlignmentIterator attribute) (Bio.Align.chain.AlignmentWriter attribute) (Bio.Align.clustal.AlignmentIterator attribute) (Bio.Align.clustal.AlignmentWriter attribute) (Bio.Align.emboss.AlignmentIterator attribute) (Bio.Align.exonerate.AlignmentIterator attribute) (Bio.Align.exonerate.AlignmentWriter attribute) (Bio.Align.fasta.AlignmentIterator attribute) (Bio.Align.fasta.AlignmentWriter attribute) (Bio.Align.hhr.AlignmentIterator attribute) (Bio.Align.interfaces.AlignmentIterator attribute) (Bio.Align.interfaces.AlignmentWriter attribute) (Bio.Align.maf.AlignmentIterator attribute) (Bio.Align.maf.AlignmentWriter attribute) (Bio.Align.mauve.AlignmentIterator attribute) (Bio.Align.mauve.AlignmentWriter attribute) (Bio.Align.msf.AlignmentIterator attribute) (Bio.Align.nexus.AlignmentIterator attribute) (Bio.Align.nexus.AlignmentWriter attribute) (Bio.Align.phylip.AlignmentIterator attribute) (Bio.Align.phylip.AlignmentWriter attribute) (Bio.Align.psl.AlignmentIterator attribute) (Bio.Align.psl.AlignmentWriter attribute) (Bio.Align.sam.AlignmentIterator attribute) (Bio.Align.sam.AlignmentWriter attribute) (Bio.Align.stockholm.AlignmentIterator attribute) (Bio.Align.stockholm.AlignmentWriter attribute) (Bio.Align.tabular.AlignmentIterator attribute) (Bio.SeqIO.AlignmentSequenceIterator property)

fmt_() (in module Bio.Blast.NCBIXML) format() (Bio.Align.Alignment method) (Bio.Align.substitution_matrices.Array method) (Bio.motifs.Motif method) (Bio.Phylo.BaseTree.Tree method) (Bio.SeqRecord.SeqRecord method) format_alignment() (Bio.Align.a2m.AlignmentWriter method) (Bio.Align.bed.AlignmentWriter method) (Bio.Align.chain.AlignmentWriter method) (Bio.Align.clustal.AlignmentWriter method) (Bio.Align.fasta.AlignmentWriter method) (Bio.Align.interfaces.AlignmentWriter method) (Bio.Align.maf.AlignmentWriter method) (Bio.Align.mauve.AlignmentWriter method) (Bio.Align.nexus.AlignmentWriter method) (Bio.Align.phylip.AlignmentWriter method) (Bio.Align.psl.AlignmentWriter method) (Bio.Align.sam.AlignmentWriter method) (Bio.Align.stockholm.AlignmentWriter method) (in module Bio.pairwise2) format_label() (in module Bio.Phylo.CDAOIO) format_output() (Bio.Restriction.PrintFormat.PrintFormat method) format_phylip() (Bio.Phylo.TreeConstruction.DistanceMatrix method) forward_algorithm() (Bio.HMM.DynamicProgramming.AbstractDPAlgorithms method) forward_table (Bio.Data.CodonTable.CodonTable attribute) Fragment (class in Bio.PDB.FragmentMapper) FragmentMapper (class in Bio.PDB.FragmentMapper) frequencies (Bio.Align.Alignment property) FrequencyPositionMatrix (class in Bio.motifs.matrix) from_bytes() (Bio.Align.bigbed.AutoSQLTable class method) from_clade() (Bio.Phylo.BaseTree.Tree class method) (Bio.Phylo.PhyloXML.Clade class method) (Bio.Phylo.PhyloXML.Phylogeny class method) from_hex() (Bio.Phylo.BaseTree.BranchColor class method) from_msa() (Bio.codonalign.codonalignment.CodonAlignment class method) from_name() (Bio.Phylo.BaseTree.BranchColor class method) from_seq() (Bio.codonalign.codonseq.CodonSeq class method) from_seqfeature() (Bio.Phylo.PhyloXML.ProteinDomain class method) from_seqrecord() (Bio.Phylo.PhyloXML.Sequence class method) from_string() (Bio.Align.bigbed.AutoSQLTable class method) (Bio.Phylo.CDAOIO.Parser class method) (Bio.Phylo.NewickIO.Parser class method) (Bio.Phylo.NeXMLIO.Parser class method) from_tree() (Bio.Phylo.PhyloXML.Phylogeny class method) fromstring() (Bio.SeqFeature.Location method) (Bio.SeqFeature.Position static method) (Bio.SeqFeature.SimpleLocation static method) full_string (Bio.SeqIO.QualityIO.InvalidCharError attribute) full_translate() (Bio.codonalign.codonseq.CodonSeq method)

G

gafbyproteiniterator() (in module Bio.UniProt.GOA) gafiterator() (in module Bio.UniProt.GOA) gaponly() (Bio.Nexus.Nexus.Nexus method) gaps (Bio.Align.AlignmentCounts property) GB_BASE_INDENT (Bio.GenBank.Record.Record attribute) GB_FEATURE_INDENT (Bio.GenBank.Record.Record attribute) GB_FEATURE_INTERNAL_INDENT (Bio.GenBank.Record.Record attribute) GB_INTERNAL_INDENT (Bio.GenBank.Record.Record attribute) GB_LINE_LENGTH (Bio.GenBank.Record.Record attribute) GB_OTHER_INTERNAL_INDENT (Bio.GenBank.Record.Record attribute) GB_SEQUENCE_INDENT (Bio.GenBank.Record.Record attribute) GC123() (in module Bio.SeqUtils) gc_content (Bio.motifs.matrix.GenericPositionMatrix property) (Bio.motifs.matrix.PositionSpecificScoringMatrix property) gc_fraction() (in module Bio.SeqUtils) gc_mapping (Bio.Align.stockholm.AlignmentIterator attribute) (Bio.Align.stockholm.AlignmentWriter attribute) GC_skew() (in module Bio.SeqUtils) gcg() (in module Bio.SeqUtils.CheckSum) GckIterator (class in Bio.SeqIO.GckIO) gen_key() (Bio.PDB.internal_coords.Edron static method) gen_tuple() (Bio.PDB.internal_coords.Edron static method) GENBANK_INDENT (Bio.GenBank.Scanner.GenBankScanner attribute) GENBANK_SPACER (Bio.GenBank.Scanner.GenBankScanner attribute) GenBankCdsFeatureIterator (class in Bio.SeqIO.InsdcIO) GenBankIterator (class in Bio.SeqIO.InsdcIO) GenBankScanner (class in Bio.GenBank.Scanner) GenBankWriter (class in Bio.SeqIO.InsdcIO) Generic_dbutils (class in BioSQL.DBUtils) GenericPositionMatrix (class in Bio.motifs.matrix) genes (Bio.KEGG.KGML.KGML_pathway.Pathway property) get() (Bio.Align.substitution_matrices.Array method) (Bio.Data.CodonTable.AmbiguousForwardTable method) get_acgt() (Bio.motifs.xms.XMSScanner method) get_alignment_length() (Bio.Align.MultipleSeqAlignment method) get_all_assemblies() (Bio.PDB.PDBList.PDBList method) get_all_entries() (Bio.PDB.PDBList.PDBList method) get_all_obsolete() (Bio.PDB.PDBList.PDBList method) get_aln_length() (Bio.codonalign.codonalignment.CodonAlignment method) get_altloc() (Bio.PDB.Atom.Atom method) get_amino_acids_percent() (Bio.SeqUtils.ProtParam.ProteinAnalysis method) get_angle() (Bio.PDB.internal_coords.IC_Residue method) get_anisou() (Bio.PDB.Atom.Atom method) get_area() (in module Bio.phenotype.pm_fitting) get_array() (Bio.PDB.vectors.Vector method) get_artemis_colorscheme() (Bio.Graphics.GenomeDiagram.ColorTranslator method) get_atoms() (Bio.PDB.Chain.Chain method) (Bio.PDB.Model.Model method) (Bio.PDB.Residue.Residue method) (Bio.PDB.Structure.Structure method) get_bfactor() (Bio.PDB.Atom.Atom method) get_blank_emissions() (Bio.HMM.MarkovModel.HiddenMarkovModel method) get_blank_transitions() (Bio.HMM.MarkovModel.HiddenMarkovModel method) get_ca_list() (Bio.PDB.Polypeptide.Polypeptide method) get_chains() (Bio.PDB.Model.Model method) (Bio.PDB.Structure.Structure method) get_charge() (Bio.PDB.Atom.Atom method) get_codon() (Bio.codonalign.codonseq.CodonSeq method) get_codon_num() (Bio.codonalign.codonseq.CodonSeq method) get_color_dict() (in module Bio.Graphics.ColorSpiral) get_colors() (Bio.Graphics.ColorSpiral.ColorSpiral method) (in module Bio.Graphics.ColorSpiral) get_colorscheme() (Bio.Graphics.GenomeDiagram.ColorTranslator method) get_column() (Bio.Align.AlignInfo.SummaryInfo method) (Bio.phenotype.phen_micro.PlateRecord method) get_coord() (Bio.PDB.Atom.Atom method) get_coords() (Bio.PDB.FragmentMapper.Fragment method) get_data() (Bio.Graphics.GenomeDiagram.GraphData method) (Bio.Nexus.Nodes.Node method) get_dbutils() (in module BioSQL.DBUtils) get_distance() (Bio.Phylo.TreeConstruction.DistanceCalculator method) get_dn_ds_matrix() (Bio.codonalign.codonalignment.CodonAlignment method) get_dn_ds_tree() (Bio.codonalign.codonalignment.CodonAlignment method) get_drawn_levels() (Bio.Graphics.GenomeDiagram.Diagram method) get_feature() (Bio.Graphics.GenomeDiagram.Feature method) get_features() (Bio.Graphics.GenomeDiagram.FeatureSet method) get_from_decoded() (in module Bio.PDB.mmtf) get_full_id() (Bio.PDB.Atom.Atom method) (Bio.PDB.Entity.Entity method) get_full_rf_table() (Bio.codonalign.codonseq.CodonSeq method) get_fullname() (Bio.PDB.Atom.Atom method) get_graphs() (Bio.Graphics.GenomeDiagram.GraphSet method) get_guide_coord_from_structure() (Bio.PDB.cealign.CEAligner method) get_header() (Bio.PDB.PDBParser.PDBParser method) get_id() (Bio.Nexus.Nodes.Node method) (Bio.PDB.Atom.Atom method) (Bio.PDB.Entity.DisorderedEntityWrapper method) (Bio.PDB.Entity.Entity method) (Bio.PDB.FragmentMapper.Fragment method) get_ids() (Bio.Graphics.GenomeDiagram.FeatureSet method) (Bio.Graphics.GenomeDiagram.GraphSet method) (Bio.Graphics.GenomeDiagram.Track method) get_indiv() (in module Bio.PopGen.GenePop) (in module Bio.PopGen.GenePop.LargeFileParser) get_individual() (Bio.PopGen.GenePop.FileParser.FileRecord method) get_init_rms() (Bio.PDB.qcprot.QCPSuperimposer method) (Bio.SVDSuperimposer.SVDSuperimposer method) get_iterator() (Bio.PDB.Entity.Entity method) (Bio.PDB.StructureAlignment.StructureAlignment method) get_KGML() (Bio.KEGG.KGML.KGML_pathway.Pathway method) get_length() (Bio.PDB.internal_coords.Hedron method) (Bio.PDB.internal_coords.IC_Residue method) get_level() (Bio.PDB.Atom.Atom method) (Bio.PDB.Entity.Entity method) get_levels() (Bio.Graphics.GenomeDiagram.Diagram method) get_list() (Bio.PDB.Entity.Entity method) get_maps() (Bio.PDB.StructureAlignment.StructureAlignment method) get_markov_model() (Bio.HMM.MarkovModel.MarkovModelBuilder method) get_models() (Bio.PDB.Structure.Structure method) get_name() (Bio.PDB.Atom.Atom method) get_node_info() (Bio.Phylo.CDAOIO.Parser method) get_nonterminals() (Bio.Phylo.BaseTree.TreeMixin method) get_occupancy() (Bio.PDB.Atom.Atom method) get_parent() (Bio.PDB.Atom.Atom method) (Bio.PDB.Entity.DisorderedEntityWrapper method) (Bio.PDB.Entity.Entity method) get_path() (Bio.Phylo.BaseTree.TreeMixin method) get_phi_psi_list() (Bio.PDB.Polypeptide.Polypeptide method)

get_predictions() (in module Bio.PDB.alphafold_db) get_prev() (Bio.Nexus.Nodes.Node method) get_prodoc_entry() (in module Bio.ExPASy) get_property_value() (Bio.motifs.xms.XMSScanner method) get_prosite_entry() (in module Bio.ExPASy) get_prosite_raw() (in module Bio.ExPASy) get_qresult_id() (Bio.SearchIO.ExonerateIO.exonerate_cigar.ExonerateCigarIndexer method) (Bio.SearchIO.ExonerateIO.exonerate_text.ExonerateTextIndexer method) (Bio.SearchIO.ExonerateIO.exonerate_vulgar.ExonerateVulgarIndexer method) get_radius() (Bio.PDB.Atom.Atom method) get_raw() (Bio.phenotype.phen_micro.WellRecord method) (Bio.SearchIO.BlastIO.blast_tab.BlastTabIndexer method) (Bio.SearchIO.BlastIO.blast_xml.BlastXmlIndexer method) (Bio.SearchIO.BlatIO.BlatPslIndexer method) (Bio.SearchIO.ExonerateIO.exonerate_text.ExonerateTextIndexer method) (Bio.SearchIO.ExonerateIO.exonerate_vulgar.ExonerateVulgarIndexer method) (Bio.SearchIO.FastaIO.FastaM10Indexer method) (Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabIndexer method) get_recent_changes() (Bio.PDB.PDBList.PDBList method) get_residues() (Bio.PDB.Chain.Chain method) (Bio.PDB.Model.Model method) (Bio.PDB.Structure.Structure method) get_resname() (Bio.PDB.Residue.Residue method) get_resname_list() (Bio.PDB.FragmentMapper.Fragment method) get_rms() (Bio.PDB.qcprot.QCPSuperimposer method) (Bio.SVDSuperimposer.SVDSuperimposer method) get_rotran() (Bio.PDB.qcprot.QCPSuperimposer method) (Bio.SVDSuperimposer.SVDSuperimposer method) get_row() (Bio.phenotype.phen_micro.PlateRecord method) get_score() (Bio.Phylo.TreeConstruction.ParsimonyScorer method) (Bio.Phylo.TreeConstruction.Scorer method) get_segid() (Bio.PDB.Residue.Residue method) get_segment_info() (Bio.Graphics.DisplayRepresentation.ChromosomeCounts method) get_seq() (Bio.PDB.PSEA.PSEA method) get_Seq_by_acc() (BioSQL.BioSeqDatabase.BioSeqDatabase method) get_Seq_by_id() (BioSQL.BioSeqDatabase.BioSeqDatabase method) get_Seq_by_ver() (BioSQL.BioSeqDatabase.BioSeqDatabase method) get_seqres_file() (Bio.PDB.PDBList.PDBList method) get_Seqs_by_acc() (BioSQL.BioSeqDatabase.BioSeqDatabase method) get_sequence() (Bio.PDB.Polypeptide.Polypeptide method) get_serial_number() (Bio.PDB.Atom.Atom method) get_sets() (Bio.Graphics.GenomeDiagram.Track method) get_sigatm() (Bio.PDB.Atom.Atom method) get_signals() (Bio.phenotype.phen_micro.WellRecord method) get_siguij() (Bio.PDB.Atom.Atom method) get_spherical_coordinates() (in module Bio.PDB.vectors) get_spliced() (Bio.AlignIO.MafIO.MafIndex method) get_sprot_raw() (in module Bio.ExPASy) get_start_end() (in module Bio.Nexus.Nexus) get_status_list() (Bio.PDB.PDBList.PDBList static method) get_structural_models_for() (in module Bio.PDB.alphafold_db) get_structure() (Bio.PDB.binary_cif.BinaryCIFParser method) (Bio.PDB.MMCIFParser.FastMMCIFParser method) (Bio.PDB.MMCIFParser.MMCIFParser method) (Bio.PDB.mmtf.MMTFParser static method) (Bio.PDB.PDBMLParser.PDBMLParser method) (Bio.PDB.PDBParser.PDBParser method) (Bio.PDB.StructureBuilder.StructureBuilder method) get_structure_from_url() (Bio.PDB.mmtf.MMTFParser static method) get_subseq_as_string() (BioSQL.BioSeqDatabase.Adaptor method) get_succ() (Bio.Nexus.Nodes.Node method) get_support() (in module Bio.Phylo.Consensus) get_surface() (in module Bio.PDB.ResidueDepth) get_tau_list() (Bio.PDB.Polypeptide.Polypeptide method) get_taxa() (Bio.Nexus.Trees.Tree method) get_temp_imagefilename() (in module Bio.Graphics.KGML_vis) get_terminals() (Bio.Nexus.Trees.Tree method) (Bio.Phylo.BaseTree.TreeMixin method) get_text() (Bio.motifs.xms.XMSScanner method) get_theta_list() (Bio.PDB.Polypeptide.Polypeptide method) get_times() (Bio.phenotype.phen_micro.WellRecord method) get_tracks() (Bio.Graphics.GenomeDiagram.Diagram method) get_trailer() (Bio.PDB.PDBParser.PDBParser method) get_transformed() (Bio.PDB.qcprot.QCPSuperimposer method) (Bio.SVDSuperimposer.SVDSuperimposer method) get_unique_parents() (in module Bio.PDB.Selection) get_unpacked_list() (Bio.PDB.Chain.Chain method) (Bio.PDB.Residue.Residue method) get_vector() (Bio.PDB.Atom.Atom method) getAscendent() (Bio.SCOP.Node method) getAscendentFromSQL() (Bio.SCOP.Scop method) getAstralDomainsFromFile() (Bio.SCOP.Astral method) getAstralDomainsFromSQL() (Bio.SCOP.Astral method) getAtoms() (Bio.SCOP.Raf.SeqMap method) getChildren() (Bio.SCOP.Node method) getDescendents() (Bio.SCOP.Node method) getDescendentsFromSQL() (Bio.SCOP.Scop method) getDomainBySid() (Bio.SCOP.Scop method) getDomainFromSQL() (Bio.SCOP.Scop method) getDomains() (Bio.SCOP.Scop method) getNodeBySunid() (Bio.SCOP.Scop method) getParent() (Bio.SCOP.Node method) getRoot() (Bio.SCOP.Scop method) getSeq() (Bio.SCOP.Astral method) getSeqBySid() (Bio.SCOP.Astral method) getSeqMap() (Bio.SCOP.Raf.SeqMapIndex method) gf_mapping (Bio.Align.stockholm.AlignmentIterator attribute) (Bio.Align.stockholm.AlignmentWriter attribute) Gfa1Iterator (class in Bio.SeqIO.GfaIO) Gfa2Iterator (class in Bio.SeqIO.GfaIO) global_dtd_dir (Bio.Entrez.Parser.DataHandler attribute) global_xsd_dir (Bio.Entrez.Parser.DataHandler attribute) gly_Cbeta (Bio.PDB.internal_coords.IC_Residue attribute) gompertz() (in module Bio.phenotype.pm_fitting) gpa_iterator() (in module Bio.UniProt.GOA) gpi_iterator() (in module Bio.UniProt.GOA) gr_mapping (Bio.Align.stockholm.AlignmentIterator attribute) (Bio.Align.stockholm.AlignmentWriter attribute) Graph (class in Bio.Pathway.Rep.Graph) GraphData (class in Bio.Graphics.GenomeDiagram) Graphics (class in Bio.KEGG.KGML.KGML_pathway) GraphSet (class in Bio.Graphics.GenomeDiagram) gravy() (Bio.SeqUtils.ProtParam.ProteinAnalysis method) green() (Bio.Phylo.PhyloXMLIO.Writer method) gs_mapping (Bio.Align.stockholm.AlignmentIterator attribute) (Bio.Align.stockholm.AlignmentWriter attribute) guess_lag() (in module Bio.phenotype.pm_fitting) guess_plateau() (in module Bio.phenotype.pm_fitting)

H

handle_motif() (Bio.motifs.xms.XMSScanner method) handleMissingDocumentDefinition() (Bio.Entrez.Parser.DataHandler method) has_id() (Bio.PDB.Chain.Chain method) (Bio.PDB.Entity.Entity method) has_support() (Bio.Nexus.Trees.Tree method) hashedDomainsByEv() (Bio.SCOP.Astral method) hashedDomainsById() (Bio.SCOP.Astral method) Header (class in Bio.Blast.NCBIXML) HEADER_WIDTH (Bio.GenBank.Scanner.EmblScanner attribute) (Bio.GenBank.Scanner.GenBankScanner attribute) (Bio.GenBank.Scanner.InsdcScanner attribute) (Bio.SeqIO.InsdcIO.EmblWriter attribute) (Bio.SeqIO.InsdcIO.GenBankWriter attribute) (Bio.SeqIO.InsdcIO.ImgtWriter attribute) Hedron (class in Bio.PDB.internal_coords) HedronMatchError height (Bio.KEGG.KGML.KGML_pathway.Graphics property) Hhsuite2TextParser (class in Bio.SearchIO.HHsuiteIO.hhsuite2_text) HiddenMarkovModel (class in Bio.HMM.MarkovModel) Hit (class in Bio.Blast) hit_coverage() (Bio.Compass.Record method) hmm_as_hit (Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmhitParser attribute) (Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmhitWriter attribute) (Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmqueryParser attribute) (Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmqueryWriter attribute)

Hmmer2TextIndexer (class in Bio.SearchIO.HmmerIO.hmmer2_text) Hmmer2TextParser (class in Bio.SearchIO.HmmerIO.hmmer2_text) Hmmer3DomtabHmmhitIndexer (class in Bio.SearchIO.HmmerIO.hmmer3_domtab) Hmmer3DomtabHmmhitParser (class in Bio.SearchIO.HmmerIO.hmmer3_domtab) Hmmer3DomtabHmmhitWriter (class in Bio.SearchIO.HmmerIO.hmmer3_domtab) Hmmer3DomtabHmmqueryIndexer (class in Bio.SearchIO.HmmerIO.hmmer3_domtab) Hmmer3DomtabHmmqueryParser (class in Bio.SearchIO.HmmerIO.hmmer3_domtab) Hmmer3DomtabHmmqueryWriter (class in Bio.SearchIO.HmmerIO.hmmer3_domtab) Hmmer3TabIndexer (class in Bio.SearchIO.HmmerIO.hmmer3_tab) Hmmer3TabParser (class in Bio.SearchIO.HmmerIO.hmmer3_tab) Hmmer3TabWriter (class in Bio.SearchIO.HmmerIO.hmmer3_tab) Hmmer3TextIndexer (class in Bio.SearchIO.HmmerIO.hmmer3_text) Hmmer3TextParser (class in Bio.SearchIO.HmmerIO.hmmer3_text) homog_rot_mtx() (in module Bio.PDB.vectors) homog_scale_mtx() (in module Bio.PDB.vectors) homog_trans_mtx() (in module Bio.PDB.vectors) HSExposureCA (class in Bio.PDB.HSExposure) HSExposureCB (class in Bio.PDB.HSExposure) HSP (class in Bio.Blast) (class in Bio.Blast.NCBIXML)

I

IC_Chain (class in Bio.PDB.internal_coords) IC_duplicate() (in module Bio.PDB.ic_rebuild) IC_Residue (class in Bio.PDB.internal_coords) id (Bio.KEGG.KGML.KGML_pathway.Component property) (Bio.KEGG.KGML.KGML_pathway.Entry property) (Bio.KEGG.KGML.KGML_pathway.Reaction property) (Bio.PDB.Entity.Entity property) Id (class in Bio.Phylo.PhyloXML) id() (Bio.Phylo.PhyloXMLIO.Parser method) (Bio.Phylo.PhyloXMLIO.Writer method) id_width (Bio.AlignIO.PhylipIO.PhylipIterator attribute) identities (Bio.Align.AlignmentCounts property) identity_match (class in Bio.pairwise2) IgIterator (class in Bio.SeqIO.IgIO) ImgtIterator (class in Bio.SeqIO.InsdcIO) ImgtWriter (class in Bio.SeqIO.InsdcIO) Indent (Bio.Restriction.PrintFormat.PrintFormat attribute) index (Bio.SeqIO.QualityIO.InvalidCharError attribute) Index (class in Bio.SCOP.Cla) index() (Bio.Blast.Record method) (Bio.SCOP.Raf.SeqMap method) (Bio.Seq.SequenceDataAbstractBaseClass method) (in module Bio.SearchIO) (in module Bio.SeqIO) index_db() (in module Bio.SearchIO) (in module Bio.SeqIO) index_to_one() (in module Bio.PDB.Polypeptide) index_to_three() (in module Bio.PDB.Polypeptide) indices (Bio.Align.Alignment property) infer_coordinates() (Bio.Align.Alignment class method) init_atom() (Bio.PDB.StructureBuilder.StructureBuilder method) init_atom_coords() (Bio.PDB.internal_coords.IC_Chain method) init_chain() (Bio.PDB.StructureBuilder.StructureBuilder method) init_edra() (Bio.PDB.internal_coords.IC_Chain method) init_model() (Bio.PDB.StructureBuilder.StructureBuilder method) init_residue() (Bio.PDB.StructureBuilder.StructureBuilder method) init_seg() (Bio.PDB.StructureBuilder.StructureBuilder method) init_structure() (Bio.PDB.mmtf.DefaultParser.StructureDecoder method) (Bio.PDB.StructureBuilder.StructureBuilder method) InputRecord (class in Bio.Emboss.PrimerSearch) InsdcScanner (class in Bio.GenBank.Scanner) insert() (Bio.PDB.Entity.Entity method) (Bio.Seq.MutableSeq method) insert_gap() (Bio.Nexus.Nexus.Nexus method) insertions (Bio.Align.AlignmentCounts property) instability_index() (Bio.SeqUtils.ProtParam.ProteinAnalysis method) Instance (class in Bio.motifs.meme) int255_color() (Bio.Graphics.GenomeDiagram.ColorTranslator method) IntegerElement (class in Bio.Entrez.Parser) integers (Bio.ExPASy.ScanProsite.ContentHandler attribute) Interaction (class in Bio.Pathway)

interactions() (Bio.Pathway.Network method) internal_deletions (Bio.Align.AlignmentCounts property) INTERNAL_FEATURE_FORMAT (Bio.GenBank.Record.Record attribute) INTERNAL_FORMAT (Bio.GenBank.Record.Record attribute) internal_gaps (Bio.Align.AlignmentCounts property) internal_insertions (Bio.Align.AlignmentCounts property) internal_to_atom_coordinates() (Bio.PDB.Chain.Chain method) (Bio.PDB.internal_coords.IC_Chain method) (Bio.PDB.Model.Model method) (Bio.PDB.Structure.Structure method) InterproscanXmlParser (class in Bio.SearchIO.InterproscanIO.interproscan_xml) InvalidCharError inverse_indices (Bio.Align.Alignment property) invert() (Bio.Nexus.Nexus.Nexus method) is_aa() (in module Bio.PDB.Polypeptide) is_backbone() (Bio.PDB.internal_coords.AtomKey method) (Bio.PDB.internal_coords.Edron method) is_bifurcating() (Bio.Nexus.Trees.Tree method) (Bio.Phylo.BaseTree.TreeMixin method) is_compatible() (Bio.Nexus.Trees.Tree method) is_disordered() (Bio.PDB.Atom.Atom method) (Bio.PDB.Entity.DisorderedEntityWrapper method) (Bio.PDB.Residue.Residue method) is_identical() (Bio.Nexus.Trees.Tree method) is_internal() (Bio.Nexus.Trees.Tree method) is_monophyletic() (Bio.Nexus.Trees.Tree method) (Bio.Phylo.BaseTree.TreeMixin method) is_nucleic() (in module Bio.PDB.Polypeptide) is_parent_of() (Bio.Nexus.Nodes.Chain method) (Bio.Phylo.BaseTree.TreeMixin method) is_preterminal() (Bio.Nexus.Trees.Tree method) (Bio.Phylo.BaseTree.TreeMixin method) is_reactant (Bio.KEGG.KGML.KGML_pathway.Entry property) is_terminal() (Bio.Nexus.Trees.Tree method) (Bio.Phylo.BaseTree.Clade method) (Bio.Phylo.BaseTree.Tree method) isatty() (Bio.bgzf.BgzfReader method) (Bio.bgzf.BgzfWriter method) isDomainInEv() (Bio.SCOP.Astral method) isDomainInId() (Bio.SCOP.Astral method) islower() (Bio.Seq.SequenceDataAbstractBaseClass method) (Bio.SeqRecord.SeqRecord method) isoelectric_point() (Bio.SeqUtils.ProtParam.ProteinAnalysis method) IsoelectricPoint (class in Bio.SeqUtils.IsoelectricPoint) isupper() (Bio.Seq.SequenceDataAbstractBaseClass method) (Bio.SeqRecord.SeqRecord method) items() (Bio.Align.substitution_matrices.Array method) (Bio.Phylo.PhyloXML.Events method) (BioSQL.BioSeqDatabase.BioSeqDatabase method) (BioSQL.BioSeqDatabase.DBServer method) Iterator (class in Bio.GenBank)

J

JASPAR5 (class in Bio.motifs.jaspar.db) jitter (Bio.Graphics.ColorSpiral.ColorSpiral property)

JsonIterator() (in module Bio.phenotype.phen_micro) JsonWriter (class in Bio.phenotype.phen_micro)

K

kcluster() (Bio.Cluster.Record method) (in module Bio.Cluster) kegg_conv() (in module Bio.KEGG.REST) kegg_find() (in module Bio.KEGG.REST) kegg_get() (in module Bio.KEGG.REST) kegg_info() (in module Bio.KEGG.REST) kegg_link() (in module Bio.KEGG.REST) kegg_list() (in module Bio.KEGG.REST) key (Bio.Align.stockholm.AlignmentIterator attribute) keys() (Bio.Align.substitution_matrices.Array method) (Bio.Blast.Record method) (Bio.PDB.AbstractPropertyMap.AbstractPropertyMap method) (Bio.Phylo.PhyloXML.Events method) (Bio.SeqIO.TwoBitIO.TwoBitIterator method) (BioSQL.BioSeqDatabase.BioSeqDatabase method) (BioSQL.BioSeqDatabase.DBServer method)

keys_to_process (Bio.GenBank.utils.FeatureValueCleaner attribute) keyword (Bio.Align.stockholm.AlignmentIterator attribute) KGMLCanvas (class in Bio.Graphics.KGML_vis) KGMLParser (class in Bio.KEGG.KGML.KGML_parser) kill() (Bio.Nexus.Nodes.Chain method) kmedoids() (in module Bio.Cluster) KnownStateTrainer (class in Bio.HMM.Trainer)

L

labels() (Bio.Pathway.Rep.Graph.Graph method) (Bio.Pathway.Rep.MultiGraph.MultiGraph method) ladderize() (Bio.Phylo.BaseTree.TreeMixin method) last_id() (BioSQL.BioSeqDatabase.Adaptor method) (BioSQL.DBUtils.Generic_dbutils method) (BioSQL.DBUtils.Mysql_dbutils method) lat() (Bio.Phylo.PhyloXMLIO.Writer method) lcc_mult() (in module Bio.SeqUtils.lcc) lcc_simp() (in module Bio.SeqUtils.lcc) left_deletions (Bio.Align.AlignmentCounts property) left_gaps (Bio.Align.AlignmentCounts property) left_insertions (Bio.Align.AlignmentCounts property) left_multiply() (Bio.PDB.vectors.Vector method) len12 (Bio.PDB.internal_coords.Hedron property) len23 (Bio.PDB.internal_coords.Hedron property) length (Bio.Align.Alignment property) letter_annotations (Bio.SeqRecord.SeqRecord property) LETTERS_PER_BLOCK (Bio.SeqIO.InsdcIO.EmblWriter attribute) LETTERS_PER_LINE (Bio.SeqIO.InsdcIO.EmblWriter attribute) (Bio.SeqIO.InsdcIO.GenBankWriter attribute) level (Bio.PDB.Entity.Entity attribute) LineDistribution (class in Bio.Graphics.Distribution) linesize (Bio.Restriction.PrintFormat.PrintFormat attribute) link() (Bio.Nexus.Nodes.Chain method) list_ambiguous_codons() (in module Bio.Data.CodonTable)

list_any_ids() (BioSQL.BioSeqDatabase.Adaptor method) list_biodatabase_names() (BioSQL.BioSeqDatabase.Adaptor method) list_bioentry_display_ids() (BioSQL.BioSeqDatabase.Adaptor method) list_bioentry_ids() (BioSQL.BioSeqDatabase.Adaptor method) list_possible_proteins() (in module Bio.Data.CodonTable) ListElement (class in Bio.Entrez.Parser) load() (BioSQL.BioSeqDatabase.BioSeqDatabase method) (in module Bio.Align.substitution_matrices) load_database_sql() (BioSQL.BioSeqDatabase.DBServer method) load_seqrecord() (BioSQL.Loader.DatabaseLoader method) local_dtd_dir (Bio.Entrez.Parser.DataHandler attribute) local_xsd_dir (Bio.Entrez.Parser.DataHandler attribute) Location (class in Bio.SeqFeature) location() (Bio.Phylo.PhyloXMLIO.Writer method) LocationParserError log_likelihood() (Bio.HMM.Trainer.AbstractTrainer method) log_odds() (Bio.motifs.matrix.PositionWeightMatrix method) LogDPAlgorithms (class in Bio.HMM.DynamicProgramming) logistic() (in module Bio.phenotype.pm_fitting) long() (Bio.Phylo.PhyloXMLIO.Writer method) lookup() (BioSQL.BioSeqDatabase.BioSeqDatabase method) losses() (Bio.Phylo.PhyloXMLIO.Writer method) lower() (Bio.Seq.SequenceDataAbstractBaseClass method) (Bio.SeqRecord.SeqRecord method) lstrip() (Bio.Seq.SequenceDataAbstractBaseClass method)

M

m2rotaxis() (in module Bio.PDB.vectors) MafIndex (class in Bio.AlignIO.MafIO) MafIterator() (in module Bio.AlignIO.MafIO) MafWriter (class in Bio.AlignIO.MafIO) majority_consensus() (in module Bio.Phylo.Consensus) make_back_table() (in module Bio.Data.CodonTable) make_dssp_dict() (in module Bio.PDB.DSSP) make_extended() (Bio.PDB.internal_coords.IC_Chain method) make_format() (Bio.Restriction.PrintFormat.PrintFormat method) make_table() (in module Bio.SeqUtils.MeltingTemp) make_virtual_offset() (in module Bio.bgzf) map() (Bio.Align.Alignment method) mapall() (Bio.Align.Alignment method) maps (Bio.KEGG.KGML.KGML_pathway.Pathway property) MarkovModelBuilder (class in Bio.HMM.MarkovModel) mask (Bio.motifs.Motif property) MATCH (Bio.Align.tabular.State attribute) matches() (in module Bio.Phylo.NeXMLIO) MauveIterator (class in Bio.AlignIO.MauveIO) MauveWriter (class in Bio.AlignIO.MauveIO) max (Bio.motifs.matrix.PositionSpecificScoringMatrix property) maximum() (Bio.Phylo.PhyloXMLIO.Writer method) MaxPeptideBond (Bio.PDB.internal_coords.IC_Chain attribute) MaxSize (Bio.Restriction.PrintFormat.PrintFormat attribute) mean() (Bio.Graphics.GenomeDiagram.GraphData method) (Bio.motifs.matrix.PositionSpecificScoringMatrix method) merge_with_support() (Bio.Nexus.Trees.Tree method) methods (Bio.Phylo.TreeConstruction.DistanceTreeConstructor attribute) min (Bio.motifs.matrix.PositionSpecificScoringMatrix property) min_dist() (in module Bio.PDB.ResidueDepth) minimum() (Bio.Phylo.PhyloXMLIO.Writer method) mismatches (Bio.Align.AlignmentCounts property) MissingAtomError MissingExternalDependencyError MissingPythonDependencyError mktest() (in module Bio.Align.analysis) (in module Bio.codonalign.codonalignment) ml_estimator() (Bio.HMM.Trainer.AbstractTrainer method) MMCIF2Dict (class in Bio.PDB.MMCIF2Dict) MMCIFIO (class in Bio.PDB.mmcifio) MMCIFParser (class in Bio.PDB.MMCIFParser) MMTFIO (class in Bio.PDB.mmtf.mmtfio) MMTFParser (class in Bio.PDB.mmtf) mode (Bio.Align.bigbed.AlignmentIterator attribute) (Bio.Align.bigbed.AlignmentWriter attribute) (Bio.Align.bigmaf.AlignmentIterator attribute) (Bio.Align.interfaces.AlignmentIterator attribute) (Bio.Align.interfaces.AlignmentWriter attribute) Model (class in Bio.PDB.Model) models (Bio.Phylo.TreeConstruction.DistanceCalculator attribute) modes (Bio.SeqIO.AbiIO.AbiIterator attribute) (Bio.SeqIO.AceIO.AceIterator attribute) (Bio.SeqIO.AlignmentSequenceIterator attribute) (Bio.SeqIO.AlignmentSequenceWriter attribute) (Bio.SeqIO.FastaIO.FastaBlastIterator attribute) (Bio.SeqIO.FastaIO.FastaIterator attribute) (Bio.SeqIO.FastaIO.FastaPearsonIterator attribute) (Bio.SeqIO.FastaIO.FastaTwoLineIterator attribute) (Bio.SeqIO.FastaIO.FastaWriter attribute) (Bio.SeqIO.GckIO.GckIterator attribute) (Bio.SeqIO.GfaIO.Gfa1Iterator attribute) (Bio.SeqIO.GfaIO.Gfa2Iterator attribute) (Bio.SeqIO.IgIO.IgIterator attribute) (Bio.SeqIO.InsdcIO.EmblCdsFeatureIterator attribute) (Bio.SeqIO.InsdcIO.EmblIterator attribute) (Bio.SeqIO.InsdcIO.GenBankCdsFeatureIterator attribute) (Bio.SeqIO.InsdcIO.GenBankIterator attribute) (Bio.SeqIO.InsdcIO.ImgtIterator attribute) (Bio.SeqIO.Interfaces.SequenceIterator property) (Bio.SeqIO.Interfaces.SequenceWriter property) (Bio.SeqIO.NibIO.NibIterator attribute) (Bio.SeqIO.NibIO.NibWriter attribute) (Bio.SeqIO.PdbIO.CifAtomIterator attribute) (Bio.SeqIO.PdbIO.CifSeqresIterator attribute) (Bio.SeqIO.PdbIO.PdbAtomIterator attribute) (Bio.SeqIO.PdbIO.PdbSeqresIterator attribute) (Bio.SeqIO.PhdIO.PhdIterator attribute) (Bio.SeqIO.PhdIO.PhdWriter attribute) (Bio.SeqIO.PirIO.PirIterator attribute) (Bio.SeqIO.PirIO.PirWriter attribute) (Bio.SeqIO.QualityIO.FastqIlluminaWriter attribute) (Bio.SeqIO.QualityIO.FastqIteratorAbstractBaseClass attribute) (Bio.SeqIO.QualityIO.FastqPhredWriter attribute) (Bio.SeqIO.QualityIO.FastqSolexaWriter attribute) (Bio.SeqIO.QualityIO.QualPhredIterator attribute) (Bio.SeqIO.QualityIO.QualPhredWriter attribute) (Bio.SeqIO.SeqXmlIO.SeqXmlIterator attribute) (Bio.SeqIO.SeqXmlIO.SeqXmlWriter attribute) (Bio.SeqIO.SffIO.SffIterator attribute) (Bio.SeqIO.SffIO.SffWriter attribute) (Bio.SeqIO.SnapGeneIO.SnapGeneIterator attribute) (Bio.SeqIO.SwissIO.SwissIterator attribute) (Bio.SeqIO.TabIO.TabIterator attribute) (Bio.SeqIO.TabIO.TabWriter attribute) (Bio.SeqIO.TwoBitIO.TwoBitIterator attribute) (Bio.SeqIO.UniprotIO.UniprotIterator attribute) (Bio.SeqIO.XdnaIO.XdnaIterator attribute) (Bio.SeqIO.XdnaIO.XdnaWriter attribute) modify() (Bio.motifs.thresholds.ScoreDistribution method) module Bio Bio.Affy Bio.Affy.CelFile Bio.Align Bio.Align.a2m Bio.Align.AlignInfo Bio.Align.analysis Bio.Align.bed Bio.Align.bigbed Bio.Align.bigmaf Bio.Align.bigpsl Bio.Align.chain Bio.Align.clustal Bio.Align.emboss Bio.Align.exonerate Bio.Align.fasta Bio.Align.hhr Bio.Align.interfaces Bio.Align.maf Bio.Align.mauve Bio.Align.msf Bio.Align.nexus Bio.Align.phylip Bio.Align.psl Bio.Align.sam Bio.Align.stockholm Bio.Align.substitution_matrices Bio.Align.tabular Bio.AlignIO Bio.AlignIO.ClustalIO Bio.AlignIO.EmbossIO Bio.AlignIO.FastaIO Bio.AlignIO.Interfaces Bio.AlignIO.MafIO Bio.AlignIO.MauveIO Bio.AlignIO.MsfIO Bio.AlignIO.NexusIO Bio.AlignIO.PhylipIO Bio.AlignIO.StockholmIO Bio.bgzf Bio.Blast Bio.Blast.NCBIWWW Bio.Blast.NCBIXML Bio.CAPS Bio.Cluster Bio.codonalign Bio.codonalign.codonalignment Bio.codonalign.codonseq Bio.Compass Bio.Data Bio.Data.CodonTable Bio.Data.IUPACData Bio.Data.PDBData Bio.Emboss Bio.Emboss.Primer3 Bio.Emboss.PrimerSearch Bio.Entrez Bio.Entrez.Parser Bio.ExPASy Bio.ExPASy.cellosaurus Bio.ExPASy.Enzyme Bio.ExPASy.Prodoc Bio.ExPASy.Prosite Bio.ExPASy.ScanProsite Bio.File Bio.GenBank Bio.GenBank.Record Bio.GenBank.Scanner Bio.GenBank.utils Bio.Geo Bio.Geo.Record Bio.Graphics Bio.Graphics.BasicChromosome Bio.Graphics.ColorSpiral Bio.Graphics.Comparative Bio.Graphics.DisplayRepresentation Bio.Graphics.Distribution Bio.Graphics.GenomeDiagram Bio.Graphics.KGML_vis Bio.HMM Bio.HMM.DynamicProgramming Bio.HMM.MarkovModel Bio.HMM.Trainer Bio.HMM.Utilities Bio.KEGG Bio.KEGG.Compound Bio.KEGG.Enzyme Bio.KEGG.Gene Bio.KEGG.KGML Bio.KEGG.KGML.KGML_parser Bio.KEGG.KGML.KGML_pathway Bio.KEGG.Map Bio.KEGG.REST Bio.Medline Bio.motifs Bio.motifs.alignace Bio.motifs.clusterbuster Bio.motifs.jaspar Bio.motifs.jaspar.db Bio.motifs.mast Bio.motifs.matrix Bio.motifs.meme Bio.motifs.minimal Bio.motifs.pfm Bio.motifs.thresholds Bio.motifs.transfac Bio.motifs.xms Bio.Nexus Bio.Nexus.Nexus Bio.Nexus.Nodes Bio.Nexus.StandardData Bio.Nexus.Trees Bio.NMR Bio.NMR.NOEtools Bio.NMR.xpktools Bio.pairwise2 Bio.Pathway Bio.Pathway.Rep Bio.Pathway.Rep.Graph Bio.Pathway.Rep.MultiGraph Bio.PDB Bio.PDB.AbstractPropertyMap Bio.PDB.alphafold_db Bio.PDB.Atom Bio.PDB.binary_cif Bio.PDB.cealign Bio.PDB.Chain Bio.PDB.Dice Bio.PDB.DSSP Bio.PDB.Entity Bio.PDB.FragmentMapper Bio.PDB.HSExposure Bio.PDB.ic_data Bio.PDB.ic_rebuild Bio.PDB.internal_coords Bio.PDB.MMCIF2Dict Bio.PDB.mmcifio Bio.PDB.MMCIFParser Bio.PDB.mmtf Bio.PDB.mmtf.DefaultParser Bio.PDB.mmtf.mmtfio Bio.PDB.Model Bio.PDB.NACCESS Bio.PDB.NeighborSearch Bio.PDB.parse_pdb_header Bio.PDB.PDBExceptions Bio.PDB.PDBIO Bio.PDB.PDBList Bio.PDB.PDBMLParser Bio.PDB.PDBParser Bio.PDB.PICIO Bio.PDB.Polypeptide Bio.PDB.PSEA Bio.PDB.qcprot Bio.PDB.Residue Bio.PDB.ResidueDepth Bio.PDB.SASA Bio.PDB.SCADIO Bio.PDB.Selection Bio.PDB.Structure Bio.PDB.StructureAlignment Bio.PDB.StructureBuilder Bio.PDB.Superimposer Bio.PDB.vectors Bio.phenotype Bio.phenotype.phen_micro Bio.phenotype.pm_fitting Bio.Phylo Bio.Phylo.BaseTree Bio.Phylo.CDAO Bio.Phylo.CDAOIO Bio.Phylo.Consensus Bio.Phylo.Newick Bio.Phylo.NewickIO Bio.Phylo.NeXML Bio.Phylo.NeXMLIO Bio.Phylo.NexusIO Bio.Phylo.PAML Bio.Phylo.PAML.baseml Bio.Phylo.PAML.chi2 Bio.Phylo.PAML.codeml Bio.Phylo.PAML.yn00 Bio.Phylo.PhyloXML Bio.Phylo.PhyloXMLIO Bio.Phylo.TreeConstruction Bio.PopGen Bio.PopGen.GenePop Bio.PopGen.GenePop.FileParser Bio.PopGen.GenePop.LargeFileParser Bio.Restriction Bio.Restriction.PrintFormat Bio.Restriction.Restriction_Dictionary Bio.SCOP Bio.SCOP.Cla Bio.SCOP.Des Bio.SCOP.Dom Bio.SCOP.Hie Bio.SCOP.Raf Bio.SCOP.Residues Bio.SearchIO Bio.SearchIO.BlastIO Bio.SearchIO.BlastIO.blast_tab Bio.SearchIO.BlastIO.blast_xml Bio.SearchIO.BlatIO Bio.SearchIO.ExonerateIO Bio.SearchIO.ExonerateIO.exonerate_cigar Bio.SearchIO.ExonerateIO.exonerate_text Bio.SearchIO.ExonerateIO.exonerate_vulgar Bio.SearchIO.FastaIO Bio.SearchIO.HHsuiteIO Bio.SearchIO.HHsuiteIO.hhsuite2_text Bio.SearchIO.HmmerIO Bio.SearchIO.HmmerIO.hmmer2_text Bio.SearchIO.HmmerIO.hmmer3_domtab Bio.SearchIO.HmmerIO.hmmer3_tab Bio.SearchIO.HmmerIO.hmmer3_text Bio.SearchIO.InterproscanIO Bio.SearchIO.InterproscanIO.interproscan_xml Bio.Seq Bio.SeqFeature Bio.SeqIO Bio.SeqIO.AbiIO Bio.SeqIO.AceIO Bio.SeqIO.FastaIO Bio.SeqIO.GckIO Bio.SeqIO.GfaIO Bio.SeqIO.IgIO Bio.SeqIO.InsdcIO Bio.SeqIO.Interfaces Bio.SeqIO.NibIO Bio.SeqIO.PdbIO Bio.SeqIO.PhdIO Bio.SeqIO.PirIO Bio.SeqIO.QualityIO Bio.SeqIO.SeqXmlIO Bio.SeqIO.SffIO Bio.SeqIO.SnapGeneIO Bio.SeqIO.SwissIO Bio.SeqIO.TabIO Bio.SeqIO.TwoBitIO Bio.SeqIO.UniprotIO Bio.SeqIO.XdnaIO Bio.SeqRecord Bio.Sequencing Bio.Sequencing.Ace Bio.Sequencing.Phd Bio.SeqUtils Bio.SeqUtils.CheckSum Bio.SeqUtils.IsoelectricPoint Bio.SeqUtils.lcc Bio.SeqUtils.MeltingTemp Bio.SeqUtils.ProtParam Bio.SeqUtils.ProtParamData Bio.SVDSuperimposer Bio.SwissProt Bio.SwissProt.KeyWList Bio.TogoWS Bio.UniGene Bio.UniProt Bio.UniProt.GOA BioSQL BioSQL.BioSeq BioSQL.BioSeqDatabase BioSQL.DBUtils BioSQL.Loader

mol_seq() (Bio.Phylo.PhyloXMLIO.Parser method) (Bio.Phylo.PhyloXMLIO.Writer method) molar_extinction_coefficient() (Bio.SeqUtils.ProtParam.ProteinAnalysis method) molecular_weight() (Bio.SeqUtils.ProtParam.ProteinAnalysis method) (in module Bio.SeqUtils) MolSeq (class in Bio.Phylo.PhyloXML) Motif (class in Bio.motifs) (class in Bio.motifs.jaspar) (class in Bio.motifs.meme) (class in Bio.motifs.transfac) move_track() (Bio.Graphics.GenomeDiagram.Diagram method) MsfIterator (class in Bio.AlignIO.MsfIO) multi_coord_space() (in module Bio.PDB.vectors) multi_rot_Y() (in module Bio.PDB.vectors) multi_rot_Z() (in module Bio.PDB.vectors) MultiGraph (class in Bio.Pathway.Rep.MultiGraph) multiple_value_keys (Bio.motifs.transfac.Motif attribute) MultipleAlignment (class in Bio.Blast.NCBIXML) MultipleSeqAlignment (class in Bio.Align) MutableSeq (class in Bio.Seq) Mysql_dbutils (class in BioSQL.DBUtils) MysqlConnectorAdaptor (class in BioSQL.BioSeqDatabase)

N

NACCESS (class in Bio.PDB.NACCESS) NACCESS_atomic (class in Bio.PDB.NACCESS) name (Bio.Align.bigbed.Field attribute) (Bio.KEGG.KGML.KGML_pathway.Entry property) (Bio.KEGG.KGML.KGML_pathway.Pathway property) (Bio.KEGG.KGML.KGML_pathway.Reaction property) name() (Bio.Phylo.PhyloXMLIO.Writer method) NameWidth (Bio.Restriction.PrintFormat.PrintFormat attribute) NCBICodonTable (class in Bio.Data.CodonTable) NCBICodonTableDNA (class in Bio.Data.CodonTable) NCBICodonTableRNA (class in Bio.Data.CodonTable) NeighborSearch (class in Bio.PDB.NeighborSearch) Network (class in Bio.Pathway) new_clade() (Bio.Phylo.CDAOIO.Parser method) (Bio.Phylo.NewickIO.Parser method) new_database() (BioSQL.BioSeqDatabase.DBServer method) new_graph() (Bio.Graphics.GenomeDiagram.GraphSet method) new_label() (Bio.Phylo.NeXMLIO.Writer method) new_set() (Bio.Graphics.GenomeDiagram.Track method) new_track() (Bio.Graphics.GenomeDiagram.Diagram method) NewickError NeXMLError next_nonwhitespace() (Bio.Nexus.Nexus.CharBuffer method) next_until() (Bio.Nexus.Nexus.CharBuffer method) next_word() (Bio.Nexus.Nexus.CharBuffer method) Nexus (class in Bio.Nexus.Nexus) NexusError, [1] NexusIterator() (in module Bio.AlignIO.NexusIO)

NexusWriter (class in Bio.AlignIO.NexusIO) NibIterator (class in Bio.SeqIO.NibIO) NibWriter (class in Bio.SeqIO.NibIO) nj() (Bio.Phylo.TreeConstruction.DistanceTreeConstructor method) NNITreeSearcher (class in Bio.Phylo.TreeConstruction) no_altloc (Bio.PDB.internal_coords.IC_Residue attribute) Node (class in Bio.Cluster) (class in Bio.Nexus.Nodes) (class in Bio.SCOP) node() (Bio.Nexus.Trees.Tree method) node_id() (Bio.Phylo.PhyloXMLIO.Writer method) NodeData (class in Bio.Nexus.Trees) NodeException nodes() (Bio.Pathway.Rep.Graph.Graph method) (Bio.Pathway.Rep.MultiGraph.MultiGraph method) NONE (Bio.Align.tabular.State attribute) NoneElement (class in Bio.Entrez.Parser) norm() (Bio.PDB.vectors.Vector method) normalize() (Bio.motifs.matrix.FrequencyPositionMatrix method) (Bio.PDB.vectors.Vector method) normalize_letters() (in module Bio.SCOP.Raf) normalized() (Bio.PDB.vectors.Vector method) normsq() (Bio.PDB.vectors.Vector method) NotXMLError, [1] nt_search() (in module Bio.SeqUtils) nucleotide_alphabet (Bio.Data.CodonTable.NCBICodonTable attribute) (Bio.Data.CodonTable.NCBICodonTableDNA attribute) (Bio.Data.CodonTable.NCBICodonTableRNA attribute) number (Bio.KEGG.KGML.KGML_pathway.Pathway property)

O

ok_applies_to (Bio.Phylo.PhyloXML.Property attribute) ok_datatype (Bio.Phylo.PhyloXML.Property attribute) ok_rank (Bio.Phylo.PhyloXML.Taxonomy attribute) ok_type (Bio.Phylo.PhyloXML.Events attribute) (Bio.Phylo.PhyloXML.SequenceRelation attribute) one_to_index() (in module Bio.PDB.Polypeptide) OneOfPosition (class in Bio.SeqFeature) open() (in module Bio.bgzf) open_database() (in module BioSQL.BioSeqDatabase) open_dtd_file() (Bio.Entrez.Parser.DataHandler method)

open_xsd_file() (Bio.Entrez.Parser.DataHandler method) optimize() (Bio.SeqUtils.CodonAdaptationIndex method) OrderedListElement (class in Bio.Entrez.Parser) Organism (class in Bio.Graphics.BasicChromosome) orthologs (Bio.KEGG.KGML.KGML_pathway.Pathway property) Other (class in Bio.Phylo.PhyloXML) other() (Bio.Phylo.PhyloXMLIO.Parser method) (Bio.Phylo.PhyloXMLIO.Writer method) OTHER_INTERNAL_FORMAT (Bio.GenBank.Record.Record attribute) out_block() (in module Bio.Geo.Record) OutputRecord (class in Bio.Emboss.PrimerSearch)

P

PairedFastaQualIterator() (in module Bio.SeqIO.QualityIO) PairwiseAligner (class in Bio.Align) PairwiseAlignments (class in Bio.Align) ParallelAssembleResidues (Bio.PDB.internal_coords.IC_Chain attribute) Parameters (class in Bio.Blast.NCBIXML) parent (Bio.PDB.Entity.Entity attribute) parent_edges() (Bio.Pathway.Rep.Graph.Graph method) (Bio.Pathway.Rep.MultiGraph.MultiGraph method) parents() (Bio.Pathway.Rep.Graph.Graph method) (Bio.Pathway.Rep.MultiGraph.MultiGraph method) parse() (Bio.Entrez.Parser.DataHandler method) (Bio.GenBank.FeatureParser method) (Bio.GenBank.RecordParser method) (Bio.GenBank.Scanner.InsdcScanner method) (Bio.KEGG.KGML.KGML_parser.KGMLParser method) (Bio.Phylo.CDAOIO.Parser method) (Bio.Phylo.NewickIO.Parser method) (Bio.Phylo.NeXMLIO.Parser method) (Bio.Phylo.PhyloXMLIO.Parser method) (in module Bio.Align) (in module Bio.AlignIO) (in module Bio.Blast) (in module Bio.Blast.NCBIXML) (in module Bio.Compass) (in module Bio.Emboss.Primer3) (in module Bio.Entrez) (in module Bio.ExPASy.cellosaurus) (in module Bio.ExPASy.Enzyme) (in module Bio.ExPASy.Prodoc) (in module Bio.ExPASy.Prosite) (in module Bio.GenBank) (in module Bio.Geo) (in module Bio.KEGG.Compound) (in module Bio.KEGG.Enzyme) (in module Bio.KEGG.Gene) (in module Bio.KEGG.KGML.KGML_parser) (in module Bio.KEGG.Map) (in module Bio.Medline) (in module Bio.motifs) (in module Bio.phenotype) (in module Bio.Phylo.CDAOIO) (in module Bio.Phylo.NewickIO) (in module Bio.Phylo.NeXMLIO) (in module Bio.Phylo.NexusIO) (in module Bio.Phylo.PhyloXMLIO) (in module Bio.SCOP.Cla) (in module Bio.SCOP.Des) (in module Bio.SCOP.Dom) (in module Bio.SCOP.Hie) (in module Bio.SCOP.Raf) (in module Bio.SearchIO) (in module Bio.SeqIO) (in module Bio.Sequencing.Ace) (in module Bio.Sequencing.Phd) (in module Bio.SwissProt) (in module Bio.SwissProt.KeyWList) (in module Bio.UniGene) parse_alignment_block() (Bio.SearchIO.ExonerateIO.exonerate_cigar.ExonerateCigarParser method) (Bio.SearchIO.ExonerateIO.exonerate_text.ExonerateTextParser method) (Bio.SearchIO.ExonerateIO.exonerate_vulgar.ExonerateVulgarParser method) parse_btop() (Bio.Align.tabular.AlignmentIterator method) parse_cds_features() (Bio.GenBank.Scanner.InsdcScanner method) parse_children() (Bio.Phylo.CDAOIO.Parser method) parse_cigar() (Bio.Align.tabular.AlignmentIterator method) parse_domain() (in module Bio.SCOP) parse_feature() (Bio.GenBank.Scanner.InsdcScanner method) parse_features() (Bio.GenBank.Scanner.InsdcScanner method) parse_footer() (Bio.GenBank.Scanner.EmblScanner method) (Bio.GenBank.Scanner.GenBankScanner method) (Bio.GenBank.Scanner.InsdcScanner method) parse_graph() (Bio.Phylo.CDAOIO.Parser method) parse_handle_to_graph() (Bio.Phylo.CDAOIO.Parser method) parse_header() (Bio.GenBank.Scanner.InsdcScanner method) parse_hits() (Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser method) parse_hsp_alignments() (Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser method) parse_hsps() (Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser method) parse_key_value() (Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser method) parse_pdb_header() (in module Bio.PDB.parse_pdb_header) parse_preamble() (Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser method) parse_printed_alignment() (Bio.Align.Alignment class method) parse_qresult() (Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser method) parse_records() (Bio.GenBank.Scanner.InsdcScanner method) parse_xsd() (Bio.Entrez.Parser.DataHandler method) Parser (class in Bio.ExPASy.ScanProsite) (class in Bio.Phylo.CDAOIO) (class in Bio.Phylo.NewickIO) (class in Bio.Phylo.NeXMLIO) (class in Bio.Phylo.PhyloXMLIO) ParserError ParserFailureError ParsimonyScorer (class in Bio.Phylo.TreeConstruction) ParsimonyTreeConstructor (class in Bio.Phylo.TreeConstruction) parts (Bio.SeqFeature.SimpleLocation property) Pathway (class in Bio.KEGG.KGML.KGML_pathway) pca() (in module Bio.Cluster) pcb_vectors_pymol() (Bio.PDB.HSExposure.HSExposureCA method)

pdb_date() (in module Bio.PDB.PICIO) PDB_REF (Bio.PDB.PDBList.PDBList attribute) pdb_residue_string() (Bio.PDB.internal_coords.IC_Residue method) PdbAtomIterator (class in Bio.SeqIO.PdbIO) PDBConstructionException PDBConstructionWarning PDBException PDBIO (class in Bio.PDB.PDBIO) PDBIOException PDBList (class in Bio.PDB.PDBList) PDBMLParser (class in Bio.PDB.PDBMLParser) PDBParser (class in Bio.PDB.PDBParser) PdbSeqresIterator (class in Bio.SeqIO.PdbIO) Peaklist (class in Bio.NMR.xpktools) peek() (Bio.Nexus.Nexus.CharBuffer method) peek_nonwhitespace() (Bio.Nexus.Nexus.CharBuffer method) peek_word() (Bio.Nexus.Nexus.CharBuffer method) pfam_gc_mapping (Bio.AlignIO.StockholmIO.StockholmIterator attribute) (Bio.AlignIO.StockholmIO.StockholmWriter attribute) pfam_gr_mapping (Bio.AlignIO.StockholmIO.StockholmIterator attribute) (Bio.AlignIO.StockholmIO.StockholmWriter attribute) pfam_gs_mapping (Bio.AlignIO.StockholmIO.StockholmIterator attribute) (Bio.AlignIO.StockholmIO.StockholmWriter attribute) Pgdb_dbutils (class in BioSQL.DBUtils) PhdIterator (class in Bio.SeqIO.PhdIO) PhdWriter (class in Bio.SeqIO.PhdIO) phred_quality_from_solexa() (in module Bio.SeqIO.QualityIO) PhylipIterator (class in Bio.AlignIO.PhylipIO) PhylipWriter (class in Bio.AlignIO.PhylipIO) PhyloElement (class in Bio.Phylo.PhyloXML) Phylogeny (class in Bio.Phylo.PhyloXML) phylogeny() (Bio.Phylo.PhyloXMLIO.Writer method) Phyloxml (class in Bio.Phylo.PhyloXML) phyloxml() (Bio.Phylo.PhyloXMLIO.Writer method) PhyloXMLError PhyloXMLWarning pi() (Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint method) pic_accuracy (Bio.PDB.internal_coords.IC_Residue attribute) pic_flags (Bio.PDB.internal_coords.IC_Residue attribute) picFlagsDefault (Bio.PDB.internal_coords.IC_Residue attribute) picFlagsDict (Bio.PDB.internal_coords.IC_Residue attribute) pick_angle() (Bio.PDB.internal_coords.IC_Residue method) pick_length() (Bio.PDB.internal_coords.IC_Residue method) PirIterator (class in Bio.SeqIO.PirIO) PirWriter (class in Bio.SeqIO.PirIO) PlateRecord (class in Bio.phenotype.phen_micro) Point (class in Bio.Phylo.PhyloXML) point() (Bio.Phylo.PhyloXMLIO.Parser method) (Bio.Phylo.PhyloXMLIO.Writer method) Polygon (class in Bio.Phylo.PhyloXML) polygon() (Bio.Phylo.PhyloXMLIO.Parser method) (Bio.Phylo.PhyloXMLIO.Writer method) Polypeptide (class in Bio.PDB.Polypeptide) pop() (Bio.Seq.MutableSeq method) Position (class in Bio.SeqFeature) POSITION_PADDING (Bio.SeqIO.InsdcIO.EmblWriter attribute) PositionSpecificScoringMatrix (class in Bio.motifs.matrix) PositionWeightMatrix (class in Bio.motifs.matrix) positives (Bio.Align.AlignmentCounts property) PPBuilder (class in Bio.PDB.Polypeptide) predictNOE() (in module Bio.NMR.NOEtools) prefixes (Bio.Phylo.CDAOIO.Writer attribute) PrefWidth (Bio.Restriction.PrintFormat.PrintFormat attribute) pretty_print_prediction() (in module Bio.HMM.Utilities) pretty_str() (Bio.PDB.internal_coords.IC_Residue method) Primers (class in Bio.Emboss.Primer3) print_as() (Bio.Restriction.PrintFormat.PrintFormat method) print_matrix() (in module Bio.pairwise2) print_options() (Bio.Phylo.PAML.codeml.Codeml method) print_that() (Bio.Restriction.PrintFormat.PrintFormat method) PrintFormat (class in Bio.Restriction.PrintFormat) process_asa_data() (in module Bio.PDB.NACCESS) process_clade() (Bio.Phylo.CDAOIO.Writer method) (Bio.Phylo.NewickIO.Parser method) process_rsa_data() (in module Bio.PDB.NACCESS) products (Bio.KEGG.KGML.KGML_pathway.Reaction property) propagate_changes() (Bio.PDB.internal_coords.IC_Chain method) Property (class in Bio.Phylo.PhyloXML) property() (Bio.Phylo.PhyloXMLIO.Parser method) (Bio.Phylo.PhyloXMLIO.Writer method) protein_alphabet (Bio.Data.CodonTable.NCBICodonTable attribute) protein_models (Bio.Phylo.TreeConstruction.DistanceCalculator attribute) protein_scale() (Bio.SeqUtils.ProtParam.ProteinAnalysis method) ProteinAnalysis (class in Bio.SeqUtils.ProtParam) ProteinDomain (class in Bio.Phylo.PhyloXML) ProtsimLine (class in Bio.UniGene) prune() (Bio.Nexus.Trees.Tree method) (Bio.Phylo.BaseTree.TreeMixin method) PSEA (class in Bio.PDB.PSEA) psea() (in module Bio.PDB.PSEA) psea2HEC() (in module Bio.PDB.PSEA) pseudocounts (Bio.motifs.Motif property) PSIBlast (class in Bio.Blast.NCBIXML) pssm (Bio.motifs.Motif property) Psycopg2_dbutils (class in BioSQL.DBUtils) push_back() (Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser method) pwm (Bio.motifs.Motif property)

Q

q_key (Bio.SeqIO.QualityIO.FastqIlluminaIterator attribute) (Bio.SeqIO.QualityIO.FastqIteratorAbstractBaseClass property) (Bio.SeqIO.QualityIO.FastqPhredIterator attribute) (Bio.SeqIO.QualityIO.FastqSolexaIterator attribute) q_mapping (Bio.SeqIO.QualityIO.FastqIlluminaIterator attribute) (Bio.SeqIO.QualityIO.FastqIteratorAbstractBaseClass property) (Bio.SeqIO.QualityIO.FastqPhredIterator attribute) (Bio.SeqIO.QualityIO.FastqSolexaIterator attribute) qa (class in Bio.Sequencing.Ace) qblast() (in module Bio.Blast) (in module Bio.Blast.NCBIWWW) qcp() (in module Bio.PDB.qcprot) QCPSuperimposer (class in Bio.PDB.qcprot) qend_mark (Bio.SearchIO.BlastIO.blast_xml.BlastXmlIndexer attribute) qresult_end (Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextIndexer attribute) (Bio.SearchIO.HmmerIO.hmmer3_text.Hmmer3TextIndexer attribute) qresult_start (Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextIndexer attribute) (Bio.SearchIO.HmmerIO.hmmer3_text.Hmmer3TextIndexer attribute)

qstart_mark (Bio.SearchIO.BlastIO.blast_xml.BlastXmlIndexer attribute) Qualifier (class in Bio.GenBank.Record) QUALIFIER_INDENT (Bio.SeqIO.InsdcIO.EmblWriter attribute) (Bio.SeqIO.InsdcIO.GenBankWriter attribute) (Bio.SeqIO.InsdcIO.ImgtWriter attribute) QUALIFIER_INDENT_STR (Bio.SeqIO.InsdcIO.EmblWriter attribute) (Bio.SeqIO.InsdcIO.ImgtWriter attribute) QUALIFIER_INDENT_TMP (Bio.SeqIO.InsdcIO.EmblWriter attribute) (Bio.SeqIO.InsdcIO.ImgtWriter attribute) QualPhredIterator (class in Bio.SeqIO.QualityIO) QualPhredWriter (class in Bio.SeqIO.QualityIO) quartiles() (Bio.Graphics.GenomeDiagram.GraphData method) query (Bio.Align.Alignment property) query_coverage() (Bio.Compass.Record method) QUERY_GAP (Bio.Align.tabular.State attribute) quotestrip() (in module Bio.Nexus.Nexus) qUri() (in module Bio.Phylo.CDAOIO) (in module Bio.Phylo.NeXMLIO)

R

r (Bio.SeqIO.QualityIO.InvalidCharError attribute) rak() (Bio.PDB.internal_coords.IC_Residue method) randomize() (Bio.Nexus.Trees.Tree method) randomized() (Bio.Phylo.BaseTree.Tree class method) range() (Bio.Graphics.GenomeDiagram.Diagram method) (Bio.Graphics.GenomeDiagram.FeatureSet method) (Bio.Graphics.GenomeDiagram.GraphData method) (Bio.Graphics.GenomeDiagram.GraphSet method) (Bio.Graphics.GenomeDiagram.Track method) rank() (Bio.Phylo.PhyloXMLIO.Writer method) raw() (Bio.Nexus.StandardData.StandardData method) rd (class in Bio.Sequencing.Ace) re_code (Bio.Phylo.PhyloXML.Taxonomy attribute) re_doi (Bio.Phylo.PhyloXML.Reference attribute) re_ref (Bio.Phylo.PhyloXML.Annotation attribute) (Bio.Phylo.PhyloXML.Property attribute) re_symbol (Bio.Phylo.PhyloXML.Sequence attribute) re_value (Bio.Phylo.PhyloXML.MolSeq attribute) reactant_ids (Bio.KEGG.KGML.KGML_pathway.Reaction property) reaction (Bio.KEGG.KGML.KGML_pathway.Entry property) Reaction (class in Bio.KEGG.KGML.KGML_pathway) (class in Bio.Pathway) reaction_entries (Bio.KEGG.KGML.KGML_pathway.Pathway property) reactions (Bio.KEGG.KGML.KGML_pathway.Pathway property) reactions() (Bio.Pathway.System method) read() (Bio.bgzf.BgzfReader method) (Bio.Entrez.Parser.DataHandler method) (Bio.Nexus.Nexus.Nexus method) (Bio.Phylo.PhyloXMLIO.Parser method) (in module Bio.Affy.CelFile) (in module Bio.Align) (in module Bio.Align.substitution_matrices) (in module Bio.AlignIO) (in module Bio.Blast) (in module Bio.Blast.NCBIXML) (in module Bio.Cluster) (in module Bio.Compass) (in module Bio.Emboss.Primer3) (in module Bio.Emboss.PrimerSearch) (in module Bio.Entrez) (in module Bio.ExPASy.cellosaurus) (in module Bio.ExPASy.Enzyme) (in module Bio.ExPASy.Prodoc) (in module Bio.ExPASy.Prosite) (in module Bio.ExPASy.ScanProsite) (in module Bio.GenBank) (in module Bio.KEGG.Enzyme) (in module Bio.KEGG.KGML.KGML_parser) (in module Bio.Medline) (in module Bio.motifs) (in module Bio.motifs.alignace) (in module Bio.motifs.clusterbuster) (in module Bio.motifs.jaspar) (in module Bio.motifs.mast) (in module Bio.motifs.meme) (in module Bio.motifs.minimal) (in module Bio.motifs.pfm) (in module Bio.motifs.transfac) (in module Bio.motifs.xms) (in module Bio.phenotype) (in module Bio.Phylo.PAML.baseml) (in module Bio.Phylo.PAML.codeml) (in module Bio.Phylo.PAML.yn00) (in module Bio.Phylo.PhyloXMLIO) (in module Bio.PopGen.GenePop) (in module Bio.PopGen.GenePop.FileParser) (in module Bio.PopGen.GenePop.LargeFileParser) (in module Bio.SearchIO) (in module Bio.SeqIO) (in module Bio.Sequencing.Ace) (in module Bio.Sequencing.Phd) (in module Bio.SwissProt) (in module Bio.UniGene) read_colorscheme() (Bio.Graphics.GenomeDiagram.ColorTranslator method) read_ctl_file() (Bio.Phylo.PAML.baseml.Baseml method) (Bio.Phylo.PAML.codeml.Codeml method) (Bio.Phylo.PAML.yn00.Yn00 method) read_header_fmt (Bio.SeqIO.SffIO.SffIterator attribute) read_header_size (Bio.SeqIO.SffIO.SffIterator attribute) read_next() (Bio.SearchIO.HmmerIO.hmmer2_text.Hmmer2TextParser method) read_PIC() (in module Bio.PDB.PICIO) read_PIC_seq() (in module Bio.PDB.PICIO) readline() (Bio.bgzf.BgzfReader method) ReadRocheXmlManifest() (in module Bio.SeqIO.SffIO) Reads (class in Bio.Sequencing.Ace) Record (class in Bio.Affy.CelFile) (class in Bio.Blast) (class in Bio.Cluster) (class in Bio.Compass) (class in Bio.Emboss.Primer3) (class in Bio.ExPASy.cellosaurus) (class in Bio.ExPASy.Enzyme) (class in Bio.ExPASy.Prodoc) (class in Bio.ExPASy.Prosite) (class in Bio.ExPASy.ScanProsite) (class in Bio.GenBank.Record) (class in Bio.Geo.Record) (class in Bio.KEGG.Compound) (class in Bio.KEGG.Enzyme) (class in Bio.KEGG.Gene) (class in Bio.Medline) (class in Bio.motifs.alignace) (class in Bio.motifs.clusterbuster) (class in Bio.motifs.jaspar) (class in Bio.motifs.mast) (class in Bio.motifs.meme) (class in Bio.motifs.minimal) (class in Bio.motifs.pfm) (class in Bio.motifs.transfac) (class in Bio.motifs.xms) (class in Bio.PopGen.GenePop) (class in Bio.PopGen.GenePop.LargeFileParser) (class in Bio.SCOP.Cla) (class in Bio.SCOP.Des) (class in Bio.SCOP.Dom) (class in Bio.SCOP.Hie) (class in Bio.Sequencing.Phd) (class in Bio.SwissProt) (class in Bio.SwissProt.KeyWList) (class in Bio.UniGene)

record_has() (in module Bio.UniProt.GOA) RECORD_START (Bio.GenBank.Scanner.EmblScanner attribute) (Bio.GenBank.Scanner.GenBankScanner attribute) (Bio.GenBank.Scanner.InsdcScanner attribute) RecordParser (class in Bio.GenBank) Records (class in Bio.Blast) red() (Bio.Phylo.PhyloXMLIO.Writer method) ref (Bio.SeqFeature.CompoundLocation property) ref_db (Bio.SeqFeature.CompoundLocation property) Reference (class in Bio.ExPASy.Prodoc) (class in Bio.GenBank.Record) (class in Bio.Phylo.PhyloXML) (class in Bio.SeqFeature) (class in Bio.SwissProt) reference() (Bio.Phylo.PhyloXMLIO.Parser method) (Bio.Phylo.PhyloXMLIO.Writer method) reference_keys (Bio.motifs.transfac.Motif attribute) refmat() (in module Bio.PDB.vectors) register_ncbi_table() (in module Bio.Data.CodonTable) Relation (class in Bio.KEGG.KGML.KGML_pathway) relations (Bio.KEGG.KGML.KGML_pathway.Pathway property) relative_entropy (Bio.motifs.Motif property) RelaxedPhylipIterator (class in Bio.AlignIO.PhylipIO) RelaxedPhylipWriter (class in Bio.AlignIO.PhylipIO) remove() (Bio.Seq.MutableSeq method) (BioSQL.Loader.DatabaseRemover method) remove_component() (Bio.KEGG.KGML.KGML_pathway.Entry method) remove_edge() (Bio.Pathway.Rep.Graph.Graph method) (Bio.Pathway.Rep.MultiGraph.MultiGraph method) remove_entry() (Bio.KEGG.KGML.KGML_pathway.Pathway method) remove_graphics() (Bio.KEGG.KGML.KGML_pathway.Entry method) remove_loci_by_name() (Bio.PopGen.GenePop.FileParser.FileRecord method) remove_loci_by_position() (Bio.PopGen.GenePop.FileParser.FileRecord method) remove_locus_by_name() (Bio.PopGen.GenePop.FileParser.FileRecord method) (Bio.PopGen.GenePop.Record method) remove_locus_by_position() (Bio.PopGen.GenePop.FileParser.FileRecord method) (Bio.PopGen.GenePop.Record method) remove_node() (Bio.Pathway.Rep.Graph.Graph method) (Bio.Pathway.Rep.MultiGraph.MultiGraph method) remove_population() (Bio.PopGen.GenePop.FileParser.FileRecord method) (Bio.PopGen.GenePop.Record method) remove_reaction() (Bio.KEGG.KGML.KGML_pathway.Pathway method) (Bio.Pathway.System method) remove_relation() (Bio.KEGG.KGML.KGML_pathway.Pathway method) remove_succ() (Bio.Nexus.Nodes.Node method) removeprefix() (Bio.Seq.SequenceDataAbstractBaseClass method) removesuffix() (Bio.Seq.SequenceDataAbstractBaseClass method) renumber_tracks() (Bio.Graphics.GenomeDiagram.Diagram method) replace() (Bio.Seq.SequenceDataAbstractBaseClass method) replace_entry() (in module Bio.NMR.xpktools) report_IC() (in module Bio.PDB.ic_rebuild) Res (class in Bio.SCOP.Raf) reset() (Bio.Blast.NCBIXML.BlastParser method) Residue (class in Bio.PDB.Residue) residue_depth() (in module Bio.PDB.ResidueDepth) residue_dict() (Bio.NMR.xpktools.Peaklist method) ResidueDepth (class in Bio.PDB.ResidueDepth) Residues (class in Bio.SCOP.Residues) rest() (Bio.Nexus.Nexus.CharBuffer method) retrieve_assembly_file() (Bio.PDB.PDBList.PDBList method) retrieve_pdb_file() (Bio.PDB.PDBList.PDBList method) reverse() (Bio.Pathway.Reaction method) (Bio.Seq.MutableSeq method) reverse_complement() (Bio.Align.Alignment method) (Bio.motifs.matrix.GenericPositionMatrix method) (Bio.motifs.Motif method) (Bio.SeqRecord.SeqRecord method) (in module Bio.Seq) reverse_complement_rna() (in module Bio.Seq) rewind() (Bio.Align.Alignments method) (Bio.Align.AlignmentsAbstractBaseClass method) (Bio.Align.interfaces.AlignmentIterator method) (Bio.Align.PairwiseAlignments method) rfind() (Bio.Seq.SequenceDataAbstractBaseClass method) richards() (in module Bio.phenotype.pm_fitting) right_deletions (Bio.Align.AlignmentCounts property) right_gaps (Bio.Align.AlignmentCounts property) right_insertions (Bio.Align.AlignmentCounts property) right_multiply() (Bio.PDB.vectors.Vector method) rindex() (Bio.Seq.SequenceDataAbstractBaseClass method) rollback() (BioSQL.BioSeqDatabase.Adaptor method) (BioSQL.BioSeqDatabase.DBServer method) root (Bio.Phylo.BaseTree.Clade property) root_at_midpoint() (Bio.Phylo.BaseTree.Tree method) root_with_outgroup() (Bio.Nexus.Trees.Tree method) (Bio.Phylo.BaseTree.Tree method) rotaxis() (in module Bio.PDB.vectors) rotaxis2m() (in module Bio.PDB.vectors) rotmat() (in module Bio.PDB.vectors) Round (class in Bio.Blast.NCBIXML) rsplit() (Bio.Seq.SequenceDataAbstractBaseClass method) rstrip() (Bio.Seq.SequenceDataAbstractBaseClass method) rt (class in Bio.Sequencing.Ace) run() (Bio.PDB.qcprot.QCPSuperimposer method) (Bio.Phylo.PAML.baseml.Baseml method) (Bio.Phylo.PAML.codeml.Codeml method) (Bio.Phylo.PAML.yn00.Yn00 method) (Bio.SVDSuperimposer.SVDSuperimposer method) run_naccess() (in module Bio.PDB.NACCESS) run_psea() (in module Bio.PDB.PSEA)

S

safename() (in module Bio.Nexus.Nexus) salt_correction() (in module Bio.SeqUtils.MeltingTemp) sanitize_name() (in module Bio.AlignIO.PhylipIO) save() (Bio.Cluster.Record method) (Bio.PDB.mmcifio.MMCIFIO method) (Bio.PDB.mmtf.mmtfio.MMTFIO method) (Bio.PDB.PDBIO.PDBIO method) save_dtd_file() (Bio.Entrez.Parser.DataHandler method) save_xsd_file() (Bio.Entrez.Parser.DataHandler method) scale_segment_value() (Bio.Graphics.DisplayRepresentation.ChromosomeCounts method) ScaledDPAlgorithms (class in Bio.HMM.DynamicProgramming) scan() (in module Bio.ExPASy.ScanProsite) schemaHandler() (Bio.Entrez.Parser.DataHandler method) scheme_color() (Bio.Graphics.GenomeDiagram.ColorTranslator method) scientific_name() (Bio.Phylo.PhyloXMLIO.Writer method) Scop (class in Bio.SCOP) score (Bio.pairwise2.Alignment attribute) score() (Bio.Align.CodonAligner method) (Bio.Align.PairwiseAligner method) ScoreDistribution (class in Bio.motifs.thresholds) Scorer (class in Bio.Phylo.TreeConstruction) search() (Bio.Align.bigbed.AlignmentIterator method) (Bio.AlignIO.MafIO.MafIndex method) (Bio.motifs.matrix.PositionSpecificScoringMatrix method) (Bio.PDB.NeighborSearch.NeighborSearch method) (Bio.Phylo.TreeConstruction.NNITreeSearcher method) (Bio.Phylo.TreeConstruction.TreeSearcher method) (in module Bio.SCOP) (in module Bio.TogoWS) (in module Bio.UniProt) search_all() (Bio.PDB.NeighborSearch.NeighborSearch method) search_count() (in module Bio.TogoWS) search_iter() (in module Bio.TogoWS) search_taxon() (Bio.Nexus.Trees.Tree method) secondary_structure_fraction() (Bio.SeqUtils.ProtParam.ProteinAnalysis method) seek() (Bio.bgzf.BgzfReader method) seek_position() (Bio.PopGen.GenePop.FileParser.FileRecord method) seekable() (Bio.bgzf.BgzfReader method) (Bio.bgzf.BgzfWriter method) seguid() (in module Bio.SeqUtils.CheckSum) Select (class in Bio.PDB.PDBIO) select() (Bio.Align.substitution_matrices.Array method) seq (Bio.SeqRecord.SeqRecord property) (BioSQL.BioSeq.DBSeqRecord property) Seq (class in Bio.Seq) seq1() (in module Bio.SeqUtils) seq3() (in module Bio.SeqUtils) seqA (Bio.pairwise2.Alignment attribute) seqB (Bio.pairwise2.Alignment attribute) SeqFeature (class in Bio.SeqFeature) SeqMap (class in Bio.SCOP.Raf) SeqMapIndex (class in Bio.SCOP.Raf) SeqRecord (class in Bio.SeqRecord) Sequence (class in Bio.Phylo.PhyloXML) sequence() (Bio.Phylo.PhyloXMLIO.Writer method) SEQUENCE_FORMAT (Bio.GenBank.Record.Record attribute) SEQUENCE_HEADERS (Bio.GenBank.Scanner.EmblScanner attribute) (Bio.GenBank.Scanner.GenBankScanner attribute) (Bio.GenBank.Scanner.InsdcScanner attribute) SEQUENCE_INDENT (Bio.SeqIO.InsdcIO.GenBankWriter attribute) sequence_relation() (Bio.Phylo.PhyloXMLIO.Parser method) (Bio.Phylo.PhyloXMLIO.Writer method) SequenceDataAbstractBaseClass (class in Bio.Seq) SequenceIterator (class in Bio.SeqIO.Interfaces) SequenceLine (class in Bio.UniGene) SequenceRelation (class in Bio.Phylo.PhyloXML) SequenceWriter (class in Bio.SeqIO.Interfaces) SequentialAlignmentWriter (class in Bio.AlignIO.Interfaces) SequentialPhylipIterator (class in Bio.AlignIO.PhylipIO) SequentialPhylipWriter (class in Bio.AlignIO.PhylipIO) SeqXmlIterator (class in Bio.SeqIO.SeqXmlIO) SeqXmlWriter (class in Bio.SeqIO.SeqXmlIO) set() (Bio.Nexus.Nexus.StepMatrix method) (Bio.PDB.qcprot.QCPSuperimposer method) (Bio.SVDSuperimposer.SVDSuperimposer method) set_accuracy_95() (in module Bio.PDB.internal_coords) set_all_features() (Bio.Graphics.GenomeDiagram.FeatureSet method) set_all_tracks() (Bio.Graphics.GenomeDiagram.Diagram method) set_altloc() (Bio.PDB.Atom.Atom method) set_angle() (Bio.PDB.internal_coords.IC_Residue method) set_anisou() (Bio.PDB.Atom.Atom method) (Bio.PDB.StructureBuilder.StructureBuilder method) set_atom_info() (Bio.PDB.mmtf.DefaultParser.StructureDecoder method) set_atoms() (Bio.PDB.qcprot.QCPSuperimposer method) (Bio.PDB.Superimposer.Superimposer method) set_bfactor() (Bio.PDB.Atom.Atom method) set_bio_assembly_trans() (Bio.PDB.mmtf.DefaultParser.StructureDecoder method) set_chain_info() (Bio.PDB.mmtf.DefaultParser.StructureDecoder method) set_charge() (Bio.PDB.Atom.Atom method) set_color() (Bio.Graphics.GenomeDiagram.Feature method) set_colour() (Bio.Graphics.GenomeDiagram.Feature method) set_coord() (Bio.PDB.Atom.Atom method) set_data() (Bio.Graphics.GenomeDiagram.GraphData method) (Bio.Nexus.Nodes.Node method) set_dict() (Bio.PDB.mmcifio.MMCIFIO method) set_emission_pseudocount() (Bio.HMM.MarkovModel.MarkovModelBuilder method) set_emission_score() (Bio.HMM.MarkovModel.MarkovModelBuilder method) set_entity_info() (Bio.PDB.mmtf.DefaultParser.StructureDecoder method) set_equal_probabilities() (Bio.HMM.MarkovModel.MarkovModelBuilder method) set_feature() (Bio.Graphics.GenomeDiagram.Feature method) set_flexible() (Bio.PDB.internal_coords.IC_Residue method) set_group_bond() (Bio.PDB.mmtf.DefaultParser.StructureDecoder method) set_group_info() (Bio.PDB.mmtf.DefaultParser.StructureDecoder method) set_handle() (Bio.GenBank.Scanner.InsdcScanner method) set_hbond() (Bio.PDB.internal_coords.IC_Residue method) set_header() (Bio.PDB.StructureBuilder.StructureBuilder method) set_header_info() (Bio.PDB.mmtf.DefaultParser.StructureDecoder method) set_hit_accession() (Bio.Blast.NCBIXML.BlastParser method) set_hit_def() (Bio.Blast.NCBIXML.BlastParser method) set_hit_id() (Bio.Blast.NCBIXML.BlastParser method) set_hit_len() (Bio.Blast.NCBIXML.BlastParser method) set_homog_trans_mtx() (in module Bio.PDB.vectors) set_id() (Bio.Nexus.Nodes.Node method) set_initial_probabilities() (Bio.HMM.MarkovModel.MarkovModelBuilder method) set_inter_group_bond() (Bio.PDB.mmtf.DefaultParser.StructureDecoder method) set_length() (Bio.PDB.internal_coords.Hedron method) (Bio.PDB.internal_coords.IC_Residue method) set_line_counter() (Bio.PDB.StructureBuilder.StructureBuilder method) set_model_info() (Bio.PDB.mmtf.DefaultParser.StructureDecoder method) set_occupancy() (Bio.PDB.Atom.Atom method) set_parent() (Bio.PDB.Atom.Atom method) (Bio.PDB.Entity.DisorderedEntityWrapper method) (Bio.PDB.Entity.Entity method) set_prev() (Bio.Nexus.Nodes.Node method) set_radius() (Bio.PDB.Atom.Atom method) set_random_emission_probabilities() (Bio.HMM.MarkovModel.MarkovModelBuilder method) set_random_initial_probabilities() (Bio.HMM.MarkovModel.MarkovModelBuilder method) set_random_probabilities() (Bio.HMM.MarkovModel.MarkovModelBuilder method) set_random_transition_probabilities() (Bio.HMM.MarkovModel.MarkovModelBuilder method) set_reference() (Bio.PDB.cealign.CEAligner method)

set_scale() (Bio.Graphics.DisplayRepresentation.ChromosomeCounts method) set_serial_number() (Bio.PDB.Atom.Atom method) set_sigatm() (Bio.PDB.Atom.Atom method) (Bio.PDB.StructureBuilder.StructureBuilder method) set_siguij() (Bio.PDB.Atom.Atom method) (Bio.PDB.StructureBuilder.StructureBuilder method) set_structure() (Bio.PDB.PDBIO.StructureIO method) set_subtree() (Bio.Nexus.Trees.Tree method) set_succ() (Bio.Nexus.Nodes.Node method) set_symmetry() (Bio.PDB.StructureBuilder.StructureBuilder method) set_transition_pseudocount() (Bio.HMM.MarkovModel.MarkovModelBuilder method) set_transition_score() (Bio.HMM.MarkovModel.MarkovModelBuilder method) set_X_homog_rot_mtx() (in module Bio.PDB.vectors) set_xtal_info() (Bio.PDB.mmtf.DefaultParser.StructureDecoder method) set_Y_homog_rot_mtx() (in module Bio.PDB.vectors) set_Z_homog_rot_mtx() (in module Bio.PDB.vectors) SffIterator (class in Bio.SeqIO.SffIO) SffWriter (class in Bio.SeqIO.SffIO) shape (Bio.Align.Alignment property) ShrakeRupley (class in Bio.PDB.SASA) SimpleFastaParser() (in module Bio.SeqIO.FastaIO) SimpleLocation (class in Bio.SeqFeature) sink() (Bio.Pathway.Network method) sink_interactions() (Bio.Pathway.Network method) six_frame_translations() (in module Bio.SeqUtils) skip_header() (Bio.PopGen.GenePop.FileParser.FileRecord method) skip_population() (Bio.PopGen.GenePop.FileParser.FileRecord method) skip_whitespace() (Bio.Nexus.Nexus.CharBuffer method) skipCharacterDataHandler() (Bio.Entrez.Parser.DataHandler method) smprint() (Bio.Nexus.Nexus.StepMatrix method) SnapGeneIterator (class in Bio.SeqIO.SnapGeneIO) solexa_quality_from_phred() (in module Bio.SeqIO.QualityIO) somcluster() (Bio.Cluster.Record method) (in module Bio.Cluster) sort() (Bio.Align.Alignment method) (Bio.Align.MultipleSeqAlignment method) (Bio.Cluster.Tree method) (Bio.PDB.Residue.DisorderedResidue method) (Bio.Sequencing.Ace.ACEFileRecord method) source() (Bio.Pathway.Network method) source_interactions() (Bio.Pathway.Network method) SpacerSegment (class in Bio.Graphics.BasicChromosome) speciations() (Bio.Phylo.PhyloXMLIO.Writer method) species() (Bio.Pathway.Network method) (Bio.Pathway.Reaction method) (Bio.Pathway.System method) split() (Bio.Nexus.Trees.Tree method) (Bio.Phylo.BaseTree.TreeMixin method) (Bio.Seq.SequenceDataAbstractBaseClass method) split_akl() (Bio.PDB.internal_coords.IC_Residue method) split_in_loci() (Bio.PopGen.GenePop.Record method) split_in_pops() (Bio.PopGen.GenePop.Record method) split_jaspar_id() (in module Bio.motifs.jaspar) split_virtual_offset() (in module Bio.bgzf) Sqlite_dbutils (class in BioSQL.DBUtils) ss_to_index() (in module Bio.PDB.DSSP) StandardData (class in Bio.Nexus.StandardData) start (Bio.pairwise2.Alignment attribute) (Bio.SeqFeature.CompoundLocation property) (Bio.SeqFeature.SimpleLocation property) start_codons (Bio.Data.CodonTable.CodonTable attribute) start_read() (Bio.PopGen.GenePop.FileParser.FileRecord method) startA (Bio.Graphics.GenomeDiagram.CrossLink property) startB (Bio.Graphics.GenomeDiagram.CrossLink property) startDBRefElement() (Bio.SeqIO.SeqXmlIO.ContentHandler method) startDescriptionElement() (Bio.SeqIO.SeqXmlIO.ContentHandler method) startDocument() (Bio.SeqIO.SeqXmlIO.ContentHandler method) startElement() (Bio.ExPASy.ScanProsite.ContentHandler method) startElementHandler() (Bio.Entrez.Parser.DataHandler method) startEntryElement() (Bio.SeqIO.SeqXmlIO.ContentHandler method) startEntryFieldElement() (Bio.SeqIO.SeqXmlIO.ContentHandler method) startEntryFieldElementVersion01() (Bio.SeqIO.SeqXmlIO.ContentHandler method) startNamespaceDeclHandler() (Bio.Entrez.Parser.DataHandler method) startPropertyElement() (Bio.SeqIO.SeqXmlIO.ContentHandler method) startRawElementHandler() (Bio.Entrez.Parser.DataHandler method) startSequenceElement() (Bio.SeqIO.SeqXmlIO.ContentHandler method) startSeqXMLElement() (Bio.SeqIO.SeqXmlIO.ContentHandler method) startSkipElementHandler() (Bio.Entrez.Parser.DataHandler method) startSpeciesElement() (Bio.SeqIO.SeqXmlIO.ContentHandler method) startswith() (Bio.Seq.SequenceDataAbstractBaseClass method) State (class in Bio.Align.tabular) status_characters (Bio.Align.maf.AlignmentIterator attribute) std() (Bio.motifs.matrix.PositionSpecificScoringMatrix method) stdev() (Bio.Graphics.GenomeDiagram.GraphData method) StepMatrix (class in Bio.Nexus.Nexus) stochiometry() (Bio.Pathway.System method) StockholmIterator (class in Bio.AlignIO.StockholmIO) StockholmWriter (class in Bio.AlignIO.StockholmIO) stop_codons (Bio.Data.CodonTable.CodonTable attribute) store() (Bio.Entrez.Parser.DictionaryElement method) (Bio.Entrez.Parser.ListElement method) (Bio.Entrez.Parser.OrderedListElement method) strand (Bio.SeqFeature.CompoundLocation property) (Bio.SeqFeature.SimpleLocation property) StreamModeError strict_consensus() (in module Bio.Phylo.Consensus) strictly_equals() (Bio.PDB.Atom.Atom method) (Bio.PDB.Entity.DisorderedEntityWrapper method) (Bio.PDB.Entity.Entity method) (Bio.PDB.Residue.Residue method) StringElement (class in Bio.Entrez.Parser) strings (Bio.ExPASy.ScanProsite.ContentHandler attribute) strip() (Bio.Seq.SequenceDataAbstractBaseClass method) Structure (class in Bio.PDB.Structure) structure_rebuild_test() (in module Bio.PDB.ic_rebuild) StructureAlignment (class in Bio.PDB.StructureAlignment) StructureBuilder (class in Bio.PDB.StructureBuilder) STRUCTURED_COMMENT_DELIM (Bio.GenBank.Scanner.GenBankScanner attribute) (Bio.SeqIO.InsdcIO.GenBankWriter attribute) STRUCTURED_COMMENT_END (Bio.GenBank.Scanner.GenBankScanner attribute) (Bio.SeqIO.InsdcIO.GenBankWriter attribute) STRUCTURED_COMMENT_START (Bio.GenBank.Scanner.GenBankScanner attribute) (Bio.SeqIO.InsdcIO.GenBankWriter attribute) StructureDecoder (class in Bio.PDB.mmtf.DefaultParser) StructureIO (class in Bio.PDB.PDBIO) STSLine (class in Bio.UniGene) subcomponent_size() (Bio.Graphics.BasicChromosome.Chromosome method) substitutions (Bio.Align.Alignment property) (Bio.Align.MultipleSeqAlignment property) substrates (Bio.KEGG.KGML.KGML_pathway.Reaction property) subtract_control() (Bio.phenotype.phen_micro.PlateRecord method) sum() (Bio.Nexus.Nexus.StepMatrix method) sum_branchlength() (Bio.Nexus.Trees.Tree method) SummaryInfo (class in Bio.Align.AlignInfo) Superimposer (class in Bio.PDB.Superimposer) SVDSuperimposer (class in Bio.SVDSuperimposer) SwissIterator (class in Bio.SeqIO.SwissIO) SwissProtParserError symbol() (Bio.Phylo.PhyloXMLIO.Writer method) synonym() (Bio.Phylo.PhyloXMLIO.Writer method) System (class in Bio.Pathway)

T

TabIterator (class in Bio.SeqIO.TabIO) TabWriter (class in Bio.SeqIO.TabIO) target (Bio.Align.Alignment property) TARGET_GAP (Bio.Align.tabular.State attribute) taxonomy (Bio.Phylo.PhyloXML.Clade property) Taxonomy (class in Bio.Phylo.PhyloXML) taxonomy() (Bio.Phylo.PhyloXMLIO.Writer method) tell() (Bio.bgzf.BgzfReader method) (Bio.bgzf.BgzfWriter method) TelomereSegment (class in Bio.Graphics.BasicChromosome) terminal_gap_to_missing() (Bio.Nexus.Nexus.Nexus method) three_to_index() (in module Bio.PDB.Polypeptide) threshold_balanced() (Bio.motifs.thresholds.ScoreDistribution method) threshold_fnr() (Bio.motifs.thresholds.ScoreDistribution method) threshold_fpr() (Bio.motifs.thresholds.ScoreDistribution method) threshold_patser() (Bio.motifs.thresholds.ScoreDistribution method) Tm_GC() (in module Bio.SeqUtils.MeltingTemp) Tm_NN() (in module Bio.SeqUtils.MeltingTemp) Tm_Wallace() (in module Bio.SeqUtils.MeltingTemp) tname() (BioSQL.DBUtils.Generic_dbutils method) to_alignment() (Bio.Phylo.PhyloXML.Phylogeny method) to_dict() (Bio.motifs.jaspar.Record method) (in module Bio.SearchIO) (in module Bio.SeqIO) to_generic() (Bio.Blast.NCBIXML.MultipleAlignment method) to_hex() (Bio.Phylo.BaseTree.BranchColor method) to_phylogeny() (Bio.Phylo.PhyloXML.Clade method) to_phyloxml_container() (Bio.Phylo.PhyloXML.Phylogeny method) to_rgb() (Bio.Phylo.BaseTree.BranchColor method) to_seqfeature() (Bio.Phylo.PhyloXML.ProteinDomain method) to_seqrecord() (Bio.Phylo.PhyloXML.Sequence method) to_string() (Bio.Graphics.GenomeDiagram.FeatureSet method) (Bio.Graphics.GenomeDiagram.GraphSet method) (Bio.Graphics.GenomeDiagram.Track method) (Bio.Nexus.Trees.Tree method) (Bio.SeqIO.FastaIO.FastaTwoLineWriter class method) (Bio.SeqIO.FastaIO.FastaWriter class method) (Bio.SeqIO.Interfaces.SequenceWriter class method) (Bio.SeqIO.QualityIO.FastqIlluminaWriter class method) (Bio.SeqIO.QualityIO.FastqPhredWriter class method) (Bio.SeqIO.QualityIO.FastqSolexaWriter class method) (Bio.SeqIO.QualityIO.QualPhredWriter class method) (Bio.SeqIO.TabIO.TabWriter class method) to_strings() (Bio.Phylo.NewickIO.Writer method)

toClaRecord() (Bio.SCOP.Domain method) toDesRecord() (Bio.SCOP.Domain method) (Bio.SCOP.Node method) toHieRecord() (Bio.SCOP.Node method) toMultipleSeqAlignment() (Bio.codonalign.codonalignment.CodonAlignment method) toSeq() (Bio.codonalign.codonseq.CodonSeq method) total_branch_length() (Bio.Phylo.BaseTree.TreeMixin method) trace() (Bio.Nexus.Nodes.Chain method) (Bio.Phylo.BaseTree.TreeMixin method) Track (class in Bio.Graphics.GenomeDiagram) train() (Bio.HMM.Trainer.BaumWelchTrainer method) (Bio.HMM.Trainer.KnownStateTrainer method) TrainingSequence (class in Bio.HMM.Trainer) transcribe() (in module Bio.Seq) transform() (Bio.PDB.Atom.Atom method) (Bio.PDB.Atom.DisorderedAtom method) (Bio.PDB.Entity.Entity method) transformation() (Bio.Nexus.Nexus.StepMatrix method) transitions_from() (Bio.HMM.MarkovModel.HiddenMarkovModel method) transitions_to() (Bio.HMM.MarkovModel.HiddenMarkovModel method) translate() (Bio.codonalign.codonseq.CodonSeq method) (Bio.Graphics.GenomeDiagram.ColorTranslator method) (Bio.Seq.SequenceDataAbstractBaseClass method) (Bio.SeqFeature.SeqFeature method) (Bio.SeqRecord.SeqRecord method) (in module Bio.Seq) TranslationError transpose() (Bio.Align.substitution_matrices.Array method) Tree (class in Bio.Cluster) (class in Bio.Nexus.Trees) (class in Bio.Phylo.BaseTree) (class in Bio.Phylo.CDAO) (class in Bio.Phylo.Newick) (class in Bio.Phylo.NeXML) treecluster() (Bio.Cluster.Record method) (in module Bio.Cluster) TreeConstructor (class in Bio.Phylo.TreeConstruction) TreeElement (class in Bio.Phylo.BaseTree) TreeError TreeMixin (class in Bio.Phylo.BaseTree) TreeSearcher (class in Bio.Phylo.TreeConstruction) TwoBitIterator (class in Bio.SeqIO.TwoBitIO) type() (Bio.Phylo.PhyloXMLIO.Writer method) types (Bio.Phylo.PhyloXML.Sequence attribute)

U

UncertainPosition (class in Bio.SeqFeature) UndefinedSequenceError unfold_entities() (in module Bio.PDB.Selection) ungap() (Bio.codonalign.codonseq.CodonSeq method) UniprotIterator (class in Bio.SeqIO.UniprotIO) uniqueify() (in module Bio.PDB.Selection) UnknownPosition (class in Bio.SeqFeature) unlink() (Bio.Nexus.Nodes.Chain method) unroot() (Bio.Nexus.Trees.Tree method) update() (Bio.Align.substitution_matrices.Array method)

update_dCoordSpace() (Bio.PDB.internal_coords.IC_Chain method) update_emissions() (Bio.HMM.Trainer.BaumWelchTrainer method) update_pdb() (Bio.PDB.PDBList.PDBList method) update_transitions() (Bio.HMM.Trainer.BaumWelchTrainer method) upgma() (Bio.Phylo.TreeConstruction.DistanceTreeConstructor method) upper() (Bio.Seq.SequenceDataAbstractBaseClass method) (Bio.SeqRecord.SeqRecord method) Uri (class in Bio.Phylo.PhyloXML) uri() (Bio.Phylo.PhyloXMLIO.Parser method) (Bio.Phylo.PhyloXMLIO.Writer method)

V

v_final (Bio.Graphics.ColorSpiral.ColorSpiral property) v_init (Bio.Graphics.ColorSpiral.ColorSpiral property) ValidationError value (Bio.Align.stockholm.AlignmentIterator attribute) (Bio.Phylo.PhyloXML.Confidence property) value() (Bio.Phylo.PhyloXMLIO.Writer method) values() (Bio.Align.substitution_matrices.Array method) (Bio.Phylo.PhyloXML.Events method) (BioSQL.BioSeqDatabase.BioSeqDatabase method) (BioSQL.BioSeqDatabase.DBServer method)

Vector (class in Bio.PDB.vectors) vector_to_axis() (in module Bio.PDB.vectors) version (Bio.motifs.jaspar.Motif property) version() (in module Bio.PDB.DSSP) viterbi() (Bio.HMM.MarkovModel.HiddenMarkovModel method)

W

wa (class in Bio.Sequencing.Ace) weblogo() (Bio.motifs.Motif method) weighted_stepmatrix() (Bio.Nexus.Nexus.Nexus method) weighting() (Bio.Nexus.Nexus.StepMatrix method) WellRecord (class in Bio.phenotype.phen_micro) width (Bio.KEGG.KGML.KGML_pathway.Graphics property) width() (Bio.Phylo.PhyloXMLIO.Writer method) WithinPosition (class in Bio.SeqFeature) wr (class in Bio.Sequencing.Ace) write() (Bio.Align.interfaces.AlignmentWriter method) (Bio.bgzf.BgzfWriter method) (Bio.Graphics.GenomeDiagram.Diagram method) (Bio.phenotype.phen_micro.JsonWriter method) (Bio.Phylo.CDAOIO.Writer method) (Bio.Phylo.NewickIO.Writer method) (Bio.Phylo.NeXMLIO.Writer method) (Bio.Phylo.PhyloXMLIO.Writer method) (in module Bio.Align) (in module Bio.AlignIO) (in module Bio.Blast) (in module Bio.motifs) (in module Bio.motifs.clusterbuster) (in module Bio.motifs.jaspar) (in module Bio.motifs.pfm) (in module Bio.motifs.transfac) (in module Bio.phenotype) (in module Bio.Phylo.CDAOIO) (in module Bio.Phylo.NewickIO) (in module Bio.Phylo.NeXMLIO) (in module Bio.Phylo.NexusIO) (in module Bio.Phylo.PhyloXMLIO) (in module Bio.SearchIO) (in module Bio.SeqIO) write_alignment() (Bio.Align.nexus.AlignmentWriter method) (Bio.AlignIO.ClustalIO.ClustalWriter method) (Bio.AlignIO.Interfaces.SequentialAlignmentWriter method) (Bio.AlignIO.MafIO.MafWriter method) (Bio.AlignIO.MauveIO.MauveWriter method) (Bio.AlignIO.NexusIO.NexusWriter method) (Bio.AlignIO.PhylipIO.PhylipWriter method) (Bio.AlignIO.PhylipIO.RelaxedPhylipWriter method) (Bio.AlignIO.PhylipIO.SequentialPhylipWriter method) (Bio.AlignIO.StockholmIO.StockholmWriter method) write_alignments() (Bio.Align.a2m.AlignmentWriter method) (Bio.Align.bigbed.AlignmentWriter method) (Bio.Align.interfaces.AlignmentWriter method) (Bio.Align.nexus.AlignmentWriter method) write_cla() (Bio.SCOP.Scop method) write_cla_sql() (Bio.SCOP.Scop method) write_ctl_file() (Bio.Phylo.PAML.baseml.Baseml method) (Bio.Phylo.PAML.codeml.Codeml method) (Bio.Phylo.PAML.yn00.Yn00 method) write_des() (Bio.SCOP.Scop method) write_des_sql() (Bio.SCOP.Scop method) write_file() (Bio.Align.bigbed.AlignmentWriter method) (Bio.Align.bigmaf.AlignmentWriter method) (Bio.Align.bigpsl.AlignmentWriter method) (Bio.Align.interfaces.AlignmentWriter method) (Bio.Align.mauve.AlignmentWriter method) (Bio.Align.nexus.AlignmentWriter method) (Bio.AlignIO.Interfaces.AlignmentWriter method) (Bio.AlignIO.Interfaces.SequentialAlignmentWriter method) (Bio.AlignIO.NexusIO.NexusWriter method) (Bio.SearchIO.BlastIO.blast_tab.BlastTabWriter method) (Bio.SearchIO.BlastIO.blast_xml.BlastXmlWriter method) (Bio.SearchIO.BlatIO.BlatPslWriter method) (Bio.SearchIO.HmmerIO.hmmer3_domtab.Hmmer3DomtabHmmhitWriter method) (Bio.SearchIO.HmmerIO.hmmer3_tab.Hmmer3TabWriter method) (Bio.SeqIO.Interfaces.SequenceWriter method)

write_footer() (Bio.Align.exonerate.AlignmentWriter method) (Bio.Align.interfaces.AlignmentWriter method) (Bio.AlignIO.Interfaces.SequentialAlignmentWriter method) (Bio.SeqIO.SeqXmlIO.SeqXmlWriter method) write_header() (Bio.Align.clustal.AlignmentWriter method) (Bio.Align.exonerate.AlignmentWriter method) (Bio.Align.interfaces.AlignmentWriter method) (Bio.Align.maf.AlignmentWriter method) (Bio.Align.mauve.AlignmentWriter method) (Bio.Align.psl.AlignmentWriter method) (Bio.Align.sam.AlignmentWriter method) (Bio.AlignIO.Interfaces.SequentialAlignmentWriter method) (Bio.AlignIO.MafIO.MafWriter method) (Bio.NMR.xpktools.Peaklist method) (Bio.SeqIO.NibIO.NibWriter method) (Bio.SeqIO.SeqXmlIO.SeqXmlWriter method) (Bio.SeqIO.SffIO.SffWriter method) write_hie() (Bio.SCOP.Scop method) write_hie_sql() (Bio.SCOP.Scop method) write_multiple_alignments() (Bio.Align.interfaces.AlignmentWriter method) write_nexus_data() (Bio.Nexus.Nexus.Nexus method) write_nexus_data_partitions() (Bio.Nexus.Nexus.Nexus method) write_PDB() (in module Bio.PDB.ic_rebuild) write_PIC() (in module Bio.PDB.PICIO) write_record() (Bio.SeqIO.FastaIO.FastaWriter method) (Bio.SeqIO.InsdcIO.EmblWriter method) (Bio.SeqIO.InsdcIO.GenBankWriter method) (Bio.SeqIO.Interfaces.SequenceWriter method) (Bio.SeqIO.NibIO.NibWriter method) (Bio.SeqIO.PhdIO.PhdWriter method) (Bio.SeqIO.PirIO.PirWriter method) (Bio.SeqIO.QualityIO.FastqIlluminaWriter method) (Bio.SeqIO.QualityIO.FastqPhredWriter method) (Bio.SeqIO.QualityIO.FastqSolexaWriter method) (Bio.SeqIO.QualityIO.QualPhredWriter method) (Bio.SeqIO.SeqXmlIO.SeqXmlWriter method) (Bio.SeqIO.SffIO.SffWriter method) (Bio.SeqIO.TabIO.TabWriter method) write_records() (Bio.SeqIO.AlignmentSequenceWriter method) (Bio.SeqIO.Interfaces.SequenceWriter method) (Bio.SeqIO.NibIO.NibWriter method) (Bio.SeqIO.SeqXmlIO.SeqXmlWriter method) (Bio.SeqIO.SffIO.SffWriter method) (Bio.SeqIO.XdnaIO.XdnaWriter method) write_SCAD() (in module Bio.PDB.SCADIO) write_single_alignment() (Bio.Align.interfaces.AlignmentWriter method) write_to_string() (Bio.Graphics.GenomeDiagram.Diagram method) writebyproteinrec() (in module Bio.UniProt.GOA) Writer (class in Bio.Phylo.CDAOIO) (class in Bio.Phylo.NewickIO) (class in Bio.Phylo.NeXMLIO) (class in Bio.Phylo.PhyloXMLIO) writerec() (in module Bio.UniProt.GOA) writeToSQL() (Bio.SCOP.Astral method)

X

x (Bio.KEGG.KGML.KGML_pathway.Graphics property) XdnaIterator (class in Bio.SeqIO.XdnaIO) XdnaWriter (class in Bio.SeqIO.XdnaIO)

xGC_skew() (in module Bio.SeqUtils) xmlDeclHandler() (Bio.Entrez.Parser.DataHandler method) XMSScanner (class in Bio.motifs.xms) XpkEntry (class in Bio.NMR.xpktools)

Y

y (Bio.KEGG.KGML.KGML_pathway.Graphics property)

Yn00 (class in Bio.Phylo.PAML.yn00) Yn00Error