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]
S
s_
(in
Bio.Affy.CelFile
)
set_data()
(in
Node
)
square
(in
Bio.distance
)
s_
(in
Bio.distance
)
set_dna_matrix()
(in
MultipleAlignCL
)
ss1
(in
align
)
safe_exp()
(in
Bio.mathfns
)
set_emission_pseudocount()
(in
MarkovModelBuilder
)
ss_to_index()
(in
Bio.PDB.DSSP'
)
safe_log()
(in
Bio.mathfns
)
set_emission_score()
(in
MarkovModelBuilder
)
Stabilizing
(in
Bio.GA.Repair
)
safe_log2()
(in
Bio.mathfns
)
set_equal_probabilities()
(in
MarkovModelBuilder
)
standard_aa_names
(in
Bio.PDB.DSSP'
)
safe_peekline()
(in
Bio.ParserSupport
)
set_feature()
(in
Feature
)
standard_aa_names
(in
Bio.PDB.FragmentMapper'
)
safe_readline()
(in
Bio.ParserSupport
)
set_guide_tree()
(in
MultipleAlignCL
)
standard_aa_names
(in
Bio.PDB.HSExposure
)
SafeFitnessCrossover
(in
Bio.GA.Crossover.General
)
set_handle()
(in
InsdcScanner
)
standard_aa_names
(in
Bio.PDB.PSEA
)
SafeFitnessMutation
(in
Bio.GA.Mutation.General
)
set_header()
(in
StructureBuilder
)
standard_aa_names
(in
Bio.PDB.Polypeptide
)
safename()
(in
Bio.Nexus.Nexus
)
set_id()
(in
Node
)
standard_aa_names
(in
Bio.PDB.ResidueDepth'
)
SANGER_SCORE_OFFSET
(in
Bio.SeqIO.QualityIO
)
set_input()
(in
_GenePopCommandline
)
standard_aa_names
(in
Bio.PDB.StructureAlignment'
)
save()
(in
Record
)
set_line_counter()
(in
StructureBuilder
)
standard_dna_table
(in
Bio.Data.CodonTable
)
save()
(in
Bio.MarkovModel
)
set_margins()
(in
AbstractDrawer
)
standard_rna_table
(in
Bio.Data.CodonTable
)
save()
(in
PDBIO
)
set_mask()
(in
Motif
)
start
(in
Bio.Restriction._Update.RestrictionCompiler
)
saveline()
(in
UndoHandle
)
set_mask()
(in
Motif
)
start
(in
FeatureLocation
)
sbjct()
(in
_HSPConsumer
)
set_menu()
(in
_GenePopCommandline
)
start()
(in
Location
)
ScalarType
(in
Bio.Affy.CelFile
)
set_new_guide_tree()
(in
MultipleAlignCL
)
start()
(in
PrositeMatch
)
ScalarType
(in
Bio.distance
)
set_occupancy()
(in
Atom
)
start_a()
(in
InterProParser
)
scale_segment_value()
(in
ChromosomeCounts
)
set_original_taxon_order()
(in
Nexus
)
start_a()
(in
ExtractUrls
)
ScaledDPAlgorithms
(in
Bio.HMM.DynamicProgramming
)
set_output()
(in
MultipleAlignCL
)
start_aa_list
(in
align
)
scan()
(in
Bio.ExPASy.ScanProsite
)
set_page_size()
(in
AbstractDrawer
)
start_alignment()
(in
_AlignmentConsumer
)
scan()
(in
Bio.GenBank.LocationParser
)
set_parameter()
(in
AbstractCommandline
)
start_codons
(in
CodonTable
)
scan_sequence_expasy()
(in
Bio.Prosite
)
set_parameter()
(in
PrimerSearchCommandline
)
start_database_report()
(in
_DatabaseReportConsumer
)
Scanner
(in
Bio.AlignAce
)
set_parent()
(in
Atom
)
start_descriptions()
(in
_DescriptionConsumer
)
Scanner
(in
Bio.GenBank
)
set_parent()
(in
DisorderedEntityWrapper
)
start_descriptions()
(in
_PSIBlastConsumer
)
ScanProsite
(in
Bio.ExPASy
)
set_parent()
(in
Entity
)
start_feature_table()
(in
_FeatureConsumer
)
scanprosite1()
(in
Bio.ExPASy
)
set_prev()
(in
Node
)
start_feature_table()
(in
_RecordConsumer
)
scanPWM()
(in
Motif
)
set_prop
(in
Bio.Encodings.IUPACEncoding
)
start_h1()
(in
NdbParser
)
Schema
(in
Bio.NeuralNetwork.Gene
)
set_protein_matrix()
(in
MultipleAlignCL
)
start_h2()
(in
InterProParser
)
Schema
(in
Bio.NeuralNetwork.Gene.Schema
)
set_random_probabilities()
(in
MarkovModelBuilder
)
start_h2()
(in
NdbParser
)
SchemaCoder
(in
Bio.NeuralNetwork.Gene.Schema
)
set_scale()
(in
ChromosomeCounts
)
start_header()
(in
_BlastConsumer
)
SchemaDNAAlphabet
(in
Bio.NeuralNetwork.Gene.Schema
)
set_serial_number()
(in
Atom
)
start_header()
(in
_HeaderConsumer
)
SchemaFactory
(in
Bio.NeuralNetwork.Gene.Schema
)
set_sigatm()
(in
Atom
)
start_header()
(in
_PSIBlastConsumer
)
SchemaFinder
(in
Bio.NeuralNetwork.Gene.Schema
)
set_sigatm()
(in
StructureBuilder
)
start_hsp()
(in
_HSPConsumer
)
scheme_color()
(in
ColorTranslator
)
set_siguij()
(in
Atom
)
start_i()
(in
InterProParser
)
SCOP
(in
Bio
)
set_siguij()
(in
StructureBuilder
)
start_i()
(in
NdbParser
)
Scop
(in
Bio.SCOP
)
set_structure()
(in
PDBIO
)
start_li()
(in
InterProParser
)
score()
(in
_HSPConsumer
)
set_subtree()
(in
Tree
)
start_li()
(in
NdbParser
)
score_hit()
(in
Motif
)
set_succ()
(in
Node
)
start_ol()
(in
InterProParser
)
score_hit()
(in
Motif
)
set_symmetry()
(in
StructureBuilder
)
start_parameters()
(in
_ParametersConsumer
)
ScoreDistribution
(in
Bio.Motif.Thresholds
)
set_track_heights()
(in
CircularDrawer
)
start_pop()
(in
_RecordConsumer
)
scores()
(in
_Consumer
)
set_track_heights()
(in
LinearDrawer
)
start_record()
(in
_RecordConsumer
)
sctypeDict
(in
Bio.Affy.CelFile
)
set_transition_pseudocount()
(in
MarkovModelBuilder
)
start_record()
(in
_RecordConsumer
)
sctypeDict
(in
Bio.distance
)
set_transition_score()
(in
MarkovModelBuilder
)
start_record()
(in
_RecordConsumer
)
sctypeNA
(in
Bio.Affy.CelFile
)
set_type()
(in
MultipleAlignCL
)
start_record()
(in
_RecordConsumer
)
sctypeNA
(in
Bio.distance
)
set_weight()
(in
AbstractLayer
)
start_record()
(in
_RecordConsumer
)
sctypes
(in
Bio.Affy.CelFile
)
set_weight()
(in
OutputLayer
)
start_record()
(in
_SequenceConsumer
)
sctypes
(in
Bio.distance
)
setdefault()
(in
Crystal
)
start_sub()
(in
NdbParser
)
Search
(in
Bio
)
SGMLHandle
(in
Bio.File
)
start_table()
(in
InterProParser
)
Search
(in
Bio.Search
)
SGMLStripper
(in
Bio.File
)
start_td()
(in
InterProParser
)
search()
(in
KDTree
)
SGMLStrippingConsumer
(in
Bio.ParserSupport
)
start_ul()
(in
InterProParser
)
search()
(in
NeighborSearch
)
SharpEcoliIndex
(in
Bio.SeqUtils.CodonUsageIndices
)
start_ul()
(in
NdbParser
)
search()
(in
Prosite
)
SHIFT_DIVIDEBYZERO
(in
Bio.Affy.CelFile
)
start_work()
(in
Local
)
search()
(in
AbstractCut
)
SHIFT_DIVIDEBYZERO
(in
Bio.distance
)
startElement()
(in
_XMLparser
)
search()
(in
RestrictionBatch
)
SHIFT_INVALID
(in
Bio.Affy.CelFile
)
startElement()
(in
DataHandler
)
search()
(in
Bio.SCOP
)
SHIFT_INVALID
(in
Bio.distance
)
startElement()
(in
ContentHandler
)
search_all()
(in
NeighborSearch
)
SHIFT_OVERFLOW
(in
Bio.Affy.CelFile
)
startElement()
(in
EventGenerator
)
search_for()
(in
Bio.PubMed
)
SHIFT_OVERFLOW
(in
Bio.distance
)
StartIntensity()
(in
CelConsumer
)
search_instances()
(in
Motif
)
SHIFT_UNDERFLOW
(in
Bio.Affy.CelFile
)
startswith()
(in
Seq
)
search_instances()
(in
Motif
)
SHIFT_UNDERFLOW
(in
Bio.distance
)
Statistics
(in
Bio
)
search_pwm()
(in
Motif
)
ShortQueryBlastError
(in
Bio.Blast.NCBIStandalone
)
Statistics
(in
Bio.Wise.dnal
)
search_pwm()
(in
Motif
)
show_codes()
(in
RestrictionBatch
)
stdev()
(in
GraphData
)
search_taxon()
(in
Tree
)
show_only_between()
(in
Analysis
)
stdevs()
(in
CelRecord
)
secondary_structure_fraction()
(in
ProteinAnalysis
)
sign
(in
Bio.Affy.CelFile
)
SteadyStateEvolver
(in
Bio.GA.Evolver
)
SecondaryStructure
(in
Bio.Alphabet
)
sign
(in
Bio.distance
)
StepMatrix
(in
Bio.Nexus.Nexus
)
seek()
(in
UndoHandle
)
Signature
(in
Bio.NeuralNetwork.Gene
)
stochiometry()
(in
System
)
Segment
(in
Bio.GFF
)
SignatureCoder
(in
Bio.NeuralNetwork.Gene.Signature
)
StockholmIO
(in
Bio.AlignIO
)
segment()
(in
Connection
)
SignatureFinder
(in
Bio.NeuralNetwork.Gene.Signature
)
StockholmIterator
(in
Bio.AlignIO.StockholmIO
)
segment()
(in
_FeatureConsumer
)
signbit
(in
Bio.Affy.CelFile
)
StockholmWriter
(in
Bio.AlignIO.StockholmIO
)
segment()
(in
_RecordConsumer
)
signbit
(in
Bio.distance
)
stop_codons
(in
CodonTable
)
seguid()
(in
Bio.SeqUtils.CheckSum
)
sim()
(in
Motif
)
stopping_criteria()
(in
ValidationIncreaseStop
)
Select
(in
Bio.PDB.PDBIO'
)
SimCoal
(in
Bio.PopGen
)
StopTraining
(in
Bio.NeuralNetwork
)
select()
(in
AbstractSelection
)
SimCoalCache
(in
Bio.PopGen.SimCoal.Async
)
strand()
(in
_HSPConsumer
)
select()
(in
DiversitySelection
)
SimCoalCache
(in
Bio.PopGen.SimCoal.Cache
)
StringElement
(in
Bio.Entrez.Parser
)
select()
(in
RouletteWheelSelection
)
SimCoalController
(in
Bio.PopGen.SimCoal.Controller
)
stringfns
(in
Bio
)
select()
(in
TournamentSelection
)
Simple
(in
Bio.GA.Mutation
)
strings
(in
ContentHandler
)
Selection
(in
Bio.GA
)
SIMPLE
(in
MMCIF2Dict
)
StringTypes
(in
Bio.AlignAce.Parser
)
Selection
(in
Bio.PDB
)
SimpleFinisher
(in
Bio.NeuralNetwork.Gene.Schema
)
StringTypes
(in
Bio.Blast.NCBIStandalone
)
SEMICOLONS
(in
MMCIF2Dict
)
sin
(in
Bio.Affy.CelFile
)
StringTypes
(in
Bio.Compass
)
Seq
(in
Bio
)
sin
(in
Bio.distance
)
StringTypes
(in
Bio.Enzyme
)
Seq
(in
Bio.Seq
)
single_feature()
(in
Segment
)
StringTypes
(in
Bio.MEME.Parser
)
seq
(in
SeqRecord
)
single_letter_alphabet
(in
Bio.Alphabet
)
StringTypes
(in
Bio.Motif.Parsers.AlignAce
)
seq
(in
DBSeqRecord
)
SingleLetterAlphabet
(in
Bio.Alphabet
)
StringTypes
(in
Bio.Motif.Parsers.MEME
)
seq()
(in
Feature
)
SinglePointCrossover
(in
Bio.GA.Crossover.Point
)
StringTypes
(in
Bio.UniGene
)
seq()
(in
FeatureAggregate
)
SinglePositionMutation
(in
Bio.GA.Mutation.Simple
)
strip()
(in
SGMLStripper
)
seq3()
(in
Bio.SeqUtils
)
sinh
(in
Bio.Affy.CelFile
)
strip()
(in
Seq
)
SEQ_TYPES
(in
TCoffeeCommandline
)
sinh
(in
Bio.distance
)
struct_wrap()
(in
Bio.KEGG.Compound
)
SeqFeature
(in
Bio
)
sink()
(in
Network
)
struct_wrap()
(in
Bio.KEGG.Enzyme
)
SeqFeature
(in
Bio.SeqFeature
)
sink_interactions()
(in
Network
)
Structure
(in
Bio.PDB
)
SeqIO
(in
Bio
)
six_frame_translations()
(in
Bio.SeqUtils
)
Structure
(in
Bio.PDB.Structure
)
SeqMap
(in
Bio.SCOP.Raf
)
size
(in
Alphabet
)
structure
(in
Bio.SubsMat.MatrixInfo
)
SeqMapIndex
(in
Bio.SCOP.Raf
)
size
(in
HPModel
)
StructureAlignment
(in
Bio.PDB.StructureAlignment'
)
SeqMat
(in
Bio.SubsMat
)
size
(in
Murphy10
)
StructureAlignment'
(in
Bio.PDB
)
SeqRecord
(in
Bio
)
size
(in
Murphy15
)
StructureBuilder
(in
Bio.PDB
)
SeqRecord
(in
Bio.SeqRecord
)
size
(in
Murphy4
)
StructureBuilder
(in
Bio.PDB.StructureBuilder
)
SeqretCommandline
(in
Bio.Emboss.Applications
)
size
(in
Murphy8
)
StructureElement
(in
Bio.Entrez.Parser
)
sequence()
(in
AlignAceConsumer
)
size
(in
PC5
)
STS()
(in
_RecordConsumer
)
sequence()
(in
FSSPAlignDict
)
size
(in
SingleLetterAlphabet
)
STSLine
(in
Bio.UniGene
)
sequence()
(in
_FeatureConsumer
)
size
(in
ThreeLetterProtein
)
subcomponent_size()
(in
Chromosome
)
sequence()
(in
_RecordConsumer
)
size()
(in
CelRecord
)
sublocation()
(in
Location
)
sequence()
(in
AlignAceConsumer
)
size()
(in
_FeatureConsumer
)
SUBS
(in
Bio.SubsMat
)
SEQUENCE()
(in
_RecordConsumer
)
size()
(in
_RecordConsumer
)
SubsMat
(in
Bio
)
sequence_data()
(in
_RecordConsumer
)
skip_whitespace()
(in
CharBuffer
)
SubstitutionMatrix
(in
Bio.SubsMat
)
sequence_data()
(in
_SequenceConsumer
)
smprint()
(in
StepMatrix
)
subtract
(in
Bio.Affy.CelFile
)
SEQUENCE_FORMAT
(in
Record
)
solexa_quality_from_phred()
(in
Bio.SeqIO.QualityIO
)
subtract
(in
Bio.distance
)
sequence_header()
(in
_RecordConsumer
)
SOLEXA_SCORE_OFFSET
(in
Bio.SeqIO.QualityIO
)
suffix
(in
Query
)
SEQUENCE_HEADERS
(in
EmblScanner
)
somcluster()
(in
Record
)
sum()
(in
StepMatrix
)
SEQUENCE_HEADERS
(in
GenBankScanner
)
sort()
(in
DisorderedResidue
)
sum()
(in
SeqMat
)
SEQUENCE_HEADERS
(in
InsdcScanner
)
sort()
(in
Residue
)
sum()
(in
Bio.utils
)
SequenceIterator
(in
Bio.SeqIO.Interfaces
)
sort()
(in
ACEFileRecord
)
sum_2ple()
(in
Bio.utils
)
SequenceLine
(in
Bio.UniGene
)
source()
(in
_FeatureConsumer
)
sum_branchlength()
(in
Tree
)
SequenceParser
(in
Bio.Fasta
)
source()
(in
_RecordConsumer
)
summary_rec
(in
Bio.FSSP
)
SequenceParser
(in
Bio.SwissProt.SProt
)
source()
(in
Network
)
summary_title
(in
Bio.FSSP
)
sequences()
(in
AlignAceConsumer
)
source_interactions()
(in
Network
)
SummaryInfo
(in
Bio.Align.AlignInfo
)
sequences()
(in
AlignAceConsumer
)
span()
(in
PrositeMatch
)
Superimposer
(in
Bio.PDB.Superimposer'
)
SequenceWriter
(in
Bio.SeqIO.Interfaces
)
spark
(in
Bio.Parsers
)
Superimposer'
(in
Bio.PDB
)
Sequencing
(in
Bio
)
SPECIAL_COMMANDS
(in
Bio.Nexus.Nexus
)
suppl_codes()
(in
RestrictionBatch
)
SequentialAlignmentWriter
(in
Bio.AlignIO.Interfaces
)
SPECIALCOMMENTS
(in
Bio.Nexus.Nexus
)
supplier_list()
(in
Commercially_available
)
SequentialSequenceWriter
(in
Bio.SeqIO.Interfaces
)
species()
(in
Network
)
supplier_list()
(in
Not_available
)
SeqUtils
(in
Bio
)
species()
(in
Reaction
)
suppliers
(in
Bio.Restriction.Restriction_Dictionary
)
set()
(in
StepMatrix
)
species()
(in
System
)
suppliers()
(in
Commercially_available
)
set()
(in
SVDSuperimposer
)
split()
(in
Tree
)
suppliers()
(in
Not_available
)
set_all_features()
(in
FeatureSet
)
split()
(in
RestrictionBatch
)
suppliersdict
(in
Bio.Restriction._Update.RestrictionCompiler
)
set_all_tracks()
(in
Diagram
)
split()
(in
Seq
)
Surrogate
set_altloc()
(in
Atom
)
split_in_loci()
(in
Record
)
SurrogateNotInitedError
set_anisou()
(in
Atom
)
split_in_pops()
(in
Record
)
SVDSuperimposer
(in
Bio
)
set_anisou()
(in
StructureBuilder
)
splitany()
(in
Bio.stringfns
)
SVDSuperimposer
(in
Bio.SVDSuperimposer.SVDSuperimposer'
)
set_atoms()
(in
Superimposer
)
SplitFDist
(in
Bio.PopGen.FDist.Async
)
SVDSuperimposer'
(in
Bio.SVDSuperimposer
)
set_bfactor()
(in
Atom
)
SProt
(in
Bio.SwissProt
)
SwissDict
(in
Bio.SeqIO._index
)
set_bounds()
(in
AbstractDrawer
)
sprot_search_de()
(in
Bio.ExPASy
)
SwissIO
(in
Bio.SeqIO
)
set_cai_index()
(in
CodonAdaptationIndex
)
sprot_search_ful()
(in
Bio.ExPASy
)
SwissIterator()
(in
Bio.SeqIO.SwissIO
)
set_color()
(in
Feature
)
sqrt
(in
Bio.Affy.CelFile
)
SwissProt
(in
Bio
)
set_colour()
(in
Feature
)
sqrt
(in
Bio.SVDSuperimposer.SVDSuperimposer'
)
Symbol
(in
Bio.GenBank.LocationParser
)
set_coord()
(in
Atom
)
sqrt
(in
Bio.SVDSuperimposer
)
SynonymousCodons
(in
Bio.SeqUtils.CodonUsage
)
set_coords()
(in
KDTree
)
sqrt
(in
Bio.distance
)
System
(in
Bio.Pathway
)
set_data()
(in
GraphData
)
square
(in
Bio.Affy.CelFile
)
Trees
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