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]
S
s
(in
Martel.test.test_swissprot38
)
set_text()
(in
IndentedText
)
start_hit_description_block()
(in
BuildSearch
)
s1
(in
Martel.test.test_swissprot38
)
set_transition_pseudocount()
(in
MarkovModelBuilder
)
start_hit_length()
(in
BuildSearch
)
s1_info
(in
Bio.expressions.blast.ncbiblast
)
set_transition_score()
(in
MarkovModelBuilder
)
start_hsp()
(in
_HSPConsumer
)
s2
(in
Martel.test.test_swissprot38
)
set_type()
(in
MultipleAlignCL
)
start_hsp()
(in
Handle_hsp
)
s2_info
(in
Bio.expressions.blast.ncbiblast
)
set_weight()
(in
AbstractLayer
)
start_hsp()
(in
Handle_hsp_seqalign
)
s3
(in
Martel.test.test_swissprot38
)
set_weight()
(in
OutputLayer
)
start_hsp_frame()
(in
Handle_hsp
)
Saf
(in
Bio
)
setCharacterSaver()
(in
DispatchHandler
)
start_hsp_seqalign()
(in
Handle_hsp_seqalign
)
saf_format
(in
Bio.Saf
)
setdefault()
(in
Crystal
)
start_hsp_seqalign_homology_seq()
(in
Handle_hsp_seqalign
)
saf_record
(in
Bio.Saf.saf_format
)
setDocumentLocator()
(in
ObjectParserHandler
)
start_hsp_seqalign_query_end()
(in
Handle_hsp_seqalign
)
safe_exp()
(in
Bio.mathfns
)
SetGroupValue
(in
Martel.Generate
)
start_hsp_seqalign_query_leader()
(in
Handle_hsp_seqalign
)
safe_int()
(in
Bio.Decode
)
setLocation()
(in
ParserException
)
start_hsp_seqalign_query_name()
(in
Handle_hsp_seqalign
)
safe_load_module()
(in
Bio.config._support
)
setName()
(in
Task
)
start_hsp_seqalign_query_seq()
(in
Handle_hsp_seqalign
)
safe_log()
(in
Bio.mathfns
)
setnode()
(in
POMDocument
)
start_hsp_seqalign_query_start()
(in
Handle_hsp_seqalign
)
safe_log2()
(in
Bio.mathfns
)
setup
(in
Bio.EUtils
)
start_hsp_seqalign_subject_end()
(in
Handle_hsp_seqalign
)
safe_peekline()
(in
Bio.ParserSupport
)
setup
(in
Martel
)
start_hsp_seqalign_subject_name()
(in
Handle_hsp_seqalign
)
safe_readline()
(in
Bio.ParserSupport
)
severity
(in
ErrorProblem
)
start_hsp_seqalign_subject_seq()
(in
Handle_hsp_seqalign
)
SafeFitnessCrossover
(in
Bio.GA.Crossover.General
)
severity
(in
FieldNotFound
)
start_hsp_seqalign_subject_start()
(in
Handle_hsp_seqalign
)
SafeFitnessMutation
(in
Bio.GA.Mutation.General
)
severity
(in
WarningProblem
)
start_hsp_strand()
(in
Handle_hsp
)
safename()
(in
Bio.Nexus.Nexus
)
SGMLExtractor
(in
Bio
)
start_hsp_value()
(in
Handle_hsp
)
sample_dir
(in
Martel.test.test_delimiter
)
SGMLExtractor
(in
Bio.SGMLExtractor
)
start_i()
(in
InterProParser
)
save()
(in
DataFile
)
SGMLExtractorHandle
(in
Bio.SGMLExtractor
)
start_i()
(in
NdbParser
)
save()
(in
Bio.MarkovModel
)
SGMLHandle
start_keywords()
(in
_ListConsumer
)
save()
(in
PDBIO
)
SGMLStripper
start_li()
(in
InterProParser
)
save_characters()
(in
DispatchHandler
)
SGMLStrippingConsumer
(in
Bio.ParserSupport
)
start_li()
(in
NdbParser
)
save_characters()
(in
Dispatcher
)
SharpEcoliIndex
(in
Bio.SeqUtils.CodonUsageIndices
)
start_locus_line()
(in
_RecordConsumer
)
save_info()
(in
GrabXPathNodes
)
ShortQueryBlastError
(in
Bio.Blast.NCBIStandalone
)
start_ol()
(in
InterProParser
)
save_key()
(in
_RecordConsumer
)
show_codes()
(in
RestrictionBatch
)
start_parameters()
(in
_ParametersConsumer
)
saveline()
(in
UndoHandle
)
show_only_between()
(in
Analysis
)
start_phenotype_block()
(in
_RecordConsumer
)
sbjct()
(in
_HSPConsumer
)
Signature
(in
Bio.NeuralNetwork.Gene
)
start_pop()
(in
_RecordConsumer
)
scale_segment_value()
(in
ChromosomeCounts
)
SignatureCoder
(in
Bio.NeuralNetwork.Gene.Signature
)
start_primer
(in
Bio.Emboss.primer3_format
)
ScaledDPAlgorithms
(in
Bio.HMM.DynamicProgramming
)
SignatureFinder
(in
Bio.NeuralNetwork.Gene.Signature
)
start_primer()
(in
_Primer3RecordConsumer
)
scan()
(in
Bio.Decode
)
sim()
(in
Motif
)
start_query_description()
(in
Handle_search_header
)
scan()
(in
Bio.GenBank.LocationParser
)
Simple
(in
Bio.GA.Mutation
)
start_query_description_block()
(in
Handle_search_header
)
scan_sequence_expasy()
(in
Bio.Prosite
)
SIMPLE
(in
MMCIF2Dict
)
start_query_size()
(in
Handle_search_header
)
Scanner
(in
Bio.AlignAce
)
Simple()
(in
Bio.expressions.swissprot.sprot38
)
start_range_contents_multiline()
(in
_RecordConsumer
)
Scanner
(in
Bio.GenBank
)
Simple()
(in
Martel.test.testformats.swissprot38
)
start_range_tag()
(in
_RecordConsumer
)
scanprosite1()
(in
Bio.WWW.ExPASy
)
simple_elem()
(in
Bio.Medline.nlmmedline_001211_format
)
start_record()
(in
_RecordConsumer
)
Scheduler
(in
Bio.MultiProc
)
simple_elem()
(in
Bio.Medline.nlmmedline_010319_format
)
start_record()
(in
_RecordConsumer
)
Scheduler
(in
Bio.MultiProc.Scheduler
)
simple_elem()
(in
Bio.Medline.nlmmedline_011101_format
)
start_record()
(in
_RecordConsumer
)
Schema
(in
Bio.NeuralNetwork.Gene
)
simple_elem()
(in
Bio.Medline.nlmmedline_031101_format
)
start_record()
(in
_RecordConsumer
)
Schema
(in
Bio.NeuralNetwork.Gene.Schema
)
SimpleFinisher
(in
Bio.NeuralNetwork.Gene.Schema
)
start_record()
(in
_RecordConsumer
)
SchemaCoder
(in
Bio.NeuralNetwork.Gene.Schema
)
SimpleIndexer
(in
Bio.Mindy.SimpleSeqRecord
)
start_record()
(in
_RecordConsumer
)
SchemaDNAAlphabet
(in
Bio.NeuralNetwork.Gene.Schema
)
SimpleRecordFilter()
(in
Martel
)
start_record()
(in
_SequenceConsumer
)
SchemaFactory
(in
Bio.NeuralNetwork.Gene.Schema
)
SimpleSeqRecord
(in
Bio.Mindy
)
start_record()
(in
BuildSeqRecord
)
SchemaFinder
(in
Bio.NeuralNetwork.Gene.Schema
)
simplify()
(in
Multicall
)
start_reference_contents_multiline()
(in
_RecordConsumer
)
SCOP
(in
Bio
)
sin
(in
Bio.Affy.CelFile
)
start_representative_contents_multiline()
(in
_RecordConsumer
)
Scop
(in
Bio.SCOP
)
sin
(in
Bio.LogisticRegression
)
start_representative_tag()
(in
_RecordConsumer
)
SCOP
(in
Bio.WWW
)
sin
(in
Bio.MarkovModel
)
start_saf_record()
(in
_RecordConsumer
)
Score
(in
Bio.EUtils.DTDs.eLink_020511
)
sin
(in
Bio.MaxEntropy
)
start_search_parameter()
(in
Handle_search_info
)
score
(in
Bio.expressions.blast.ncbiblast
)
sin
(in
Bio.NaiveBayes
)
start_search_statistic()
(in
Handle_search_info
)
score()
(in
_HSPConsumer
)
sin
(in
Bio.PDB.Vector'
)
start_search_table()
(in
Handle_search_table
)
score_hit()
(in
Motif
)
sin
(in
Bio.Statistics.lowess
)
start_search_table_description()
(in
Handle_search_table
)
scores()
(in
_Consumer
)
sin
(in
Bio.distance
)
start_search_table_entry()
(in
Handle_search_table
)
scramble()
(in
Immune
)
sin
(in
Bio.kNN
)
start_search_table_value()
(in
Handle_search_table
)
Search
(in
Bio
)
single_comment
(in
Bio.expressions.swissprot.sprot38
)
start_sequence()
(in
_RecordConsumer
)
Search
(in
Bio.Search
)
single_comment
(in
Martel.test.test_swissprot38
)
start_sequence()
(in
Handle_sequence
)
Search
(in
Bio.builders
)
single_comment
(in
Martel.test.testformats.swissprot38
)
start_sequence_block()
(in
Handle_sequence
)
search
(in
Bio.builders.Search
)
single_feature()
(in
Segment
)
start_sequence_contents_multiline()
(in
_RecordConsumer
)
search
(in
Bio.formatdefs
)
single_letter_alphabet
(in
Bio.Alphabet
)
start_sequence_tag()
(in
_RecordConsumer
)
search
(in
Bio.formatdefs.search
)
single_primer_line
(in
Bio.Emboss.primer3_format
)
start_source_contents_multiline()
(in
_RecordConsumer
)
search()
(in
DBIdsClient
)
single_primer_line()
(in
_Primer3RecordConsumer
)
start_source_tag()
(in
_RecordConsumer
)
search()
(in
HistoryClient
)
SingleLetterAlphabet
start_status_contents_multiline()
(in
_RecordConsumer
)
search()
(in
KDTree
)
SinglePointCrossover
(in
Bio.GA.Crossover.Point
)
start_status_tag()
(in
_RecordConsumer
)
search()
(in
NeighborSearch
)
SinglePositionMutation
(in
Bio.GA.Mutation.Simple
)
start_sub()
(in
NdbParser
)
search()
(in
Prosite
)
SingleToken
(in
Bio.EUtils.DTDs.eInfo_020511
)
start_table()
(in
InterProParser
)
search()
(in
AbstractCut
)
sinh
(in
Bio.Affy.CelFile
)
start_table()
(in
LocusLinkParser
)
search()
(in
RestrictionBatch
)
sinh
(in
Bio.LogisticRegression
)
start_table_entry()
(in
_RecordConsumer
)
search()
(in
Bio.WWW.SCOP
)
sinh
(in
Bio.MarkovModel
)
start_taxonomy_contents_multiline()
(in
_RecordConsumer
)
search_accum_weight()
(in
Immune
)
sinh
(in
Bio.MaxEntropy
)
start_taxonomy_tag()
(in
_RecordConsumer
)
search_all()
(in
NeighborSearch
)
sinh
(in
Bio.NaiveBayes
)
start_td()
(in
InterProParser
)
search_center_radius()
(in
KDTree
)
sinh
(in
Bio.Statistics.lowess
)
start_td()
(in
LocusLinkParser
)
search_for()
(in
Bio.PubMed
)
sinh
(in
Bio.distance
)
start_th()
(in
LocusLinkParser
)
search_header()
(in
Bio.Std
)
sinh
(in
Bio.kNN
)
start_tr()
(in
LocusLinkParser
)
search_instances()
(in
Motif
)
sink()
(in
Network
)
start_ul()
(in
InterProParser
)
search_parameter()
(in
Bio.Std
)
sink_interactions()
(in
Network
)
start_ul()
(in
NdbParser
)
search_pwm()
(in
Motif
)
SITE_FREQUENCY_LINE
(in
Bio.expressions.transfac
)
start_work()
(in
Local
)
search_statistic()
(in
Bio.Std
)
six_frame_translations()
(in
Bio.SeqUtils
)
startDocument()
(in
ObjectParserHandler
)
search_table()
(in
Bio.Std
)
size
(in
Alphabet
)
startDocument()
(in
_RecordConsumer
)
search_table_description()
(in
Bio.Std
)
size
(in
HPModel
)
startDocument()
(in
GrabXPathNodes
)
search_table_entry()
(in
Bio.Std
)
size
(in
Murphy10
)
startDocument()
(in
_RecordConsumer
)
search_table_value()
(in
Bio.Std
)
size
(in
Murphy15
)
startDocument()
(in
ConvertHandler
)
search_taxon()
(in
Tree
)
size
(in
Murphy4
)
startDocument()
(in
Dispatcher
)
SearchResult
(in
Bio.EUtils.Datatypes
)
size
(in
Murphy8
)
startDocument()
(in
StoreEvents
)
Season
(in
Bio.Medline.nlmmedline_001211_format
)
size
(in
PC5
)
startDocument()
(in
LAX
)
Season
(in
Bio.Medline.nlmmedline_010319_format
)
size
(in
SingleLetterAlphabet
)
startDocument()
(in
CheckGood
)
Season
(in
Bio.Medline.nlmmedline_011101_format
)
size
(in
ThreeLetterProtein
)
startDocument()
(in
Dump
)
Season
(in
Bio.Medline.nlmmedline_031101_format
)
size
(in
Bio.expressions.genbank
)
startDocument()
(in
GrabElements
)
Second
(in
Bio.Medline.nlmmedline_001211_format
)
size()
(in
CelRecord
)
startDocument()
(in
Capture
)
Second
(in
Bio.Medline.nlmmedline_010319_format
)
size()
(in
_FeatureConsumer
)
startDocument()
(in
GetErrorPos
)
Second
(in
Bio.Medline.nlmmedline_011101_format
)
size()
(in
_RecordConsumer
)
startElement()
(in
_XMLparser
)
Second
(in
Bio.Medline.nlmmedline_031101_format
)
SIZEHINT
(in
Martel.RecordReader
)
startElement()
(in
_AlignCreator
)
secondary_id
(in
Bio.expressions.swissprot.sprot38
)
skip_empty_group()
(in
Martel.optimize
)
startElement()
(in
ObjectParserHandler
)
secondary_key_names()
(in
_FastaFunctionIndexer
)
skip_whitespace()
(in
CharBuffer
)
startElement()
(in
_IndexerHandler
)
secondary_key_names()
(in
_FastaTitleIndexer
)
SkipLinesTo()
(in
Martel
)
startElement()
(in
GrabXPathNodes
)
secondary_key_names()
(in
BaseSeqRecordIndexer
)
SkipLinesToNoEOL()
(in
Bio.expressions.swissprot.speclist
)
startElement()
(in
EventGenerator
)
secondary_key_names()
(in
FunctionIndexer
)
SkipLinesUntil()
(in
Martel
)
startElement()
(in
ConvertHandler
)
secondary_key_names()
(in
SimpleIndexer
)
small_indent_space
(in
Bio.expressions.genbank
)
startElement()
(in
Dispatcher
)
secondary_source_id()
(in
_RecordConsumer
)
smprint()
(in
StepMatrix
)
startElement()
(in
StoreEvents
)
secondary_structure_fraction()
(in
ProteinAnalysis
)
somcluster()
(in
DataFile
)
startElement()
(in
LAX
)
SecondaryNamespace
(in
Bio.Mindy.BerkeleyDB
)
sort()
(in
DisorderedResidue
)
startElement()
(in
Dump
)
SecondaryNamespace
(in
Bio.Mindy.FlatDB
)
sort()
(in
Residue
)
startElement()
(in
CountRecords
)
SecondaryStructure
sort()
(in
ACEFileRecord
)
startElement()
(in
GrabElements
)
SecondaryTable
(in
Bio.Mindy.FlatDB
)
source()
(in
_FeatureConsumer
)
startElement()
(in
CatchFields
)
seek()
(in
ReseekFile
)
source()
(in
_RecordConsumer
)
startElement()
(in
Capture
)
seek()
(in
UndoHandle
)
source()
(in
_RecordConsumer
)
StartIntensity()
(in
CelConsumer
)
seek()
(in
Tokenizer
)
source()
(in
Network
)
StartPage
(in
Bio.Medline.nlmmedline_001211_format
)
Segment
(in
Bio.GFF
)
source()
(in
_RecordConsumer
)
StartPage
(in
Bio.Medline.nlmmedline_010319_format
)
segment
(in
Bio.expressions.blocks
)
source_block
(in
Bio.CDD.cdd_format
)
StartPage
(in
Bio.Medline.nlmmedline_011101_format
)
segment
(in
Bio.expressions.genbank
)
source_block
(in
Bio.expressions.genbank
)
StartPage
(in
Bio.Medline.nlmmedline_031101_format
)
segment()
(in
Connection
)
source_contents_line
(in
Bio.CDD.cdd_format
)
starts_with()
(in
Bio.stringfns
)
segment()
(in
_FeatureConsumer
)
source_contents_multiline
(in
Bio.CDD.cdd_format
)
StartsWith
(in
Martel.RecordReader
)
segment()
(in
_RecordConsumer
)
source_interactions()
(in
Network
)
Statistics
(in
Bio
)
segment_block
(in
Bio.expressions.blocks
)
source_key_line
(in
Bio.CDD.cdd_format
)
Statistics
(in
Bio.Wise.dnal
)
segment_line
(in
Bio.expressions.genbank
)
source_tag
(in
Bio.CDD.cdd_format
)
statistics
(in
Bio.expressions.blast.wublast
)
seguid()
(in
Bio.SeqUtils.CheckSum
)
SourceFile
(in
Bio.EUtils.sourcegen
)
status_block
(in
Bio.CDD.cdd_format
)
Select
(in
Bio.PDB.PDBIO'
)
sourcegen
(in
Bio.EUtils
)
status_contents_line
(in
Bio.CDD.cdd_format
)
select()
(in
AbstractSelection
)
SourceGen
(in
Bio.EUtils.sourcegen
)
status_contents_multiline
(in
Bio.CDD.cdd_format
)
select()
(in
DiversitySelection
)
sp_sample
(in
Martel.test.test_RecordReader
)
status_key_line
(in
Bio.CDD.cdd_format
)
select()
(in
RouletteWheelSelection
)
space
(in
Bio.Medline.nlmmedline_001211_format
)
status_tag
(in
Bio.CDD.cdd_format
)
select()
(in
TournamentSelection
)
space
(in
Bio.Medline.nlmmedline_010319_format
)
Std
(in
Bio
)
select_at_random()
(in
Immune
)
space
(in
Bio.Medline.nlmmedline_011101_format
)
stdevs()
(in
CelRecord
)
select_names()
(in
Martel
)
space
(in
Bio.Medline.nlmmedline_031101_format
)
StdHandler
(in
Bio
)
Selection
(in
Bio.GA
)
SpaceFlightMission
(in
Bio.Medline.nlmmedline_001211_format
)
StdTerm
(in
Bio.Std
)
Selection
(in
Bio.PDB
)
SpaceFlightMission
(in
Bio.Medline.nlmmedline_010319_format
)
SteadyStateEvolver
(in
Bio.GA.Evolver
)
SEMICOLONS
(in
MMCIF2Dict
)
SpaceFlightMission
(in
Bio.Medline.nlmmedline_011101_format
)
StepMatrix
(in
Bio.Nexus.Nexus
)
sentinel_line
(in
Bio.CDD.cdd_format
)
SpaceFlightMission
(in
Bio.Medline.nlmmedline_031101_format
)
stochiometry()
(in
System
)
Separator
(in
Bio.EUtils.DTDs.LinkOut
)
spaceformat
(in
Martel.test.testformats.delimiter
)
StockholmIO
(in
Bio.SeqIO
)
Seq
(in
Bio
)
Spaces()
(in
Martel
)
StockholmIterator
(in
Bio.SeqIO.StockholmIO
)
Seq
(in
Bio.Seq
)
spaces_line
(in
Bio.expressions.blast.ncbiblast
)
StockholmWriter
(in
Bio.SeqIO.StockholmIO
)
seq
(in
DBSeqRecord
)
spaces_line
(in
Bio.expressions.blast.wublast
)
stoichiometric_block
(in
Bio.MetaTool.metatool_format
)
Seq
(in
Martel.Expression
)
span()
(in
PrositeMatch
)
stoichiometric_line
(in
Bio.MetaTool.metatool_format
)
seq()
(in
Feature
)
spark
(in
Bio.Parsers
)
stoichiometric_tag
(in
Bio.MetaTool.metatool_format
)
seq()
(in
FeatureAggregate
)
spec
(in
Martel.Time
)
stoichiometric_tag()
(in
_RecordConsumer
)
Seq()
(in
Martel
)
SPECIAL_CHARS
(in
Martel.msre_parse
)
stop_codons
(in
CodonTable
)
seq3()
(in
Bio.SeqUtils
)
SPECIAL_COMMANDS
(in
Bio.Nexus.Nexus
)
stop_symbol
(in
HasStopCodon
)
seq_id
(in
Bio.Clustalw.clustal_format
)
special_list()
(in
_RecordConsumer
)
stopping_criteria()
(in
ValidationIncreaseStop
)
seq_indent
(in
Bio.Emboss.primersearch_format
)
SPECIALCOMMENTS
(in
Bio.Nexus.Nexus
)
StopTraining
(in
Bio.NeuralNetwork
)
seq_info
(in
Bio.Clustalw.clustal_format
)
species()
(in
Network
)
Storage
(in
Martel.test.support
)
seq_line
(in
Bio.Clustalw.clustal_format
)
species()
(in
Reaction
)
StoreEvents
(in
Martel.Iterator
)
seq_num
(in
Bio.Clustalw.clustal_format
)
species()
(in
System
)
Str
(in
Martel.Expression
)
seq_space
(in
Bio.Clustalw.clustal_format
)
speclist
(in
Bio.expressions.swissprot
)
Str()
(in
Martel
)
seqdb
(in
Bio.config.SeqDBRegistry
)
split()
(in
Tree
)
Str1()
(in
Martel
)
SeqDBRegistry
(in
Bio.config
)
split()
(in
RestrictionBatch
)
strand
(in
Bio.expressions.blast.ncbiblast
)
SeqDBRegistry
(in
Bio.config.SeqDBRegistry
)
split_in_loci()
(in
Record
)
strand()
(in
_HSPConsumer
)
SeqFeature
(in
Bio
)
split_in_pops()
(in
Record
)
String
(in
Bio.Decode
)
SeqFeature
(in
Bio.SeqFeature
)
splitany()
(in
Bio.stringfns
)
stringfns
(in
Bio
)
SeqIO
(in
Bio
)
SplitFDist
(in
Bio.PopGen.FDist.Async
)
StringTypes
(in
Bio.AlignAce.AlignAceStandalone
)
seqline
(in
Bio.expressions.fasta
)
SponsoringAgency
(in
Bio.Medline.nlmmedline_001211_format
)
StringTypes
(in
Bio.AlignAce.Parser
)
seqline_nonewline
(in
Bio.expressions.fasta
)
SProt
(in
Bio.SwissProt
)
StringTypes
(in
Bio.Blast.NCBIStandalone
)
SeqMap
(in
Bio.SCOP.Raf
)
sprot38
(in
Bio.expressions.swissprot
)
StringTypes
(in
Bio.Blast.NCBIWWW
)
SeqMapIndex
(in
Bio.SCOP.Raf
)
sprot38
(in
Bio.formatdefs.swissprot
)
StringTypes
(in
Bio.Compass
)
SeqMat
(in
Bio.SubsMat
)
sprot40
(in
Bio.expressions.swissprot
)
StringTypes
(in
Bio.Enzyme
)
SeqRecord
(in
Bio.SeqIO.generic
)
sprot40
(in
Bio.formatdefs.swissprot
)
StringTypes
(in
Bio.MEME.Parser
)
SeqRecord
(in
Bio
)
sprot_search_de()
(in
Bio.WWW.ExPASy
)
StringTypes
(in
Bio.Medline.NLMMedlineXML
)
SeqRecord
(in
Bio.SeqRecord
)
sprot_search_ful()
(in
Bio.WWW.ExPASy
)
StringTypes
(in
Bio.UniGene
)
SeqRecord
(in
Bio.builders
)
SQ
(in
Bio.expressions.swissprot.sprot38
)
strip
(in
Bio.EUtils.DTDs.LinkOut
)
SeqRecord
(in
Bio.writers
)
SQ
(in
Martel.test.test_swissprot38
)
strip()
(in
SGMLStripper
)
sequence
(in
Bio.Emboss.primer3_format
)
SQ
(in
Martel.test.testformats.swissprot38
)
strip()
(in
SGMLExtractor
)
sequence
(in
Bio.builders.SeqRecord
)
SQ_block
(in
Bio.expressions.embl.embl65
)
struct_wrap()
(in
Bio.KEGG.Compound
)
sequence
(in
Bio.expressions.fasta
)
SQ_data
(in
Bio.expressions.embl.embl65
)
struct_wrap()
(in
Bio.KEGG.Enzyme
)
sequence
(in
Bio.expressions.genbank
)
SQ_data
(in
Bio.expressions.swissprot.sprot38
)
Structure
(in
Bio.PDB
)
sequence
(in
Bio.expressions.swissprot.sprot38
)
SQ_data
(in
Martel.test.test_swissprot38
)
Structure
(in
Bio.PDB.Structure
)
sequence
(in
Bio.formatdefs
)
SQ_data
(in
Martel.test.testformats.swissprot38
)
structure
(in
Bio.SubsMat.MatrixInfo
)
sequence
(in
Bio.formatdefs.sequence
)
SQ_exp
(in
Bio.expressions.swissprot.sprot40
)
StructureAlignment
(in
Bio.PDB.StructureAlignment'
)
sequence
(in
Martel.test.test_swissprot38
)
SQ_line
(in
Bio.expressions.embl.embl65
)
StructureAlignment'
(in
Bio.PDB
)
sequence
(in
Martel.test.testformats.swissprot38
)
sqrt
(in
Bio.Affy.CelFile
)
StructureBuilder
(in
Bio.PDB
)
sequence()
(in
AlignAceConsumer
)
sqrt
(in
Bio.LogisticRegression
)
StructureBuilder
(in
Bio.PDB.StructureBuilder
)
sequence()
(in
FSSPAlignDict
)
sqrt
(in
Bio.MarkovModel
)
STS()
(in
_RecordConsumer
)
sequence()
(in
_FeatureConsumer
)
sqrt
(in
Bio.MaxEntropy
)
subcollection()
(in
BiblioCollection
)
sequence()
(in
_RecordConsumer
)
sqrt
(in
Bio.NaiveBayes
)
subcomponent_size()
(in
Chromosome
)
sequence()
(in
_RecordConsumer
)
sqrt
(in
Bio.PDB.ResidueDepth'
)
SubHeading
(in
Bio.Medline.nlmmedline_001211_format
)
sequence()
(in
_RecordConsumer
)
sqrt
(in
Bio.PDB.Vector'
)
SubHeading
(in
Bio.Medline.nlmmedline_010319_format
)
sequence()
(in
Bio.Std
)
sqrt
(in
Bio.SVDSuperimposer.SVDSuperimposer'
)
SubHeading
(in
Bio.Medline.nlmmedline_011101_format
)
SEQUENCE()
(in
_RecordConsumer
)
sqrt
(in
Bio.SVDSuperimposer
)
SubHeading
(in
Bio.Medline.nlmmedline_031101_format
)
sequence_block
(in
Bio.CDD.cdd_format
)
sqrt
(in
Bio.Statistics.lowess
)
subheadings()
(in
_RecordConsumer
)
sequence_block
(in
Bio.NBRF.nbrf_format
)
sqrt
(in
Bio.distance
)
subject_line
(in
Bio.expressions.blast.ncbiblast
)
sequence_block()
(in
Bio.Std
)
sqrt
(in
Bio.kNN
)
SubjectType
(in
Bio.EUtils.DTDs.LinkOut
)
sequence_contents_line
(in
Bio.CDD.cdd_format
)
SRE_FLAG_DEBUG
(in
Martel.msre_constants
)
SubjectType
(in
Bio.EUtils.DTDs.eLink_020511
)
sequence_contents_multiline
(in
Bio.CDD.cdd_format
)
SRE_FLAG_DEBUG
(in
Martel.msre_parse
)
sublocation()
(in
Location
)
sequence_data()
(in
_RecordConsumer
)
SRE_FLAG_DOTALL
(in
Martel.msre_constants
)
SubObjectSelector
(in
Bio.EUtils.DTDs.LinkOut
)
sequence_data()
(in
_SequenceConsumer
)
SRE_FLAG_DOTALL
(in
Martel.msre_parse
)
SUBPATTERN
(in
Martel.msre_constants
)
sequence_descr
(in
Bio.Emboss.primersearch_format
)
SRE_FLAG_IGNORECASE
(in
Martel.msre_constants
)
SUBPATTERN
(in
Martel.msre_parse
)
sequence_entry
(in
Bio.expressions.genbank
)
SRE_FLAG_IGNORECASE
(in
Martel.msre_parse
)
SubPattern
(in
Martel.msre_parse
)
sequence_final_line
(in
Bio.NBRF.nbrf_format
)
SRE_FLAG_LOCALE
(in
Martel.msre_constants
)
SubProvider
(in
Bio.EUtils.DTDs.LinkOut
)
sequence_final_text()
(in
_RecordConsumer
)
SRE_FLAG_LOCALE
(in
Martel.msre_parse
)
subs
(in
Bio.EUtils.DTDs.LinkOut
)
SEQUENCE_FORMAT
(in
Record
)
SRE_FLAG_MULTILINE
(in
Martel.msre_constants
)
SUBS
(in
Bio.SubsMat
)
sequence_header()
(in
_RecordConsumer
)
SRE_FLAG_MULTILINE
(in
Martel.msre_parse
)
subsets_block
(in
Bio.MetaTool.metatool_format
)
SEQUENCE_HEADERS
(in
EmblScanner
)
SRE_FLAG_TEMPLATE
(in
Martel.msre_constants
)
subsets_line
(in
Bio.MetaTool.metatool_format
)
SEQUENCE_HEADERS
(in
GenBankScanner
)
SRE_FLAG_TEMPLATE
(in
Martel.msre_parse
)
subsets_tag
(in
Bio.MetaTool.metatool_format
)
SEQUENCE_HEADERS
(in
InsdcScanner
)
SRE_FLAG_UNICODE
(in
Martel.msre_constants
)
subsets_tag()
(in
_RecordConsumer
)
sequence_id
(in
Bio.Emboss.primersearch_format
)
SRE_FLAG_UNICODE
(in
Martel.msre_parse
)
SubsMat
(in
Bio
)
sequence_info
(in
Bio.Emboss.primersearch_format
)
SRE_FLAG_VERBOSE
(in
Martel.msre_constants
)
substance_block
(in
Bio.ECell.ecell_format
)
sequence_info
(in
Bio.expressions.hmmpfam
)
SRE_FLAG_VERBOSE
(in
Martel.msre_parse
)
substance_line
(in
Bio.ECell.ecell_format
)
sequence_key_line
(in
Bio.CDD.cdd_format
)
SRE_INFO_CHARSET
(in
Martel.msre_constants
)
substance_multiline
(in
Bio.ECell.ecell_format
)
sequence_line
(in
Bio.NBRF.nbrf_format
)
SRE_INFO_CHARSET
(in
Martel.msre_parse
)
substance_multiline()
(in
_RecordConsumer
)
sequence_line
(in
Bio.expressions.genbank
)
SRE_INFO_LITERAL
(in
Martel.msre_constants
)
substance_name()
(in
_RecordConsumer
)
SEQUENCE_LINE
(in
Bio.expressions.transfac
)
SRE_INFO_LITERAL
(in
Martel.msre_parse
)
substance_tag
(in
Bio.ECell.ecell_format
)
sequence_line()
(in
_RecordConsumer
)
SRE_INFO_PREFIX
(in
Martel.msre_constants
)
subtract
(in
Bio.Affy.CelFile
)
sequence_name()
(in
_RecordConsumer
)
SRE_INFO_PREFIX
(in
Martel.msre_parse
)
subtract
(in
Bio.LogisticRegression
)
sequence_plus_spaces
(in
Bio.expressions.genbank
)
SS()
(in
Bio.expressions.transfac
)
subtract
(in
Bio.MarkovModel
)
sequence_tag
(in
Bio.CDD.cdd_format
)
ss1
(in
align
)
subtract
(in
Bio.MaxEntropy
)
sequence_text
(in
Bio.NBRF.nbrf_format
)
ss_to_index()
(in
Bio.PDB.DSSP'
)
subtract
(in
Bio.NaiveBayes
)
SEQUENCE_TYPE
(in
Bio.EUtils.Config
)
Stabilizing
(in
Bio.GA.Repair
)
subtract
(in
Bio.Statistics.lowess
)
sequence_type
(in
Bio.NBRF.nbrf_format
)
standard_aa_names
(in
Bio.PDB.DSSP'
)
subtract
(in
Bio.distance
)
sequence_type()
(in
_RecordConsumer
)
standard_aa_names
(in
Bio.PDB.FragmentMapper'
)
subtract
(in
Bio.kNN
)
sequence_types
(in
Bio.NBRF.nbrf_format
)
standard_aa_names
(in
Bio.PDB.HSExposure
)
SUCCESS
(in
Martel.msre_constants
)
SequenceDBIdsFetchMixin
(in
Bio.EUtils.DBIdsClient
)
standard_aa_names
(in
Bio.PDB.PSEA
)
SUCCESS
(in
Martel.msre_parse
)
SequenceDBIdsRecord
(in
Bio.EUtils.DBIdsClient
)
standard_aa_names
(in
Bio.PDB.Polypeptide
)
suffix
(in
Query
)
SequenceDBIdsRecordSet
(in
Bio.EUtils.DBIdsClient
)
standard_aa_names
(in
Bio.PDB.ResidueDepth'
)
Suffix
(in
Bio.Medline.nlmmedline_001211_format
)
SequenceFetchMixin
(in
Bio.EUtils.Mixins
)
standard_aa_names
(in
Bio.PDB.StructureAlignment'
)
Suffix
(in
Bio.Medline.nlmmedline_010319_format
)
SequenceHistoryFetchMixin
(in
Bio.EUtils.HistoryClient
)
standard_dna_table
(in
Bio.Data.CodonTable
)
Suffix
(in
Bio.Medline.nlmmedline_011101_format
)
SequenceHistoryRecord
(in
Bio.EUtils.HistoryClient
)
standard_rna_table
(in
Bio.Data.CodonTable
)
Suffix
(in
Bio.Medline.nlmmedline_031101_format
)
SequenceHistoryRecordSet
(in
Bio.EUtils.HistoryClient
)
standard_translator
(in
Bio.GFF
)
sum()
(in
StepMatrix
)
SequenceIterator
(in
Bio.SeqIO.Interfaces
)
Stanza
(in
Bio.config._stanzaformat
)
sum()
(in
Bio.utils
)
SequenceParser
(in
Bio.Fasta
)
StanzaFormat
(in
Bio.config._stanzaformat
)
sum_2ple()
(in
Bio.utils
)
SequenceParser
(in
Bio.SwissProt.SProt
)
start
(in
Bio.Restriction._Update.RestrictionCompiler
)
sum_branchlength()
(in
Tree
)
SequenceRecord
(in
Bio.Gobase
)
start()
(in
Location
)
sum_is_constant_block
(in
Bio.MetaTool.metatool_format
)
sequences()
(in
AlignAceConsumer
)
start()
(in
Task
)
sum_is_constant_line
(in
Bio.MetaTool.metatool_format
)
SEQUENCES_LENGTH_LINE
(in
Bio.expressions.transfac
)
start()
(in
PrositeMatch
)
sum_is_constant_line()
(in
_RecordConsumer
)
SequenceWriter
(in
Bio.SeqIO.Interfaces
)
start()
(in
LAX
)
Summary
(in
Bio.EUtils.Datatypes
)
Sequencing
(in
Bio
)
start_()
(in
Handle_search_header
)
summary()
(in
DBIdsLookup
)
SequentialSequenceWriter
(in
Bio.SeqIO.Interfaces
)
start_()
(in
Handle_search_info
)
summary()
(in
DBIdsRecord
)
SeqUtils
(in
Bio
)
start_()
(in
Handle_sequence
)
summary()
(in
HistoryLookup
)
set()
(in
StepMatrix
)
start_()
(in
BuildSearch
)
summary()
(in
HistoryRecord
)
set()
(in
SVDSuperimposer
)
start_a()
(in
InterProParser
)
summary_line
(in
Bio.CDD.cdd_format
)
set()
(in
DBObject
)
start_a()
(in
LocusLinkParser
)
summary_rec
(in
Bio.FSSP
)
set_altloc()
(in
Atom
)
start_a()
(in
ExtractUrls
)
summary_title
(in
Bio.FSSP
)
set_anisou()
(in
Atom
)
start_aa_list
(in
align
)
summary_type_parser_table
(in
Bio.EUtils.parse
)
set_anisou()
(in
StructureBuilder
)
start_accnum_block()
(in
_RecordConsumer
)
SummaryForPatientsIn
(in
Bio.Medline.nlmmedline_010319_format
)
set_atoms()
(in
Superimposer
)
start_aligned_contents_multiline()
(in
_RecordConsumer
)
SummaryForPatientsIn
(in
Bio.Medline.nlmmedline_011101_format
)
set_attribute()
(in
ElementNode
)
start_aligned_tag()
(in
_RecordConsumer
)
SummaryForPatientsIn
(in
Bio.Medline.nlmmedline_031101_format
)
set_bfactor()
(in
Atom
)
start_alignment()
(in
_AlignmentConsumer
)
SummaryForPatientsIn_end
(in
Bio.Medline.nlmmedline_010319_format
)
set_cai_index()
(in
CodonAdaptationIndex
)
start_alphabet()
(in
Handle_sequence
)
SummaryForPatientsIn_end
(in
Bio.Medline.nlmmedline_011101_format
)
set_coord()
(in
Atom
)
start_application_name()
(in
Handle_search_header
)
SummaryForPatientsIn_end
(in
Bio.Medline.nlmmedline_031101_format
)
set_coords()
(in
KDTree
)
start_application_version()
(in
Handle_search_header
)
SummaryForPatientsIn_start
(in
Bio.Medline.nlmmedline_010319_format
)
set_data()
(in
KDTree
)
start_b()
(in
LocusLinkParser
)
SummaryForPatientsIn_start
(in
Bio.Medline.nlmmedline_011101_format
)
set_data()
(in
Node
)
start_candidate_line()
(in
_RecordConsumer
)
SummaryForPatientsIn_start
(in
Bio.Medline.nlmmedline_031101_format
)
set_defaults()
(in
Immune
)
start_cd_contents_multiline()
(in
_RecordConsumer
)
SummaryInfo
(in
Bio.Align.AlignInfo
)
set_dirty()
(in
POMDocument
)
start_cd_tag()
(in
_RecordConsumer
)
superdir()
(in
Martel.Dispatch
)
set_dna_matrix()
(in
MultipleAlignCL
)
start_codons
(in
CodonTable
)
Superimposer
(in
Bio.PDB.Superimposer'
)
set_emission_pseudocount()
(in
MarkovModelBuilder
)
start_database_name()
(in
Handle_search_header
)
Superimposer'
(in
Bio.PDB
)
set_emission_score()
(in
MarkovModelBuilder
)
start_database_num_letters()
(in
Handle_search_header
)
suppl_codes()
(in
RestrictionBatch
)
set_equal_probabilities()
(in
MarkovModelBuilder
)
start_database_num_sequences()
(in
Handle_search_header
)
supplier_list()
(in
Commercially_available
)
set_guide_tree()
(in
MultipleAlignCL
)
start_database_report()
(in
_DatabaseReportConsumer
)
supplier_list()
(in
Not_available
)
set_handle()
(in
InsdcScanner
)
start_date_contents_multiline()
(in
_RecordConsumer
)
suppliers
(in
Bio.Restriction.Restriction_Dictionary
)
set_header()
(in
StructureBuilder
)
start_date_tag()
(in
_RecordConsumer
)
suppliers()
(in
Commercially_available
)
set_id()
(in
Node
)
start_db_block()
(in
_RecordConsumer
)
suppliers()
(in
Not_available
)
set_indented()
(in
ElementNode
)
start_dbid()
(in
Handle_dbid
)
suppliersdict
(in
Bio.Restriction._Update.RestrictionCompiler
)
set_inline()
(in
ElementNode
)
start_dbxref()
(in
Handle_dbxref
)
support
(in
Martel.test
)
set_interest_tags()
(in
_RecordConsumer
)
start_dbxref_dbid()
(in
Handle_dbxref
)
supports_lookahead
(in
Martel.Generate
)
set_interest_tags()
(in
_RecordConsumer
)
start_dbxref_dbname()
(in
Handle_dbxref
)
supports_lookahead
(in
Martel.test.test_Generate
)
set_interest_tags()
(in
_RecordConsumer
)
start_dbxref_negate()
(in
Handle_dbxref
)
Surrogate
set_level()
(in
ElementNode
)
start_description()
(in
Handle_description
)
SurrogateNotInitedError
set_level()
(in
IndentedText
)
start_description_block()
(in
Handle_description
)
SV_line
(in
Bio.expressions.embl.embl65
)
set_line_counter()
(in
StructureBuilder
)
start_description_contents_multiline()
(in
_RecordConsumer
)
SVDSuperimposer
(in
Bio
)
set_mask()
(in
Motif
)
start_description_tag()
(in
_RecordConsumer
)
SVDSuperimposer
(in
Bio.SVDSuperimposer.SVDSuperimposer'
)
set_namespace()
(in
ElementNode
)
start_descriptions()
(in
_DescriptionConsumer
)
SVDSuperimposer'
(in
Bio.SVDSuperimposer
)
set_new_guide_tree()
(in
MultipleAlignCL
)
start_descriptions()
(in
_PSIBlastConsumer
)
SwissIO
(in
Bio.SeqIO
)
set_occupancy()
(in
Atom
)
start_fast_dbxref()
(in
Handle_dbxref
)
SwissIterator()
(in
Bio.SeqIO.SwissIO
)
set_original_taxon_order()
(in
Nexus
)
start_feature()
(in
Handle_feature_location
)
SwissProt
(in
Bio
)
set_output()
(in
MultipleAlignCL
)
start_feature()
(in
Handle_features
)
swissprot
(in
Bio.dbdefs
)
set_parameter()
(in
AbstractCommandline
)
start_feature_block()
(in
Handle_features
)
swissprot
(in
Bio.dbdefs.swissprot
)
set_parent()
(in
Atom
)
start_feature_description()
(in
Handle_features
)
swissprot
(in
Bio.expressions
)
set_parent()
(in
DisorderedEntityWrapper
)
start_feature_location()
(in
Handle_feature_location
)
swissprot
(in
Bio.formatdefs
)
set_parent()
(in
Entity
)
start_feature_location_end()
(in
Handle_feature_location
)
swissprot
(in
Bio.formatdefs.swissprot
)
set_prev()
(in
Node
)
start_feature_location_start()
(in
Handle_feature_location
)
swissprot38
(in
Martel.test.testformats
)
set_prop
(in
Bio.Encodings.IUPACEncoding
)
start_feature_name()
(in
Handle_features
)
swissprot_expasy_cgi
(in
Bio.dbdefs.swissprot
)
set_protein_matrix()
(in
MultipleAlignCL
)
start_feature_qualifier()
(in
Handle_feature_qualifier
)
swissprot_usmirror_cgi
(in
Bio.dbdefs.swissprot
)
set_random_probabilities()
(in
MarkovModelBuilder
)
start_feature_qualifier_description()
(in
Handle_feature_qualifier
)
Symbol
(in
Bio.GenBank.LocationParser
)
set_scale()
(in
ChromosomeCounts
)
start_feature_qualifier_name()
(in
Handle_feature_qualifier
)
symbol_forward
(in
Bio.expressions.hmmpfam
)
set_serial_number()
(in
Atom
)
start_feature_table()
(in
_FeatureConsumer
)
symbol_reverse
(in
Bio.expressions.hmmpfam
)
set_sigatm()
(in
Atom
)
start_feature_table()
(in
_RecordConsumer
)
SynonymousCodons
(in
Bio.SeqUtils.CodonUsage
)
set_sigatm()
(in
StructureBuilder
)
start_h1()
(in
NdbParser
)
System
(in
Bio.Pathway
)
set_siguij()
(in
Atom
)
start_h2()
(in
InterProParser
)
system_block
(in
Bio.ECell.ecell_format
)
set_siguij()
(in
StructureBuilder
)
start_h2()
(in
NdbParser
)
system_line
(in
Bio.ECell.ecell_format
)
set_structure()
(in
PDBIO
)
start_header()
(in
_BlastConsumer
)
system_line()
(in
_RecordConsumer
)
set_subtree()
(in
Tree
)
start_header()
(in
_HeaderConsumer
)
system_tag
(in
Bio.ECell.ecell_format
)
set_succ()
(in
Node
)
start_header()
(in
_PSIBlastConsumer
)
system_to_metatool()
(in
Bio.MetaTool.Input
)
set_symmetry()
(in
StructureBuilder
)
start_hit()
(in
BuildSearch
)
set_text()
(in
Comment
)
start_hit_description()
(in
BuildSearch
)
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