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]
P
p_absolute_location()
(in
LocationParser
)
parse_neighbor_links()
(in
Bio.EUtils.parse
)
PrefWidth
(in
PrintFormat
)
p_arg()
(in
DecodeParser
)
parse_pdb_header'
(in
Bio.PDB
)
preorder()
(in
GenericASTTraversal
)
p_args()
(in
DecodeParser
)
parse_pdb_header()
(in
Bio.PDB.parse_pdb_header'
)
prepare_input_source()
(in
Bio.EUtils.ReseekFile
)
p_base_position()
(in
LocationParser
)
parse_post()
(in
Bio.EUtils.parse
)
preprocess()
(in
GenericASTBuilder
)
p_base_range()
(in
LocationParser
)
parse_records()
(in
InsdcScanner
)
preprocess()
(in
GenericASTMatcher
)
p_between_position()
(in
LocationParser
)
parse_search()
(in
Bio.EUtils.parse
)
preprocess()
(in
GenericParser
)
p_database()
(in
LocationParser
)
parse_simple_xpath()
(in
Bio.Mindy.XPath
)
pretty_print_prediction()
(in
Bio.HMM.Utilities
)
p_expression()
(in
DecodeParser
)
parse_single()
(in
Bio.EZRetrieve
)
primary()
(in
_RecordConsumer
)
p_feature_label()
(in
LocationParser
)
parse_str()
(in
AbstractParser
)
primary_key_name()
(in
BaseSeqRecordIndexer
)
p_feature_name()
(in
LocationParser
)
parse_string()
(in
RecordParser
)
primary_key_name()
(in
FunctionIndexer
)
p_function()
(in
LocationParser
)
parse_string()
(in
SequenceParser
)
primary_key_name()
(in
SimpleIndexer
)
p_functional_operator()
(in
LocationParser
)
parse_summary_xml()
(in
Bio.EUtils.parse
)
primary_ref_line()
(in
_RecordConsumer
)
p_high_base_bound()
(in
LocationParser
)
parse_template()
(in
Martel.msre_parse
)
PrimaryNamespace
(in
Bio.Mindy.BerkeleyDB
)
p_local_location()
(in
LocationParser
)
parse_using_dtd()
(in
UsePOMParser
)
PrimaryNamespace
(in
Bio.Mindy.FlatDB
)
p_location()
(in
LocationParser
)
ParseBlastTable
(in
Bio.Blast
)
PrimaryTable
(in
Bio.Mindy.FlatDB
)
p_location_list()
(in
LocationParser
)
parseFile()
(in
POMDocument
)
Primer
(in
Bio.Emboss
)
p_low_base_bound()
(in
LocationParser
)
parseFile()
(in
HeaderFooterParser
)
Primer3
(in
Bio.Emboss
)
p_path()
(in
LocationParser
)
parseFile()
(in
Parser
)
primer3_format
(in
Bio.Emboss
)
p_primary_accession()
(in
LocationParser
)
parseFile()
(in
RecordParser
)
Primer3Commandline
(in
Bio.Emboss.Applications
)
p_term()
(in
DecodeParser
)
parseline()
(in
DictionaryBuilder
)
Primer3Parser
(in
Bio.Emboss.Primer
)
p_two_base_bound_1()
(in
LocationParser
)
Parser
(in
Bio.AlignAce
)
Primer3Primers
(in
Bio.Emboss.Primer
)
p_two_base_bound_2()
(in
LocationParser
)
Parser
(in
Bio.Entrez
)
Primer3Record
(in
Bio.Emboss.Primer
)
pad
(in
Bio.EUtils.DTDs.LinkOut
)
Parser
(in
Bio.MEME
)
primer_name
(in
Bio.Emboss.primersearch_format
)
pagination()
(in
_RecordConsumer
)
Parser
(in
Bio.SCOP.Cla
)
primer_name()
(in
_PrimerSearchRecordConsumer
)
pairlist_to_dict()
(in
Bio.InterPro
)
Parser
(in
Bio.SCOP.Des
)
primer_name_line
(in
Bio.Emboss.primersearch_format
)
pairwise2
(in
Bio
)
Parser
(in
Bio.SCOP.Dom
)
primer_space
(in
Bio.Emboss.primer3_format
)
PalindromeCommandline
(in
Bio.Emboss.Applications
)
Parser
(in
Bio.SCOP.Hie
)
primer_start_line
(in
Bio.Emboss.primer3_format
)
Palindromic
(in
Bio.Restriction.Restriction
)
Parser
(in
Bio.SCOP.Raf
)
Primers
(in
Bio.Emboss.Primer3
)
pam120
(in
Bio.SubsMat.MatrixInfo
)
Parser
(in
Martel
)
PrimerSearch
(in
Bio.Emboss
)
pam180
(in
Bio.SubsMat.MatrixInfo
)
Parser
(in
Martel.Parser
)
primersearch_format
(in
Bio.Emboss
)
pam250
(in
Bio.SubsMat.MatrixInfo
)
ParseRecords
PrimerSearchAmplifier
(in
Bio.Emboss.Primer
)
pam30
(in
Bio.SubsMat.MatrixInfo
)
ParserException
(in
Martel.Parser
)
PrimerSearchCommandline
(in
Bio.Emboss.Applications
)
pam300
(in
Bio.SubsMat.MatrixInfo
)
ParserFailureError
PrimerSearchInputRecord
(in
Bio.Emboss.Primer
)
pam60
(in
Bio.SubsMat.MatrixInfo
)
ParserIncompleteException
(in
Martel.Parser
)
PrimerSearchOutputRecord
(in
Bio.Emboss.Primer
)
pam90
(in
Bio.SubsMat.MatrixInfo
)
ParserPositionException
(in
Martel.Parser
)
PrimerSearchParser
(in
Bio.Emboss.Primer
)
parameter()
(in
AlignAceConsumer
)
ParserRecordException
(in
Martel.Parser
)
print_as()
(in
PrintFormat
)
Parameters
(in
Bio.Blast.Record
)
Parsers
(in
Bio
)
print_debug
(in
Martel.Generate
)
parameters()
(in
AlignAceConsumer
)
ParserSupport
(in
Bio
)
print_full_mat()
(in
SeqMat
)
parent_edges()
(in
Graph
)
parseString()
(in
HeaderFooterParser
)
print_index()
(in
CodonAdaptationIndex
)
parent_edges()
(in
MultiGraph
)
parseString()
(in
Parser
)
print_info
(in
Martel.Generate
)
parents()
(in
Graph
)
parseString()
(in
RecordParser
)
print_info_content()
(in
Bio.Align.AlignInfo
)
parents()
(in
MultiGraph
)
PassThrough
print_mat()
(in
SeqMat
)
parse
(in
Bio.EUtils
)
Path
(in
Bio.GenBank.LocationParser
)
print_matrix()
(in
Bio.pairwise2
)
parse()
(in
CelParser
)
pathname()
(in
ElementNode
)
print_that()
(in
PrintFormat
)
parse()
(in
AlignAceParser
)
Pathway
(in
Bio
)
print_that()
(in
Analysis
)
parse()
(in
CompareAceParser
)
PathwayTransform
PrintFormat
(in
Bio.Restriction
)
parse()
(in
Bio.AlignIO
)
Pattern
(in
Bio.NeuralNetwork.Gene
)
PrintFormat
(in
Bio.Restriction.PrintFormat
)
parse()
(in
BlastErrorParser
)
Pattern
(in
Bio.Prosite
)
prlinks()
(in
LinkMixin
)
parse()
(in
BlastParser
)
Pattern
(in
Martel.msre_parse
)
Problem
(in
Bio.EUtils.Datatypes
)
parse()
(in
PSIBlastParser
)
pattern()
(in
_RecordConsumer
)
problem_category_mapping
(in
Bio.EUtils.Datatypes
)
parse()
(in
BlastParser
)
pattern_mapping()
(in
Bio.Prosite.Pattern
)
process_asa_data()
(in
Bio.PDB.NACCESS
)
parse()
(in
BlastParser
)
PatternHit
(in
Bio.Prosite
)
process_para()
(in
Bio.PopGen.SimCoal.Template
)
parse()
(in
Bio.Blast.NCBIXML
)
PatternIO
(in
Bio.NeuralNetwork.Gene.Pattern
)
process_row()
(in
QueryAll
)
parse()
(in
RecordParser
)
PatternRepository
(in
Bio.NeuralNetwork.Gene.Pattern
)
process_row()
(in
QueryAllFirstItem
)
parse()
(in
Bio.Decode
)
PC5
(in
Bio.Alphabet.Reduced
)
process_rsa_data()
(in
Bio.PDB.NACCESS
)
parse()
(in
POMDocument
)
pc_5_table
(in
Bio.Alphabet.Reduced
)
process_text()
(in
Bio.PopGen.SimCoal.Template
)
parse()
(in
Primer3Parser
)
pcb_vectors_pymol()
(in
HSExposureCA
)
processing_instruction()
(in
ElementNode
)
parse()
(in
PrimerSearchParser
)
PDB
(in
Bio
)
processingInstruction()
(in
ObjectParserHandler
)
parse()
(in
RecordParser
)
pdb()
(in
FSSPAlignDict
)
Prodoc
(in
Bio.Prosite
)
parse()
(in
RecordParser
)
PDB_REF
(in
PDBList
)
product_size
(in
Bio.Emboss.primer3_format
)
parse()
(in
SequenceParser
)
pdb_reference()
(in
_RecordConsumer
)
product_size()
(in
_Primer3RecordConsumer
)
parse()
(in
FeatureParser
)
pdb_res_num
(in
align
)
profilewidth()
(in
_Consumer
)
parse()
(in
Bio.GenBank.LocationParser
)
PDBConstructionException
(in
Bio.PDB.PDBExceptions
)
project()
(in
_FeatureConsumer
)
parse()
(in
RecordParser
)
PDBException
(in
Bio.PDB.PDBExceptions
)
project()
(in
_RecordConsumer
)
parse()
(in
InsdcScanner
)
PDBExceptions
(in
Bio.PDB
)
prompt_user_passwd()
(in
RebaseUpdate
)
parse()
(in
Bio.Geo
)
PDBIO
(in
Bio.PDB.PDBIO'
)
property
(in
Bio.Encodings.IUPACEncoding
)
parse()
(in
RecordParser
)
PDBIO'
(in
Bio.PDB
)
PropertyManager
(in
Bio
)
parse()
(in
InterProParser
)
PDBList
(in
Bio.PDB.PDBList'
)
PropertyManager
(in
Bio.PropertyManager
)
parse()
(in
Bio.KEGG.Compound
)
PDBList'
(in
Bio.PDB
)
prorule()
(in
_RecordConsumer
)
parse()
(in
Bio.KEGG.Enzyme
)
PDBParser
(in
Bio.PDB.PDBParser'
)
Prosite
(in
Bio
)
parse()
(in
Bio.KEGG.Map
)
PDBParser'
(in
Bio.PDB
)
Prosite
(in
Bio.Prosite.Pattern
)
parse()
(in
MASTParser
)
Peaklist
(in
Bio.NMR.xpktools
)
prosite_alphabet
(in
Bio.Prosite.Pattern
)
parse()
(in
MEMEParser
)
peek()
(in
CharBuffer
)
prosite_re
(in
Bio.Prosite.Pattern
)
parse()
(in
RecordParser
)
peek_nonwhitespace()
(in
CharBuffer
)
prosite_reference()
(in
_RecordConsumer
)
parse()
(in
Bio.Medline
)
peek_word()
(in
CharBuffer
)
prosite_reference()
(in
_RecordConsumer
)
parse()
(in
RecordParser
)
peekline()
(in
UndoHandle
)
prosite_term_re
(in
Bio.Prosite.Pattern
)
parse()
(in
RecordParser
)
percent_monomers()
(in
Bio.utils
)
prosite_to_grouped_re()
(in
Bio.Prosite.Pattern
)
parse()
(in
NdbParser
)
personal_name_as_subject()
(in
_RecordConsumer
)
prosite_to_re()
(in
Bio.Prosite.Pattern
)
parse()
(in
AbstractParser
)
pfam_gr_mapping
(in
StockholmIterator
)
PrositeAlphabet
(in
Bio.Prosite.Pattern
)
parse()
(in
GenericParser
)
pfam_gr_mapping
(in
StockholmWriter
)
PrositeMatch
(in
Bio.Prosite.Pattern
)
parse()
(in
RecordParser
)
pfam_gs_mapping
(in
StockholmIterator
)
PrositeTerm
(in
Bio.Prosite.Pattern
)
parse()
(in
RecordParser
)
pfam_gs_mapping
(in
StockholmWriter
)
protein
(in
Bio.Alphabet.IUPAC
)
parse()
(in
Bio.PopGen.GenePop
)
Pgdb_dbutils
(in
BioSQL.DBUtils
)
Protein20Random
(in
Bio.Align.AlignInfo
)
parse()
(in
RecordParser
)
Phd
(in
Bio.Sequencing
)
protein_alphabet
(in
CodonTable
)
parse()
(in
Bio.Prosite.Prodoc
)
PhdIO
(in
Bio.SeqIO
)
protein_alphabet
(in
NCBICodonTable
)
parse()
(in
RecordParser
)
PhdIterator()
(in
Bio.SeqIO.PhdIO
)
protein_existence()
(in
_RecordConsumer
)
parse()
(in
Bio.Prosite
)
PhraseIgnored
(in
Bio.EUtils.DTDs.eSearch_020511
)
protein_letters
(in
Bio.Data.IUPACData
)
parse()
(in
Parser
)
PhraseIgnored
(in
Bio.EUtils.Datatypes
)
PROTEIN_MATRIX
(in
MultipleAlignCL
)
parse()
(in
Bio.SCOP.Cla
)
PhraseNotFound
(in
Bio.EUtils.DTDs.eSearch_020511
)
protein_scale()
(in
ProteinAnalysis
)
parse()
(in
Parser
)
PhraseNotFound
(in
Bio.EUtils.Datatypes
)
protein_weight_ranges
(in
Bio.Data.IUPACData
)
parse()
(in
Bio.SCOP.Des
)
phred_version()
(in
_RecordConsumer
)
protein_weights
(in
Bio.Data.IUPACData
)
parse()
(in
Parser
)
PhylipIO
(in
Bio.AlignIO
)
ProteinAlphabet
(in
Bio.Alphabet
)
parse()
(in
Bio.SCOP.Dom
)
PhylipIterator
(in
Bio.AlignIO.PhylipIO
)
ProteinAnalysis
(in
Bio.SeqUtils.ProtParam
)
parse()
(in
Parser
)
PhylipWriter
(in
Bio.AlignIO.PhylipIO
)
ProteinX
(in
Bio.SeqUtils
)
parse()
(in
Bio.SCOP.Hie
)
pi
(in
Bio.Affy.CelFile
)
proteinX
(in
Bio.SeqUtils
)
parse()
(in
Parser
)
pi
(in
Bio.distance
)
ProtParam
(in
Bio.SeqUtils
)
parse()
(in
Bio.SCOP.Raf
)
pi()
(in
IsoelectricPoint
)
ProtParamData
(in
Bio.SeqUtils
)
parse()
(in
RecordParser
)
pid()
(in
_FeatureConsumer
)
PROTSIM()
(in
_RecordConsumer
)
parse()
(in
Bio.SeqIO
)
pid()
(in
_RecordConsumer
)
Provider
(in
Bio.EUtils.DTDs.LinkOut
)
parse()
(in
ACEParser
)
PINF
(in
Bio.Affy.CelFile
)
Provider
(in
Bio.EUtils.DTDs.eLink_020511
)
parse()
(in
RecordParser
)
PINF
(in
Bio.distance
)
Provider
(in
Bio.EUtils.Datatypes
)
parse()
(in
Bio.Sequencing.Ace
)
PirIO
(in
Bio.SeqIO
)
ProviderId
(in
Bio.EUtils.DTDs.LinkOut
)
parse()
(in
RecordParser
)
PirIterator()
(in
Bio.SeqIO.PirIO
)
prune()
(in
Tree
)
parse()
(in
Bio.Sequencing.Phd
)
pKcterminal
(in
Bio.SeqUtils.IsoelectricPoint
)
prune()
(in
GenericASTTraversal
)
parse()
(in
ListParser
)
pKnterminal
(in
Bio.SeqUtils.IsoelectricPoint
)
PSEA
(in
Bio.PDB
)
parse()
(in
Bio.SwissProt.KeyWList
)
PLUS_STRAND
(in
Bio.EUtils
)
PSEA
(in
Bio.PDB.PSEA
)
parse()
(in
RecordParser
)
Point
(in
Bio.GA.Crossover
)
psea()
(in
Bio.PDB.PSEA
)
parse()
(in
SequenceParser
)
Polypeptide
(in
Bio.PDB
)
psea2HEC()
(in
Bio.PDB.PSEA
)
parse()
(in
Bio.SwissProt
)
Polypeptide
(in
Bio.PDB.Polypeptide
)
PSIBlast
(in
Bio.Blast.Record
)
parse()
(in
RecordParser
)
POM
(in
Bio.EUtils
)
PSIBlastParser
(in
Bio.Blast.NCBIStandalone
)
parse()
(in
Bio.Wise.psw
)
POMDocument
PSSM
(in
Bio.Align.AlignInfo
)
parse()
(in
HeaderFooterParser
)
pop()
(in
MutableSeq
)
psw
(in
Bio.Wise
)
parse()
(in
Parser
)
PopGen
(in
Bio
)
Psycopg2_dbutils
(in
BioSQL.DBUtils
)
parse()
(in
RecordParser
)
popitem()
(in
Crystal
)
Psycopg_dbutils
(in
BioSQL.DBUtils
)
parse()
(in
Martel.msre_parse
)
pos_align_list2dict()
(in
FSSPAlignRec
)
publication_date()
(in
_RecordConsumer
)
parse_cds_features()
(in
InsdcScanner
)
pos_specific_score_matrix()
(in
SummaryInfo
)
PUBLICATION_TYPE
(in
Bio.EUtils.Config
)
parse_domain()
(in
Bio.SCOP
)
PosAlign
(in
Bio.FSSP
)
publication_type()
(in
_RecordConsumer
)
parse_feature()
(in
InsdcScanner
)
PositionGap
(in
Bio.SeqFeature
)
PublicationDBIdsFetchMixin
(in
Bio.EUtils.DBIdsClient
)
parse_features()
(in
InsdcScanner
)
positive_alignment()
(in
_Consumer
)
PublicationDBIdsRecord
(in
Bio.EUtils.DBIdsClient
)
parse_fetch_identifiers()
(in
Bio.EUtils.parse
)
positive_pKs
(in
Bio.SeqUtils.IsoelectricPoint
)
PublicationDBIdsRecordSet
(in
Bio.EUtils.DBIdsClient
)
parse_fetch_publication_xml()
(in
Bio.EUtils.parse
)
post()
(in
HistoryClient
)
PublicationFetchMixin
(in
Bio.EUtils.Mixins
)
parse_fetch_sequence_xml()
(in
Bio.EUtils.parse
)
posted_date()
(in
_DatabaseReportConsumer
)
PublicationHistoryFetchMixin
(in
Bio.EUtils.HistoryClient
)
parse_file()
(in
Bio.Clustalw
)
postorder()
(in
GenericASTTraversal
)
PublicationHistoryRecord
(in
Bio.EUtils.HistoryClient
)
parse_file()
(in
Bio.Fasta.FastaAlign
)
postprocessing()
(in
_RecordConsumer
)
PublicationHistoryRecordSet
(in
Bio.EUtils.HistoryClient
)
parse_file()
(in
AbstractParser
)
PostResult
(in
Bio.EUtils.Datatypes
)
PubMed
(in
Bio
)
parse_footer()
(in
EmblScanner
)
power
(in
Bio.Affy.CelFile
)
pubmed_id()
(in
_FeatureConsumer
)
parse_footer()
(in
GenBankScanner
)
power
(in
Bio.distance
)
pubmed_id()
(in
_RecordConsumer
)
parse_footer()
(in
InsdcScanner
)
PPBuilder
(in
Bio.PDB.Polypeptide
)
pubmed_id()
(in
_RecordConsumer
)
parse_header()
(in
InsdcScanner
)
PRECISION_BRANCHLENGTH
(in
Bio.Nexus.Trees
)
PUNCTUATION
(in
Bio.Nexus.Nexus
)
parse_lcheck()
(in
Bio.EUtils.parse
)
PRECISION_SUPPORT
(in
Bio.Nexus.Trees
)
Punctuation()
(in
Martel
)
parse_line()
(in
Bio.Wise.psw
)
predict()
(in
BasicNetwork
)
pwm()
(in
Motif
)
parse_link_xml()
(in
Bio.EUtils.parse
)
predictNOE()
(in
Bio.NMR.NOEtools
)
PZERO
(in
Bio.Affy.CelFile
)
parse_llinks()
(in
Bio.EUtils.parse
)
prefix
(in
Query
)
PZERO
(in
Bio.distance
)
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