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P
p_absolute_location()
(in
LocationParser
)
parse_records()
(in
InsdcScanner
)
postorder()
(in
GenericASTTraversal
)
p_base_position()
(in
LocationParser
)
parse_siteclass_omegas()
(in
Bio.Phylo.PAML._parse_codeml
)
power
(in
Bio.Affy.CelFile
)
p_base_range()
(in
LocationParser
)
parse_siteclass_proportions()
(in
Bio.Phylo.PAML._parse_codeml
)
PPBuilder
(in
Bio.PDB.Polypeptide
)
p_between_position()
(in
LocationParser
)
parse_str()
(in
AbstractParser
)
PpiI
(in
Bio.Restriction.Restriction
)
p_database()
(in
LocationParser
)
parse_yn00()
(in
Bio.Phylo.PAML._parse_yn00
)
PpsI
(in
Bio.Restriction.Restriction
)
p_feature_label()
(in
LocationParser
)
ParseBlastTable
(in
Bio.Blast
)
Ppu10I
(in
Bio.Restriction.Restriction
)
p_feature_name()
(in
LocationParser
)
parseline()
(in
DictionaryBuilder
)
Ppu21I
(in
Bio.Restriction.Restriction
)
p_function()
(in
LocationParser
)
Parser
(in
Bio.Entrez
)
PpuMI
(in
Bio.Restriction.Restriction
)
p_functional_operator()
(in
LocationParser
)
Parser
(in
Bio.ExPASy.ScanProsite
)
PrankCommandline
(in
Bio.Align.Applications._Prank
)
p_high_base_bound()
(in
LocationParser
)
Parser
(in
Bio.Phylo.NewickIO
)
PRECISION_BRANCHLENGTH
(in
Bio.Nexus.Trees
)
p_local_location()
(in
LocationParser
)
Parser
(in
Bio.Phylo.PhyloXMLIO
)
PRECISION_SUPPORT
(in
Bio.Nexus.Trees
)
p_location()
(in
LocationParser
)
Parser
(in
Bio.SeqIO.UniprotIO
)
predict()
(in
BasicNetwork
)
p_location_list()
(in
LocationParser
)
ParserFailureError
predictNOE()
(in
Bio.NMR.NOEtools
)
p_low_base_bound()
(in
LocationParser
)
Parsers
(in
Bio.Motif
)
prefix
(in
Query
)
p_path()
(in
LocationParser
)
Parsers
(in
Bio
)
prefix
(in
Bio.Phylo.PhyloXMLIO
)
p_primary_accession()
(in
LocationParser
)
ParserSupport
(in
Bio
)
PrefWidth
(in
PrintFormat
)
p_two_base_bound_1()
(in
LocationParser
)
PasI
(in
Bio.Restriction.Restriction
)
preorder()
(in
GenericASTTraversal
)
p_two_base_bound_2()
(in
LocationParser
)
Path
(in
Bio.GenBank.LocationParser
)
preprocess()
(in
GenericASTBuilder
)
PabI
(in
Bio.Restriction.Restriction
)
Pathway
(in
Bio
)
preprocess()
(in
GenericASTMatcher
)
PacI
(in
Bio.Restriction.Restriction
)
Pattern
(in
Bio.NeuralNetwork.Gene
)
preprocess()
(in
GenericParser
)
PaeI
(in
Bio.Restriction.Restriction
)
PatternIO
(in
Bio.NeuralNetwork.Gene.Pattern
)
pretty_print_prediction()
(in
Bio.HMM.Utilities
)
PaeR7I
(in
Bio.Restriction.Restriction
)
PatternRepository
(in
Bio.NeuralNetwork.Gene.Pattern
)
primary()
(in
_RecordConsumer
)
page_sizes()
(in
Bio.Graphics.GenomeDiagram._AbstractDrawer
)
PauI
(in
Bio.Restriction.Restriction
)
primary_ref_line()
(in
_RecordConsumer
)
PagI
(in
Bio.Restriction.Restriction
)
PC5
(in
Bio.Alphabet.Reduced
)
Primer3
(in
Bio.Emboss
)
PairedFastaQualIterator()
(in
Bio.SeqIO.QualityIO
)
pc_5_table
(in
Bio.Alphabet.Reduced
)
Primer3Commandline
(in
Bio.Emboss.Applications
)
pairwise2
(in
Bio
)
pcb_vectors_pymol()
(in
HSExposureCA
)
Primers
(in
Bio.Emboss.Primer3
)
PalAI
(in
Bio.Restriction.Restriction
)
PceI
(in
Bio.Restriction.Restriction
)
PrimerSearch
(in
Bio.Emboss
)
PalindromeCommandline
(in
Bio.Emboss.Applications
)
PciI
(in
Bio.Restriction.Restriction
)
PrimerSearchCommandline
(in
Bio.Emboss.Applications
)
Palindromic
(in
Bio.Restriction.Restriction
)
PciSI
(in
Bio.Restriction.Restriction
)
print_as()
(in
PrintFormat
)
pam120
(in
Bio.SubsMat.MatrixInfo
)
PctI
(in
Bio.Restriction.Restriction
)
print_full_mat()
(in
SeqMat
)
pam180
(in
Bio.SubsMat.MatrixInfo
)
PDB
(in
Bio
)
print_index()
(in
CodonAdaptationIndex
)
pam250
(in
Bio.SubsMat.MatrixInfo
)
pdb()
(in
FSSPAlignDict
)
print_info_content()
(in
Bio.Align.AlignInfo
)
pam30
(in
Bio.SubsMat.MatrixInfo
)
PDB_REF
(in
PDBList
)
print_item()
(in
UniGeneParser
)
pam300
(in
Bio.SubsMat.MatrixInfo
)
pdb_res_num
(in
align
)
print_mat()
(in
SeqMat
)
pam60
(in
Bio.SubsMat.MatrixInfo
)
PDBConstructionException
(in
Bio.PDB.PDBExceptions
)
print_matrix()
(in
Bio.pairwise2
)
pam90
(in
Bio.SubsMat.MatrixInfo
)
PDBConstructionWarning
(in
Bio.PDB.PDBExceptions
)
print_options()
(in
Paml
)
PAML
(in
Bio.Phylo
)
PDBException
(in
Bio.PDB.PDBExceptions
)
print_options()
(in
Codeml
)
Paml
(in
Bio.Phylo.PAML._paml
)
PDBExceptions
(in
Bio.PDB
)
print_tags()
(in
UniGeneParser
)
PamlError
(in
Bio.Phylo.PAML._paml
)
PDBIO
(in
Bio.PDB.PDBIO'
)
print_that()
(in
PrintFormat
)
Parameters
(in
Bio.Blast.Record
)
PDBIO'
(in
Bio.PDB
)
print_that()
(in
Analysis
)
parent_edges()
(in
Graph
)
PDBList
(in
Bio.PDB.PDBList'
)
PrintFormat
(in
Bio.Restriction
)
parent_edges()
(in
MultiGraph
)
PDBList'
(in
Bio.PDB
)
PrintFormat
(in
Bio.Restriction.PrintFormat
)
parents()
(in
Graph
)
PDBParser
(in
Bio.PDB.PDBParser'
)
ProbconsCommandline
(in
Bio.Align.Applications._Probcons
)
parents()
(in
MultiGraph
)
PDBParser'
(in
Bio.PDB
)
process_asa_data()
(in
Bio.PDB.NACCESS
)
parse()
(in
CelParser
)
PdiI
(in
Bio.Restriction.Restriction
)
process_para()
(in
Bio.PopGen.SimCoal.Template
)
parse()
(in
Bio.AlignIO
)
PdmI
(in
Bio.Restriction.Restriction
)
process_row()
(in
QueryAll
)
parse()
(in
BlastErrorParser
)
Peaklist
(in
Bio.NMR.xpktools
)
process_row()
(in
QueryAllFirstItem
)
parse()
(in
BlastParser
)
peek()
(in
CharBuffer
)
process_rsa_data()
(in
Bio.PDB.NACCESS
)
parse()
(in
PSIBlastParser
)
peek_nonwhitespace()
(in
CharBuffer
)
process_text()
(in
Bio.PopGen.SimCoal.Template
)
parse()
(in
Bio.Blast.NCBIXML
)
peek_word()
(in
CharBuffer
)
Prodoc
(in
Bio.ExPASy
)
parse()
(in
RecordParser
)
peekline()
(in
UndoHandle
)
profilewidth()
(in
_Consumer
)
parse()
(in
Bio.Compass
)
pfam_gr_mapping
(in
StockholmIterator
)
project()
(in
_FeatureConsumer
)
parse()
(in
Bio.Emboss.Primer3
)
pfam_gr_mapping
(in
StockholmWriter
)
project()
(in
_RecordConsumer
)
parse()
(in
DataHandler
)
pfam_gs_mapping
(in
StockholmIterator
)
prompt_user_passwd()
(in
RebaseUpdate
)
parse()
(in
Bio.Entrez
)
pfam_gs_mapping
(in
StockholmWriter
)
Property
(in
Bio.Phylo.PhyloXML
)
parse()
(in
Bio.ExPASy.Enzyme
)
PfeI
(in
Bio.Restriction.Restriction
)
property()
(in
Parser
)
parse()
(in
Bio.ExPASy.Prodoc
)
Pfl1108I
(in
Bio.Restriction.Restriction
)
property()
(in
Writer
)
parse()
(in
Bio.ExPASy.Prosite
)
Pfl23II
(in
Bio.Restriction.Restriction
)
Prosite
(in
Bio.ExPASy
)
parse()
(in
FeatureParser
)
PflFI
(in
Bio.Restriction.Restriction
)
protein
(in
Bio.Alphabet.IUPAC
)
parse()
(in
Bio.GenBank.LocationParser
)
PflMI
(in
Bio.Restriction.Restriction
)
Protein20Random
(in
Bio.Align.AlignInfo
)
parse()
(in
RecordParser
)
PfoI
(in
Bio.Restriction.Restriction
)
protein_alphabet
(in
CodonTable
)
parse()
(in
InsdcScanner
)
Pgdb_dbutils
(in
BioSQL.DBUtils
)
protein_alphabet
(in
NCBICodonTable
)
parse()
(in
Bio.Geo
)
Phd
(in
Bio.Sequencing
)
protein_letters
(in
Bio.Data.IUPACData
)
parse()
(in
Bio.KEGG.Compound
)
PhdIO
(in
Bio.SeqIO
)
protein_scale()
(in
ProteinAnalysis
)
parse()
(in
Bio.KEGG.Enzyme
)
PhdIterator()
(in
Bio.SeqIO.PhdIO
)
protein_weight_ranges
(in
Bio.Data.IUPACData
)
parse()
(in
Bio.KEGG.Map
)
PhdWriter
(in
Bio.SeqIO.PhdIO
)
protein_weights
(in
Bio.Data.IUPACData
)
parse()
(in
Bio.Medline
)
PhoI
(in
Bio.Restriction.Restriction
)
ProteinAlphabet
(in
Bio.Alphabet
)
parse()
(in
Bio.Motif
)
phred_quality_from_solexa()
(in
Bio.SeqIO.QualityIO
)
ProteinAnalysis
(in
Bio.SeqUtils.ProtParam
)
parse()
(in
AbstractParser
)
PhylipIO
(in
Bio.AlignIO
)
ProteinDomain
(in
Bio.Phylo.PhyloXML
)
parse()
(in
GenericParser
)
PhylipIterator
(in
Bio.AlignIO.PhylipIO
)
ProtParam
(in
Bio.SeqUtils
)
parse()
(in
Parser
)
PhylipWriter
(in
Bio.AlignIO.PhylipIO
)
ProtParamData
(in
Bio.SeqUtils
)
parse()
(in
Bio.Phylo.NewickIO
)
Phylo
(in
Bio
)
PROTSIM()
(in
_RecordConsumer
)
parse()
(in
Bio.Phylo.NexusIO
)
PhyloElement
(in
Bio.Phylo.PhyloXML
)
ProtsimLine
(in
Bio.UniGene
)
parse()
(in
Parser
)
Phylogeny
(in
Bio.Phylo.PhyloXML
)
prune()
(in
Tree
)
parse()
(in
Bio.Phylo.PhyloXMLIO
)
phylogeny()
(in
Writer
)
prune()
(in
GenericASTTraversal
)
parse()
(in
Bio.Phylo._io
)
PhyloXML
(in
Bio.Phylo
)
prune()
(in
TreeMixin
)
parse()
(in
Bio.SCOP.Cla
)
Phyloxml
(in
Bio.Phylo.PhyloXML
)
PscI
(in
Bio.Restriction.Restriction
)
parse()
(in
Bio.SCOP.Des
)
phyloxml()
(in
Writer
)
PSEA
(in
Bio.PDB
)
parse()
(in
Bio.SCOP.Dom
)
PhyloXMLError
(in
Bio.Phylo.PhyloXMLIO
)
PSEA
(in
Bio.PDB.PSEA
)
parse()
(in
Bio.SCOP.Hie
)
PhyloXMLIO
(in
Bio.Phylo
)
psea()
(in
Bio.PDB.PSEA
)
parse()
(in
Bio.SCOP.Raf
)
PhyloXMLWarning
(in
Bio.Phylo.PhyloXML
)
psea2HEC()
(in
Bio.PDB.PSEA
)
parse()
(in
Parser
)
PhymlCommandline
(in
Bio.Phylo.Applications._Phyml
)
PshAI
(in
Bio.Restriction.Restriction
)
parse()
(in
Bio.SeqIO
)
pi
(in
Bio.Affy.CelFile
)
PshBI
(in
Bio.Restriction.Restriction
)
parse()
(in
Bio.Sequencing.Ace
)
pi()
(in
IsoelectricPoint
)
PSIBlast
(in
Bio.Blast.Record
)
parse()
(in
Bio.Sequencing.Phd
)
pid()
(in
_FeatureConsumer
)
PSIBlastParser
(in
Bio.Blast.NCBIStandalone
)
parse()
(in
Bio.SwissProt.KeyWList
)
pid()
(in
_RecordConsumer
)
PsiI
(in
Bio.Restriction.Restriction
)
parse()
(in
Bio.SwissProt
)
PinAI
(in
Bio.Restriction.Restriction
)
Psp03I
(in
Bio.Restriction.Restriction
)
parse()
(in
RecordParser
)
PINF
(in
Bio.Affy.CelFile
)
Psp124BI
(in
Bio.Restriction.Restriction
)
parse()
(in
UniGeneParser
)
PirIO
(in
Bio.SeqIO
)
Psp1406I
(in
Bio.Restriction.Restriction
)
parse()
(in
Bio.UniGene
)
PirIterator()
(in
Bio.SeqIO.PirIO
)
Psp5II
(in
Bio.Restriction.Restriction
)
parse()
(in
Bio.Wise.psw
)
pKcterminal
(in
Bio.SeqUtils.IsoelectricPoint
)
Psp6I
(in
Bio.Restriction.Restriction
)
parse_basics()
(in
Bio.Phylo.PAML._parse_baseml
)
pKnterminal
(in
Bio.SeqUtils.IsoelectricPoint
)
PspCI
(in
Bio.Restriction.Restriction
)
parse_basics()
(in
Bio.Phylo.PAML._parse_codeml
)
PlaDI
(in
Bio.Restriction.Restriction
)
PspEI
(in
Bio.Restriction.Restriction
)
parse_branch_site_a()
(in
Bio.Phylo.PAML._parse_codeml
)
Ple19I
(in
Bio.Restriction.Restriction
)
PspGI
(in
Bio.Restriction.Restriction
)
parse_cds_features()
(in
InsdcScanner
)
PleI
(in
Bio.Restriction.Restriction
)
PspLI
(in
Bio.Restriction.Restriction
)
parse_clademodelc()
(in
Bio.Phylo.PAML._parse_codeml
)
PmaCI
(in
Bio.Restriction.Restriction
)
PspN4I
(in
Bio.Restriction.Restriction
)
parse_distances()
(in
Bio.Phylo.PAML._parse_codeml
)
PmeI
(in
Bio.Restriction.Restriction
)
PspOMI
(in
Bio.Restriction.Restriction
)
parse_domain()
(in
Bio.SCOP
)
PmlI
(in
Bio.Restriction.Restriction
)
PspOMII
(in
Bio.Restriction.Restriction
)
parse_feature()
(in
InsdcScanner
)
Point
(in
Bio.GA.Crossover
)
PspPI
(in
Bio.Restriction.Restriction
)
parse_features()
(in
InsdcScanner
)
Point
(in
Bio.Phylo.PhyloXML
)
PspPPI
(in
Bio.Restriction.Restriction
)
parse_features()
(in
_ImgtScanner
)
point()
(in
Parser
)
PspPRI
(in
Bio.Restriction.Restriction
)
parse_file()
(in
AbstractParser
)
point()
(in
Writer
)
PspXI
(in
Bio.Restriction.Restriction
)
parse_footer()
(in
EmblScanner
)
Polygon
(in
Bio.Phylo.PhyloXML
)
PsrI
(in
Bio.Restriction.Restriction
)
parse_footer()
(in
GenBankScanner
)
polygon()
(in
Parser
)
PssI
(in
Bio.Restriction.Restriction
)
parse_footer()
(in
InsdcScanner
)
polygon()
(in
Writer
)
PSSM
(in
Bio.Align.AlignInfo
)
parse_freqs()
(in
Bio.Phylo.PAML._parse_baseml
)
Polypeptide
(in
Bio.PDB
)
PstI
(in
Bio.Restriction.Restriction
)
parse_header()
(in
InsdcScanner
)
Polypeptide
(in
Bio.PDB.Polypeptide
)
PsuI
(in
Bio.Restriction.Restriction
)
parse_kappas()
(in
Bio.Phylo.PAML._parse_baseml
)
pop()
(in
MutableSeq
)
psw
(in
Bio.Wise
)
parse_line()
(in
Bio.Wise.psw
)
pop()
(in
_IndexedSeqFileDict
)
Psycopg2_dbutils
(in
BioSQL.DBUtils
)
parse_model()
(in
Bio.Phylo.PAML._parse_codeml
)
PopGen
(in
Bio
)
PsyI
(in
Bio.Restriction.Restriction
)
parse_ng86()
(in
Bio.Phylo.PAML._parse_yn00
)
popitem()
(in
Crystal
)
PteI
(in
Bio.Restriction.Restriction
)
parse_nssites()
(in
Bio.Phylo.PAML._parse_codeml
)
popitem()
(in
_IndexedSeqFileDict
)
pubmed_id()
(in
_FeatureConsumer
)
parse_others()
(in
Bio.Phylo.PAML._parse_yn00
)
pos_align_list2dict()
(in
FSSPAlignRec
)
pubmed_id()
(in
_RecordConsumer
)
parse_pairwise()
(in
Bio.Phylo.PAML._parse_codeml
)
pos_specific_score_matrix()
(in
SummaryInfo
)
PUNCTUATION
(in
Bio.Nexus.Nexus
)
parse_parameter_list()
(in
Bio.Phylo.PAML._parse_baseml
)
PosAlign
(in
Bio.FSSP
)
PvuI
(in
Bio.Restriction.Restriction
)
parse_parameters()
(in
Bio.Phylo.PAML._parse_baseml
)
PositionGap
(in
Bio.SeqFeature
)
PvuII
(in
Bio.Restriction.Restriction
)
parse_pdb_header'
(in
Bio.PDB
)
positive_alignment()
(in
_Consumer
)
pwm()
(in
Motif
)
parse_pdb_header()
(in
Bio.PDB.parse_pdb_header'
)
positive_pKs
(in
Bio.SeqUtils.IsoelectricPoint
)
PZERO
(in
Bio.Affy.CelFile
)
parse_rates()
(in
Bio.Phylo.PAML._parse_baseml
)
posted_date()
(in
_DatabaseReportConsumer
)
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