### Home Classes Methods

### In Files

- lib/bio/db/pdb/pdb.rb
- lib/bio/db/pdb/residue.rb
- lib/bio/db/pdb/utils.rb
- lib/bio/db/pdb/chain.rb
- lib/bio/db/pdb/atom.rb
- lib/bio/db/pdb/chemicalcomponent.rb
- lib/bio/db/pdb/model.rb
- lib/bio/db/pdb.rb

### Parent

Object

### Namespace

- MODULE Bio::PDB::AtomFinder
- MODULE Bio::PDB::ChainFinder
- MODULE Bio::PDB::DataType
- MODULE Bio::PDB::HetatmFinder
- MODULE Bio::PDB::HeterogenFinder
- MODULE Bio::PDB::ModelFinder
- MODULE Bio::PDB::ResidueFinder
- MODULE Bio::PDB::Utils
- CLASS Bio::PDB::Chain
- CLASS Bio::PDB::ChemicalComponent
- CLASS Bio::PDB::Coordinate
- CLASS Bio::PDB::Heterogen
- CLASS Bio::PDB::Model
- CLASS Bio::PDB::Record
- CLASS Bio::PDB::Residue

### Methods

- ::new
- #[]
- #accession
- #addModel
- #authors
- #classification
- #dbref
- #definition
- #each
- #each_model
- #entry_id
- #helix
- #inspect
- #jrnl
- #keywords
- #record
- #remark
- #seqres
- #sheet
- #ssbond
- #to_s
- #turn
- #version

### Included Modules

- Bio::PDB::Utils
- Bio::PDB::AtomFinder
- Bio::PDB::ResidueFinder
- Bio::PDB::ChainFinder
- Bio::PDB::ModelFinder
- Bio::PDB::HetatmFinder
- Bio::PDB::HeterogenFinder
- Enumerable

### Files

- ChangeLog
- KNOWN_ISSUES.rdoc
- LEGAL
- README.rdoc
- README_DEV.rdoc
- RELEASE_NOTES.rdoc
- Changes-1.3.rdoc
- RELEASE_NOTES-1.4.0.rdoc
- RELEASE_NOTES-1.4.1.rdoc
- RELEASE_NOTES-1.4.2.rdoc

### Class/Module Index

Quicksearch

- Bio
- Bio::AAindex
- Bio::AAindex1
- Bio::AAindex2
- Bio::Abif
- Bio::Abif::DirectoryEntry
- Bio::Alignment
- Bio::Alignment::ArrayExtension
- Bio::Alignment::EnumerableExtension
- Bio::Alignment::FactoryTemplate
- Bio::Alignment::FactoryTemplate::FileInFileOut
- Bio::Alignment::FactoryTemplate::FileInFileOutWithTree
- Bio::Alignment::FactoryTemplate::FileInStdoutOut
- Bio::Alignment::FactoryTemplate::Simple
- Bio::Alignment::FactoryTemplate::StdinInFileOut
- Bio::Alignment::FactoryTemplate::WrapInputStdin
- Bio::Alignment::FactoryTemplate::WrapInputTempfile
- Bio::Alignment::FactoryTemplate::WrapOutputStdout
- Bio::Alignment::FactoryTemplate::WrapOutputTempfile
- Bio::Alignment::GAP
- Bio::Alignment::HashExtension
- Bio::Alignment::MultiFastaFormat
- Bio::Alignment::OriginalAlignment
- Bio::Alignment::OriginalPrivate
- Bio::Alignment::Output
- Bio::Alignment::PropertyMethods
- Bio::Alignment::SequenceArray
- Bio::Alignment::SequenceHash
- Bio::Alignment::Site
- Bio::Alignment::SiteMethods
- Bio::AminoAcid
- Bio::AminoAcid::Data
- Bio::Blast
- Bio::Blast::Bl2seq
- Bio::Blast::Bl2seq::Report
- Bio::Blast::Bl2seq::Report::HSP
- Bio::Blast::Bl2seq::Report::Hit
- Bio::Blast::Bl2seq::Report::Iteration
- Bio::Blast::Default
- Bio::Blast::Default::Report
- Bio::Blast::Default::Report::HSP
- Bio::Blast::Default::Report::Hit
- Bio::Blast::Default::Report::Iteration
- Bio::Blast::Default::Report_TBlast
- Bio::Blast::Fastacmd
- Bio::Blast::NCBIOptions
- Bio::Blast::RPSBlast
- Bio::Blast::RPSBlast::RPSBlastSplitter
- Bio::Blast::RPSBlast::Report
- Bio::Blast::RPSBlast::Report::FLATFILE_SPLITTER
- Bio::Blast::RPSBlast::Report::Iteration
- Bio::Blast::Remote
- Bio::Blast::Remote::DDBJ
- Bio::Blast::Remote::DDBJ::Information
- Bio::Blast::Remote::Ddbj
- Bio::Blast::Remote::GenomeNet
- Bio::Blast::Remote::GenomeNet::Information
- Bio::Blast::Remote::Genomenet
- Bio::Blast::Remote::Information
- Bio::Blast::Report
- Bio::Blast::Report::BlastXmlSplitter
- Bio::Blast::Report::FLATFILE_SPLITTER
- Bio::Blast::Report::Hit
- Bio::Blast::Report::Hsp
- Bio::Blast::Report::Iteration
- Bio::Blast::Report_tab
- Bio::Blast::WU
- Bio::Blast::WU::Report
- Bio::Blast::WU::Report::HSP
- Bio::Blast::WU::Report::Hit
- Bio::Blast::WU::Report::Iteration
- Bio::Blast::WU::Report_TBlast
- Bio::Blat
- Bio::Blat::Report
- Bio::Blat::Report::FLATFILE_SPLITTER
- Bio::Blat::Report::Hit
- Bio::Blat::Report::SegmentPair
- Bio::Blat::Report::SeqDesc
- Bio::ClustalW
- Bio::ClustalW::Report
- Bio::CodonTable
- Bio::ColorScheme
- Bio::Command
- Bio::Command::Tmpdir
- Bio::Command::Tmpdir::Remover
- Bio::ContingencyTable
- Bio::DAS
- Bio::DAS::DNA
- Bio::DAS::DSN
- Bio::DAS::ENTRY_POINT
- Bio::DAS::FEATURE
- Bio::DAS::GFF
- Bio::DAS::GROUP
- Bio::DAS::LINK
- Bio::DAS::SEGMENT
- Bio::DAS::SEQUENCE
- Bio::DAS::TARGET
- Bio::DAS::TYPE
- Bio::DAS::TYPES
- Bio::DB
- Bio::DBGET
- Bio::DDBJ
- Bio::DDBJ::REST
- Bio::DDBJ::REST::Blast
- Bio::DDBJ::REST::ClustalW
- Bio::DDBJ::REST::DDBJ
- Bio::DDBJ::REST::Mafft
- Bio::DDBJ::REST::RequestManager
- Bio::DDBJ::REST::WABItemplate
- Bio::DDBJ::XML
- Bio::DDBJ::XML::Blast
- Bio::DDBJ::XML::ClustalW
- Bio::DDBJ::XML::DDBJ
- Bio::DDBJ::XML::Fasta
- Bio::DDBJ::XML::GetEntry
- Bio::DDBJ::XML::Gib
- Bio::DDBJ::XML::Gtop
- Bio::DDBJ::XML::PML
- Bio::DDBJ::XML::RequestManager
- Bio::DDBJ::XML::RequestManager::REST
- Bio::DDBJ::XML::SRS
- Bio::DDBJ::XML::TxSearch
- Bio::EBI
- Bio::EBI::SOAP
- Bio::EBI::SOAP::Citation
- Bio::EBI::SOAP::ClustalW
- Bio::EBI::SOAP::Dbfetch
- Bio::EBI::SOAP::Emboss
- Bio::EBI::SOAP::Fasta
- Bio::EBI::SOAP::InterProScan
- Bio::EBI::SOAP::MPsrch
- Bio::EBI::SOAP::MSD
- Bio::EBI::SOAP::Muscle
- Bio::EBI::SOAP::Ontology
- Bio::EBI::SOAP::ScanPS
- Bio::EBI::SOAP::TCoffee
- Bio::EBI::SOAP::WUBlast
- Bio::EMBL
- Bio::EMBLDB
- Bio::EMBLDB::Common
- Bio::EMBOSS
- Bio::Ensembl
- Bio::Ensembl::Base
- Bio::Ensembl::Human
- Bio::Ensembl::Mouse
- Bio::FANTOM
- Bio::FANTOM::MaXML
- Bio::FANTOM::MaXML::Annotation
- Bio::FANTOM::MaXML::Annotation::DataSrc
- Bio::FANTOM::MaXML::Annotations
- Bio::FANTOM::MaXML::Cluster
- Bio::FANTOM::MaXML::Sequence
- Bio::FANTOM::MaXML::Sequences
- Bio::Fasta
- Bio::Fasta::Report
- Bio::Fasta::Report::FLATFILE_SPLITTER
- Bio::Fasta::Report::FastaFormat10Splitter
- Bio::Fasta::Report::Hit
- Bio::Fasta::Report::Hit::Query
- Bio::Fasta::Report::Hit::Target
- Bio::Fasta::Report::Program
- Bio::FastaDefline
- Bio::FastaFormat
- Bio::FastaNumericFormat
- Bio::Fastq
- Bio::Fastq::Error
- Bio::Fastq::Error::Diff_ids
- Bio::Fastq::Error::Long_qual
- Bio::Fastq::Error::No_atmark
- Bio::Fastq::Error::No_ids
- Bio::Fastq::Error::No_qual
- Bio::Fastq::Error::No_seq
- Bio::Fastq::Error::Qual_char
- Bio::Fastq::Error::Qual_range
- Bio::Fastq::Error::Seq_char
- Bio::Fastq::Error::Short_qual
- Bio::Fastq::Error::Skipped_unformatted_lines
- Bio::Fastq::FLATFILE_SPLITTER
- Bio::Fastq::FormatData
- Bio::Fastq::FormatData::FASTQ_ILLUMINA
- Bio::Fastq::FormatData::FASTQ_SANGER
- Bio::Fastq::FormatData::FASTQ_SOLEXA
- Bio::Feature
- Bio::Feature::Qualifier
- Bio::Features
- Bio::Fetch
- Bio::FlatFile
- Bio::FlatFile::AutoDetect
- Bio::FlatFile::AutoDetect::RuleDebug
- Bio::FlatFile::AutoDetect::RuleProc
- Bio::FlatFile::AutoDetect::RuleRegexp
- Bio::FlatFile::AutoDetect::RuleRegexp2
- Bio::FlatFile::AutoDetect::RuleSpecial
- Bio::FlatFile::AutoDetect::RuleTemplate
- Bio::FlatFile::AutoDetect::RulesArray
- Bio::FlatFile::BufferedInputStream
- Bio::FlatFile::Splitter
- Bio::FlatFile::Splitter::Default
- Bio::FlatFile::Splitter::LineOriented
- Bio::FlatFile::Splitter::Template
- Bio::FlatFile::UnknownDataFormatError
- Bio::FlatFileIndex
- Bio::FlatFileIndex::BDB_1
- Bio::FlatFileIndex::BDB_1::BDBMappingFile
- Bio::FlatFileIndex::BDB_1::PrimaryNameSpace
- Bio::FlatFileIndex::BDB_1::SecondaryNameSpace
- Bio::FlatFileIndex::BDBdefault
- Bio::FlatFileIndex::BDBwrapper
- Bio::FlatFileIndex::DEBUG
- Bio::FlatFileIndex::DataBank
- Bio::FlatFileIndex::FileID
- Bio::FlatFileIndex::FileIDs
- Bio::FlatFileIndex::Flat_1
- Bio::FlatFileIndex::Flat_1::FlatMappingFile
- Bio::FlatFileIndex::Flat_1::PrimaryNameSpace
- Bio::FlatFileIndex::Flat_1::Record
- Bio::FlatFileIndex::Flat_1::SecondaryNameSpace
- Bio::FlatFileIndex::Indexer
- Bio::FlatFileIndex::Indexer::NameSpace
- Bio::FlatFileIndex::Indexer::NameSpaces
- Bio::FlatFileIndex::Indexer::Parser
- Bio::FlatFileIndex::Indexer::Parser::BlastDefaultParser
- Bio::FlatFileIndex::Indexer::Parser::EMBLParser
- Bio::FlatFileIndex::Indexer::Parser::FastaFormatParser
- Bio::FlatFileIndex::Indexer::Parser::GenBankParser
- Bio::FlatFileIndex::Indexer::Parser::GenPeptParser
- Bio::FlatFileIndex::Indexer::Parser::MaXMLClusterParser
- Bio::FlatFileIndex::Indexer::Parser::MaXMLSequenceParser
- Bio::FlatFileIndex::Indexer::Parser::PDBChemicalComponentParser
- Bio::FlatFileIndex::Indexer::Parser::SPTRParser
- Bio::FlatFileIndex::Indexer::Parser::TemplateParser
- Bio::FlatFileIndex::NameSpaces
- Bio::FlatFileIndex::Results
- Bio::FlatFileIndex::Template
- Bio::FlatFileIndex::Template::NameSpace
- Bio::GCG
- Bio::GCG::Msf
- Bio::GCG::Seq
- Bio::GFF
- Bio::GFF::GFF2
- Bio::GFF::GFF2::Escape
- Bio::GFF::GFF2::MetaData
- Bio::GFF::GFF2::Record
- Bio::GFF::GFF2::Record::Value
- Bio::GFF::GFF3
- Bio::GFF::GFF3::Escape
- Bio::GFF::GFF3::Record
- Bio::GFF::GFF3::Record::Gap
- Bio::GFF::GFF3::Record::Gap::Code
- Bio::GFF::GFF3::Record::Target
- Bio::GFF::GFF3::RecordBoundary
- Bio::GFF::GFF3::SequenceRegion
- Bio::GFF::Record
- Bio::GO
- Bio::GO::External2go
- Bio::GO::GeneAssociation
- Bio::GO::Ontology
- Bio::GenBank
- Bio::GenBank::Locus
- Bio::GenPept
- Bio::GenPept::Locus
- Bio::Genscan
- Bio::Genscan::Report
- Bio::Genscan::Report::Exon
- Bio::Genscan::Report::Gene
- Bio::HGC
- Bio::HGC::HiGet
- Bio::HMMER
- Bio::HMMER::Report
- Bio::HMMER::Report::Hit
- Bio::HMMER::Report::Hsp
- Bio::Hinv
- Bio::Hinv::Acc2hit
- Bio::Hinv::Common
- Bio::Hinv::Hit2acc
- Bio::Hinv::HitCnt
- Bio::Hinv::HitDefinition
- Bio::Hinv::HitPubmedId
- Bio::Hinv::HitXML
- Bio::Hinv::Hix2hit
- Bio::Hinv::HixCnt
- Bio::Hinv::HixRepresent
- Bio::Hinv::HixXML
- Bio::Hinv::IdSearch
- Bio::Hinv::KeywordSearch
- Bio::Iprscan
- Bio::Iprscan::Report
- Bio::Iprscan::Report::Match
- Bio::KEGG
- Bio::KEGG::API
- Bio::KEGG::BRITE
- Bio::KEGG::COMPOUND
- Bio::KEGG::Common
- Bio::KEGG::Common::DblinksAsHash
- Bio::KEGG::Common::GenesAsHash
- Bio::KEGG::Common::ModulesAsHash
- Bio::KEGG::Common::OrthologsAsHash
- Bio::KEGG::Common::PathwaysAsHash
- Bio::KEGG::Common::References
- Bio::KEGG::Common::StringsAsHash
- Bio::KEGG::DRUG
- Bio::KEGG::ENZYME
- Bio::KEGG::EXPRESSION
- Bio::KEGG::GENES
- Bio::KEGG::GENOME
- Bio::KEGG::GLYCAN
- Bio::KEGG::KGML
- Bio::KEGG::KGML::Entry
- Bio::KEGG::KGML::Graphics
- Bio::KEGG::KGML::Product
- Bio::KEGG::KGML::Reaction
- Bio::KEGG::KGML::Relation
- Bio::KEGG::KGML::Substrate
- Bio::KEGG::KGML::SubstrateProduct
- Bio::KEGG::Keggtab
- Bio::KEGG::Keggtab::DB
- Bio::KEGG::MODULE
- Bio::KEGG::ORTHOLOGY
- Bio::KEGG::PATHWAY
- Bio::KEGG::REACTION
- Bio::KEGG::Taxonomy
- Bio::KEGGDB
- Bio::LITDB
- Bio::Lasergene
- Bio::Location
- Bio::Locations
- Bio::MAFFT
- Bio::MAFFT::Report
- Bio::MEDLINE
- Bio::Map
- Bio::Map::ActsLikeMap
- Bio::Map::ActsLikeMarker
- Bio::Map::Mapping
- Bio::Map::Marker
- Bio::Map::SimpleMap
- Bio::Meme
- Bio::Meme::Mast
- Bio::Meme::Mast::Report
- Bio::Meme::Motif
- Bio::Muscle
- Bio::NBRF
- Bio::NCBI
- Bio::NCBI::REST
- Bio::NCBI::REST::EFetch
- Bio::NCBI::REST::EFetch::Methods
- Bio::NCBI::REST::ESearch
- Bio::NCBI::REST::ESearch::Methods
- Bio::NCBI::SOAP
- Bio::NCBI::SOAP::EFetch
- Bio::NCBI::SOAP::EFetchLite
- Bio::NCBI::SOAP::EUtils
- Bio::NCBI::SOAP::EUtilsLite
- Bio::NCBIDB
- Bio::NCBIDB::Common
- Bio::Newick
- Bio::Newick::Edge
- Bio::Newick::Node
- Bio::Newick::ParseError
- Bio::Nexus
- Bio::Nexus::CharactersBlock
- Bio::Nexus::DataBlock
- Bio::Nexus::DistancesBlock
- Bio::Nexus::GenericBlock
- Bio::Nexus::NexusMatrix
- Bio::Nexus::NexusMatrix::NexusMatrixError
- Bio::Nexus::NexusParseError
- Bio::Nexus::TaxaBlock
- Bio::Nexus::TreesBlock
- Bio::Nexus::Util
- Bio::NucleicAcid
- Bio::NucleicAcid::Data
- Bio::PAML
- Bio::PAML::Baseml
- Bio::PAML::Baseml::Report
- Bio::PAML::Codeml
- Bio::PAML::Codeml::Model
- Bio::PAML::Codeml::PositiveSite
- Bio::PAML::Codeml::PositiveSites
- Bio::PAML::Codeml::Rates
- Bio::PAML::Codeml::Report
- Bio::PAML::Codeml::ReportError
- Bio::PAML::Codeml::ReportSingle
- Bio::PAML::Common
- Bio::PAML::Common::Report
- Bio::PAML::Yn00
- Bio::PAML::Yn00::Report
- Bio::PDB
- Bio::PDB::AtomFinder
- Bio::PDB::Chain
- Bio::PDB::ChainFinder
- Bio::PDB::ChemicalComponent
- Bio::PDB::ChemicalComponent::Record
- Bio::PDB::Coordinate
- Bio::PDB::DataType
- Bio::PDB::DataType::ConstLikeMethod
- Bio::PDB::DataType::Pdb_AChar
- Bio::PDB::DataType::Pdb_Atom
- Bio::PDB::DataType::Pdb_Character
- Bio::PDB::DataType::Pdb_Date
- Bio::PDB::DataType::Pdb_IDcode
- Bio::PDB::DataType::Pdb_Integer
- Bio::PDB::DataType::Pdb_LString
- Bio::PDB::DataType::Pdb_List
- Bio::PDB::DataType::Pdb_Real
- Bio::PDB::DataType::Pdb_Residue_name
- Bio::PDB::DataType::Pdb_SList
- Bio::PDB::DataType::Pdb_Specification_list
- Bio::PDB::DataType::Pdb_String
- Bio::PDB::DataType::Pdb_StringRJ
- Bio::PDB::DataType::Pdb_SymOP
- Bio::PDB::HetatmFinder
- Bio::PDB::Heterogen
- Bio::PDB::HeterogenFinder
- Bio::PDB::Model
- Bio::PDB::ModelFinder
- Bio::PDB::Record
- Bio::PDB::Record::ANISOU
- Bio::PDB::Record::ATOM
- Bio::PDB::Record::HETATM
- Bio::PDB::Record::Jrnl
- Bio::PDB::Record::Remark1
- Bio::PDB::Record::Remark2
- Bio::PDB::Residue
- Bio::PDB::ResidueFinder
- Bio::PDB::Utils
- Bio::PROSITE
- Bio::PSORT
- Bio::PSORT::CGIDriver
- Bio::PSORT::IPSORT
- Bio::PSORT::PSORT1
- Bio::PSORT::PSORT1::Remote
- Bio::PSORT::PSORT1::Report
- Bio::PSORT::PSORT2
- Bio::PSORT::PSORT2::Remote
- Bio::PSORT::PSORT2::Report
- Bio::PSORT::PSORTB
- Bio::PSORT::WoLF_PSORT
- Bio::PTS1
- Bio::PTS1::Report
- Bio::Pathway
- Bio::Phylip
- Bio::Phylip::DistanceMatrix
- Bio::Phylip::PhylipFormat
- Bio::PhyloXML
- Bio::PhyloXML::Accession
- Bio::PhyloXML::Annotation
- Bio::PhyloXML::BinaryCharacters
- Bio::PhyloXML::BranchColor
- Bio::PhyloXML::CladeRelation
- Bio::PhyloXML::Confidence
- Bio::PhyloXML::Date
- Bio::PhyloXML::Distribution
- Bio::PhyloXML::DomainArchitecture
- Bio::PhyloXML::Events
- Bio::PhyloXML::Id
- Bio::PhyloXML::Node
- Bio::PhyloXML::Other
- Bio::PhyloXML::Parser
- Bio::PhyloXML::Point
- Bio::PhyloXML::Polygon
- Bio::PhyloXML::Property
- Bio::PhyloXML::ProteinDomain
- Bio::PhyloXML::Reference
- Bio::PhyloXML::Sequence
- Bio::PhyloXML::SequenceRelation
- Bio::PhyloXML::Taxonomy
- Bio::PhyloXML::Tree
- Bio::PhyloXML::Uri
- Bio::PhyloXML::Writer
- Bio::Probcons
- Bio::PubMed
- Bio::REBASE
- Bio::RefSeq
- Bio::Reference
- Bio::References
- Bio::Registry
- Bio::Registry::DB
- Bio::RestrictionEnzyme
- Bio::RestrictionEnzyme::Analysis
- Bio::RestrictionEnzyme::CutSymbol
- Bio::RestrictionEnzyme::CutSymbol::CutSymbol__
- Bio::RestrictionEnzyme::DenseIntArray
- Bio::RestrictionEnzyme::DoubleStranded
- Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands
- Bio::RestrictionEnzyme::DoubleStranded::CutLocationPair
- Bio::RestrictionEnzyme::DoubleStranded::CutLocationPairInEnzymeNotation
- Bio::RestrictionEnzyme::DoubleStranded::CutLocations
- Bio::RestrictionEnzyme::DoubleStranded::CutLocationsInEnzymeNotation
- Bio::RestrictionEnzyme::DoubleStranded::EnzymeAction
- Bio::RestrictionEnzyme::Fragments
- Bio::RestrictionEnzyme::Range
- Bio::RestrictionEnzyme::Range::CutRange
- Bio::RestrictionEnzyme::Range::CutRanges
- Bio::RestrictionEnzyme::Range::HorizontalCutRange
- Bio::RestrictionEnzyme::Range::SequenceRange
- Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts
- Bio::RestrictionEnzyme::Range::SequenceRange::Fragment
- Bio::RestrictionEnzyme::Range::SequenceRange::Fragments
- Bio::RestrictionEnzyme::Range::VerticalCutRange
- Bio::RestrictionEnzyme::SingleStrand
- Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation
- Bio::RestrictionEnzyme::SingleStrandComplement
- Bio::RestrictionEnzyme::SortedNumArray
- Bio::RestrictionEnzyme::StringFormatting
- Bio::SOAPWSDL
- Bio::SOFT
- Bio::SOSUI
- Bio::SOSUI::Report
- Bio::SOSUI::Report::TMH
- Bio::SPTR
- Bio::SQL
- Bio::SQL::Biodatabase
- Bio::SQL::Bioentry
- Bio::SQL::BioentryDbxref
- Bio::SQL::BioentryPath
- Bio::SQL::BioentryQualifierValue
- Bio::SQL::BioentryReference
- Bio::SQL::BioentryRelationship
- Bio::SQL::Biosequence
- Bio::SQL::Comment
- Bio::SQL::Dbxref
- Bio::SQL::DbxrefQualifierValue
- Bio::SQL::DummyBase
- Bio::SQL::Location
- Bio::SQL::LocationQualifierValue
- Bio::SQL::Ontology
- Bio::SQL::Reference
- Bio::SQL::Seqfeature
- Bio::SQL::SeqfeatureDbxref
- Bio::SQL::SeqfeaturePath
- Bio::SQL::SeqfeatureQualifierValue
- Bio::SQL::SeqfeatureRelationship
- Bio::SQL::Sequence
- Bio::SQL::Taxon
- Bio::SQL::TaxonName
- Bio::SQL::Term
- Bio::SQL::TermDbxref
- Bio::SQL::TermPath
- Bio::SQL::TermRelationship
- Bio::SQL::TermRelationshipTerm
- Bio::SQL::TermSynonym
- Bio::SangerChromatogram
- Bio::Scf
- Bio::Sequence
- Bio::Sequence::AA
- Bio::Sequence::Adapter
- Bio::Sequence::Adapter::BioSQL
- Bio::Sequence::Adapter::EMBL
- Bio::Sequence::Adapter::FastaFormat
- Bio::Sequence::Adapter::FastaNumericFormat
- Bio::Sequence::Adapter::Fastq
- Bio::Sequence::Adapter::GenBank
- Bio::Sequence::Adapter::SangerChromatogram
- Bio::Sequence::Common
- Bio::Sequence::DBLink
- Bio::Sequence::Format
- Bio::Sequence::Format::AminoFormatter
- Bio::Sequence::Format::Formatter
- Bio::Sequence::Format::Formatter::Fasta
- Bio::Sequence::Format::Formatter::Fasta_ncbi
- Bio::Sequence::Format::Formatter::Fasta_numeric
- Bio::Sequence::Format::Formatter::Fastq
- Bio::Sequence::Format::Formatter::Fastq_illumina
- Bio::Sequence::Format::Formatter::Fastq_sanger
- Bio::Sequence::Format::Formatter::Fastq_solexa
- Bio::Sequence::Format::Formatter::Qual
- Bio::Sequence::Format::Formatter::Raw
- Bio::Sequence::Format::FormatterBase
- Bio::Sequence::Format::INSDFeatureHelper
- Bio::Sequence::Format::NucFormatter
- Bio::Sequence::Format::NucFormatter::Embl
- Bio::Sequence::Format::NucFormatter::Genbank
- Bio::Sequence::NA
- Bio::Sequence::NA::MidiTrack
- Bio::Sequence::QualityScore
- Bio::Sequence::QualityScore::Converter
- Bio::Sequence::QualityScore::Phred
- Bio::Sequence::QualityScore::Solexa
- Bio::Sequence::SequenceMasker
- Bio::Shell
- Bio::Shell::ColoredCodonTable
- Bio::Shell::Core
- Bio::Shell::Demo
- Bio::Shell::Ghost
- Bio::Shell::Irb
- Bio::Shell::Private
- Bio::Shell::Script
- Bio::Shell::Setup
- Bio::Shell::Web
- Bio::Shell::Web::Results
- Bio::SiRNA
- Bio::SiRNA::Pair
- Bio::SiRNA::ShRNA
- Bio::Sim4
- Bio::Sim4::Report
- Bio::Sim4::Report::Hit
- Bio::Sim4::Report::Segment
- Bio::Sim4::Report::SegmentPair
- Bio::Sim4::Report::SeqDesc
- Bio::Spidey
- Bio::Spidey::Report
- Bio::Spidey::Report::Hit
- Bio::Spidey::Report::Segment
- Bio::Spidey::Report::SegmentPair
- Bio::Spidey::Report::SeqDesc
- Bio::SwissProt
- Bio::TMHMM
- Bio::TMHMM::Report
- Bio::TMHMM::TMH
- Bio::TRANSFAC
- Bio::TRANSFAC::CELL
- Bio::TRANSFAC::CLASS
- Bio::TRANSFAC::FACTOR
- Bio::TRANSFAC::GENE
- Bio::TRANSFAC::MATRIX
- Bio::TRANSFAC::SITE
- Bio::TargetP
- Bio::TargetP::Report
- Bio::Taxonomy
- Bio::Tcoffee
- Bio::Tcoffee::DEFAULT_PARSER
- Bio::TogoWS
- Bio::TogoWS::AccessWait
- Bio::TogoWS::REST
- Bio::TrEMBL
- Bio::Tree
- Bio::Tree::Edge
- Bio::Tree::NoPathError
- Bio::Tree::Node
- Bio::UniProt
- BiorubyController
- BiorubyGenerator
- BiorubyHelper
- Hash
- Object
- String

No matching classes.

# Bio::PDB

This is the main PDB class which takes care of parsing, annotations and is the entry way to the co-ordinate data held in models.

There are many related classes.

Bio::PDB::Model Bio::PDB::Chain Bio::PDB::Residue Bio::PDB::Heterogen Bio::PDB::Record::ATOM Bio::PDB::Record::HETATM Bio::PDB::Record::* Bio::PDB::Coordinate

### Constants

Coordinate_fileds
DELIMITER

  delimiter for reading via Bio::FlatFile

### Attributes

data[R]

all records in this entry as an array.

hash[R]

all records in this entry as an hash accessed by record names.

models[R]

models in this entry (array).

### Public Class Methods

new(str) click to toggle source

Creates a new Bio::PDB object from given str.

    # File lib/bio/db/pdb/pdb.rb, line 1445
    def initialize(str)
      #Aha! Our entry into the world of PDB parsing, we initialise a PDB
      #object with the whole PDB file as a string
      #each PDB has an array of the lines of the original file
      #a bit memory-tastic! A hash of records and an array of models
      #also has an id

      @data = str.split(/[\r\n]+/)
      @hash = {}
      @models = []
      @id = nil

      #Flag to say whether the current line is part of a continuation
      cont = false

      #Empty current model
      cModel    = Model.new
      cChain    = nil #Chain.new
      cResidue  = nil #Residue.new
      cLigand   = nil #Heterogen.new
      c_atom    = nil

      #Goes through each line and replace that line with a PDB::Record
      @data.collect! do |line|
        #Go to next if the previous line was contiunation able, and
        #add_continuation returns true. Line is added by add_continuation
        next if cont and cont = cont.add_continuation(line)

        #Make the new record
        f = Record.get_record_class(line).new.initialize_from_string(line)
        #p f
        #Set cont
        cont = f if f.continue?
        #Set the hash to point to this record either by adding to an
        #array, or on it's own
        key = f.record_name
        if a = @hash[key] then
          a << f
        else
          @hash[key] = [ f ]
        end

        # Do something for ATOM and HETATM
        if key == 'ATOM' or key == 'HETATM' then
          if cChain and f.chainID == cChain.id
            chain = cChain
          else
            if chain = cModel[f.chainID]
              cChain = chain unless cChain
            else
              # If we don't have chain, add a new chain
              newChain = Chain.new(f.chainID, cModel)
              cModel.addChain(newChain)
              cChain = newChain
              chain = newChain
            end
            # chain might be changed, clearing cResidue and cLigand
            cResidue = nil
            cLigand = nil
          end
        end

        case key
        when 'ATOM'
          c_atom = f
          residueID = Residue.get_residue_id_from_atom(f)

          if cResidue and residueID == cResidue.id
            residue = cResidue
          else
            if residue = chain.get_residue_by_id(residueID)
              cResidue = residue unless cResidue
            else
              # add a new residue
              newResidue = Residue.new(f.resName, f.resSeq, f.iCode, chain)
              chain.addResidue(newResidue)
              cResidue = newResidue
              residue = newResidue
            end
          end

          f.residue = residue
          residue.addAtom(f)

        when 'HETATM'
          c_atom = f
          residueID = Heterogen.get_residue_id_from_atom(f)

          if cLigand and residueID == cLigand.id
            ligand = cLigand
          else
            if ligand = chain.get_heterogen_by_id(residueID)
              cLigand = ligand unless cLigand
            else
              # add a new heterogen
              newLigand = Heterogen.new(f.resName, f.resSeq, f.iCode, chain)
              chain.addLigand(newLigand)
              cLigand = newLigand
              ligand = newLigand
              #Each model has a special solvent chain. (for compatibility)
              if f.resName == 'HOH'
                cModel.addSolvent(newLigand)
              end
            end
          end

          f.residue = ligand
          ligand.addAtom(f)

        when 'MODEL'
          c_atom = nil
          cChain = nil
          cResidue = nil
          cLigand = nil
          if cModel.model_serial or cModel.chains.size > 0 then
            self.addModel(cModel)
          end
          cModel = Model.new(f.serial)

        when 'TER'
          if c_atom
            c_atom.ter = f
          else
            #$stderr.puts "Warning: stray TER?"
          end
        when 'SIGATM'
          if c_atom
            #$stderr.puts "Warning: duplicated SIGATM?" if c_atom.sigatm
            c_atom.sigatm = f
          else
            #$stderr.puts "Warning: stray SIGATM?"
          end
        when 'ANISOU'
          if c_atom
            #$stderr.puts "Warning: duplicated ANISOU?" if c_atom.anisou
            c_atom.anisou = f
          else
            #$stderr.puts "Warning: stray ANISOU?"
          end
        when 'SIGUIJ'
          if c_atom and c_atom.anisou
            #$stderr.puts "Warning: duplicated SIGUIJ?" if c_atom.anisou.siguij
            c_atom.anisou.siguij = f
          else
            #$stderr.puts "Warning: stray SIGUIJ?"
          end

        else
          c_atom = nil

        end
        f
      end #each
      #At the end we need to add the final model
      self.addModel(cModel)
      @data.compact!
    end

### Public Instance Methods

[](key) click to toggle source

Provides keyed access to the models based on serial number returns nil if it's not there

    # File lib/bio/db/pdb/pdb.rb, line 1633
    def [](key)
      @models.find{ |model| key == model.model_serial }
    end

accession() click to toggle source

Same as `Bio::PDB#entry_id`.

    # File lib/bio/db/pdb/pdb.rb, line 1887
    def accession
      self.entry_id
    end

addModel(model) click to toggle source

Adds a `Bio::Model` object to the current strucutre. Adds a model to the current structure. Returns self.

    # File lib/bio/db/pdb/pdb.rb, line 1615
    def addModel(model)
      raise "Expecting a Bio::PDB::Model" if not model.is_a? Bio::PDB::Model
      @models.push(model)
      self
    end

authors() click to toggle source

Get authors in "AUTHOR".

    # File lib/bio/db/pdb/pdb.rb, line 1869
    def authors
      self.record('AUTHOR').collect { |f| f.authorList }.flatten
    end

classification() click to toggle source

Classification in "HEADER".

    # File lib/bio/db/pdb/pdb.rb, line 1863
    def classification
      f = self.record('HEADER').first
      f ? f.classification : nil
    end

dbref(chainID = nil) click to toggle source

Gets DBREF records. Returns an array of Bio::PDB::Record::DBREF objects.

If chainID is given, it returns corresponding DBREF records.

    # File lib/bio/db/pdb/pdb.rb, line 1848
    def dbref(chainID = nil)
      if chainID then
        self.record('DBREF').find_all { |f| f.chainID == chainID }
      else
        self.record('DBREF')
      end
    end

definition() click to toggle source

Title of this entry in "TITLE".

    # File lib/bio/db/pdb/pdb.rb, line 1892
    def definition
      f = self.record('TITLE').first
      f ? f.title : nil
    end

each() click to toggle source

Iterates over each model. Iterates over each of the models in the structure. Returns `self`.

    # File lib/bio/db/pdb/pdb.rb, line 1624
    def each
      @models.each{ |model| yield model }
      self
    end

Also aliased as: each_model
each_model() click to toggle source

Alias needed for Bio::PDB::ModelFinder

Alias for: each
entry_id() click to toggle source

PDB identifier written in "HEADER". (e.g. 1A00)

    # File lib/bio/db/pdb/pdb.rb, line 1878
    def entry_id
      unless @id
        f = self.record('HEADER').first
        @id = f ? f.idCode : nil
      end
      @id
    end

helix(helixID = nil) click to toggle source

Gets HELIX records. If no arguments are given, it returns all HELIX records. (Returns an array of `Bio::PDB::Record::HELIX` instances.) If helixID is given, it only returns records corresponding to given helixID. (Returns an `Bio::PDB::Record::HELIX` instance.)

    # File lib/bio/db/pdb/pdb.rb, line 1749
    def helix(helixID = nil)
      if helixID then
        self.record('HELIX').find { |f| f.helixID == helixID }
      else
        self.record('HELIX')
      end
    end

inspect() click to toggle source

returns a string containing human-readable representation of this object.

    # File lib/bio/db/pdb/pdb.rb, line 1905
    def inspect
      "#<#{self.class.to_s} entry_id=#{entry_id.inspect}>"
    end

jrnl(sub_record = nil) click to toggle source

Gets JRNL records. If no arguments, it returns all JRNL records as a hash. If sub record name is specified, it returns only corresponding records as an array of Bio::PDB::Record instances.

    # File lib/bio/db/pdb/pdb.rb, line 1730
    def jrnl(sub_record = nil)
      unless defined?(@jrnl)
        @jrnl = make_hash(self.record('JRNL'), :sub_record)
      end
      sub_record ? @jrnl[sub_record] : @jrnl
    end

keywords() click to toggle source

Keywords in "KEYWDS". Returns an array of string.

    # File lib/bio/db/pdb/pdb.rb, line 1858
    def keywords
      self.record('KEYWDS').collect { |f| f.keywds }.flatten
    end

record(name = nil) click to toggle source

Gets all records whose record type is name. Returns an array of `Bio::PDB::Record::*` objects.

if name is nil, returns hash storing all record data.

Example: p pdb.record('HETATM') p pdb.record

    # File lib/bio/db/pdb/pdb.rb, line 1696
    def record(name = nil)
      name ? (@hash[name] || []) : @hash
    end

remark(nn = nil) click to toggle source

Gets REMARK records. If no arguments, it returns all REMARK records as a hash. If remark number is specified, returns only corresponding REMARK records. If number == 1 or 2 ("REMARK 1" or "REMARK 2"), returns an array of Bio::PDB::Record instances. Otherwise, returns an array of strings.

    # File lib/bio/db/pdb/pdb.rb, line 1711
    def remark(nn = nil)
      unless defined?(@remark)
        h = make_hash(self.record('REMARK'), :remarkNum)
        h.each do |i, a|
            a.shift # remove first record (= space only)
          if i != 1 and i != 2 then
            a.collect! { |f| f.text.gsub(/\s+\z/, '') }
          end
        end
        @remark = h
      end
      nn ? @remark[nn] : @remark
    end

seqres(chainID = nil) click to toggle source

Amino acid or nucleic acid sequence of backbone residues in "SEQRES". If chainID is given, it returns corresponding sequence as an array of string. Otherwise, returns a hash which contains all sequences.

    # File lib/bio/db/pdb/pdb.rb, line 1802
    def seqres(chainID = nil)
      unless defined?(@seqres)
        h = make_hash(self.record('SEQRES'), :chainID)
        newHash = {}
        h.each do |k, a|
          a.collect! { |f| f.resName }
          a.flatten!
          # determine nuc or aa?
          tmp = Hash.new(0)
          a[0,13].each { |x| tmp[x.to_s.strip.size] += 1 }
          if tmp[3] >= tmp[1] then
            # amino acid sequence
            a.collect! do |aa|
              #aa is three letter code: i.e. ALA
              #need to look up with Ala
              aa = aa.capitalize
              (begin
                 Bio::AminoAcid.three2one(aa)
               rescue ArgumentError
                 nil
               end || 'X')
            end
            seq = Bio::Sequence::AA.new(a.join(''))
          else
            # nucleic acid sequence
            a.collect! do |na|
              na = na.delete('^a-zA-Z')
              na.size == 1 ? na : 'n'
            end
            seq = Bio::Sequence::NA.new(a.join(''))
          end
          newHash[k] = seq
        end
        @seqres = newHash
      end
      if chainID then
        @seqres[chainID]
      else
        @seqres
      end
    end

sheet(sheetID = nil) click to toggle source

Gets SHEET records. If no arguments are given, it returns all SHEET records as an array of arrays of `Bio::PDB::Record::SHEET` instances. If sheetID is given, it returns an array of `Bio::PDB::Record::SHEET` instances.

    # File lib/bio/db/pdb/pdb.rb, line 1777
    def sheet(sheetID = nil)
      unless defined?(@sheet)
        @sheet = make_grouping(self.record('SHEET'), :sheetID)
      end
      if sheetID then
        @sheet.find_all { |f| f.first.sheetID == sheetID }
      else
        @sheet
      end
    end

ssbond() click to toggle source

Gets SSBOND records.

    # File lib/bio/db/pdb/pdb.rb, line 1789
    def ssbond
      self.record('SSBOND')
    end

to_s() click to toggle source

Returns a string of Bio::PDB::Models. This propogates down the heirarchy till you get to Bio::PDB::Record::ATOM which are outputed in PDB format

    # File lib/bio/db/pdb/pdb.rb, line 1647
    def to_s
      string = ""
      @models.each{ |model| string << model.to_s }
      string << "END\n"
      return string
    end

turn(turnId = nil) click to toggle source

Gets TURN records. If no arguments are given, it returns all TURN records. (Returns an array of `Bio::PDB::Record::TURN` instances.) If turnId is given, it only returns a record corresponding to given turnId. (Returns an `Bio::PDB::Record::TURN` instance.)

    # File lib/bio/db/pdb/pdb.rb, line 1764
    def turn(turnId = nil)
      if turnId then
        self.record('TURN').find { |f| f.turnId == turnId }
      else
        self.record('TURN')
      end
    end

version() click to toggle source

Current modification number in "REVDAT".

    # File lib/bio/db/pdb/pdb.rb, line 1898
    def version
      f = self.record('REVDAT').first
      f ? f.modNum : nil
    end

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