Class | Bio::PDB
In: | lib/bio/db/pdb.rb lib/bio/db/pdb/atom.rb lib/bio/db/pdb/chain.rb lib/bio/db/pdb/chemicalcomponent.rb lib/bio/db/pdb/model.rb lib/bio/db/pdb/pdb.rb lib/bio/db/pdb/residue.rb lib/bio/db/pdb/utils.rb
Parent: | Object

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

### Methods

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

### Included Modules

Utils AtomFinder ResidueFinder ChainFinder ModelFinder HetatmFinder HeterogenFinder Enumerable

### Classes and Modules

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

### Constants

DELIMITER | = | RS = nil |  | delimiter for reading via Bio::FlatFile
Coordinate_fileds | = | { 'MODEL' => true, :MODEL => true, 'ENDMDL' => true, :ENDMDL => true, 'ATOM' => true, :ATOM => true, 'HETATM' => true, :HETATM => true, 'SIGATM' => true, :SIGATM => true, 'SIGUIJ' => true, :SIGUIJ => true, 'ANISOU' => true, :ANISOU => true, 'TER' => true, :TER => true, }

### 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)

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

[Source]

          # File lib/bio/db/pdb/pdb.rb, line 1445
    1445:     def initialize(str)
    1446:       #Aha! Our entry into the world of PDB parsing, we initialise a PDB
    1447:       #object with the whole PDB file as a string
    1448:       #each PDB has an array of the lines of the original file
    1449:       #a bit memory-tastic! A hash of records and an array of models
    1450:       #also has an id
    1451:
    1452:       @data = str.split(/[\r\n]+/)
    1453:       @hash = {}
    1454:       @models = []
    1455:       @id = nil
    1456:
    1457:       #Flag to say whether the current line is part of a continuation
    1458:       cont = false
    1459:
    1460:       #Empty current model
    1461:       cModel    = Model.new
    1462:       cChain    = nil #Chain.new
    1463:       cResidue  = nil #Residue.new
    1464:       cLigand   = nil #Heterogen.new
    1465:       c_atom    = nil
    1466:
    1467:       #Goes through each line and replace that line with a PDB::Record
    1468:       @data.collect! do |line|
    1469:         #Go to next if the previous line was contiunation able, and
    1470:         #add_continuation returns true. Line is added by add_continuation
    1471:         next if cont and cont = cont.add_continuation(line)
    1472:
    1473:         #Make the new record
    1474:         f = Record.get_record_class(line).new.initialize_from_string(line)
    1475:         #p f
    1476:         #Set cont
    1477:         cont = f if f.continue?
    1478:         #Set the hash to point to this record either by adding to an
    1479:         #array, or on it's own
    1480:         key = f.record_name
    1481:         if a = @hash[key] then
    1482:           a << f
    1483:         else
    1484:           @hash[key] = [ f ]
    1485:         end
    1486:
    1487:         # Do something for ATOM and HETATM
    1488:         if key == 'ATOM' or key == 'HETATM' then
    1489:           if cChain and f.chainID == cChain.id
    1490:             chain = cChain
    1491:           else
    1492:             if chain = cModel[f.chainID]
    1493:               cChain = chain unless cChain
    1494:             else
    1495:               # If we don't have chain, add a new chain
    1496:               newChain = Chain.new(f.chainID, cModel)
    1497:               cModel.addChain(newChain)
    1498:               cChain = newChain
    1499:               chain = newChain
    1500:             end
    1501:             # chain might be changed, clearing cResidue and cLigand
    1502:             cResidue = nil
    1503:             cLigand = nil
    1504:           end
    1505:         end
    1506:
    1507:         case key
    1508:         when 'ATOM'
    1509:           c_atom = f
    1510:           residueID = Residue.get_residue_id_from_atom(f)
    1511:
    1512:           if cResidue and residueID == cResidue.id
    1513:             residue = cResidue
    1514:           else
    1515:             if residue = chain.get_residue_by_id(residueID)
    1516:               cResidue = residue unless cResidue
    1517:             else
    1518:               # add a new residue
    1519:               newResidue = Residue.new(f.resName, f.resSeq, f.iCode, chain)
    1520:               chain.addResidue(newResidue)
    1521:               cResidue = newResidue
    1522:               residue = newResidue
    1523:             end
    1524:           end
    1525:
    1526:           f.residue = residue
    1527:           residue.addAtom(f)
    1528:
    1529:         when 'HETATM'
    1530:           c_atom = f
    1531:           residueID = Heterogen.get_residue_id_from_atom(f)
    1532:
    1533:           if cLigand and residueID == cLigand.id
    1534:             ligand = cLigand
    1535:           else
    1536:             if ligand = chain.get_heterogen_by_id(residueID)
    1537:               cLigand = ligand unless cLigand
    1538:             else
    1539:               # add a new heterogen
    1540:               newLigand = Heterogen.new(f.resName, f.resSeq, f.iCode, chain)
    1541:               chain.addLigand(newLigand)
    1542:               cLigand = newLigand
    1543:               ligand = newLigand
    1544:               #Each model has a special solvent chain. (for compatibility)
    1545:               if f.resName == 'HOH'
    1546:                 cModel.addSolvent(newLigand)
    1547:               end
    1548:             end
    1549:           end
    1550:
    1551:           f.residue = ligand
    1552:           ligand.addAtom(f)
    1553:
    1554:         when 'MODEL'
    1555:           c_atom = nil
    1556:           cChain = nil
    1557:           cResidue = nil
    1558:           cLigand = nil
    1559:           if cModel.model_serial or cModel.chains.size > 0 then
    1560:             self.addModel(cModel)
    1561:           end
    1562:           cModel = Model.new(f.serial)
    1563:
    1564:         when 'TER'
    1565:           if c_atom
    1566:             c_atom.ter = f
    1567:           else
    1568:             #$stderr.puts "Warning: stray TER?"
    1569:           end
    1570:         when 'SIGATM'
    1571:           if c_atom
    1572:             #$stderr.puts "Warning: duplicated SIGATM?" if c_atom.sigatm
    1573:             c_atom.sigatm = f
    1574:           else
    1575:             #$stderr.puts "Warning: stray SIGATM?"
    1576:           end
    1577:         when 'ANISOU'
    1578:           if c_atom
    1579:             #$stderr.puts "Warning: duplicated ANISOU?" if c_atom.anisou
    1580:             c_atom.anisou = f
    1581:           else
    1582:             #$stderr.puts "Warning: stray ANISOU?"
    1583:           end
    1584:         when 'SIGUIJ'
    1585:           if c_atom and c_atom.anisou
    1586:             #$stderr.puts "Warning: duplicated SIGUIJ?" if c_atom.anisou.siguij
    1587:             c_atom.anisou.siguij = f
    1588:           else
    1589:             #$stderr.puts "Warning: stray SIGUIJ?"
    1590:           end
    1591:
    1592:         else
    1593:           c_atom = nil
    1594:
    1595:         end
    1596:         f
    1597:       end #each
    1598:       #At the end we need to add the final model
    1599:       self.addModel(cModel)
    1600:       @data.compact!
    1601:     end

### Public Instance methods

[](key)

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

[Source]

          # File lib/bio/db/pdb/pdb.rb, line 1633
    1633:     def [](key)
    1634:       @models.find{ |model| key == model.model_serial }
    1635:     end

accession()

Same as `Bio::PDB#entry_id`.

[Source]

          # File lib/bio/db/pdb/pdb.rb, line 1887
    1887:     def accession
    1888:       self.entry_id
    1889:     end

addModel(model)

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

[Source]

          # File lib/bio/db/pdb/pdb.rb, line 1615
    1615:     def addModel(model)
    1616:       raise "Expecting a Bio::PDB::Model" if not model.is_a? Bio::PDB::Model
    1617:       @models.push(model)
    1618:       self
    1619:     end

authors()

Get authors in "AUTHOR".

[Source]

          # File lib/bio/db/pdb/pdb.rb, line 1869
    1869:     def authors
    1870:       self.record('AUTHOR').collect { |f| f.authorList }.flatten
    1871:     end

classification()

Classification in "HEADER".

[Source]

          # File lib/bio/db/pdb/pdb.rb, line 1863
    1863:     def classification
    1864:       f = self.record('HEADER').first
    1865:       f ? f.classification : nil
    1866:     end

dbref(chainID = nil)

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

If chainID is given, it returns corresponding DBREF records.

[Source]

          # File lib/bio/db/pdb/pdb.rb, line 1848
    1848:     def dbref(chainID = nil)
    1849:       if chainID then
    1850:         self.record('DBREF').find_all { |f| f.chainID == chainID }
    1851:       else
    1852:         self.record('DBREF')
    1853:       end
    1854:     end

definition()

Title of this entry in "TITLE".

[Source]

          # File lib/bio/db/pdb/pdb.rb, line 1892
    1892:     def definition
    1893:       f = self.record('TITLE').first
    1894:       f ? f.title : nil
    1895:     end

each() {|model| ...}

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

[Source]

          # File lib/bio/db/pdb/pdb.rb, line 1624
    1624:     def each
    1625:       @models.each{ |model| yield model }
    1626:       self
    1627:     end

each_model()

Alias for each

entry_id()

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

[Source]

          # File lib/bio/db/pdb/pdb.rb, line 1878
    1878:     def entry_id
    1879:       unless @id
    1880:         f = self.record('HEADER').first
    1881:         @id = f ? f.idCode : nil
    1882:       end
    1883:       @id
    1884:     end

helix(helixID = nil)

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.)

[Source]

          # File lib/bio/db/pdb/pdb.rb, line 1749
    1749:     def helix(helixID = nil)
    1750:       if helixID then
    1751:         self.record('HELIX').find { |f| f.helixID == helixID }
    1752:       else
    1753:         self.record('HELIX')
    1754:       end
    1755:     end

inspect()

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

[Source]

          # File lib/bio/db/pdb/pdb.rb, line 1905
    1905:     def inspect
    1906:       "#<#{self.class.to_s} entry_id=#{entry_id.inspect}>"
    1907:     end

jrnl(sub_record = nil)

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.

[Source]

          # File lib/bio/db/pdb/pdb.rb, line 1730
    1730:     def jrnl(sub_record = nil)
    1731:       unless defined?(@jrnl)
    1732:         @jrnl = make_hash(self.record('JRNL'), :sub_record)
    1733:       end
    1734:       sub_record ? @jrnl[sub_record] : @jrnl
    1735:     end

keywords()

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

[Source]

          # File lib/bio/db/pdb/pdb.rb, line 1858
    1858:     def keywords
    1859:       self.record('KEYWDS').collect { |f| f.keywds }.flatten
    1860:     end

record(name = nil)

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[‘HETATM’]

[Source]

          # File lib/bio/db/pdb/pdb.rb, line 1696
    1696:     def record(name = nil)
    1697:       name ? (@hash[name] || []) : @hash
    1698:     end

remark(nn = nil)

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.

[Source]

          # File lib/bio/db/pdb/pdb.rb, line 1711
    1711:     def remark(nn = nil)
    1712:       unless defined?(@remark)
    1713:         h = make_hash(self.record('REMARK'), :remarkNum)
    1714:         h.each do |i, a|
    1715:             a.shift # remove first record (= space only)
    1716:           if i != 1 and i != 2 then
    1717:             a.collect! { |f| f.text.gsub(/\s+\z/, '') }
    1718:           end
    1719:         end
    1720:         @remark = h
    1721:       end
    1722:       nn ? @remark[nn] : @remark
    1723:     end

seqres(chainID = nil)

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.

[Source]

          # File lib/bio/db/pdb/pdb.rb, line 1802
    1802:     def seqres(chainID = nil)
    1803:       unless defined?(@seqres)
    1804:         h = make_hash(self.record('SEQRES'), :chainID)
    1805:         newHash = {}
    1806:         h.each do |k, a|
    1807:           a.collect! { |f| f.resName }
    1808:           a.flatten!
    1809:           # determine nuc or aa?
    1810:           tmp = Hash.new(0)
    1811:           a[0,13].each { |x| tmp[x.to_s.strip.size] += 1 }
    1812:           if tmp[3] >= tmp[1] then
    1813:             # amino acid sequence
    1814:             a.collect! do |aa|
    1815:               #aa is three letter code: i.e. ALA
    1816:               #need to look up with Ala
    1817:               aa = aa.capitalize
    1818:               (begin
    1819:                  Bio::AminoAcid.three2one(aa)
    1820:                rescue ArgumentError
    1821:                  nil
    1822:                end || 'X')
    1823:             end
    1824:             seq = Bio::Sequence::AA.new(a.join(''))
    1825:           else
    1826:             # nucleic acid sequence
    1827:             a.collect! do |na|
    1828:               na = na.delete('^a-zA-Z')
    1829:               na.size == 1 ? na : 'n'
    1830:             end
    1831:             seq = Bio::Sequence::NA.new(a.join(''))
    1832:           end
    1833:           newHash[k] = seq
    1834:         end
    1835:         @seqres = newHash
    1836:       end
    1837:       if chainID then
    1838:         @seqres[chainID]
    1839:       else
    1840:         @seqres
    1841:       end
    1842:     end

sheet(sheetID = nil)

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.

[Source]

          # File lib/bio/db/pdb/pdb.rb, line 1777
    1777:     def sheet(sheetID = nil)
    1778:       unless defined?(@sheet)
    1779:         @sheet = make_grouping(self.record('SHEET'), :sheetID)
    1780:       end
    1781:       if sheetID then
    1782:         @sheet.find_all { |f| f.first.sheetID == sheetID }
    1783:       else
    1784:         @sheet
    1785:       end
    1786:     end

ssbond()

Gets SSBOND records.

[Source]

          # File lib/bio/db/pdb/pdb.rb, line 1789
    1789:     def ssbond
    1790:       self.record('SSBOND')
    1791:     end

to_s()

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

[Source]

          # File lib/bio/db/pdb/pdb.rb, line 1647
    1647:     def to_s
    1648:       string = ""
    1649:       @models.each{ |model| string << model.to_s }
    1650:       string << "END\n"
    1651:       return string
    1652:     end

turn(turnId = nil)

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.)

[Source]

          # File lib/bio/db/pdb/pdb.rb, line 1764
    1764:     def turn(turnId = nil)
    1765:       if turnId then
    1766:         self.record('TURN').find { |f| f.turnId == turnId }
    1767:       else
    1768:         self.record('TURN')
    1769:       end
    1770:     end

version()

Current modification number in "REVDAT".

[Source]

          # File lib/bio/db/pdb/pdb.rb, line 1898
    1898:     def version
    1899:       f = self.record('REVDAT').first
    1900:       f ? f.modNum : nil
    1901:     end

[Validate]