Class: Bio::PDB

Inherits:
Object show all
Includes:
AtomFinder, ChainFinder, HetatmFinder, HeterogenFinder, ModelFinder, ResidueFinder, Utils, Enumerable
Defined in:
lib/bio/db/pdb/pdb.rb,
lib/bio/db/pdb.rb,
lib/bio/db/pdb/atom.rb,
lib/bio/db/pdb/chain.rb,
lib/bio/db/pdb/model.rb,
lib/bio/db/pdb/utils.rb,
lib/bio/db/pdb/residue.rb,
lib/bio/db/pdb/chemicalcomponent.rb

Overview

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

Defined Under Namespace

Modules: AtomFinder, ChainFinder, DataType, HetatmFinder, HeterogenFinder, ModelFinder, ResidueFinder, Utils Classes: Chain, ChemicalComponent, Coordinate, Heterogen, Model, Record, Residue

Constant Summary collapse

DELIMITER =

delimiter for reading via Bio::FlatFile

RS = nil
Coordinate_fileds =

class Record

{
  '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,
}

Constants included from Utils

Utils::ElementMass

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from HeterogenFinder

#each_heterogen, #find_heterogen, #heterogens

Methods included from HetatmFinder

#each_hetatm, #find_hetatm, #hetatms

Methods included from ModelFinder

#find_model

Methods included from ChainFinder

#chains, #each_chain, #find_chain

Methods included from ResidueFinder

#each_residue, #find_residue, #residues

Methods included from AtomFinder

#atoms, #each_atom, #find_atom

Methods included from Utils

acos, calculatePlane, #centreOfGravity, convert_to_xyz, dihedral_angle, distance, #finder, #geometricCentre, rad2deg, to_xyz

Constructor Details

#initialize(str) ⇒ PDB

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



1445
1446
1447
1448
1449
1450
1451
1452
1453
1454
1455
1456
1457
1458
1459
1460
1461
1462
1463
1464
1465
1466
1467
1468
1469
1470
1471
1472
1473
1474
1475
1476
1477
1478
1479
1480
1481
1482
1483
1484
1485
1486
1487
1488
1489
1490
1491
1492
1493
1494
1495
1496
1497
1498
1499
1500
1501
1502
1503
1504
1505
1506
1507
1508
1509
1510
1511
1512
1513
1514
1515
1516
1517
1518
1519
1520
1521
1522
1523
1524
1525
1526
1527
1528
1529
1530
1531
1532
1533
1534
1535
1536
1537
1538
1539
1540
1541
1542
1543
1544
1545
1546
1547
1548
1549
1550
1551
1552
1553
1554
1555
1556
1557
1558
1559
1560
1561
1562
1563
1564
1565
1566
1567
1568
1569
1570
1571
1572
1573
1574
1575
1576
1577
1578
1579
1580
1581
1582
1583
1584
1585
1586
1587
1588
1589
1590
1591
1592
1593
1594
1595
1596
1597
1598
1599
1600
1601
# 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

Instance Attribute Details

#dataObject (readonly)

all records in this entry as an array.



1604
1605
1606
# File 'lib/bio/db/pdb/pdb.rb', line 1604

def data
  @data
end

#hashObject (readonly)

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



1607
1608
1609
# File 'lib/bio/db/pdb/pdb.rb', line 1607

def hash
  @hash
end

#modelsObject (readonly)

models in this entry (array).



1610
1611
1612
# File 'lib/bio/db/pdb/pdb.rb', line 1610

def models
  @models
end

Instance Method Details

#[](key) ⇒ Object

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



1633
1634
1635
# File 'lib/bio/db/pdb/pdb.rb', line 1633

def [](key)
  @models.find{ |model| key == model.model_serial }
end

#accessionObject

Same as Bio::PDB#entry_id.



1887
1888
1889
# File 'lib/bio/db/pdb/pdb.rb', line 1887

def accession
  self.entry_id
end

#addModel(model) ⇒ Object

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



1615
1616
1617
1618
1619
# 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

#authorsObject

Get authors in “AUTHOR”.



1869
1870
1871
# File 'lib/bio/db/pdb/pdb.rb', line 1869

def authors
  self.record('AUTHOR').collect { |f| f.authorList }.flatten
end

#classificationObject

Classification in “HEADER”.



1863
1864
1865
1866
# File 'lib/bio/db/pdb/pdb.rb', line 1863

def classification
  f = self.record('HEADER').first
  f ? f.classification : nil
end

#dbref(chainID = nil) ⇒ Object

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

If chainID is given, it returns corresponding DBREF records.



1848
1849
1850
1851
1852
1853
1854
# 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

#definitionObject

Title of this entry in “TITLE”.



1892
1893
1894
1895
# File 'lib/bio/db/pdb/pdb.rb', line 1892

def definition
  f = self.record('TITLE').first
  f ? f.title : nil
end

#eachObject Also known as: each_model

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



1624
1625
1626
1627
# File 'lib/bio/db/pdb/pdb.rb', line 1624

def each
  @models.each{ |model| yield model }
  self
end

#entry_idObject

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



1878
1879
1880
1881
1882
1883
1884
# 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) ⇒ Object

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.)



1749
1750
1751
1752
1753
1754
1755
# 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

#inspectObject

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



1905
1906
1907
# 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) ⇒ Object

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.



1730
1731
1732
1733
1734
1735
# 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

#keywordsObject

Keywords in “KEYWDS”. Returns an array of string.



1858
1859
1860
# File 'lib/bio/db/pdb/pdb.rb', line 1858

def keywords
  self.record('KEYWDS').collect { |f| f.keywds }.flatten
end

#record(name = nil) ⇒ Object

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



1696
1697
1698
# File 'lib/bio/db/pdb/pdb.rb', line 1696

def record(name = nil)
  name ? (@hash[name] || []) : @hash
end

#remark(nn = nil) ⇒ Object

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.



1711
1712
1713
1714
1715
1716
1717
1718
1719
1720
1721
1722
1723
# 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) ⇒ Object

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.



1802
1803
1804
1805
1806
1807
1808
1809
1810
1811
1812
1813
1814
1815
1816
1817
1818
1819
1820
1821
1822
1823
1824
1825
1826
1827
1828
1829
1830
1831
1832
1833
1834
1835
1836
1837
1838
1839
1840
1841
1842
# 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) ⇒ Object

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.



1777
1778
1779
1780
1781
1782
1783
1784
1785
1786
# 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

#ssbondObject

Gets SSBOND records.



1789
1790
1791
# File 'lib/bio/db/pdb/pdb.rb', line 1789

def ssbond
  self.record('SSBOND')
end

#to_sObject

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



1647
1648
1649
1650
1651
1652
# 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) ⇒ Object

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.)



1764
1765
1766
1767
1768
1769
1770
# 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

#versionObject

Current modification number in “REVDAT”.



1898
1899
1900
1901
# File 'lib/bio/db/pdb/pdb.rb', line 1898

def version
  f = self.record('REVDAT').first
  f ? f.modNum : nil
end