class 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
all records in this entry as an array.
all records in this entry as an hash accessed by record names.
models in this entry (array).
Public Class Methods
Creates a new Bio::PDB object from given str.
# File lib/bio/db/pdb/pdb.rb 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
Provides keyed access to the models based on serial number returns nil if it’s not there
# File lib/bio/db/pdb/pdb.rb 1633 def [](key) 1634 @models.find{ |model| key == model.model_serial } 1635 end
Same as Bio::PDB#entry_id.
# File lib/bio/db/pdb/pdb.rb 1887 def accession 1888 self.entry_id 1889 end
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 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
Classification in “HEADER”.
# File lib/bio/db/pdb/pdb.rb 1863 def classification 1864 f = self.record('HEADER').first 1865 f ? f.classification : nil 1866 end
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 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
Title of this entry in “TITLE”.
# File lib/bio/db/pdb/pdb.rb 1892 def definition 1893 f = self.record('TITLE').first 1894 f ? f.title : nil 1895 end
Iterates over each model. Iterates over each of the models in the structure. Returns self.
# File lib/bio/db/pdb/pdb.rb 1624 def each 1625 @models.each{ |model| yield model } 1626 self 1627 end
PDB identifier written in “HEADER”. (e.g. 1A00)
# File lib/bio/db/pdb/pdb.rb 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
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 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
returns a string containing human-readable representation of this object.
# File lib/bio/db/pdb/pdb.rb 1905 def inspect 1906 "#<#{self.class.to_s} entry_id=#{entry_id.inspect}>" 1907 end
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 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 in “KEYWDS”. Returns an array of string.
# File lib/bio/db/pdb/pdb.rb 1858 def keywords 1859 self.record('KEYWDS').collect { |f| f.keywds }.flatten 1860 end
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 1696 def record(name = nil) 1697 name ? (@hash[name] || []) : @hash 1698 end
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 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
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 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
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 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
Gets SSBOND records.
# File lib/bio/db/pdb/pdb.rb 1789 def ssbond 1790 self.record('SSBOND') 1791 end
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 1647 def to_s 1648 string = "" 1649 @models.each{ |model| string << model.to_s } 1650 string << "END\n" 1651 return string 1652 end
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 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
Current modification number in “REVDAT”.
# File lib/bio/db/pdb/pdb.rb 1898 def version 1899 f = self.record('REVDAT').first 1900 f ? f.modNum : nil 1901 end