Class Bio::PDB::Record::ATOM
In: lib/bio/db/pdb/pdb.rb  (CVS)
Parent: Object

ATOM record class

Methods

<=>   do_parse   to_a   to_s   xyz  

Included Modules

Utils Comparable

External Aliases

occupancy -> occ
  for backward compatibility
tempFactor -> bfac
  for backward compatibility

Attributes

anisou  [RW]  ANISOU record
residue  [RW]  residue the atom belongs to.
sigatm  [RW]  SIGATM record
ter  [RW]  TER record

Public Instance methods

Sorts based on serial numbers

[Source]

# File lib/bio/db/pdb/pdb.rb, line 973
        def <=>(other)
          return serial <=> other.serial
        end

[Source]

# File lib/bio/db/pdb/pdb.rb, line 977
        def do_parse
          return self if @parsed or !@str
          self.serial     = @str[6..10].to_i
          self.name       = @str[12..15].strip
          self.altLoc     = @str[16..16]
          self.resName    = @str[17..19].strip
          self.chainID    = @str[21..21]
          self.resSeq     = @str[22..25].to_i
          self.iCode      = @str[26..26].strip
          self.x          = @str[30..37].to_f
          self.y          = @str[38..45].to_f
          self.z          = @str[46..53].to_f
          self.occupancy  = @str[54..59].to_f
          self.tempFactor = @str[60..65].to_f
          self.segID      = @str[72..75].to_s.rstrip
          self.element    = @str[76..77].to_s.lstrip
          self.charge     = @str[78..79].to_s.strip
          @parsed = true
          self
        end

Returns an array of the xyz positions

[Source]

# File lib/bio/db/pdb/pdb.rb, line 968
        def to_a
          [ x, y, z ]
        end

[Source]

# File lib/bio/db/pdb/pdb.rb, line 1045
        def to_s
          atomname = justify_atomname
          sprintf("%-6s%5d %-4s%-1s%3s %-1s%4d%-1s   %8.3f%8.3f%8.3f%6.2f%6.2f      %-4s%2s%-2s\n",
                  self.record_name,
                  self.serial, 
                  atomname,
                  self.altLoc,
                  self.resName,
                  self.chainID,
                  self.resSeq,
                  self.iCode,
                  self.x, self.y, self.z,
                  self.occupancy,
                  self.tempFactor,
                  self.segID,
                  self.element,
                  self.charge)
        end

Returns a Coordinate class instance of the xyz positions

[Source]

# File lib/bio/db/pdb/pdb.rb, line 963
        def xyz
          Coordinate[ x, y, z ]
        end

[Validate]