class Bio::PDB::Record::ATOM

ATOM record class

Attributes

anisou[RW]

ANISOU record

residue[RW]

residue the atom belongs to.

sigatm[RW]

SIGATM record

ter[RW]

TER record

Public Instance Methods

<=>(other) click to toggle source

Sorts based on serial numbers

# File lib/bio/db/pdb/pdb.rb, line 974
def <=>(other)
  return serial <=> other.serial
end
do_parse() click to toggle source
# File lib/bio/db/pdb/pdb.rb, line 978
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
to_a() click to toggle source

Returns an array of the xyz positions

# File lib/bio/db/pdb/pdb.rb, line 969
def to_a
  [ x, y, z ]
end
to_s() click to toggle source
# File lib/bio/db/pdb/pdb.rb, line 1046
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
xyz() click to toggle source

Returns a Coordinate class instance of the xyz positions

# File lib/bio/db/pdb/pdb.rb, line 964
def xyz
  Coordinate[ x, y, z ]
end