Class Bio::PDB::Record::ATOM
In: lib/bio/db/pdb/pdb.rb
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

<=>(other)

Sorts based on serial numbers

[Source]

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

[Source]

     # File lib/bio/db/pdb/pdb.rb, line 977
977:         def do_parse
978:           return self if @parsed or !@str
979:           self.serial     = @str[6..10].to_i
980:           self.name       = @str[12..15].strip
981:           self.altLoc     = @str[16..16]
982:           self.resName    = @str[17..19].strip
983:           self.chainID    = @str[21..21]
984:           self.resSeq     = @str[22..25].to_i
985:           self.iCode      = @str[26..26].strip
986:           self.x          = @str[30..37].to_f
987:           self.y          = @str[38..45].to_f
988:           self.z          = @str[46..53].to_f
989:           self.occupancy  = @str[54..59].to_f
990:           self.tempFactor = @str[60..65].to_f
991:           self.segID      = @str[72..75].to_s.rstrip
992:           self.element    = @str[76..77].to_s.lstrip
993:           self.charge     = @str[78..79].to_s.strip
994:           @parsed = true
995:           self
996:         end
to_a()

Returns an array of the xyz positions

[Source]

     # File lib/bio/db/pdb/pdb.rb, line 968
968:         def to_a
969:           [ x, y, z ]
970:         end
to_s()

[Source]

      # File lib/bio/db/pdb/pdb.rb, line 1045
1045:         def to_s
1046:           atomname = justify_atomname
1047:           sprintf("%-6s%5d %-4s%-1s%3s %-1s%4d%-1s   %8.3f%8.3f%8.3f%6.2f%6.2f      %-4s%2s%-2s\n",
1048:                   self.record_name,
1049:                   self.serial, 
1050:                   atomname,
1051:                   self.altLoc,
1052:                   self.resName,
1053:                   self.chainID,
1054:                   self.resSeq,
1055:                   self.iCode,
1056:                   self.x, self.y, self.z,
1057:                   self.occupancy,
1058:                   self.tempFactor,
1059:                   self.segID,
1060:                   self.element,
1061:                   self.charge)
1062:         end
xyz()

Returns a Coordinate class instance of the xyz positions

[Source]

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

[Validate]