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]