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)
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Sorts based on serial numbers
# File lib/bio/db/pdb/pdb.rb 974 def <=>(other) 975 return serial <=> other.serial 976 end
do_parse()
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# File lib/bio/db/pdb/pdb.rb 978 def do_parse 979 return self if @parsed or !@str 980 self.serial = @str[6..10].to_i 981 self.name = @str[12..15].strip 982 self.altLoc = @str[16..16] 983 self.resName = @str[17..19].strip 984 self.chainID = @str[21..21] 985 self.resSeq = @str[22..25].to_i 986 self.iCode = @str[26..26].strip 987 self.x = @str[30..37].to_f 988 self.y = @str[38..45].to_f 989 self.z = @str[46..53].to_f 990 self.occupancy = @str[54..59].to_f 991 self.tempFactor = @str[60..65].to_f 992 self.segID = @str[72..75].to_s.rstrip 993 self.element = @str[76..77].to_s.lstrip 994 self.charge = @str[78..79].to_s.strip 995 @parsed = true 996 self 997 end
to_a()
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Returns an array of the xyz positions
# File lib/bio/db/pdb/pdb.rb 969 def to_a 970 [ x, y, z ] 971 end
to_s()
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# File lib/bio/db/pdb/pdb.rb 1046 def to_s 1047 atomname = justify_atomname 1048 sprintf("%-6s%5d %-4s%-1s%3s %-1s%4d%-1s %8.3f%8.3f%8.3f%6.2f%6.2f %-4s%2s%-2s\n", 1049 self.record_name, 1050 self.serial, 1051 atomname, 1052 self.altLoc, 1053 self.resName, 1054 self.chainID, 1055 self.resSeq, 1056 self.iCode, 1057 self.x, self.y, self.z, 1058 self.occupancy, 1059 self.tempFactor, 1060 self.segID, 1061 self.element, 1062 self.charge) 1063 end
xyz()
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Returns a Coordinate
class instance of the xyz positions
# File lib/bio/db/pdb/pdb.rb 964 def xyz 965 Coordinate[ x, y, z ] 966 end