Class | Bio::PDB::Record::ATOM |
In: |
lib/bio/db/pdb/pdb.rb
|
Parent: | Object |
occupancy | -> | occ |
for backward compatibility | ||
tempFactor | -> | bfac |
for backward compatibility |
anisou | [RW] | ANISOU record |
residue | [RW] | residue the atom belongs to. |
sigatm | [RW] | SIGATM record |
ter | [RW] | TER record |
Sorts based on serial numbers
# File lib/bio/db/pdb/pdb.rb, line 974 974: def <=>(other) 975: return serial <=> other.serial 976: end
# File lib/bio/db/pdb/pdb.rb, line 978 978: 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
# File lib/bio/db/pdb/pdb.rb, line 1046 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
Returns a Coordinate class instance of the xyz positions
# File lib/bio/db/pdb/pdb.rb, line 964 964: def xyz 965: Coordinate[ x, y, z ] 966: end