Module Bio::AminoAcid::Data
In: lib/bio/data/aa.rb

Methods

[]   aa   name   name2one   name2three   names   one   one2name   one2three   three   three2name   three2one   to_1   to_3   to_re   weight  

Constants

NAMES = { 'A' => 'Ala', 'C' => 'Cys', 'D' => 'Asp', 'E' => 'Glu', 'F' => 'Phe', 'G' => 'Gly', 'H' => 'His', 'I' => 'Ile', 'K' => 'Lys', 'L' => 'Leu', 'M' => 'Met', 'N' => 'Asn', 'P' => 'Pro', 'Q' => 'Gln', 'R' => 'Arg', 'S' => 'Ser', 'T' => 'Thr', 'V' => 'Val', 'W' => 'Trp', 'Y' => 'Tyr', 'B' => 'Asx', # D/N 'Z' => 'Glx', # E/Q 'J' => 'Xle', # I/L 'U' => 'Sec', # 'uga' (stop) 'O' => 'Pyl', # 'uag' (stop) 'X' => 'Xaa', # (unknown) 'Ala' => 'alanine', 'Cys' => 'cysteine', 'Asp' => 'aspartic acid', 'Glu' => 'glutamic acid', 'Phe' => 'phenylalanine', 'Gly' => 'glycine', 'His' => 'histidine', 'Ile' => 'isoleucine', 'Lys' => 'lysine', 'Leu' => 'leucine', 'Met' => 'methionine', 'Asn' => 'asparagine', 'Pro' => 'proline', 'Gln' => 'glutamine', 'Arg' => 'arginine', 'Ser' => 'serine', 'Thr' => 'threonine', 'Val' => 'valine', 'Trp' => 'tryptophan', 'Tyr' => 'tyrosine', 'Asx' => 'asparagine/aspartic acid [DN]', 'Glx' => 'glutamine/glutamic acid [EQ]', 'Xle' => 'isoleucine/leucine [IL]', 'Sec' => 'selenocysteine', 'Pyl' => 'pyrrolysine', 'Xaa' => 'unknown [A-Z]', }   IUPAC code
WEIGHT = { 'A' => 89.09, 'C' => 121.15, # 121.16 according to the Wikipedia 'D' => 133.10, 'E' => 147.13, 'F' => 165.19, 'G' => 75.07, 'H' => 155.16, 'I' => 131.17, 'K' => 146.19, 'L' => 131.17, 'M' => 149.21, 'N' => 132.12, 'P' => 115.13, 'Q' => 146.15, 'R' => 174.20, 'S' => 105.09, 'T' => 119.12, 'U' => 168.06, 'V' => 117.15, 'W' => 204.23, 'Y' => 181.19, }   AAindex FASG760101 - Molecular weight (Fasman, 1976)
  Fasman, G.D., ed.
  Handbook of Biochemistry and Molecular Biology", 3rd ed.,
  Proteins - Volume 1, CRC Press, Cleveland (1976)

Public Instance methods

[Source]

     # File lib/bio/data/aa.rb, line 131
131:     def [](x)
132:       NAMES[x]
133:     end
aa()

Alias for names

[Source]

     # File lib/bio/data/aa.rb, line 141
141:     def name(x)
142:       str = NAMES[x]
143:       if str and str.length == 3
144:         NAMES[str]
145:       else
146:         str
147:       end
148:     end

[Source]

     # File lib/bio/data/aa.rb, line 198
198:     def name2one(x)
199:       str = reverse[x.to_s.downcase]
200:       if str and str.length == 3
201:         three2one(str)
202:       else
203:         str
204:       end
205:     end

[Source]

     # File lib/bio/data/aa.rb, line 215
215:     def name2three(x)
216:       reverse[x.downcase]
217:     end

backward compatibility

[Source]

     # File lib/bio/data/aa.rb, line 136
136:     def names
137:       NAMES
138:     end
one(x)

Alias for to_1

[Source]

     # File lib/bio/data/aa.rb, line 190
190:     def one2name(x)
191:       if x and x.length != 1
192:         raise ArgumentError
193:       else
194:         three2name(NAMES[x])
195:       end
196:     end

[Source]

     # File lib/bio/data/aa.rb, line 174
174:     def one2three(x)
175:       if x and x.length != 1
176:         raise ArgumentError
177:       else
178:         NAMES[x]
179:       end
180:     end
three(x)

Alias for to_3

[Source]

     # File lib/bio/data/aa.rb, line 207
207:     def three2name(x)
208:       if x and x.length != 3
209:         raise ArgumentError
210:       else
211:         NAMES[x]
212:       end
213:     end

[Source]

     # File lib/bio/data/aa.rb, line 182
182:     def three2one(x)
183:       if x and x.length != 3
184:         raise ArgumentError
185:       else
186:         reverse[x]
187:       end
188:     end

[Source]

     # File lib/bio/data/aa.rb, line 150
150:     def to_1(x)
151:       case x.to_s.length
152:       when 1
153:         x
154:       when 3
155:         three2one(x)
156:       else
157:         name2one(x)
158:       end
159:     end

[Source]

     # File lib/bio/data/aa.rb, line 162
162:     def to_3(x)
163:       case x.to_s.length
164:       when 1
165:         one2three(x)
166:       when 3
167:         x
168:       else
169:         name2three(x)
170:       end
171:     end

[Source]

     # File lib/bio/data/aa.rb, line 219
219:     def to_re(seq)
220:       replace = {
221:         'B' => '[DNB]',
222:         'Z' => '[EQZ]',
223:         'J' => '[ILJ]',
224:         'X' => '[ACDEFGHIKLMNPQRSTVWYUOX]',
225:       }
226:       replace.default = '.'
227: 
228:       str = seq.to_s.upcase
229:       str.gsub!(/[^ACDEFGHIKLMNPQRSTVWYUO]/) { |aa|
230:         replace[aa]
231:       }
232:       Regexp.new(str)
233:     end

[Source]

     # File lib/bio/data/aa.rb, line 110
110:     def weight(x = nil)
111:       if x
112:         if x.length > 1
113:           total = 0.0
114:           x.each_byte do |byte|
115:             aa = byte.chr.upcase
116:             if WEIGHT[aa]
117:               total += WEIGHT[aa]
118:             else
119:               raise "Error: invalid amino acid '#{aa}'"
120:             end
121:           end
122:           total -= NucleicAcid.weight[:water] * (x.length - 1)
123:         else
124:           WEIGHT[x]
125:         end
126:       else
127:         WEIGHT
128:       end
129:     end

[Validate]