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