mirror of
https://github.com/biopython/biopython.git
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57056bbfc4
Reverted unwanted changes (mostly arrays in tests, but also some whitespace in doctests). Remaining changes are standardising spacing between module docstring and imports, and lower-case \x<hex> in strings.
421 lines
9.0 KiB
Python
421 lines
9.0 KiB
Python
# Copyright 2000 Andrew Dalke. All rights reserved.
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#
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# This file is part of the Biopython distribution and governed by your
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# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
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# Please see the LICENSE file that should have been included as part of this
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# package.
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"""Information about the IUPAC alphabets."""
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protein_letters = "ACDEFGHIKLMNPQRSTVWY"
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extended_protein_letters = "ACDEFGHIKLMNPQRSTVWYBXZJUO"
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# B = "Asx"; aspartic acid or asparagine (D or N)
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# X = "Xxx"; unknown or 'other' amino acid
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# Z = "Glx"; glutamic acid or glutamine (E or Q)
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# http://www.chem.qmul.ac.uk/iupac/AminoAcid/A2021.html#AA212
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#
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# J = "Xle"; leucine or isoleucine (L or I, used in NMR)
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# Mentioned in http://www.chem.qmul.ac.uk/iubmb/newsletter/1999/item3.html
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# Also the International Nucleotide Sequence Database Collaboration (INSDC)
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# (i.e. GenBank, EMBL, DDBJ) adopted this in 2006
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# http://www.ddbj.nig.ac.jp/insdc/icm2006-e.html
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#
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# Xle (J); Leucine or Isoleucine
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# The residue abbreviations, Xle (the three-letter abbreviation) and J
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# (the one-letter abbreviation) are reserved for the case that cannot
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# experimentally distinguish leucine from isoleucine.
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#
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# U = "Sec"; selenocysteine
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# http://www.chem.qmul.ac.uk/iubmb/newsletter/1999/item3.html
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#
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# O = "Pyl"; pyrrolysine
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# http://www.chem.qmul.ac.uk/iubmb/newsletter/2009.html#item35
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protein_letters_1to3 = {
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"A": "Ala",
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"C": "Cys",
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"D": "Asp",
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"E": "Glu",
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"F": "Phe",
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"G": "Gly",
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"H": "His",
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"I": "Ile",
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"K": "Lys",
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"L": "Leu",
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"M": "Met",
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"N": "Asn",
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"P": "Pro",
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"Q": "Gln",
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"R": "Arg",
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"S": "Ser",
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"T": "Thr",
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"V": "Val",
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"W": "Trp",
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"Y": "Tyr",
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}
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protein_letters_1to3_extended = {
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**protein_letters_1to3,
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**{"B": "Asx", "X": "Xaa", "Z": "Glx", "J": "Xle", "U": "Sec", "O": "Pyl"},
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}
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protein_letters_3to1 = {value: key for key, value in protein_letters_1to3.items()}
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protein_letters_3to1_extended = {
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value: key for key, value in protein_letters_1to3_extended.items()
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}
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ambiguous_dna_letters = "GATCRYWSMKHBVDN"
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unambiguous_dna_letters = "GATC"
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ambiguous_rna_letters = "GAUCRYWSMKHBVDN"
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unambiguous_rna_letters = "GAUC"
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# B == 5-bromouridine
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# D == 5,6-dihydrouridine
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# S == thiouridine
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# W == wyosine
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extended_dna_letters = "GATCBDSW"
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# are there extended forms?
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# extended_rna_letters = "GAUCBDSW"
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# "X" is included in the following _values and _complement dictionaries,
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# for historical reasons although it is not an IUPAC nucleotide,
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# and so is not in the corresponding _letters strings above
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ambiguous_dna_values = {
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"A": "A",
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"C": "C",
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"G": "G",
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"T": "T",
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"M": "AC",
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"R": "AG",
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"W": "AT",
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"S": "CG",
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"Y": "CT",
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"K": "GT",
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"V": "ACG",
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"H": "ACT",
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"D": "AGT",
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"B": "CGT",
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"X": "GATC",
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"N": "GATC",
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}
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ambiguous_rna_values = {
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"A": "A",
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"C": "C",
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"G": "G",
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"U": "U",
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"M": "AC",
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"R": "AG",
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"W": "AU",
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"S": "CG",
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"Y": "CU",
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"K": "GU",
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"V": "ACG",
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"H": "ACU",
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"D": "AGU",
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"B": "CGU",
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"X": "GAUC",
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"N": "GAUC",
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}
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ambiguous_dna_complement = {
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"A": "T",
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"C": "G",
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"G": "C",
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"T": "A",
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"M": "K",
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"R": "Y",
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"W": "W",
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"S": "S",
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"Y": "R",
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"K": "M",
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"V": "B",
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"H": "D",
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"D": "H",
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"B": "V",
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"X": "X",
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"N": "N",
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}
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ambiguous_rna_complement = {
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"A": "U",
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"C": "G",
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"G": "C",
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"U": "A",
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"M": "K",
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"R": "Y",
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"W": "W",
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"S": "S",
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"Y": "R",
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"K": "M",
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"V": "B",
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"H": "D",
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"D": "H",
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"B": "V",
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"X": "X",
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"N": "N",
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}
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def _make_ranges(mydict):
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d = {}
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for key, value in mydict.items():
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d[key] = (value, value)
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return d
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# Mass data taken from PubChem
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# Average masses of monophosphate deoxy nucleotides
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unambiguous_dna_weights = {"A": 331.2218, "C": 307.1971, "G": 347.2212, "T": 322.2085}
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# Monoisotopic masses of monophospate deoxy nucleotides
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monoisotopic_unambiguous_dna_weights = {
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"A": 331.06817,
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"C": 307.056936,
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"G": 347.063084,
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"T": 322.056602,
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}
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unambiguous_dna_weight_ranges = _make_ranges(unambiguous_dna_weights)
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unambiguous_rna_weights = {"A": 347.2212, "C": 323.1965, "G": 363.2206, "U": 324.1813}
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monoisotopic_unambiguous_rna_weights = {
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"A": 347.063084,
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"C": 323.051851,
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"G": 363.057999,
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"U": 324.035867,
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}
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unambiguous_rna_weight_ranges = _make_ranges(unambiguous_rna_weights)
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def _make_ambiguous_ranges(mydict, weight_table):
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range_d = {}
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avg_d = {}
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for letter, values in mydict.items():
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# Following line is a quick hack to skip undefined weights for U and O
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if len(values) == 1 and values[0] not in weight_table:
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continue
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weights = [weight_table.get(x) for x in values]
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range_d[letter] = (min(weights), max(weights))
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total_w = 0.0
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for w in weights:
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total_w = total_w + w
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avg_d[letter] = total_w / len(weights)
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return range_d, avg_d
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ambiguous_dna_weight_ranges, avg_ambiguous_dna_weights = _make_ambiguous_ranges(
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ambiguous_dna_values, unambiguous_dna_weights
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)
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ambiguous_rna_weight_ranges, avg_ambiguous_rna_weights = _make_ambiguous_ranges(
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ambiguous_rna_values, unambiguous_rna_weights
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)
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protein_weights = {
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"A": 89.0932,
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"C": 121.1582,
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"D": 133.1027,
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"E": 147.1293,
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"F": 165.1891,
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"G": 75.0666,
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"H": 155.1546,
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"I": 131.1729,
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"K": 146.1876,
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"L": 131.1729,
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"M": 149.2113,
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"N": 132.1179,
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"O": 255.3134,
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"P": 115.1305,
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"Q": 146.1445,
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"R": 174.201,
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"S": 105.0926,
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"T": 119.1192,
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"U": 168.0532,
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"V": 117.1463,
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"W": 204.2252,
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"Y": 181.1885,
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}
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monoisotopic_protein_weights = {
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"A": 89.047678,
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"C": 121.019749,
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"D": 133.037508,
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"E": 147.053158,
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"F": 165.078979,
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"G": 75.032028,
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"H": 155.069477,
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"I": 131.094629,
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"K": 146.105528,
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"L": 131.094629,
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"M": 149.051049,
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"N": 132.053492,
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"O": 255.158292,
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"P": 115.063329,
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"Q": 146.069142,
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"R": 174.111676,
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"S": 105.042593,
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"T": 119.058243,
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"U": 168.964203,
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"V": 117.078979,
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"W": 204.089878,
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"Y": 181.073893,
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}
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extended_protein_values = {
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"A": "A",
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"B": "ND",
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"C": "C",
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"D": "D",
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"E": "E",
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"F": "F",
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"G": "G",
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"H": "H",
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"I": "I",
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"J": "IL",
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"K": "K",
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"L": "L",
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"M": "M",
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"N": "N",
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"O": "O",
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"P": "P",
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"Q": "Q",
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"R": "R",
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"S": "S",
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"T": "T",
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"U": "U",
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"V": "V",
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"W": "W",
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"X": "ACDEFGHIKLMNPQRSTVWY",
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# TODO - Include U and O in the possible values of X?
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# This could alter the extended_protein_weight_ranges ...
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# by MP: Won't do this, because they are so rare.
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"Y": "Y",
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"Z": "QE",
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}
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protein_weight_ranges = _make_ranges(protein_weights)
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extended_protein_weight_ranges, avg_extended_protein_weights = _make_ambiguous_ranges(
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extended_protein_values, protein_weights
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)
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# For Center of Mass Calculation.
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# Taken from http://www.chem.qmul.ac.uk/iupac/AtWt/ & PyMol
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atom_weights = {
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"H": 1.00794,
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"D": 2.01410,
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"He": 4.002602,
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"Li": 6.941,
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"Be": 9.012182,
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"B": 10.811,
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"C": 12.0107,
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"N": 14.0067,
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"O": 15.9994,
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"F": 18.9984032,
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"Ne": 20.1797,
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"Na": 22.989770,
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"Mg": 24.3050,
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"Al": 26.981538,
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"Si": 28.0855,
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"P": 30.973761,
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"S": 32.065,
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"Cl": 35.453,
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"Ar": 39.948,
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"K": 39.0983,
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"Ca": 40.078,
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"Sc": 44.955910,
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"Ti": 47.867,
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"V": 50.9415,
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"Cr": 51.9961,
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"Mn": 54.938049,
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"Fe": 55.845,
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"Co": 58.933200,
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"Ni": 58.6934,
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"Cu": 63.546,
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"Zn": 65.39,
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"Ga": 69.723,
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"Ge": 72.64,
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"As": 74.92160,
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"Se": 78.96,
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"Br": 79.904,
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"Kr": 83.80,
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"Rb": 85.4678,
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"Sr": 87.62,
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"Y": 88.90585,
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"Zr": 91.224,
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"Nb": 92.90638,
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"Mo": 95.94,
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"Tc": 98.0,
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"Ru": 101.07,
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"Rh": 102.90550,
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"Pd": 106.42,
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"Ag": 107.8682,
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"Cd": 112.411,
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"In": 114.818,
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"Sn": 118.710,
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"Sb": 121.760,
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"Te": 127.60,
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"I": 126.90447,
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"Xe": 131.293,
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"Cs": 132.90545,
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"Ba": 137.327,
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"La": 138.9055,
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"Ce": 140.116,
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"Pr": 140.90765,
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"Nd": 144.24,
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"Pm": 145.0,
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"Sm": 150.36,
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"Eu": 151.964,
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"Gd": 157.25,
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"Tb": 158.92534,
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"Dy": 162.50,
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"Ho": 164.93032,
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"Er": 167.259,
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"Tm": 168.93421,
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"Yb": 173.04,
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"Lu": 174.967,
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"Hf": 178.49,
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"Ta": 180.9479,
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"W": 183.84,
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"Re": 186.207,
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"Os": 190.23,
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"Ir": 192.217,
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"Pt": 195.078,
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"Au": 196.96655,
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"Hg": 200.59,
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"Tl": 204.3833,
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"Pb": 207.2,
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"Bi": 208.98038,
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"Po": 208.98,
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"At": 209.99,
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"Rn": 222.02,
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"Fr": 223.02,
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"Ra": 226.03,
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"Ac": 227.03,
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"Th": 232.0381,
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"Pa": 231.03588,
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"U": 238.02891,
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"Np": 237.05,
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"Pu": 244.06,
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"Am": 243.06,
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"Cm": 247.07,
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"Bk": 247.07,
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"Cf": 251.08,
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"Es": 252.08,
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"Fm": 257.10,
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"Md": 258.10,
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"No": 259.10,
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"Lr": 262.11,
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"Rf": 261.11,
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"Db": 262.11,
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"Sg": 266.12,
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"Bh": 264.12,
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"Hs": 269.13,
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"Mt": 268.14,
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}
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