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[jabaws.git] / website / archive / binaries / mac / src / disembl / biopython-1.50 / Bio / Alphabet / Reduced.py

diff --git a/website/archive/binaries/mac/src/disembl/biopython-1.50/Bio/Alphabet/Reduced.py b/website/archive/binaries/mac/src/disembl/biopython-1.50/Bio/Alphabet/Reduced.py
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-# Copyright 2004 by Iddo Friedberg.
-# All rights reserved.
-# This code is part of the Biopython distribution and governed by its
-# license.  Please see the LICENSE file that should have been included
-# as part of this package.
-
-"""Reduced alphabets which lump together several amino-acids into one letter.
-
-Reduced (redundant or simplified) alphabets are used to represent protein sequences using an
-alternative alphabet which lumps together several amino-acids into one letter, based
-on physico-chemical traits. For example, all the aliphatics (I,L,V) are usually
-quite interchangeable, so many sequence studies group them into one letter
-
-Examples of reduced alphabets are available in:
-
-http://viscose.ifg.uni-muenster.de/html/alphabets.html
-
-Bio.utils.reduce_sequence is used to take a Protein alphabet, and reduce it using one of
-the tables here, or a user-defined table.
-"""
-
-from Bio import Alphabet
-
-# The Murphy tables are from here:
-#      Murphy L.R., Wallqvist A, Levy RM. (2000) Simplified amino acid alphabets for protein
-#      fold recognition and implications for folding. Protein Eng. 13(3):149-152
-
-murphy_15_tab = {"L": "L",
-             "V": "L",
-             "I": "L",
-             "M": "L",
-             "C": "C",
-             "A": "A",
-             "G": "G",
-             "S": "S",
-             "T": "T",
-             "P": "P",
-             "F": "F",
-             "Y": "F",
-             "W": "W",
-             "E": "E",
-             "D": "D",
-             "N": "N",
-             "Q": "Q",
-             "K": "K",
-             "R": "K",
-             "H": "H"}
-
-class Murphy15(Alphabet.ProteinAlphabet):
-   letters = "LCAGSTPFWEDNQKH"
-   size = 15
-murphy_15 = Murphy15()
-
-murphy_10_tab = {"L": "L",
-             "V": "L",
-             "I": "L",
-             "M": "L",
-             "C": "C",
-             "A": "A",
-             "G": "G",
-             "S": "S",
-             "T": "S",
-             "P": "P",
-             "F": "F",
-             "Y": "F",
-             "W": "F",
-             "E": "E",
-             "D": "E",
-             "N": "E",
-             "Q": "E",
-             "K": "K",
-             "R": "K",
-             "H": "H"}
-class Murphy10(Alphabet.ProteinAlphabet):
-   letters = "LCAGSPFEKH"
-   size = 10
-murphy_10 = Murphy10()
-
-murphy_8_tab  = {"L": "L",
-             "V": "L",
-             "I": "L",
-             "M": "L",
-             "C": "L",
-             "A": "A",
-             "G": "A",
-             "S": "S",
-             "T": "S",
-             "P": "P",
-             "F": "F",
-             "Y": "F",
-             "W": "F",
-             "E": "E",
-             "D": "E",
-             "N": "E",
-             "Q": "E",
-             "K": "K",
-             "R": "K",
-             "H": "H"}
-
-class Murphy8(Alphabet.ProteinAlphabet):
-   letters = "LASPFEKH"
-   size = 8
-murphy_8 = Murphy8()
-
-murphy_4_tab  = {"L": "L",
-             "V": "L",
-             "I": "L",
-             "M": "L",
-             "C": "L",
-             "A": "A",
-             "G": "A",
-             "S": "A",
-             "T": "A",
-             "P": "A",
-             "F": "F",
-             "Y": "F",
-             "W": "F",
-             "E": "E",
-             "D": "E",
-             "N": "E",
-             "Q": "E",
-             "K": "E",
-             "R": "E",
-             "H": "E"}
-
-class Murphy4(Alphabet.ProteinAlphabet):
-   letters = "LAFE"
-   size = 4
-murphy_4 = Murphy4()
-
-hp_model_tab = {"A": "P",   # Hydrophilic
-            "G": "P",
-            "T": "P",
-            "S": "P",
-            "N": "P",
-            "Q": "P",
-            "D": "P",
-            "E": "P",
-            "H": "P",
-            "R": "P",
-            "K": "P",
-            "P": "P",
-            "C": "H",  # Hydrophobic
-            "M": "H",
-            "F": "H",
-            "I": "H",
-            "L": "H",
-            "V": "H",
-            "W": "H",
-            "Y": "H"}
-
-class HPModel(Alphabet.ProteinAlphabet):
-   letters = "HP"
-   size = 2
-hp_model = HPModel()
-
-pc_5_table  = {"I": "A", # Aliphatic
-         "V": "A",
-         "L": "A",
-         "F": "R", # Aromatic
-         "Y": "R",
-         "W": "R",
-         "H": "R",
-         "K": "C", # Charged
-         "R": "C",
-         "D": "C",
-         "E": "C",
-         "G": "T", # Tiny
-         "A": "T",
-         "C": "T",
-         "S": "T",
-         "T": "D", # Diverse
-         "M": "D",
-         "Q": "D",
-         "N": "D",
-         "P": "D"}
-
-class PC5(Alphabet.ProteinAlphabet):
-   letters = "ARCTD"
-   size = 5
-hp_model = HPModel()