Class ProteinTools


  • public class ProteinTools
    extends Object
    The central port-of-call for all information and functionality specific to SymbolLists over the protein alphabet.
    Author:
    Matthew Pocock, Greg Cox, Thomas Down, MarkSchreiber, Jonathan Warren, gwaldon (pyrrolysine, pKs)
    • Method Detail

      • getTAlphabet

        public static final FiniteAlphabet getTAlphabet()
        Gets the protein alphabet including the translation termination symbols
      • ala

        public static AtomicSymbol ala()
        Returns the AtomicSymbol for the amino acid Alanine (A)
      • a

        public static AtomicSymbol a()
        Returns the AtomicSymbol for the amino acid Alanine
      • arg

        public static AtomicSymbol arg()
        Returns the AtomicSymbol for the amino acid Arginine (R)
      • r

        public static AtomicSymbol r()
        Returns the AtomicSymbol for the amino acid Arginine
      • asn

        public static AtomicSymbol asn()
        Returns the AtomicSymbol for the amino acid Asparagine (N)
      • n

        public static AtomicSymbol n()
        Returns the AtomicSymbol for the amino acid Asparagine
      • asp

        public static AtomicSymbol asp()
        Returns the AtomicSymbol for the amino acid Aspartic Acid (D)
      • d

        public static AtomicSymbol d()
        Returns the AtomicSymbol for the amino acid Aspartic Acid
      • cys

        public static AtomicSymbol cys()
        Returns the AtomicSymbol for the amino acid Cysteine (C)
      • c

        public static AtomicSymbol c()
        Returns the AtomicSymbol for the amino acid Cysteine
      • gln

        public static AtomicSymbol gln()
        Returns the AtomicSymbol for the amino acid Glutamine (Q)
      • q

        public static AtomicSymbol q()
        Returns the AtomicSymbol for the amino acid Glutamine
      • glu

        public static AtomicSymbol glu()
        Returns the AtomicSymbol for the amino acid Glutamic Acid (E)
      • e

        public static AtomicSymbol e()
        Returns the AtomicSymbol for the amino acid Glutamic Acid
      • gly

        public static AtomicSymbol gly()
        Returns the AtomicSymbol for the amino acid Glycine (G)
      • g

        public static AtomicSymbol g()
        Returns the AtomicSymbol for the amino acid Glycine
      • his

        public static AtomicSymbol his()
        Returns the AtomicSymbol for the amino acid Histidine (H)
      • h

        public static AtomicSymbol h()
        Returns the AtomicSymbol for the amino acid Histidine
      • ile

        public static AtomicSymbol ile()
        Returns the AtomicSymbol for the amino acid Isoleucine (I)
      • i

        public static AtomicSymbol i()
        Returns the AtomicSymbol for the amino acid Isoleucine
      • leu

        public static AtomicSymbol leu()
        Returns the AtomicSymbol for the amino acid Leucine (L)
      • l

        public static AtomicSymbol l()
        Returns the AtomicSymbol for the amino acid Leucine
      • lys

        public static AtomicSymbol lys()
        Returns the AtomicSymbol for the amino acid Lysine (K)
      • k

        public static AtomicSymbol k()
        Returns the AtomicSymbol for the amino acid Lysine
      • met

        public static AtomicSymbol met()
        Returns the AtomicSymbol for the amino acid Methionine (M)
      • m

        public static AtomicSymbol m()
        Returns the AtomicSymbol for the amino acid Methionine
      • phe

        public static AtomicSymbol phe()
        Returns the AtomicSymbol for the amino acid Phenylalanine (F)
      • f

        public static AtomicSymbol f()
        Returns the AtomicSymbol for the amino acid Phenylalanine
      • pro

        public static AtomicSymbol pro()
        Returns the AtomicSymbol for the amino acid Proline (P)
      • p

        public static AtomicSymbol p()
        Returns the AtomicSymbol for the amino acid Proline
      • pyl

        public static AtomicSymbol pyl()
        Returns the AtomicSymbol for the amino acid Pyrrolysine (O)
      • o

        public static AtomicSymbol o()
        Returns the AtomicSymbol for the amino acid Pyrrolysine
      • sec

        public static AtomicSymbol sec()
        Returns the AtomicSymbol for the amino acid Selenocysteine (U)
      • u

        public static AtomicSymbol u()
        Returns the AtomicSymbol for the amino acid Selenocysteine
      • ser

        public static AtomicSymbol ser()
        Returns the AtomicSymbol for the amino acid Serine (S)
      • s

        public static AtomicSymbol s()
        Returns the AtomicSymbol for the amino acid Serine
      • thr

        public static AtomicSymbol thr()
        Returns the AtomicSymbol for the amino acid Threonine (T)
      • t

        public static AtomicSymbol t()
        Returns the AtomicSymbol for the amino acid Threonine
      • trp

        public static AtomicSymbol trp()
        Returns the AtomicSymbol for the amino acid Tryptophan (W)
      • w

        public static AtomicSymbol w()
        Returns the AtomicSymbol for the amino acid Tryptophan
      • tyr

        public static AtomicSymbol tyr()
        Returns the AtomicSymbol for the amino acid Tyrosine (Y)
      • y

        public static AtomicSymbol y()
        Returns the AtomicSymbol for the amino acid Tyrosine
      • val

        public static AtomicSymbol val()
        Returns the AtomicSymbol for the amino acid Valine (V)
      • v

        public static AtomicSymbol v()
        Returns the AtomicSymbol for the amino acid Valine
      • ter

        public static AtomicSymbol ter()
        Returns the AtomicSymbol for the termination (*) placeholder