Package org.biojava.bio.seq

Class ProteinTools

java.lang.Object
org.biojava.bio.seq.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 Details

    • getAlphabet

      public static final FiniteAlphabet getAlphabet()
      Gets the protein alphabet

    • getTAlphabet

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

    • getSymbolPropertyTable

      public static final SymbolPropertyTable getSymbolPropertyTable(String name)

    • createProtein

      public static SymbolList createProtein(String theProtein) throws IllegalSymbolException
      Return a new Protein SymbolList for protein.
      Parameters:
      theProtein - a String to parse into Protein
      Returns:
      a SymbolList created form Protein
      Throws:
      IllegalSymbolException - if dna contains any non-Amino Acid characters.

    • createGappedProteinSequence

      public static GappedSequence createGappedProteinSequence(String theProtein, String name) throws IllegalSymbolException
      Get a new protein as a GappedSequence
      Throws:
      IllegalSymbolException

    • createProteinSequence

      public static Sequence createProteinSequence(String protein, String name) throws IllegalSymbolException
      Return a new PROTEIN Sequence for protein.
      Parameters:
      protein - a String to parse into PROTEIN
      name - a String to use as the name
      Returns:
      a Sequence created form protein
      Throws:
      IllegalSymbolException - if protein contains any non-PROTEIN characters

    • 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