public abstract class AminoAcid extends ExperimentObject
Modifier and Type | Class and Description |
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static class |
AminoAcid.Property
Properties of the amino acids.
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Modifier and Type | Field and Description |
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static AminoAcid |
A |
static String[] |
AMINO_ACID_STRINGS
The amino acid one letter codes as string array.
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protected char[] |
aminoAcidCombinations
The amino acid combinations.
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static AminoAcid |
B |
static AminoAcid |
C |
static AminoAcid |
D |
static AminoAcid |
E |
static AminoAcid |
F |
static AminoAcid |
G |
static AminoAcid |
H |
static AminoAcid |
I |
static AminoAcid |
J |
static AminoAcid |
K |
static AminoAcid |
L |
static AminoAcid |
M |
protected AtomChain |
monoisotopicAtomChain
The monoisotopic atom chain.
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static AminoAcid |
N |
String |
name
Name of the amino acid.
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static AminoAcid |
O |
static AminoAcid |
P |
static AminoAcid |
Q |
static AminoAcid |
R |
static AminoAcid |
S |
String |
singleLetterCode
Single letter code of the amino acid.
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protected String[] |
standardGeneticCode
The standard genetic code.
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protected char[] |
subAminoAcidsWithCombination
The sub amino acids with combination.
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protected char[] |
subAminoAcidsWithoutCombination
The sub amino acids without combination.
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static AminoAcid |
T |
String |
threeLetterCode
Three letter code of the amino acid.
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static AminoAcid |
U |
static AminoAcid |
V |
static AminoAcid |
W |
static AminoAcid |
X |
static AminoAcid |
Y |
static AminoAcid |
Z |
NO_KEY
Constructor and Description |
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AminoAcid()
Empty default constructor.
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Modifier and Type | Method and Description |
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boolean |
equals(Object obj) |
static AminoAcid |
getAminoAcid(char aa)
Returns the amino acid corresponding to the single letter code given.
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static AminoAcid |
getAminoAcid(String aa)
Returns the amino acid corresponding to the letter given.
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static AminoAcid |
getAminoAcidFromGeneticCode(String geneticCode)
Returns the amino acid from the standard genetic code.
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static char[] |
getAminoAcids()
Convenience method returning an array of all implemented amino acids
represented by their singe letter code.
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static List<String> |
getAminoAcidsList()
Convenience method returning an arrayList of all implemented amino acids.
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abstract double |
getBasicity()
Returns the basicity according to PMID 14730315.
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char[] |
getCombinations()
Returns the amino acids combinations which might represent this amino
acid.
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abstract double |
getHelicity()
Returns the helicity according to PMID 14730315.
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abstract double |
getHydrophobicity()
Returns the hydrophobicity according to PMID 14730315.
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static int |
getIndex(char aa)
Returns an index for the amino acid excluding combinations.
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static char |
getMatchingAminoAcid(char aa,
SequenceMatchingParameters sequenceMatchingPreferences)
Returns a matching amino acid using the given preferences.
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static String |
getMatchingSequence(String sequence,
SequenceMatchingParameters sequenceMatchingPreferences)
Returns the matching sequence of a given sequence.
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AtomChain |
getMonoisotopicAtomChain()
Returns the monoisotopic atom chain representing this amino acid.
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double |
getMonoisotopicMass()
Returns the mass of the amino acid.
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static int |
getNUnique()
Returns the number of amino acids excluding combinations.
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abstract double |
getPI()
Returns the pI.
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abstract double |
getPK1()
Returns the pK1.
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abstract double |
getPK2()
Returns the pK2.
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abstract double |
getPKa()
Returns the pKa.
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double |
getProperty(AminoAcid.Property property)
Returns a property of the amino acid.
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char |
getSingleLetterCodeAsChar()
Returns the single letter code as character.
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String[] |
getStandardGeneticCode()
Returns the standard genetic triplets associated to this amino acid.
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protected String[] |
getStandardGeneticCodeForCombination()
Returns the genetic code as combination of the sub amino acid genetic
codes.
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char[] |
getSubAminoAcids()
In case of a combination of amino acids, returns the comprised amino
acids or amino acid groups represented by their single letter code
including sub combinations.
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char[] |
getSubAminoAcids(boolean includeCombinations)
In case of a combination of amino acids, returns the comprised amino
acids or amino acid groups represented by their single letter code.
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static char[] |
getUniqueAminoAcids()
Returns a char array of the one letter code of amino acids without
combinations of amino acids.
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static int |
getUniqueIndex(char aa)
Returns an index for the amino acid excluding combinations.
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abstract int |
getVanDerWaalsVolume()
Returns the van der Waals volume in Å3.
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static boolean |
isAa(char aa)
Returns a boolean indicating whether the given character is a supported
amino acid.
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static boolean |
isAa(int aa)
Returns a boolean indicating whether the given character is a supported
amino acid.
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abstract boolean |
iscombination()
Indicates whether the amino acid object refers to a combination of amino
acids like B, J, Z or X.
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static boolean |
isUniqueAa(char aa)
Returns a boolean indicating whether the given character is a supported
amino acid excluding combinations.
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addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
public static final AminoAcid A
public static final AminoAcid C
public static final AminoAcid D
public static final AminoAcid E
public static final AminoAcid F
public static final AminoAcid G
public static final AminoAcid H
public static final AminoAcid I
public static final AminoAcid K
public static final AminoAcid L
public static final AminoAcid M
public static final AminoAcid N
public static final AminoAcid P
public static final AminoAcid Q
public static final AminoAcid R
public static final AminoAcid S
public static final AminoAcid T
public static final AminoAcid V
public static final AminoAcid W
public static final AminoAcid Y
public static final AminoAcid U
public static final AminoAcid O
public static final AminoAcid B
public static final AminoAcid J
public static final AminoAcid Z
public static final AminoAcid X
public String singleLetterCode
public String threeLetterCode
public String name
protected AtomChain monoisotopicAtomChain
protected char[] subAminoAcidsWithoutCombination
protected char[] subAminoAcidsWithCombination
protected char[] aminoAcidCombinations
protected String[] standardGeneticCode
public static final String[] AMINO_ACID_STRINGS
public static char[] getAminoAcids()
public char getSingleLetterCodeAsChar()
public static List<String> getAminoAcidsList()
public static char[] getUniqueAminoAcids()
public static AminoAcid getAminoAcid(String aa) throws IllegalArgumentException
aa
- the amino acid single letter code as a StringIllegalArgumentException
- if the amino acid is not implementedpublic static AminoAcid getAminoAcid(char aa) throws IllegalArgumentException
aa
- the single letter code of the amino acidIllegalArgumentException
- if the amino acid is not implementedpublic abstract boolean iscombination()
public char[] getSubAminoAcids()
public char[] getSubAminoAcids(boolean includeCombinations)
includeCombinations
- if true, sub-amino acids which are amino acids
combinations like Z will also be includedpublic char[] getCombinations()
public static char getMatchingAminoAcid(char aa, SequenceMatchingParameters sequenceMatchingPreferences)
aa
- the single letter code of the amino acid of interestsequenceMatchingPreferences
- the sequence matching preferencespublic static String getMatchingSequence(String sequence, SequenceMatchingParameters sequenceMatchingPreferences)
sequence
- the sequence of interestsequenceMatchingPreferences
- the sequence matching preferencespublic String[] getStandardGeneticCode()
public static AminoAcid getAminoAcidFromGeneticCode(String geneticCode)
geneticCode
- the three letter genetic code of the desired amino
acidprotected String[] getStandardGeneticCodeForCombination()
public AtomChain getMonoisotopicAtomChain()
public double getMonoisotopicMass()
public abstract double getHydrophobicity()
public abstract double getHelicity()
public abstract double getBasicity()
public abstract double getPI()
public abstract double getPK1()
public abstract double getPK2()
public abstract double getPKa()
public abstract int getVanDerWaalsVolume()
public double getProperty(AminoAcid.Property property)
property
- the property of interestpublic static int getNUnique()
public static int getUniqueIndex(char aa)
aa
- the upper case single letter code of the amino acid.public static int getIndex(char aa)
aa
- the upper case single letter code of the amino acid.public static boolean isAa(char aa)
aa
- the amino acid as single character codepublic static boolean isAa(int aa)
aa
- the amino acid as single character codepublic static boolean isUniqueAa(char aa)
aa
- the amino acid as single character codeCopyright © 2021. All rights reserved.