Package | Description |
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com.compomics.util.experiment.biology.aminoacids |
The amino acid classes.
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com.compomics.util.experiment.biology.aminoacids.impl |
The amino acid implementations.
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com.compomics.util.experiment.biology.aminoacids.sequence |
Classes related to the handling of protein sequences.
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com.compomics.util.experiment.biology.ions.impl |
Ion implementations.
|
Modifier and Type | Field and Description |
---|---|
static AminoAcid |
AminoAcid.A |
static AminoAcid |
AminoAcid.B |
static AminoAcid |
AminoAcid.C |
static AminoAcid |
AminoAcid.D |
static AminoAcid |
AminoAcid.E |
static AminoAcid |
AminoAcid.F |
static AminoAcid |
AminoAcid.G |
static AminoAcid |
AminoAcid.H |
static AminoAcid |
AminoAcid.I |
static AminoAcid |
AminoAcid.J |
static AminoAcid |
AminoAcid.K |
static AminoAcid |
AminoAcid.L |
static AminoAcid |
AminoAcid.M |
static AminoAcid |
AminoAcid.N |
static AminoAcid |
AminoAcid.O |
static AminoAcid |
AminoAcid.P |
static AminoAcid |
AminoAcid.Q |
static AminoAcid |
AminoAcid.R |
static AminoAcid |
AminoAcid.S |
static AminoAcid |
AminoAcid.T |
static AminoAcid |
AminoAcid.U |
static AminoAcid |
AminoAcid.V |
static AminoAcid |
AminoAcid.W |
static AminoAcid |
AminoAcid.X |
static AminoAcid |
AminoAcid.Y |
static AminoAcid |
AminoAcid.Z |
Modifier and Type | Method and Description |
---|---|
static AminoAcid |
AminoAcid.getAminoAcid(char aa)
Returns the amino acid corresponding to the single letter code given.
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static AminoAcid |
AminoAcid.getAminoAcid(String aa)
Returns the amino acid corresponding to the letter given.
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static AminoAcid |
AminoAcid.getAminoAcidFromGeneticCode(String geneticCode)
Returns the amino acid from the standard genetic code.
|
Modifier and Type | Class and Description |
---|---|
class |
Alanine
Alanine.
|
class |
Arginine
Arginine.
|
class |
Asparagine
Asparagine.
|
class |
AsparticAcid
Aspartic Acid.
|
class |
B
Asn or Asp: Asx (Mascot).
|
class |
Cysteine
Cysteine.
|
class |
GlutamicAcid
Glutamic Acid.
|
class |
Glutamine
Glutamine.
|
class |
Glycine
Glycine.
|
class |
Histidine
Histidine.
|
class |
Isoleucine
Isoleucine.
|
class |
J
Isoleucine or Leucine.
|
class |
Leucine
Leucine.
|
class |
Lysine
Lysine.
|
class |
Methionine
Methionine.
|
class |
Phenylalanine
Phenylalanine.
|
class |
Proline
Proline.
|
class |
Pyrrolysine
Pyrrolysine.
|
class |
Selenocysteine
SeC (U) (Mascot)-
|
class |
Serine
Serine.
|
class |
Threonine
Threonine.
|
class |
Tryptophan
Tryptophan.
|
class |
Tyrosine
Tyrosine.
|
class |
Valine
Valine.
|
class |
X
Unknown amino acid (Mascot).
|
class |
Z
Glu or Gln: Glx (Mascot).
|
Modifier and Type | Method and Description |
---|---|
AminoAcid |
AminoAcidSequence.getAminoAcidAt(int aa)
Returns the amino acid at the given index on the sequence.
|
Modifier and Type | Method and Description |
---|---|
static ArrayList<RelatedIon> |
RelatedIon.getRelatedIons(AminoAcid aminoAcidTarget)
Returns the list of related ions for the given amino acid.
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Constructor and Description |
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RelatedIon(AminoAcid aminoAcidTarget,
AtomChain atomChain,
int subType)
Constructor for a related ion.
|
RelatedIon(AminoAcid aminoAcidTarget,
AtomChain atomChain,
int subType,
boolean save)
Constructor for a related ion.
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