belka.chem
Class Compound

java.lang.Object
  extended by belka.chem.Compound
All Implemented Interfaces:
Serializable

public class Compound
extends Object
implements Serializable

Objects of this class represent chemical compounds.

Author:
Alexej Abyzov
See Also:
Serialized Form

Field Summary
static Compound Adenine
          Adenine
static Compound Alanine
          Alanine
static Compound Arginine
          Arginine
static Compound Asparagine
          Asparagine
static Compound Aspartate
          Aspartate
static Compound Aspartate_or_Asparagine
          Aspartate or asparagine (uncertain result of hydrolysis)
static Compound Cysteine
          Cysteine
static Compound Cytosine
          Cytosine
static Compound Glutamate
          Glutamate
static Compound Glutamate_or_Glutamine
          Glutamate or glutamine (uncertain result of hydrolysis)
static Compound Glutamine
          Glutamine
static Compound Glycine
          Glycine
static Compound Guanine
          Guanine
static Compound h2o
           
static Compound Histidine
          Histidine
static Compound hoh
          Water
static Compound Isoleucine
          Isoleucine
static Compound Leucine
          Leucine
static Compound Leucine_or_Isoleucine
          Leucine or isoleucine (uncertain result of mass-spec)
static Compound Lysine
          Lysine
static Compound Methionine
          Methionine
static Compound Phenylalanine
          Phenylalanine
static Compound Proline
          Proline
static Compound Pyrrolysine
          Pyrrolysine (non-standard)
static Compound Selenocysteine
          Selenocysteine (non-standard)
static Compound Selenomethionine
          Selenomethionine (non-standard)
static Compound Serine
          Serine
static Compound Threonine
          Threonine
static Compound Thymine
          Thymine
static Compound Tryptophan
          Tryptophan
static Compound Tyrosine
          Tyrosine
static Compound Uracil
          Uracil
static Compound Valine
          Valine
 
Constructor Summary
Compound(String short_name)
           
Compound(String name, String short_name, char letter, Color col)
           
 
Method Summary
 Color getColor()
          Returns compound's color to be used to draw it.
static Compound getCompoundByName(String name)
          Returns compound with given name.
static Compound getCompoundByShortName(String short_name)
          Returns compound with short (three-letter) name.
 char getLetterName()
          Returns compound's one letter name, for example 'A' for Alanine.
 String getName()
          Returns compound's full name, for example "Alanine".
 String getShortName()
          Returns compound's short name (three-letter), for example "Ala".
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

Alanine

public static final Compound Alanine
Alanine


Arginine

public static final Compound Arginine
Arginine


Asparagine

public static final Compound Asparagine
Asparagine


Aspartate

public static final Compound Aspartate
Aspartate


Cysteine

public static final Compound Cysteine
Cysteine


Glutamate

public static final Compound Glutamate
Glutamate


Glutamine

public static final Compound Glutamine
Glutamine


Glycine

public static final Compound Glycine
Glycine


Histidine

public static final Compound Histidine
Histidine


Isoleucine

public static final Compound Isoleucine
Isoleucine


Leucine

public static final Compound Leucine
Leucine


Lysine

public static final Compound Lysine
Lysine


Methionine

public static final Compound Methionine
Methionine


Selenomethionine

public static final Compound Selenomethionine
Selenomethionine (non-standard)


Phenylalanine

public static final Compound Phenylalanine
Phenylalanine


Proline

public static final Compound Proline
Proline


Serine

public static final Compound Serine
Serine


Threonine

public static final Compound Threonine
Threonine


Tyrosine

public static final Compound Tyrosine
Tyrosine


Tryptophan

public static final Compound Tryptophan
Tryptophan


Valine

public static final Compound Valine
Valine


Selenocysteine

public static final Compound Selenocysteine
Selenocysteine (non-standard)


Pyrrolysine

public static final Compound Pyrrolysine
Pyrrolysine (non-standard)


Aspartate_or_Asparagine

public static final Compound Aspartate_or_Asparagine
Aspartate or asparagine (uncertain result of hydrolysis)


Leucine_or_Isoleucine

public static final Compound Leucine_or_Isoleucine
Leucine or isoleucine (uncertain result of mass-spec)


Glutamate_or_Glutamine

public static final Compound Glutamate_or_Glutamine
Glutamate or glutamine (uncertain result of hydrolysis)


Adenine

public static final Compound Adenine
Adenine


Cytosine

public static final Compound Cytosine
Cytosine


Guanine

public static final Compound Guanine
Guanine


Thymine

public static final Compound Thymine
Thymine


Uracil

public static final Compound Uracil
Uracil


hoh

public static final Compound hoh
Water


h2o

public static final Compound h2o
Constructor Detail

Compound

public Compound(String name,
                String short_name,
                char letter,
                Color col)

Compound

public Compound(String short_name)
Method Detail

getName

public String getName()
Returns compound's full name, for example "Alanine".

Returns:
compound's full name.

getShortName

public String getShortName()
Returns compound's short name (three-letter), for example "Ala".

Returns:
compound's short name.

getLetterName

public char getLetterName()
Returns compound's one letter name, for example 'A' for Alanine.

Returns:
compound's one letter name.

getColor

public Color getColor()
Returns compound's color to be used to draw it.

Returns:
compound's color to be used to draw it.

getCompoundByName

public static Compound getCompoundByName(String name)
Returns compound with given name.

Parameters:
name - compounds's name.
Returns:
compound with inputed name. Null if there is not such compound.

getCompoundByShortName

public static Compound getCompoundByShortName(String short_name)
Returns compound with short (three-letter) name.

Parameters:
short_name - compounds's short name.
Returns:
compound with inputed short name. Null if there is not such compound.