Molecule (com.hfg API Documentation)

java.lang.Object
- com.hfg.chem.Molecule

All Implemented Interfaces:

Matter, HfgXMLSerializable, Cloneable, Comparable

Direct Known Subclasses:

AminoAcid, BioSequenceImpl, CTerminalGroup, Glycan, Monosaccharide, NTerminalGroup, Nucleotide, ProteinXLink, ProteinXLinkType
```
public class Molecule
extends Object
implements Matter, HfgXMLSerializable, Cloneable, Comparable
```
Generic chemical entity.

Field Summary

Fields
Modifier and Type Field and Description

static Molecule H2O

protected boolean mLocked

protected String mName

static Molecule NaCl

static Molecule NH3

Fields
Modifier and Type	Field and Description
`static Molecule`	`H2O`
`protected boolean`	`mLocked`
`protected String`	`mName`
`static Molecule`	`NaCl`
`static Molecule`	`NH3`

Constructor Summary

Constructors
Constructor and Description
`Molecule()`
`Molecule(Map<Element,Float> inElementalComposition)`
`Molecule(Matter inInitialValue)`
`Molecule(String inName)`
`Molecule(String inName, Map<Element,Float> inElementalComposition)`
`Molecule(XMLNode inXML)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`Molecule`	`add(Matter inValue)`
`Molecule`	`add(Matter inValue, int inCount)`
`Molecule`	`addAtom(Atom inAtom)`
`Molecule`	`addAtoms(Element inElement, float inNum)`
`Molecule`	`addAtoms(Element inElement, int inNum)`
`Molecule`	`addAtoms(List<Atom> inAtoms)`
`Molecule`	`addElementalComposition(ElementalComposition inElementalComposition, int inNum)`
`Molecule`	`addElementalComposition(Map<Element,Float> inMap)`
`Molecule`	`addElementalComposition(Map<Element,Float> inMap, int inNum)`
`Molecule`	`addKa(IonizableGroup inValue)`
`Molecule`	`addKa(IonizableGroup inValue, int inCount)`
`protected void`	`calculateMassFromElementalComposition()`
`void`	`clearAttributes()`
`void`	`clearCalculatedProperties()`
`void`	`clearElementalComposition()`
`Molecule`	`clone()` Returns an unlocked copy of the Molecule.
`int`	`compareTo(Object inObj)`
`boolean`	`equals(Object inObj)`
`protected static String`	`formatMassString(double inValue)`
`List<Atom>`	`getAtoms()`
`Object`	`getAttribute(String inName)`
`Collection<String>`	`getAttributeNames()`
`Double`	`getAverageMass()`
`String`	`getChemicalFormula()` Returns a chemical formula String like 'C5H11NO'.
`String`	`getChemicalFormulaWithSubscripts()` Returns a chemical formula String like 'C₅H₁₁NO'.
`Map<Element,Float>`	`getElementalComposition()` Returns the elemental composition as an unmodifiable Map.
`List<IonizableGroup>`	`getKas()` Returns a List of IonizableGroup objects.
`Atom`	`getLastAtom()`
`Double`	`getMonoisotopicMass()`
`Double`	`getOrganicAverageMass()`
`Double`	`getPhysicalProperty(PhysicalProperty inProperty)`
`boolean`	`hasAttribute(String inName)`
`boolean`	`hasAttributes()`
`int`	`hashCode()`
`boolean`	`isLocked()`
`Molecule`	`lock()`
`protected boolean`	`massesAreUserSet()`
`String`	`name()`
`Molecule`	`remove(Matter inValue)`
`Molecule`	`remove(Matter inValue, int inCount)`
`Object`	`removeAttribute(String inName)`
`void`	`setAttribute(String inName, Object inValue)`
`Molecule`	`setAverageMass(Double inValue)` If the elemental composition is known, use setElementalComposition() and the masses will be derived automatically; this method is for use in those (hopefully) rare times when the mass is known but not the elemental composition.
`Molecule`	`setChemicalFormula(String inValue)`
`void`	`setElementalComposition(Map<Element,Float> inMap)`
`Molecule`	`setMonoisotopicMass(Double inValue)` If the elemental composition is known, use setElementalComposition() and the masses will be derived automatically; this method is for use in those (hopefully) rare times when the mass is known but not the elemental composition.
`Molecule`	`setName(String inValue)`
`Molecule`	`setOrganicAverageMass(Double inValue)` If the elemental composition is known, use setElementalComposition() and the masses will be derived automatically; this method is for use in those (hopefully) rare times when the mass is known but not the elemental composition.
`Molecule`	`setPhysicalProperty(PhysicalProperty inProperty, Double inValue)`
`String`	`toString()`
`XMLNode`	`toXMLNode()`

Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

mName
```
protected String mName
```

mLocked
```
protected boolean mLocked
```

H2O
```
public static final Molecule H2O
```

NH3
```
public static final Molecule NH3
```

NaCl
```
public static final Molecule NaCl
```

Constructor Detail

Molecule
```
public Molecule()
```

Molecule
```
public Molecule(String inName)
```

Molecule

public Molecule(Map<Element,Float> inElementalComposition)

Molecule

public Molecule(String inName,
                Map<Element,Float> inElementalComposition)

Molecule

public Molecule(Matter inInitialValue)

Molecule
```
public Molecule(XMLNode inXML)
```

Method Detail
- setName
```
public Molecule setName(String inValue)
```
- name
```
public String name()
```
- toString
```
public String toString()
```
  Overrides:
  
  toString in class Object
- hashCode
```
public int hashCode()
```
  Overrides:
  
  hashCode in class Object
- equals
```
public boolean equals(Object inObj)
```
  Overrides:
  
  equals in class Object
- compareTo
```
public int compareTo(Object inObj)
```
  Specified by:
  
  compareTo in interface Comparable
- clone
```
public Molecule clone()
```
  Returns an unlocked copy of the Molecule.
  
  Overrides:
  
  clone in class Object
  
  Returns:
  
  an unlocked copy of the Molecule
- isLocked
```
public boolean isLocked()
```
- lock
```
public Molecule lock()
```
- setElementalComposition
```
public void setElementalComposition(Map<Element,Float> inMap)
```
- clearElementalComposition
```
public void clearElementalComposition()
```
- addElementalComposition
```
public Molecule addElementalComposition(Map<Element,Float> inMap)
```
- addElementalComposition
```
public Molecule addElementalComposition(Map<Element,Float> inMap,
                                        int inNum)
```
- addElementalComposition
```
public Molecule addElementalComposition(ElementalComposition inElementalComposition,
                                        int inNum)
```
- add
```
public Molecule add(Matter inValue)
```
- add
```
public Molecule add(Matter inValue,
                    int inCount)
```
- remove
```
public Molecule remove(Matter inValue)
```
- remove
```
public Molecule remove(Matter inValue,
                       int inCount)
```
- addAtoms
```
public Molecule addAtoms(Element inElement,
                         int inNum)
```
- addAtoms
```
public Molecule addAtoms(Element inElement,
                         float inNum)
```
- addAtom
```
public Molecule addAtom(Atom inAtom)
```
- addAtoms
```
public Molecule addAtoms(List<Atom> inAtoms)
```
- getAtoms
```
public List<Atom> getAtoms()
```
- getLastAtom
```
public Atom getLastAtom()
```
- setMonoisotopicMass
```
public Molecule setMonoisotopicMass(Double inValue)
```
  If the elemental composition is known, use setElementalComposition() and the masses will be derived automatically; this method is for use in those (hopefully) rare times when the mass is known but not the elemental composition.
  
  Parameters:
  
  inValue - the mass to use as the monoisotopic mass for this object
  
  Returns:
  
  this Molecule object to enable method chaining
- getMonoisotopicMass
```
public Double getMonoisotopicMass()
```
  Specified by:
  
  getMonoisotopicMass in interface Matter
- setAverageMass
```
public Molecule setAverageMass(Double inValue)
```
  If the elemental composition is known, use setElementalComposition() and the masses will be derived automatically; this method is for use in those (hopefully) rare times when the mass is known but not the elemental composition.
  
  Parameters:
  
  inValue - the mass to use as the average mass for this object
  
  Returns:
  
  this Molecule object to enable method chaining
- getAverageMass
```
public Double getAverageMass()
```
  Specified by:
  
  getAverageMass in interface Matter
- setOrganicAverageMass
```
public Molecule setOrganicAverageMass(Double inValue)
```
  If the elemental composition is known, use setElementalComposition() and the masses will be derived automatically; this method is for use in those (hopefully) rare times when the mass is known but not the elemental composition.
  
  Parameters:
  
  inValue - the mass to use as the organic average mass for this object
  
  Returns:
  
  this Molecule object to enable method chaining
- getOrganicAverageMass
```
public Double getOrganicAverageMass()
```
  Specified by:
  
  getOrganicAverageMass in interface Matter
- getElementalComposition
```
public Map<Element,Float> getElementalComposition()
```
  Returns the elemental composition as an unmodifiable Map.
  
  Specified by:
  
  getElementalComposition in interface Matter
  
  Returns:
  
  Map containing the elemental composition
- setChemicalFormula
```
public Molecule setChemicalFormula(String inValue)
```
- getChemicalFormula
```
public String getChemicalFormula()
```
  Returns a chemical formula String like 'C5H11NO'. If carbon is present, it is listed first followed by the other elements in ascending mass order. Symbols for isotopes are enclosed in square brackets such as '[2H]2O' for deuterated water.
  
  Specified by:
  
  getChemicalFormula in interface Matter
  
  Returns:
  
  the chemical formula string
- getChemicalFormulaWithSubscripts
```
public String getChemicalFormulaWithSubscripts()
```
  Returns a chemical formula String like 'C₅H₁₁NO'. If carbon is present, it is listed first followed by the other elements in ascending mass order. Symbols for isotopes are enclosed in square brackets such as '[²H]₂O' for deuterated water.
  
  Returns:
  
  the chemical formula string
- clearCalculatedProperties
```
public void clearCalculatedProperties()
```
- addKa
```
public Molecule addKa(IonizableGroup inValue)
```
- addKa
```
public Molecule addKa(IonizableGroup inValue,
                      int inCount)
```
- getKas
```
public List<IonizableGroup> getKas()
```
  Returns a List of IonizableGroup objects.
  
  Returns:
  
  List of IonizableGroups
- getPhysicalProperty
```
public Double getPhysicalProperty(PhysicalProperty inProperty)
```
- setPhysicalProperty
```
public Molecule setPhysicalProperty(PhysicalProperty inProperty,
                                    Double inValue)
```
- setAttribute
```
public void setAttribute(String inName,
                         Object inValue)
```
- hasAttributes
```
public boolean hasAttributes()
```
- hasAttribute
```
public boolean hasAttribute(String inName)
```
- getAttribute
```
public Object getAttribute(String inName)
```
- getAttributeNames
```
public Collection<String> getAttributeNames()
```
- clearAttributes
```
public void clearAttributes()
```
- removeAttribute
```
public Object removeAttribute(String inName)
```
- toXMLNode
```
public XMLNode toXMLNode()
```
  Specified by:
  
  toXMLNode in interface HfgXMLSerializable
- calculateMassFromElementalComposition
```
protected void calculateMassFromElementalComposition()
```
- massesAreUserSet
```
protected boolean massesAreUserSet()
```
- formatMassString
```
protected static String formatMassString(double inValue)
```

Class Molecule

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

mName

mLocked

H2O

NH3

NaCl

Constructor Detail

Molecule

Molecule

Molecule

Molecule

Molecule

Molecule

Method Detail

setName

name

toString

hashCode

equals

compareTo

clone

isLocked

lock

setElementalComposition

clearElementalComposition

addElementalComposition

addElementalComposition

addElementalComposition

add

add

remove

remove

addAtoms

addAtoms

addAtom

addAtoms

getAtoms

getLastAtom

setMonoisotopicMass

getMonoisotopicMass

setAverageMass

getAverageMass

setOrganicAverageMass

getOrganicAverageMass

getElementalComposition

setChemicalFormula

getChemicalFormula

getChemicalFormulaWithSubscripts

clearCalculatedProperties

addKa

addKa

getKas

getPhysicalProperty

setPhysicalProperty

setAttribute

hasAttributes

hasAttribute

getAttribute

getAttributeNames

clearAttributes

removeAttribute

toXMLNode

calculateMassFromElementalComposition

massesAreUserSet

formatMassString