Packages

c

apps.montecarlo

MassSpectra

class MassSpectra extends Error

The MassSpectra class calculates the masses and corresponding probabilities for organic molecules, providing a Monte Carlo simulation of their mass spectra.

Linear Supertypes
Error, AnyRef, Any
Ordering
  1. Alphabetic
  2. By Inheritance
Inherited
  1. MassSpectra
  2. Error
  3. AnyRef
  4. Any
  1. Hide All
  2. Show All
Visibility
  1. Public
  2. All

Instance Constructors

  1. new MassSpectra(thres: Double = 1E-6, noise: Double = 1E-5)

    thres

    the lowest detectable relative abundance (probability) level

    noise

    the noise level of the mass spectrometer

Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
    AnyRef → Any
  3. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  4. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  5. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  6. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  7. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  8. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  9. final def flaw(method: String, message: String): Unit
    Definition Classes
    Error
  10. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
  11. def getElementMasses(e: String, n: Int): Set[(Double, Double)]

    Get all the masses for n atoms of element e, so long as its relative abundance (probability) is above threshold 'thres'.

    Get all the masses for n atoms of element e, so long as its relative abundance (probability) is above threshold 'thres'. Return a set '(mass, prob)' tuples.

    e

    the given element (e.g., "O" for Oxygen)

    n

    the number of such atoms in the molecule (e.g., 2 in 'CO2')

  12. def hashCode(): Int
    Definition Classes
    AnyRef → Any
  13. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  14. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  15. final def notify(): Unit
    Definition Classes
    AnyRef
  16. final def notifyAll(): Unit
    Definition Classes
    AnyRef
  17. def simulate(comp: Set[(String, Int)]): Set[(Double, Double)]

    Given an elemental composition, a set of (element, atom count) tuples, of an organic molecule, simulate its spectrum, a set of (mass, probability) tuples.

    Given an elemental composition, a set of (element, atom count) tuples, of an organic molecule, simulate its spectrum, a set of (mass, probability) tuples.

    comp

    the elemental composition of an organic molecule

  18. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  19. def toString(): String
    Definition Classes
    AnyRef → Any
  20. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  21. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  22. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Error

Inherited from AnyRef

Inherited from Any

Ungrouped