net.sf.octet.util
Class MoleculeKit

java.lang.Object
  net.sf.octet.util.MoleculeKit

public final class MoleculeKit

extends java.lang.Object

MoleculeKit is a collection of static utility methods for the manipulation and analysis of Molecule objects.

Author:

Richard Apodaca

Method Summary

static void	copyMolecule(Molecule molecule, RepresentationBuilder builder) Directs the specifed RepresentationBuilder by using the specifed Molecule as a template.
static boolean	exactStructureMatch(Molecule input, Molecule model) Returns true if input and model are exact structure matches, or false otherwise.
static double	getExactMass(Molecule molecule) Returns the exact mass of the specified Molecule, in unified atomic mass units (u), using the most abundant isotope of each Atom.
static double	getFormalBondOrder(Atom source, Atom target, Molecule molecule) Returns the formal bond order between source and target.
static double	getFormalCharge(Atom atom, Molecule molecule) Returns the formal charge of atom.
static double	getMass(Molecule molecule) Returns the sum of all atomic masses, in unified atomic mass units (u), of molecule.
static double	getValence(Atom atom, Molecule molecule) Returns the simple sum of bond orders for all atom pairs in which atom participates.
static void	printMolecule(Molecule molecule, java.io.PrintStream out) Prints a text-only representation of the indicated Molecule to the indicated PrintStream.
static boolean	substructureMatch(Molecule input, Molecule model) Returns true if input matches model as a substructure, or false otherwise.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

getFormalCharge

public static double getFormalCharge(Atom atom,
                                     Molecule molecule)

Returns the formal charge of atom. This value is determined as outlined in JCICS 1995 35, 787-802.

Parameters:

atom - the atom

molecule - the molecule

Returns:

the formal charge.

getValence

public static double getValence(Atom atom,
                                Molecule molecule)

Returns the simple sum of bond orders for all atom pairs in which atom participates.

Parameters:

atom - the atom

Returns:

the total valence of atom

getFormalBondOrder

public static double getFormalBondOrder(Atom source,
                                        Atom target,
                                        Molecule molecule)

Returns the formal bond order between source and target. This value is determined as outlined in JCICS 1995 35, 787-802.

Parameters:

source - the source atom

target - the target atom

Returns:

the formal bond order between source and target

getMass

public static double getMass(Molecule molecule)

Returns the sum of all atomic masses, in unified atomic mass units (u), of molecule.

Parameters:

molecule - the Molecule

Returns:

the sum of all atomic masses, in unified atomic mass units (u), including implicit hydrogen atoms

getExactMass

public static double getExactMass(Molecule molecule)

Returns the exact mass of the specified Molecule, in unified atomic mass units (u), using the most abundant isotope of each Atom.

Parameters:

molecule - the Molecule

Returns:

the exact mass of the specified Molecule in unified atomic mass units (u)

printMolecule

public static void printMolecule(Molecule molecule,
                                 java.io.PrintStream out)

Prints a text-only representation of the indicated Molecule to the indicated PrintStream.

Parameters:

molecule - the molecule

out - the PrintStream

copyMolecule

public static void copyMolecule(Molecule molecule,
                                RepresentationBuilder builder)

Directs the specifed RepresentationBuilder by using the specifed Molecule as a template. This implementation does not copy Configuration or Conformation. Typical usage:

 Molecule molecule = ... ;
 MoleculeBuilder builder = ... ;
 
 MoleculeKit.copyMolecule(molecule, builder);
 
 Molecule newMolecule = builder.releaseMolecule();
 

This implementation does not currently copy atomic Configuration or Conformation.

Parameters:

molecule - the Molecule to copy

builder - the RepresentationBuilder to use

exactStructureMatch

public static boolean exactStructureMatch(Molecule input,
                                          Molecule model)

Returns true if input and model are exact structure matches, or false otherwise. The designations input and model are interchangeable.

Parameters:

input - the input Molecule

model - the model Molecule

Returns:

true if input and model match exactly, or false otherwise

See Also:

TemplateMoleculeQuery

substructureMatch

public static boolean substructureMatch(Molecule input,
                                        Molecule model)

Returns true if input matches model as a substructure, or false otherwise.

Parameters:

input - the Molecule to be tested as a substructure of model

model - the Molecule to be tested as a superstructure of input

Returns:

true if input matches model as a substructure, or false otherwise

See Also:

TemplateMoleculeQuery