org.expasy.mzjava.core.mol

Class AtomicCompositionParser

java.lang.Object

org.expasy.mzjava.core.mol.AtomicCompositionParser

public final class AtomicCompositionParser
extends Object

Parsing atomic composition.

Atom definition

An atom is defined by a symbol with an optional explicit mass number (nucleon number)
Example: hydrogen atom could be described like "H" or "H[1]"

Atom occurrence definition

The number of atoms directly follows the atom definition else there is only one occurrence. This number can be positive or negative, signed or not.
Example 1: "O2" or "O+2" means 2 atoms of oxygen (main isotope O[16])
Example 2: "H-1" defines a loss of H

Composition definition

A composition is an assembling of atoms (or groups of atom) and is simply described as a sequence of previously defined atoms.
Example: "CH4", "H2O" or "C2H6OH"

A composition may also contains groups of atoms simplifying some composition definition
Example: "CH3(CH2)2OH"
Observe the two occurrences of CH2 group in the previous propanol molecule.

Composition charge definition

A composition can be neutral or charged. The charge has to close the composition. The charge, surrounded with parenthesis, may be positive or negative with the sign placed at the end
Example: "H3O(+)", "OH(-)", "SO4(2-)"

Grammar

 Composition      :   AtomicExpression+ ('(' Charge ')') ?
 AtomicExpression :   HomoAtoms | AtomGroup
 HomoAtoms        :   AtomicSymbol ('[' MassNumber ']')? Count?
 AtomGroup        :   '(' HomoAtoms ')' Count
 AtomicSymbol     :   [A-Z][a-z]?
 MassNumber       :   [0-9]+
 Count            :   [+-]?[0-9]+
 Charge           :   [0-9]* [+-]
 

Remark

Sometimes things can be a bit tricky with the overall charge state when atoms are removed. Let's take an example by describing an expression for proton removal.

An intuitive way of writing it would be "H-1(+)" but it is wrong as it leads to subtracting an hydrogen and an electron (-H-e) whereas it should be subtracting an hydrogen and adding an electron (H+ = H-1e => -H+ = -H+1e).

As a result the right way of defining it is "H-1(-)" with the correct overall deduced charge given to the parser.

Version:

1.0

Author:

nikitin

Method Summary

Methods

Modifier and Type	Method and Description
static AtomicCompositionParser	getInstance()
int	parse(String content, gnu.trove.map.TObjectIntMap<Atom> composition) Parses the given string content and transmit data to builder.

Methods inherited from class java.lang.Object

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

Method Detail

getInstance

public static AtomicCompositionParser getInstance()

Returns:

the singleton

parse

public int parse(String content,
        gnu.trove.map.TObjectIntMap<Atom> composition)

Parses the given string content and transmit data to builder.

Parameters:

content - the data string to parse.