org.openscience.cdk.formula.MolecularFormula Maven / Gradle / Ivy
/* Copyright (C) 2007 Miguel Rojasch
*
* Contact: [email protected]
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
*/
package org.openscience.cdk.formula;
import java.util.HashMap;
import java.util.Hashtable;
import java.util.Iterator;
import java.util.Map;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.interfaces.IIsotope;
import org.openscience.cdk.interfaces.IMolecularFormula;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
/**
* Class defining a molecular formula object. It maintains
* a list of list {@link IIsotope}.
*
* Examples:
*
* [C5H5]-C6H612C513CH6
*
* @cdk.module data
* @author miguelrojasch
* @cdk.created 2007-11-20
* @cdk.keyword molecular formula
* @cdk.githash
*/
public class MolecularFormula implements IMolecularFormula {
/**
* Determines if a de-serialized object is compatible with this class.
*
* This value must only be changed if and only if the new version
* of this class is incompatible with the old version. See Sun docs
* for details.
*/
private static final long serialVersionUID = -2011407700837295287L;
private Map isotopes;
/**
* The partial charge of the molecularFormula. The default value is Double.NaN.
*/
private Integer charge = null;
/**
* A hashtable for the storage of any kind of properties of this IChemObject.
*/
private Map properties;
/**
* Constructs an empty MolecularFormula.
*/
public MolecularFormula() {
isotopes = new HashMap();
}
/**
* Adds an molecularFormula to this MolecularFormula.
*
* @param formula The molecularFormula to be added to this chemObject
* @return The IMolecularFormula
*/
@Override
public IMolecularFormula add(IMolecularFormula formula) {
for (IIsotope newIsotope : formula.isotopes()) {
addIsotope(newIsotope, formula.getIsotopeCount(newIsotope));
}
if (formula.getCharge() != null) {
if (charge != null)
charge += formula.getCharge();
else
charge = formula.getCharge();
}
return this;
}
/**
* Adds an Isotope to this MolecularFormula one time.
*
* @param isotope The isotope to be added to this MolecularFormula
* @see #addIsotope(IIsotope, int)
*/
@Override
public IMolecularFormula addIsotope(IIsotope isotope) {
return this.addIsotope(isotope, 1);
}
/**
* Adds an Isotope to this MolecularFormula in a number of occurrences.
*
* @param isotope The isotope to be added to this MolecularFormula
* @param count The number of occurrences to add
* @see #addIsotope(IIsotope)
*/
@Override
public IMolecularFormula addIsotope(IIsotope isotope, int count) {
boolean flag = false;
for (IIsotope thisIsotope : isotopes()) {
if (isTheSame(thisIsotope, isotope)) {
isotopes.put(thisIsotope, isotopes.get(thisIsotope) + count);
flag = true;
break;
}
}
if (!flag) {
isotopes.put(isotope, count);
}
return this;
}
/**
* True, if the MolecularFormula contains the given IIsotope object and not
* the instance. The method looks for other isotopes which has the same
* symbol, natural abundance and exact mass.
*
* @param isotope The IIsotope this MolecularFormula is searched for
* @return True, if the MolecularFormula contains the given isotope object
*/
@Override
public boolean contains(IIsotope isotope) {
for (IIsotope thisIsotope : isotopes()) {
if (isTheSame(thisIsotope, isotope)) {
return true;
}
}
return false;
}
/**
* {@inheritDoc}
*/
@Override
public Integer getCharge() {
return charge;
}
/**
* Checks a set of Nodes for the occurrence of the isotope in the
* IMolecularFormula from a particular isotope. It returns 0 if the does not exist.
*
* @param isotope The IIsotope to look for
* @return The occurrence of this isotope in this IMolecularFormula
* @see #getIsotopeCount()
*/
@Override
public int getIsotopeCount(IIsotope isotope) {
return !contains(isotope) ? 0 : isotopes.get(getIsotope(isotope));
}
/**
* Checks a set of Nodes for the number of different isotopes in the
* IMolecularFormula.
*
* @return The the number of different isotopes in this IMolecularFormula
* @see #getIsotopeCount(IIsotope)
*/
@Override
public int getIsotopeCount() {
return isotopes.size();
}
/**
* Get the isotope instance given an IIsotope. The instance is those
* that has the isotope with the same symbol, natural abundance and
* exact mass.
*
* @param isotope The IIsotope for looking for
* @return The IIsotope instance
* @see #isotopes
*/
private IIsotope getIsotope(IIsotope isotope) {
for (IIsotope thisIsotope : isotopes()) {
if (isTheSame(isotope, thisIsotope)) return thisIsotope;
}
return null;
}
/**
* Returns an Iterator for looping over all isotopes in this IMolecularFormula.
*
* @return An Iterator with the isotopes in this IMolecularFormula
*/
@Override
public Iterable isotopes() {
return isotopes.keySet();
}
/**
* {@inheritDoc}
*/
@Override
public void setCharge(Integer charge) {
this.charge = charge;
}
/**
* Removes all isotopes of this molecular formula.
*/
@Override
public void removeAllIsotopes() {
isotopes.clear();
}
/**
* Removes the given isotope from the MolecularFormula.
*
* @param isotope The IIsotope to be removed
*/
@Override
public void removeIsotope(IIsotope isotope) {
isotopes.remove(getIsotope(isotope));
}
/**
* Clones this MolecularFormula object and its content. I should
* integrate into ChemObject.
*
* @return The cloned object
*/
@Override
public Object clone() throws CloneNotSupportedException {
// /* it is not a super class of chemObject */
// MolecularFormula clone = (MolecularFormula) super.clone();
// // start from scratch
// clone.removeAllIsotopes();
// // clone all isotopes
// Iterator iterIso = this.isotopes();
// while(iterIso.hasNext()){
// IIsotope isotope = iterIso.next();
// clone.addIsotope((IIsotope) isotope.clone(),getIsotopeCount(isotope));
// }
MolecularFormula clone = new MolecularFormula();
for (IIsotope isotope : isotopes()) {
clone.addIsotope((IIsotope) isotope.clone(), getIsotopeCount(isotope));
}
clone.setCharge(getCharge());
return clone;
}
/**
* Lazy creation of properties hash. I should
* integrate into ChemObject.
*
* @return Returns in instance of the properties
*/
private Map lazyProperties() {
if (properties == null) {
properties = new Hashtable();
}
return properties;
}
/**
* Sets a property for a IChemObject. I should
* integrate into ChemObject.
*
*@param description An object description of the property (most likely a
* unique string)
*@param property An object with the property itself
*@see #getProperty
*@see #removeProperty
*/
@Override
public void setProperty(Object description, Object property) {
lazyProperties().put(description, property);
}
/**
* Removes a property for a IChemObject. I should
* integrate into ChemObject.
*
*@param description The object description of the property (most likely a
* unique string)
*@see #setProperty
*@see #getProperty
*/
@Override
public void removeProperty(Object description) {
if (properties == null) {
return;
}
lazyProperties().remove(description);
}
/**
*{@inheritDoc}
*/
@Override
public T getProperty(Object description) {
if (properties == null) return null;
// can't check the type
@SuppressWarnings("unchecked")
T value = (T) lazyProperties().get(description);
return value;
}
/**
*{@inheritDoc}
*/
@Override
public T getProperty(Object description, Class c) {
Object value = lazyProperties().get(description);
if (c.isInstance(value)) {
@SuppressWarnings("unchecked")
T typed = (T) value;
return typed;
} else if (value != null) {
throw new IllegalArgumentException("attempted to access a property of incorrect type, expected "
+ c.getSimpleName() + " got " + value.getClass().getSimpleName());
}
return null;
}
/**
* Returns a Map with the IChemObject's properties.I should
* integrate into ChemObject.
*
*@return The object's properties as an Hashtable
*@see #setProperties
*/
@Override
public Map getProperties() {
return lazyProperties();
}
/**
* Sets the properties of this object.
*
*@param properties a Hashtable specifying the property values
*@see #getProperties
*/
@Override
public void setProperties(Map properties) {
Iterator