kekule
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Open source JavaScript toolkit for chemoinformatics
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JavaScript
/**
* @fileoverview
* This file contains basic classes related with electrons (bond, lone pair...).
* @author Partridge Jiang
*/
/*
* requires /lan/classes.js
* requires /core/kekule.common.js
* requires /utils/kekule.utils.js
*/
/**
* Represent an abstract electron set (bond, lone pair, etc.).
* @class
* @augments Kekule.ChemObject
* @param {Float} electronCount Count of electrons in this set.
* Note that there may be partial electron in set, so a float value is used here.
*
* @property {Float} electronCount Count of electrons in this set.
* Note that there may be partial electron in set, so a float value is used here.
*/
Kekule.ElectronSet = Class.create(Kekule.ChemObject,
/** @lends Kekule.ElectronSet# */
{
/** @private */
CLASS_NAME: 'Kekule.ElectronSet',
/**
* @constructs
*/
initialize: function(/*$super, */electronCount)
{
this.tryApplySuper('initialize') /* $super() */;
this.setElectronCount(electronCount || Kekule.ElectronSet.UNSET_ELECTRONCOUNT);
},
/** @private */
initProperties: function()
{
this.defineProp('electronCount', {'dataType': DataType.FLOAT});
}
});
/**
* Indicate the electron count is uncertain.
* @constant
*/
Kekule.ElectronSet.UNSET_ELECTRONCOUNT = null;
/**
* Represent unbonded form of electron sets.
* @class
* @augments Kekule.ElectronSet
* @param {Float} electronCount Count of electrons in this set. If this param is not set,
* electron count will be regarded as bondOrder * 2.
*/
Kekule.UnbondedElectronSet = Class.create(Kekule.ElectronSet,
/** @lends Kekule.UnbondedElectronSet# */
{
/** @private */
CLASS_NAME: 'Kekule.UnBondedElectronSet',
/**
* @constructs
*/
initialize: function(/*$super, */electronCount)
{
this.tryApplySuper('initialize', [electronCount]) /* $super(electronCount) */;
},
/** @private */
initProperties: function()
{
}
});
/**
* Enumeration of bond types
* @class
*/
Kekule.BondType = {
/** Covalent bond, the default bond type */
COVALENT: 'covalent',
/** Ionic bond */
IONIC: 'ionic',
/** Coordinate bond */
COORDINATE: 'coordinate',
/** Metallic bond' */
METALLIC: 'metallic',
/** HYDROGEN bond */
HYDROGEN: 'hydrogen',
/** Trasition bond, bond forming or breaking in transition state */
TRANSITION: 'transition',
/** Unknown */
UNKNOWN: null,
/** Default type is covalent bond */
DEFAULT: 'covalent'
};
/**
* Enumeration of bond orders
* @class
*/
Kekule.BondOrder = {
/** Single bond */
SINGLE: 1,
/** Double bond. */
DOUBLE: 2,
/** Triple bond. */
TRIPLE: 3,
/** Quadruple bond. */
QUAD: 4,
/** Explicit Aromatic bond. */
EXPLICIT_AROMATIC: 10,
/** Other form of bond. */
OTHER: 20,
/** Uncertain bond. */
UNSET: null,
/** Default is a single bond */
DEFAULT: 1,
/**
* Get min valence of an atom to connect to a bond.
* @param {Object} bondOrder
* @returns {Float} Aromatic bond will return 1.5, means it is between single and double bond.
*/
getBondValence: function(bondOrder)
{
if (bondOrder === Kekule.BondOrder.UNSET)
return 0;
else if (bondOrder == Kekule.BondOrder.EXPLICIT_AROMATIC)
return 1.5;
else
return bondOrder;
}
};
/**
* Represent a typical bond form of molecule.
* @class
* @augments Kekule.ElectronSet
* @param {Int} bondOrder Order of bond. Usually electronCount / 2.
* @param {Float} electronCount Count of electrons in this set. If this param is not set,
* electron count will be regarded as bondOrder * 2.
* @param {String} bondType Type of bond, a value from {@link Kekule.BondType}.
* If not specified, the bond will be regarded as a covalent one.
*
* @property {String} bondType Type of bond, a value from {@link Kekule.BondType}.
* @property {Num} bondOrder Order of bond. Values should be retrieved from {@link Kekule.BondOrder}.
* @property {Num} bondValence Valence comsumed of an atom to connect to this bond. Note this value is different from {@link Kekule.BondForm#bondOrder},
* For example, bondOrder value for {@link Kekule.BondOrder.EXPLICIT_AROMATIC} is 10, but the valence is 1.5. This property is read only.
*/
Kekule.BondForm = Class.create(Kekule.ElectronSet,
/** @lends Kekule.BondForm# */
{
/** @private */
CLASS_NAME: 'Kekule.BondForm',
/**
* @constructs
*/
initialize: function(/*$super, */bondOrder, electronCount, bondType)
{
this.tryApplySuper('initialize', [electronCount]) /* $super(electronCount) */;
this.setBondOrder(bondOrder || Kekule.BondOrder.DEFAULT);
if (Kekule.ObjUtils.notUnset(bondType))
this.setBondType(bondType);
if (Kekule.ObjUtils.notUnset(electronCount))
this.setElectronCount(electronCount);
},
/** @private */
initProperties: function()
{
this.defineProp('bondType', {
'dataType': DataType.STRING,
'enumSource': Kekule.BondType,
'getter': function() { var r = this.getPropStoreFieldValue('bondType'); return (r? r: Kekule.BondType.DEFAULT); }
});
this.defineProp('bondOrder', {
'dataType': DataType.FLOAT,
'enumSource': Kekule.BondOrder,
'setter': function(value)
{
if (this.getPropStoreFieldValue('bondOrder') != value)
{
this.setPropStoreFieldValue('bondOrder', value);
if (value)
{
if (this.getBondType() == Kekule.BondType.COVALENT)
{
this.setElectronCount(this.getBondValence() * 2);
}
}
else if (value === Kekule.BondOrder.UNSET)
this.setElectronCount(Kekule.ElectronSet.UNSET_ELECTRONCOUNT);
}
}
});
this.defineProp('electronCount', {
'dataType': DataType.FLOAT
});
this.defineProp('bondValence', {
'dataType': DataType.FLOAT,
'serializable': false,
'getter': function() { return Kekule.BondOrder.getBondValence(this.getBondOrder()); },
'setter': null
});
}
});
/*
* Indicate the bond order is uncertain.
* @constant
*/
//Kekule.BondForm.UNSET_BONDORDER = null;
//======================================================
/**
* Factory to create and get suitable bond form objects.
* @class
*/
Kekule.BondFormFactory = {
/** @private */
_bondForms: {},
/** @private */
getBondFormId: function(bondOrder, electronCount, bondType)
{
var result = '';
if (bondType)
result += bondType + '_';
if (bondOrder)
result += Number(bondOrder).toString();
if (electronCount)
result += '_' + Number(electronCount).toString();
return result;
},
/**
* Returns a suitable {@link Kekule.BondForm} object.
* @param {Int} bondOrder Order of bond.
* @param {Float} electronCount Number of electrons. Usually you can bypass this param.
* @param {String} bondType Type of bond.
* @returns {Kekule.BondForm}
*/
getBondForm: function(bondOrder, electronCount, bondType)
{
if ((!bondOrder) && (!electronCount) && (!bondType))
return undefined;
if (!bondType)
bondType = Kekule.BondType.DEFAULT;
if ((!electronCount) && (bondOrder) && (bondType === Kekule.BondType.COVALENT))
{
var bondValence = Kekule.BondOrder.getBondValence(bondOrder);
electronCount = bondValence * 2;
}
var id = Kekule.BondFormFactory.getBondFormId(bondOrder, electronCount, bondType);
if (!Kekule.BondFormFactory._bondForms[id])
Kekule.BondFormFactory._bondForms[id] = new Kekule.BondForm(bondOrder, electronCount, bondType);
return Kekule.BondFormFactory._bondForms[id];
}
};
/**
* Enumeration of radical types
* @class
*/
Kekule.RadicalOrder = {
NONE: 0,
SINGLET: 1,
DOUBLET: 2,
TRIPLET: 3,
DEFAULT: 0,
/**
* Returns the electron number of this radical.
* @param {Int} radicalOrder Value from {@link Kekule.RadicalOrder}.
* @returns {Int}
*/
getRadicalElectronCount: function(radicalOrder)
{
var O = Kekule.RadicalOrder;
if (Kekule.ObjUtils.isUnset(radicalOrder) || (radicalOrder === O.NONE))
return 0;
else if (radicalOrder === O.DOUBLET)
return 1;
else
return 2;
}
};
/**
* Enumeration of hybridization types
* @class
*/
Kekule.HybridizationType = {
/** hybridization type is not determined. **/
UNKNOWN: null,
/** sp. **/
SP: 1,
/** sp2 **/
SP2: 2,
/** sp3 **/
SP3: 3,
/** Explicitly no hybridization. */
NONE: 0
};