kekule
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Open source JavaScript toolkit for chemoinformatics
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JavaScript
/**
* @fileoverview
* This file helps to determine the valence of a neutral, anion(-) or cation(+) atom.
* @author Partridge Jiang
*/
/**
* A class to help to determinate the valence of atom, especially with charge.
* @class
*/
Kekule.ValenceUtils = {
/**
* Returns possible valence according to atomic number and charge.
* @param {Int} atomicNumber
* @param {Int} charge
* @returns {Hash} A special hash containing fields {valences: array, valenceElectronCount: int(in no charge form), unexpectedCharge: a special flag, indicating that the input charge is not a normal one}
*/
getPossibleMdlValenceInfo: function(atomicNumber, charge)
{
var q = Math.round(charge);
var valences = [];
var valenceElectronCount = 0;
var unexpectedCharge = false;
var result = {};
switch (atomicNumber) {
case 1: // H
case 3: // Li
case 11: // Na
case 19: // K
case 37: // Rb
case 55: // Cs
case 87: // Fr
if (q === 0)
valences = [1];
else if (q === 1)
valences = [0];
else
unexpectedCharge = true;
valenceElectronCount = 1;
break;
case 4: // Be
case 12: // Mg
case 20: // Ca
case 38: // Sr
case 56: // Ba
case 88: // Ra
switch (q) {
case 0: valences = [2]; break;
case 1: valences = [1]; break;
case 2: valences = [0]; break;
default: unexpectedCharge = true; break;
}
valenceElectronCount = 2;
break;
case 5: // B
switch (q) {
case -4: valences = [1]; break;
case -3: valences = [2]; break;
case -2: valences = [3, 5]; break;
case -1: valences = [4]; break;
case 0: valences = [3]; break;
case 1: valences = [2]; break;
case 2: valences = [1]; break;
case 3: valences = [0]; break;
default: unexpectedCharge = true; break;
}
valenceElectronCount = 3;
break;
case 6: // C
switch (q) {
case -4: valences = [0]; break;
case -3: valences = [1]; break;
case -2: valences = [2]; break;
case -1: valences = [3, 5]; break;
case 0: valences = [4]; break;
case 1: valences = [3]; break;
case 2: valences = [2]; break;
case 3: valences = [1]; break;
case 4: valences = [0]; break;
default: unexpectedCharge = true; break;
}
valenceElectronCount = 4;
break;
case 7: // N
switch (q) {
case -3: valences = [0]; break;
case -2: valences = [1]; break;
case -1: valences = [2]; break;
case 0: valences = [3, 5]; break;
case 1: valences = [4]; break;
case 2: valences = [3]; break;
case 3: valences = [2]; break;
case 4: valences = [1]; break;
case 5: valences = [0]; break;
default: unexpectedCharge = true; break;
}
valenceElectronCount = 5;
break;
case 8: // O
switch (q) {
case -2: valences = [0]; break;
case -1: valences = [1]; break;
case 0: valences = [2]; break;
case 1: valences = [3, 5]; break;
case 2: valences = [4]; break;
case 3: valences = [3]; break;
case 4: valences = [2]; break;
case 5: valences = [1]; break;
case 6: valences = [0]; break;
default: unexpectedCharge = true; break;
}
valenceElectronCount = 6;
break;
case 9: // F
switch (q) {
case -1: valences = [0]; break;
case 0: valences = [1]; break;
case 1: valences = [2]; break;
case 2: valences = [3, 5]; break;
case 3: valences = [4]; break;
case 4: valences = [3]; break;
case 5: valences = [2]; break;
case 6: valences = [1]; break;
case 7: valences = [0]; break;
default: unexpectedCharge = true; break;
}
valenceElectronCount = 7;
break;
case 13: // Al
switch (q) {
case -4: valences = [1, 3, 5, 7]; break;
case -3: valences = [2, 4, 6]; break;
case -2: valences = [3, 5]; break;
case -1: valences = [4]; break;
case 0: valences = [3]; break;
case 1: valences = [2]; break;
case 2: valences = [1]; break;
case 3: valences = [0]; break;
default: unexpectedCharge = true; break;
}
valenceElectronCount = 3;
break;
case 14: // Si
switch (q) {
case -4: valences = [0]; break;
case -3: valences = [1, 3, 5, 7]; break;
case -2: valences = [2, 4, 6]; break;
case -1: valences = [3, 5]; break;
case 0: valences = [4]; break;
case 1: valences = [3]; break;
case 2: valences = [2]; break;
case 3: valences = [1]; break;
case 4: valences = [0]; break;
}
valenceElectronCount = 4;
break;
case 15: // P
switch (q) {
case -3: valences = [0]; break;
case -2: valences = [1, 3, 5, 7]; break;
case -1: valences = [2, 4, 6]; break;
case 0: valences = [3, 5]; break;
case 1: valences = [4]; break;
case 2: valences = [3]; break;
case 3: valences = [2]; break;
case 4: valences = [1]; break;
case 5: valences = [0]; break;
}
valenceElectronCount = 5;
break;
case 16: // S
switch (q) {
case -2: valences = [0]; break;
case -1: valences = [1, 3, 5, 7]; break;
case 0: valences = [2, 4, 6]; break;
case 1: valences = [3, 5]; break;
case 2: valences = [4]; break;
case 3: valences = [3]; break;
case 4: valences = [2]; break;
case 5: valences = [1]; break;
case 6: valences = [0]; break;
}
valenceElectronCount = 6;
break;
case 17: // Cl
switch (q) {
case -1: valences = [0]; break;
case 0: valences = [1, 3, 5, 7]; break;
case 1: valences = [2, 4, 6]; break;
case 2: valences = [3, 5]; break;
case 3: valences = [4]; break;
case 4: valences = [3]; break;
case 5: valences = [2]; break;
case 6: valences = [1]; break;
case 7: valences = [0]; break;
}
valenceElectronCount = 7;
break;
case 31: // Ga
switch (q) {
case -4: valences = [1, 3, 5, 7]; break;
case -3: valences = [2, 4, 6]; break;
case -2: valences = [3, 5]; break;
case -1: valences = [4]; break;
case 0: valences = [3]; break;
case 2: valences = [1]; break;
case 3: valences = [0]; break;
default: unexpectedCharge = true; break;
}
valenceElectronCount = 3;
break;
case 32: // Ge
switch (q) {
case -4: valences = [0]; break;
case -3: valences = [1, 3, 5, 7]; break;
case -2: valences = [2, 4, 6]; break;
case -1: valences = [3, 5]; break;
case 0: valences = [4]; break;
case 1: valences = [3]; break;
case 3: valences = [1]; break;
case 4: valences = [0]; break;
}
valenceElectronCount = 4;
break;
case 33: // As
switch (q) {
case -3: valences = [0]; break;
case -2: valences = [1, 3, 5, 7]; break;
case -1: valences = [2, 4, 6]; break;
case 0: valences = [3, 5]; break;
case 1: valences = [4]; break;
case 2: valences = [3]; break;
case 4: valences = [1]; break;
case 5: valences = [0]; break;
}
valenceElectronCount = 5;
break;
case 34: // Se
switch (q) {
case -2: valences = [0]; break;
case -1: valences = [1, 3, 5, 7]; break;
case 0: valences = [2, 4, 6]; break;
case 1: valences = [3, 5]; break;
case 2: valences = [4]; break;
case 3: valences = [3]; break;
case 5: valences = [1]; break;
case 6: valences = [0]; break;
}
valenceElectronCount = 6;
break;
case 35: // Br
switch (q) {
case -1: valences = [0]; break;
case 0: valences = [1, 3, 5, 7]; break;
case 1: valences = [2, 4, 6]; break;
case 2: valences = [3, 5]; break;
case 3: valences = [4]; break;
case 4: valences = [3]; break;
case 6: valences = [1]; break;
case 7: valences = [0]; break;
}
valenceElectronCount = 7;
break;
case 49: // In
switch (q) {
case -4: valences = [1, 3, 5, 7]; break;
case -3: valences = [2, 4, 6]; break;
case -2: valences = [3, 5]; break;
case -1: valences = [4]; break;
case 0: valences = [3]; break;
case 2: valences = [1]; break;
case 3: valences = [0]; break;
default: unexpectedCharge = true; break;
}
valenceElectronCount = 3;
break;
case 50: // Sn
case 82: // Pb
switch (q) {
case -4: valences = [0]; break;
case -3: valences = [1, 3, 5, 7]; break;
case -2: valences = [2, 4, 6]; break;
case -1: valences = [3, 5]; break;
case 0: valences = [2, 4]; break;
case 1: valences = [3]; break;
case 3: valences = [1]; break;
case 4: valences = [0]; break;
}
valenceElectronCount = 4;
break;
case 51: // Sb
case 83: // Bi
switch (q) {
case -3: valences = [0]; break;
case -2: valences = [1, 3, 5, 7]; break;
case -1: valences = [2, 4, 6]; break;
case 0: valences = [3, 5]; break;
case 1: valences = [2, 4]; break;
case 2: valences = [3]; break;
case 4: valences = [1]; break;
case 5: valences = [0]; break;
}
valenceElectronCount = 5;
break;
case 52: // Te
case 84: // Po
switch (q) {
case -2: valences = [0]; break;
case -1: valences = [1, 3, 5, 7]; break;
case 0: valences = [2, 4, 6]; break;
case 1: valences = [3, 5]; break;
case 2: valences = [2, 4]; break;
case 3: valences = [3]; break;
case 5: valences = [1]; break;
case 6: valences = [0]; break;
}
valenceElectronCount = 6;
break;
case 53: // I
case 85: // At
switch (q) {
case -1: valences = [0]; break;
case 0: valences = [1, 3, 5, 7]; break;
case 1: valences = [2, 4, 6]; break;
case 2: valences = [3, 5]; break;
case 3: valences = [2, 4]; break;
case 4: valences = [3]; break;
case 6: valences = [1]; break;
case 7: valences = [0]; break;
}
valenceElectronCount = 7;
break;
case 81: // Tl
switch (q) {
case -4: valences = [1, 3, 5, 7]; break;
case -3: valences = [2, 4, 6]; break;
case -2: valences = [3, 5]; break;
case -1: valences = [2, 4]; break;
case 0: valences = [1, 3]; break;
case 3: valences = [0]; break;
default: unexpectedCharge = true; break;
}
valenceElectronCount = 3;
break;
}
if (unexpectedCharge) // calculate the valence direct from outer shell valence electron count
{
var eCount = valenceElectronCount - charge;
if (eCount < 0 || eCount > 8) // related to the inner shell, complex and we do not handle here
valences = [];
}
return {'valences': valences, 'valenceElectronCount': valenceElectronCount, 'unexpectedCharge': unexpectedCharge};
},
/**
* Returns the max possible MDL valence value.
* @param {Int} atomicNumber
* @param {Int} charge
* @returns {Int} Returns 0 when there is no provided value.
*/
getMaxPossibleMdlValence: function(atomicNumber, charge)
{
var valenceInfos = Kekule.ValenceUtils.getPossibleMdlValenceInfo(atomicNumber, charge);
var valences = valenceInfos.valences;
return valences.length? valences[valences.length - 1]: 0;
},
/**
* Returns the implicit MDL valence for element with charge and known (explicit) valence.
* e.g. C+ valence is 3 while C- valence is also 3.
* The code is copy from mdlvalence.h of OpenBabel.
* See https://github.com/openbabel/openbabel/blob/master/src/formats/mdlvalence.h
* @param {Int} atomicNumber
* @param {Int} charge
* @param {Int} explicitValence
* @returns {Int}
*/
getImplicitMdlValence: function(atomicNumber, charge, explicitValence)
{
var q = charge;
var val = explicitValence;
switch (atomicNumber) {
case 1: // H
case 3: // Li
case 11: // Na
case 19: // K
case 37: // Rb
case 55: // Cs
case 87: // Fr
if (q == 0 && val <= 1)
return 1;
break;
case 4: // Be
case 12: // Mg
case 20: // Ca
case 38: // Sr
case 56: // Ba
case 88: // Ra
switch (q) {
case 0: if (val <= 2) return 2; break;
case 1: if (val <= 1) return 1; break;
}
break;
case 5: // B
switch (q) {
case -4: if (val <= 1) return 1; break;
case -3: if (val <= 2) return 2; break;
case -2: if (val <= 3) return 3;
if (val <= 5) return 5; break;
case -1: if (val <= 4) return 4; break;
case 0: if (val <= 3) return 3; break;
case 1: if (val <= 2) return 2; break;
case 2: if (val <= 1) return 1; break;
}
break;
case 6: // C
switch (q) {
case -3: if (val <= 1) return 1; break;
case -2: if (val <= 2) return 2; break;
case -1: if (val <= 3) return 3;
if (val <= 5) return 5; break;
case 0: if (val <= 4) return 4; break;
case 1: if (val <= 3) return 3; break;
case 2: if (val <= 2) return 2; break;
case 3: if (val <= 1) return 1; break;
}
break;
case 7: // N
switch (q) {
case -2: if (val <= 1) return 1; break;
case -1: if (val <= 2) return 2; break;
case 0: if (val <= 3) return 3;
if (val <= 5) return 5; break;
case 1: if (val <= 4) return 4; break;
case 2: if (val <= 3) return 3; break;
case 3: if (val <= 2) return 2; break;
case 4: if (val <= 1) return 1; break;
}
break;
case 8: // O
switch (q) {
case -1: if (val <= 1) return 1; break;
case 0: if (val <= 2) return 2; break;
case 1: if (val <= 3) return 3;
if (val <= 5) return 5; break;
case 2: if (val <= 4) return 4; break;
case 3: if (val <= 3) return 3; break;
case 4: if (val <= 2) return 2; break;
case 5: if (val <= 1) return 1; break;
}
break;
case 9: // F
switch (q) {
case 0: if (val <= 1) return 1; break;
case 1: if (val <= 2) return 2; break;
case 2: if (val <= 3) return 3;
if (val <= 5) return 5; break;
case 3: if (val <= 4) return 4; break;
case 4: if (val <= 3) return 3; break;
case 5: if (val <= 2) return 2; break;
case 6: if (val <= 1) return 1; break;
}
break;
case 13: // Al
switch (q) {
case -4: if (val <= 1) return 1;
if (val <= 3) return 3;
if (val <= 5) return 5;
if (val <= 7) return 7; break;
case -3: if (val <= 2) return 2;
if (val <= 4) return 4;
if (val <= 6) return 6; break;
case -2: if (val <= 3) return 3;
if (val <= 5) return 5; break;
case -1: if (val <= 4) return 4; break;
case 0: if (val <= 3) return 3; break;
case 1: if (val <= 2) return 2; break;
case 2: if (val <= 1) return 1; break;
}
break;
case 14: // Si
switch (q) {
case -3: if (val <= 1) return 1;
if (val <= 3) return 3;
if (val <= 5) return 5;
if (val <= 7) return 7; break;
case -2: if (val <= 2) return 2;
if (val <= 4) return 4;
if (val <= 6) return 6; break;
case -1: if (val <= 3) return 3;
if (val <= 5) return 5; break;
case 0: if (val <= 4) return 4; break;
case 1: if (val <= 3) return 3; break;
case 2: if (val <= 2) return 2; break;
case 3: if (val <= 1) return 1; break;
}
break;
case 15: // P
switch (q) {
case -2: if (val <= 1) return 1;
if (val <= 3) return 3;
if (val <= 5) return 5;
if (val <= 7) return 7; break;
case -1: if (val <= 2) return 2;
if (val <= 4) return 4;
if (val <= 6) return 6; break;
case 0: if (val <= 3) return 3;
if (val <= 5) return 5; break;
case 1: if (val <= 4) return 4; break;
case 2: if (val <= 3) return 3; break;
case 3: if (val <= 2) return 2; break;
case 4: if (val <= 1) return 1; break;
}
break;
case 16: // S
switch (q) {
case -1: if (val <= 1) return 1;
if (val <= 3) return 3;
if (val <= 5) return 5;
if (val <= 7) return 7; break;
case 0: if (val <= 2) return 2;
if (val <= 4) return 4;
if (val <= 6) return 6; break;
case 1: if (val <= 3) return 3;
if (val <= 5) return 5; break;
case 2: if (val <= 4) return 4; break;
case 3: if (val <= 3) return 3; break;
case 4: if (val <= 2) return 2; break;
case 5: if (val <= 1) return 1; break;
}
break;
case 17: // Cl
switch (q) {
case 0: if (val <= 1) return 1;
if (val <= 3) return 3;
if (val <= 5) return 5;
if (val <= 7) return 7; break;
case 1: if (val <= 2) return 2;
if (val <= 4) return 4;
if (val <= 6) return 6; break;
case 2: if (val <= 3) return 3;
if (val <= 5) return 5; break;
case 3: if (val <= 4) return 4; break;
case 4: if (val <= 3) return 3; break;
case 5: if (val <= 2) return 2; break;
case 6: if (val <= 1) return 1; break;
}
break;
case 31: // Ga
switch (q) {
case -4: if (val <= 1) return 1;
if (val <= 3) return 3;
if (val <= 5) return 5;
if (val <= 7) return 7; break;
case -3: if (val <= 2) return 2;
if (val <= 4) return 4;
if (val <= 6) return 6; break;
case -2: if (val <= 3) return 3;
if (val <= 5) return 5; break;
case -1: if (val <= 4) return 4; break;
case 0: if (val <= 3) return 3; break;
case 2: if (val <= 1) return 1; break;
}
break;
case 32: // Ge
switch (q) {
case -3: if (val <= 1) return 1;
if (val <= 3) return 3;
if (val <= 5) return 5;
if (val <= 7) return 7; break;
case -2: if (val <= 2) return 2;
if (val <= 4) return 4;
if (val <= 6) return 6; break;
case -1: if (val <= 3) return 3;
if (val <= 5) return 5; break;
case 0: if (val <= 4) return 4; break;
case 1: if (val <= 3) return 3; break;
case 3: if (val <= 1) return 1; break;
}
break;
case 33: // As
switch (q) {
case -2: if (val <= 1) return 1;
if (val <= 3) return 3;
if (val <= 5) return 5;
if (val <= 7) return 7; break;
case -1: if (val <= 2) return 2;
if (val <= 4) return 4;
if (val <= 6) return 6; break;
case 0: if (val <= 3) return 3;
if (val <= 5) return 5; break;
case 1: if (val <= 4) return 4; break;
case 2: if (val <= 3) return 3; break;
case 4: if (val <= 1) return 1; break;
}
break;
case 34: // Se
switch (q) {
case -1: if (val <= 1) return 1;
if (val <= 3) return 3;
if (val <= 5) return 5;
if (val <= 7) return 7; break;
case 0: if (val <= 2) return 2;
if (val <= 4) return 4;
if (val <= 6) return 6; break;
case 1: if (val <= 3) return 3;
if (val <= 5) return 5; break;
case 2: if (val <= 4) return 4; break;
case 3: if (val <= 3) return 3; break;
case 5: if (val <= 1) return 1; break;
}
break;
case 35: // Br
switch (q) {
case 0: if (val <= 1) return 1;
if (val <= 3) return 3;
if (val <= 5) return 5;
if (val <= 7) return 7; break;
case 1: if (val <= 2) return 2;
if (val <= 4) return 4;
if (val <= 6) return 6; break;
case 2: if (val <= 3) return 3;
if (val <= 5) return 5; break;
case 3: if (val <= 4) return 4; break;
case 4: if (val <= 3) return 3; break;
case 6: if (val <= 1) return 1; break;
}
break;
case 49: // In
switch (q) {
case -4: if (val <= 1) return 1;
if (val <= 3) return 3;
if (val <= 5) return 5;
if (val <= 7) return 7; break;
case -3: if (val <= 2) return 2;
if (val <= 4) return 4;
if (val <= 6) return 6; break;
case -2: if (val <= 3) return 3;
if (val <= 5) return 5; break;
case -1: if (val <= 2) return 2;
if (val <= 4) return 4; break;
case 0: if (val <= 3) return 3; break;
case 2: if (val <= 1) return 1; break;
}
break;
case 50: // Sn
case 82: // Pb
switch (q) {
case -3: if (val <= 1) return 1;
if (val <= 3) return 3;
if (val <= 5) return 5;
if (val <= 7) return 7; break;
case -2: if (val <= 2) return 2;
if (val <= 4) return 4;
if (val <= 6) return 6; break;
case -1: if (val <= 3) return 3;
if (val <= 5) return 5; break;
case 0: if (val <= 2) return 2;
if (val <= 4) return 4; break;
case 1: if (val <= 3) return 3; break;
case 3: if (val <= 1) return 1; break;
}
break;
case 51: // Sb
case 83: // Bi
switch (q) {
case -2: if (val <= 1) return 1;
if (val <= 3) return 3;
if (val <= 5) return 5;
if (val <= 7) return 7; break;
case -1: if (val <= 2) return 2;
if (val <= 4) return 4;
if (val <= 6) return 6; break;
case 0: if (val <= 3) return 3;
if (val <= 5) return 5; break;
case 1: if (val <= 2) return 2;
if (val <= 4) return 4; break;
case 2: if (val <= 3) return 3; break;
case 4: if (val <= 1) return 1; break;
}
break;
case 52: // Te
case 84: // Po
switch (q) {
case -1: if (val <= 1) return 1;
if (val <= 3) return 3;
if (val <= 5) return 5;
if (val <= 7) return 7; break;
case 0: if (val <= 2) return 2;
if (val <= 4) return 4;
if (val <= 6) return 6; break;
case 1: if (val <= 3) return 3;
if (val <= 5) return 5; break;
case 2: if (val <= 2) return 2;
if (val <= 4) return 4; break;
case 3: if (val <= 3) return 3; break;
case 5: if (val <= 1) return 1; break;
}
break;
case 53: // I
case 85: // At
switch (q) {
case 0: if (val <= 1) return 1;
if (val <= 3) return 3;
if (val <= 5) return 5;
if (val <= 7) return 7; break;
case 1: if (val <= 2) return 2;
if (val <= 4) return 4;
if (val <= 6) return 6; break;
case 2: if (val <= 3) return 3;
if (val <= 5) return 5; break;
case 3: if (val <= 2) return 2;
if (val <= 4) return 4; break;
case 4: if (val <= 3) return 3; break;
case 6: if (val <= 1) return 1; break;
}
break;
case 81: // Tl
switch (q) {
case -4: if (val <= 1) return 1;
if (val <= 3) return 3;
if (val <= 5) return 5;
if (val <= 7) return 7; break;
case -3: if (val <= 2) return 2;
if (val <= 4) return 4;
if (val <= 6) return 6; break;
case -2: if (val <= 3) return 3;
if (val <= 5) return 5; break;
case -1: if (val <= 2) return 2;
if (val <= 4) return 4; break;
case 0: if (val <= 1) return 1;
if (val <= 3) return 3; break;
}
break;
}
return val;
},
/**
* Returns the implicit HYD valence for element with charge and known (explicit) valence.
* The code is copy from mdlvalence.h of OpenBabel.
* See https://github.com/openbabel/openbabel/blob/master/src/formats/mdlvalence.h
* @param {Int} atomicNumber
* @param {Int} charge
* @param {Int} explicitValence
* @returns {Int}
*/
getImplicitHydValence: function(atomicNumber, charge, explicitValence)
{
var elem = atomicNumber;
var q = charge;
var val = explicitValence;
var impval = 0;
if (elem == 6) { // C
impval = 4 - Math.abs(q);
} else if (elem == 7 || elem == 15) { // N or P
impval = 3 + q;
} else if (elem == 8 || elem == 16) { // O or S
impval = 2 + q;
}
if (impval < 0) {
impval = 0;
}
if (val > impval) {
impval = val;
}
return impval;
}
};
// defaultly the valence determination method is MDL.
Kekule.ValenceUtils.getImplicitValence = Kekule.ValenceUtils.getImplicitMdlValence;
Kekule.ValenceUtils.getMaxPossibleValence = Kekule.ValenceUtils.getMaxPossibleMdlValence;