kekule
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Open source JavaScript toolkit for chemoinformatics
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JavaScript
/**
* @fileoverview
* Methods about basic chem structures searching and matching.
* @author Partridge Jiang
*/
/*
* requires /lan/classes.js
* requires /core/kekule.common.js
* requires /core/kekule.structures.js
* requires /utils/kekule.utils.js
* requires /algorithm/kekule.canonicalizers.js
*/
(function(){
"use strict";
var AU = Kekule.ArrayUtils;
//var SC = Kekule.UnivChemStructObjComparer;
/*
* Default options to do sub structure search.
* @object
*/
Kekule.globalOptions.add('algorithm.structureSearch', {
doStandardize: true
});
/**
* A util class to search sub structures in ctab based molecule.
* @class
*/
Kekule.ChemStructureSearcher = {
/* @private */
//OPS_SKELETAL: {'compareAtom': false, 'compareCharge': false, 'compareBondOrder': false, 'compareStereo': false, 'compareHydrogenCount': false},
/* @private */
//OPS_CONSTITUTION: {'compareStereo': false},
/* @private */
//OPS_CONFIGRATION: {'compareStereo': true},
/**
* Search sub structure in molecule.
* @param {Kekule.StructureFragment} subStructure Structure to find.
* @param {Kekule.StructureFragment} sourceMol
* @param {Hash} options Search options, can include the following fields:
* {
* doStandardize: Bool, whether standardize molecule (especially perceive aromatic rings) before searching,
* default is true.
* exactMatch: Bool, if true, only the same structure with subStructure will be matched.
* structureLevel: comparation level, value from {@link Kekule.StructureComparationLevel}. Default is constitution.
* atom: Bool, if false, all node will be regarded as same. Default is true.
* mass: Bool, whether mass number is compared. Default is false.
* charge: Bool, whether charge of node is compared. Default is false.
* bondOrder: Bool, whether order of bond is compared. Default is true.
* stereo: Bool, whether stereo feature (chiral center, cis/trans of double bond) is taken into consideration. Default is false.
* }
* @returns {Variant} If sub structure is found, an array of matching node and connectors will be returned.
* Otherwise false will be returned.
*/
findSubStructure: function(subStructure, sourceMol, options)
{
// TODO: configuration search need to be rechecked
var op = Object.extend(Object.extend({}, Kekule.globalOptions.algorithm.structureSearch), options);
if (op.exactMatch)
{
var matched = sourceMol.isSameStructureWith(subStructure, op);
if (matched)
return [].concat(sourceMol.getNodes()).concat(sourceMol.getConnectors());
else
return false;
}
/*
var KS = Kekule.ChemStructureSearcher;
var initialCompareOptions = op.compareConfiguration? KS.OPS_CONFIGRATION:
op.compareConstitution? KS.OPS_CONSTITUTION:
op.compareSkeletal? KS.OPS_SKELETAL:
{};
op = Object.extend(op, initialCompareOptions);
var objCompareOptions = Object.create({
compareAtom: op.compareAtom,
compareMass: op.compareMass,
compareStereo: op.compareStereo,
compareLinkedConnectorCount: false,
compareCharge: op.compareCharge,
compareHydrogenCount: false,
compareConnectedObjCount: false,
compareBondOrder: op.compareBondOrder
});
*/
// initial options
op = Object.extend({level: Kekule.StructureComparationLevel.CONSTITUTION,
compareLinkedConnectorCount: false, compareHydrogenCount: false, compareConnectedObjCount: false}, op);
/*
var op1 = Kekule.UnivChemStructObjComparer.prepareCompareOptions(op);
var op2 = Kekule.ObjComparer.getStructureComparisonDetailOptions(op);
op = op2;
console.log(op1);
console.log(op2);
console.log('===================');
*/
op = Kekule.ObjComparer.getStructureComparisonDetailOptions(op);
var objCompareOptions = op;
// standardize structures first, perceive aromatic rings
//console.log(op);
if (op.doStandardize)
{
var standardizeOps = {
unmarshalSubFragments: !true,
doCanonicalization: true,
doAromaticPerception: true,
hucklizeStructure: true
};
if (!op.compareStereo) // do not need perceive stereo
standardizeOps.doCanonicalization = false;
// here we ensure two structures are standardized (with their flattened shadows).
subStructure.standardize(standardizeOps);
sourceMol.standardize(standardizeOps);
}
var flattenedSrcMol = sourceMol.getFlattenedShadowFragment(true);
var flattenedSubStruct = subStructure.getFlattenedShadowFragment(true);
/*
var targetStartingNode = subStructure.getNonHydrogenNodes()[0]; //subStructure.getNodeAt(0);
var srcNodes = sourceMol.getNonHydrogenNodes(); //sourceMol.getNodes();
*/
var targetStartingNode = flattenedSubStruct.getNonHydrogenNodes()[0]; //subStructure.getNodeAt(0);
var srcNodes = flattenedSrcMol.getNonHydrogenNodes(); //sourceMol.getNodes();
var srcNodeCount = srcNodes.length;
var srcIndex = 0;
var initComparedTargetObjs = [];
var initComparedSrcObjs = [];
//console.log(options, objCompareOptions);
var compareResult = false;
while (!compareResult && (srcIndex < srcNodeCount))
{
compareResult = SM._compareNode(targetStartingNode, srcNodes[srcIndex], initComparedTargetObjs, initComparedSrcObjs, objCompareOptions);
++srcIndex;
}
//if (srcIndex >= srcNodeCount) // can not find
if (!compareResult)
return false;
else
{
var matchedObjs = AU.toUnique(compareResult);
// map back to original structure
var result = sourceMol.getFlatternedShadowSourceObjs(matchedObjs);
return result;
}
},
/*
__reportComparedObjsChange: function(objs, tag)
{
var nodeIds = [];
for (var i = 0, l = objs.length; i < l; ++i)
{
var o = objs[i];
if (o.getId)
nodeIds.push(o.getId());
}
var s = '[' + nodeIds.join(', ') + ']';
if (tag)
s = '(' + tag + ') ' + s;
console.log(s);
},
*/
/** @private */
_addToComparedObjs: function(obj, comparedObjs, tag)
{
/*
if (comparedObjs.indexOf(obj) >= 0)
console.log('dup', tag, obj.getId());
*/
//AU.pushUnique(comparedObjs, obj);
comparedObjs.push(obj);
//obj.setRenderOption('color', 'red');
//SM.__reportComparedObjsChange(comparedObjs, tag);
},
/** @private */
_removeFromComparedObjs: function(obj, comparedObjs, tag)
{
//AU.remove(comparedObjs, obj);
var index = comparedObjs.indexOf(obj);
comparedObjs.length = index;
//obj.setRenderOption('color', null);
//SM.__reportComparedObjsChange(comparedObjs, tag);
},
/** @private */
_isSameMappedObj: function(targetObj, srcObj, comparedTargetObjs, comparedSrcObjs)
{
var srcIndex = comparedSrcObjs.indexOf(srcObj);
var targetIndex = comparedTargetObjs.indexOf(targetObj);
return (srcIndex >= 0) && (srcIndex === targetIndex);
},
/** @private */
_compareComparedNeighbors: function(targetObjs, srcObjs, allComparedTargetObjs, allComparedSrcObjs)
{
if (targetObjs.length > srcObjs.length)
return false;
var targetIndexes = [];
for (var i = 0, l = targetObjs.length; i < l; ++i)
{
targetIndexes.push(allComparedTargetObjs.indexOf(targetObjs[i]));
}
//targetIndexes.sort();
var srcIndexes = [];
for (var i = 0, l = srcObjs.length; i < l; ++i)
{
srcIndexes.push(allComparedSrcObjs.indexOf(srcObjs[i]));
}
//srcIndexes.sort();
for (var i = 0, l = targetIndexes.length; i < l; ++i)
{
if (srcIndexes.indexOf(targetIndexes[i]) < 0)
return false;
}
return true;
},
/** @private */
_compareNode: function(targetNode, srcNode, comparedTargetObjs, comparedSrcObjs, compareOptions)
{
/*
if (SM._isSameMappedObj(targetNode, srcNode, comparedTargetObjs, comparedSrcObjs))
return true;
var compareOptions = {
compareLinkedConnectorCount: false,
compareCharge: false,
compareHydrogenCount: false
};
*/
//if (SC.compare(targetNode, srcNode, compareOptions) !== 0)
if (targetNode.compareStructure(srcNode, compareOptions) !== 0)
return false;
else
{
var targetConnectors = targetNode.getLinkedNonHydrogenConnectors(); // AU.clone(targetNode.getLinkedConnectors());
var srcConnectors = srcNode.getLinkedNonHydrogenConnectors(); //AU.clone(srcNode.getLinkedConnectors());
var targetConnectorCount = targetConnectors.length; //targetNode.getLinkedConnectorCount();
var srcConnectorCount = srcConnectors.length; //srcNode.getLinkedConnectorCount();
if (targetConnectorCount > srcConnectorCount)
return false;
var dupComparedTargetObjs = AU.clone(comparedTargetObjs);
var dupComparedSrcObjs = AU.clone(comparedSrcObjs);
SM._addToComparedObjs(targetNode, dupComparedTargetObjs, 'target');
SM._addToComparedObjs(srcNode, dupComparedSrcObjs, 'src');
/*
SM._addToComparedObjs(targetNode, comparedTargetObjs, 'target');
SM._addToComparedObjs(srcNode, comparedSrcObjs, 'src');
*/
/*
var targetConnectors = AU.exclude(AU.clone(targetNode.getLinkedConnectors()), comparedTargetObjs);
var srcConnectors = AU.exclude(AU.clone(srcNode.getLinkedConnectors()), comparedSrcObjs);
*/
var targetComparedConnectors = AU.intersect(targetConnectors, dupComparedTargetObjs);
var srcComparedConnectors = AU.intersect(srcConnectors, dupComparedSrcObjs);
var result = true;
if (!SM._compareComparedNeighbors(targetComparedConnectors, srcComparedConnectors, dupComparedTargetObjs, dupComparedSrcObjs))
result = false;
else
{
targetConnectors = AU.exclude(targetConnectors, targetComparedConnectors);
srcConnectors = AU.exclude(srcConnectors, srcComparedConnectors);
if (targetConnectors.length > srcConnectors.length)
result = false;
}
var nextComparedObjs = [];
while (result && targetConnectors.length)
{
var compareResult = false;
var targetConn = targetConnectors.shift();
var srcIndex = 0;
var srcConn;
while (srcConnectors.length && !compareResult && (srcIndex < srcConnectors.length))
{
srcConn = srcConnectors[srcIndex];
compareResult = SM._compareConnector(targetConn, srcConn, dupComparedTargetObjs, dupComparedSrcObjs, compareOptions);
if (compareResult)
nextComparedObjs = nextComparedObjs.concat(compareResult);
++srcIndex;
}
if (!compareResult) // can not find match connector
{
result = false;
break;
}
else
AU.remove(srcConnectors, srcConn);
}
/*
if (!result) // remove targetConn and srcConn from compared
{
SM._removeFromComparedObjs(targetNode, comparedTargetObjs, 'target');
SM._removeFromComparedObjs(srcNode, comparedSrcObjs, 'src');
}
*/
if (result) // compare success, returns all compared objects
result = [srcNode].concat(nextComparedObjs) //dupComparedSrcObjs;
return result;
}
},
/** @private */
_compareConnector: function(targetConn, srcConn, comparedTargetObjs, comparedSrcObjs, compareOptions)
{
// targetConn and srcConn are surely not connected to hydrogen atom
/*
if (SM._isSameMappedObj(targetConn, srcConn, comparedTargetObjs, comparedSrcObjs))
return true;
var compareOptions = {
compareConnectedObjCount: false
};
*/
//if (SC.compare(targetConn, srcConn, compareOptions) !== 0)
if (targetConn.compareStructure(srcConn, compareOptions) !== 0)
return false;
else
{
var targetConnectedObjCount = targetConn.getConnectedObjCount();
var srcConnectedObjCount = srcConn.getConnectedObjCount();
if (targetConnectedObjCount > srcConnectedObjCount)
return false;
var dupComparedTargetObjs = AU.clone(comparedTargetObjs);
var dupComparedSrcObjs = AU.clone(comparedSrcObjs);
SM._addToComparedObjs(targetConn, dupComparedTargetObjs, 'target');
SM._addToComparedObjs(srcConn, dupComparedSrcObjs, 'src');
/*
SM._addToComparedObjs(targetConn, comparedTargetObjs, 'target');
SM._addToComparedObjs(srcConn, comparedSrcObjs, 'src');
*/
/*
var targetConnectedObjs = AU.exclude(AU.clone(targetConn.getConnectedObjs()), comparedTargetObjs);
var srcConnectedObjs = AU.exclude(AU.clone(srcConn.getConnectedObjs()), comparedSrcObjs);
*/
var targetConnectedObjs = AU.clone(targetConn.getConnectedObjs());
var srcConnectedObjs = AU.clone(srcConn.getConnectedObjs());
var targetComparedObjs = AU.intersect(targetConnectedObjs, dupComparedTargetObjs);
var srcComparedObjs = AU.intersect(srcConnectedObjs, dupComparedSrcObjs);
var result = true;
if (!SM._compareComparedNeighbors(targetComparedObjs, srcComparedObjs, dupComparedTargetObjs, dupComparedSrcObjs))
result = false;
else
{
targetConnectedObjs = AU.exclude(targetConnectedObjs, targetComparedObjs);
srcConnectedObjs = AU.exclude(srcConnectedObjs, srcComparedObjs);
if (targetConnectedObjs.length > srcConnectedObjs.length)
result = false;
}
var nextComparedObjs = [];
while (result && targetConnectedObjs.length)
{
var compareResult = false;
var targetObj = targetConnectedObjs.shift();
var srcIndex = 0;
var srcObj;
while (srcConnectedObjs.length && !compareResult && (srcIndex < srcConnectedObjs.length))
{
srcObj = srcConnectedObjs[srcIndex];
if (srcObj.getClass() !== targetObj.getClass())
compareResult = false;
else if (srcObj instanceof Kekule.ChemStructureNode)
compareResult = SM._compareNode(targetObj, srcObj, dupComparedTargetObjs, dupComparedSrcObjs, compareOptions);
else if (srcObj instanceof Kekule.ChemStructureConnector)
compareResult = SM._compareConnector(targetObj, srcObj, dupComparedTargetObjs, dupComparedSrcObjs, compareOptions);
else
compareResult = false;
if (compareResult)
nextComparedObjs = nextComparedObjs.concat(compareResult);
++srcIndex;
}
if (!compareResult) // can not find match connector
{
result = false;
break;
}
else
AU.remove(srcConnectedObjs, srcObj);
}
/*
if (!result) // remove targetConn and srcConn from compared
{
SM._removeFromComparedObjs(targetConn, comparedTargetObjs, 'target');
SM._removeFromComparedObjs(srcConn, comparedSrcObjs, 'src');
}
*/
if (result) // compare success, returns all compared objects
result = [srcConn].concat(nextComparedObjs); //dupComparedSrcObjs;
return result;
}
}
};
var SM = Kekule.ChemStructureSearcher;
ClassEx.extend(Kekule.StructureFragment,
/** @lends Kekule.StructureFragment# */
{
/**
* Search sub structure in this fragment.
* @param {Kekule.StructureFragment} subStructure Structure to find.
* @param {Hash} options Search options, can include the following fields:
* {
* doStandardize: Bool, whether standardize molecule (especially perceive aromatic rings) before searching.
* exactMatch: Bool, if true, only the same structure with subStructure will be matched.
* ignoreCharge: Bool
* ignoreBondOrder: Bool
* }
* @returns {Variant} If sub structure is found, an array of matching node and connectors will be returned.
* Otherwise false will be returned.
*/
search: function(subStructure, options)
{
return SM.findSubStructure(subStructure, this, options);
}
});
})();