Current Dev State

static/js/ketcher2/script/chem/smiles/cis_trans.js

@@ -0,0 +1,212 @@
+/****************************************************************************
+ * Copyright 2017 EPAM Systems
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ ***************************************************************************/
+
+var Map = require('../../util/map');
+var Vec2 = require('../../util/vec2');
+
+var Struct = require('../struct');
+
+function CisTrans(mol, neighborsFunc, context) {
+	this.molecule = mol;
+	this.bonds = new Map();
+	this.getNeighbors = neighborsFunc;
+	this.context = context;
+}
+
+CisTrans.PARITY = {
+	NONE: 0,
+	CIS: 1,
+	TRANS: 2
+};
+
+CisTrans.prototype.each = function (func, context) {
+	this.bonds.each(func, context);
+};
+
+CisTrans.prototype.getParity = function (idx) {
+	return this.bonds.get(idx).parity;
+};
+
+CisTrans.prototype.getSubstituents = function (idx) {
+	return this.bonds.get(idx).substituents;
+};
+
+CisTrans.prototype.sameside = function (beg, end, neiBeg, neiEnd) {
+	var diff = Vec2.diff(beg, end);
+	var norm = new Vec2(-diff.y, diff.x);
+
+	if (!norm.normalize())
+		return 0;
+
+	var normBeg = Vec2.diff(neiBeg, beg);
+	var normEnd = Vec2.diff(neiEnd, end);
+
+	if (!normBeg.normalize())
+		return 0;
+	if (!normEnd.normalize())
+		return 0;
+
+	var prodBeg = Vec2.dot(normBeg, norm);
+	var prodEnd = Vec2.dot(normEnd, norm);
+
+	if (Math.abs(prodBeg) < 0.001 || Math.abs(prodEnd) < 0.001)
+		return 0;
+
+	return (prodBeg * prodEnd > 0) ? 1 : -1;
+};
+
+CisTrans.prototype.samesides = function (iBeg, iEnd, iNeiBeg, iNeiEnd) {
+	return this.sameside(this.molecule.atoms.get(iBeg).pp, this.molecule.atoms.get(iEnd).pp,
+		this.molecule.atoms.get(iNeiBeg).pp, this.molecule.atoms.get(iNeiEnd).pp);
+};
+
+CisTrans.prototype.sortSubstituents = function (substituents) { // eslint-disable-line max-statements
+	var h0 = this.molecule.atoms.get(substituents[0]).pureHydrogen();
+	var h1 = substituents[1] < 0 || this.molecule.atoms.get(substituents[1]).pureHydrogen();
+	var h2 = this.molecule.atoms.get(substituents[2]).pureHydrogen();
+	var h3 = substituents[3] < 0 || this.molecule.atoms.get(substituents[3]).pureHydrogen();
+
+	if (h0 && h1)
+		return false;
+	if (h2 && h3)
+		return false;
+
+	if (h1) {
+		substituents[1] = -1;
+	} else if (h0) {
+		substituents[0] = substituents[1];
+		substituents[1] = -1;
+	} else if (substituents[0] > substituents[1]) {
+		swap(substituents, 0, 1);
+	}
+
+	if (h3) {
+		substituents[3] = -1;
+	} else if (h2) {
+		substituents[2] = substituents[3];
+		substituents[3] = -1;
+	} else if (substituents[2] > substituents[3]) {
+		swap(substituents, 2, 3);
+	}
+
+	return true;
+};
+
+CisTrans.prototype.isGeomStereoBond = function (bondIdx, substituents) { // eslint-disable-line max-statements
+	// it must be [C,N,Si]=[C,N,Si] bond
+	var bond = this.molecule.bonds.get(bondIdx);
+
+	if (bond.type != Struct.Bond.PATTERN.TYPE.DOUBLE)
+		return false;
+
+	var label1 = this.molecule.atoms.get(bond.begin).label;
+	var label2 = this.molecule.atoms.get(bond.end).label;
+
+	if (label1 != 'C' && label1 != 'N' && label1 != 'Si' && label1 != 'Ge')
+		return false;
+	if (label2 != 'C' && label2 != 'N' && label2 != 'Si' && label2 != 'Ge')
+		return false;
+
+	// the atoms should have 1 or 2 single bonds
+	// (apart from the double bond under consideration)
+	var neiBegin = this.getNeighbors.call(this.context, bond.begin);
+	var neiЕnd = this.getNeighbors.call(this.context, bond.end);
+
+	if (
+	neiBegin.length < 2 || neiBegin.length > 3 ||
+	neiЕnd.length < 2 || neiЕnd.length > 3
+	)
+		return false;
+
+	substituents[0] = -1;
+	substituents[1] = -1;
+	substituents[2] = -1;
+	substituents[3] = -1;
+
+	var i;
+	var nei;
+
+	for (i = 0; i < neiBegin.length; i++) {
+		nei = neiBegin[i];
+
+		if (nei.bid == bondIdx)
+			continue; // eslint-disable-line no-continue
+
+		if (this.molecule.bonds.get(nei.bid).type != Struct.Bond.PATTERN.TYPE.SINGLE)
+			return false;
+
+		if (substituents[0] == -1)
+			substituents[0] = nei.aid;
+		else // (substituents[1] == -1)
+			substituents[1] = nei.aid;
+	}
+
+	for (i = 0; i < neiЕnd.length; i++) {
+		nei = neiЕnd[i];
+
+		if (nei.bid == bondIdx)
+			continue;  // eslint-disable-line no-continue
+
+		if (this.molecule.bonds.get(nei.bid).type != Struct.Bond.PATTERN.TYPE.SINGLE)
+			return false;
+
+		if (substituents[2] == -1)
+			substituents[2] = nei.aid;
+		else // (substituents[3] == -1)
+			substituents[3] = nei.aid;
+	}
+
+	if (substituents[1] != -1 && this.samesides(bond.begin, bond.end, substituents[0], substituents[1]) != -1)
+		return false;
+	if (substituents[3] != -1 && this.samesides(bond.begin, bond.end, substituents[2], substituents[3]) != -1)
+		return false;
+
+	return true;
+};
+
+CisTrans.prototype.build = function (excludeBonds) {
+	this.molecule.bonds.each(function (bid, bond) {
+		var ct = this.bonds.set(bid,
+			{
+				parity: 0,
+				substituents: []
+			});
+
+		if (Array.isArray(excludeBonds) && excludeBonds[bid])
+			return;
+
+		if (!this.isGeomStereoBond(bid, ct.substituents))
+			return;
+
+		if (!this.sortSubstituents(ct.substituents))
+			return;
+
+		var sign = this.samesides(bond.begin, bond.end, ct.substituents[0], ct.substituents[2]);
+
+		if (sign == 1)
+			ct.parity = CisTrans.PARITY.CIS;
+		else if (sign == -1)
+			ct.parity = CisTrans.PARITY.TRANS;
+	}, this);
+};
+
+function swap(arr, i1, i2) {
+	var tmp = arr[i1];
+	arr[i1] = arr[i2];
+	arr[i2] = tmp;
+}
+
+module.exports = CisTrans;