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• PlaneRule.java

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org.openmolecules.chem.conf.so.PlaneRule Maven / Gradle / Ivy

/*
 * Copyright 2013-2020 Thomas Sander, openmolecules.org
 *
 * Redistribution and use in source and binary forms, with or without modification,
 * are permitted provided that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright notice,
 *    this list of conditions and the following disclaimer.
 * 2. Redistributions in binary form must reproduce the above copyright notice,
 *    this list of conditions and the following disclaimer in the documentation
 *    and/or other materials provided with the distribution.
 * 3. Neither the name of the copyright holder nor the names of its contributors
 *    may be used to endorse or promote products derived from this software without
 *    specific prior written permission.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY
 * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
 * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT
 * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
 * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
 * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
 * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
 * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 *
 * @author Thomas Sander
 */

package org.openmolecules.chem.conf.so;

import com.actelion.research.chem.Coordinates;
import com.actelion.research.chem.RingCollection;
import com.actelion.research.chem.StereoMolecule;
import com.actelion.research.chem.conf.Conformer;

import java.util.ArrayList;

public class PlaneRule extends ConformationRule {
	private int[] mPlaneAtom;	// these are the atoms that define the plane

	public PlaneRule(int[] atom, StereoMolecule mol) {
		super(atom);
		int count = 0;
		for (int i=0; i 2) {
			mPlaneAtom = new int[count];
			count = 0;
			for (int i=0; i ruleList, StereoMolecule mol) {
		boolean[] isFlatBond = new boolean[mol.getBonds()];

		RingCollection ringSet = mol.getRingSet();
		boolean[] isAromaticRing = new boolean[ringSet.getSize()];
		ringSet.determineAromaticity(isAromaticRing, new boolean[ringSet.getSize()], new int[ringSet.getSize()], true);
		for (int ring=0; ring 1
							 && mol.getAllConnAtoms(bondAtom2) > 1));
			if (!isFlatBond[bond]) {
					// check if bond is an amide or ester bond
				if (mol.getBondOrder(bond) == 1) {
					for (int i=0; i<2; i++) {
						if ((atomicNo[i] == 7 || atomicNo[i] == 8) && atomicNo[1-i] == 6) {
							int carbon = mol.getBondAtom(1-i, bond);
							for (int j=0; j 1)
				 || (mol.isFlatNitrogen(atom) && mol.getAtomPi(atom) != 2 && mol.getAllConnAtoms(atom) > 1)) {
					int[] atomList = new int[1+mol.getAllConnAtoms(atom)];
					for (int i=0; i=0; i--) {
			if (mol.getAtomicNo(fragmentAtom[i]) <= 8) {
				for (int j=0; j