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• AtomFunctionAnalyzer.java

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com.actelion.research.chem.AtomFunctionAnalyzer Maven / Gradle / Ivy

/*
 * Copyright (c) 1997 - 2016
 * Actelion Pharmaceuticals Ltd.
 * Gewerbestrasse 16
 * CH-4123 Allschwil, Switzerland
 *
 * All rights reserved.
 *
 * 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 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 OWNER 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 com.actelion.research.chem;

public class AtomFunctionAnalyzer {
	/**
	 * @param mol
	 * @param atom
	 * @return number of double-bonded O
	 */
	private static int getOxoCount(StereoMolecule mol, int atom) {
		int count = 0;
		for (int i=0; i-1)&&(indexDoubleBondedO>-1)) {
			nitro = true;
		}
			
		return nitro;
	}

	
	
	public static boolean isBasicNitrogen(StereoMolecule mol, int atom) {
		if (mol.getAtomicNo(atom) != 7
		 || mol.getAtomCharge(atom) != 0
		 || (mol.getConnAtoms(atom) + mol.getAtomPi(atom) > 3))
			return false;

		if (mol.isAromaticAtom(atom)) {
			if (mol.getAtomPi(atom) != 1)
				return false;	// pyrrol type

			if (mol.getAtomRingCount(atom, 7) != 1)
				return false;

			RingCollection rc = mol.getRingSet();
			for (int r=0; r 0;
						}
					break;
					}
				}
			return false;
			}

		if (mol.getAtomPi(atom) > 1)
			return false;	// nitrile

		if (mol.getAtomPi(atom) == 1) {
			int imineC = -1;
			int supporterCount = 0;
			for (int i=0; i= 0);
			}

		// non-aromatic nitrogen without pi-bond
		for (int i=0; i