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• ConformationRule.java

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org.openmolecules.chem.conf.so.ConformationRule 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.calc.SingularValueDecomposition;
import com.actelion.research.chem.Coordinates;
import com.actelion.research.chem.StereoMolecule;
import com.actelion.research.chem.conf.Conformer;

public abstract class ConformationRule {
	public static final int RULE_TYPE_DISTANCE = 0;
	public static final int RULE_TYPE_PLANE = 1;
	public static final int RULE_TYPE_LINE = 2;
	public static final int RULE_TYPE_TORSION = 3;
	public static final int RULE_TYPE_STEREO = 4;
	public static final int RULE_TYPE_BINAP = 5;

	public static final String[] RULE_NAME = { "distance", "plane", "line", "torsion", "stereo", "binap" };

	protected int[] mAtom;
	protected boolean mIsEnabled;

	public ConformationRule(int[] atom) {
		mAtom = atom;
		mIsEnabled = true;
		}

	public boolean isEnabled() {
		return mIsEnabled;
		}

	public void setEnabled(boolean b) {
		mIsEnabled = b;
		}

	public abstract boolean apply(Conformer conformer, double cycleFactor);
	public abstract double addStrain(Conformer conformer, double[] atomStrain);
	public abstract int getRuleType();
	public abstract String toString();

	protected int[] getAtomList() {
		return mAtom;
		}

	protected void addAtomList(StringBuilder sb) {
		if (mAtom == null) {
		    sb.append(" atoms:");
			}
		else {
		    sb.append(" atoms:"+mAtom[0]);
	        for (int i=1; i