org.openmolecules.chem.conf.so.StraightLineRule Maven / Gradle / Ivy
Go to download
Show more of this group Show more artifacts with this name
Show all versions of openchemlib Show documentation
Show all versions of openchemlib Show documentation
Open Source Chemistry Library
/*
* 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.IDCodeParser;
import com.actelion.research.chem.StereoMolecule;
import com.actelion.research.chem.conf.Conformer;
import java.util.ArrayList;
public class StraightLineRule extends ConformationRule {
/**
* Test code...
* @param args
*/
public static void main(String args[]) {
final int LINE_ATOMS = 7;
final int FIRST_LINE_ATOM = 4;
final int LAST_LINE_ATOM = FIRST_LINE_ATOM+LINE_ATOMS-1;
int[] atom = new int[LINE_ATOMS];
for (int i=0; i ruleList, StereoMolecule mol) {
boolean[] atomHandled = new boolean[mol.getAllAtoms()];
for (int atom=0; atom S[maxIndex])
maxIndex = i;
double[][] U = svd.getU();
double[] n = new double[3]; // normal vector of fitted line
for (int i=0; i<3; i++)
n[i] = U[i][maxIndex];
double[] lambda = new double[mAtom.length];
for (int i=0; i s1);
double delta = isIncreasing ? max-min : min-max;
lambda[0] = isIncreasing ? min : max;
for (int i=1; i S[maxIndex])
maxIndex = i;
double[][] U = svd.getU();
double[] n = new double[3]; // normal vector of fitted line
for (int i=0; i<3; i++)
n[i] = U[i][maxIndex];
double totalStrain = 0;
for (int i=0; i